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Sample records for major lignin qtl

  1. A knockout mutation in the lignin biosynthesis gene CCR1 explains a major QTL for acid detergent lignin content in Brassica napus seeds.

    PubMed

    Liu, Liezhao; Stein, Anna; Wittkop, Benjamin; Sarvari, Pouya; Li, Jiana; Yan, Xingying; Dreyer, Felix; Frauen, Martin; Friedt, Wolfgang; Snowdon, Rod J

    2012-05-01

    Seed coat phenolic compounds represent important antinutritive fibre components that cause a considerable reduction in value of seed meals from oilseed rape (Brassica napus). The nutritionally most important fibre compound is acid detergent lignin (ADL), to which a significant contribution is made by phenylpropanoid-derived lignin precursors. In this study, we used bulked-segregant analysis in a population of recombinant inbred lines (RILs) from a cross of the Chinese oilseed rape lines GH06 (yellow seed, low ADL) and P174 (black seed, high ADL) to identify markers with tight linkage to a major quantitative trait locus (QTL) for seed ADL content. Fine mapping of the QTL was performed in a backcross population comprising 872 BC(1)F(2) plants from a cross of an F(7) RIL from the above-mentioned population, which was heterozygous for this major QTL and P174. A 3:1 phenotypic segregation for seed ADL content indicated that a single, dominant, major locus causes a substantial reduction in ADL. This locus was successively narrowed to 0.75 cM using in silico markers derived from a homologous Brassica rapa sequence contig spanning the QTL. Subsequently, we located a B. rapa orthologue of the key lignin biosynthesis gene CINNAMOYL CO-A REDUCTASE 1 (CCR1) only 600 kbp (0.75 cM) upstream of the nearest linked marker. Sequencing of PCR amplicons, covering the full-length coding sequences of Bna.CCR1 homologues, revealed a locus in P174 whose sequence corresponds to the Brassica oleracea wild-type allele from chromosome C8. In GH06, however, this allele is replaced by a homologue derived from chromosome A9 that contains a loss-of-function frameshift mutation in exon 1. Genetic and physical map data infer that this loss-of-function allele has replaced a functional Bna.CCR1 locus on chromosome C8 in GH06 by homoeologous non-reciprocal translocation.

  2. Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea.

    PubMed

    Das, Shouvik; Upadhyaya, Hari D; Bajaj, Deepak; Kujur, Alice; Badoni, Saurabh; Laxmi; Kumar, Vinod; Tripathi, Shailesh; Gowda, C L Laxmipathi; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

    2015-06-01

    A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R(2) at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/genotypes, but not in any wild species/genotypes of primary, secondary and tertiary gene pools. This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the

  3. mQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea.

    PubMed

    Das, Shouvik; Singh, Mohar; Srivastava, Rishi; Bajaj, Deepak; Saxena, Maneesha S; Rana, Jai C; Bansal, Kailash C; Tyagi, Akhilesh K; Parida, Swarup K

    2016-02-01

    The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 × ILWC 46 and Pusa 256 × ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8-10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in Δ (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (Caq(a)PN4.1: 867.8 kb and Caq(a)PN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (Caq(b)PN4.1: 637.5 kb and Caq(b)PN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (∼3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby

  4. Consistent effects of a major QTL for thermal resistance in field-released Drosophila melanogaster.

    PubMed

    Loeschcke, Volker; Kristensen, Torsten Nygaard; Norry, Fabian M

    2011-09-01

    Molecular genetic markers can be used to identify quantitative trait loci (QTL) for thermal resistance and this has allowed characterization of a major QTL for knockdown resistance to high temperature in Drosophila melanogaster. The QTL showed trade-off associations with cold resistance under laboratory conditions. However, assays of thermal tolerance conducted in the laboratory may not necessarily reflect performance at varying temperatures in the field. Here we tested if lines with different genotypes in this QTL show different thermal performance under high and low temperatures in the field using a release recapture assay. We found that lines carrying the QTL genotype for high thermal tolerance were significantly better at locating resources in the field releases under hot temperatures while the QTL line carrying the contrasting genotype were superior at cold temperatures. Further, we studied copulatory success between the different QTL genotypes at different temperatures. We found higher copulatory success in males of the high tolerance QTL genotype under hot temperature conditions, while there was no difference in females at cold temperatures. The results allow relating components of field fitness at different environmental temperatures with genotypic variation in a QTL for thermal tolerance.

  5. A consensus linkage map of oil palm and a major QTL for stem height

    PubMed Central

    Lee, May; Xia, Jun Hong; Zou, Zhongwei; Ye, Jian; Rahmadsyah; Alfiko, Yuzer; Jin, Jingjing; Lieando, Jessica Virginia; Purnamasari, Maria Indah; Lim, Chin Huat; Suwanto, Antonius; Wong, Limsoon; Chua, Nam-Hai; Yue, Gen Hua

    2015-01-01

    Oil palm (Elaeis guinensis Jacquin) is the most important source of vegetable oil and fat. Several linkage maps had been constructed using dominant and co-dominant markers to facilitate mapping of QTL. However, dominant markers are not easily transferable among different laboratories. We constructed a consensus linkage map for oil palm using co-dominant markers (i.e. microsatellite and SNPs) and two F1 breeding populations generated by crossing Dura and Pisifera individuals. Four hundreds and forty-four microsatellites and 36 SNPs were mapped onto 16 linkage groups. The map length was 1565.6 cM, with an average marker space of 3.72 cM. A genome-wide scan of QTL identified a major QTL for stem height on the linkage group 5, which explained 51% of the phenotypic variation. Genes in the QTL were predicted using the palm genome sequence and bioinformatic tools. The linkage map supplies a base for mapping QTL for accelerating the genetic improvement, and will be also useful in the improvement of the assembly of the genome sequences. Markers linked to the QTL may be used in selecting dwarf trees. Genes within the QTL will be characterized to understand the mechanisms underlying dwarfing. PMID:25648560

  6. Dissection and fine mapping of a major QTL for preharvest sprouting resistance in white wheat Rio Blanco.

    PubMed

    Liu, Shubing; Bai, Guihua

    2010-11-01

    Preharvest sprouting (PHS) is a major constraint to white wheat production. Previously, we mapped quantitative trait loci (QTL) for PHS resistance in white wheat by using a recombinant inbred line (RIL) population derived from the cross Rio Blanco/NW97S186. One QTL, QPhs.pseru-3A, showed a major effect on PHS resistance, and three simple sequence repeat (SSR) markers were mapped in the QTL region. To determine the flanking markers for the QTL and narrow down the QTL to a smaller chromosome region, we developed a new fine mapping population of 1,874 secondary segregating F(2) plants by selfing an F6 RIL (RIL25) that was heterozygous in the three SSR marker loci. Segregation of PHS resistance in the population fitted monogenic inheritance. An additive effect of the QTL played a major role on PHS resistance, but a dominant effect was also observed. Fifty-six recombinants among the three SSR markers were identified in the population and selfed to produce homozygous recombinants or QTL near-isogenic lines (NIL). PHS evaluation of the recombinants delineated the QTL in the region close to Xbarc57 flanked by Xbarc321 and Xbarc12. To saturate the QTL region, 11 amplified fragment length polymorphism (AFLP) markers were mapped in the QTL region with 7 AFLP co-segregated with Xbarc57 by using the NIL population. Dissection of the QTL as a Mendelian factor and saturation of the QTL region with additional markers created a solid foundation for positional cloning of the major QTL. PMID:20607209

  7. Mapping of yield influencing QTL in Brassica juncea: implications for breeding of a major oilseed crop of dryland areas.

    PubMed

    Ramchiary, N; Padmaja, K L; Sharma, S; Gupta, V; Sodhi, Y S; Mukhopadhyay, A; Arumugam, N; Pental, D; Pradhan, A K

    2007-10-01

    Quantitative trait loci (QTL) analysis of yield influencing traits was carried out in Brassica juncea (AABB) using a doubled haploid (DH) mapping population of 123 lines derived from a cross between Varuna (a line representing the Indian gene pool) and Heera (representing the east European gene pool) to identify potentially useful alleles from both the parents. The existing AFLP based map of B. juncea was further saturated with RFLP and SSR markers which led to the identification of the linkage groups belonging to the A (B. rapa) and B (B. nigra) genome components of B. juncea. For QTL dissection, the DH lines were evaluated at three different environments and phenotyped for 12 quantitative traits. A total of 65 QTL spread over 13 linkage groups (LG) were identified from the three environments. QTL analysis showed that the A genome has contributed more than the B genome to productivity (68% of the total QTL detected) suggesting a more prominent role of the A genome towards domestication of this crop. The east European line, Heera, carried favorable alleles for 42% of the detected QTL and the remaining 58% were in the Indian gene pool line, Varuna. We observed clustering of major QTL in a few linkage groups, particularly in J7 and J10 of the A genome, with QTL of different traits having agronomically antagonistic allelic effects co-mapping to the same genetic interval. QTL analysis also identified some well-separated QTL which could be readily transferred between the two pools. Based on the QTL analysis, we propose that improvement in yield could be achieved more readily by heterosis breeding rather than by pure line breeding.

  8. A major QTL controls susceptibility to spinal curvature in the curveback guppy

    PubMed Central

    2011-01-01

    Background Understanding the genetic basis of heritable spinal curvature would benefit medicine and aquaculture. Heritable spinal curvature among otherwise healthy children (i.e. Idiopathic Scoliosis and Scheuermann kyphosis) accounts for more than 80% of all spinal curvatures and imposes a substantial healthcare cost through bracing, hospitalizations, surgery, and chronic back pain. In aquaculture, the prevalence of heritable spinal curvature can reach as high as 80% of a stock, and thus imposes a substantial cost through production losses. The genetic basis of heritable spinal curvature is unknown and so the objective of this work is to identify quantitative trait loci (QTL) affecting heritable spinal curvature in the curveback guppy. Prior work with curveback has demonstrated phenotypic parallels to human idiopathic-type scoliosis, suggesting shared biological pathways for the deformity. Results A major effect QTL that acts in a recessive manner and accounts for curve susceptibility was detected in an initial mapping cross on LG 14. In a second cross, we confirmed this susceptibility locus and fine mapped it to a 5 cM region that explains 82.6% of the total phenotypic variance. Conclusions We identify a major QTL that controls susceptibility to curvature. This locus contains over 100 genes, including MTNR1B, a candidate gene for human idiopathic scoliosis. The identification of genes associated with heritable spinal curvature in the curveback guppy has the potential to elucidate the biological basis of spinal curvature among humans and economically important teleosts. PMID:21269476

  9. QTL Mapping of Kernel Number-Related Traits and Validation of One Major QTL for Ear Length in Maize

    PubMed Central

    Huo, Dongao; Ning, Qiang; Shen, Xiaomeng; Liu, Lei; Zhang, Zuxin

    2016-01-01

    The kernel number is a grain yield component and an important maize breeding goal. Ear length, kernel number per row and ear row number are highly correlated with the kernel number per ear, which eventually determines the ear weight and grain yield. In this study, two sets of F2:3 families developed from two bi-parental crosses sharing one inbred line were used to identify quantitative trait loci (QTL) for four kernel number-related traits: ear length, kernel number per row, ear row number and ear weight. A total of 39 QTLs for the four traits were identified in the two populations. The phenotypic variance explained by a single QTL ranged from 0.4% to 29.5%. Additionally, 14 overlapping QTLs formed 5 QTL clusters on chromosomes 1, 4, 5, 7, and 10. Intriguingly, six QTLs for ear length and kernel number per row overlapped in a region on chromosome 1. This region was designated qEL1.10 and was validated as being simultaneously responsible for ear length, kernel number per row and ear weight in a near isogenic line-derived population, suggesting that qEL1.10 was a pleiotropic QTL with large effects. Furthermore, the performance of hybrids generated by crossing 6 elite inbred lines with two near isogenic lines at qEL1.10 showed the breeding value of qEL1.10 for the improvement of the kernel number and grain yield of maize hybrids. This study provides a basis for further fine mapping, molecular marker-aided breeding and functional studies of kernel number-related traits in maize. PMID:27176215

  10. Identification of a major QTL controlling the content of B-type starch granules in Aegilops

    PubMed Central

    Howard, Thomas; Rejab, Nur Ardiyana; Griffiths, Simon; Leigh, Fiona; Leverington-Waite, Michelle; Simmonds, James; Uauy, Cristobal; Trafford, Kay

    2011-01-01

    Starch within the endosperm of most species of the Triticeae has a unique bimodal granule morphology comprising large lenticular A-type granules and smaller near-spherical B-type granules. However, a few wild wheat species (Aegilops) are known to lack B-granules. Ae. peregrina and a synthetic tetraploid Aegilops with the same genome composition (SU) were found to differ in B-granule number. The synthetic tetraploid had normal A- and B-type starch granules whilst Ae. peregrina had only A-granules because the B-granules failed to initiate. A population segregating for B-granule number was generated by crossing these two accessions and was used to study the genetic basis of B-granule initiation. A combination of Bulked Segregant Analysis and QTL mapping identified a major QTL located on the short arm of chromosome 4S that accounted for 44.4% of the phenotypic variation. The lack of B-granules in polyploid Aegilops with diverse genomes suggests that the B-granule locus has been lost several times independently during the evolution of the Triticeae. It is proposed that the B-granule locus is susceptible to silencing during polyploidization and a model is presented to explain the observed data based on the assumption that the initiation of B-granules is controlled by a single major locus per haploid genome. PMID:21227932

  11. fs3.1: a major fruit shape QTL conserved in Capsicum.

    PubMed

    Ben Chaim, Arnon; Borovsky, Yelena; Rao, G U; Tanyolac, Bahattin; Paran, Ilan

    2003-02-01

    fs3.1 is a major fruit shape (defined as the ratio of fruit length to fruit width) quantitative trait locus (QTL) originally detected in an intraspecific cross of Capsicum annuum between the blocky and elongated-fruited inbreds 'Maor' and 'Perennial', respectively. In addition to increasing fruit shape index, the 'Perennial' allele at fs3.1 increased fruit elongation and decreased fruit width and pericarp thickness. We verified the effect of fs3.1 in backcross inbred lines (BILs) derived from crossing 'Perennial' with 'Maor' and with a second blocky-type inbred line of C. annuum. To determine the effect of the fs3.1 region in additional Capsicum species, we constructed an advanced backcross population from the cross of 'Maor' and the oval-fruited Capsicum frutescens BG 2816 and an F2 of the introgression line IL 152 that contains an introgression of the fs3.1 region from Capsicum chinense PI 152225. QTLs for fruit shape, fruit width, and pericarp thickness, but not for fruit length, were detected in both crosses, indicating the conservation of the fs3.1 region as a QTL affecting fruit shape in pepper. We also tested tomato (Lycopersicon spp.) introgression lines containing the corresponding fs3.1 region from L. pennellii and L. hirsutum, but we did not detect a significant fruit shape QTL in these lines. The effect of fs3.1 on the growth of fruit dimensions varied with the genetic background. By measuring the length and width of ovaries and fruits of near-isogenic C. annuum lines that differ in fs3.1 during fruit development, we determined that fs3.1 controls shape predominantly by increasing the growth rate of the longitudinal axis in the first 2 weeks after pollination. However, in the crosses of C. annuum with C. frutescens and C. chinense, fs3.1 predominantly exerted its effect on the width dimension.

  12. A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia

    PubMed Central

    Liu, Feng; Sun, Fei; Xia, Jun Hong; Li, Jian; Fu, Gui Hong; Lin, Grace; Tu, Rong Jian; Wan, Zi Yi; Quek, Delia; Yue, Gen Hua

    2014-01-01

    Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140 dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growth traits was identified in the sex-determining locus in LG1, explaining 71.7%, 67.2% and 64.9% of the phenotypic variation (PV) of body weight, total length and standard length, respectively. In addition, a candidate gene GHR2 in a QTL was significantly associated with body weight, explaining 13.1% of PV. Real-time qPCR revealed that different genotypes at the GHR2 locus influenced the IGF-1 expression level. The markers located in the major QTL for growth traits could be used in marker-assisted selection of tilapia. The associations between GHR2 variants and growth traits suggest that the GHR2 gene should be an important gene that explains the difference in growth among tilapia species. PMID:25435025

  13. Inheritance and Identification of a Major Quantitative Trait Locus (QTL) that Confers Resistance to Meloidogyne incognita and a Novel QTL for Plant Height in Sweet Sorghum.

    PubMed

    Harris-Shultz, Karen R; Davis, Richard F; Knoll, Joseph E; Anderson, William; Wang, Hongliang

    2015-12-01

    Southern root-knot nematodes (Meloidogyne incognita) are a pest on many economically important row crop and vegetable species and management relies on chemicals, plant resistance, and cultural practices such as crop rotation. Little is known about the inheritance of resistance to M. incognita or the genomic regions associated with resistance in sorghum (Sorghum bicolor). In this study, an F2 population (n = 130) was developed between the resistant sweet sorghum cultivar 'Honey Drip' and the susceptible sweet cultivar 'Collier'. Each F2 plant was phenotyped for stalk weight, height, juice Brix, root weight, total eggs, and eggs per gram of root. Strong correlations were observed between eggs per gram of root and total eggs, height and stalk weight, and between two measurements of Brix. Genotyping-by-sequencing was used to generate single nucleotide polymorphism markers. The G-Model, single marker analysis, interval mapping, and composite interval mapping were used to identify a major quantitative trait locus (QTL) on chromosome 3 for total eggs and eggs per gram of root. Furthermore, a new QTL for plant height was also discovered on chromosome 3. Simple sequence repeat markers were developed in the total eggs and eggs per gram of root QTL region and the markers flanking the resistance gene are 4.7 and 2.4 cM away. These markers can be utilized to move the southern root-knot nematode resistance gene from Honey Drip to any sorghum line. PMID:26574655

  14. Inheritance and Identification of a Major Quantitative Trait Locus (QTL) that Confers Resistance to Meloidogyne incognita and a Novel QTL for Plant Height in Sweet Sorghum.

    PubMed

    Harris-Shultz, Karen R; Davis, Richard F; Knoll, Joseph E; Anderson, William; Wang, Hongliang

    2015-12-01

    Southern root-knot nematodes (Meloidogyne incognita) are a pest on many economically important row crop and vegetable species and management relies on chemicals, plant resistance, and cultural practices such as crop rotation. Little is known about the inheritance of resistance to M. incognita or the genomic regions associated with resistance in sorghum (Sorghum bicolor). In this study, an F2 population (n = 130) was developed between the resistant sweet sorghum cultivar 'Honey Drip' and the susceptible sweet cultivar 'Collier'. Each F2 plant was phenotyped for stalk weight, height, juice Brix, root weight, total eggs, and eggs per gram of root. Strong correlations were observed between eggs per gram of root and total eggs, height and stalk weight, and between two measurements of Brix. Genotyping-by-sequencing was used to generate single nucleotide polymorphism markers. The G-Model, single marker analysis, interval mapping, and composite interval mapping were used to identify a major quantitative trait locus (QTL) on chromosome 3 for total eggs and eggs per gram of root. Furthermore, a new QTL for plant height was also discovered on chromosome 3. Simple sequence repeat markers were developed in the total eggs and eggs per gram of root QTL region and the markers flanking the resistance gene are 4.7 and 2.4 cM away. These markers can be utilized to move the southern root-knot nematode resistance gene from Honey Drip to any sorghum line.

  15. Characterization of a major QTL for adult plant resistance to stripe rust in US soft red winter wheat.

    PubMed

    Hao, Yuanfeng; Chen, Zhenbang; Wang, Yingying; Bland, Dan; Buck, James; Brown-Guedira, Gina; Johnson, Jerry

    2011-12-01

    Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of soft red winter wheat in the eastern region of the USA. Pioneer 26R61 has provided effective resistance to stripe rust for 10 years. To elucidate the genetic basis of the resistance, a mapping population of 178 recombinant inbred lines (RILs) was developed using single-seed descent from a cross between Pioneer 26R61 and the susceptible cultivar AGS 2000. A genetic map with 895 markers covering all 21 chromosomes was used for QTL analysis. One major QTL was detected, explaining up to 56.0% of the mean phenotypic variation, flanked by markers Xbarc124 and Xgwm359, and assigned to the distal 22% of the short arm of wheat chromosome 2A. Evidence showed that it was different from Yr17 derived from Ae. ventricosa, the only formally named Yr gene in 2AS, and the QTL was temporarily designated as YrR61. In addition, a minor QTL, QYr.uga-6AS, probably conditioned high-temperature adult plant resistance. The QTL explained 6-7% of the trait variation. Preliminary test of the flanking markers for YrR61, in two cultivars and two promising breeding lines with Pioneer 26R61 in their pedigree, indicated that YrR61 was present in these cultivars and lines, and these markers could therefore be used in marker-assisted selection.

  16. Foreword to the international workshop on major genes and QTL in sheep and goats

    PubMed Central

    2005-01-01

    This is the third international meeting dealing with major genes in small ruminants. The first was held in Armidale (NSW, Australia) in 1980, just after the discovery of the Booroola gene by B. Bindon and L. Piper. The discovery of a gene having such a large effect on ovulation rate and prolificacy in sheep was totally unsuspected at this time and a number of research teams all over the world concentrated their efforts to study its effects and identify the causal mutation. About 20 years were finally needed to obtain this information, which opened a new approach to the physiological regulation of reproduction. The second meeting was organised in 1990 in Toulouse along the same lines. Although its main concern was the Booroola gene, other major genes influencing ovulation in sheep were also considered. Indeed, an increasing amount of evidence demonstrated that, on the contrary to the current opinion in quantitative genetics laboratories before 1980, prolificacy is not always controlled by a very large number of genes each exhibiting a very small effect, but may also be influenced by genes with large effects, generalising the Booroola situation to other populations. Since then, mixed inheritance was also found for other production traits such as body conformation, seasonality or milk composition. However, the major evolution has been the inexpensive large-scale access to molecular genetic information, using PCR, microsatellites and SNP technologies. QTL detection experiments are performed in all domestic species, including sheep and goats, and the identification of genes having an average effect on the performance trait variability is now possible. The utilisation of these polymorphisms should also be a great help for a better management of populations, either through the selection of breeders or through the preservation of genetic diversity. This third meeting on major genes and QTL in sheep and goats was a unique occasion for the researchers involved in this area

  17. Major quality trait analysis and QTL detection in hexaploid wheat in humid rain-fed agriculture.

    PubMed

    Li, H M; Tang, Z X; Zhang, H Q; Yan, B J; Ren, Z L

    2013-05-21

    Humid rain-fed agriculture is a special environment for wheat (Triticum aestivum) culture that tends to negatively affect wheat yield and quality. To identify quality characters of wheat in a humid environment, we conducted quality analysis and quantitative trait loci (QTL) detection in a recombinant inbred line whose parent had a high level of quality for several years. We found that high-quality wheat had less gluten content and lower protein content. Apparently, wheat quality and associated quantity traits were in a dynamic state of equilibrium. We detected 83 QTL for 10 wheat quality traits in this recombinant inbred line population. Nine QTL were detected in both evaluation years; Q.DT.scau-2A, linked to Xwmc522-2A, was detected at the same genetic location in both years. Other QTL for different traits were detected simultaneously in more than one location. Consequently, there appeared to be pleiotropic genes that control wheat quality. Based on previous studies and our research on QTL analysis of grain protein content, we conclude that there must be one or more genes for grain protein content on chromosome 6B, whose expression was little affected by environment. We constructed a consensus map and projected the QTL on it. It was useful for choosing optimal markers for marker-assisted breeding and map-based cloning.

  18. QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance.

    PubMed

    Yao, Nasser; Lee, Cheng-Ruei; Semagn, Kassa; Sow, Mounirou; Nwilene, Francis; Kolade, Olufisayo; Bocco, Roland; Oyetunji, Olumoye; Mitchell-Olds, Thomas; Ndjiondjop, Marie-Noëlle

    2016-01-01

    African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders. PMID:27508500

  19. QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance

    PubMed Central

    Semagn, Kassa; Sow, Mounirou; Nwilene, Francis; Kolade, Olufisayo; Bocco, Roland; Oyetunji, Olumoye; Mitchell-Olds, Thomas; Ndjiondjop, Marie-Noëlle

    2016-01-01

    African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders. PMID:27508500

  20. A major QTL for resistance to Gibberella stalk rot in maize.

    PubMed

    Yang, Qin; Yin, Guangming; Guo, Yanling; Zhang, Dongfeng; Chen, Shaojiang; Xu, Mingliang

    2010-08-01

    Fusarium graminearum Schwabe, the conidial form of Gibberella zeae, is the causal fungal pathogen responsible for Gibberella stalk rot of maize. Using a BC(1)F(1) backcross mapping population derived from a cross between '1145' (donor parent, completely resistant) and 'Y331' (recurrent parent, highly susceptible), two quantitative trait loci (QTLs), qRfg1 and qRfg2, conferring resistance to Gibberella stalk rot have been detected. The major QTL qRfg1 was further confirmed in the double haploid, F(2), BC(2)F(1), and BC(3)F(1) populations. Within a qRfg1 confidence interval, single/low-copy bacterial artificial chromosome sequences, anchored expressed sequence tags, and insertion/deletion polymorphisms, were exploited to develop 59 markers to saturate the qRfg1 region. A step by step narrowing-down strategy was adopted to pursue fine mapping of the qRfg1 locus. Recombinants within the qRfg1 region, screened from each backcross generation, were backcrossed to 'Y331' to produce the next backcross progenies. These progenies were individually genotyped and evaluated for resistance to Gibberella stalk rot. Significant (or no significant) difference in resistance reactions between homozygous and heterozygous genotypes in backcross progeny suggested presence (or absence) of qRfg1 in '1145' donor fragments. The phenotypes were compared to sizes of donor fragments among recombinants to delimit the qRfg1 region. Sequential fine mapping of BC(4)F(1) to BC(6)F(1) generations enabled us to progressively refine the qRfg1 locus to a ~500-kb interval flanked by the markers SSR334 and SSR58. Meanwhile, resistance of qRfg1 to Gibberella stalk rot was also investigated in BC(3)F(1) to BC(6)F(1) generations. Once introgressed into the 'Y331' genome, the qRfg1 locus could steadily enhance the frequency of resistant plants by 32-43%. Hence, the qRfg1 locus was capable of improving maize resistance to Gibberella stalk rot. PMID:20401458

  1. A major QTL for resistance to Gibberella stalk rot in maize.

    PubMed

    Yang, Qin; Yin, Guangming; Guo, Yanling; Zhang, Dongfeng; Chen, Shaojiang; Xu, Mingliang

    2010-08-01

    Fusarium graminearum Schwabe, the conidial form of Gibberella zeae, is the causal fungal pathogen responsible for Gibberella stalk rot of maize. Using a BC(1)F(1) backcross mapping population derived from a cross between '1145' (donor parent, completely resistant) and 'Y331' (recurrent parent, highly susceptible), two quantitative trait loci (QTLs), qRfg1 and qRfg2, conferring resistance to Gibberella stalk rot have been detected. The major QTL qRfg1 was further confirmed in the double haploid, F(2), BC(2)F(1), and BC(3)F(1) populations. Within a qRfg1 confidence interval, single/low-copy bacterial artificial chromosome sequences, anchored expressed sequence tags, and insertion/deletion polymorphisms, were exploited to develop 59 markers to saturate the qRfg1 region. A step by step narrowing-down strategy was adopted to pursue fine mapping of the qRfg1 locus. Recombinants within the qRfg1 region, screened from each backcross generation, were backcrossed to 'Y331' to produce the next backcross progenies. These progenies were individually genotyped and evaluated for resistance to Gibberella stalk rot. Significant (or no significant) difference in resistance reactions between homozygous and heterozygous genotypes in backcross progeny suggested presence (or absence) of qRfg1 in '1145' donor fragments. The phenotypes were compared to sizes of donor fragments among recombinants to delimit the qRfg1 region. Sequential fine mapping of BC(4)F(1) to BC(6)F(1) generations enabled us to progressively refine the qRfg1 locus to a ~500-kb interval flanked by the markers SSR334 and SSR58. Meanwhile, resistance of qRfg1 to Gibberella stalk rot was also investigated in BC(3)F(1) to BC(6)F(1) generations. Once introgressed into the 'Y331' genome, the qRfg1 locus could steadily enhance the frequency of resistant plants by 32-43%. Hence, the qRfg1 locus was capable of improving maize resistance to Gibberella stalk rot.

  2. A major QTL located on chromosome V associates with in vitro tuberization in a tetraploid potato population.

    PubMed

    Zhou, Jun; Fang, Hui; Shan, Jianwei; Gao, Xiaoxi; Chen, Lin; Xie, Conghua; Xie, Tingting; Liu, Jun

    2014-08-01

    The cultivated potato (Solanum tuberosum L.) is an autotetraploid species. The complexity of tetrasomic inheritance and the lack of pure lines increase the difficulty of genetic analysis of the inherited characteristics. Tuberization is the determinant step for economic yield of potato. To understand the complex genetic basis of tuberization of the cultivated potato, we developed linkage maps for a tetraploid population (F1) of 237 genotypes and mapped QTLs for the percent of in vitro tuberized plantlets (% IVT). The paternal map for E108 (well tuberized) covered 948 cM and included 12 linkage groups, all of which contained all four homologous chromosomes. The maternal map for E20 (nontuberized) covered 1,286 cM and included 14 linkage groups, 12 of which contained all four homologous chromosomes. All 12 chromosomes of potato were tagged using the SSR markers. A major QTL (MT05) with additive effect was detected on chromosome V of E108 which explained 16.23 % of the variation for % IVT, and two minor QTLs (mt05 and mt09) displaying simplex dominant effects were located on chromosome V and chromosome IX of E20 which explained 5.33 and 4.59 % of the variation for % IVT, respectively. Based on the additive model of MT05, the segregation ratio of the gametic genotypes (Q-: qq = 5:1) matched the ratio of the tuberized genotypes to the nontuberized genotypes in the population suggesting that the segregation of in vitro tuberization in this population is controlled by a major-effect gene or genes. The mapping results of three important candidate genes indicated that the QTL causal genes detected in our study are new. In this study, we developed the almost complete linkage maps of a tetraploid population, identified a major QTL on chromosome V affecting in vitro tuberization, suggested a major-effect gene with minor modifiers model controlling this trait and found that the QTLs identified here correspond to new tuberization genes. Our work provides new and useful

  3. Development of selective markers linked to a major QTL for parthenocarpy in eggplant (Solanum melongena L.).

    PubMed

    Miyatake, Koji; Saito, Takeo; Negoro, Satomi; Yamaguchi, Hirotaka; Nunome, Tsukasa; Ohyama, Akio; Fukuoka, Hiroyuki

    2012-05-01

    Parthenocarpy, the ability to set fruits without pollination, is a useful trait for setting fruit under unfavorable conditions. To identify the loci controlling parthenocarpy in eggplant (Solanum melongena L.), we constructed linkage maps by using co-dominant simple sequence repeat and single nucleotide polymorphism markers in F(2) populations derived from intraspecific crosses between two non-parthenocarpic lines (LS1934 and Nakate-Shinkuro) and a parthenocarpic line (AE-P03). Total map distances were 1,414.6 cM (ALF2: LS1934 x AE-P03) and 1,153.8 cM (NAF2: Nakate-Shinkuro x AE-P03), respectively. Quantitative trait locus (QTL) analyses revealed two QTLs on chromosomes 3 and 8, which we denoted as Controlling parthenocarpy3.1 (Cop3.1) and Cop8.1, respectively. The percentage of phenotypic variance explained (PVE) of Cop3.1 was 6.3% in ALF2 (LOD = 4.2) and 10.6% in NAF2 (LOD = 3.0). The PVE of Cop8.1 was 45.7% in ALF2 (LOD = 23.8) and 29.7% in NAF2 (LOD = 7.9). Using a population of backcross inbred lines, we confirmed the effect of Cop8.1, but there was no evidence to support the contribution of Cop3.1. We need to verify the effect of Cop3.1 under various temperature conditions. In addition, we clarified the effectiveness of selective SSR markers, emf21H22 and emh11J10, mapped on each side of Cop8.1 in other F(2) populations derived from various parental combinations. This is the first report concerning QTL analysis of parthenocarpy in eggplant using molecular markers. It will be useful in marker-assisted selection and in revealing the genomic mechanism underlying parthenocarpy in eggplant. PMID:22301906

  4. Development of selective markers linked to a major QTL for parthenocarpy in eggplant (Solanum melongena L.).

    PubMed

    Miyatake, Koji; Saito, Takeo; Negoro, Satomi; Yamaguchi, Hirotaka; Nunome, Tsukasa; Ohyama, Akio; Fukuoka, Hiroyuki

    2012-05-01

    Parthenocarpy, the ability to set fruits without pollination, is a useful trait for setting fruit under unfavorable conditions. To identify the loci controlling parthenocarpy in eggplant (Solanum melongena L.), we constructed linkage maps by using co-dominant simple sequence repeat and single nucleotide polymorphism markers in F(2) populations derived from intraspecific crosses between two non-parthenocarpic lines (LS1934 and Nakate-Shinkuro) and a parthenocarpic line (AE-P03). Total map distances were 1,414.6 cM (ALF2: LS1934 x AE-P03) and 1,153.8 cM (NAF2: Nakate-Shinkuro x AE-P03), respectively. Quantitative trait locus (QTL) analyses revealed two QTLs on chromosomes 3 and 8, which we denoted as Controlling parthenocarpy3.1 (Cop3.1) and Cop8.1, respectively. The percentage of phenotypic variance explained (PVE) of Cop3.1 was 6.3% in ALF2 (LOD = 4.2) and 10.6% in NAF2 (LOD = 3.0). The PVE of Cop8.1 was 45.7% in ALF2 (LOD = 23.8) and 29.7% in NAF2 (LOD = 7.9). Using a population of backcross inbred lines, we confirmed the effect of Cop8.1, but there was no evidence to support the contribution of Cop3.1. We need to verify the effect of Cop3.1 under various temperature conditions. In addition, we clarified the effectiveness of selective SSR markers, emf21H22 and emh11J10, mapped on each side of Cop8.1 in other F(2) populations derived from various parental combinations. This is the first report concerning QTL analysis of parthenocarpy in eggplant using molecular markers. It will be useful in marker-assisted selection and in revealing the genomic mechanism underlying parthenocarpy in eggplant.

  5. Heading Date QTL in Winter Wheat (Triticum aestivum L.) Coincide with Major Developmental Genes VERNALIZATION1 and PHOTOPERIOD1

    PubMed Central

    Hao, Yuan Feng; Johnson, Jerry; Harrison, Steve; Marshall, David

    2016-01-01

    In wheat (Triticum aestivum L.), time from planting to spike emergence is influenced by genes controlling vernalization requirement and photoperiod response. Characterizing the available genetic diversity of known and novel alleles of VERNALIZATION1 (VRN1) and PHOTOPERIOD1 (PPD1) in winter wheat can inform approaches for breeding climate resilient cultivars. This study identified QTL for heading date (HD) associated with multiple VRN1 and PPD1 loci in a population developed from a cross between two early flowering winter wheat cultivars. When the population was grown in the greenhouse after partial vernalization treatment, major heading date QTLs co-located with the VRN-A1 and VRN-B1 loci. Copy number variation at the VRN-A1 locus influenced HD such that RIL having three copies required longer cold exposure to transition to flowering than RIL having two VRN-A1 copies. Sequencing vrn-B1 winter alleles of the parents revealed multiple polymorphisms in the first intron that were the basis of mapping a major HD QTL coinciding with VRN-B1. A 36 bp deletion in the first intron of VRN-B1 was associated with earlier HD after partial vernalization in lines having either two or three haploid copies of VRN-A1. The VRN1 loci interacted significantly and influenced time to heading in field experiments in Louisiana, Georgia and North Carolina. The PPD1 loci were significant determinants of heading date in the fully vernalized treatment in the greenhouse and in all field environments. Heading date QTL were associated with alleles having large deletions in the upstream regions of PPD-A1 and PPD-D1 and with copy number variants at the PPD-B1 locus. The PPD-D1 locus was determined to have the largest genetic effect, followed by PPD-A1 and PPD-B1. Our results demonstrate that VRN1 and PPD1 alleles of varying strength allow fine tuning of flowering time in diverse winter wheat growing environments. PMID:27163605

  6. High-resolution mapping of a major effect QTL from wild tomato Solanum habrochaites that influences water relations under root chilling.

    PubMed

    Arms, Erin M; Bloom, Arnold J; St Clair, Dina A

    2015-09-01

    QTL stm9 controlling rapid-onset water stress tolerance in S. habrochaites was high-resolution mapped to a chromosome 9 region that contains genes associated with abiotic stress tolerances. Wild tomato (Solanum habrochaites) exhibits tolerance to abiotic stresses, including drought and chilling. Root chilling (6 °C) induces rapid-onset water stress by impeding water movement from roots to shoots. S. habrochaites responds to such changes by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) fails to close stomata and wilts. This response (shoot turgor maintenance under root chilling) is controlled by a major QTL (designated stm9) on chromosome 9, which was previously fine-mapped to a 2.7-cM region. Recombinant sub-near-isogenic lines for chromosome 9 were marker-selected, phenotyped for shoot turgor maintenance under root chilling in two sets of replicated experiments (Fall and Spring), and the data were used to high-resolution map QTL stm9 to a 0.32-cM region. QTL mapping revealed a single QTL that was coincident for both the Spring and Fall datasets, suggesting that the gene or genes contributing to shoot turgor maintenance under root chilling reside within the marker interval H9-T1673. In the S. lycopersicum reference genome sequence, this chromosome 9 region is gene-rich and contains representatives of gene families that have been associated with abiotic stress tolerance.

  7. A High-Density Genetic Map Identifies a Novel Major QTL for Boron Efficiency in Oilseed Rape (Brassica napus L.)

    PubMed Central

    Wang, Xiaohua; Zhao, Hua; Shi, Lei; Xu, Fangsen

    2014-01-01

    Low boron (B) seriously limits the growth of oilseed rape (Brassica napus L.), a high B demand species that is sensitive to low B conditions. Significant genotypic variations in response to B deficiency have been observed among B. napus cultivars. To reveal the genetic basis for B efficiency in B. napus, quantitative trait loci (QTLs) for the plant growth traits, B uptake traits and the B efficiency coefficient (BEC) were analyzed using a doubled haploid (DH) population derived from a cross between a B-efficient parent, Qingyou 10, and a B-inefficient parent, Westar 10. A high-density genetic map was constructed based on single nucleotide polymorphisms (SNPs) assayed using Brassica 60 K Infinium BeadChip Array, simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs). The linkage map covered a total length of 2139.5 cM, with 19 linkage groups (LGs) and an average distance of 1.6 cM between adjacent markers. Based on hydroponic evaluation of six B efficiency traits measured in three separate repeated trials, a total of 52 QTLs were identified, accounting for 6.14–46.27% of the phenotypic variation. A major QTL for BEC, qBEC-A3a, was co-located on A3 with other QTLs for plant growth and B uptake traits under low B stress. Using a subset of substitution lines, qBEC-A3a was validated and narrowed down to the interval between CNU384 and BnGMS436. The results of this study provide a novel major locus located on A3 for B efficiency in B. napus that will be suitable for fine mapping and marker-assisted selection breeding for B efficiency in B. napus. PMID:25375356

  8. Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat

    PubMed Central

    Atkinson, Jonathan A.; Wingen, Luzie U.; Griffiths, Marcus; Pound, Michael P.; Gaju, Oorbessy; Foulkes, M. John; Le Gouis, Jacques; Griffiths, Simon; Bennett, Malcolm J.; King, Julie; Wells, Darren M.

    2015-01-01

    Seedling root traits of wheat (Triticum aestivum L.) have been shown to be important for efficient establishment and linked to mature plant traits such as height and yield. A root phenotyping pipeline, consisting of a germination paper-based screen combined with image segmentation and analysis software, was developed and used to characterize seedling traits in 94 doubled haploid progeny derived from a cross between the winter wheat cultivars Rialto and Savannah. Field experiments were conducted to measure mature plant height, grain yield, and nitrogen (N) uptake in three sites over 2 years. In total, 29 quantitative trait loci (QTLs) for seedling root traits were identified. Two QTLs for grain yield and N uptake co-localize with root QTLs on chromosomes 2B and 7D, respectively. Of the 29 root QTLs identified, 11 were found to co-localize on 6D, with four of these achieving highly significant logarithm of odds scores (>20). These results suggest the presence of a major-effect gene regulating seedling root vigour/growth on chromosome 6D. PMID:25740921

  9. Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat.

    PubMed

    Atkinson, Jonathan A; Wingen, Luzie U; Griffiths, Marcus; Pound, Michael P; Gaju, Oorbessy; Foulkes, M John; Le Gouis, Jacques; Griffiths, Simon; Bennett, Malcolm J; King, Julie; Wells, Darren M

    2015-04-01

    Seedling root traits of wheat (Triticum aestivum L.) have been shown to be important for efficient establishment and linked to mature plant traits such as height and yield. A root phenotyping pipeline, consisting of a germination paper-based screen combined with image segmentation and analysis software, was developed and used to characterize seedling traits in 94 doubled haploid progeny derived from a cross between the winter wheat cultivars Rialto and Savannah. Field experiments were conducted to measure mature plant height, grain yield, and nitrogen (N) uptake in three sites over 2 years. In total, 29 quantitative trait loci (QTLs) for seedling root traits were identified. Two QTLs for grain yield and N uptake co-localize with root QTLs on chromosomes 2B and 7D, respectively. Of the 29 root QTLs identified, 11 were found to co-localize on 6D, with four of these achieving highly significant logarithm of odds scores (>20). These results suggest the presence of a major-effect gene regulating seedling root vigour/growth on chromosome 6D.

  10. Mapping and validation of a major QTL affecting resistance to pancreas disease (salmonid alphavirus) in Atlantic salmon (Salmo salar).

    PubMed

    Gonen, S; Baranski, M; Thorland, I; Norris, A; Grove, H; Arnesen, P; Bakke, H; Lien, S; Bishop, S C; Houston, R D

    2015-11-01

    Pancreas disease (PD), caused by a salmonid alphavirus (SAV), has a large negative economic and animal welfare impact on Atlantic salmon aquaculture. Evidence for genetic variation in host resistance to this disease has been reported, suggesting that selective breeding may potentially form an important component of disease control. The aim of this study was to explore the genetic architecture of resistance to PD, using survival data collected from two unrelated populations of Atlantic salmon; one challenged with SAV as fry in freshwater (POP 1) and one challenged with SAV as post-smolts in sea water (POP 2). Analyses of the binary survival data revealed a moderate-to-high heritability for host resistance to PD in both populations (fry POP 1 h(2)~0.5; post-smolt POP 2 h(2)~0.4). Subsets of both populations were genotyped for single nucleotide polymorphism markers, and six putative resistance quantitative trait loci (QTL) were identified. One of these QTL was mapped to the same location on chromosome 3 in both populations, reaching chromosome-wide significance in both the sire- and dam-based analyses in POP 1, and genome-wide significance in a combined analysis in POP 2. This independently verified QTL explains a significant proportion of host genetic variation in resistance to PD in both populations, suggesting a common underlying mechanism for genetic resistance across lifecycle stages. Markers associated with this QTL are being incorporated into selective breeding programs to improve PD resistance.

  11. Mapping and validation of a major QTL affecting resistance to pancreas disease (salmonid alphavirus) in Atlantic salmon (Salmo salar)

    PubMed Central

    Gonen, S; Baranski, M; Thorland, I; Norris, A; Grove, H; Arnesen, P; Bakke, H; Lien, S; Bishop, S C; Houston, R D

    2015-01-01

    Pancreas disease (PD), caused by a salmonid alphavirus (SAV), has a large negative economic and animal welfare impact on Atlantic salmon aquaculture. Evidence for genetic variation in host resistance to this disease has been reported, suggesting that selective breeding may potentially form an important component of disease control. The aim of this study was to explore the genetic architecture of resistance to PD, using survival data collected from two unrelated populations of Atlantic salmon; one challenged with SAV as fry in freshwater (POP 1) and one challenged with SAV as post-smolts in sea water (POP 2). Analyses of the binary survival data revealed a moderate-to-high heritability for host resistance to PD in both populations (fry POP 1 h2~0.5; post-smolt POP 2 h2~0.4). Subsets of both populations were genotyped for single nucleotide polymorphism markers, and six putative resistance quantitative trait loci (QTL) were identified. One of these QTL was mapped to the same location on chromosome 3 in both populations, reaching chromosome-wide significance in both the sire- and dam-based analyses in POP 1, and genome-wide significance in a combined analysis in POP 2. This independently verified QTL explains a significant proportion of host genetic variation in resistance to PD in both populations, suggesting a common underlying mechanism for genetic resistance across lifecycle stages. Markers associated with this QTL are being incorporated into selective breeding programs to improve PD resistance. PMID:25990876

  12. A major QTL for acute ethanol sensitivity in the alcohol tolerant and non-tolerant selected rat lines.

    PubMed

    Radcliffe, R A; Erwin, V G; Bludeau, P; Deng, X; Fay, T; Floyd, K L; Deitrich, R A

    2009-08-01

    The Alcohol Tolerant and Alcohol Non-Tolerant rats (AT, ANT) were selectively bred for ethanol-induced ataxia as measured on the inclined plane. Here we report on a quantitative trait locus (QTL) study in an F(2) intercross population derived from inbred AT and ANT (IAT, IANT) and a follow-up study of congenics that were bred to examine one of the mapped QTLs. Over 1200 F(2) offspring were tested for inclined plane sensitivity, acute tolerance on the inclined plane, duration of the loss of righting reflex (LORR) and blood ethanol at regain of the righting reflex (BECRR). F(2) rats that were in the upper and lower 20% for inclined plane sensitivity were genotyped with 78 SSLP markers. Significant QTLs for inclined plane sensitivity were mapped on chromosomes 8 and 20; suggestive QTLs were mapped on chromosomes 1, 2 and 3. Highly significant QTLs for LORR duration (LOD = 12.4) and BECRR (LOD = 5.7) were mapped to the same locus on chromosome 1. Breeding and testing of reciprocal congenic lines confirmed the chromosome 1 LORR/BECRR QTL. A series of recombinant congenic sub-lines were bred to fine-map this QTL. Current results have narrowed the QTL to an interval of between 5 and 20 Mb. We expect to be able to narrow the interval to less than 5 Mb with additional genotyping and continued breeding of recombinant sub-congenic lines.

  13. Identification of a major QTL allele from wild soybean (Glycine soja Sieb. & Zucc.) for increasing alkaline salt tolerance in soybean.

    PubMed

    Tuyen, D D; Lal, S K; Xu, D H

    2010-07-01

    Salt-affected soils are generally classified into two main categories, sodic (alkaline) and saline. Our previous studies showed that the wild soybean accession JWS156-1 (Glycine soja) from the Kinki area of Japan was tolerant to NaCl salt, and the quantitative trait locus (QTL) for NaCl salt tolerance was located on soybean linkage group N (chromosome 3). Further investigation revealed that the wild soybean accession JWS156-1 also had a higher tolerance to alkaline salt stress. In the present study, an F(6) recombinant inbred line mapping population (n = 112) and an F(2) population (n = 149) derived from crosses between a cultivated soybean cultivar Jackson and JWS156-1 were used to identify QTL for alkaline salt tolerance in soybean. Evaluation of soybean alkaline salt tolerance was carried out based on salt tolerance rating (STR) and leaf chlorophyll content (SPAD value) after treatment with 180 mM NaHCO(3) for about 3 weeks under greenhouse conditions. In both populations, a significant QTL for alkaline salt tolerance was detected on the molecular linkage group D2 (chromosome 17), which accounted for 50.2 and 13.0% of the total variation for STR in the F(6) and the F(2) populations, respectively. The wild soybean contributed to the tolerance allele in the progenies. Our results suggest that QTL for alkaline salt tolerance is different from the QTL for NaCl salt tolerance found previously in this wild soybean genotype. The DNA markers closely associated with the QTLs might be useful for marker-assisted selection to pyramid tolerance genes in soybean for both alkaline and saline stresses.

  14. A major QTL and an SSR marker associated with glycoalkaloid content in potato tubers from Solanum tuberosum x S. sparsipilum located on chromosome I.

    PubMed

    Sørensen, Kirsten Kørup; Kirk, Hanne Grethe; Olsson, Kerstin; Labouriau, Rodrigo; Christiansen, Jørgen

    2008-06-01

    New potato (Solanum tuberosum) varieties are required to contain low levels of the toxic glycoalkaloids and a potential approach to obtain this is through marker-assisted selection (MAS). Before applying MAS it is necessary to map quantitative trait loci (QTLs) for glycoalkaloid content in potato tubers and identify markers that link tightly to this trait. In this study, tubers of a dihaploid BC(1) population, originating from a cross between 90-HAF-01 (S. tuberosum(1)) and 90-HAG-15 (S. tuberosum(2) x S. sparsipilum), were evaluated for content of alpha-solanine and alpha-chaconine (total glycoalkaloid, TGA) after field trials. In addition, tubers were assayed for TGA content after exposure to light. A detailed analysis of segregation patterns indicated that a major QTL is responsible for the TGA content in tubers of this potato population. One highly significant QTL was mapped to chromosome I of the HAG and the HAF parent. Quantitative trait loci for glycoalkaloid production in foliage of different Solanum species have previously been mapped to this chromosome. In the present research, QTLs for alpha-solanine and alpha-chaconine content were mapped to the same location as for TGA content. Similar results were observed for tubers exposed to light. The simple sequence repeat marker STM5136 was closely linked to the identified QTL.

  15. Microsomal Omega-3 Fatty Acid Desaturase Genes in Low Linolenic Acid Soybean Line RG10 and Validation of Major Linolenic Acid QTL

    PubMed Central

    Reinprecht, Yarmilla; Pauls, K. Peter

    2016-01-01

    High levels of linolenic acid (80 g kg−1) are associated with the development of off-flavors and poor stability in soybean oil. The development of low linolenic acid lines such as RG10 (20 g kg−1 linolenic acid) can reduce these problems. The level of linolenic acid in seed oil is determined by the activities of microsomal omega-3 fatty acid desaturases (FAD3). A major linolenic acid QTL (>70% of variation) on linkage group B2 (chromosome Gm14) was previously detected in a recombinant inbred line population from the RG10 × OX948 cross. The objectives of this study were to validate the major linolenic acid QTL in an independent population and characterize all the soybean FAD3 genes. Four FAD3 genes were sequenced and localized in RG10 and OX948 and compared to the genes in the reference Williams 82 genome. The FAD3A gene sequences mapped to the locus Glyma.14g194300 [on the chromosome Gm14 (B2)], which is syntenic to the FAD3B gene (locus Glyma.02g227200) on the chromosome Gm02 (D1b). The location of the FAD3A gene is the same as was previously determined for the fan allele, that conditions low linolenic acid content and several linolenic acid QTL, including Linolen 3-3, mapped previously with the RG10 × OX948 population and confirmed in the PI 361088B × OX948 population as Linolen-PO (FAD3A). The FAD3B gene-based marker, developed previously, was mapped to the chromosome Gm02 (D1b) in a region containing a newly detected linolenic acid QTL [Linolen-RO(FAD3B)] in the RG10 × OX948 genetic map and corresponds well with the in silico position of the FAD3B gene sequences. FAD3C and FAD3D gene sequences, mapped to syntenic regions on chromosomes Gm18 (locus Glyma.18g062000) and Gm11 (locus Glyma.11g227200), respectively. Association of linolenic acid QTL with the desaturase genes FAD3A and FAD3B, their validation in an independent population, and development of FAD3 gene-specific markers should simplify and accelerate breeding for low linolenic acid soybean

  16. Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye.

    PubMed

    Yun, Lan; Larson, Steve R; Mott, Ivan W; Jensen, Kevin B; Staub, Jack E

    2014-06-01

    Rhizomes are prostrate subterranean stems that provide primitive mechanisms of vegetative dispersal, survival, and regrowth of perennial grasses and other monocots. The extent of rhizome proliferation varies greatly among grasses, being absent in cereals and other annuals, strictly confined in caespitose perennials, or highly invasive in some perennial weeds. However, genetic studies of rhizome proliferation are limited and genes controlling rhizomatous growth habit have not been elucidated. Quantitative trait loci (QTLs) controlling rhizome spreading were compared in reciprocal backcross populations derived from hybrids of rhizomatous creeping wildrye (Leymus triticoides) and caespitose basin wildrye (L. cinereus), which are perennial relatives of wheat. Two recessive QTLs were unique to the creeping wildrye backcross, one dominant QTL was unique to the basin wildrye backcross, and one additive QTL was detectable in reciprocal backcrosses with high log odds (LOD = 31.6) in the basin wildrye background. The dominant QTL located on linkage group (LG)-2a was aligned to a dominant rhizome orthogene (Rhz3) of perennial rice (Oryza longistamina) and perennial sorghum (Sorghum propinquum). Nonparametric 99 % confidence bounds of the 31.6-LOD QTL were localized to a distal 3.8-centiMorgan region of LG-6a, which corresponds to a 0.7-Mb region of Brachypodium Chromosome 3 containing 106 genes. An Aux/IAA auxin signal factor gene was located at the 31.6-LOD peak, which could explain the gravitropic and aphototropic behavior of rhizomes. Findings elucidate genetic mechanisms controlling rhizome development and architectural growth habit differences among plant species. Results have possible applications to improve perennial forage and turf grasses, extend the vegetative life cycle of annual cereals, such as wheat, or control the invasiveness of highly rhizomatous weeds such as quackgrass (Elymus repens). PMID:24509730

  17. Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye.

    PubMed

    Yun, Lan; Larson, Steve R; Mott, Ivan W; Jensen, Kevin B; Staub, Jack E

    2014-06-01

    Rhizomes are prostrate subterranean stems that provide primitive mechanisms of vegetative dispersal, survival, and regrowth of perennial grasses and other monocots. The extent of rhizome proliferation varies greatly among grasses, being absent in cereals and other annuals, strictly confined in caespitose perennials, or highly invasive in some perennial weeds. However, genetic studies of rhizome proliferation are limited and genes controlling rhizomatous growth habit have not been elucidated. Quantitative trait loci (QTLs) controlling rhizome spreading were compared in reciprocal backcross populations derived from hybrids of rhizomatous creeping wildrye (Leymus triticoides) and caespitose basin wildrye (L. cinereus), which are perennial relatives of wheat. Two recessive QTLs were unique to the creeping wildrye backcross, one dominant QTL was unique to the basin wildrye backcross, and one additive QTL was detectable in reciprocal backcrosses with high log odds (LOD = 31.6) in the basin wildrye background. The dominant QTL located on linkage group (LG)-2a was aligned to a dominant rhizome orthogene (Rhz3) of perennial rice (Oryza longistamina) and perennial sorghum (Sorghum propinquum). Nonparametric 99 % confidence bounds of the 31.6-LOD QTL were localized to a distal 3.8-centiMorgan region of LG-6a, which corresponds to a 0.7-Mb region of Brachypodium Chromosome 3 containing 106 genes. An Aux/IAA auxin signal factor gene was located at the 31.6-LOD peak, which could explain the gravitropic and aphototropic behavior of rhizomes. Findings elucidate genetic mechanisms controlling rhizome development and architectural growth habit differences among plant species. Results have possible applications to improve perennial forage and turf grasses, extend the vegetative life cycle of annual cereals, such as wheat, or control the invasiveness of highly rhizomatous weeds such as quackgrass (Elymus repens).

  18. pc8.1, a major QTL for pigment content in pepper fruit, is associated with variation in plastid compartment size.

    PubMed

    Brand, Arnon; Borovsky, Yelena; Meir, Sagit; Rogachev, Ilana; Aharoni, Asaph; Paran, Ilan

    2012-03-01

    Studies on the genetic control of pigment content in pepper fruit have focused mainly on monogenic mutations leading to changes in fruit color. In addition to the qualitative variation in fruit color, quantitative variation in pigment content and color intensity exists in pepper giving rise to a range of color intensities. However, the genetic basis for this variation is poorly understood, hindering the development of peppers that are rich in these beneficial compounds. In this paper, quantitative variation in pigment content was studied in a cross between a dark-green Capsicum annuum pepper and a light-green C. chinense pepper. Two major pigment content QTLs that control chlorophyll content were identified, pc8.1 and pc10.1. The major QTL pc8.1, also affected carotenoid content in the ripe fruit. However, additional analyses in subsequent generations did not reveal a consistent effect of this QTL on carotenoid content in ripe fruit. Confocal microscopy analyses of green immature fruits of the parents and of near-isogenic lines for pc8.1 indicated that the QTL exerts its effect via increasing chloroplast compartment size in the dark-green genotypes, predominantly in a fruit-specific manner. Metabolic analyses indicated that in addition to chlorophyll, chloroplast-associated tocopherols and carotenoids are also elevated. Future identification of the genes controlling pigment content QTLs in pepper will provide a better understanding of this important trait and new opportunities for breeding peppers and other Solanaceae species with enhanced nutritional value. PMID:21987007

  19. A single major QTL controls expression of larval Cry1F resistance trait in Ostrinia nubilalis (Lepidoptera: Crambidae) and is independent of midgut receptor genes.

    PubMed

    Coates, Brad S; Sumerford, Douglas V; Lopez, Miriam D; Wang, Haichuan; Fraser, Lisa M; Kroemer, Jeremy A; Spencer, Terrence; Kim, Kyung S; Abel, Craig A; Hellmich, Richard L; Siegfried, Blair D

    2011-08-01

    The European corn borer, Ostrinia nubilalis (Lepidoptera: Crambidae), is an introduced crop pest in North America that causes major damage to corn and reduces yield of food, feed, and biofuel materials. The Cry1F toxin from Bacillus thuringiensis (Bt) expressed in transgenic hybrid corn is highly toxic to O. nubilalis larvae and effective in minimizing feeding damage. A laboratory colony of O. nubilalis was selected for high levels of Cry1F resistance (>12,000-fold compared to susceptible larvae) and is capable of survival on transgenic hybrid corn. Genetic linkage maps with segregating AFLP markers show that the Cry1F resistance trait is controlled by a single quantitative trait locus (QTL) on linkage group 12. The map position of single nucleotide polymorphism (SNP) markers indicated that midgut Bt toxin-receptor genes, alkaline phosphatase, aminopeptidase N, and cadherin, are not linked with the Cry1F QTL. Evidence suggests that genes within this genome interval may give rise to a novel Bt toxin resistance trait for Lepidoptera that appears independent of known receptor-based mechanisms of resistance.

  20. A single major QTL controls expression of larval Cry1F resistance trait in Ostrinia nubilalis (Lepidoptera: Crambidae) and is independent of midgut receptor genes.

    PubMed

    Coates, Brad S; Sumerford, Douglas V; Lopez, Miriam D; Wang, Haichuan; Fraser, Lisa M; Kroemer, Jeremy A; Spencer, Terrence; Kim, Kyung S; Abel, Craig A; Hellmich, Richard L; Siegfried, Blair D

    2011-08-01

    The European corn borer, Ostrinia nubilalis (Lepidoptera: Crambidae), is an introduced crop pest in North America that causes major damage to corn and reduces yield of food, feed, and biofuel materials. The Cry1F toxin from Bacillus thuringiensis (Bt) expressed in transgenic hybrid corn is highly toxic to O. nubilalis larvae and effective in minimizing feeding damage. A laboratory colony of O. nubilalis was selected for high levels of Cry1F resistance (>12,000-fold compared to susceptible larvae) and is capable of survival on transgenic hybrid corn. Genetic linkage maps with segregating AFLP markers show that the Cry1F resistance trait is controlled by a single quantitative trait locus (QTL) on linkage group 12. The map position of single nucleotide polymorphism (SNP) markers indicated that midgut Bt toxin-receptor genes, alkaline phosphatase, aminopeptidase N, and cadherin, are not linked with the Cry1F QTL. Evidence suggests that genes within this genome interval may give rise to a novel Bt toxin resistance trait for Lepidoptera that appears independent of known receptor-based mechanisms of resistance. PMID:21822602

  1. Exploring bacterial lignin degradation.

    PubMed

    Brown, Margaret E; Chang, Michelle C Y

    2014-04-01

    Plant biomass represents a renewable carbon feedstock that could potentially be used to replace a significant level of petroleum-derived chemicals. One major challenge in its utilization is that the majority of this carbon is trapped in the recalcitrant structural polymers of the plant cell wall. Deconstruction of lignin is a key step in the processing of biomass to useful monomers but remains challenging. Microbial systems can provide molecular information on lignin depolymerization as they have evolved to break lignin down using metalloenzyme-dependent radical pathways. Both fungi and bacteria have been observed to metabolize lignin; however, their differential reactivity with this substrate indicates that they may utilize different chemical strategies for its breakdown. This review will discuss recent advances in studying bacterial lignin degradation as an approach to exploring greater diversity in the environment. PMID:24780273

  2. From lignin association to nano-/micro-particle preparation: Extracting higher value of lignin

    DOE PAGES

    Zhao, Wenwen; Simmons, Blake; Singh, Seema; Ragauskas, Arthur J.; Cheng, Gang

    2016-09-26

    As the most abundant source of renewable aromatic compounds on the planet, lignin is gaining growing interest in replacing petroleum-based chemicals and products. Value-added applications of lignin are also essential for economic viability for future bio-refineries. It is however an under-utilized natural resource due to its structural heterogeneities. Lignin nanoparticles offer many opportunities for value-added applications of lignin. The solution structures of lignin were proposed as one of the key elements in controlling lignin nano-/micro-particle preparation. Fundamental understanding of solutionstructures of lignin aid in designing better fabrication of lignin nanoparticles. A deeper understanding of the observed experimental results also pointsmore » to the need for detailed studies of lignin in solution. Lastly, this review consists of two major topics, the solution structures of lignin and lignin nano-/micro-particle preparation. Suggestions for future studies regarding these two topics were also put forward.« less

  3. Dominance Is the Major Genetic Basis of Heterosis in Rice as Revealed by Qtl Analysis Using Molecular Markers

    PubMed Central

    Xiao, J.; Li, J.; Yuan, L.; Tanksley, S. D.

    1995-01-01

    A set of 194 F(7) lines derived from a subspecific rice cross showing strong F(1) heterosis was backcrossed to the two parents. The materials (388 BC(1)F(7) lines, 194 F(8) lines, two parents, F(1)) were phenotyped for 12 quantitative traits. A total of 37 significant QTLs (LOD >/= 2.0) was detected through 141 RFLP markers in the BC(1)F(7) populations. Twenty-seven (73%) quantitative trait loci (QTLs) were detected in only one of the BC(1)F(7) populations. In 82% of these cases, the heterozygotes were superior to the respective homozygotes. The remaining 10 (27%) QTLs were detected in both BC(1)F(7) populations, and the heterozygote had a phenotype falling between those of the two homozygotes and in no instances were the heterozygotes found to be superior to both homozygotes. These results suggest that dominance complementation is the major genetic basis of heterosis in rice. This conclusion was strengthened by the finding that there was no correlation between most traits and overall genome heterozygosity and that there were some recombinant inbred lines in the F(8) population having phenotypic values superior to the F(1) for all of the traits evaluated--a result not expected if overdominance was a major contributor to heterosis. Digenic epistasis was not evident. PMID:7498751

  4. DNL1, encodes cellulose synthase-like D4, is a major QTL for plant height and leaf width in rice (Oryza sativa L.).

    PubMed

    Ding, Zhengquan; Lin, Zefeng; Li, Qin; Wu, Hao; Xiang, Chunyan; Wang, Jianfei

    2015-02-01

    To better understand the genetic of rice agronomic traits, we selected two different rice germplasms in phenotypes, Xian80 and Suyunuo, to construct genetic population for QTL analysis. A total of 25 QTLs for six traits were found in a 175 F2 population. Major QTLs, qPH12,qLW12.2, qLL12 and qGW12.1, explaining 50.00%, 57.08%, 15.41% and 22.51% phenotypic variation for plant height, leaf width, leaf length and grain width, respectively, were located on the same interval of chromosome 12 flanking SSR markers RM519 and RM1103. In consideration of the great effects on plant height and leaf width, the locus was named DNL1 (Dwarf and Narrowed Leaf 1). Using a segregating population derived from F2 heterozygous individuals, a total of 1363 dwarfism and narrowed-leaf individuals was selected for screening recombinants. By high-resolution linkage analysis in 141 recombination events, DNL1 was narrowed to a 62.39kb region of InDel markers ID12M28 and HF43. The results of ORF analysis in target region and nucleotide sequence alignment indicated that DNL1 encodes cellulose synthase-like D4 protein, and a single nucleotide substitution (C2488T) in dnl1 result in decrease in plant height and leaf width. Bioinformatical analysis demonstrated that a conserved role for OsCSLD4 in the regulation of plant growth and development. Expression analysis for OsCSLDs showed OsCSLD4 highly expressed in roots, while other CSLD members had comparatively lower expression levels. However, no clear evidence about CSLD4/DNL1 expression was associated with its function.

  5. Genome Assembly Anchored QTL Map of Bovine Chromosome 14

    PubMed Central

    Wibowo, Tito A.; Gaskins, Charles T.; Newberry, Ruth C.; Thorgaard, Gary H.; Michal, Jennifer J.; Jiang, Zhihua

    2008-01-01

    Bovine chromosome 14 (BTA14) has been widely explored for quantitative trait loci (QTL) and genes related to economically important traits in both dairy and beef cattle. We reviewed more than 40 investigations and anchored 126 QTL to the current genome assembly (Btau 4_0). Using this anchored QTL map, we observed that, in dairy cattle, the region spanning 0 – 10 Mb on BTA14 has the highest density QTL map with a total of 56 QTL, mainly for milk production traits. It is very likely that both somatic cell score (SCS) and clinical mastitis share some common QTL in two regions: 61.48 Mb - 73.84 Mb and 7.86 Mb – 39.55 Mb, respectively. As well, both ovulation rate and twinning rate might share a common QTL region from 34.16 Mb to 65.38 Mb. However, there are no common QTL locations in three pregnancy related phenotypes: non-return rate, pregnancy rate and daughter pregnancy rate. In beef cattle, the majority of QTL are located in a broad region of 15 Mb – 45 Mb on the chromosome. Functional genes, such as CRH, CYP11B1, DGAT1, FABP4 and TG, as potential candidates for some of these QTL, were also reviewed. Therefore, our review provides a standardized QTL map anchored within the current genome assembly, which would enhance the process of selecting positional and physiological candidate genes for many important traits in cattle. PMID:19043607

  6. Ensemble Learning of QTL Models Improves Prediction of Complex Traits

    PubMed Central

    Bian, Yang; Holland, James B.

    2015-01-01

    Quantitative trait locus (QTL) models can provide useful insights into trait genetic architecture because of their straightforward interpretability but are less useful for genetic prediction because of the difficulty in including the effects of numerous small effect loci without overfitting. Tight linkage between markers introduces near collinearity among marker genotypes, complicating the detection of QTL and estimation of QTL effects in linkage mapping, and this problem is exacerbated by very high density linkage maps. Here we developed a thinning and aggregating (TAGGING) method as a new ensemble learning approach to QTL mapping. TAGGING reduces collinearity problems by thinning dense linkage maps, maintains aspects of marker selection that characterize standard QTL mapping, and by ensembling, incorporates information from many more markers-trait associations than traditional QTL mapping. The objective of TAGGING was to improve prediction power compared with QTL mapping while also providing more specific insights into genetic architecture than genome-wide prediction models. TAGGING was compared with standard QTL mapping using cross validation of empirical data from the maize (Zea mays L.) nested association mapping population. TAGGING-assisted QTL mapping substantially improved prediction ability for both biparental and multifamily populations by reducing both the variance and bias in prediction. Furthermore, an ensemble model combining predictions from TAGGING-assisted QTL and infinitesimal models improved prediction abilities over the component models, indicating some complementarity between model assumptions and suggesting that some trait genetic architectures involve a mixture of a few major QTL and polygenic effects. PMID:26276383

  7. Ensemble Learning of QTL Models Improves Prediction of Complex Traits.

    PubMed

    Bian, Yang; Holland, James B

    2015-10-01

    Quantitative trait locus (QTL) models can provide useful insights into trait genetic architecture because of their straightforward interpretability but are less useful for genetic prediction because of the difficulty in including the effects of numerous small effect loci without overfitting. Tight linkage between markers introduces near collinearity among marker genotypes, complicating the detection of QTL and estimation of QTL effects in linkage mapping, and this problem is exacerbated by very high density linkage maps. Here we developed a thinning and aggregating (TAGGING) method as a new ensemble learning approach to QTL mapping. TAGGING reduces collinearity problems by thinning dense linkage maps, maintains aspects of marker selection that characterize standard QTL mapping, and by ensembling, incorporates information from many more markers-trait associations than traditional QTL mapping. The objective of TAGGING was to improve prediction power compared with QTL mapping while also providing more specific insights into genetic architecture than genome-wide prediction models. TAGGING was compared with standard QTL mapping using cross validation of empirical data from the maize (Zea mays L.) nested association mapping population. TAGGING-assisted QTL mapping substantially improved prediction ability for both biparental and multifamily populations by reducing both the variance and bias in prediction. Furthermore, an ensemble model combining predictions from TAGGING-assisted QTL and infinitesimal models improved prediction abilities over the component models, indicating some complementarity between model assumptions and suggesting that some trait genetic architectures involve a mixture of a few major QTL and polygenic effects. PMID:26276383

  8. Development of sequence characterized amplified region (SCAR) primers for the detection of Phyto.5.2, a major QTL for resistance to Phytophthora capsici Leon. in pepper.

    PubMed

    Quirin, E A; Ogundiwin, E A; Prince, J P; Mazourek, M; Briggs, M O; Chlanda, T S; Kim, K-T; Falise, M; Kang, B-C; Jahn, M M

    2005-02-01

    Phytophthora capsici causes devastating disease on many crop species, including Capsicum. Resistance in Capsicum annuum is genetically and physiologically complex. A panel of Capsicum germplasm that included genotypes from both C. annuum and C. chinense showing highly resistant, highly susceptible and intermediate or tolerant responses to the pathogen, respectively, was screened with a series of randomly amplified polymorphic sequence primers to determine which genomic regions contribute to the highest level of resistance. One primer, OpD04, amplified a single band only in those C. annuum and C. chinense genotypes showing the highest level of resistance. The amplified product was cloned, sequenced and used to design longer primers in order to generate a sequence characterized amplified region marker which was then mapped in a reference mapping population and a screened population segregating for resistance to P. capsici. These primers were observed to define a locus on pepper chromosome 5 tightly linked to Phyto.5.2, one of six quantitative trait loci (QTL) previously reported to contribute to P. capsici resistance. These results indicate that the Phyto.5.2 QTL may be widely distributed in highly resistant germplasm and provide improved resolution for this QTL. This work also defines the first breeding tools for this system, allowing for the rapid selection of genotypes likely to be highly resistant to P. capsici.

  9. Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping.

    PubMed

    Zhang, Yu; Cui, Min; Zhang, Jimin; Zhang, Lei; Li, Chenliu; Kan, Xin; Sun, Qian; Deng, Dexiang; Yin, Zhitong

    2016-01-01

    Maize grain contamination with aflatoxin from Aspergillus flavus (A. flavus) is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs) associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS) and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs), and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM) on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs) in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD) and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS) of A. flavus resistance and a characterisation of the causal gene. PMID:27598199

  10. Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping.

    PubMed

    Zhang, Yu; Cui, Min; Zhang, Jimin; Zhang, Lei; Li, Chenliu; Kan, Xin; Sun, Qian; Deng, Dexiang; Yin, Zhitong

    2016-09-02

    Maize grain contamination with aflatoxin from Aspergillus flavus (A. flavus) is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs) associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS) and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs), and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM) on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs) in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD) and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS) of A. flavus resistance and a characterisation of the causal gene.

  11. Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping

    PubMed Central

    Zhang, Yu; Cui, Min; Zhang, Jimin; Zhang, Lei; Li, Chenliu; Kan, Xin; Sun, Qian; Deng, Dexiang; Yin, Zhitong

    2016-01-01

    Maize grain contamination with aflatoxin from Aspergillus flavus (A. flavus) is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs) associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS) and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs), and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM) on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs) in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD) and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS) of A. flavus resistance and a characterisation of the causal gene. PMID:27598199

  12. Preparation and Analysis of Biomass Lignins

    SciTech Connect

    Compere, A L; Griffith, William {Bill} L

    2009-01-01

    Lignin, comprised primarily of three randomly polymerized phenylpropenyl monomers, is, arguably, the second most common organic molecule on earth. In current biorefinery applications, lignin is burned, usually in concentrated pulping or hydrolysis liquor, as a source of process steam and both internal and exported electricity. The aromatic content of lignin makes it a potentially attractive feedstock for highly-valued aromatic chemicals, polymers, and carbon products (graphite, activated carbon, and carbon fiber). Revenue from production of lignin-based chemicals could play a major role in biorefinery profitability if cost-effective methods for lignin separation and purification can be developed. This article presents descriptions of methods for assessing and purifying biorefinery lignins so that they can be evaluated for use as feedstocks for production of chemical products. Areas covered are: 1) initial evaluations of as-received lignin samples (visual, microscopic, separable organics), 2) analysis of common contaminants (bulk and filterable ash and particulate contaminants in liquid and dry lignin samples), 3) preparation of lignins for experimental use as chemical feedstocks (prefiltration, filtration using bench-scale chemical apparatus and larger scale bag filters, one-step lignin precipitation, two-step carbohydrate and lignin precipitation, desalting of dry powdered or precipitated lignin, and lyophilization). These methods have been used successfully at bench-scale to produce the 1 50 kg amounts of wood and grass lignins typically required for bench-scale assessment as chemical feedstocks

  13. Preparation and Analysis of Biomass Lignins

    NASA Astrophysics Data System (ADS)

    Compere, Alicia L.; Griffith, William L.

    Lignin, comprised primarily of three randomly polymerized phenylpropenyl monomers, is, arguably, the second most common organic molecule on earth. In current biorefinery applications, lignin is burned, usually in concentrated pulping or hydrolysis liquor, as a source of process steam and both internal and exported electricity. The aromatic content of lignin makes it a potentially attractive feedstock for high-value aromatic chemicals, polymers, and carbon products (graphite, activated carbon, and carbon fiber). Revenue from production of lignin-based chemicals could play a major role in biorefinery profitability if cost-effective methods for lignin separation and purification can be developed. This chapter presents descriptions of methods for assessing and purifying biorefinery lignins so that they can be evaluated for use as feedstock for production of chemical products. Areas covered are: (1) initial evaluations of as-received lignin samples (visual, microscopic, separable organics); (2) analysis of common contaminants (bulk and filterable ash and particulate contaminants in liquid and dry lignin samples); (3) preparation of lignins for experimental use as chemical feedstock (prefiltration, filtration using bench-scale chemical apparatus and larger scale bag filters, one-step lignin precipitation, two-step carbohydrate and lignin precipitation, desalting of dry powdered or precipitated lignin, and lyophilization). These methods have been used successfully at the bench scale to produce the 1-50 kg amounts of wood and grass lignins typically required for bench-scale assessment as chemical feedstocks.

  14. Bacterial extracellular lignin peroxidase

    DOEpatents

    Crawford, Donald L.; Ramachandra, Muralidhara

    1993-01-01

    A newly discovered lignin peroxidase enzyme is provided. The enzyme is obtained from a bacterial source and is capable of degrading the lignin portion of lignocellulose in the presence of hydrogen peroxide. The enzyme is extracellular, oxidative, inducible by lignin, larch wood xylan, or related substrates and capable of attacking certain lignin substructure chemical bonds that are not degradable by fungal lignin peroxidases.

  15. Lignin nanoparticle synthesis

    DOEpatents

    Dirk, Shawn M.; Cicotte, Kirsten Nicole; Wheeler, David R.; Benko, David A.

    2015-08-11

    A method including reducing a particle size of lignin particles to an average particle size less than 40 nanometers; after reducing the particle size, combining the lignin particles with a polymeric material; and forming a structure of the combination. A method including exposing lignin to a diazonium precursor including a functional group; modifying the lignin by introducing the functional group to the lignin; and combining the modified lignin with a polymeric material to form a composite. An apparatus including a composite of a polymer and lignin wherein the lignin has an average particle size less than 100 micrometers.

  16. Identification of QTLs for Resistance to Sclerotinia Stem Rot and BnaC.IGMT5.a as a Candidate Gene of the Major Resistant QTL SRC6 in Brassica napus

    PubMed Central

    Wu, Jian; Cai, Guangqin; Tu, Jiangying; Li, Lixia; Liu, Sheng; Luo, Xinping; Zhou, Lipeng; Fan, Chuchuan; Zhou, Yongming

    2013-01-01

    Stem rot caused by Sclerotinia sclerotiorum in many important dicotyledonous crops, including oilseed rape (Brassica napus), is one of the most devastating fungal diseases and imposes huge yield loss each year worldwide. Currently, breeding for Sclerotinia resistance in B. napus, as in other crops, can only rely on germplasms with quantitative resistance genes. Thus, the identification of quantitative trait locus (QTL) for S. sclerotiorum resistance/tolerance in this crop holds immediate promise for the genetic improvement of the disease resistance. In this study, ten QTLs for stem resistance (SR) at the mature plant stage and three QTLs for leaf resistance (LR) at the seedling stage in multiple environments were mapped on nine linkage groups (LGs) of a whole genome map for B. napus constructed with SSR markers. Two major QTLs, LRA9 on LG A9 and SRC6 on LG C6, were repeatedly detected across all environments and explained 8.54–15.86% and 29.01%–32.61% of the phenotypic variations, respectively. Genotypes containing resistant SRC6 or LRA9 allele showed a significant reduction in disease lesion after pathogen infection. Comparative mapping with Arabidopsis and data mining from previous gene profiling experiments identified that the Arabidopsis homologous gene of IGMT5 (At1g76790) was related to the SRC6 locus. Four copies of the IGMT5 gene in B. napus were isolated through homologous cloning, among which, only BnaC.IGMT5.a showed a polymorphism between parental lines and can be associated with the SRC6. Furthermore, two parental lines exhibited a differential expression pattern of the BnaC.IGMT5.a gene in responding to pathogen inoculation. Thus, our data suggested that BnaC.IGMT5.a was very likely a candidate gene of this major resistance QTL. PMID:23844081

  17. Cell Wall Composition and Underlying QTL in an F1 Pseudo-Testcross Population of Switchgrass

    DOE PAGES

    Serba, Desalegn D.; Sykes, Robert W.; Gjersing, Erica L.; Decker, Stephen R.; Daverdin, Guillaume; Devos, Katrien M.; Brummer, E. Charles; Saha, Malay C.

    2016-04-23

    Natural genetic variation for reduced recalcitrance can be used to improve switchgrass for biofuel production. A full-sib switchgrass mapping population developed by crossing a lowland genotype, AP13, and upland genotype, VS16, was evaluated at three locations (Ardmore and Burneyville, OK and Watkinsville, GA). Biomass harvested after senescence in 2009 and 2010 was evaluated at the National Renewable Energy Laboratory (NREL) for sugar release using enzymatic hydrolysis and for lignin content and syringyl/guaiacyl lignin monomer (S/G) ratio using pyrolysis molecular beam mass spectrometry (py-MBMS). Glucose and xylose release ranged from 120 to 313 and 123 to 263 mg g-1, respectively, whilemore » lignin content ranged from 19 to 27% of the dry biomass. Statistically significant differences were observed among the genotypes and the environments for the cell wall composition traits. Regression analysis showed that a unit increase in lignin content reduced total sugar release by an average of 10 mg g-1. Quantitative trait loci (QTL) analysis detected 9 genomic regions underlying sugar release and 14 for lignin content. The phenotypic variation explained by the individual QTL identified for sugar release ranged from 4.5 to 9.4 and for lignin content from 3.8 to 11.1%. Mapping of the QTL regions to the switchgrass genome sequence (v1.1) found that some of the QTL colocalized with genes involved in carbohydrate processing and metabolism, plant development, defense systems, and transcription factors. Finally, the markers associated with QTL can be implemented in breeding programs to efficiently develop improved switchgrass cultivars for biofuel production.« less

  18. QTL mapping of resistance to gray leaf spot in maize.

    PubMed

    Zhang, Yan; Xu, Ling; Fan, Xingming; Tan, Jing; Chen, Wei; Xu, Mingliang

    2012-12-01

    Gray leaf spot (GLS), caused by the causal fungal pathogen Cercospora zeae-maydis, is one of the most serious foliar diseases of maize worldwide. In the current study, a highly resistant inbred line Y32 and a susceptible line Q11 were used to produce segregating populations for both genetic analysis and QTL mapping. The broad-sense heritability (H (2)) for GLS resistance was estimated to be as high as 0.85, indicating that genetic factors played key roles in phenotypic variation. In initial QTL analysis, four QTL, located on chromosomes 1, 2, 5, and 8, were detected to confer GLS resistance. Each QTL could explain 2.53-23.90 % of the total phenotypic variation, predominantly due to additive genetic effects. Two major QTL, qRgls1 and qRgls2 on chromosomes 8 and 5, were consistently detected across different locations and replicates. Compared to the previous results, qRgls2 is located in a 'hotspot' for GLS resistance; while, qRgls1 does not overlap with any other known resistance QTL. Furthermore, the major QTL-qRgls1 was fine-mapped into an interval of 1.4 Mb, flanked by the markers GZ204 and IDP5. The QTL-qRgls1 could enhance the resistance percentages by 19.70-61.28 %, suggesting its usefulness to improve maize resistance to GLS.

  19. Bacterial enzymes involved in lignin degradation.

    PubMed

    de Gonzalo, Gonzalo; Colpa, Dana I; Habib, Mohamed H M; Fraaije, Marco W

    2016-10-20

    Lignin forms a large part of plant biomass. It is a highly heterogeneous polymer of 4-hydroxyphenylpropanoid units and is embedded within polysaccharide polymers forming lignocellulose. Lignin provides strength and rigidity to plants and is rather resilient towards degradation. To improve the (bio)processing of lignocellulosic feedstocks, more effective degradation methods of lignin are in demand. Nature has found ways to fully degrade lignin through the production of dedicated ligninolytic enzyme systems. While such enzymes have been well thoroughly studied for ligninolytic fungi, only in recent years biochemical studies on bacterial enzymes capable of lignin modification have intensified. This has revealed several types of enzymes available to bacteria that enable them to act on lignin. Two major classes of bacterial lignin-modifying enzymes are DyP-type peroxidases and laccases. Yet, recently also several other bacterial enzymes have been discovered that seem to play a role in lignin modifications. In the present review, we provide an overview of recent advances in the identification and use of bacterial enzymes acting on lignin or lignin-derived products. PMID:27544286

  20. Bacterial enzymes involved in lignin degradation.

    PubMed

    de Gonzalo, Gonzalo; Colpa, Dana I; Habib, Mohamed H M; Fraaije, Marco W

    2016-10-20

    Lignin forms a large part of plant biomass. It is a highly heterogeneous polymer of 4-hydroxyphenylpropanoid units and is embedded within polysaccharide polymers forming lignocellulose. Lignin provides strength and rigidity to plants and is rather resilient towards degradation. To improve the (bio)processing of lignocellulosic feedstocks, more effective degradation methods of lignin are in demand. Nature has found ways to fully degrade lignin through the production of dedicated ligninolytic enzyme systems. While such enzymes have been well thoroughly studied for ligninolytic fungi, only in recent years biochemical studies on bacterial enzymes capable of lignin modification have intensified. This has revealed several types of enzymes available to bacteria that enable them to act on lignin. Two major classes of bacterial lignin-modifying enzymes are DyP-type peroxidases and laccases. Yet, recently also several other bacterial enzymes have been discovered that seem to play a role in lignin modifications. In the present review, we provide an overview of recent advances in the identification and use of bacterial enzymes acting on lignin or lignin-derived products.

  1. Lignin conversion: Opportunities and challenges for the integrated biorefinery

    DOE PAGES

    Xie, Shangxian; Ragauskas, Arthur J.; Yuan, Joshua S.

    2016-06-21

    The utilization of lignin for fungible fuels and products represents one of the most imminent challenges in the modern biorefinery because most of the bioprocesses for lignocellulosic biofuels results in a lignin-containing waste stream. Considering lignin's abundance and relatively high energy content, this waste stream can be used as a feedstock for value-added products to improve the sustainability and economic feasibility of the biorefinery. Bioconversion of lignin with microbes recently emerged as an alternative lignin-valorization approach with significant potential. Typically, the microbial bioconversion of lignin requires three major steps: lignin depolymerization, aromatic compounds catabolism, and target product biosynthesis. In thismore » review, we summarize the most recent advances in lignin bioconversion to address the challenges in each of the three steps. In conclusion, we further discuss strategies and perspectives for future research to address the challenges in bioconversion of lignin.« less

  2. Mapping dynamic QTL for plant height in triticale

    PubMed Central

    2014-01-01

    Background Plant height is a prime example of a dynamic trait that changes constantly throughout adult development. In this study we utilised a large triticale mapping population, comprising 647 doubled haploid lines derived from 4 families, to phenotype for plant height by a precision phenotyping platform at multiple time points. Results Using multiple-line cross QTL mapping we identified main effect and epistatic QTL for plant height for each of the time points. Interestingly, some QTL were detected at all time points whereas others were specific to particular developmental stages. Furthermore, the contribution of the QTL to the genotypic variance of plant height also varied with time as exemplified by a major QTL identified on chromosome 6A. Conclusions Taken together, our results in the small grain cereal triticale reveal the importance of considering temporal genetic patterns in the regulation of complex traits such as plant height. PMID:24885543

  3. Modulating lignin in plants

    SciTech Connect

    Apuya, Nestor; Bobzin, Steven Craig; Okamuro, Jack; Zhang, Ke

    2013-01-29

    Materials and methods for modulating (e.g., increasing or decreasing) lignin content in plants are disclosed. For example, nucleic acids encoding lignin-modulating polypeptides are disclosed as well as methods for using such nucleic acids to generate transgenic plants having a modulated lignin content.

  4. Solubilization of lignin by the ruminal anaerobic fungus Neocallimastix patriciarum.

    PubMed Central

    McSweeney, C S; Dulieu, A; Katayama, Y; Lowry, J B

    1994-01-01

    The ability of the ruminal anaerobic phycomycete Neocallimastix patriciarum to digest model lignin compounds and lignified structures in plant material was studied in batch culture. The fungus did not degrade or transform model lignin compounds that were representative of the predominant intermonomer linkages in lignin, nor did it solubilize acid detergent lignin that had been isolated from spear grass. In a stem fraction of sorghum, 33.6% of lignin was apparently solubilized by the fungus. Solubilization of ester- and either-linked phenolics accounted for 9.2% of the lignin released. The amounts of free phenolic acids detected in culture fluid were equivalent to the apparent loss of ester-linked phenolics from the sorghum substrate. However, the fungus was unable to cleave the ether bond in hydroxycinnamic acid bridges that cross-link lignin and polysaccharide. It is suggested that the majority of the solubilized lignin fraction was a lignin carbohydrate complex containing ether-linked hydroxycinnamic acids. The lignin carbohydrate complex was probably solubilized through dissolution of xylan in the lignin-xylan matrix rather than by lignin depolymerization. PMID:8085834

  5. Analytical pyrolysis of hardwood and softwood lignins and its use in lignin-type determination of hardwood vessel elements

    SciTech Connect

    Obst, J.R.

    1983-01-01

    Pyrolysis, GC and mass spectrometry were performed on milled wood lignins and wood samples. Among the major pyrolysis products identified from loblolly pine lignin were: guaiacol, 4-methylguaiacol, 4-vinylguaiacol, vanillin, coniferaldehyde and coniferyl alcohol. White oak lignin pyrolysis products included: guaiacol, 4-methylguaiacol, vanillin, 2,6-dimethoxyphenol, 4-methyl-2,6-dimethoxyphenol, syringaldehyde and sinapaldehyde. By the identification of pyrolysis products it is thus possible to classify lignins as either guaiacyl-type or syringyl/guaiacyl-type. Pyrolysis of isolated vessel elements from white oak, white birch (Betula papyrifera) and American elm (Ulmus americana) indicated that vessel lignin is of the syringyl/guaiacyl type. 14 references.

  6. Genetic and Molecular Basis of QTL of Diabetes in Mouse: Genes and Polymorphisms

    PubMed Central

    Gao, Peng; Jiao, Yan; Xiong, Qing; Wang, Cong-Yi; Gerling, Ivan; Gu, Weikuan

    2008-01-01

    A systematic study has been conducted of all available reports in PubMed and OMIM (Online Mendelian Inheritance in Man) to examine the genetic and molecular basis of quantitative genetic loci (QTL) of diabetes with the main focus on genes and polymorphisms. The major question is, What can the QTL tell us? Specifically, we want to know whether those genome regions differ from other regions in terms of genes relevant to diabetes. Which genes are within those QTL regions, and, among them, which genes have already been linked to diabetes? whether more polymorphisms have been associated with diabetes in the QTL regions than in the non-QTL regions. Our search revealed a total of 9038 genes from 26 type 1 diabetes QTL, which cover 667,096,006 bp of the mouse genomic sequence. On one hand, a large number of candidate genes are in each of these QTL; on the other hand, we found that some obvious candidate genes of QTL have not yet been investigated. Thus, the comprehensive search of candidate genes for known QTL may provide unexpected benefit for identifying QTL genes for diabetes. PMID:19471607

  7. Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust.

    PubMed

    Vales, M I; Schön, C C; Capettini, F; Chen, X M; Corey, A E; Mather, D E; Mundt, C C; Richardson, K L; Sandoval-Islas, J S; Utz, H F; Hayes, P M

    2005-11-01

    The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n = 409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods-resampling, selective genotyping, and selective phenotyping-to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.

  8. Computational Design of Lignin Depolymerization Catalysts

    SciTech Connect

    Kim, S.; Chmely, S. C.; Sturgeon, M.; Katahira, R.; Paton, R. S.; Beckham, G. T.

    2012-01-01

    Lignin is a major component of plant cell walls that is typically underutilized in selective conversion strategies for renewable fuels and chemicals. The mechanisms by which thermal and catalytic treatments deconstruct lignin remain elusive, for which quantum mechanical calculations can offer fundamental insights. In this work, a computational approach has been used to elucidate the reductive deconstruction pathway of a ruthenium-catalyzed system. Transition states have been computed to determine the rate-limiting steps for a catalyst that cleaves arylether linkages. Our calculations are supported by experimental synthesis and kinetic and thermodynamic measurements of the deconstruction of model lignin dimers by a ruthenium catalyst with the ultimate objective of designing new catalysts to eventually utilize lignin in biorefineries.

  9. Multivariate whole genome average interval mapping: QTL analysis for multiple traits and/or environments.

    PubMed

    Verbyla, Arūnas P; Cullis, Brian R

    2012-09-01

    A major aim in some plant-based studies is the determination of quantitative trait loci (QTL) for multiple traits or across multiple environments. Understanding these QTL by trait or QTL by environment interactions can be of great value to the plant breeder. A whole genome approach for the analysis of QTL is presented for such multivariate applications. The approach is an extension of whole genome average interval mapping in which all intervals on a linkage map are included in the analysis simultaneously. A random effects working model is proposed for the multivariate (trait or environment) QTL effects for each interval, with a variance-covariance matrix linking the variates in a particular interval. The significance of the variance-covariance matrix for the QTL effects is tested and if significant, an outlier detection technique is used to select a putative QTL. This QTL by variate interaction is transferred to the fixed effects. The process is repeated until the variance-covariance matrix for QTL random effects is not significant; at this point all putative QTL have been selected. Unlinked markers can also be included in the analysis. A simulation study was conducted to examine the performance of the approach and demonstrated the multivariate approach results in increased power for detecting QTL in comparison to univariate methods. The approach is illustrated for data arising from experiments involving two doubled haploid populations. The first involves analysis of two wheat traits, α-amylase activity and height, while the second is concerned with a multi-environment trial for extensibility of flour dough. The method provides an approach for multi-trait and multi-environment QTL analysis in the presence of non-genetic sources of variation. PMID:22692445

  10. Systems biology-guided biodesign of consolidated lignin conversion

    DOE PAGES

    Lin, Lu; Cheng, Yanbing; Pu, Yunqiao; Sun, Su; Li, Xiao; Jin, Mingjie; Pierson, Elizabeth A.; Gross, Dennis C.; Dale, Bruce E.; Dai, Susie Y.; et al

    2016-07-12

    Lignin is the second most abundant biopolymer on the earth, yet its utilization for fungible products is complicated by its recalcitrant nature and remains a major challenge for sustainable lignocellulosic biorefineries. In this study, we used a systems biology approach to reveal the carbon utilization pattern and lignin degradation mechanisms in a unique lignin-utilizing Pseudomonas putida strain (A514). The mechanistic study further guided the design of three functional modules to enable a consolidated lignin bioconversion route. First, P. putida A514 mobilized a dye peroxidase-based enzymatic system for lignin depolymerization. This system could be enhanced by overexpressing a secreted multifunctional dyemore » peroxidase to promote a two-fold enhancement of cell growth on insoluble kraft lignin. Second, A514 employed a variety of peripheral and central catabolism pathways to metabolize aromatic compounds, which can be optimized by overexpressing key enzymes. Third, the β-oxidation of fatty acid was up-regulated, whereas fatty acid synthesis was down-regulated when A514 was grown on lignin and vanillic acid. Therefore, the functional module for polyhydroxyalkanoate (PHA) production was designed to rechannel β-oxidation products. As a result, PHA content reached 73% per cell dry weight (CDW). Further integrating the three functional modules enhanced the production of PHA from kraft lignin and biorefinery waste. Furthermore, this study elucidated lignin conversion mechanisms in bacteria with potential industrial implications and laid out the concept for engineering a consolidated lignin conversion route.« less

  11. Fine-mapping of qRL6.1, a major QTL for root length of rice seedlings grown under a wide range of NH4+ concentrations in hydroponic conditions

    PubMed Central

    Tamura, Wataru; Ebitani, Takeshi; Yano, Masahiro; Sato, Tadashi; Yamaya, Tomoyuki

    2010-01-01

    Root system development is an important target for improving yield in cereal crops. Active root systems that can take up nutrients more efficiently are essential for enhancing grain yield. In this study, we attempted to identify quantitative trait loci (QTL) involved in root system development by measuring root length of rice seedlings grown in hydroponic culture. Reliable growth conditions for estimating the root length were first established to renew nutrient solutions daily and supply NH4+ as a single nitrogen source. Thirty-eight chromosome segment substitution lines derived from a cross between ‘Koshihikari’, a japonica variety, and ‘Kasalath’, an indica variety, were used to detect QTL for seminal root length of seedlings grown in 5 or 500 μM NH4+. Eight chromosomal regions were found to be involved in root elongation. Among them, the most effective QTL was detected on a ‘Kasalath’ segment of SL-218, which was localized to the long-arm of chromosome 6. The ‘Kasalath’ allele at this QTL, qRL6.1, greatly promoted root elongation under all NH4+ concentrations tested. The genetic effect of this QTL was confirmed by analysis of the near-isogenic line (NIL) qRL6.1. The seminal root length of the NIL was 13.5–21.1% longer than that of ‘Koshihikari’ under different NH4+ concentrations. Toward our goal of applying qRL6.1 in a molecular breeding program to enhance rice yield, a candidate genomic region of qRL6.1 was delimited within a 337 kb region in the ‘Nipponbare’ genome by means of progeny testing of F2 plants/F3 lines derived from a cross between SL-218 and ‘Koshihikari’. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1328-3) contains supplementary material, which is available to authorized users. PMID:20390245

  12. Mapping Isoflavone QTL with Main, Epistatic and QTL × Environment Effects in Recombinant Inbred Lines of Soybean

    PubMed Central

    Wang, Yan; Han, Yingpeng; Zhao, Xue; Li, Yongguang; Teng, Weili; Li, Dongmei; Zhan, Yong; Li, Wenbin

    2015-01-01

    Soybean (Glycine max (L.) Merr.) isoflavone is important for human health and plant defense system. To identify novel quantitative trait loci (QTL) and epistatic QTL underlying isoflavone content in soybean, F5:6, F5:7 and F5:8 populations of 130 recombinant inbred (RI) lines, derived from the cross of soybean cultivar ‘Zhong Dou 27′ (high isoflavone) and ‘Jiu Nong 20′ (low isoflavone), were analyzed with 95 new SSR markers. A new linkage map including 194 SSR markers and covering 2,312 cM with mean distance of about 12 cM between markers was constructed. Thirty four QTL for both individual and total seed isoflavone contents of soybean were identified. Six, seven, ten and eleven QTL were associated with daidzein (DZ), glycitein (GC), genistein (GT) and total isoflavone (TI), respectively. Of them 23 QTL were newly identified. The qTIF_1 between Satt423 and Satt569 shared the same marker Satt569 with qDZF_2, qGTF_1 and qTIF_2. The qGTD2_1 between Satt186 and Satt226 was detected in four environments and explained 3.41%-10.98% of the phenotypic variation. The qGTA2_1, overlapped with qGCA2_1 and detected in four environments, was close to the previously identified major QTL for GT, which were responsible for large a effects. QTL (qDZF_2, qGTF_1 and qTIF_2) between Satt144-Satt569 were either clustered or pleiotropic. The qGCM_1, qGTM_1 and qTIM_1 between Satt540-Sat_244 explained 2.02%–9.12% of the phenotypic variation over six environments. Moreover, the qGCE_1 overlapped with qGTE_1 and qTIE_1, the qTIH_2 overlapped with qGTH_1, qGCI_1 overlapped with qDZI_1, qTIL_1 overlapped with qGTL_1, and qTIO_1 overlapped with qGTO_1. In this study, some of unstable QTL were detected in different environments, which were due to weak expression of QTL, QTL by environment interaction in the opposite direction to a effects, and/or epistasis. The markers identified in multi-environments in this study could be applied in the selection of soybean cultivars for higher

  13. p-Hydroxyphenyl (H) Units Lower the Degree of Polymerization in Lignin: Chemical Control in Lignin Biosynthesis

    SciTech Connect

    Sangha, A. K.; Parks, J. M.; Davis, M. F.; Smith, J. C.

    2013-01-01

    Lignin, composed predominantly of p-hydroxyphenyl (H), guaiacyl (G) and syringyl (S) subunits, is a major component of plant cell walls that imparts resistance toward chemical and microbial deconstruction of plant biomass, rendering its conversion inefficient and costly. Previous studies have shown that alterating lignin composition, i.e., the relative abundance of H, G and S subunits, promises more efficient extraction of sugars from plant biomass. Smaller and less branched lignin chains are more easily extracted during pretreatment, making cellulose more readily degradable. Here, using density functional theory calculations, we show that the incorporation of H subunits into lignin via b-b and b-5 interunit linkages reduces the degree of polymerization in lignin. Frontier molecular orbital analyses of lignin dimers and trimers show that H as a terminal subunit on a growing lignin polymer linked via b-b and b-5 linkage cannot undergo radical formation, preventing further chain growth by endwise polymerization resulting in lignin polymers with lower degree of polymerization. These results indicate that, for endwise polymerization in lignin synthesis, there exists a chemical control that may lay a significant role in determining the structure of lignin.

  14. Experimental Study of Mechanistic Acid Deconstruction of Lignin

    SciTech Connect

    Sturgeon, M.; Kim, S.; Chmely, S. C.; Katahira, R.; Foust, T. D.; Beckham, G. T.

    2012-01-01

    Lignin is a major component of biomass, which remains highly underutilized in selective biomass conversion strategies to renewable fuels and chemicals. Here we are interested in studying the mechanisms related to the acid deconstruction of lignin with a combined theoretical and experimental approach. Quantum mechanical calculations were employed to elucidate possible deconstruction mechanisms with transition state theory. Model dimers, imitating H, S, and G lignins, were synthesized with the most abundant {beta} - O - 4 linkage in lignin. These compounds were then depolymerized using various acids and at different operating conditions. The deconstruction products were analyzed to complement the QM studies and investigate proposed mechanisms.

  15. QTL Mapping in Eggplant Reveals Clusters of Yield-Related Loci and Orthology with the Tomato Genome

    PubMed Central

    Portis, Ezio; Barchi, Lorenzo; Toppino, Laura; Lanteri, Sergio; Acciarri, Nazzareno; Felicioni, Nazzareno; Fusari, Fabio; Barbierato, Valeria; Cericola, Fabio; Valè, Giampiero; Rotino, Giuseppe Leonardo

    2014-01-01

    In spite of its widespread cultivation and nutritional and economic importance, the eggplant (Solanum melongena L.) genome has not been extensively explored. A lack of knowledge of the patterns of inheritance of key agronomic traits has hindered the exploitation of marker technologies to accelerate its genetic improvement. An already established F2 intraspecific population of eggplant bred from the cross ‘305E40’ x ‘67/3’ was phenotyped for 20 agronomically relevant traits at two sites. Up to seven quantitative trait loci (QTL) per trait were identified and the percentage of the phenotypic variance (PV) explained per QTL ranged from 4 to 93%. Not all the QTL were detectable at both sites, but for each trait at least one major QTL (PV explained ≥10%) was identified. Although no detectable QTL x environment interaction was found, some QTL identified were location-specific. Many of the fruit-related QTL clustered within specific chromosomal regions, reflecting either linkage and/or pleiotropy. Evidence for putative tomato orthologous QTL/genes was obtained for several of the eggplant QTL. Information regarding the inheritance of key agronomic traits was obtained. Some of the QTL, along with their respective linked markers, may be useful in the context of marker-assisted breeding. PMID:24586828

  16. In situ micro-spectroscopic investigation of lignin in poplar cell walls pretreated by maleic acid

    DOE PAGES

    Zeng, Yining; Zhao, Shuai; Wei, Hui; Tucker, Melvin P.; Himmel, Michael E.; Mosier, Nathan S.; Meilan, Richard; Ding, Shi -You

    2015-08-27

    In higher plant cells, lignin provides necessary physical support for plant growth and resistance to attack by microorganisms. For the same reason, lignin is considered to be a major impediment to the process of deconstructing biomass to simple sugars by hydrolytic enzymes. Furthermore, the in situ variation of lignin in plant cell walls is important for better understanding of the roles lignin play in biomass recalcitrance.

  17. QTL Characterization of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line Soru#1

    PubMed Central

    He, Xinyao; Lillemo, Morten; Shi, Jianrong; Wu, Jirong; Bjørnstad, Åsmund; Belova, Tatiana; Dreisigacker, Susanne; Duveiller, Etienne; Singh, Pawan

    2016-01-01

    Fusarium head blight (FHB) resistant line Soru#1 was hybridized with the German cultivar Naxos to generate 131 recombinant inbred lines for QTL mapping. The population was phenotyped for FHB and associated traits in spray inoculated experiments in El Batán (Mexico), spawn inoculated experiments in Ås (Norway) and point inoculated experiments in Nanjing (China), with two field trials at each location. Genotyping was performed with the Illumina iSelect 90K SNP wheat chip, along with a few SSR and STS markers. A major QTL for FHB after spray and spawn inoculation was detected on 2DLc, explaining 15–22% of the phenotypic variation in different experiments. This QTL remained significant after correction for days to heading (DH) and plant height (PH), while another QTL for FHB detected at the Vrn-A1 locus on 5AL almost disappeared after correction for DH and PH. Minor QTL were detected on chromosomes 2AS, 2DL, 4AL, 4DS and 5DL. In point inoculated experiments, QTL on 2DS, 3AS, 4AL and 5AL were identified in single environments. The mechanism of resistance of Soru#1 to FHB was mainly of Type I for resistance to initial infection, conditioned by the major QTL on 2DLc and minor ones that often coincided with QTL for DH, PH and anther extrusion (AE). This indicates that phenological and morphological traits and flowering biology play important roles in resistance/escape of FHB. SNPs tightly linked to resistance QTL, particularly 2DLc, could be utilized in breeding programs to facilitate the transfer and selection of those QTL. PMID:27351632

  18. QTL mapping of powdery mildew resistance in WI 2757 cucumber (Cucumis sativus L.).

    PubMed

    He, Xiaoming; Li, Yuhong; Pandey, Sudhakar; Yandell, Brain S; Pathak, Mamta; Weng, Yiqun

    2013-08-01

    Powdery mildew (PM) is a very important disease of cucumber (Cucumis sativus L.). Resistant cultivars have been deployed in production for a long time, but the genetic mechanisms of PM resistance in cucumber are not well understood. A 3-year QTL mapping study of PM resistance was conducted with 132 F2:3 families derived from two cucumber inbred lines WI 2757 (resistant) and True Lemon (susceptible). A genetic map covering 610.4 cM in seven linkage groups was developed with 240 SSR marker loci. Multiple QTL mapping analysis of molecular marker data and disease index of the hypocotyl, cotyledon and true leaf for responses to PM inoculation identified six genomic regions in four chromosomes harboring QTL for PM resistance in WI 2757. Among the six QTL, pm1.1 and pm1.2 in chromosome 1 conferred leaf resistance. Minor QTL pm3.1 (chromosome 3) and pm4.1 (chromosome 4) contributed to disease susceptibility. The two major QTL, pm5.1 and pm5.2 were located in an interval of ~40 cM in chromosome 5 with each explaining 21.0-74.5 % phenotypic variations. Data presented herein support two recessively inherited, linked major QTL in chromosome 5 plus minor QTL in other chromosomes that control the PM resistance in WI 2757. The QTL pm5.2 for hypocotyl resistance plays the most important role in host resistance. Multiple observations in the same year revealed the importance of scoring time in the detection of PM resistance QTL. Results of this study provided new insights into phenotypic and genetic mechanisms of powdery mildew resistance in cucumber.

  19. QTL mapping of powdery mildew resistance in WI 2757 cucumber (Cucumis sativus L.).

    PubMed

    He, Xiaoming; Li, Yuhong; Pandey, Sudhakar; Yandell, Brain S; Pathak, Mamta; Weng, Yiqun

    2013-08-01

    Powdery mildew (PM) is a very important disease of cucumber (Cucumis sativus L.). Resistant cultivars have been deployed in production for a long time, but the genetic mechanisms of PM resistance in cucumber are not well understood. A 3-year QTL mapping study of PM resistance was conducted with 132 F2:3 families derived from two cucumber inbred lines WI 2757 (resistant) and True Lemon (susceptible). A genetic map covering 610.4 cM in seven linkage groups was developed with 240 SSR marker loci. Multiple QTL mapping analysis of molecular marker data and disease index of the hypocotyl, cotyledon and true leaf for responses to PM inoculation identified six genomic regions in four chromosomes harboring QTL for PM resistance in WI 2757. Among the six QTL, pm1.1 and pm1.2 in chromosome 1 conferred leaf resistance. Minor QTL pm3.1 (chromosome 3) and pm4.1 (chromosome 4) contributed to disease susceptibility. The two major QTL, pm5.1 and pm5.2 were located in an interval of ~40 cM in chromosome 5 with each explaining 21.0-74.5 % phenotypic variations. Data presented herein support two recessively inherited, linked major QTL in chromosome 5 plus minor QTL in other chromosomes that control the PM resistance in WI 2757. The QTL pm5.2 for hypocotyl resistance plays the most important role in host resistance. Multiple observations in the same year revealed the importance of scoring time in the detection of PM resistance QTL. Results of this study provided new insights into phenotypic and genetic mechanisms of powdery mildew resistance in cucumber. PMID:23689747

  20. QTL Characterization of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line Soru#1.

    PubMed

    He, Xinyao; Lillemo, Morten; Shi, Jianrong; Wu, Jirong; Bjørnstad, Åsmund; Belova, Tatiana; Dreisigacker, Susanne; Duveiller, Etienne; Singh, Pawan

    2016-01-01

    Fusarium head blight (FHB) resistant line Soru#1 was hybridized with the German cultivar Naxos to generate 131 recombinant inbred lines for QTL mapping. The population was phenotyped for FHB and associated traits in spray inoculated experiments in El Batán (Mexico), spawn inoculated experiments in Ås (Norway) and point inoculated experiments in Nanjing (China), with two field trials at each location. Genotyping was performed with the Illumina iSelect 90K SNP wheat chip, along with a few SSR and STS markers. A major QTL for FHB after spray and spawn inoculation was detected on 2DLc, explaining 15-22% of the phenotypic variation in different experiments. This QTL remained significant after correction for days to heading (DH) and plant height (PH), while another QTL for FHB detected at the Vrn-A1 locus on 5AL almost disappeared after correction for DH and PH. Minor QTL were detected on chromosomes 2AS, 2DL, 4AL, 4DS and 5DL. In point inoculated experiments, QTL on 2DS, 3AS, 4AL and 5AL were identified in single environments. The mechanism of resistance of Soru#1 to FHB was mainly of Type I for resistance to initial infection, conditioned by the major QTL on 2DLc and minor ones that often coincided with QTL for DH, PH and anther extrusion (AE). This indicates that phenological and morphological traits and flowering biology play important roles in resistance/escape of FHB. SNPs tightly linked to resistance QTL, particularly 2DLc, could be utilized in breeding programs to facilitate the transfer and selection of those QTL. PMID:27351632

  1. QTL Characterization of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line Soru#1.

    PubMed

    He, Xinyao; Lillemo, Morten; Shi, Jianrong; Wu, Jirong; Bjørnstad, Åsmund; Belova, Tatiana; Dreisigacker, Susanne; Duveiller, Etienne; Singh, Pawan

    2016-01-01

    Fusarium head blight (FHB) resistant line Soru#1 was hybridized with the German cultivar Naxos to generate 131 recombinant inbred lines for QTL mapping. The population was phenotyped for FHB and associated traits in spray inoculated experiments in El Batán (Mexico), spawn inoculated experiments in Ås (Norway) and point inoculated experiments in Nanjing (China), with two field trials at each location. Genotyping was performed with the Illumina iSelect 90K SNP wheat chip, along with a few SSR and STS markers. A major QTL for FHB after spray and spawn inoculation was detected on 2DLc, explaining 15-22% of the phenotypic variation in different experiments. This QTL remained significant after correction for days to heading (DH) and plant height (PH), while another QTL for FHB detected at the Vrn-A1 locus on 5AL almost disappeared after correction for DH and PH. Minor QTL were detected on chromosomes 2AS, 2DL, 4AL, 4DS and 5DL. In point inoculated experiments, QTL on 2DS, 3AS, 4AL and 5AL were identified in single environments. The mechanism of resistance of Soru#1 to FHB was mainly of Type I for resistance to initial infection, conditioned by the major QTL on 2DLc and minor ones that often coincided with QTL for DH, PH and anther extrusion (AE). This indicates that phenological and morphological traits and flowering biology play important roles in resistance/escape of FHB. SNPs tightly linked to resistance QTL, particularly 2DLc, could be utilized in breeding programs to facilitate the transfer and selection of those QTL.

  2. Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL.

    PubMed

    Cavanagh, Colin R; Jonas, Elisabeth; Hobbs, Matthew; Thomson, Peter C; Tammen, Imke; Raadsma, Herman W

    2010-09-16

    An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

  3. Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL

    PubMed Central

    2010-01-01

    An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified. A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21. PMID:20846385

  4. Isolation and characterization of new lignin streams derived from extractive-ammonia (EA) pretreatment

    DOE PAGES

    da Costa Sousa, Leonardo; Foston, Marcus; Bokade, Vijay; Azarpira, Ali; Lu, Fachuang; Ragauskas, Arthur J.; Ralph, John; Dale, Bruce; Balan, Venkatesh

    2016-05-05

    One of the key challenges facing lignin conversion to fuels and chemicals is related to the level of carbohydrate and ash impurities found in extracted lignin. Structural modifications of lignin may also occur as a result of biomass pretreatment and harsh lignin extraction protocols. Extractive-Ammonia (EA) is a new pretreatment technology that uses liquid ammonia to cleave lignin–carbohydrate complexes, decrystallize cellulose, solubilize lignin, and selectively extract lignin from lignocellulosic biomass, enabling better utilization of both lignin and carbohydrate components in a biorefinery. The EA-based biorefinery produces two different lignin-rich streams, with different properties, that could potentially be upgraded to fuelsmore » and chemicals using green processes. In this work, a water/ethanol-based fractionation method was developed to enrich the ammonia-soluble extractives, resulting in a major product stream containing 92% lignin. Detailed characterization of the various streams resulting from EA treatment, including compositional analysis, structural characterization by nuclear magnetic resonance (NMR) spectrometry, elemental analysis, molecular weight analysis, and thermo-gravimetric analysis provides a broad evaluation of the EA-derived lignin product stream structures and properties, assessing their potential for commercial applications. In summary, EA-derived lignins preserve much of lignin's functionality, including the sensitive β-aryl ether units. Furthermore, nitrogen incorporation was observed in the lignin-rich streams, notably due to the presence of hydroxycinnamoyl amides formed during ammonia pretreatment.« less

  5. Fusarium Head Blight Resistance QTL in the Spring Wheat Cross Kenyon/86ISMN 2137

    PubMed Central

    McCartney, Curt A.; Brûlé-Babel, Anita L.; Fedak, George; Martin, Richard A.; McCallum, Brent D.; Gilbert, Jeannie; Hiebert, Colin W.; Pozniak, Curtis J.

    2016-01-01

    Fusarium head blight (FHB), caused by Fusarium graminearum, is a very important disease of wheat globally. Damage caused by F. graminearum includes reduced grain yield, reduced grain functional quality, and results in the presence of the trichothecene mycotoxin deoxynivalenol in Fusarium-damaged kernels. The development of FHB resistant wheat cultivars is an important component of integrated management. The objective of this study was to identify QTL for FHB resistance in a recombinant inbred line (RIL) population of the spring wheat cross Kenyon/86ISMN 2137. Kenyon is a Canadian spring wheat, while 86ISMN 2137 is an unrelated spring wheat. The RIL population was evaluated for FHB resistance in six FHB nurseries. Nine additive effect QTL for FHB resistance were identified, six from Kenyon and three from 86ISMN 2137. Rht8 and Ppd-D1a co-located with two FHB resistance QTL on chromosome arm 2DS. A major QTL for FHB resistance from Kenyon (QFhb.crc-7D) was identified on chromosome 7D. The QTL QFhb.crc-2D.4 from Kenyon mapped to the same region as a FHB resistance QTL from Wuhan-1 on chromosome arm 2DL. This result was unexpected since Kenyon does not share common ancestry with Wuhan-1. Other FHB resistance QTL on chromosomes 4A, 4D, and 5B also mapped to known locations of FHB resistance. Four digenic epistatic interactions were detected for FHB resistance, which involved eight QTL. None of these QTL were significant based upon additive effect QTL analysis. This study provides insight into the genetic basis of native FHB resistance in Canadian spring wheat. PMID:27790188

  6. Computational Mechanistic Studies of Acid-Catalyzed Lignin Model Dimers for Lignin Depolymerization

    SciTech Connect

    Kim, S.; Sturgeon, M. R.; Chmely, S. C.; Paton, R. S.; Beckham, G. T.

    2013-01-01

    Lignin is a heterogeneous alkyl-aromatic polymer that constitutes up to 30% of plant cell walls, and is used for water transport, structure, and defense. The highly irregular and heterogeneous structure of lignin presents a major obstacle in the development of strategies for its deconstruction and upgrading. Here we present mechanistic studies of the acid-catalyzed cleavage of lignin aryl-ether linkages, combining both experimental studies and quantum chemical calculations. Quantum mechanical calculations provide a detailed interpretation of reaction mechanisms including possible intermediates and transition states. Solvent effects on the hydrolysis reactions were incorporated through the use of a conductor-like polarizable continuum model (CPCM) and with cluster models including explicit water molecules in the first solvation shell. Reaction pathways were computed for four lignin model dimers including 2-phenoxy-phenylethanol (PPE), 1-(para-hydroxyphenyl)-2-phenoxy-ethanol (HPPE), 2-phenoxy-phenyl-1,3-propanediol (PPPD), and 1-(para-hydroxyphenyl)-2-phenoxy-1,3-propanediol (HPPPD). Lignin model dimers with a para-hydroxyphenyl ether (HPPE and HPPPD) show substantial differences in reactivity relative to the phenyl ether compound (PPE and PPPD) which have been clarified theoretically and experimentally. The significance of these results for acid deconstruction of lignin in plant cell walls will be discussed.

  7. Through Lignin Biodegradation to Lignin-based Plastics

    NASA Astrophysics Data System (ADS)

    Wang, Yun-Yan

    The consequences of strong noncovalent intermolecular interactions between oligomeric and/or polymeric lignin components are encountered during enzyme-catalyzed lignin degradation and in the properties of lignin-based plastics. A new chapter in the 30-year quest for functional lignin-depolymerizing enzymes has been opened. The lignin-degrading capacity of the flavin-dependent monooxygenase, salicylate hydroxylase acting as a putative lignin depolymerase, has been characterized using a water-soluble native softwood lignin substrate under mildly acidic aqueous conditions. When macromolecular lignins undergo lignin-depolymerase catalyzed degradation, the cleaved components tend to associate with one another, or with nearby associated lignin complexes, through processes mediated by the enzyme acting in a non-catalytic capacity. As a result, the radius of gyration (Rg) falls rapidly to approximately constant values, while the weight-average molecular weight (Mw) of the substrate rises more slowly to an extent dependent on enzyme concentration. Xylanase, when employed in an auxiliary capacity, is able to facilitate dissociation of the foregoing complexes through its interactions with the lignin depolymerase. The flavin-dependent lignin depolymerase must be reduced before reaction with oxygen can occur to form the hydroperoxy intermediate that hydroxylates the lignin substrate prior to cleavage. In the absence of the cofactor, NADH, the necessary reducing power can be provided (albeit more slowly) by the lignin substrate itself. Under such conditions, a simultaneous decrease in R g and Mw is initially observed during the enzymatic process through which the lignin is cleaved. The partially degraded product-lignins arising from lignin depolymerase activity can be readily converted into polymeric materials with mechanical properties that supersede those of polystyrene. Methylation and blending of ball-milled softwood lignins with miscible low-Tg polymers, or simple low

  8. Lignin-rich Enzyme Lignin (LREL), a Cellulase-treated Lignin-Carbohydrate Derived from Plants, Activates Myeloid Dendritic Cells via Toll-like Receptor 4 (TLR4)

    PubMed Central

    Tsuji, Ryohei; Koizumi, Hideki; Aoki, Dan; Watanabe, Yuta; Sugihara, Yoshihiko; Matsushita, Yasuyuki; Fukushima, Kazuhiko; Fujiwara, Daisuke

    2015-01-01

    Lignin-carbohydrates, one of the major cell wall components, are believed to be the structures that form chemical linkage between lignin and cell wall polysaccharides. Due to the molecular complexity of lignin-containing substances, their isolation and the assignment of their biological activities have so far remained a difficult task. Here, we extracted two lignin-containing carbohydrates, lignin-rich enzyme lignin (LREL) and pure enzyme lignin (PEL), from barley husk and demonstrated that they act as immune stimulators of dendritic cells (DCs), which are particularly important in linking innate and adaptive immunity. Thioacidolysis, acid hydrolysis, and mild alkali hydrolysis of both LREL and PEL revealed that their immunostimulatory activities depended on the lignin structure and/or content, neutral sugar content (especially the characteristic distribution of galactose and mannose), and presence of an ester bond. Furthermore, we showed that the immunostimulatory potency of the lignin-carbohydrate depended on its molecular weight and degree of polymerization. We also demonstrated that the LREL-induced activation of DCs was mediated via TLR4. Thus, LREL-induced increases in the expression levels of several cell surface marker proteins, production of inflammatory cytokines IL-12p40 and TNF-α, and activation and nuclear translocation of transcription factors, as was observed in the WT DCs, were completely abrogated in DCs derived from the TLR4−/− mice but not in DCs derived from the TLR2−/−, TLR7−/−, and TLR9−/− mice. We further demonstrated that LRELs isolated from other plant tissues also activated DCs. These immunostimulatory activities of lignin-carbohydrates, extracted from edible plant tissues, could have potential relevance in anti-infectious immunity and vaccine adjuvants. PMID:25548274

  9. Validation of linkage between BCWD resistance and spleen size QTL on Omy19 in rainbow trout: Pleiotropy versus linkage

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacterial cold water disease (BCWD) is caused by infection with Flavobacterium psychrophilum, and results in significant economic losses in salmonid aquaculture. Previously, we identified a major QTL for BCWD resistance on Omy19 (h2q=0.57-0.67) as well as a QTL for surrogate measures of disease resi...

  10. Validation of linked QTL for bacterial cold water disease resistance and spleen size on rainbow trout chromosome Omy19

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacterial cold water disease (BCWD) is caused by infection with Flavobacterium psychrophilum, and results in significant economic losses in salmonid aquaculture. Previously, we identified a major QTL for BCWD resistance and a QTL for spleen size (SPLW = spleen weight and SPLI = spleen index) in naï...

  11. Fluorescence analyzer for lignin

    DOEpatents

    Berthold, John W.; Malito, Michael L.; Jeffers, Larry

    1993-01-01

    A method and apparatus for measuring lignin concentration in a sample of wood pulp or black liquor comprises a light emitting arrangement for emitting an excitation light through optical fiber bundles into a probe which has an undiluted sensing end facing the sample. The excitation light causes the lignin concentration to produce fluorescent emission light which is then conveyed through the probe to analyzing equipment which measures the intensity of the emission light. Measures a This invention was made with Government support under Contract Number DOE: DE-FC05-90CE40905 awarded by the Department of Energy (DOE). The Government has certain rights in this invention.

  12. Extracting lignins from mill wastes

    NASA Technical Reports Server (NTRS)

    Humphrey, M. F.

    1977-01-01

    Addition of quaternary ammonium compound and activated charcoal to pulp and mill wastes precipitates lignins in sludge mixture. Methanol dissolves lignins for separation from resulting slurry. Mineral acid reprecipitates lignins in filtered solution. Quaternary ammonium compound, activated charcoal, as well as water may be recovered and recycled from this process.

  13. Starch-Lignin Baked Foams

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Starch-kraft lignin foams were prepared by a baking process. Replacing up to 20% of the starch with lignin has no effect on foam density or overall morphology. At 10% replacement, lignin marginally increases water resistance and modulus of elasticity but decreases strain at maximum stress. At 20% re...

  14. Construction of genetic linkage map and mapping of QTL for seed color in Brassica rapa.

    PubMed

    Kebede, Berisso; Cheema, Kuljit; Greenshields, David L; Li, Changxi; Selvaraj, Gopalan; Rahman, Habibur

    2012-12-01

    A genetic linkage map of Brassica rapa L. was constructed using recombinant inbred lines (RILs) derived from a cross between yellow-seeded cultivar Sampad and a yellowish brown seeded inbred line 3-0026.027. The RILs were evaluated for seed color under three conditions: field plot, greenhouse, and controlled growth chambers. Variation for seed color in the RILs ranged from yellow, like yellow sarson, to dark brown/black even though neither parent had shown brown/black colored seeds. One major QTL (SCA9-2) and one minor QTL (SCA9-1) on linkage group (LG) A9 and two minor QTL (SCA3-1, SCA5-1) on LG A3 and LG A5, respectively, were detected. These collectively explained about 67% of the total phenotypic variance. SCA9-2 mapped in the middle of LG A9, explained about 55% phenotypic variance, and consistently expressed in all environments. The second QTL on LG A9 was ~70 cM away from SCA9-2, suggesting that independent assortment of these QTLs is possible. A digenic epistatic interaction was found between the two main effect QTL on LG A9; and the epistasis × environment interaction was nonsignificant, suggesting stability of the interaction across the environments. The QTL effect on LG A9 was validated using simple sequence repeat (SSR) markers from the two QTL regions of this LG on a B(1)S(1) population (F(1) backcrossed to Sampad followed by self-pollination) segregating for brown and yellow seed color, and on their self-pollinated progenies (B(1)S(2)). The SSR markers from the QTL region SCA9-2 showed a stronger linkage association with seed color as compared with the marker from SCA9-1. This suggests that the QTL SCA9-2 is the major determinant of seed color in the A genome of B. rapa.

  15. Construction of genetic linkage map and mapping of QTL for seed color in Brassica rapa.

    PubMed

    Kebede, Berisso; Cheema, Kuljit; Greenshields, David L; Li, Changxi; Selvaraj, Gopalan; Rahman, Habibur

    2012-12-01

    A genetic linkage map of Brassica rapa L. was constructed using recombinant inbred lines (RILs) derived from a cross between yellow-seeded cultivar Sampad and a yellowish brown seeded inbred line 3-0026.027. The RILs were evaluated for seed color under three conditions: field plot, greenhouse, and controlled growth chambers. Variation for seed color in the RILs ranged from yellow, like yellow sarson, to dark brown/black even though neither parent had shown brown/black colored seeds. One major QTL (SCA9-2) and one minor QTL (SCA9-1) on linkage group (LG) A9 and two minor QTL (SCA3-1, SCA5-1) on LG A3 and LG A5, respectively, were detected. These collectively explained about 67% of the total phenotypic variance. SCA9-2 mapped in the middle of LG A9, explained about 55% phenotypic variance, and consistently expressed in all environments. The second QTL on LG A9 was ~70 cM away from SCA9-2, suggesting that independent assortment of these QTLs is possible. A digenic epistatic interaction was found between the two main effect QTL on LG A9; and the epistasis × environment interaction was nonsignificant, suggesting stability of the interaction across the environments. The QTL effect on LG A9 was validated using simple sequence repeat (SSR) markers from the two QTL regions of this LG on a B(1)S(1) population (F(1) backcrossed to Sampad followed by self-pollination) segregating for brown and yellow seed color, and on their self-pollinated progenies (B(1)S(2)). The SSR markers from the QTL region SCA9-2 showed a stronger linkage association with seed color as compared with the marker from SCA9-1. This suggests that the QTL SCA9-2 is the major determinant of seed color in the A genome of B. rapa. PMID:23231600

  16. Mapping of QTL Associated with Waterlogging Tolerance during the Seedling Stage in Maize

    PubMed Central

    Qiu, Fazhan; Zheng, Yonglian; Zhang, Zili; Xu, Shangzhong

    2007-01-01

    Background and Aims Soil waterlogging is a major environmental stress that suppresses maize (Zea mays) growth and yield. To identify quantitative trait loci (QTL) associated with waterlogging tolerance at the maize seedling stage, a F2 population consisting of 288 F2:3 lines was created from a cross between two maize genotypes, ‘HZ32’ (waterlogging-tolerant) and ‘K12’ (waterlogging-sensitive). Methods The F2 population was genotyped and a base-map of 1710·5 cM length was constructed with an average marker space of 11·5 cM based on 177 SSR (simple sequence repeat) markers. QTL associated with root length, root dry weight, plant height, shoot dry weight, total dry weight and waterlogging tolerance coefficient were identified via composite interval mapping (CIM) under waterlogging and control conditions in 2004 (EXP.1) and 2005 (EXP.2), respectively. Key Results and Conclusions Twenty-five and thirty-four QTL were detected in EXP.1 and EXP.2, respectively. The effects of each QTL were moderate, ranging from 3·9 to 37·3 %. Several major QTL determining shoot dry weight, root dry weight, total dry weight, plant height and their waterlogging tolerance coefficient each mapped on chromosomes 4 and 9. These QTL were detected consistently in both experiments. Secondary QTL influencing tolerance were also identified and located on chromosomes 1, 2, 3, 6, 7 and 10. These QTL were specific to particular traits or environments. Although the detected regions need to be mapped more precisely, the findings and QTL found in this study may provide useful information for marker-assisted selection (MAS) and further genetic studies on maize waterlogging tolerance. PMID:17470902

  17. Lignin blockers and uses thereof

    SciTech Connect

    Yang, Bin; Wyman, Charles E.

    2011-01-25

    Disclosed is a method for converting cellulose in a lignocellulosic biomass. The method provides for a lignin-blocking polypeptide and/or protein treatment of high lignin solids. The treatment enhances cellulase availability in cellulose conversion and allows for the determination of optimized pretreatment conditions. Additionally, ethanol yields from a Simultaneous Saccharification and Fermentation process are improved 5-25% by treatment with a lignin-blocking polypeptide and/or protein. Thus, a more efficient and economical method of processing lignin containing biomass materials utilizes a polypeptide/protein treatment step that effectively blocks lignin binding of cellulase.

  18. Fluorescence analyzer for lignin

    SciTech Connect

    Berthold, J.W.; Malito, M.L.; Jeffers, L.

    1993-06-01

    An apparatus for measuring lignin concentration with time resolved fluorescence in an undiluted wood pulp or black liquor sample, on a real-time, in situ basis is described, comprising: light source means for applying excitation light pulses at a selected wavelength and at known time intervals to the undiluted sample for causing the lignin concentration to produce fluorescent emission light with a fluorescence intensity that monotonically decreases in a quenched fluorescence regime; light detector means for measuring the emission light at the known time intervals and establishing signals indicative thereof; switching means for turning said light detector means on at precise specified time intervals after each excitation light pulse; and signal processing means connected to the light source means and the light detector means for comparing intensities of the emission light from the lignin in the quenched fluorescence regime to the intensities of the excitation light pulses on a time resolved basis for providing a measurement of the lignin concentration in the undiluted sample as a function of the time resolved emission light intensity.

  19. Main Effect QTL with Dominance Determines Heterosis for Dynamic Plant Height in Upland Cotton

    PubMed Central

    Shang, Lianguang; Ma, Lingling; Wang, Yumei; Su, Ying; Wang, Xiaocui; Li, Yuhua; Abduweli, Abdugheni; Cai, Shihu; Liu, Fang; Wang, Kunbo; Hua, Jinping

    2016-01-01

    Plant height, which shows dynamic development and heterosis, is a major trait affecting plant architecture and has an indirect influence on economic yield related to biological yield in cotton. In the present study, we carried out dynamic analysis for plant height and its heterosis by quantitative trait loci (QTL) mapping at multiple developmental stages using two recombinant inbred lines (RILs) and their backcross progeny. At the single-locus level, 47 QTL were identified at five developmental stages in two hybrids. In backcross populations, QTL identified at an early stage mainly showed partial effects and QTL detected at a later stage mostly displayed overdominance effects. At the two-locus level, we found that main effect QTL played a more important role than epistatic QTL in the expression of heterosis in backcross populations. Therefore, this study implies that the genetic basis of plant height heterosis shows dynamic character and main effect QTL with dominance determines heterosis for plant height in Upland cotton. PMID:27565885

  20. Structural Insights into the Affinity of Cel7A Carbohydrate-binding Module for Lignin*

    PubMed Central

    Strobel, Kathryn L.; Pfeiffer, Katherine A.; Blanch, Harvey W.; Clark, Douglas S.

    2015-01-01

    The high cost of hydrolytic enzymes impedes the commercial production of lignocellulosic biofuels. High enzyme loadings are required in part due to their non-productive adsorption to lignin, a major component of biomass. Despite numerous studies documenting cellulase adsorption to lignin, few attempts have been made to engineer enzymes to reduce lignin binding. In this work, we used alanine-scanning mutagenesis to elucidate the structural basis for the lignin affinity of Trichoderma reesei Cel7A carbohydrate binding module (CBM). T. reesei Cel7A CBM mutants were produced with a Talaromyces emersonii Cel7A catalytic domain and screened for their binding to cellulose and lignin. Mutation of aromatic and polar residues on the planar face of the CBM greatly decreased binding to both cellulose and lignin, supporting the hypothesis that the cellulose-binding face is also responsible for lignin affinity. Cellulose and lignin affinity of the 31 mutants were highly correlated, although several mutants displayed selective reductions in lignin or cellulose affinity. Four mutants with increased cellulose selectivity (Q2A, H4A, V18A, and P30A) did not exhibit improved hydrolysis of cellulose in the presence of lignin. Further reduction in lignin affinity while maintaining a high level of cellulose affinity is thus necessary to generate an enzyme with improved hydrolysis capability. This work provides insights into the structural underpinnings of lignin affinity, identifies residues amenable to mutation without compromising cellulose affinity, and informs engineering strategies for family one CBMs. PMID:26209638

  1. Structural insights into the affinity of Cel7A carbohydrate-binding module for lignin.

    PubMed

    Strobel, Kathryn L; Pfeiffer, Katherine A; Blanch, Harvey W; Clark, Douglas S

    2015-09-11

    The high cost of hydrolytic enzymes impedes the commercial production of lignocellulosic biofuels. High enzyme loadings are required in part due to their non-productive adsorption to lignin, a major component of biomass. Despite numerous studies documenting cellulase adsorption to lignin, few attempts have been made to engineer enzymes to reduce lignin binding. In this work, we used alanine-scanning mutagenesis to elucidate the structural basis for the lignin affinity of Trichoderma reesei Cel7A carbohydrate binding module (CBM). T. reesei Cel7A CBM mutants were produced with a Talaromyces emersonii Cel7A catalytic domain and screened for their binding to cellulose and lignin. Mutation of aromatic and polar residues on the planar face of the CBM greatly decreased binding to both cellulose and lignin, supporting the hypothesis that the cellulose-binding face is also responsible for lignin affinity. Cellulose and lignin affinity of the 31 mutants were highly correlated, although several mutants displayed selective reductions in lignin or cellulose affinity. Four mutants with increased cellulose selectivity (Q2A, H4A, V18A, and P30A) did not exhibit improved hydrolysis of cellulose in the presence of lignin. Further reduction in lignin affinity while maintaining a high level of cellulose affinity is thus necessary to generate an enzyme with improved hydrolysis capability. This work provides insights into the structural underpinnings of lignin affinity, identifies residues amenable to mutation without compromising cellulose affinity, and informs engineering strategies for family one CBMs. PMID:26209638

  2. Structural insights into the affinity of Cel7A carbohydrate-binding module for lignin.

    PubMed

    Strobel, Kathryn L; Pfeiffer, Katherine A; Blanch, Harvey W; Clark, Douglas S

    2015-09-11

    The high cost of hydrolytic enzymes impedes the commercial production of lignocellulosic biofuels. High enzyme loadings are required in part due to their non-productive adsorption to lignin, a major component of biomass. Despite numerous studies documenting cellulase adsorption to lignin, few attempts have been made to engineer enzymes to reduce lignin binding. In this work, we used alanine-scanning mutagenesis to elucidate the structural basis for the lignin affinity of Trichoderma reesei Cel7A carbohydrate binding module (CBM). T. reesei Cel7A CBM mutants were produced with a Talaromyces emersonii Cel7A catalytic domain and screened for their binding to cellulose and lignin. Mutation of aromatic and polar residues on the planar face of the CBM greatly decreased binding to both cellulose and lignin, supporting the hypothesis that the cellulose-binding face is also responsible for lignin affinity. Cellulose and lignin affinity of the 31 mutants were highly correlated, although several mutants displayed selective reductions in lignin or cellulose affinity. Four mutants with increased cellulose selectivity (Q2A, H4A, V18A, and P30A) did not exhibit improved hydrolysis of cellulose in the presence of lignin. Further reduction in lignin affinity while maintaining a high level of cellulose affinity is thus necessary to generate an enzyme with improved hydrolysis capability. This work provides insights into the structural underpinnings of lignin affinity, identifies residues amenable to mutation without compromising cellulose affinity, and informs engineering strategies for family one CBMs.

  3. Lignin-Based Thermoplastic Materials.

    PubMed

    Wang, Chao; Kelley, Stephen S; Venditti, Richard A

    2016-04-21

    Lignin-based thermoplastic materials have attracted increasing interest as sustainable, cost-effective, and biodegradable alternatives for petroleum-based thermoplastics. As an amorphous thermoplastic material, lignin has a relatively high glass-transition temperature and also undergoes radical-induced self-condensation at high temperatures, which limits its thermal processability. Additionally, lignin-based materials are usually brittle and exhibit poor mechanical properties. To improve the thermoplasticity and mechanical properties of technical lignin, polymers or plasticizers are usually integrated with lignin by blending or chemical modification. This Review attempts to cover the reported approaches towards the development of lignin-based thermoplastic materials on the basis of published information. Approaches reviewed include plasticization, blending with miscible polymers, and chemical modifications by esterification, etherification, polymer grafting, and copolymerization. Those lignin-based thermoplastic materials are expected to show applications as engineering plastics, polymeric foams, thermoplastic elastomers, and carbon-fiber precursors. PMID:27059111

  4. Lignin-Based Thermoplastic Materials.

    PubMed

    Wang, Chao; Kelley, Stephen S; Venditti, Richard A

    2016-04-21

    Lignin-based thermoplastic materials have attracted increasing interest as sustainable, cost-effective, and biodegradable alternatives for petroleum-based thermoplastics. As an amorphous thermoplastic material, lignin has a relatively high glass-transition temperature and also undergoes radical-induced self-condensation at high temperatures, which limits its thermal processability. Additionally, lignin-based materials are usually brittle and exhibit poor mechanical properties. To improve the thermoplasticity and mechanical properties of technical lignin, polymers or plasticizers are usually integrated with lignin by blending or chemical modification. This Review attempts to cover the reported approaches towards the development of lignin-based thermoplastic materials on the basis of published information. Approaches reviewed include plasticization, blending with miscible polymers, and chemical modifications by esterification, etherification, polymer grafting, and copolymerization. Those lignin-based thermoplastic materials are expected to show applications as engineering plastics, polymeric foams, thermoplastic elastomers, and carbon-fiber precursors.

  5. Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis.

    PubMed

    Wei, Qing-Zhen; Fu, Wen-Yuan; Wang, Yun-Zhu; Qin, Xiao-Dong; Wang, Jing; Li, Ji; Lou, Qun-Feng; Chen, Jin-Feng

    2016-06-07

    The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes.

  6. Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis.

    PubMed

    Wei, Qing-Zhen; Fu, Wen-Yuan; Wang, Yun-Zhu; Qin, Xiao-Dong; Wang, Jing; Li, Ji; Lou, Qun-Feng; Chen, Jin-Feng

    2016-01-01

    The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes. PMID:27271557

  7. Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis

    PubMed Central

    Wei, Qing-zhen; Fu, Wen-yuan; Wang, Yun-zhu; Qin, Xiao-dong; Wang, Jing; Li, Ji; Lou, Qun-feng; Chen, Jin-feng

    2016-01-01

    The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes. PMID:27271557

  8. Analysis of lignin-carbohydrate and lignin-lignin linkages after hydrolase treatment of xylan-lignin, glucomannan-lignin and glucan-lignin complexes from spruce wood.

    PubMed

    Du, Xueyu; Pérez-Boada, Marta; Fernández, Carmen; Rencoret, Jorge; del Río, José C; Jiménez-Barbero, Jesús; Li, Jiebing; Gutiérrez, Ana; Martínez, Angel T

    2014-05-01

    Xylan-lignin (XL), glucomannan-lignin (GML) and glucan-lignin (GL) complexes were isolated from spruce wood, hydrolyzed with xylanase or endoglucanase/β-glucosidase, and analyzed by analytical pyrolysis and 2D-NMR. The enzymatic hydrolysis removed most of the polysaccharide moieties in the complexes, and the lignin content and relative abundance of lignin-carbohydrate linkages increased. Analytical pyrolysis confirmed the action of the enzymatic hydrolysis, with strong decreases of levoglucosane and other carbohydrate-derived products. Unexpectedly it also revealed that the hydrolase treatment alters the pattern of lignin breakdown products, resulting in higher amounts of coniferyl alcohol. From the anomeric carbohydrate signals in the 2D-NMR spectra, phenyl glycoside linkages (undetectable in the original complexes) could be identified in the hydrolyzed GML complex. Lower amounts of glucuronosyl and benzyl ether linkages were also observed after the hydrolysis. From the 2D-NMR spectra of the hydrolyzed complexes, it was concluded that the lignin in GML is less condensed than in XL due to its higher content in β-O-4' ether substructures (62 % of side chains in GML vs 53 % in XL) accompanied by more coniferyl alcohol end units (16 vs 13 %). In contrast, the XL lignin has more pinoresinols (11 vs 6 %) and dibenzodioxocins (9 vs 2 %) than the GML (and both have ~13 % phenylcoumarans and 1 % spirodienones). Direct 2D-NMR analysis of the hydrolyzed GL complex was not possible due to its low solubility. However, after sample acetylation, an even less condensed lignin than in the GML complex was found (with up to 72 % β-O-4' substructures and only 1 % pinoresinols). The study provides evidence for the existence of structurally different lignins associated to hemicelluloses (xylan and glucomannan) and cellulose in spruce wood and, at the same time, offers information on some of the chemical linkages between the above polymers.

  9. Dynamic QTL Analysis and Candidate Gene Mapping for Waterlogging Tolerance at Maize Seedling Stage

    PubMed Central

    Osman, Khalid A.; Tang, Bin; Wang, Yaping; Chen, Juanhua; Yu, Feng; Li, Liu; Han, Xuesong; Zhang, Zuxin; Yan, Jianbin; Zheng, Yonglian; Yue, Bing; Qiu, Fazhan

    2013-01-01

    Soil waterlogging is one of the major abiotic stresses adversely affecting maize growth and yield. To identify dynamic expression of genes or quantitative trait loci (QTL), QTL associated with plant height, root length, root dry weight, shoot dry weight and total dry weight were identified via conditional analysis in a mixed linear model and inclusive composite interval mapping method at three respective periods under waterlogging and control conditions. A total of 13, 19 and 23 QTL were detected at stages 3D|0D (the period during 0–3 d of waterlogging), 6D|3D and 9D|6D, respectively. The effects of each QTL were moderate and distributed over nine chromosomes, singly explaining 4.14–18.88% of the phenotypic variation. Six QTL (ph6-1, rl1-2, sdw4-1, sdw7-1, tdw4-1 and tdw7-1) were identified at two consistent stages of seedling development, which could reflect a continuous expression of genes; the remaining QTL were detected at only one stage. Thus, expression of most QTL was influenced by the developmental status. In order to provide additional evidence regarding the role of corresponding genes in waterlogging tolerance, mapping of Expressed Sequence Tags markers and microRNAs were conducted. Seven candidate genes were observed to co-localize with the identified QTL on chromosomes 1, 4, 6, 7 and 9, and may be important candidate genes for waterlogging tolerance. These results are a good starting point for understanding the genetic basis for selectively expressing of QTL in different stress periods and the common genetic control mechanism of the co-localized traits. PMID:24244474

  10. Lignin down-regulation of Zea mays via dsRNAi and klason lignin analysis.

    PubMed

    Park, Sang-Hyuck; Ong, Rebecca Garlock; Mei, Chuansheng; Sticklen, Mariam

    2014-07-23

    To facilitate the use of lignocellulosic biomass as an alternative bioenergy resource, during biological conversion processes, a pretreatment step is needed to open up the structure of the plant cell wall, increasing the accessibility of the cell wall carbohydrates. Lignin, a polyphenolic material present in many cell wall types, is known to be a significant hindrance to enzyme access. Reduction in lignin content to a level that does not interfere with the structural integrity and defense system of the plant might be a valuable step to reduce the costs of bioethanol production. In this study, we have genetically down-regulated one of the lignin biosynthesis-related genes, cinnamoyl-CoA reductase (ZmCCR1) via a double stranded RNA interference technique. The ZmCCR1_RNAi construct was integrated into the maize genome using the particle bombardment method. Transgenic maize plants grew normally as compared to the wild-type control plants without interfering with biomass growth or defense mechanisms, with the exception of displaying of brown-coloration in transgenic plants leaf mid-ribs, husks, and stems. The microscopic analyses, in conjunction with the histological assay, revealed that the leaf sclerenchyma fibers were thinned but the structure and size of other major vascular system components was not altered. The lignin content in the transgenic maize was reduced by 7-8.7%, the crystalline cellulose content was increased in response to lignin reduction, and hemicelluloses remained unchanged. The analyses may indicate that carbon flow might have been shifted from lignin biosynthesis to cellulose biosynthesis. This article delineates the procedures used to down-regulate the lignin content in maize via RNAi technology, and the cell wall compositional analyses used to verify the effect of the modifications on the cell wall structure.

  11. Lignin Down-regulation of Zea mays via dsRNAi and Klason Lignin Analysis

    PubMed Central

    Park, Sang-Hyuck; Ong, Rebecca Garlock; Mei, Chuansheng; Sticklen, Mariam

    2014-01-01

    To facilitate the use of lignocellulosic biomass as an alternative bioenergy resource, during biological conversion processes, a pretreatment step is needed to open up the structure of the plant cell wall, increasing the accessibility of the cell wall carbohydrates. Lignin, a polyphenolic material present in many cell wall types, is known to be a significant hindrance to enzyme access. Reduction in lignin content to a level that does not interfere with the structural integrity and defense system of the plant might be a valuable step to reduce the costs of bioethanol production. In this study, we have genetically down-regulated one of the lignin biosynthesis-related genes, cinnamoyl-CoA reductase (ZmCCR1) via a double stranded RNA interference technique. The ZmCCR1_RNAi construct was integrated into the maize genome using the particle bombardment method. Transgenic maize plants grew normally as compared to the wild-type control plants without interfering with biomass growth or defense mechanisms, with the exception of displaying of brown-coloration in transgenic plants leaf mid-ribs, husks, and stems. The microscopic analyses, in conjunction with the histological assay, revealed that the leaf sclerenchyma fibers were thinned but the structure and size of other major vascular system components was not altered. The lignin content in the transgenic maize was reduced by 7-8.7%, the crystalline cellulose content was increased in response to lignin reduction, and hemicelluloses remained unchanged. The analyses may indicate that carbon flow might have been shifted from lignin biosynthesis to cellulose biosynthesis. This article delineates the procedures used to down-regulate the lignin content in maize via RNAi technology, and the cell wall compositional analyses used to verify the effect of the modifications on the cell wall structure. PMID:25080235

  12. Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity.

    PubMed

    Sammond, Deanne W; Yarbrough, John M; Mansfield, Elisabeth; Bomble, Yannick J; Hobdey, Sarah E; Decker, Stephen R; Taylor, Larry E; Resch, Michael G; Bozell, Joseph J; Himmel, Michael E; Vinzant, Todd B; Crowley, Michael F

    2014-07-25

    The inhibitory action of lignin on cellulase cocktails is a major challenge to the biological saccharification of plant cell wall polysaccharides. Although the mechanism remains unclear, hydrophobic interactions between enzymes and lignin are hypothesized to drive adsorption. Here we evaluate the role of hydrophobic interactions in enzyme-lignin binding. The hydrophobicity of the enzyme surface was quantified using an estimation of the clustering of nonpolar atoms, identifying potential interaction sites. The adsorption of enzymes to lignin surfaces, measured using the quartz crystal microbalance, correlates to the hydrophobic cluster scores. Further, these results suggest a minimum hydrophobic cluster size for a protein to preferentially adsorb to lignin. The impact of electrostatic contribution was ruled out by comparing the isoelectric point (pI) values to the adsorption of proteins to lignin surfaces. These results demonstrate the ability to predict enzyme-lignin adsorption and could potentially be used to design improved cellulase cocktails, thus lowering the overall cost of biofuel production. PMID:24876380

  13. Predicting Enzyme Adsorption to Lignin Films by Calculating Enzyme Surface Hydrophobicity*

    PubMed Central

    Sammond, Deanne W.; Yarbrough, John M.; Mansfield, Elisabeth; Bomble, Yannick J.; Hobdey, Sarah E.; Decker, Stephen R.; Taylor, Larry E.; Resch, Michael G.; Bozell, Joseph J.; Himmel, Michael E.; Vinzant, Todd B.; Crowley, Michael F.

    2014-01-01

    The inhibitory action of lignin on cellulase cocktails is a major challenge to the biological saccharification of plant cell wall polysaccharides. Although the mechanism remains unclear, hydrophobic interactions between enzymes and lignin are hypothesized to drive adsorption. Here we evaluate the role of hydrophobic interactions in enzyme-lignin binding. The hydrophobicity of the enzyme surface was quantified using an estimation of the clustering of nonpolar atoms, identifying potential interaction sites. The adsorption of enzymes to lignin surfaces, measured using the quartz crystal microbalance, correlates to the hydrophobic cluster scores. Further, these results suggest a minimum hydrophobic cluster size for a protein to preferentially adsorb to lignin. The impact of electrostatic contribution was ruled out by comparing the isoelectric point (pI) values to the adsorption of proteins to lignin surfaces. These results demonstrate the ability to predict enzyme-lignin adsorption and could potentially be used to design improved cellulase cocktails, thus lowering the overall cost of biofuel production. PMID:24876380

  14. Modifying lignin to improve bioenergy feedstocks: strengthening the barrier against pathogens?†

    PubMed Central

    Sattler, Scott E.; Funnell-Harris, Deanna L.

    2013-01-01

    Lignin is a ubiquitous polymer present in cell walls of all vascular plants, where it rigidifies and strengthens the cell wall structure through covalent cross-linkages to cell wall polysaccharides. The presence of lignin makes the cell wall recalcitrant to conversion into fermentable sugars for bioenergy uses. Therefore, reducing lignin content and modifying its linkages have become major targets for bioenergy feedstock development through either biotechnology or traditional plant breeding. In addition, lignin synthesis has long been implicated as an important plant defense mechanism against pathogens, because lignin synthesis is often induced at the site of pathogen attack. This article explores the impact of lignin modifications on the susceptibility of a range of plant species to their associated pathogens, and the implications for development of feedstocks for the second-generation biofuels industry. Surprisingly, there are some instances where plants modified in lignin synthesis may display increased resistance to associated pathogens, which is explored in this article. PMID:23577013

  15. QTL affecting stress response to crowding in a rainbow trout broodstock population

    PubMed Central

    2012-01-01

    Background Genomic analyses have the potential to impact selective breeding programs by identifying markers that serve as proxies for traits which are expensive or difficult to measure. Also, identifying genes affecting traits of interest enhances our understanding of their underlying biochemical pathways. To this end we conducted genome scans of seven rainbow trout families from a single broodstock population to identify quantitative trait loci (QTL) having an effect on stress response to crowding as measured by plasma cortisol concentration. Our goal was to estimate the number of major genes having large effects on this trait in our broodstock population through the identification of QTL. Results A genome scan including 380 microsatellite markers representing 29 chromosomes resulted in the de novo construction of genetic maps which were in good agreement with the NCCCWA genetic map. Unique sets of QTL were detected for two traits which were defined after observing a low correlation between repeated measurements of plasma cortisol concentration in response to stress. A highly significant QTL was detected in three independent analyses on Omy16, many additional suggestive and significant QTL were also identified. With linkage-based methods of QTL analysis such as half-sib regression interval mapping and a variance component method, we determined that the significant and suggestive QTL explain about 40-43% and 13-27% of the phenotypic trait variation, respectively. Conclusions The cortisol response to crowding stress is a complex trait controlled in a sub-sample of our broodstock population by multiple QTL on at least 8 chromosomes. These QTL are largely different from others previously identified for a similar trait, documenting that population specific genetic variants independently affect cortisol response in ways that may result in different impacts on growth. Also, mapping QTL for multiple traits associated with stress response detected trait specific QTL which

  16. QTL Analysis for Resistance to Blast Disease in U.S. Weedy Rice.

    PubMed

    Liu, Yan; Qi, Xinshuai; Gealy, Dave R; Olsen, Kenneth M; Caicedo, Ana L; Jia, Yulin

    2015-07-01

    Understanding the genetic architecture of adaptation is of great importance in evolutionary biology. U.S. weedy rice is well adapted to the local conditions in U.S. rice fields. Rice blast disease is one of the most destructive diseases of cultivated rice worldwide. However, information about resistance to blast in weedy rice is limited. Here, we evaluated the disease reactions of 60 U.S. weedy rice accessions with 14 blast races, and investigated the quantitative trait loci (QTL) associated with blast resistance in two major ecotypes of U.S. weedy rice. Our results revealed that U.S. weedy rice exhibited a broad resistance spectrum. Using genotyping by sequencing, we identified 28 resistance QTL in two U.S. weedy rice ecotypes. The resistance QTL with relatively large and small effects suggest that U.S. weedy rice groups have adapted to blast disease using two methods, both major resistance (R) genes and QTL. Three genomic loci shared by some of the resistance QTL indicated that these loci may contribute to no-race-specific resistance in weedy rice. Comparing with known blast disease R genes, we found that the R genes at these resistance QTL are novel, suggesting that U.S. weedy rice is a potential source of novel blast R genes for resistant breeding.

  17. Lignin blockers and uses thereof

    SciTech Connect

    Yang, Bin; Wyman, Charles E

    2013-11-12

    Disclosed is a method for converting cellulose in a lignocellulosic biomass. The method provides for a lignin-blocking polypeptide and/or protein treatment of high lignin solids. The treatment enhances cellulase availability in cellulose conversion and allows for the determination of optimized pretreatment conditions. Additionally, ethanol yields from a Simultaneous Saccharification and Fermentation process are improved 5-25% by treatment with a lignin-blocking polypeptide and/or protein.

  18. Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis)

    PubMed Central

    Sauvage, Christopher; Vagner, Marie; Derôme, Nicolas; Audet, Céline; Bernatchez, Louis

    2012-01-01

    Growth performance and reduced stress response are traits of major interest in fish production. Growth and stress-related quantitative trait loci (QTL) have been already identified in several salmonid species, but little effort has been devoted to charrs (genus Salvelinus). Moreover, most QTL studies to date focused on one or very few traits, and little investigation has been devoted to QTL identification for gene expression. Here, our objective was to identify QTL for 27 phenotypes related to growth and stress responses in brook charr (Salvelinus fontinalis), which is one of the most economically important freshwater aquaculture species in Canada. Phenotypes included 12 growth parameters, six blood and plasma variables, three hepatic variables, and one plasma hormone level as well as the relative expression measurements of five genes of interest linked to growth regulation. QTL analysis relied on a linkage map recently built from S. fontinalis consisting of both single-nucleotide polymorphism (SNP, n = 266) and microsatellite (n =81) markers in an F2 interstrain hybrid population (n = 171). We identified 63 growth-related QTL and four stress-related QTL across 18 of the 40 linkage groups of the brook charr linkage map. Percent variance explained, confidence interval, and allelic QTL effects also were investigated to provide insight into the genetic architecture of growth- and stress-related QTL. QTL related to growth performance and stress response that were identified could be classified into two groups: (1) a group composed of the numerous, small-effect QTL associated with some traits related to growth (i.e., weight) that may be under the control of a large number of genes or pleiotropic genes, and (2) a group of less numerous QTL associated with growth (i.e., gene expression) and with stress-related QTL that display a larger effect, suggesting that these QTL are under the control of a limited number of genes of major effect. This study represents a first step

  19. Effect of liquid hot water pretreatment severity on properties of hardwood lignin and enzymatic hydrolysis of cellulose.

    PubMed

    Ko, Ja Kyong; Kim, Youngmi; Ximenes, Eduardo; Ladisch, Michael R

    2015-02-01

    Lignin, one of the major components of lignocellulosic biomass, plays an inhibitory role on the enzymatic hydrolysis of cellulose. This work examines the role of lignin in pretreated hardwood, where extents of cellulose hydrolysis decrease, rather than increase with increasing severity of liquid hot water pretreatment. Hardwood pretreated with liquid hot water at severities ranging from log Ro  = 8.25 to 12.51 resulted in 80-90% recovery of the initial lignin in the residual solids. The ratio of acid insoluble lignin (AIL) to acid soluble lignin (ASL) increased and the formation of spherical lignin droplets on the cell wall surface was observed as previously reported in the literature. When lignins were isolated from hardwoods pretreated at increasing severities and characterized based on glass transition temperature (Tg ), the Tg of isolated lignins was found to increase from 171 to 180°C as the severity increased from log Ro  = 10.44 to 12.51. The increase in Tg suggested that the condensation reactions of lignin molecules occurred during pretreatment and altered the lignin structure. The contribution of the changes in lignin properties to enzymatic hydrolysis were examined by carrying out Avicel hydrolysis in the presence of isolated lignins. Lignins derived from more severely pretreated hardwoods had higher Tg values and showed more pronounced inhibition of enzymatic hydrolysis.

  20. Lignin valorization: improving lignin processing in the biorefinery.

    PubMed

    Ragauskas, Arthur J; Beckham, Gregg T; Biddy, Mary J; Chandra, Richard; Chen, Fang; Davis, Mark F; Davison, Brian H; Dixon, Richard A; Gilna, Paul; Keller, Martin; Langan, Paul; Naskar, Amit K; Saddler, Jack N; Tschaplinski, Timothy J; Tuskan, Gerald A; Wyman, Charles E

    2014-05-16

    Research and development activities directed toward commercial production of cellulosic ethanol have created the opportunity to dramatically increase the transformation of lignin to value-added products. Here, we highlight recent advances in this lignin valorization effort. Discovery of genetic variants in native populations of bioenergy crops and direct manipulation of biosynthesis pathways have produced lignin feedstocks with favorable properties for recovery and downstream conversion. Advances in analytical chemistry and computational modeling detail the structure of the modified lignin and direct bioengineering strategies for future targeted properties. Refinement of biomass pretreatment technologies has further facilitated lignin recovery, and this coupled with genetic engineering will enable new uses for this biopolymer, including low-cost carbon fibers, engineered plastics and thermoplastic elastomers, polymeric foams, fungible fuels, and commodity chemicals.

  1. Lignin Valorization: Improving Lignin Processing in the Biorefinery

    SciTech Connect

    Ragauskas, Arthur; Beckham, Gregg; Biddy, Mary J; Chandra, Richard; Chen, Fang; Davis, Dr. Mark F.; Davison, Brian H; Dixon, Richard; Gilna, Paul; Keller, Martin; Langan, Paul; Naskar, Amit K; Saddler, Jack N; Tschaplinski, Timothy J; Tuskan, Gerald A; Wyman, Charles E,; Harber, Karen S

    2014-01-01

    Research and development activities directed toward commercial production of cellulosic ethanol have created the opportunity to dramatically increase the transformation of lignin to value-added products. Here we highlight recent advances in this lignin valorization effort. Discovery of genetic variants in native populations of bioenergy crops and direct manipulation of biosynthesis pathways have produced lignin feedstocks with favorable properties for recovery and downstream conversion. Advances in analytical chemistry and computational modeling detail the structure of the modified lignin and direct bioengineering strategies for future targeted properties. Refinement of biomass pretreatment technologies has further facilitated lignin recovery, and this coupled with genetic engineering will enable new uses for this biopolymer, including low-cost carbon fibers, engineered plastics and thermoplastic elastomers, polymeric foams, fungible fuels, and commodity chemicals.

  2. Systematic Genetic Analysis Identifies Cis-eQTL Target Genes Associated with Glioblastoma Patient Survival

    PubMed Central

    Chen, Qing-Rong; Hu, Ying; Yan, Chunhua; Buetow, Kenneth; Meerzaman, Daoud

    2014-01-01

    Prior expression quantitative trait locus (eQTL) studies have demonstrated heritable variation determining differences in gene expression. The majority of eQTL studies were based on cell lines and normal tissues. We performed cis-eQTL analysis using glioblastoma multiforme (GBM) data sets obtained from The Cancer Genome Atlas (TCGA) to systematically investigate germline variation’s contribution to tumor gene expression levels. We identified 985 significant cis-eQTL associations (FDR<0.05) mapped to 978 SNP loci and 159 unique genes. Approximately 57% of these eQTLs have been previously linked to the gene expression in cell lines and normal tissues; 43% of these share cis associations known to be associated with functional annotations. About 25% of these cis-eQTL associations are also common to those identified in Breast Cancer from a recent study. Further investigation of the relationship between gene expression and patient clinical information identified 13 eQTL genes whose expression level significantly correlates with GBM patient survival (p<0.05). Most of these genes are also differentially expressed in tumor samples and organ-specific controls (p<0.05). Our results demonstrated a significant relationship of germline variation with gene expression levels in GBM. The identification of eQTLs-based expression associated survival might be important to the understanding of genetic contribution to GBM cancer prognosis. PMID:25133526

  3. Lignin Bioproducts to Enable Biofuels

    SciTech Connect

    Wyman, Charles E.; Ragauskas, Arthur J

    2015-09-15

    Here we report that today's and tomorrow's biofuels production facilities could benefit tremendously from increasing the value from the large amount of lignin that results from biofuels operations. Certainly, the scientific community, and biofuels industry has begun to recognize the challenges and opportunities associated with lignin.

  4. Identification of quantitative trait loci controlling fibre length and lignin content in Arabidopsis thaliana stems

    PubMed Central

    Berleth, Thomas

    2013-01-01

    Fibre properties and the biochemical composition of cell walls are important traits in many applications. For example, the lengths of fibres define the strength and quality of paper, and lignin content is a critical parameter for the use of biomass in biofuel production. Identifying genes controlling these traits is comparatively difficult in woody species, because of long generation times and limited amenability to high-resolution genetic mapping. To address this problem, this study mapped quantitative trait loci (QTLs) defining fibre length and lignin content in the Arabidopsis recombinant inbred line population Col-4×Ler-0. Adapting high-throughput phenotyping techniques for both traits for measurements in Arabidopsis inflorescence stems identified significant QTLs for fibre length on chromosomes 2 and 5, as well as one significant QTL affecting lignin content on chromosome 2. For fibre length, total variation within the population was 208% higher than between parental lines and the identified QTLs explained 50.58% of the observed variation. For lignin content, the values were 261 and 26.51%, respectively. Bioinformatics analysis of the associated intervals identified a number of candidate genes for fibre length and lignin content. This study demonstrates that molecular mapping of QTLs pertaining to wood and fibre properties is possible in Arabidopsis, which substantially broadens the use of Arabidopsis as a model species for the functional characterization of plant genes. PMID:23136168

  5. Lignin-assisted coal depolymerization. Technical report, December 1, 1991--February 29, 1992

    SciTech Connect

    Lalvani, S.B.

    1992-08-01

    Previous research has shown that addition of lignin and lignin-derived liquids to coal stirred in tetralin under mild reaction conditions (375{degrees}C and 300--500 psig) results in a marked enhancement in the rate of coal depolymerization. In this quarterly report, overall mass balances on experiments conducted with tetralin, coal, lignin and coal-lignin mixture are reported. Overall mass recoveries of 95--99% of the total mass charged to the reactor were obtained. A number of experiments were conducted on coal, lignin and coal-lignin depolymerization. A careful statistical analysis of the data shows that coal depolymerization is enhanced by 10.4%, due to the lignin addition. The liquids obtained are being examined for their elemental composition, and molecular weight determination by size exclusion chromatography. The stability of the liquid products is being examined in various environments. The gaseous product analyses show that the major gases produced during the course of depolymerization are CO, CH{sub 4}, and CO{sub 2}. When coal and lignin are reacted together, the amount of CO and CH{sub 4}produced respectively 12% and 38% greater than the corresponding amount of gases calculated, based on the weighted average of values obtained for coal and lignin alone. The data obtained show that lignin addition to coal is synergistic in that not only is the extent of coal depolymerization increased, but the gas produced contains higher concentrations of more desirable gaseous products.

  6. Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects.

    PubMed Central

    Melchinger, A E; Utz, H F; Schön, C C

    1998-01-01

    The efficiency of marker-assisted selection (MAS) depends on the power of quantitative trait locus (QTL) detection and unbiased estimation of QTL effects. Two independent samples N = 344 and 107 of F2 plants were genotyped for 89 RFLP markers. For each sample, testcross (TC) progenies of the corresponding F3 lines with two testers were evaluated in four environments. QTL for grain yield and other agronomically important traits were mapped in both samples. QTL effects were estimated from the same data as used for detection and mapping of QTL (calibration) and, based on QTL positions from calibration, from the second, independent sample (validation). For all traits and both testers we detected a total of 107 QTL with N = 344, and 39 QTL with N = 107, of which only 20 were in common. Consistency of QTL effects across testers was in agreement with corresponding genotypic correlations between the two TC series. Most QTL displayed no significant QTL x environment nor epistatic interactions. Estimates of the proportion of the phenotypic and genetic variance explained by QTL were considerably reduced when derived from the independent validation sample as opposed to estimates from the calibration sample. We conclude that, unless QTL effects are estimated from an independent sample, they can be inflated, resulting in an overly optimistic assessment of the efficiency of MAS. PMID:9584111

  7. Linkage disequilibrium with linkage analysis of multiline crosses reveals different multiallelic QTL for hybrid performance in the flint and dent heterotic groups of maize.

    PubMed

    Giraud, Héloïse; Lehermeier, Christina; Bauer, Eva; Falque, Matthieu; Segura, Vincent; Bauland, Cyril; Camisan, Christian; Campo, Laura; Meyer, Nina; Ranc, Nicolas; Schipprack, Wolfgang; Flament, Pascal; Melchinger, Albrecht E; Menz, Monica; Moreno-González, Jesús; Ouzunova, Milena; Charcosset, Alain; Schön, Chris-Carolin; Moreau, Laurence

    2014-12-01

    Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R(2) = 27%) with pleiotropic effects was detected on chromosome 10, whereas other QTL displayed milder effects (R(2) < 10%). On average, the LDLA models detected more QTL but generally explained lower percentages of variance, consistent with the fact that most QTL display complex allelic series. Only 15% of the QTL were common to the two designs. A joint analysis of the two designs detected between 15 and 21 QTL for the five traits. Of these, between 27 for silking date and 41% for tasseling date were significant in both groups. Favorable allelic effects detected in both groups open perspectives for improving biomass production.

  8. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population

    DOE PAGES

    Penning, Bryan W.; Sykes, Robert W.; Babcock, Nicholas C.; Dugard, Christopher K.; Held, Michael A.; Klimek, John F.; Shreve, Jacob T.; Fowler, Matthew; Ziebell, Angela; Davis, Mark F.; et al

    2014-06-27

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 x 3 Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yieldmore » was shared. A genome-wide association study for lignin abundance and sugar yield of the 282- member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. Finally, these results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.« less

  9. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population

    SciTech Connect

    Penning, Bryan W.; Sykes, Robert W.; Babcock, Nicholas C.; Dugard, Christopher K.; Held, Michael A.; Klimek, John F.; Shreve, Jacob T.; Fowler, Matthew; Ziebell, Angela; Davis, Mark F.; Decker, Stephen R.; Turner, Geoffrey B.; Mosier, Nathan S.; Springer, Nathan M.; Thimmapuram, Jyothi; Weil, Clifford F.; McCann, Maureen C.; Carpita, Nicholas C.

    2014-06-27

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 x 3 Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study for lignin abundance and sugar yield of the 282- member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. Finally, these results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.

  10. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population.

    PubMed

    Penning, Bryan W; Sykes, Robert W; Babcock, Nicholas C; Dugard, Christopher K; Held, Michael A; Klimek, John F; Shreve, Jacob T; Fowler, Matthew; Ziebell, Angela; Davis, Mark F; Decker, Stephen R; Turner, Geoffrey B; Mosier, Nathan S; Springer, Nathan M; Thimmapuram, Jyothi; Weil, Clifford F; McCann, Maureen C; Carpita, Nicholas C

    2014-06-27

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 × Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study for lignin abundance and sugar yield of the 282-member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. These results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.

  11. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population1[W][OPEN

    PubMed Central

    Penning, Bryan W.; Sykes, Robert W.; Babcock, Nicholas C.; Dugard, Christopher K.; Held, Michael A.; Klimek, John F.; Shreve, Jacob T.; Fowler, Matthew; Ziebell, Angela; Davis, Mark F.; Decker, Stephen R.; Turner, Geoffrey B.; Mosier, Nathan S.; Springer, Nathan M.; Thimmapuram, Jyothi; Weil, Clifford F.; McCann, Maureen C.; Carpita, Nicholas C.

    2014-01-01

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 × Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study for lignin abundance and sugar yield of the 282-member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. These results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass. PMID:24972714

  12. Lignin structural alterations in thermochemical pretreatments with limited delignification

    DOE PAGES

    Pu, Yunqiao; Hu, Fan; Huang, Fang; Ragauskas, Arthur J.

    2015-08-02

    Lignocellulosic biomass has a complex and rigid cell wall structure that makes biomass recalcitrant to biological and chemical degradation. Among the three major structural biopolymers (i.e., cellulose, hemicellulose and lignin) in plant cell walls, lignin is considered the most recalcitrant component and generally plays a negative role in the biochemical conversion of biomass to biofuels. The conversion of biomass to biofuels through a biochemical platform usually requires a pretreatment stage to reduce the recalcitrance. Pretreatment renders compositional and structural changes of biomass with these changes ultimately govern the efficiency of the subsequent enzymatic hydrolysis. Dilute acid, hot water, steam explosion,more » and ammonia fiber expansion pretreatments are among the leading thermochemical pretreatments with a limited delignification that can reduce biomass recalcitrance. Practical applications of these pretreatment are rapidly developing as illustrated by recent commercial scale cellulosic ethanol plants. While these thermochemical pretreatments generally lead to only a limited delignification and no significant change of lignin content in the pretreated biomass, the lignin transformations that occur during these pretreatments and the roles they play in recalcitrance reduction is an important research aspect. This review highlights recent advances in our understanding of lignin alterations during these limited delignification thermochemical pretreatments, with emphasis on lignin chemical structures, molecular weights, and redistributions in the pretreated biomass.« less

  13. Lignin structural alterations in thermochemical pretreatments with limited delignification

    SciTech Connect

    Pu, Yunqiao; Hu, Fan; Huang, Fang; Ragauskas, Arthur J.

    2015-08-02

    Lignocellulosic biomass has a complex and rigid cell wall structure that makes biomass recalcitrant to biological and chemical degradation. Among the three major structural biopolymers (i.e., cellulose, hemicellulose and lignin) in plant cell walls, lignin is considered the most recalcitrant component and generally plays a negative role in the biochemical conversion of biomass to biofuels. The conversion of biomass to biofuels through a biochemical platform usually requires a pretreatment stage to reduce the recalcitrance. Pretreatment renders compositional and structural changes of biomass with these changes ultimately govern the efficiency of the subsequent enzymatic hydrolysis. Dilute acid, hot water, steam explosion, and ammonia fiber expansion pretreatments are among the leading thermochemical pretreatments with a limited delignification that can reduce biomass recalcitrance. Practical applications of these pretreatment are rapidly developing as illustrated by recent commercial scale cellulosic ethanol plants. While these thermochemical pretreatments generally lead to only a limited delignification and no significant change of lignin content in the pretreated biomass, the lignin transformations that occur during these pretreatments and the roles they play in recalcitrance reduction is an important research aspect. This review highlights recent advances in our understanding of lignin alterations during these limited delignification thermochemical pretreatments, with emphasis on lignin chemical structures, molecular weights, and redistributions in the pretreated biomass.

  14. Structural characterization of the lignin from jute (Corchorus capsularis) fibers.

    PubMed

    del Río, José C; Rencoret, Jorge; Marques, Gisela; Li, Jiebing; Gellerstedt, Göran; Jiménez-Barbero, Jesús; Martínez, Angel T; Gutiérrez, Ana

    2009-11-11

    The structural characteristics of the lignin from jute (Corchorus capsularis ) fibers, which are used for high-quality paper pulp production, were studied. The lignin content (13.3% Klason lignin) was high compared to other nonwoody bast fibers used for pulp production. The lignin structure was characterized by pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), 2D-NMR, and thioacidolysis. Upon Py-GC/MS, jute fibers released predominantly products from syringylpropanoid units with the S/G ratio being 2.1 and a H/G/S composition of 2:33:65. 2D-NMR of the milled wood lignin (MWL) isolated from jute fibers showed a predominance of beta-O-4' aryl ether linkages (72% of total side chains), followed by beta-beta' resinol-type linkages (16% of total side chains) and lower amounts of beta-5' phenylcoumaran (4%) and beta-1' spirodienone-type (4%) linkages and cinnamyl end groups (4%). The high predominance of the S-lignin units, together with the high proportion of beta-O-4' aryl ether linkages, which are easily cleaved during alkaline cooking, are advantageous for pulping. On the other hand, a small percentage (ca. 4%) of the lignin side chain was found to be acetylated at the gamma-carbon, predominantly over syringyl units. The analysis of desulphurated thioacidolysis dimers provided additional information on the relative abundances of the various carbon-carbon and diaryl ether bonds and the type of units (syringyl or guaiacyl) involved in each of the above linkage types. Interestingly, the major part of the beta-beta' dimers included two syringyl units, indicating that most of the beta-beta' substructures identified in the HSQC spectra were of the syringaresinol type (pinoresinol being absent), as already observed in the lignin of other angiosperms.

  15. 21 CFR 573.600 - Lignin sulfonates.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Lignin sulfonates. 573.600 Section 573.600 Food... Additive Listing § 573.600 Lignin sulfonates. Lignin sulfonates may be safely used in animal feeds in... feeds, as liquid lignin sulfonate, in an amount not to exceed 11 percent of the molasses. (4) As...

  16. 21 CFR 573.600 - Lignin sulfonates.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 6 2011-04-01 2011-04-01 false Lignin sulfonates. 573.600 Section 573.600 Food... Additive Listing § 573.600 Lignin sulfonates. Lignin sulfonates may be safely used in animal feeds in... feeds, as liquid lignin sulfonate, in an amount not to exceed 11 percent of the molasses. (4) As...

  17. Utilization of chemically modified lignin

    SciTech Connect

    Chem, M.J.

    1996-10-01

    A chemical modification method has been developed to convert lignin into lignin graft copolymers. The graft products are macromolecular surface active agents because, within each molecule, a hydrocarbon sidechain has been gown off of a natural oxyphenylpropyl backbone. Surface activity of the graft copolymers was indicated by their capacity to form stable emulsions between incompatible fluid phases and to adhesively bond to wood surfaces. Lignin has been grafted with ethenylbenzene (styrene), 4-methyl-2-oxy-3-oxopent-4-ene (methylmethacrylate), 2-propenamide(acrylamide), 2-propene nitrile (acrylonitrile), cationic monomers, and anionic monomers. Synthesis with anionic, cationic, or polar nonionic monomers produced water soluble, lignin copolymers that were effective dispersing, flocculating, and surface active agents. The nonionic polymers and their hydrolysis products are effective thinners and suspending agents for drilling mud formulations. In reactions with ethenylbenzene, lignin was used to make thermoplastic materials. These products have been shown to be poly(lignin-g-(1-phenylethylene))-containing materials by a series of solubility and extraction tests and are formed with 90% or more grafting efficiency for lignin. These materials have been shown to be thermoplastics, coupling agents for wood and plastic, and biodegradable plastics.

  18. Tandem Catalytic Depolymerization of Lignin by Water-Tolerant Lewis Acids and Rhodium Complexes.

    PubMed

    Jastrzebski, Robin; Constant, Sandra; Lancefield, Christopher S; Westwood, Nicholas J; Weckhuysen, Bert M; Bruijnincx, Pieter C A

    2016-08-23

    Lignin is an attractive renewable feedstock for aromatic bulk and fine chemicals production, provided that suitable depolymerization procedures are developed. Here, we describe a tandem catalysis strategy for ether linkage cleavage within lignin, involving ether hydrolysis by water-tolerant Lewis acids followed by aldehyde decarbonylation by a Rh complex. In situ decarbonylation of the reactive aldehydes limits loss of monomers by recondensation, a major issue in acid-catalyzed lignin depolymerization. Rate of hydrolysis and decarbonylation were matched using lignin model compounds, allowing the method to be successfully applied to softwood, hardwood, and herbaceous dioxasolv lignins, as well as poplar sawdust, to give the anticipated decarbonylation products and, rather surprisingly, 4-(1-propenyl)phenols. Promisingly, product selectivity can be tuned by variation of the Lewis-acid strength and lignin source. PMID:27440544

  19. Constructing Confidence Intervals for Qtl Location

    PubMed Central

    Mangin, B.; Goffinet, B.; Rebai, A.

    1994-01-01

    We describe a method for constructing the confidence interval of the QTL location parameter. This method is developed in the local asymptotic framework, leading to a linear model at each position of the putative QTL. The idea is to construct a likelihood ratio test, using statistics whose asymptotic distribution does not depend on the nuisance parameters and in particular on the effect of the QTL. We show theoretical properties of the confidence interval built with this test, and compare it with the classical confidence interval using simulations. We show in particular, that our confidence interval has the correct probability of containing the true map location of the QTL, for almost all QTLs, whereas the classical confidence interval can be very biased for QTLs having small effect. PMID:7896108

  20. QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems.

    PubMed

    Zhang, Ying; Thomas, Catherine L; Xiang, Jinxia; Long, Yan; Wang, Xiaohua; Zou, Jun; Luo, Ziliang; Ding, Guangda; Cai, Hongmei; Graham, Neil S; Hammond, John P; King, Graham J; White, Philip J; Xu, Fangsen; Broadley, Martin R; Shi, Lei; Meng, Jinling

    2016-01-01

    A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and 'normal' phosphate (Pi) supply using a 'pouch and wick' system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica. PMID:27624881

  1. QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems.

    PubMed

    Zhang, Ying; Thomas, Catherine L; Xiang, Jinxia; Long, Yan; Wang, Xiaohua; Zou, Jun; Luo, Ziliang; Ding, Guangda; Cai, Hongmei; Graham, Neil S; Hammond, John P; King, Graham J; White, Philip J; Xu, Fangsen; Broadley, Martin R; Shi, Lei; Meng, Jinling

    2016-09-14

    A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and 'normal' phosphate (Pi) supply using a 'pouch and wick' system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica.

  2. QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems

    PubMed Central

    Zhang, Ying; Thomas, Catherine L.; Xiang, Jinxia; Long, Yan; Wang, Xiaohua; Zou, Jun; Luo, Ziliang; Ding, Guangda; Cai, Hongmei; Graham, Neil S.; Hammond, John P.; King, Graham J.; White, Philip J.; Xu, Fangsen; Broadley, Martin R.; Shi, Lei; Meng, Jinling

    2016-01-01

    A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and ‘normal’ phosphate (Pi) supply using a ‘pouch and wick’ system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica. PMID:27624881

  3. Quantitative Trait Locus (QTL) Mapping Reveals a Role for Unstudied Genes in Aspergillus Virulence

    PubMed Central

    Christians, Julian K.; Cheema, Manjinder S.; Vergara, Ismael A.; Watt, Cortney A.; Pinto, Linda J.; Chen, Nansheng; Moore, Margo M.

    2011-01-01

    Infections caused by the fungus Aspergillus are a major cause of morbidity and mortality in immunocompromised populations. To identify genes required for virulence that could be used as targets for novel treatments, we mapped quantitative trait loci (QTL) affecting virulence in the progeny of a cross between two strains of A. nidulans (FGSC strains A4 and A91). We genotyped 61 progeny at 739 single nucleotide polymorphisms (SNP) spread throughout the genome, and constructed a linkage map that was largely consistent with the genomic sequence, with the exception of one potential inversion of ∼527 kb on Chromosome V. The estimated genome size was 3705 cM and the average intermarker spacing was 5.0 cM. The average ratio of physical distance to genetic distance was 8.1 kb/cM, which is similar to previous estimates, and variation in recombination rate was significantly positively correlated with GC content, a pattern seen in other taxa. To map QTL affecting virulence, we measured the ability of each progeny strain to kill model hosts, larvae of the wax moth Galleria mellonella. We detected three QTL affecting in vivo virulence that were distinct from QTL affecting in vitro growth, and mapped the virulence QTL to regions containing 7–24 genes, excluding genes with no sequence variation between the parental strains and genes with only synonymous SNPs. None of the genes in our QTL target regions have been previously associated with virulence in Aspergillus, and almost half of these genes are currently annotated as “hypothetical”. This study is the first to map QTL affecting the virulence of a fungal pathogen in an animal host, and our results illustrate the power of this approach to identify a short list of unknown genes for further investigation. PMID:21559404

  4. Degradation of carbohydrates and lignins in buried woods

    USGS Publications Warehouse

    Hedges, J.I.; Cowie, G.L.; Ertel, J.R.; James, Barbour R.; Hatcher, P.G.

    1985-01-01

    Spruce, alder, and oak woods deposited in coastal sediments were characterized versus their modern counterparts by quantification of individual neutral sugars and lignin-derived phenols as well as by scanning electron microscopy, 13C NMR, and elemental analysis. The buried spruce wood from a 2500 yr old deposit was unaltered whereas an alder wood from the same horizon and an oak wood from an open ocean sediment were profoundly degraded. Individual sugar and lignin phenol analyses indicate that at least 90 and 98 wt% of the initial total polysaccharides in the buried alder and oak woods, respectively, have been degraded along with 15-25 wt% of the lignin. At least 75% of the degraded biopolymer has been physically lost from these samples. This evidence is supported by the SEM, 13C NMR and elemental analyses, all of which indicate selective loss of the carbohydrate moiety. The following order of stability was observed for the major biochemical constituents of both buried hardwoods: vanillyl and p-hydroxyl lignin structural units > syringyl lignin structural units > pectin > ??-cellulose > hemicellulose. This sequence can be explained by selective preservation of the compound middle lamella regions of the wood cell walls. The magnitude and selectivity of the indicated diagenetic reactions are sufficient to cause major changes in the chemical compositions of wood-rich sedimentary organic mixtures and to provide a potentially large in situ nutrient source. ?? 1985.

  5. Roles of silica and lignin in horsetail (Equisetum hyemale), with special reference to mechanical properties

    NASA Astrophysics Data System (ADS)

    Yamanaka, Shigeru; Sato, Kanna; Ito, Fuyu; Komatsubara, Satoshi; Ohata, Hiroshi; Yoshino, Katsumi

    2012-02-01

    This research deals with detailed analyses of silica and lignin distribution in horsetail with special reference to mechanical strength. Scanning electron images of a cross-section of an internode showed silica deposited densely only around the outer epidermis. Detailed histochemical analyses of lignin showed no lignin deposition in the silica-rich outer internodes of horsetail, while a characteristic lignin deposition was noticed in the vascular bundle in inner side of internodes. To analyze the structure of horsetail from a mechanical viewpoint, we calculated the response of a model structure of horsetail to a mechanical force applied perpendicularly to the long axis by a finite element method. We found that silica distributed in the outer epidermis may play the major structural role, with lignin's role being limited ensuring that the vascular bundle keep waterproof. These results were in contrast to more modern tall trees like gymnosperms, for which lignin provides mechanical strength. Lignin has the advantage of sticking to cellulose, hemicellulose, and other materials. Such properties make it possible for plants containing lignin to branch. Branching of tree stems aids in competing for light and other atmospheric resources. This type of branching was impossible for ancient horsetails, which relied on the physical properties of silica. From the evolutional view points, over millennia in trees with high lignin content, true branching, and many chlorophyll-containing leaves developed.

  6. Connecting thermal performance curve variation to the genotype: a multivariate QTL approach.

    PubMed

    Latimer, C A L; Foley, B R; Chenoweth, S F

    2015-01-01

    Thermal performance curves (TPCs) are continuous reaction norms that describe the relationship between organismal performance and temperature and are useful for understanding trade-offs involved in thermal adaptation. Although thermal trade-offs such as those between generalists and specialists or between hot- and cold-adapted phenotypes are known to be genetically variable and evolve during thermal adaptation, little is known of the genetic basis to TPCs - specifically, the loci involved and the directionality of their effects across different temperatures. To address this, we took a multivariate approach, mapping quantitative trait loci (QTL) for locomotor activity TPCs in the fly, Drosophila serrata, using a panel of 76 recombinant inbred lines. The distribution of additive genetic (co)variance in the mapping population was remarkably similar to the distribution of mutational (co)variance for these traits. We detected 11 TPC QTL in females and 4 in males. Multivariate QTL effects were closely aligned with the major axes genetic (co)variation between temperatures; most QTL effects corresponded to variation for either overall increases or decreases in activity with a smaller number indicating possible trade-offs between activity at high and low temperatures. QTL representing changes in curve shape such as the 'generalist-specialist' trade-off, thought key to thermal adaptation, were poorly represented in the data. We discuss these results in the light of genetic constraints on thermal adaptation.

  7. Strategies for the Conversion of Lignin to High-Value Polymeric Materials: Review and Perspective.

    PubMed

    Upton, Brianna M; Kasko, Andrea M

    2016-02-24

    The majority of commodity plastics and materials are derived from petroleum-based chemicals, illustrating the strong dependence on products derived from non-renewable energy sources. As the most accessible, renewable form of carbon (in comparison to CO2), lignocellulosic biomass (defined as organic matter available on a renewable basis) has been acknowledged as the most logical carbon-based feedstock for a variety of materials such as biofuels and chemicals. This Review focuses on methods developed to synthesize polymers derived from lignin, monolignols, and lignin-derived chemicals. Major topics include the structure and processing of lignocellulosic biomass to lignin, polymers utilizing lignin as a macromonomer, synthesis of monomers and polymers from monolignols, and polymers from lignin-derived chemicals, such as vanillin. PMID:26654678

  8. Mechanochemical modification of lignin and application of the modified lignin for thermoplastics and thermosets

    NASA Astrophysics Data System (ADS)

    Guo, Xiaojie; Zhang, Jinwen; Xin, Junna

    In this work, mechanochemical modification of lignin and use of the modified lignin in thermoplastics and thermosets were studied. Oleated lignin was successfully prepared by transesterification between lignin and methyl, and the oleation reaction was performed in a solvent-free and room temperature ball milling process with a relatively short time. PLA/lignin blends were prepared through melt extrusion. Compared with the PLA/lignin blends, the PLA/oleated lignin blends exhibited finer dispersion of lignin in the blends, increased glass transition temperature and higher tensile properties, suggesting improved compatibility between lignin and PLA. Carboxylic and anhydride groups were also introduced into the structure of lignin via mechanochemical modification, and the resulting lignin derivatives were used as curing agents for epoxies. The dynamic mechanical properties and thermal stability of the cured epoxy resins were studied using dynamic mechanical analysis (DMA) and thermogravimetric analysis (TGA).

  9. Lignin-Derived Advanced Carbon Materials.

    PubMed

    Chatterjee, Sabornie; Saito, Tomonori

    2015-12-01

    Lignin is a highly abundant source of renewable carbon that can be considered as a valuable sustainable source of biobased materials. By applying specific pretreatments and manufacturing methods, lignin can be converted into a variety of value-added carbon materials. However, the physical and chemical heterogeneities of lignin complicate its use as a feedstock. Herein lignin manufacturing process, the effects of pretreatments and manufacturing methods on the properties of product lignin, and structure-property relationships in various applications of lignin-derived carbon materials, such as carbon fibers, carbon mats, activated carbons, carbon films, and templated carbon, are discussed.

  10. Lignin-Derived Advanced Carbon Materials

    SciTech Connect

    Chatterjee, Sabornie; Saito, Tomonori

    2015-11-16

    Lignin is a highly abundant source of renewable carbon that can be considered as a valuable sustainable source of biobased materials. By applying specific pretreatments and manufacturing methods, it has been found that lignin can be converted into a variety of value-added carbon materials. However, the physical and chemical heterogeneities of lignin complicate its use as a feedstock. Herein, we discuss the lignin manufacturing process, the effects of pretreatments and manufacturing methods on the properties of product lignin, and structure–property relationships in various applications of lignin-derived carbon materials, such as carbon fibers, carbon mats, activated carbons, carbon films, and templated carbon.

  11. Identification of QTL associated with flower and runner production in octoploid strawberry (Fragaria × ananassa)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seasonal flowering of strawberry is described as remontant and non-remontant. The genetic basis of this trait is important for breeding. This study was conducted to validate the existence of a major QTL for remontancy and weeks of flowering in F. × ananassa on LG IV, to determine if the level of flo...

  12. The fate of lignin during hydrothermal pretreatment

    PubMed Central

    2013-01-01

    Background Effective enzymatic hydrolysis of lignocellulosic biomass benefits from lignin removal, relocation, and/or modification during hydrothermal pretreatment. Phase transition, depolymerization/repolymerization, and solubility effects may all influence these lignin changes. To better understand how lignin is altered, Populus trichocarpa x P. deltoides wood samples and cellulolytic enzyme lignin (CEL) isolated from P. trichocarpa x P. deltoides were subjected to batch and flowthrough pretreatments. The residual solids and liquid hydrolysate were characterized by gel permeation chromatography, heteronuclear single quantum coherence NMR, compositional analysis, and gas chromatography–mass spectrometry. Results Changes in the structure of the solids recovered after the pretreatment of CEL and the production of aromatic monomers point strongly to depolymerization and condensation being primary mechanisms for lignin extraction and redeposition. The differences in lignin removal and phenolic compound production from native P. trichocarpa x P. deltoides and CEL suggested that lignin-carbohydrate interactions increased lignin extraction and the extractability of syringyl groups relative to guaiacyl groups. Conclusions These insights into delignification during hydrothermal pretreatment point to desirable pretreatment strategies and plant modifications. Because depolymerization followed by repolymerization appears to be the dominant mode of lignin modification, limiting the residence time of depolymerized lignin moieties in the bulk liquid phase should reduce lignin content in pretreated biomass. In addition, the increase in lignin removal in the presence of polysaccharides suggests that increasing lignin-carbohydrate cross-links in biomass would increase delignification during pretreatment. PMID:23902789

  13. Does elevated N make lignin more recalcitrant?

    NASA Astrophysics Data System (ADS)

    Weintraub, M. N.; Rinkes, Z. L.; Grandy, S.; Wickings, K.; Bertrand, I.

    2014-12-01

    Increases in nitrogen (N) availability are often found to reduce decomposition rates of lignin-rich plant litter. However, the biological and chemical mechanisms that cause this inhibitory effect are still unclear. Our goal was to determine why increased N availability inhibits lignin decomposition. We tested two competing hypotheses: 1) decomposers degrade lignin to obtain protected N compounds and stop producing lignin-degrading enzymes if mineral N is available; or 2) chemical reactions between lignin and mineral N make lignin more recalcitrant, thereby limiting the ability of decomposers to break it down. To test these hypotheses, we followed changes in carbon (C) mineralization, microbial biomass and enzyme activities, litter chemistry, and lignin monomer concentrations over a 478-day laboratory incubation of three genotypes of maize stem internodes varying in litter quality. They were factorially combined with either an acidic or neutral pH sandy soil, with and without added N. Adding N reduced C mineralization, microbial biomass, and lignin-degrading enzyme activities in all treatments. Furthermore, our data on litter chemistry and lignin monomers indicate that N addition did not significantly alter the quantity or quality of lignin in any treatment. These results suggest that abiotic interactions between N and lignin compounds did not alter the ability of decomposers to breakdown lignin. Thus, we conclude that mineral N alters microbial enzyme and biomass dynamics, but not lignin chemistry during maize decomposition.

  14. ''The control of lignin synthesis''

    SciTech Connect

    Carlson, John E.

    2005-04-07

    In this project we tested the hypothesis that regulation of the synthesis of lignin in secondary xylem cells in conifer trees involves the transport of glucosylated lignin monomers to the wall of xylem cells, followed by de-glucosylation in the cell wall by monolignol-specific glucosidase enzymes, which activates the monomers for lignin polymerization. The information we gathered is relevant to the fundamental understanding of how trees make wood, and to the applied goal of more environmentally friendly pulp and paper production. We characterized the complete genomic structure of the Coniferin-specific Beta-glucosidase (CBG) gene family in the conifers loblolly pine (Pinus taeda) and lodgepole pine (Pinus contorta), and partial genomic sequences were obtained in several other tree species. Both pine species contain multiple CBG genes which raises the possibility of differential regulation, perhaps related to the multiple roles of lignin in development and defense. Subsequent projects will need to include detailed gene expression studies of each gene family member during tree growth and development, and testing the role of each monolignol-specific glucosidase gene in controlling lignin content.

  15. Lignin-assisted coal depolymerization

    SciTech Connect

    Lalvani, S.B.

    1991-01-01

    Previous research has shown that addition of lignin-derived liquids to coal stirred in tetralin under mild reaction conditions (375{degree}C and 300--500 psig) results in a marked enhancement in the rate of coal depolymerization. A mathematical model was developed to study the kinetics of coal depolymerization in the presence of liquid-derived liquids. In the present study, a reaction pathway was formulated to explain the enhancement in coal depolymerization due to lignin (solid) addition. The model postulated assumes that the products of lignin obtained during thermolysis interact with the reactive moieties present in coal while simultaneous depolymerization of coal occurs. A good fit between the experimental data and the kinetic model was found. The results show that in addition to the enhancement in the rate of coal depolymerization, lignin also reacts (and enhances the extent of depolymerization of coal) with those reaction sites in coal that are not susceptible to depolymerization when coal alone is reacted in tetralin under identical reaction conditions. Additional work is being carried out to determine a thorough materials balance on the lignin-assisted coal depolymerization process. A number of liquid samples have been obtained which are being studied for their stability in various environments. 5 refs., 4 figs., 1 tab.

  16. Unravelling lignin formation and structure

    SciTech Connect

    Lewis, N.G. . Inst. of Biological Chemistry)

    1991-01-01

    During this study, we established that the Fagaceae exclusively accumulate Z-monolignois/glucosides, and not the E-isomers. Evidence for the presence of a novel E{yields}Z isomerse has been obtained. Our pioneering work in lignin biosynthesis and structure in situ has also progressed smoothly. We established the bonding environments of a woody angiosperm, Leucanea leucocephala, as well as wheat (T. aestivum) and tobacco (N. tabacum). A cell culture system from Pinus taeda was developed which seems ideal for investigating the early stages of lignification. These cultures excrete peroxidase isozymes, considered to be specifically involved in lignin deposition. We also studied the effect of the putative lignin-degrading enzyme, lignin peroxidase, on monolignols and dehydropolymerisates therefrom. In all cases, polymerization was observed, and not degradation; these polymers are identical to that obtained with horseradish peroxidases/H{sub 2}O{sub 2}. It seems inconceivable that these enzymes can be considered as being primarily responsible for lignin biodegradation.

  17. Lignin analysis by FT-Raman spectroscopy

    SciTech Connect

    Agarwal, U.P.; Obst, J.R.; Cannon, A.B.

    1996-10-01

    Traditional methods of lignin analysis, such as Klason (acid insoluble) lignin determinations, give satisfactory results, are widely accepted, and often are considered as standard analyses. However, the Klason lignin method is laborious and time consuming; it also requires a fairly large-amount of isolated analyte. FT-Raman spectroscopy offers an opportunity to simplify and speed up lignin analyses. FT-Raman data for a number of hardwoods (angiosperms) and softwoods (gymnosperms) are compared with data obtained using other analytical methods, including Klason lignin (with corrections for acid soluble lignin), acetyl bromide, and FT-IR determinations. In addition, 10 different specimens of Nothofagus dombeyii (chosen because of the widely varying syringyl:guaiacyl monomer compositions of their lignins) were also analyzed. Lignin monomer compositions were determined by thioacidolysis of by nitrobenzene oxidation.

  18. ISSUES IN LIGNIN CHEMISTRY. "THE HELSINKI CONNECTION"

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This presentation covers advances in lignin chemistry (and our Helsinki connection) on dibenzodioxocins, spirodienones, and reduced structures in lignins. It also explores the various roles in defending lignification theory (based on Freudenberg's original hypothesis) against a supposed new contende...

  19. Detection and validation of QTL affecting bacterial cold water disease resistance in rainbow trout using restriction-site associated DNA sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. Using microsatellites genome scan we have previously detected significant and suggestive QTL with major effects on the phenotypic variation of survival following challenge with Flavobacterium psychrophilum...

  20. Lignin degradation during plant litter photodegradation

    NASA Astrophysics Data System (ADS)

    Lin, Y.; King, J. Y.

    2014-12-01

    Lignin is the second most abundant compound, after cellulose, synthesized by plants. Numerous studies have demonstrated that initial lignin concentration is negatively correlated with litter decomposition rate under both laboratory and field conditions. Thus lignin is commonly considered to be a "recalcitrant" compound during litter decomposition. However, lignin can also serve as a radiation-absorbing compound during photodegradation, the process through which solar radiation breaks down organic matter. Here, we synthesize recent studies concerning lignin degradation during litter photodegradation and report results from our study on how photodegradation changes lignin chemistry at a molecular scale. Recent field studies have found that litter with high initial lignin concentration does not necessarily exhibit high mass loss during photodegradation. A meta-analysis (King et al. 2012) even found a weak negative correlation between initial lignin concentration and photodegradation rate. Contradicting results have been reported with regard to the change in lignin concentration during photodegradation. Some studies have found significant loss of lignin during photodegradation, while others have not. In most studies, loss of lignin only accounts for a small proportion of the overall mass loss. Using NMR spectroscopy, we found significant loss of lignin structural units containing beta-aryl ether linkages during photodegradation of a common grass litter, Bromus diandrus, even though conventional forage fiber analysis did not reveal changes in lignin concentration. Both our NMR and fiber analyses supported the idea that photodegradation induced loss of hemicellulose, which was mainly responsible for the litter mass loss during photodegradation. Our results suggest that photodegradation induces degradation, but not necessarily complete breakdown, of lignin structures and consequently exposes hemicellulose and cellulose to microbial decomposition. We conclude that lignin

  1. Development of novel assays for lignin degradation: comparative analysis of bacterial and fungal lignin degraders.

    PubMed

    Ahmad, Mark; Taylor, Charles R; Pink, David; Burton, Kerry; Eastwood, Daniel; Bending, Gary D; Bugg, Timothy D H

    2010-05-01

    Two spectrophotometric assays have been developed to monitor breakdown of the lignin component of plant lignocellulose: a continuous fluorescent assay involving fluorescently modified lignin, and a UV-vis assay involving chemically nitrated lignin. These assays have been used to analyse lignin degradation activity in bacterial and fungal lignin degraders, and to identify additional soil bacteria that show activity for lignin degradation. Two soil bacteria known to act as aromatic degraders, Pseudomonas putida and Rhodococcus sp. RHA1, consistently showed activity in these assays, and these strains were shown in a small scale experiment to breakdown lignocellulose, producing a number of monocyclic phenolic products. Using milled wood lignin prepared from wheat straw, pine, and miscanthus, some bacterial lignin degraders were found to show specificity for lignin type. These assays could be used to identify novel lignin degraders for breakdown of plant lignocellulose. PMID:20567767

  2. Cationic electrodepositable coating composition comprising lignin

    DOEpatents

    Fenn, David; Bowman, Mark P; Zawacky, Steven R; Van Buskirk, Ellor J; Kamarchik, Peter

    2013-07-30

    A cationic electrodepositable coating composition is disclosed. The present invention in directed to a cationic electrodepositable coating composition comprising a lignin-containing cationic salt resin, that comprises (A) the reaction product of: lignin, an amine, and a carbonyl compound; (B) the reaction product of lignin, epichlorohydrin, and an amine; or (C) combinations thereof.

  3. Disinfection byproduct formation from lignin precursors.

    PubMed

    Hua, Guanghui; Kim, Junsung; Reckhow, David A

    2014-10-15

    Lignin is the most abundant aromatic plant component in terrestrial ecosystems. This study was conducted to determine the contribution of lignin residues in natural water to the formation of disinfection byproducts (DBPs) in drinking water. We investigated the formation of different classes of DBPs from lignin model compounds, lignin polymers, and humic substances using two common disinfection techniques, chlorination and chloramination. The contributions of lignin to the overall formation of DBPs from these organic products were determined based on the observed abundances of individual lignin phenols and their DBP yields. Model lignin phenols generally produced higher trichloroacetic acid (TCAA) yields than chloroform and dichloroacetic acid (DCAA) during chlorination. Lignin phenols generally produced higher DBP yields but lower percentages of unknown total organic halogen compared to bulk humic substances and lignin polymers. The relative significance of lignin phenols as chlorination DBP precursors generally follows the order of TCAA > DCAA&chloroform. The relative significance of lignin phenols to DBP formation by chloramination follows the order: TCAA > DCAA&DCAN > chloroform. Overall, lignin phenols are more important as TCAA precursors than as chloroform and DCAA precursors.

  4. Liquid Fuels from Lignins: Annual Report

    SciTech Connect

    Chum, H. L.; Johnson, D. K.

    1986-01-01

    This task was initiated to assess the conversion of lignins into liquid fuels, primarily of lignins relevant to biomass-to-ethanol conversion processes. The task was composed of a literature review of this area and an experimental part to obtain pertinent data on the conversion of lignins germane to biomass-to-ethanol conversion processes.

  5. 40 CFR 721.5460 - Organosolv lignin.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Organosolv lignin. 721.5460 Section... Substances § 721.5460 Organosolv lignin. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as an organosolv lignin (PMN P-95-1584; CAS No. 8068-03-9)...

  6. Experimental Investigation of the Kinetics of a Ruthenium-Catalyzed Deconstruction of Lignin Model Compounds

    SciTech Connect

    Bu, L.; Nimlos, M. R.; Shirts, M. R.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T.

    2012-01-01

    Lignin is a major component of plant cell walls that is typically underutilized in selective conversion strategies for renewable fuels and chemicals. The mechanisms by which thermal and catalytic treatments deconstruct lignin remain elusive. In this work, we have investigated the kinetics of the catalytic deconstruction of lignin model compounds using a ruthenium catalyst reported by Bergman et al. in 2010. A series of investigations using NMR spectroscopy and GC/MS will be presented. In addition, we propose detailed mechanisms for lignin depolymerization with ruthenium catalysts. We have also used DFT to compute transition state geometries of catalytic cycle intermediates and compare the values determined computationally with those observed experimentally. Ultimately, our objective is to apply our methods to the design of new homogeneous and heterogeneous catalysts for the effective deconstruction and valorization of lignin.

  7. The Paleozoic origin of enzymatic mechanisms for lignin degradation reconstructed using 31 fungal genomes

    SciTech Connect

    Floudas, Dimitrios; Binder, Manfred; Riley, Robert; Barry, Kerrie; Blanchette, Robert A; Henrissat, Bernard; Martinez, Angel T.; Otillar, Robert; Spatafora, Joseph W.; Yadav, Jagit S.; Aerts, Andrea; Benoit, Isabelle; Boyd, Alex; Carlson, Alexis; Copeland, Alex; Coutinho, Pedro M.; de Vries, Ronald P.; Ferreira, Patricia; Findley, Keisha; Foster, Brian; Gaskell, Jill; Glotzer, Dylan; Gorecki, Pawel; Heitman, Joseph; Hesse, Cedar; Hori, Chiaki; Igarashi, Kiyohiko; Jurgens, Joel A.; Kallen, Nathan; Kersten, Phil; Kohler, Annegret; Kues, Ursula; Kumar, T. K. Arun; Kuo, Alan; LaButti, Kurt; Larrondo, Luis F.; Lindquist, Erika; Ling, Albee; Lombard, Vincent; Lucas, Susan; Lundell, Taina; Martin, Rachael; McLaughlin, David J.; Morgenstern, Ingo; Morin, Emanuelle; Murat, Claude; Nagy, Laszlo G.; Nolan, Matt; Ohm, Robin A.; Patyshakuliyeva, Aleksandrina; Rokas, Antonis; Ruiz-Duenas, Francisco J.; Sabat, Grzegorz; Salamov, Asaf; Samejima, Masahiro; Schmutz, Jeremy; Slot, Jason C.; John, Franz; Stenlid, Jan; Sun, Hui; Sun, Sheng; Syed, Khajamohiddin; Tsang, Adrian; Wiebenga, Ad; Young, Darcy; Pisabarro, Antonio; Eastwood, Daniel C.; Martin, Francis; Cullen, Dan; Grigoriev, Igor V.; Hibbett, David S.

    2012-03-12

    Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non?lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.

  8. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes.

    PubMed

    Floudas, Dimitrios; Binder, Manfred; Riley, Robert; Barry, Kerrie; Blanchette, Robert A; Henrissat, Bernard; Martínez, Angel T; Otillar, Robert; Spatafora, Joseph W; Yadav, Jagjit S; Aerts, Andrea; Benoit, Isabelle; Boyd, Alex; Carlson, Alexis; Copeland, Alex; Coutinho, Pedro M; de Vries, Ronald P; Ferreira, Patricia; Findley, Keisha; Foster, Brian; Gaskell, Jill; Glotzer, Dylan; Górecki, Paweł; Heitman, Joseph; Hesse, Cedar; Hori, Chiaki; Igarashi, Kiyohiko; Jurgens, Joel A; Kallen, Nathan; Kersten, Phil; Kohler, Annegret; Kües, Ursula; Kumar, T K Arun; Kuo, Alan; LaButti, Kurt; Larrondo, Luis F; Lindquist, Erika; Ling, Albee; Lombard, Vincent; Lucas, Susan; Lundell, Taina; Martin, Rachael; McLaughlin, David J; Morgenstern, Ingo; Morin, Emanuelle; Murat, Claude; Nagy, Laszlo G; Nolan, Matt; Ohm, Robin A; Patyshakuliyeva, Aleksandrina; Rokas, Antonis; Ruiz-Dueñas, Francisco J; Sabat, Grzegorz; Salamov, Asaf; Samejima, Masahiro; Schmutz, Jeremy; Slot, Jason C; St John, Franz; Stenlid, Jan; Sun, Hui; Sun, Sheng; Syed, Khajamohiddin; Tsang, Adrian; Wiebenga, Ad; Young, Darcy; Pisabarro, Antonio; Eastwood, Daniel C; Martin, Francis; Cullen, Dan; Grigoriev, Igor V; Hibbett, David S

    2012-06-29

    Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.

  9. Lignin depolymerization/repolymerization and its critical role for delignification of aspen wood by steam explosion.

    PubMed

    Li, Jiebing; Henriksson, Gunnar; Gellerstedt, Göran

    2007-11-01

    Steam explosion is an important process for the fractionation of biomass components. In order to understand the behaviour of lignin under the conditions encountered in the steam explosion process, as well as in other types of steam treatment, aspen wood and isolated lignin from aspen were subjected to steam treatment under various conditions. The lignin portion was analyzed using NMR and size exclusion chromatography as major analytical techniques. Thereby, the competition between lignin depolymerization and repolymerization was revealed and the conditions required for these two types of reaction identified. Addition of a reactive phenol, 2-naphthol, was shown to inhibit the repolymerization reaction strongly, resulting in a highly improved delignification by subsequent solvent extraction and an extracted lignin of uniform structure.

  10. Enzymatic monitoring of lignin and lignin derivatives biooxidation.

    PubMed

    Ibrahim, Victor; Mamo, Gashaw

    2016-01-01

    Lignin oxidation was enzymatically monitored by measuring methanol released during the reaction. The methanol was oxidized to formaldehyde and hydrogen peroxide, and the latter used to oxidize ABTS to a product measured spectrophotometrically. The efficiency was comparable to the commonly used gas chromatography method. The assay was fast and inexpensive. PMID:26632344

  11. QTL for the thermotolerance effect of heat hardening, knockdown resistance to heat and chill-coma recovery in an intercontinental set of recombinant inbred lines of Drosophila melanogaster.

    PubMed

    Norry, Fabian M; Scannapieco, Alejandra C; Sambucetti, Pablo; Bertoli, Carlos I; Loeschcke, Volker

    2008-10-01

    The thermotolerance effect of heat hardening (also called short-term acclimation), knockdown resistance to high temperature (KRHT) with and without heat hardening and chill-coma recovery (CCR) are important phenotypes of thermal adaptation in insects and other organisms. Drosophila melanogaster from Denmark and Australia were previously selected for low and high KRHT, respectively. These flies were crossed to construct recombinant inbred lines (RIL). KRHT was higher in heat-hardened than in nonhardened RIL. We quantify the heat-hardening effect (HHE) as the ratio in KRHT between heat-hardened and nonhardened RIL. Composite interval mapping revealed a more complex genetic architecture for KRHT without heat-hardening than for KRHT in heat-hardened insects. Five quantitative trait loci (QTL) were found for KRHT, but only two of them were significant after heat hardening. KRHT and CCR showed trade-off associations for QTL both in the middle of chromosome 2 and the right arm of chromosome 3, which should be the result of either pleiotropy or linkage. The major QTL on chromosome 2 explained 18% and 27-33% of the phenotypic variance in CCR and KRHT in nonhardened flies, respectively, but its KRHT effects decreased by heat hardening. We discuss candidate loci for each QTL. One HHE-QTL was found in the region of small heat-shock protein genes. However, HHE-QTL explained only a small fraction of the phenotypic variance. Most heat-resistance QTL did not colocalize with CCR-QTL. Large-effect QTL for CCR and KRHT without hardening (basal thermotolerance) were consistent across continents, with apparent transgressive segregation for CCR. HHE (inducible thermotolerance) was not regulated by large-effect QTL.

  12. Look before you leap: a new approach to mapping QTL.

    PubMed

    Huang, B Emma; George, Andrew W

    2009-09-01

    In this paper, we present an innovative and powerful approach for mapping quantitative trait loci (QTL) in experimental populations. This deviates from the traditional approach of (composite) interval mapping which uses a QTL profile to simultaneously determine the number and location of QTL. Instead, we look before we leap by employing separate detection and localization stages. In the detection stage, we use an iterative variable selection process coupled with permutation to identify the number and synteny of QTL. In the localization stage, we position the detected QTL through a series of one-dimensional interval mapping scans. Results from a detailed simulation study and real analysis of wheat data are presented. We achieve impressive increases in the power of QTL detection compared to composite interval mapping. We also accurately estimate the size and position of QTL. An R library, DLMap, implements the methods described here and is freely available from CRAN ( http://cran.r-project.org/ ). PMID:19585099

  13. Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization (Towards Lignin valorization: How a soil bacterium extracts building blocks and metabolic energy from "Lignolysis")

    DOE PAGES

    Varman, Arul M.; He, Lian; Follenfant, Rhiannon; Wu, Weihua; Wemmer, Sarah; Wrobel, Steven A.; Tang, Yinjie J.; Singh, Seema

    2016-09-15

    Lignin is a major resources for the production of next generation renewable aromatics. Sphingobium sp. SYK-6 is a bacterium that has been well-studied for the breakdown of lignin-derived compounds. There has been a lot of interest in SYK-6 lignolytic activity and many recent works have focused on understanding the unique catabolic pathway it possesses for the degradation of lignin derived monomers and oligomers. Furthermore, there has been no prior effort in understanding the central fluxome based on lignin derived substrates into value-added chemicals.

  14. QTL analysis for sugar-regulated leaf senescence supports flowering-dependent and -independent senescence pathways.

    PubMed

    Wingler, Astrid; Purdy, Sarah Jane; Edwards, Sally-Anne; Chardon, Fabien; Masclaux-Daubresse, Céline

    2010-01-01

    *The aim of this work was to determine the genetic basis of sugar-regulated senescence and to explore the relationship with other traits, including flowering and nitrogen-use efficiency. *Quantitative trait loci (QTLs) for senescence were mapped in the Arabidopsis Bay-0 x Shahdara recombinant-inbred line (RIL) population after growth on glucose-containing medium, which accelerates senescence. The extent of whole-rosette senescence was determined by imaging the maximum quantum yield of photosystem II (F(v)/F(m)). *A major QTL on the top of chromosome 4 colocalized with FRI, a major determinant of flowering. This QTL interacted epistatically with a QTL on chromosome 5, where the floral repressor FLC localizes. Vernalization accelerated senescence in late-flowering lines with functional FRI and FLC alleles. Comparison with previous results using the Bay-0 x Shahdara population showed that rapid rosette senescence on glucose-containing medium was correlated with early flowering and high sugar content in compost-grown plants. In addition, correlation was found between the expression of flowering and senescence-associated genes in Arabidopsis accessions. However, an additional QTL on chromosome 3 was not linked to flowering, but to nitrogen-use efficiency. *The results show that whole-rosette senescence is genetically linked to the vernalization-dependent control of flowering, but is also controlled by flowering-independent pathways.

  15. QTL analysis of fertility restoration in cytoplasmic male sterile pepper.

    PubMed

    Wang, L H; Zhang, B X; Lefebvre, V; Huang, S W; Daubèze, A M; Palloix, A

    2004-09-01

    Fertility restoration of Peterson's cytoplasmic male-sterility in pepper (Capsicum annuum L.) is quantitative and environment-dependent. QTL analysis of fertility restoration was performed based on the test-cross progeny of 77013A (a strict cytoplasmic-genetic male sterile line) and a doubled haploid population of 114 lines obtained from an F1 hybrid between Yolo wonder (a sterility maintainer line) and Perennial (a fertility-restorer line). The fertility of the test-crossed lines was assessed under greenhouse and open field conditions using three criteria related to pollen or seed production. One major QTL for fertility restoration was mapped to chromosome P6. It was significant in all the environments and for all the traits, accounting for 20-69% of the phenotypic variation, depending on the trait. Four additional minor QTLs were also detected on chromosomes P5, P2, and linkage groups PY3 and PY1, accounting for 7-17% of the phenotypic variation. Most of the alleles increasing fertility originated from the restorer parent, except for two alleles at minor QTLs. Phenotypic analysis and genetic dissection indicated that breeding pepper for complete sterility of female lines and high hybrid fertility requires complex combinations of alleles from both parents and a strict control of the environment. PMID:15173931

  16. Mapping of angular leaf spot resistance QTL in common bean (Phaseolus vulgaris L.) under different environments

    PubMed Central

    2012-01-01

    Background Common bean (Phaseolus vulgaris L.) is the most important grain legume for human diet worldwide and the angular leaf spot (ALS) is one of the most devastating diseases of this crop, leading to yield losses as high as 80%. In an attempt to breed resistant cultivars, it is important to first understand the inheritance mode of resistance and to develop tools that could be used in assisted breeding. Therefore, the aim of this study was to identify quantitative trait loci (QTL) controlling resistance to ALS under natural infection conditions in the field and under inoculated conditions in the greenhouse. Results QTL analyses were made using phenotypic data from 346 recombinant inbreed lines from the IAC-UNA x CAL 143 cross, gathered in three experiments, two of which were conducted in the field in different seasons and one in the greenhouse. Joint composite interval mapping analysis of QTL x environment interaction was performed. In all, seven QTLs were mapped on five linkage groups. Most of them, with the exception of two, were significant in all experiments. Among these, ALS10.1DG,UC presented major effects (R2 between 16% - 22%). This QTL was found linked to the GATS11b marker of linkage group B10, which was consistently amplified across a set of common bean lines and was associated with the resistance. Four new QTLs were identified. Between them the ALS5.2 showed an important effect (9.4%) under inoculated conditions in the greenhouse. ALS4.2 was another major QTL, under natural infection in the field, explaining 10.8% of the variability for resistance reaction. The other QTLs showed minor effects on resistance. Conclusions The results indicated a quantitative inheritance pattern of ALS resistance in the common bean line CAL 143. QTL x environment interactions were observed. Moreover, the major QTL identified on linkage group B10 could be important for bean breeding, as it was stable in all the environments. Thereby, the GATS11b marker is a potential tool

  17. Isolation and structural characterization of the milled wood lignin, dioxane lignin, and cellulolytic lignin preparations from brewer's spent grain.

    PubMed

    Rencoret, Jorge; Prinsen, Pepijn; Gutiérrez, Ana; Martínez, Ángel T; Del Río, José C

    2015-01-21

    The structure of the lignin from brewer's spent grain (BSG) has been studied in detail. Three different lignin preparations, the so-called "milled-wood" lignin (MWL), dioxane lignin (DL), and cellulolytic lignin (CEL), were isolated from BSG and then thoroughly characterized by pyrolysis GC/MS, 2D-NMR, and derivatization followed by reductive cleavage (DFRC). The data indicated that BSG lignin presents a predominance of guaiacyl units (syringyl/guaiacyl ratio of 0.4-0.5) with significant amounts of associated p-coumarates and ferulates. The flavone tricin was also present in the lignin from BSG, as also occurred in other grasses. 2D-NMR (HSQC) revealed that the main substructures present are β-O-4' alkyl-aryl ethers (77-79%) followed by β-5' phenylcoumarans (11-13%) and lower amounts of β-β' resinols (5-6%) and 5-5' dibenzodioxocins (3-5%). The results from 2D-NMR (HMBC) and DFRC indicated that p-coumarates are acylating the γ-carbon of lignin side chains and are mostly involved in condensed structures. DFRC analyses also indicated a minor degree of γ-acylation with acetate groups, which takes place preferentially on S lignin (6% of S units are acetylated) over G lignin (only 1% of G units are acetylated).

  18. Genetic dissection of fruit quality traits in the octoploid cultivated strawberry highlights the role of homoeo-QTL in their control.

    PubMed

    Lerceteau-Köhler, E; Moing, A; Guérin, G; Renaud, C; Petit, A; Rothan, C; Denoyes, Béatrice

    2012-04-01

    Fruit quality traits are major breeding targets in the Rosaceae. Several of the major Rosaceae species are current or ancient polyploids. To dissect the inheritance of fruit quality traits in polyploid fleshy fruit species, we used a cultivated strawberry segregating population comprising a 213 full-sibling F1 progeny from a cross between the variety 'Capitola' and the genotype 'CF1116'. We previously developed the most comprehensive strawberry linkage map, which displays seven homoeology groups (HG), including each four homoeology linkage groups (Genetics 179:2045-2060, 2008). The map was used to identify quantitative trait loci (QTL) for 19 fruit traits related to fruit development, texture, colour, anthocyanin, sugar and organic acid contents. Analyses were carried out over two or three successive years on field-grown plants. QTL were detected for all the analysed traits. Because strawberry is an octopolyploid species, QTL controlling a given trait and located at orthologous positions on different homoeologous linkage groups within one HG are considered as homoeo-QTL. We found that, for various traits, about one-fourth of QTL were putative homoeo-QTL and were localised on two linkage groups. Several homoeo-QTL could be detected the same year, suggesting that several copies of the gene underlying the QTL are functional. The detection of some other homoeo-QTL was year-dependent. Therefore, changes in allelic expression could take place in response to environmental changes. We believe that, in strawberry as in other polyploid fruit species, the mechanisms unravelled in the present study may play a crucial role in the variations of fruit quality.

  19. Biodegradable lignin/polyolefin composite films

    SciTech Connect

    Kosikova, B.; Demjanova, V.; Mikulasova, M.; Lora, J.H.

    1993-12-31

    From the view point of environmental protection, the plastic wastes, especially from packing materials, represent a potential waste problem. Various approaches were examined to develop partially or completely biodegradable plastics. New type of partially biodegradable polyolefins was prepared by blending of polypropylene with lignin, which was recovered in the ALCELL process, an organosolv pulping process that uses ethanol-water as the delignifying agent. Films of blends with up to 10% wt ALCELL lignin, prepared in absence of commercial stabilizers, had acceptable mechanical strengths. The effect of lignin on biodegradability of the composite films was examined by comparison of behaviour of both pure and lignin containing films during treatment with fungus Phanerochaete chrysosporium. It was found that this fungus is able to grow and to produce lignolytic enzymes in the presence of the films containing lignin. Biodegradation of lignin in the composite film was confirmed by the releasing of lignin fragments into the extracellular fluid. Because of measurement of mechanical properties offers a mean of direct estimation of polymer degradation, the degree of biodegradation of the films tested was followed by monitoring of elongation at break. The changes of break at elongation in the course of enzymatic treatment revealed that the lignin/PP composite films are potentially environmentally nonpersisting. The micrographs of the lignin containing films obtained by scanning electron microscopy show the significant changes of the film surface upon degradation with Phanerochaete chrysosporium in contrast to unchanged lignin free film.

  20. Identification of Novel QTL Governing Root Architectural Traits in an Interspecific Soybean Population

    PubMed Central

    Musket, Theresa A.; Chaky, Julian; Deshmukh, Rupesh; Vuong, Tri D.; Song, Li; Cregan, Perry B.; Nelson, James C.; Shannon, J. Grover; Specht, James E.; Nguyen, Henry T.

    2015-01-01

    Cultivated soybean (Glycine max L.) cv. Dunbar (PI 552538) and wild G. soja (PI 326582A) exhibited significant differences in root architecture and root-related traits. In this study, phenotypic variability for root traits among 251 BC2F5 backcross inbred lines (BILs) developed from the cross Dunbar/PI 326582A were identified. The root systems of the parents and BILs were evaluated in controlled environmental conditions using a cone system at seedling stage. The G. max parent Dunbar contributed phenotypically favorable alleles at a major quantitative trait locus on chromosome 8 (Satt315-I locus) that governed root traits (tap root length and lateral root number) and shoot length. This QTL accounted for >10% of the phenotypic variation of both tap root and shoot length. This QTL region was found to control various shoot- and root-related traits across soybean genetic backgrounds. Within the confidence interval of this region, eleven transcription factors (TFs) were identified. Based on RNA sequencing and Affymetrix expression data, key TFs including MYB, AP2-EREBP and bZIP TFs were identified in this QTL interval with high expression in roots and nodules. The backcross inbred lines with different parental allelic combination showed different expression pattern for six transcription factors selected based on their expression pattern in root tissues. It appears that the marker interval Satt315–I locus on chromosome 8 contain an essential QTL contributing to early root and shoot growth in soybean. PMID:25756528

  1. A growth QTL on chicken chromosome 1 affects emotionality and sociality.

    PubMed

    Wirén, Anna; Jensen, Per

    2011-03-01

    Domestication of animals, regardless of species, is often accompanied by simultaneous changes in several physiological and behavioral traits (e.g. growth rate and fearfulness). In this study we compared the social behavior and emotional reactivity, as measured in a battery of behavioral tests, of two groups of chickens selected from a common genetic background, an advanced intercross line between the ancestral red junglefowl ("RJF") and the domesticated White Leghorn layer ("WL"). The birds were selected for homozygosity for alternative alleles at one locus (a microsatellite marker), centrally positioned in a previously identified pleiotropic growth QTL on chromosome 1, closely linked to one major candidate gene (AVPR1a) for certain aspects of social behavior. Birds homozygous for the WL allele ("WL genotype") had a modified pattern of social and emotional reactions than birds homozygous for the RJF allele ("RJF genotype"), shown by different scores in a principal components analysis. These results suggest that the growth QTL affects a number of domestication related behavioral traits, and may have been a primary target of selection during domestication. The QTL contains a multitude of genes, several of which have been linked to social behavior (for example the vasotocin receptor AVPR1a targeted in this experiment). Future studies aimed at making a higher resolution genotypic characterization of the QTL should give more information about which of these genes may be considered the strongest candidates for bringing about the behavioral changes associated with animal domestication. PMID:20596888

  2. A new method to infer causal phenotype networks using QTL and phenotypic information.

    PubMed

    Wang, Huange; van Eeuwijk, Fred A

    2014-01-01

    In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at quantitative trait loci (QTLs) to learn about causal relationships among phenotypic traits. A requirement for using these approaches is that at least one unique QTL has been identified for each trait studied. However, in practice, especially for molecular phenotypes such as metabolites, this prerequisite is often not met due to limited sample sizes, high noise levels and small QTL effects. Here, we present a novel heuristic search algorithm called the QTL+phenotype supervised orientation (QPSO) algorithm to infer causal directions for edges in undirected phenotype networks. The two main advantages of this algorithm are: first, it does not require QTLs for each and every trait; second, it takes into account associated phenotypic interactions in addition to detected QTLs when orienting undirected edges between traits. We evaluate and compare the performance of QPSO with another state-of-the-art approach, the QTL-directed dependency graph (QDG) algorithm. Simulation results show that our method has broader applicability and leads to more accurate overall orientations. We also illustrate our method with a real-life example involving 24 metabolites and a few major QTLs measured on an association panel of 93 tomato cultivars. Matlab source code implementing the proposed algorithm is freely available upon request. PMID:25144184

  3. QTL involved in the modification of cyanidin compounds in black and red raspberry fruit.

    PubMed

    Bushakra, J M; Krieger, C; Deng, D; Stephens, M J; Allan, A C; Storey, R; Symonds, V V; Stevenson, D; McGhie, T; Chagné, D; Buck, E J; Gardiner, S E

    2013-03-01

    Fruit from Rubus species are highly valued for their flavor and nutritive qualities. Anthocyanin content contributes to these qualities, and although many studies have been conducted to identify and quantify the major anthocyanin compounds from various Rubus species, the genetic control of the accumulation of these complex traits in Rubus is not yet well understood. The identification of the regions of the genome involved in the production of anthocyanins is an important first step in identifying the genes underlying their expression. In this study, ultra and high-performance liquid chromatography (UHPLC and HPLC) and two newly developed Rubus linkage maps were used to conduct QTL analyses to explore the presence of associations between concentrations of five anthocyanins in fruit and genotype. In total, 27 QTL were identified on the Rubus linkage maps, four of which are associated with molecular markers designed from transcription factors and three of which are associated with molecular markers designed from anthocyanin biosynthetic pathway candidate genes. The results of this study suggest that, while QTL for anthocyanin accumulation have been identified on six of seven Rubus linkage groups (RLG), the QTL on RLG2 and RLG7 may be very important for genetic control of cyanidin modification in Rubus.

  4. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL

    PubMed Central

    Rinaldi, Riccardo; Van Deynze, Allen; Portis, Ezio; Rotino, Giuseppe L.; Toppino, Laura; Hill, Theresa; Ashrafi, Hamid; Barchi, Lorenzo; Lanteri, Sergio

    2016-01-01

    Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5–0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous

  5. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL.

    PubMed

    Rinaldi, Riccardo; Van Deynze, Allen; Portis, Ezio; Rotino, Giuseppe L; Toppino, Laura; Hill, Theresa; Ashrafi, Hamid; Barchi, Lorenzo; Lanteri, Sergio

    2016-01-01

    Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous

  6. Lignin phenols derivatives in lichens.

    PubMed

    Zavarzina, A G; Romankevich, E A; Peresypkin, V I; Ulyantzev, A S; Belyaev, N A; Zavarzin, A A

    2015-01-01

    Lignin monophenols have been measured in the cupric oxide oxidation products from lichens of different systematic groups. It is shown for the first time that syringyl structures in most lichens strongly dominate over vanillyl and p-hydroxyl ones (S/V 7-583, S/P 3-30). This distinguishes lichens from algae and mosses (p-hydroxyl phenols are dominant) and from higher plants (S/V ratios are from 0 in gymnosperms to 1.1-5.2 in angiosperms). Molecular ratios of phenols as well as the ratios of acids to aldehydes in lichens were different from lignin of higher plants, suggesting contribution of non-lignin phenols in CuO oxidation products. The contents of syringyl and vanillyl phenols in some lichen species were comparable to non-woody tissues of higher plants. Results of the study suggest that lichens can be important source of aromatic structures in soils and hydrosphere, particularly in the regions were lichens are abundant. PMID:26728733

  7. Lignin phenols derivatives in lichens.

    PubMed

    Zavarzina, A G; Romankevich, E A; Peresypkin, V I; Ulyantzev, A S; Belyaev, N A; Zavarzin, A A

    2015-01-01

    Lignin monophenols have been measured in the cupric oxide oxidation products from lichens of different systematic groups. It is shown for the first time that syringyl structures in most lichens strongly dominate over vanillyl and p-hydroxyl ones (S/V 7-583, S/P 3-30). This distinguishes lichens from algae and mosses (p-hydroxyl phenols are dominant) and from higher plants (S/V ratios are from 0 in gymnosperms to 1.1-5.2 in angiosperms). Molecular ratios of phenols as well as the ratios of acids to aldehydes in lichens were different from lignin of higher plants, suggesting contribution of non-lignin phenols in CuO oxidation products. The contents of syringyl and vanillyl phenols in some lichen species were comparable to non-woody tissues of higher plants. Results of the study suggest that lichens can be important source of aromatic structures in soils and hydrosphere, particularly in the regions were lichens are abundant.

  8. Preparing spherical lignin from rice husk.

    PubMed

    Zhang, Hongxi; Zhao, Xu; Ding, Xuefeng; Lei, Hong; Wang, Zichen

    2013-08-01

    Lignin is one of the important branched amorphous polymers, which generally has the irregular and fractal morphology. The preparation of regular sphere of lignin needs long steps and special conditions. In this study, the regular sphere of lignin can be simply prepared from rice husk (RH) under certain conditions. Namely, RH is mixed with 35% ethanol aqueous solution in the proportion of 1:10 (g:mL), non-isothermally heated to 493 K and kept for 5 h. After filtration and air-drying at room temperature, the regular lignin sphere with the diameter of 100-400 nm is obtained. The regular sphere of lignin has the potential utilization in fields such as reactive functional materials, photo sensing materials and surface active materials in cosmetics. The mechanism of formation of the regular spherical lignin is proposed and discussed in this paper.

  9. Lignin-Derived Advanced Carbon Materials

    DOE PAGES

    Chatterjee, Sabornie; Saito, Tomonori

    2015-11-16

    Lignin is a highly abundant source of renewable carbon that can be considered as a valuable sustainable source of biobased materials. By applying specific pretreatments and manufacturing methods, it has been found that lignin can be converted into a variety of value-added carbon materials. However, the physical and chemical heterogeneities of lignin complicate its use as a feedstock. Herein, we discuss the lignin manufacturing process, the effects of pretreatments and manufacturing methods on the properties of product lignin, and structure–property relationships in various applications of lignin-derived carbon materials, such as carbon fibers, carbon mats, activated carbons, carbon films, and templatedmore » carbon.« less

  10. Lignin-Based Triple Shape Memory Polymers.

    PubMed

    Sivasankarapillai, Gopakumar; Li, Hui; McDonald, Armando G

    2015-09-14

    Lignin-based triple shape memory polymers comprised of both permanent covalent cross-links and physical cross-links have been synthesized. A mixing phase with poly(ester-amine) and poly(ester-amide) network having two distinct glass transitions was hot mixed with more structurally homogenized methanol soluble lignin fraction by one-pot, two-step method. Triple shape properties arise from the combined effect of the glass transition of polyester copolymers and lignin and the dissociation of self-complementary hydrogen bonding and cross-link density. The percentage of recovery in each stage was investigated and it was proved that the first recovery is related with lignin-poly(ester-amine) rich network and the second recovery stage is related with lignin-poly(ester-amide) rich network. The thermal and mechanical properties of the lignin-copolymer networks were also investigated using differential scanning calorimetry and dynamic mechanical analysis.

  11. Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation

    SciTech Connect

    Petridis, Loukas; Pingali, Sai Venkatesh; Urban, Volker; Heller, William T; O'Neill, Hugh Michael; Foston, Marcus B; Ragauskas, Arthur J; Smith, Jeremy C

    2011-01-01

    Lignin, a major polymeric component of plant cell walls, forms aggregates in vivo and poses a barrier to cellulosic ethanol production. Here, neutron scattering experiments and molecular dynamics simulations reveal that lignin aggregates are characterized by a surface fractal dimension that is invariant under change of scale from 1 1000 A. The simulations also reveal extensive water penetration of the aggregates and heterogeneous chain dynamics corresponding to a rigid core with a fluid surface.

  12. Integrated Metabolo-Transcriptomics Reveals Fusarium Head Blight Candidate Resistance Genes in Wheat QTL-Fhb2

    PubMed Central

    Dhokane, Dhananjay; Karre, Shailesh; Kushalappa, Ajjamada C.; McCartney, Curt

    2016-01-01

    Background Fusarium head blight (FHB) caused by Fusarium graminearum not only causes severe losses in yield, but also reduces quality of wheat grain by accumulating mycotoxins. Breeding for host plant resistance is considered as the best strategy to manage FHB. Resistance in wheat to FHB is quantitative in nature, involving cumulative effects of many genes governing resistance. The poor understanding of genetics and lack of precise phenotyping has hindered the development of FHB resistant cultivars. Though more than 100 QTLs imparting FHB resistance have been reported, none discovered the specific genes localized within the QTL region, nor the underlying mechanisms of resistance. Findings In our study recombinant inbred lines (RILs) carrying resistant (R-RIL) and susceptible (S-RIL) alleles of QTL-Fhb2 were subjected to metabolome and transcriptome profiling to discover the candidate genes. Metabolome profiling detected a higher abundance of metabolites belonging to phenylpropanoid, lignin, glycerophospholipid, flavonoid, fatty acid, and terpenoid biosynthetic pathways in R-RIL than in S-RIL. Transcriptome analysis revealed up-regulation of several receptor kinases, transcription factors, signaling, mycotoxin detoxification and resistance related genes. The dissection of QTL-Fhb2 using flanking marker sequences, integrating metabolomic and transcriptomic datasets, identified 4-Coumarate: CoA ligase (4CL), callose synthase (CS), basic Helix Loop Helix (bHLH041) transcription factor, glutathione S-transferase (GST), ABC transporter-4 (ABC4) and cinnamyl alcohol dehydrogenase (CAD) as putative resistance genes localized within the QTL-Fhb2 region. Conclusion Some of the identified genes within the QTL region are associated with structural resistance through cell wall reinforcement, reducing the spread of pathogen through rachis within a spike and few other genes that detoxify DON, the virulence factor, thus eventually reducing disease severity. In conclusion, we

  13. Conversion of lignin into value-added materials and chemicals via laccase-assisted copolymerization

    DOE PAGES

    Cannatelli, Mark D.; Ragauskas, Arthur J.

    2016-09-19

    With today’s environmental concerns and the diminishing supply of the world’s petroleum-based chemicals and materials, much focus has been directed toward alternative sources. Woody biomass presents a promising option due to its sheer abundance, renewability, and biodegradability. Lignin, a highly irregular polyphenolic compound, is one of the major chemical constituents of woody biomass and is the second most abundant biopolymer on Earth, surpassed only by cellulose. The pulp and paper and cellulosic ethanol industries produce lignin on the scale of millions of tons each year as a by-product. Traditionally, lignin has been viewed as a waste material and burned asmore » an inefficient fuel. However, in recent decades, research has focused on more economical ways to convert lignin into value-added commodities, such as biofuels, biomaterials, and biochemicals, thus developing and strengthening the concept of fully integrated biorefineries. Owing to the phenolic structure of lignin, it is possible to enzymatically graft molecules onto its surface using laccases (benzenediol:oxygen oxidoreductases, EC 1.10.3.2) to create exciting novel biomaterials. These environmentally friendly enzymes use oxygen as their only co-substrate and produce water as their sole by-product, and have thus found great industrial application. Furthermore, this mini-review highlights recent advances in the field of laccase-facilitated functionalization of lignin as well as promising future directions for lignin-based polymers.« less

  14. Conversion of lignin into value-added materials and chemicals via laccase-assisted copolymerization.

    PubMed

    Cannatelli, Mark D; Ragauskas, Arthur J

    2016-10-01

    With today's environmental concerns and the diminishing supply of the world's petroleum-based chemicals and materials, much focus has been directed toward alternative sources. Woody biomass presents a promising option due to its sheer abundance, renewability, and biodegradability. Lignin, a highly irregular polyphenolic compound, is one of the major chemical constituents of woody biomass and is the second most abundant biopolymer on Earth, surpassed only by cellulose. The pulp and paper and cellulosic ethanol industries produce lignin on the scale of millions of tons each year as a by-product. Traditionally, lignin has been viewed as a waste material and burned as an inefficient fuel. However, in recent decades, research has focused on more economical ways to convert lignin into value-added commodities, such as biofuels, biomaterials, and biochemicals, thus developing and strengthening the concept of fully integrated biorefineries. Owing to the phenolic structure of lignin, it is possible to enzymatically graft molecules onto its surface using laccases (benzenediol:oxygen oxidoreductases, EC 1.10.3.2) to create exciting novel biomaterials. These environmentally friendly enzymes use oxygen as their only co-substrate and produce water as their sole by-product, and have thus found great industrial application. This mini-review highlights recent advances in the field of laccase-facilitated functionalization of lignin as well as promising future directions for lignin-based polymers. PMID:27645296

  15. Fractionation of hemp hurds by organosolv pretreatment and its effect on production of lignin and sugars.

    PubMed

    Gandolfi, Stefano; Ottolina, Gianluca; Consonni, Roberto; Riva, Sergio; Patel, Ilabahen

    2014-07-01

    Fractionation of hemp hurds into its three main components, cellulose, hemicellulose, and lignin, was carried out using organosolv pretreatment. The effect of processing parameters, such as temperature, catalyst concentration, reaction time, and methanol (MeOH) concentration, on the dissolution and recovery of hemicellulose and lignin was determined. More than 75% of total hemicellulose and 75% of total lignin was removed in a single step with low amounts of degradation products under the following conditions: 165 °C, 3% H2 SO4 , 20 min reaction time, and 45% MeOH. Enzymatic hydrolysis of the residual pretreated biomass yielded up to 60% of cellulose-to-glucose conversion. The maximum recovery of the main components was obtained at a combined severity factor value of around one. Characterization of pretreated biomass and isolated lignin was carried out with FTIR and 2D (13) C-(1) H correlation HSQC NMR spectroscopy, the latter technique providing detailed structural information about the obtained methanol organosolv lignin (MOSL). Results suggested that xylopyranoside is the major carbohydrate associated with hemp lignin. The chemical properties of MOSL samples in terms of their phenolic group content and antioxidant capacity were also investigated. The results showed that MOSL samples have a high phenolic group content and antioxidant capacity relative to Klason lignin.

  16. Conversion of lignin into value-added materials and chemicals via laccase-assisted copolymerization.

    PubMed

    Cannatelli, Mark D; Ragauskas, Arthur J

    2016-10-01

    With today's environmental concerns and the diminishing supply of the world's petroleum-based chemicals and materials, much focus has been directed toward alternative sources. Woody biomass presents a promising option due to its sheer abundance, renewability, and biodegradability. Lignin, a highly irregular polyphenolic compound, is one of the major chemical constituents of woody biomass and is the second most abundant biopolymer on Earth, surpassed only by cellulose. The pulp and paper and cellulosic ethanol industries produce lignin on the scale of millions of tons each year as a by-product. Traditionally, lignin has been viewed as a waste material and burned as an inefficient fuel. However, in recent decades, research has focused on more economical ways to convert lignin into value-added commodities, such as biofuels, biomaterials, and biochemicals, thus developing and strengthening the concept of fully integrated biorefineries. Owing to the phenolic structure of lignin, it is possible to enzymatically graft molecules onto its surface using laccases (benzenediol:oxygen oxidoreductases, EC 1.10.3.2) to create exciting novel biomaterials. These environmentally friendly enzymes use oxygen as their only co-substrate and produce water as their sole by-product, and have thus found great industrial application. This mini-review highlights recent advances in the field of laccase-facilitated functionalization of lignin as well as promising future directions for lignin-based polymers.

  17. Fatness QTL on chicken chromosome 5 and interaction with sex

    PubMed Central

    Abasht, Behnam; Pitel, Frédérique; Lagarrigue, Sandrine; Le Bihan-Duval, Elisabeth; Le Roy, Pascale; Demeure, Olivier; Vignoles, Florence; Simon, Jean; Cogburn, Larry; Aggrey, Sammy; Vignal, Alain; Douaire, Madeleine

    2006-01-01

    Quantitative trait loci (QTL) affecting fatness in male chickens were previously identified on chromosome 5 (GGA5) in a three-generation design derived from two experimental chicken lines divergently selected for abdominal fat weight. A new design, established from the same pure lines, produced 407 F2 progenies (males and females) from 4 F1-sire families. Body weight and abdominal fat were measured on the F2 at 9 wk of age. In each sire family, selective genotyping was carried out for 48 extreme individuals for abdominal fat using seven microsatellite markers from GGA5. QTL analyses confirmed the presence of QTL for fatness on GGA5 and identified a QTL by sex interaction. By crossing one F1 sire heterozygous at the QTL with lean line dams, three recombinant backcross 1 (BC1) males were produced and their QTL genotypes were assessed in backcross 2 (BC2) progenies. These results confirmed the QTL by sex interaction identified in the F2 generation and they allow mapping of the female QTL to less than 8 Mb at the distal part of the GGA5. They also indicate that fat QTL alleles were segregating in both fat and lean lines. PMID:16635451

  18. Abiotic stress QTL in lettuce crop–wild hybrids: comparing greenhouse and field experiments

    PubMed Central

    Hartman, Yorike; Hooftman, Danny A P; Uwimana, Brigitte; Schranz, M Eric; van de Wiel, Clemens C M; Smulders, Marinus J M; Visser, Richard G F; Michelmore, Richard W; van Tienderen, Peter H

    2014-01-01

    The development of stress-tolerant crops is an increasingly important goal of current crop breeding. A higher abiotic stress tolerance could increase the probability of introgression of genes from crops to wild relatives. This is particularly relevant to the discussion on the risks of new GM crops that may be engineered to increase abiotic stress resistance. We investigated abiotic stress QTL in greenhouse and field experiments in which we subjected recombinant inbred lines from a cross between cultivated Lactuca sativa cv. Salinas and its wild relative L. serriola to drought, low nutrients, salt stress, and aboveground competition. Aboveground biomass at the end of the rosette stage was used as a proxy for the performance of plants under a particular stress. We detected a mosaic of abiotic stress QTL over the entire genome with little overlap between QTL from different stresses. The two QTL clusters that were identified reflected general growth rather than specific stress responses and colocated with clusters found in earlier studies for leaf shape and flowering time. Genetic correlations across treatments were often higher among different stress treatments within the same experiment (greenhouse or field), than among the same type of stress applied in different experiments. Moreover, the effects of the field stress treatments were more correlated with those of the greenhouse competition treatments than to those of the other greenhouse stress experiments, suggesting that competition rather than abiotic stress is a major factor in the field. In conclusion, the introgression risk of stress tolerance (trans-)genes under field conditions cannot easily be predicted based on genomic background selection patterns from controlled QTL experiments in greenhouses, especially field data will be needed to assess potential (negative) ecological effects of introgression of these transgenes into wild relatives. PMID:25360276

  19. Genetic and environmental effects influencing fruit colour and QTL analysis in raspberry.

    PubMed

    McCallum, Susan; Woodhead, Mary; Hackett, Christine A; Kassim, Angzzas; Paterson, Alistair; Graham, Julie

    2010-08-01

    Raspberry (Rubus idaeus) fruit colour was assessed in the Latham x Glen Moy mapping population using a colour meter and visual scores over three seasons and three environments. The colour measurements were found to be significantly associated with pigment content, have high heritability, and stable QTL were identified across environments and seasons. Anthocyanin content has previously been shown to be the major contributor to fruit colour in red raspberry. Major structural genes (F3'H, FLS, DFR, IFR, OMT and GST) and transcription factors (bZIP, bHLH and MYB) influencing flavonoid biosynthesis have been identified, mapped and shown to underlie QTL for quantitative and qualitative anthocyanin composition. Favourable alleles for the selected traits were identified for the aspects of fruit colour and partitioning of individual pigments.

  20. Quantitative trait locus (QTL) isogenic recombinant analysis: a method for high-resolution mapping of QTL within a single population.

    PubMed

    Peleman, Johan D; Wye, Crispin; Zethof, Jan; Sørensen, Anker P; Verbakel, Henk; van Oeveren, Jan; Gerats, Tom; van der Voort, Jeroen Rouppe

    2005-11-01

    In the quest for fine mapping quantitative trait loci (QTL) at a subcentimorgan scale, several methods that involve the construction of inbred lines and the generation of large progenies of such inbred lines have been developed (Complex Trait Consortium 2003). Here we present an alternative method that significantly speeds up QTL fine mapping by using one segregating population. As a first step, a rough mapping analysis is performed on a small part of the population. Once the QTL have been mapped to a chromosomal interval by standard procedures, a large population of 1000 plants or more is analyzed with markers flanking the defined QTL to select QTL isogenic recombinants (QIRs). QIRs bear a recombination event in the QTL interval of interest, while other QTL have the same homozygous genotype. Only these QIRs are subsequently phenotyped to fine map the QTL. By focusing at an early stage on the informative individuals in the population only, the efforts in population genotyping and phenotyping are significantly reduced as compared to prior methods. The principles of this approach are demonstrated by fine mapping an erucic acid QTL of rapeseed at a subcentimorgan scale.

  1. Lignin phenols used to infer organic matter sources to Sepetiba Bay - RJ, Brasil

    NASA Astrophysics Data System (ADS)

    Rezende, C. E.; Pfeiffer, W. C.; Martinelli, L. A.; Tsamakis, E.; Hedges, J. I.; Keil, R. G.

    2010-04-01

    Lignin phenols were measured in the sediments of Sepitiba Bay, Rio de Janeiro, Brazil and in bedload sediments and suspended sediments of the four major fluvial inputs to the bay; São Francisco and Guandu Channels and the Guarda and Cação Rivers. Fluvial suspended lignin yields (Σ8 3.5-14.6 mgC 10 g dw -1) vary little between the wet and dry seasons and are poorly correlated with fluvial chlorophyll concentrations (0.8-50.2 μgC L -1). Despite current land use practices that favor grassland agriculture or industrial uses, fluvial lignin compositions are dominated by a degraded leaf-sourced material. The exception is the Guarda River, which has a slight influence from grasses. The Lignin Phenol Vegetation Index, coupled with acid/aldehyde and 3.5 Db/V ratios, indicate that degraded leaf-derived phenols are also the primary preserved lignin component in the bay. The presence of fringe Typha sp. and Spartina sp. grass beds surrounding portions of the Bay are not reflected in the lignin signature. Instead, lignin entering the bay appears to reflect the erosion of soils containing a degraded signature from the former Atlantic rain forest that once dominated the watershed, instead of containing a significant signature derived from current agricultural uses. A three-component mixing model using the LPVI, atomic N:C ratios, and stable carbon isotopes (which range between -26.8 and -21.8‰) supports the hypothesis that fluvial inputs to the bay are dominated by planktonic matter (78% of the input), with lignin dominated by leaf (14% of the input) over grass (6%). Sediments are composed of a roughly 50-50 mixture of autochthonous material and terrigenous material, with lignin being primarily sourced from leaf.

  2. Mimicry on the QT(L): genetics of speciation in Mimulus.

    PubMed

    Bleiweiss, R

    2001-08-01

    Ecological studies suggest that hummingbird-pollinated plants in North America mimic each other to increase visitation by birds. Published quantitative trait locus (QTL) data for two Mimulus species indicate that floral traits associated with hummingbird versus bee pollination results from a few loci with major effects on morphology, as predicted by classical models for the evolution of mimicry. Thus, the architecture of genetic divergence associated with speciation may depend on the ecological context.

  3. Bio-inspired MOF-based Catalysts for Lignin Valorization.

    SciTech Connect

    Allendorf, Mark D.; Stavila, Vitalie; Ramakrishnan, Parthasarathi; Davis, Ryan Wesley

    2014-09-01

    for the C-O bond hydrogenolysis in model compounds, which mimic the b-O-4, a-O-4, and 4-O-5 linkages of natural lignin. The versatile IRMOF-74(n) series is proposed as a platform for creating efficient hydrogenolysis catalysts as it not only displays tunable pore sizes, but also has the required thermal and chemical stability. The catalytic C-O bond cleavage occurs at 10 bar hydrogen pressure and temperatures as low as 120 degC. The conversion efficiency of the aromatic ether substrates into the corresponding hydrocarbons and phenols varies as PhCH 2 CH 2 OPh > PhCH 2 OPh > PhOPh (Ph = phenyl), while the catalytic activity generally follows the following trend Ni@IRMOF-74>Ti@IRMOF-74>IRMOF-74. Conversions as high as 80%, coupled with good selectivity for hydrogenolysis vs. hydrogenation, highlight the potential of MOF-based catalysts for the selective cleavage of recalcitrant aryl-ether bonds found in lignin and other biopolymers. This project supports the DOE Integrated Biorefinery Program goals, the objective of which is to convert biomass to fuels and high-value chemicals, by addressing an important technology gap: the lack of low-temperature catalysts suitable for industrial lignin degradation. Biomass, which is %7E30 wt% lignin, constitutes a potentially major source of platform chemicals that could improve overall profitability and productivity of all energy-related products, thereby benefiting consumers and reducing national dependence on imported oil. Additionally, DoD has a strong interest in low-cost drop-in fuels (Navy Biofuel Initiative) and has signed a Memorandum of Understanding with DOE and USDA to develop a sustainable biofuels industry.

  4. Linkage mapping and identification of QTL affecting deoxynivalenol (DON) content (Fusarium resistance) in oats (Avena sativa L.).

    PubMed

    He, Xinyao; Skinnes, Helge; Oliver, Rebekah E; Jackson, Eric W; Bjørnstad, Asmund

    2013-10-01

    Mycotoxins caused by Fusarium spp. is a major concern on food and feed safety in oats, although Fusarium head blight (FHB) is often less apparent than in other small grain cereals. Breeding resistant cultivars is an economic and environment-friendly way to reduce toxin content, either by the identification of resistance QTL or phenotypic evaluation. Both are little explored in oats. A recombinant-inbred line population, Hurdal × Z595-7 (HZ595, with 184 lines), was used for QTL mapping and was phenotyped for 3 years. Spawn inoculation was applied and deoxynivalenol (DON) content, FHB severity, days to heading and maturity (DH and DM), and plant height (PH) were measured. The population was genotyped with DArTs, AFLPs, SSRs and selected SNPs, and a linkage map of 1,132 cM was constructed, covering all 21 oat chromosomes. A QTL for DON on chromosome 17A/7C, tentatively designated as Qdon.umb-17A/7C, was detected in all experiments using composite interval mapping, with phenotypic effects of 12.2–26.6 %. In addition, QTL for DON were also found on chromosomes 5C, 9D, 13A, 14D and unknown_3, while a QTL for FHB was found on 11A. Several of the DON/FHB QTL coincided with those for DH, DM and/or PH. A half-sib population of HZ595, Hurdal × Z615-4 (HZ615, with 91 lines), was phenotyped in 2011 for validation of QTL found in HZ595, and Qdon.umb-17A/7C was again localized with a phenotypic effect of 12.4 %. Three SNPs closely linked to Qdon.umb-17A/7C were identified in both populations, and one each for QTL on 5C, 11A and 13A were identified in HZ595. These SNPs, together with those yet to be identified, could be useful in marker-assisted selection to pyramiding resistance QTL.

  5. QTL for bacterial cold water disease resistance and spleen size are located on rainbow trout chromosome Omy19

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Selective breeding of aquatic animals for improved disease resistance has become a major focus in aquaculture, although little is known about underlying QTL or correlated traits. At the National Center for Cool and Cold Water Aquaculture (NCCCWA), we have pursued a selective breeding program with t...

  6. Identification of quantitative trait loci (QTL) for fruit quality traits and number of weeks of flowering in the cultivated strawberry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fruit quality traits and dayneutrality are two major foci of several strawberry breeding programs. The identification of quantitative trait loci (QTL) and molecular markers linked to these traits could improve breeding efficiency. In this work, an F1 population derived from the cross ‘Delmarvel’ × ...

  7. Method for recovering and using lignin in adhesive resins by extracting demethylated lignin

    DOEpatents

    Schroeder, Herbert A.

    1991-01-01

    Lignin, or a lignin derived material, which has been significantly demethylated (e.g., the demethylated lignin found in the raffinate produced as a by-product of dimethyl sulfide production which can be carried out using the spent liquor from wood pulping operations) can be isolated by a process wherein an organic solvent is added to a lignin-containing aqueous solution. The organic solvent is typically a polar, and at least a partially water-immiscible substance such as, for example, ethyl acetate. The resulting lignin-containing aqueous solution/organic solvent mixture is acidified to produce a water layer which is discarded and an organic solvent layer which contains the demethylated lignin. Upon its recovery, the demethylated lignin is preferably dried and stored until it is used (along with an alkali, an aldehyde and an adhesive filler) in compounding an adhesive of the type generally used in the manufacture of plywood.

  8. Method for recovering and using lignin in adhesive resins by extracting demethylated lignin

    DOEpatents

    Schroeder, Herbert A.

    1991-01-01

    Lignin, or a lignin derived material, which has been significantly demethylated (e.g., the demethylated lignin found in the raffinate produced as a by-product of dimethyl sulfide production which can be carried out using the spent liquor from wood pulping operations) can be isolated by a process wherein an organic solvent is added to a lignin-containing aqueous solution. The organic solvent is typically a polar, and at least a partially water-immiscible substance such as, for example, ethyl acetate. The resulting lignin-containing aqueous solution/organic solvent mixture is acidified to produce a water layer which is discarded and an organic solvent layer which contains the demethylated lignin. Upon its recovery, the demethylated lignin is dissolved in an alkaline solution to which an aldehyde source is added to produce a resol-type resin. The aldehyde source may be formaldehyde in solution, paraformaldehyde, hexamethylenetetramine, or other aldehydes including acetaldehyde, furfural, and their derivatives.

  9. Combination of different methods to assess the fate of lignin in decomposing needle and leave litter

    NASA Astrophysics Data System (ADS)

    Klotzbücher, Thimo; Filley, Timothy; Kaiser, Klaus; Kalbitz, Karsten

    2010-05-01

    Lignin is a major component of plant litter. However, its fate during litter decay is still poorly understood. One reason is the difficult analysis. Commonly used methods utilize different methodological approaches and focus on different aspects, e.g., content of lignin and/or of lignin-derived phenols and the degree of oxidation. The comparability and feasibility of the methods has not been tested so far. Our aims were: (1) to compare different methods with respect to track lignin degradation during plant litter decay and (2) to evaluate possible advantages of combining the different results. We assessed lignin degradation in decaying litter by 13C-TMAH thermochemolysis and CuO oxidation (each combined with GC/MS) and by determination of acid-detergent lignin (ADL) combined with near infrared spectroscopy. Furthermore, water-extractable organic matter produced during litter decay was examined for indicators of lignin-derived compounds by UV absorbance at 280 nm, fluorescence spectroscopy, and 13C-TMAH GC/MS. The study included litter samples from 5 different tree species (acer, ash, beech, pine, spruce), exposed in litterbags to degradation in a spruce stand for 27 months. First results suggested stronger lignin degradation in coniferous than in deciduous litter. This was indicated by complementary results from various methods: Conifer litter showed a more pronounced decrease in ADL content and a stronger increase in oxidation degree of side chains (Ac/Al ratios of CuO oxidation and 13C-TMAH products). Furthermore water extracted organic matter from needles showed a higher aromaticity and molecule complexity. Thus properties of water extractable organic matter seemed to reflect the extents of lignin degradation in solid litter samples. Contents of lignin-derived phenols determined with the CuO method (VSC content) hardly changed during decay of needles and leaves. These results thus not matched the trends found with the ADL method. Our results suggested that water

  10. (Characterization of lignin peroxidases from Phanerochaete)

    SciTech Connect

    Not Available

    1990-11-14

    Work has continued on characterizing the kinetics of lignin peroxidases and has now expanded to include the chemistry of Mn peroxidases. Progress in these two area in addition to the authors work on the molecular biology of lignin biodegradation is briefly described below. Copies of two reprints and one preprint which have resulted from the work are attached.

  11. Lignin: Characterization of a Multifaceted Crop Component

    PubMed Central

    2013-01-01

    Lignin is a plant component with important implications for various agricultural disciplines. It confers rigidity to cell walls, and is therefore associated with tolerance to abiotic and biotic stresses and the mechanical stability of plants. In animal nutrition, lignin is considered an antinutritive component of forages as it cannot be readily fermented by rumen microbes. In terms of energy yield from biomass, the role of lignin depends on the conversion process. It contains more gross energy than other cell wall components and therefore confers enhanced heat value in thermochemical processes such as direct combustion. Conversely, it negatively affects biological energy conversion processes such as bioethanol or biogas production, as it inhibits microbial fermentation of the cell wall. Lignin from crop residues plays an important role in the soil organic carbon cycling, as it constitutes a recalcitrant carbon pool affecting nutrient mineralization and carbon sequestration. Due to the significance of lignin in several agricultural disciplines, the modification of lignin content and composition by breeding is becoming increasingly important. Both mapping of quantitative trait loci and transgenic approaches have been adopted to modify lignin in crops. However, breeding goals must be defined considering the conflicting role of lignin in different agricultural disciplines. PMID:24348159

  12. Method for regulation of plant lignin composition

    DOEpatents

    Chapple, Clint

    1999-01-01

    A method is disclosed for the regulation of lignin composition in plant tissue. Plants are transformed with a gene encoding an active F5H gene. The expression of the F5H gene results in increased levels of syringyl monomer providing a lignin composition more easily degraded with chemicals and enzymes.

  13. Development of Lignin-Based Polyurethane Thermoplastics

    SciTech Connect

    Saito, Tomonori; Perkins, Joshua H; Jackson, Daniel C; Trammell, Neil E; Hunt, Marcus A; Naskar, Amit K

    2013-01-01

    In our continued effort to develop value-added thermoplastics from lignin, here we report utilizing a tailored feedstock to synthesize mechanically robust thermoplastic polyurethanes at very high lignin contents (75 65 wt %). The molecular weight and glass transition temperature (Tg) of lignin were altered through cross-linking with formaldehyde. The cross-linked lignin was coupled with diisocyanate-based telechelic polybutadiene as a network-forming soft segment. The appearance of two Tg s, around 35 and 154 C, for the polyurethanes indicates the existence of two-phase morphology, a characteristic of thermoplastic copolymers. A calculated Flory-Huggins interaction parameter of 7.71 also suggests phase immiscibility in the synthesized lignin polyurethanes. An increase in lignin loading increased the modulus, and an increase in crosslink-density increased the modulus in the rubbery plateau region of the thermoplastic. This path for synthesis of novel lignin-based polyurethane thermoplastics provides a design tool for high performance lignin-based biopolymers.

  14. Educational Software for Mapping Quantitative Trait Loci (QTL)

    ERIC Educational Resources Information Center

    Helms, T. C.; Doetkott, C.

    2007-01-01

    This educational software was developed to aid teachers and students in their understanding of how the process of identifying the most likely quantitative trait loci (QTL) position is determined between two flanking DNA markers. The objective of the software that we developed was to: (1) show how a QTL is mapped to a position on a chromosome using…

  15. Biodegradation of lignin by Agaricus Bisporus

    SciTech Connect

    Vane, C.H.; Abbott, G.D.; Head, I.M.

    1996-12-31

    The lignolytic activity of Agaricus bisporus will be addressed in this paper. Sound and fungally degraded lignins were characterized by Pyrolysis-Gas Chromatography-Mass Spectrometry (Py-GC-MS), Fourier Transform Infrared Spectroscopy (FnR) and elemental analysis. Fungally degraded lignins displayed increased wt%N, wt%H and wt%O content and decreased wt%C content The FTIR spectrum of decayed lignin showed an increase in the relative intensity of absorption bands assigned to carbonyl and carboxyl functional groups located on the aliphatic side chain and a decrease in absorption bands assigned to aromatic skeletal vibration modes. Semiquantitative Py-GC-MS revealed an 82% decrease in lignin derived pyrolysis products upon biodegradation. No significant increase in pyrolysis products with an oxygenated aliphatic side chain were detected in the fungally degraded lignin however shortening of the aliphatic side chain via cleavage at the {alpha}, {beta} and {gamma} positions was observed.

  16. Micro-Spectroscopic Imaging of Lignin-Carbohydrate Complexes in Plant Cell Walls and Their Migration During Biomass Pretreatment

    SciTech Connect

    Zeng, Yining; Zhao, Shuai; Wei, Hui; Tucker, Melvin P.; Johnson, David K.; Himmel, Michael E.; Mosier, Nathan S.; Meilan, Richard; Ding, Shi-You

    2015-04-27

    In lignocellulosic biomass, lignin is the second most abundant biopolymer. In plant cell walls, lignin is associated with polysaccharides to form lignin-carbohydrate complexes (LCC). LCC have been considered to be a major factor that negatively affects the process of deconstructing biomass to simple sugars by cellulosic enzymes. Here, we report a micro-spectroscopic approach that combines fluorescence lifetime imaging microscopy and Stimulated Raman Scattering microscopy to probe in situ lignin concentration and conformation at each cell wall layer. This technique does not require extensive sample preparation or any external labels. Using poplar as a feedstock, for example, we observe variation of LCC in untreated tracheid poplar cell walls. The redistribution of LCC at tracheid poplar cell wall layers is also investigated when the chemical linkages between lignin and hemicellulose are cleaved during pretreatment. Our study would provide new insights into further improvement of the biomass pretreatment process.

  17. Mechanistic Study of the Acid Degradation of Lignin Model Compounds

    SciTech Connect

    Sturgeon, M.; Kim, S.; Chmely, S. C.; Foust, T. D.; Beckham, G. T.

    2012-01-01

    Lignin is a major constituent of biomass, which remains underutilized in selective biomass conversion strategies to renewable fuels and chemicals. Here we are interested in understanding the mechanisms related to the acid deconstruction of lignin with a combined theoretical and experimental approach. Two model dimers with a b-O-4 aryl ether linkage (2-phenoxy-1-phenethanol and 2-phenoxy-1-phenyl-1,3 propanediol) and model dimmers with an a-O-4 aryl ether linkage were synthesized and deconstructed in H2SO4. The major products of the acidolysis of the b-O-4 compounds consisted of phenol and two aldehydes, phenylacetaldehyde and benzaldehyde. Quantum mechanical calculations were employed to elucidate possible deconstruction mechanisms with transition state theory. To confirm proposed mechanisms several possible intermediates were studied under similar acidolysis conditions. Although the resonance time for cleavage was on the order several hours, we have shown that the cleavage of the aryl ether linkage affords phenol and aldehydes. We would next like to utilize our mechanism of aryl ether cleavage in actual lignin.

  18. Genotypic effects of the Texel Muscling QTL (TM-QTL) on meat quality in purebred Texel lambs.

    PubMed

    Lambe, N R; Richardson, R I; Macfarlane, J M; Nevison, I; Haresign, W; Matika, O; Bünger, L

    2011-10-01

    Texel Muscling QTL (TM-QTL) increases loin muscling in lambs inheriting it from their sire only. This study investigated TM-QTL effects on meat quality in 209 Texel lambs that were CT-scanned then slaughtered at 20weeks (carcasses aged for ~1week). Loin meat quality traits included: CT-measured muscle density (predicting intramuscular fat); mechanical tenderness using Volodkevich-type jaws or MIRINZ tenderometer; intramuscular fat; sensory eating quality (sub-sample of 40 lambs). Volodkevich tenderness was also measured in the leg (Vastis lateralis). TM-QTL genotypes were determined, giving 40 non-carriers (+/+), 70 heterozygotes-53 inheriting TM-QTL from the sire (TM/+) and 17 from the dam (+/TM), 34 homozygote TM-QTL lambs (TM/TM) and 65 uncertain. Multiple regression identified no genotype effects on meat quality. For MIRINZ-measured loin tenderness only, contrasts revealed a significant additive effect of TM-QTL (1.27kgF difference between homozygotes). However, the taste panel identified no significant differences between +/+ and TM/TM lambs. Results show little evidence of TM-QTL affecting meat quality.

  19. Genotypic effects of the Texel Muscling QTL (TM-QTL) on meat quality in purebred Texel lambs.

    PubMed

    Lambe, N R; Richardson, R I; Macfarlane, J M; Nevison, I; Haresign, W; Matika, O; Bünger, L

    2011-10-01

    Texel Muscling QTL (TM-QTL) increases loin muscling in lambs inheriting it from their sire only. This study investigated TM-QTL effects on meat quality in 209 Texel lambs that were CT-scanned then slaughtered at 20weeks (carcasses aged for ~1week). Loin meat quality traits included: CT-measured muscle density (predicting intramuscular fat); mechanical tenderness using Volodkevich-type jaws or MIRINZ tenderometer; intramuscular fat; sensory eating quality (sub-sample of 40 lambs). Volodkevich tenderness was also measured in the leg (Vastis lateralis). TM-QTL genotypes were determined, giving 40 non-carriers (+/+), 70 heterozygotes-53 inheriting TM-QTL from the sire (TM/+) and 17 from the dam (+/TM), 34 homozygote TM-QTL lambs (TM/TM) and 65 uncertain. Multiple regression identified no genotype effects on meat quality. For MIRINZ-measured loin tenderness only, contrasts revealed a significant additive effect of TM-QTL (1.27kgF difference between homozygotes). However, the taste panel identified no significant differences between +/+ and TM/TM lambs. Results show little evidence of TM-QTL affecting meat quality. PMID:21592676

  20. QTL analysis of body weight and carcass body length traits in an F2 intercross between Landrace and Korean native pigs.

    PubMed

    Yoo, C K; Park, H B; Lee, J B; Jung, E J; Kim, B M; Kim, H I; Ahn, S J; Ko, M S; Cho, I C; Lim, H T

    2014-08-01

    Growth traits, such as body weight and carcass body length, directly affect productivity and economic efficiency in the livestock industry. We performed a genome-wide linkage analysis to detect the quantitative trait loci (QTL) that affect body weight, growth curve parameters and carcass body length in an F2 intercross between Landrace and Korean native pigs. Eight phenotypes related to growth were measured in approximately 1000 F2 progeny. All experimental animals were subjected to genotypic analysis using 173 microsatellite markers located throughout the pig genome. The least squares regression approach was used to conduct the QTL analysis. For body weight traits, we mapped 16 genome-wide significant QTL on SSC1, 3, 5, 6, 8, 9 and 12 as well as 22 suggestive QTL on SSC2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16 and 17. On SSC12, we identified a major QTL affecting body weight at 140 days of age that accounted for 4.3% of the phenotypic variance, which was the highest test statistic (F-ratio = 45.6 under the additive model, nominal P = 2.4 × 10(-11) ) observed in this study. We also showed that there were significant QTL on SSC2, 5, 7, 8, 9 and 12 affecting carcass body length and growth curve parameters. Interestingly, the QTL on SSC2, 3, 5, 6, 8, 9, 10, 12 and 17 influencing the growth-related traits showed an obvious trend for co-localization. In conclusion, the identified QTL may play an important role in investigating the genetic structure underlying the phenotypic variation of growth in pigs.

  1. QTL analysis of body weight and carcass body length traits in an F2 intercross between Landrace and Korean native pigs.

    PubMed

    Yoo, C K; Park, H B; Lee, J B; Jung, E J; Kim, B M; Kim, H I; Ahn, S J; Ko, M S; Cho, I C; Lim, H T

    2014-08-01

    Growth traits, such as body weight and carcass body length, directly affect productivity and economic efficiency in the livestock industry. We performed a genome-wide linkage analysis to detect the quantitative trait loci (QTL) that affect body weight, growth curve parameters and carcass body length in an F2 intercross between Landrace and Korean native pigs. Eight phenotypes related to growth were measured in approximately 1000 F2 progeny. All experimental animals were subjected to genotypic analysis using 173 microsatellite markers located throughout the pig genome. The least squares regression approach was used to conduct the QTL analysis. For body weight traits, we mapped 16 genome-wide significant QTL on SSC1, 3, 5, 6, 8, 9 and 12 as well as 22 suggestive QTL on SSC2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16 and 17. On SSC12, we identified a major QTL affecting body weight at 140 days of age that accounted for 4.3% of the phenotypic variance, which was the highest test statistic (F-ratio = 45.6 under the additive model, nominal P = 2.4 × 10(-11) ) observed in this study. We also showed that there were significant QTL on SSC2, 5, 7, 8, 9 and 12 affecting carcass body length and growth curve parameters. Interestingly, the QTL on SSC2, 3, 5, 6, 8, 9, 10, 12 and 17 influencing the growth-related traits showed an obvious trend for co-localization. In conclusion, the identified QTL may play an important role in investigating the genetic structure underlying the phenotypic variation of growth in pigs. PMID:24797173

  2. Genome-Wide Association Mapping in the Global Diversity Set Reveals New QTL Controlling Root System and Related Shoot Variation in Barley

    PubMed Central

    Reinert, Stephan; Kortz, Annika; Léon, Jens; Naz, Ali A.

    2016-01-01

    The fibrous root system is a visible sign of ecological adaptation among barley natural populations. In the present study, we utilized rich barley diversity to dissect the genetic basis of root system variation and its link with shoot attributes under well-water and drought conditions. Genome-wide association mapping of phenotype data using a dense genetic map (5892 SNP markers) revealed 17 putative QTL for root and shoot traits. Among these, at 14 loci the preeminence of exotic QTL alleles resulted in trait improvements. The most promising QTL were quantified using haplotype analysis at local and global genome levels. The strongest QTL was found on chromosome 1H which accounted for root dry weight and tiller number simultaneously. Candidate gene analysis across the targeted region detected a crucial amino acid substitution mutation in the conserved domain of a WRKY29 transcription factor among genotypes bearing major and minor QTL alleles. Similarly, the drought inducible QTL QRdw.5H (5H, 95.0 cM) seems to underlie 37 amino acid deletion and substitution mutations in the conserved domain of two related genes CBF10B and CBF10A, respectively. The identification and further characterization of these candidate genes will be essential to decipher genetics behind developmental and natural adaptation mechanisms of barley. PMID:27486472

  3. Genome-Wide Association Mapping in the Global Diversity Set Reveals New QTL Controlling Root System and Related Shoot Variation in Barley.

    PubMed

    Reinert, Stephan; Kortz, Annika; Léon, Jens; Naz, Ali A

    2016-01-01

    The fibrous root system is a visible sign of ecological adaptation among barley natural populations. In the present study, we utilized rich barley diversity to dissect the genetic basis of root system variation and its link with shoot attributes under well-water and drought conditions. Genome-wide association mapping of phenotype data using a dense genetic map (5892 SNP markers) revealed 17 putative QTL for root and shoot traits. Among these, at 14 loci the preeminence of exotic QTL alleles resulted in trait improvements. The most promising QTL were quantified using haplotype analysis at local and global genome levels. The strongest QTL was found on chromosome 1H which accounted for root dry weight and tiller number simultaneously. Candidate gene analysis across the targeted region detected a crucial amino acid substitution mutation in the conserved domain of a WRKY29 transcription factor among genotypes bearing major and minor QTL alleles. Similarly, the drought inducible QTL QRdw.5H (5H, 95.0 cM) seems to underlie 37 amino acid deletion and substitution mutations in the conserved domain of two related genes CBF10B and CBF10A, respectively. The identification and further characterization of these candidate genes will be essential to decipher genetics behind developmental and natural adaptation mechanisms of barley. PMID:27486472

  4. Methanol fractionation of softwood Kraft lignin: impact on the lignin properties.

    PubMed

    Saito, Tomonori; Perkins, Joshua H; Vautard, Frederic; Meyer, Harry M; Messman, Jamie M; Tolnai, Balazs; Naskar, Amit K

    2014-01-01

    The development of technologies to tune lignin properties for high-performance lignin-based materials is crucial for the utilization of lignin in various applications. Here, the effect of methanol (MeOH) fractionation on the molecular weight, molecular weight distribution, glass transition temperature (Tg ), thermal decomposition, and chemical structure of lignin were investigated. Repeated MeOH fractionation of softwood Kraft lignin successfully removed the low-molecular-weight fraction. The separated high-molecular-weight lignin showed a Tg of 211 °C and a char yield of 47 %, much higher than those of as-received lignin (Tg 153 °C, char yield 41 %). The MeOH-soluble fraction of lignin showed an increased low-molecular-weight fraction and a lower Tg (117 °C) and char yield (32%). The amount of low-molecular-weight fraction showed a quantitative correlation with both 1/Tg and char yield in a linear regression. This study demonstrated the efficient purification or fractionation technology for lignin; it also established a theoretical and empirical correlation between the physical characteristics of fractionated lignins. PMID:24458739

  5. QTL mapping for a trade-off between leaf and bud production in a recombinant inbred population of Microseris douglasii and M. bigelovii (Asteraceae, Lactuceae): a potential preadaptation for the colonization of serpentine soils.

    PubMed

    Gailing, O; Macnair, M R; Bachmann, K

    2004-07-01

    The different response to growth on serpentine soil is a major autecological difference between the annual asteracean species Microseris douglasii and M. bigelovii, with nearly non-overlapping distribution ranges in California. Early flowering and seed set is regarded as a crucial character contributing to escape drought and thus is strongly correlated with survival and reproductive success on serpentine as naturally toxic soil. M. bigelovii (strain C94) from non-serpentine soil produces more leaves at the expense of bud production in the first growing phase than M. douglasii (B14) from serpentine soil. A QTL mapping study for this trade-off and for other growth-related traits was performed after six generations of inbreeding (F7) from a single interspecific hybrid between B14 and C94 on plants that were grown on serpentine and alternatively on normal potting soil. The trade-off is mainly correlated with markers on one map region on linkage group 03a (lg03a) with major phenotypic effects (phenotypic variance explained [PVE] = 18.8 - 31.7 %). Plants with the M. douglasii allele in QTL-B1 (QTL-NL1) produce more buds but fewer leaves in the first 119 days on both soil types. Three modifier QTL could be mapped for bud and leaf production. In one modifier (QTL-B2 = QTL-NL4) the M. douglasii allele is again associated with more buds but fewer leaves. QTL mapped for bud set in the F6 co-localize with QTL-B1 (major QTL) and QTL-B3. Two additional QTL for leaf length and red coloration of leaves could be mapped to one map region on lg03a. Co-localization of the two QTL loci with major phenotypic effects on bud and leaf production strongly suggests that a major genetic locus controls the trade-off between the two adaptive traits. The importance of mutational changes in major genes for the adaptation to stressful environments is discussed.

  6. Genetic Augmentation of Syringyl Lignin in Low-lignin Aspen Trees, Final Report

    SciTech Connect

    Chung-Jui Tsai; Mark F. Davis; Vincent L. Chiang

    2004-11-10

    As a polysaccharide-encrusting component, lignin is critical to cell wall integrity and plant growth but also hinders recovery of cellulose fibers during the wood pulping process. To improve pulping efficiency, it is highly desirable to genetically modify lignin content and/or structure in pulpwood species to maximize pulp yields with minimal energy consumption and environmental impact. This project aimed to genetically augment the syringyl-to-guaiacyl lignin ratio in low-lignin transgenic aspen in order to produce trees with reduced lignin content, more reactive lignin structures and increased cellulose content. Transgenic aspen trees with reduced lignin content have already been achieved, prior to the start of this project, by antisense downregulation of a 4-coumarate:coenzyme A ligase gene (Hu et al., 1999 Nature Biotechnol 17: 808- 812). The primary objective of this study was to genetically augment syringyl lignin biosynthesis in these low-lignin trees in order to enhance lignin reactivity during chemical pulping. To accomplish this, both aspen and sweetgum genes encoding coniferaldehyde 5-hydroxylase (Osakabe et al., 1999 PNAS 96: 8955-8960) were targeted for over-expression in wildtype or low-lignin aspen under control of either a constitutive or a xylem-specific promoter. A second objective for this project was to develop reliable and cost-effective methods, such as pyrolysis Molecular Beam Mass Spectrometry and NMR, for rapid evaluation of cell wall chemical components of transgenic wood samples. With these high-throughput techniques, we observed increased syringyl-to-guaiacyl lignin ratios in the transgenic wood samples, regardless of the promoter used or gene origin. Our results confirmed that the coniferaldehyde 5-hydroxylase gene is key to syringyl lignin biosynthesis. The outcomes of this research should be readily applicable to other pulpwood species, and promise to bring direct economic and environmental benefits to the pulp and paper industry.

  7. Genetic linkage map construction and QTL mapping of cadmium accumulation in radish (Raphanus sativus L.).

    PubMed

    Xu, Liang; Wang, Liangju; Gong, Yiqin; Dai, Wenhao; Wang, Yan; Zhu, Xianwen; Wen, Tiancai; Liu, Liwang

    2012-08-01

    Cadmium (Cd) is a widespread soil pollutant and poses a significant threat to human health via the food chain. Large phenotypic variations in Cd concentration of radish roots and shoots have been observed. However, the genetic and molecular mechanisms of Cd accumulation in radish remain to be elucidated. In this study, a genetic linkage map was constructed using an F(2) mapping population derived from a cross between a high Cd-accumulating cultivar NAU-Dysx and a low Cd-accumulating cultivar NAU-Yh. The linkage map consisted of 523 SRAP, RAPD, SSR, ISSR, RAMP, and RGA markers and had a total length of 1,678.2 cM with a mean distance of 3.4 cM between two markers. All mapped markers distributed on nine linkage groups (LGs) having sizes between 134.7 and 236.8 cM. Four quantitative trait loci (QTLs) for root Cd accumulation were mapped on LGs 1, 4, 6, and 9, which accounted for 9.86 to 48.64 % of all phenotypic variance. Two QTLs associated with shoot Cd accumulation were detected on LG1 and 3, which accounted for 17.08 and 29.53 % of phenotypic variance, respectively. A major-effect QTL, qRCd9 (QTL for root Cd accumulation on LG9), was identified on LG 9 flanked by NAUrp011_754 and EM5me6_286 markers with a high LOD value of 23.6, which accounted for 48.64 % of the total phenotypic variance in Cd accumulation of F(2) lines. The results indicated that qRCd9 is a novel QTL responsible for controlling root Cd accumulation in radish, and the identification of specific molecular markers tightly linked to the major QTL could be further applied for marker-assisted selection (MAS) in low-Cd content radish breeding program.

  8. A Tomato Peroxidase Involved in the Synthesis of Lignin and Suberin1

    PubMed Central

    Quiroga, Mónica; Guerrero, Consuelo; Botella, Miguel A.; Barceló, Araceli; Amaya, Iraida; Medina, María I.; Alonso, Francisco J.; de Forchetti, Silvia Milrad; Tigier, Horacio; Valpuesta, Victoriano

    2000-01-01

    The last step in the synthesis of lignin and suberin has been proposed to be catalyzed by peroxidases, although other proteins may also be involved. To determine which peroxidases are involved in the synthesis of lignin and suberin, five peroxidases from tomato (Lycopersicon esculentum) roots, representing the majority of the peroxidase activity in this organ, have been partially purified and characterized kinetically. The purified peroxidases with isoelectric point (pI) values of 3.6 and 9.6 showed the highest catalytic efficiency when the substrate used was syringaldazine, an analog of lignin monomer. Using a combination of transgenic expression and antibody recognition, we now show that the peroxidase pI 9.6 is probably encoded by TPX1, a tomato peroxidase gene we have previously isolated. In situ RNA hybridization revealed that TPX1 expression is restricted to cells undergoing synthesis of lignin and suberin. Salt stress has been reported to induce the synthesis of lignin and/or suberin. This stress applied to tomato caused changes in the expression pattern of TPX1 and induced the TPX1 protein. We propose that the TPX1 product is involved in the synthesis of lignin and suberin. PMID:10759507

  9. Characterization of electrospun lignin based carbon fibers

    NASA Astrophysics Data System (ADS)

    Poursorkhabi, Vida; Mohanty, Amar; Misra, Manjusri

    2015-05-01

    The production of lignin fibers has been studied in order to replace the need for petroleum based precursors for carbon fiber production. In addition to its positive environmental effects, it also benefits the economics of the industries which cannot take advantage of carbon fiber properties because of their high price. A large amount of lignin is annually produced as the byproduct of paper and growing cellulosic ethanol industry. Therefore, finding high value applications for this low cost, highly available material is getting more attention. Lignin is a biopolymer making about 15 - 30 % of the plant cell walls and has a high carbon yield upon carbonization. However, its processing is challenging due to its low molecular weight and also variations based on its origin and the method of separation from cellulose. In this study, alkali solutions of organosolv lignin with less than 1 wt/v% of poly (ethylene oxide) and two types of lignin (hardwood and softwood) were electrospun followed by carbonization. Different heating programs for carbonization were tested. The carbonized fibers had a smooth surface with an average diameter of less than 5 µm and the diameter could be controlled by the carbonization process and lignin type. Scanning electron microscopy (SEM) was used to study morphology of the fibers before and after carbonization. Thermal conductivity of a sample with amorphous carbon was 2.31 W/m.K. The electrospun lignin carbon fibers potentially have a large range of application such as in energy storage devices and water or gas purification systems.

  10. Characterization of asparagus lignin by HPLC.

    PubMed

    Jaramillo-Carmona, S; Fuentes-Alventosa, J M; Rodríguez-Gutiérrez, G; Waldron, K W; Smith, A C; Guillén-Bejarano, R; Fernández-Bolaños, J; Jiménez-Araujo, A; Rodríguez-Arcos, R

    2008-09-01

    Lignin is the cell wall component most frequently associated with hardening. Its characterization and quantification are very important to understand the biochemical modifications related to the changes in texture of vegetables such as asparagus (Asparagus officinalis), in which this organoleptic attribute is a very important quality factor. In this study, asparagus lignin from the basal sections of fresh and stored spears was analyzed using 2 methods, the traditional (Klason lignin) and the recently developed derivatization, followed by reductive cleavage (DFRC) method. The latter is a simple and reproducible technique for lignin characterization based on a degradation procedure that produces analyzable monomers and dimers by cleaving alpha- and beta-aryl ethers in lignins. The primary monomers derived from DFRC degradation of lignins are essentially p-coumaryl peracetate, coniferyl peracetate, and sinapyl peracetate. To evaluate the efficiency of the DFRC method, our investigations have been carried on distinct sample types, including wood (data not shown), straw, and asparagus samples. The results have confirmed that lignin composition is affected by plant nature. It has been found that whereas wood samples mostly contain coniferyl units, plant foods, such as straw and asparagus, contain both coniferyl and guaiacyl units. PMID:18803697

  11. Challenging/interesting lignin times

    DOE PAGES

    Ragauskas, Arthur J.

    2016-08-31

    Anyone who is working in the fuels industry knows that we are living in challenging times. On a personal note, I recall that ~5 years ago, some of my children's friends headed out into the petroleum industry to start their careers and several have now returned because of the retrenching work force. Despite these challenging times, the cellulosic ethanol industry continues to develop commercial operations, but with today's cost structure, biofuels production facilities have certainly slowed their pace of development and roll-out. Furthermore, the biological technology platform for biorefining plant polysaccharides to biofuels has been reported to have an intrinsicmore » advantage, if it can convert its waste lignin stream to value-added components.[1]« less

  12. Pseudo-lignin formation and its impact on enzymatic hydrolysis.

    PubMed

    Hu, Fan; Jung, Seokwon; Ragauskas, Arthur

    2012-08-01

    Pseudo-lignin, which can be broadly defined as aromatic material that yields a positive Klason lignin value and is not derived from native lignin, has been recently reported to form during the dilute acid pretreatment of poplar holocellulose. To investigate the chemistry of pseudo-lignin formation, GPC, FT-IR and 13C NMR were utilized to characterize pseudo-lignin extracted from dilute-acid pretreated α-cellulose and holocellulose. The results showed that pseudo-lignin consisting of carbonyl, carboxylic, aromatic and aliphatic structures was produced from dilute acid pretreated cellulose and hemicellulose. Pseudo-lignin extracted from holocellulose pretreated at different conditions had similar molecular weights (Mn∼1000 g/mol; Mw∼5000 g/mol) and structural features (carbonyl, carboxylic, aromatic and methoxy structures). These characterizations have provided the pseudo-lignin formation mechanisms during pretreatment. The presence and structure of pseudo-lignin is important since pseudo-lignin decreases the enzymatic conversion. PMID:22609707

  13. Microbial conversions of lignin to useful chemicals using a lignin-degrading Streptomyces

    SciTech Connect

    Crawford, D.L.

    1981-01-01

    The lignocellulose-decomposing abilities of an actinomycete, Streptomyces viridosporus T7A, were studied in relation to the potential utilization of this strain for the bioconversion of lignin to useful chemicals. Both carbohydrate and lignin components were degraded. The grass and corn lignocelluloses were degraded much more extensively than the spruce and maple lignocelluloses; therefore the former were considered preferable as substrates for bioconversion. Both inoculated and control culture supernatants contained solvent extractible, phenolic, lignin-derived compounds with recoveries ranging between 3.1 and 12.2% of the initial lignin substrate. Lignin fragments that were identified included p-hydroxybenzoic acid, vanillic acid, protocatechuic acid, p-coumaric acid, syringic acid, ferulic acid, and the ketol (1-hydroxy-3-(4-hydroxy-3-methoxyphenyl)-2-propanone). The potential for using S. viridosporus in lignin to chemical bioconversions was discussed.

  14. Lignin Sensor Based On Flash-Pyrolysis Mass Spectrometry

    NASA Technical Reports Server (NTRS)

    Kwack, Eug Y.; Lawson, Daniel D.; Shakkottai, Parthasarathy

    1990-01-01

    New lignin sensor takes only few minutes to measure lignin content of specimen of wood, pulp, paper, or similar material. Includes flash pyrolizer and ion-trap detector that acts as mass spectrometer. Apparatus measures amount of molecular fragments of lignin in pyrolysis products of samples. Helpful in controlling digestors in paper mills to maintain required lignin content, and also in bleaching plants, where good control of bleaching becomes possible if quick determination of lignin content made.

  15. Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.).

    PubMed

    Lee, Gyu-Ho; Kang, In-Kyu; Kim, Kyung-Min

    2016-01-01

    The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH) population of rice (Oryza sativa L.). A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interval of 9.6 cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS) were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1 Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning. PMID:27419124

  16. A global search reveals epistatic interaction between QTL for early growth in the chicken.

    PubMed

    Carlborg, Orjan; Kerje, Susanne; Schütz, Karin; Jacobsson, Lina; Jensen, Per; Andersson, Leif

    2003-03-01

    We have identified quantitative trait loci (QTL) explaining a large proportion of the variation in body weights at different ages and growth between chronological ages in an F(2) intercross between red junglefowl and White Leghorn chickens. QTL were mapped using forward selection for loci with significant marginal genetic effects and with a simultaneous search for epistatic QTL pairs. We found 22 significant loci contributing to these traits, nine of these were only found by the simultaneous two-dimensional search, which demonstrates the power of this approach for detecting loci affecting complex traits. We have also estimated the relative contribution of additive, dominance, and epistasis effects to growth and the contribution of epistasis was more pronounced prior to 46 days of age, whereas additive genetic effects explained the major portion of the genetic variance later in life. Several of the detected loci affected either early or late growth but not both. Very few loci affected the entire growth process, which points out that early and late growth, at least to some extent, have different genetic regulation. PMID:12618372

  17. Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.)

    PubMed Central

    Lee, Gyu-Ho; Kang, In-Kyu

    2016-01-01

    The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH) population of rice (Oryza sativa L.). A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interval of 9.6 cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS) were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1 Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning. PMID:27419124

  18. QTL affecting fitness of hybrids between wild and cultivated soybeans in experimental fields.

    PubMed

    Kuroda, Yosuke; Kaga, Akito; Tomooka, Norihiko; Yano, Hiroshi; Takada, Yoshitake; Kato, Shin; Vaughan, Duncan

    2013-07-01

    The objective of this study was to identify quantitative trait loci (QTL) affecting fitness of hybrids between wild soybean (Glycine soja) and cultivated soybean (Glycine max). Seed dormancy and seed number, both of which are important for fitness, were evaluated by testing artificial hybrids of G. soja × G. max in a multiple-site field trial. Generally, the fitness of the F1 hybrids and hybrid derivatives from self-pollination was lower than that of G. soja due to loss of seed dormancy, whereas the fitness of hybrid derivatives with higher proportions of G. soja genetic background was comparable with that of G. soja. These differences were genetically dissected into QTL for each population. Three QTLs for seed dormancy and one QTL for total seed number were detected in the F2 progenies of two diverse cross combinations. At those four QTLs, the G. max alleles reduced seed number and severely reduced seed survival during the winter, suggesting that major genes acquired during soybean adaptation to cultivation have a selective disadvantage in natural habitats. In progenies with a higher proportion of G. soja genetic background, the genetic effects of the G. max alleles were not expressed as phenotypes because the G. soja alleles were dominant over the G. max alleles. Considering the highly inbreeding nature of these species, most hybrid derivatives would disappear quickly in early self-pollinating generations in natural habitats because of the low fitness of plants carrying G. max alleles.

  19. Genetic and QTL analysis of resistance to Xiphinema index in a grapevine cross.

    PubMed

    Xu, K; Riaz, S; Roncoroni, N C; Jin, Y; Hu, R; Zhou, R; Walker, M A

    2008-01-01

    Resistance to the dagger nematode Xiphinema index has been an important objective in grape rootstock breeding programs. This nematode not only causes severe feeding damage to the root system, but it also vectors grapevine fanleaf virus (GFLV), the causal agent of fanleaf degeneration and one of the most severe viral diseases of grape. The established screening procedures for dagger nematode resistance are time consuming and can produce inconsistent results. A fast and reliable greenhouse-based system for screening resistance to X. index that is suitable for genetic studies and capable of evaluating breeding populations is needed. In this report, the dynamics of nematode numbers, gall formation, and root weight loss were investigated using a variety of soil mixes and pot sizes over a 52-week period. Results indicated that the number of galls formed was correlated with the size of the nematode population and with the degree of root weight loss. After inoculation with 100 nematodes, gall formation could be reliably evaluated in 4-8 weeks in most plant growth conditions and results were obtained 6 months more rapidly than past evaluation methods. This modified X. index resistance screening method was successfully applied to 185 of the 188 F(1) progeny from a cross of D8909-15 x F8909-17 (the 9621 population), which segregates for a form of X. index resistance originally derived from Vitis arizonica. Quantitative trait loci (QTL) analysis was carried out on both parental genetic maps of 255 markers using MapQTL 4.0. Results revealed that X. index resistance is controlled by a major QTL, designated Xiphinema index Resistance 1 (XiR1), near marker VMC5a10 on chromosome 19. The XiR1 QTL was supported by a LOD score of 36.9 and explained 59.9% of the resistance variance in the mapping population.

  20. QTL analysis of pasta quality using a composite microsatellite and SNP map of durum wheat.

    PubMed

    Zhang, W; Chao, S; Manthey, F; Chicaiza, O; Brevis, J C; Echenique, V; Dubcovsky, J

    2008-11-01

    Bright yellow color, firmness and low cooking loss are important factors for the production of good-quality pasta products. However, the genetic factors underlying those traits are still poorly understood. To fill this gap we developed a population of 93 recombinant inbred lines (RIL) from the cross between experimental line UC1113 (intermediate pasta quality) with the cultivar Kofa (excellent pasta quality). A total of 269 markers, including 23 SNP markers, were arranged on 14 linkage groups covering a total length of 2,140 cM. Samples from each RIL from five different environments were used for complete pasta quality testing and the results from each year were used for QTL analyses. The combined effect of different loci, environment and their interactions were analyzed using factorial ANOVAs for each trait. We identified major QTLs for pasta color on chromosomes 1B, 4B, 6A, 7A and 7B. The 4B QTL was linked to a polymorphic deletion in the Lpx-B1.1 lipoxygenase locus, suggesting that it was associated with pigment degradation during pasta processing. The 7B QTL for pasta color was linked to the Phytoene synthase 1 (Psy-B1) locus suggesting difference in pigment biosynthesis. QTLs affecting pasta firmness and cooking loss were detected on chromosomes 5A and 7B, and in both cases they were overlapping with QTL for grain protein content and wet gluten content. These last two parameters were highly correlated with pasta firmness (R > 0.71) and inversely correlated to cooking loss (R < -0.37). The location and effect of other QTLs affecting grain size and weight, gluten strength, mixing properties, and ash content are also discussed. PMID:18781292

  1. The effect of the Texel muscling QTL (TM-QTL) on meat quality traits in crossbred lambs.

    PubMed

    Lambe, N R; Macfarlane, J M; Richardson, R I; Matika, O; Haresign, W; Bünger, L

    2010-08-01

    A quantitative trait locus (QTL) has been identified on chromosome 18 in Texel sheep (TM-QTL) that increases depth and area of the longissimus dorsi muscle. The study aimed to assess the pleiotropic QTL effects on key meat quality traits (toughness and intramuscular fat content after >or=7 days aging) of crossbred lambs carrying one copy of the TM-QTL. The results showed that male TexelxMule lambs carrying the TM-QTL had significantly less intramuscular fat (1.86% versus 2.25%) and higher toughness, with increased variation, in the loin muscle, compared to non-carrier males. Similar conclusions were obtained using two different types of tenderometer equipment: one using the Volodkevitch test (average shear force of 4.17 kgF or 40.9N for carrier males, 2.61 kgF or 25.6N for non-carrier males) and one using the MIRINZ test (average shear force of 6.18 kgF or 60.6N for carrier males, 5.22 kgF or 51.2N for non-carrier males). Although most toughness measurements were within published consumer acceptability limits, a few individual TM-QTL carrier lambs had unacceptably tough meat, despite enhanced post-slaughter processing. The TM-QTL did not significantly affect loin toughness in female lambs, leg toughness in either sex, or intramuscular fat content. These results should be considered, alongside direct effects of the TM-QTL on muscling and carcass composition, in recommendations for the use of this QTL by sheep breeders. PMID:20416795

  2. Genetic mapping of two QTL from the wild tomato Solanum pimpinellifolium L. controlling resistance against two-spotted spider mite (Tetranychus urticae Koch).

    PubMed

    Salinas, María; Capel, Carmen; Alba, Juan Manuel; Mora, Blanca; Cuartero, Jesús; Fernández-Muñoz, Rafael; Lozano, Rafael; Capel, Juan

    2013-01-01

    A novel source of resistance to two-spotted spider mite (Tetranychus urticae Koch) was found in Solanum pimpinellifolium L. accession TO-937 and thereby a potential source of desirable traits that could be introduced into new tomato varieties. This resistance was found to be controlled by a major locus modulated by minor loci of unknown location in the genome of this wild tomato. We first applied a bulked segregant analysis (BSA) approach in an F(4) population as a method for rapidly identifying a genomic region of 17 cM on chromosome 2, flanked by two simple sequence repeat markers, harboring Rtu2.1, one of the major QTL involved in the spider mite resistance. A population of 169 recombinant inbred lines was also evaluated for spider mite infestation and a highly saturated genetic map was developed from this population. QTL mapping corroborated that chromosome 2 harbored the Rtu2.1 QTL in the same region that our previous BSA findings pointed out, but an even more robust QTL was found in the telomeric region of this chromosome. This QTL, we termed Rtu2.2, had a LOD score of 15.43 and accounted for more than 30% of the variance of two-spotted spider mite resistance. Several candidate genes involved in trichome formation, synthesis of trichomes exudates and plant defense signaling have been sequenced. However, either the lack of polymorphisms between the parental lines or their map position, away from the QTL, led to their rejection as candidate genes responsible for the two-spotted spider mite resistance. The Rtu2 QTL not only serve as a valuable target for marker-assisted selection of new spider mite-resistant tomato varieties, but also as a starting point for a better understanding of the molecular genetic functions underlying the resistance to this pest.

  3. Association of sugar content QTL and PQL with physiological traits relevant to frost damage resistance in pea under field and controlled conditions.

    PubMed

    Dumont, Estelle; Fontaine, Véronique; Vuylsteker, Christophe; Sellier, Hélène; Bodèle, Sylvie; Voedts, Najia; Devaux, Rosemonde; Frise, Marlène; Avia, Komlan; Hilbert, Jean-Louis; Bahrman, Nasser; Hanocq, Eric; Lejeune-Hénaut, Isabelle; Delbreil, Bruno

    2009-05-01

    To increase yield in pea (Pisum sativum L.), autumn sowing would be preferable. Hence, frost tolerance of pea became a major trait of interest for breeders. In order to better understand the cold acclimation in pea, Champagne a frost tolerant line and Terese, a frost sensitive line, and their recombinant inbred lines (RIL) were studied. RIL frost tolerance was evaluated by a frost damage scale under field as well as controlled conditions. A quantitative trait loci (QTL) approach was used to identify chromosomal regions linked to frost tolerance. The detected QTL explained from 6.5 to 46.5% of the phenotypic variance. Amongst them, those located on linkage groups 5 and 6 were consistent with over all experiments, in field as well as in controlled environments. In order to improve the understanding of the frost tolerance mechanisms, several cold acclimation key characters such as concentration of sugars, electrolyte leakage, osmotic pressure, and activity of RuBisCO were assessed. Some of these physiological QTL colocalised with QTL for frost damage, in particular two raffinose QTL on LG5 and LG6 and one RuBisCO activity QTL on LG6, explaining 8.8 to 27.0% of the phenotypic variance. In addition, protein quantitative loci were mapped; some of them colocalised with frost damage and physiological QTL on LG5 and LG6, explaining 16.0-43.6% of the phenotypic variance. Raffinose metabolism and RuBisCO activity and its effect on photosynthesis might play a major role in cold acclimation of pea.

  4. Sequestration and Transport of Lignin Monomeric Precursors

    SciTech Connect

    Liu, C.J.; Miao, Y.-C.; Zhang, K.-W.

    2011-01-18

    Lignin is the second most abundant terrestrial biopolymer after cellulose. It is essential for the viability of vascular plants. Lignin precursors, the monolignols, are synthesized within the cytosol of the cell. Thereafter, these monomeric precursors are exported into the cell wall, where they are polymerized and integrated into the wall matrix. Accordingly, transport of monolignols across cell membranes is a critical step affecting deposition of lignin in the secondarily thickened cell wall. While the biosynthesis of monolignols is relatively well understood, our knowledge of sequestration and transport of these monomers is sketchy. In this article, we review different hypotheses on monolignol transport and summarize the recent progresses toward the understanding of the molecular mechanisms underlying monolignol sequestration and transport across membranes. Deciphering molecular mechanisms for lignin precursor transport will support a better biotechnological solution to manipulate plant lignification for more efficient agricultural and industrial applications of cell wall biomass.

  5. Biologically produced acid precipitable polymeric lignin

    DOEpatents

    Crawford, Don L.; Pometto, III, Anthony L.

    1984-01-01

    A water soluble, acid precipitable polymeric degraded lignin (APPL), having a molecular weight of at least 12,000 daltons, and comprising, by percentage of total weight, at least three times the number of phenolic hydroxyl groups and carboxylic acid groups present in native lignin. The APPL may be modified by chemical oxidation and reduction to increase its phenolic hydroxyl content and reduce the number of its antioxidant inhibitory side chains, thereby improving antioxidant properties.

  6. Use of lignin extracted from different plant sources as standards in the spectrophotometric acetyl bromide lignin method.

    PubMed

    Fukushima, Romualdo S; Kerley, Monty S

    2011-04-27

    A nongravimetric acetyl bromide lignin (ABL) method was evaluated to quantify lignin concentration in a variety of plant materials. The traditional approach to lignin quantification required extraction of lignin with acidic dioxane and its isolation from each plant sample to construct a standard curve via spectrophotometric analysis. Lignin concentration was then measured in pre-extracted plant cell walls. However, this presented a methodological complexity because extraction and isolation procedures are lengthy and tedious, particularly if there are many samples involved. This work was targeted to simplify lignin quantification. Our hypothesis was that any lignin, regardless of its botanical origin, could be used to construct a standard curve for the purpose of determining lignin concentration in a variety of plants. To test our hypothesis, lignins were isolated from a range of diverse plants and, along with three commercial lignins, standard curves were built and compared among them. Slopes and intercepts derived from these standard curves were close enough to allow utilization of a mean extinction coefficient in the regression equation to estimate lignin concentration in any plant, independent of its botanical origin. Lignin quantification by use of a common regression equation obviates the steps of lignin extraction, isolation, and standard curve construction, which substantially expedites the ABL method. Acetyl bromide lignin method is a fast, convenient analytical procedure that may routinely be used to quantify lignin.

  7. Chemical factors that control lignin polymerization.

    PubMed

    Sangha, Amandeep K; Davison, Brian H; Standaert, Robert F; Davis, Mark F; Smith, Jeremy C; Parks, Jerry M

    2014-01-01

    Lignin is a complex, branched polymer that reinforces plant tissue. Understanding the factors that govern lignin structure is of central importance to the development of technologies for converting lignocellulosic biomass into fuels because lignin imparts resistance to chemical, enzymatic, and mechanical deconstruction. Lignin is formed by enzymatic oxidation of phenolic monomers (monolignols) of three main types, guaiacyl (G), syringyl (S), and p-hydroxyphenyl (H) subunits. It is known that increasing the relative abundance of H subunits results in lower molecular weight lignin polymers and hence more easily deconstructed biomass, but it is not known why. Here, we report an analysis of frontier molecular orbitals in mono-, di-, and trilignols, calculated using density functional theory, which points to a requirement of strong p-electron density on the reacting phenolic oxygen atom of the neutral precursor for enzymatic oxidation to occur. This model is consistent with a proton-coupled electron transfer (PCET) mechanism and for the first time explains why H subunits in certain linkages (β-β or β-5) react poorly and tend to "cap" the polymer. In general, β-5 linkages with either a G or H terminus are predicted to inhibit elongation. More broadly, the model correctly accounts for the reactivity of the phenolic groups in a diverse set of dilignols comprising H and G subunits. Thus, we provide a coherent framework for understanding the propensity toward growth or termination of different terminal subunits in lignin.

  8. Metagenomic scaffolds enable combinatorial lignin transformation

    PubMed Central

    Strachan, Cameron R.; Singh, Rahul; VanInsberghe, David; Ievdokymenko, Kateryna; Budwill, Karen; Mohn, William W.; Eltis, Lindsay D.; Hallam, Steven J.

    2014-01-01

    Engineering the microbial transformation of lignocellulosic biomass is essential to developing modern biorefining processes that alleviate reliance on petroleum-derived energy and chemicals. Many current bioprocess streams depend on the genetic tractability of Escherichia coli with a primary emphasis on engineering cellulose/hemicellulose catabolism, small molecule production, and resistance to product inhibition. Conversely, bioprocess streams for lignin transformation remain embryonic, with relatively few environmental strains or enzymes implicated. Here we develop a biosensor responsive to monoaromatic lignin transformation products compatible with functional screening in E. coli. We use this biosensor to retrieve metagenomic scaffolds sourced from coal bed bacterial communities conferring an array of lignin transformation phenotypes that synergize in combination. Transposon mutagenesis and comparative sequence analysis of active clones identified genes encoding six functional classes mediating lignin transformation phenotypes that appear to be rearrayed in nature via horizontal gene transfer. Lignin transformation activity was then demonstrated for one of the predicted gene products encoding a multicopper oxidase to validate the screen. These results illuminate cellular and community-wide networks acting on aromatic polymers and expand the toolkit for engineering recombinant lignin transformation based on ecological design principles. PMID:24982175

  9. Chemical factors that control lignin polymerization

    SciTech Connect

    Sangha, Amandeep K; Davison, Brian H; Standaert, Robert F; Davis, Dr. Mark F.; Smith, Jeremy C; Parks, Jerry M

    2014-01-01

    Lignin is a complex, branched polymer that reinforces plant tissue. Understanding the factors that govern lignin structure is of central importance to the development of technologies for converting lignocellulosic biomass into fuels because lignin imparts resistance to chemical, enzymatic and mechanical deconstruction. Lignin is formed by enzymatic oxidation of phenolic monomers (monolignols) of three main types, guaiacyl (G), syringyl (S) and p- hydroxyphenyl (H). It is known that increasing the relative abundance of H subunits results in lower molecular-weight lignin polymers, and hence more easily deconstructed biomass, but it is not known why. Here, we report an analysis of frontier molecular orbitals in mono-, di- and trilignols, calculated using density functional theory, which points to a requirement of strong p- electron density on the reacting phenolic oxygen atom of the neutral precursor for enzymatic oxidation to occur. This model is consistent with a proton-coupled electron transfer (PCET) mechanism and for the first time explains why H subunits in certain linkages ( - or -5) react poorly and tend to cap the polymer. In general, -5 linkages with either a G or H terminus are predicted to inhibit elongation. More broadly, the model correctly accounts for the reactivity of the phenolic groups in a diverse set of dilignols comprising H and G subunits. Thus, we provide a coherent framework for understanding the propensity toward growth or termination of different terminal subunits in lignin.

  10. eQTL Mapping Using RNA-seq Data

    PubMed Central

    Hu, Yijuan

    2012-01-01

    As RNA-seq is replacing gene expression microarrays to assess genome-wide transcription abundance, gene expression Quantitative Trait Locus (eQTL) studies using RNA-seq have emerged. RNA-seq delivers two novel features that are important for eQTL studies. First, it provides information on allele-specific expression (ASE), which is not available from gene expression microarrays. Second, it generates unprecedentedly rich data to study RNA-isoform expression. In this paper, we review current methods for eQTL mapping using ASE and discuss some future directions. We also review existing works that use RNA-seq data to study RNA-isoform expression and we discuss the gaps between these works and isoform-specific eQTL mapping. PMID:23667399

  11. Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model.

    PubMed

    Bogard, Matthieu; Ravel, Catherine; Paux, Etienne; Bordes, Jacques; Balfourier, François; Chapman, Scott C; Le Gouis, Jacques; Allard, Vincent

    2014-11-01

    Prediction of wheat phenology facilitates the selection of cultivars with specific adaptations to a particular environment. However, while QTL analysis for heading date can identify major genes controlling phenology, the results are limited to the environments and genotypes tested. Moreover, while ecophysiological models allow accurate predictions in new environments, they may require substantial phenotypic data to parameterize each genotype. Also, the model parameters are rarely related to all underlying genes, and all the possible allelic combinations that could be obtained by breeding cannot be tested with models. In this study, a QTL-based model is proposed to predict heading date in bread wheat (Triticum aestivum L.). Two parameters of an ecophysiological model (V sat and P base , representing genotype vernalization requirements and photoperiod sensitivity, respectively) were optimized for 210 genotypes grown in 10 contrasting location × sowing date combinations. Multiple linear regression models predicting V sat and P base with 11 and 12 associated genetic markers accounted for 71 and 68% of the variance of these parameters, respectively. QTL-based V sat and P base estimates were able to predict heading date of an independent validation data set (88 genotypes in six location × sowing date combinations) with a root mean square error of prediction of 5 to 8.6 days, explaining 48 to 63% of the variation for heading date. The QTL-based model proposed in this study may be used for agronomic purposes and to assist breeders in suggesting locally adapted ideotypes for wheat phenology.

  12. Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model

    PubMed Central

    Bogard, Matthieu; Ravel, Catherine; Paux, Etienne; Bordes, Jacques; Balfourier, François; Chapman, Scott C.; Le Gouis, Jacques; Allard, Vincent

    2014-01-01

    Prediction of wheat phenology facilitates the selection of cultivars with specific adaptations to a particular environment. However, while QTL analysis for heading date can identify major genes controlling phenology, the results are limited to the environments and genotypes tested. Moreover, while ecophysiological models allow accurate predictions in new environments, they may require substantial phenotypic data to parameterize each genotype. Also, the model parameters are rarely related to all underlying genes, and all the possible allelic combinations that could be obtained by breeding cannot be tested with models. In this study, a QTL-based model is proposed to predict heading date in bread wheat (Triticum aestivum L.). Two parameters of an ecophysiological model (V sat and P base, representing genotype vernalization requirements and photoperiod sensitivity, respectively) were optimized for 210 genotypes grown in 10 contrasting location × sowing date combinations. Multiple linear regression models predicting V sat and P base with 11 and 12 associated genetic markers accounted for 71 and 68% of the variance of these parameters, respectively. QTL-based V sat and P base estimates were able to predict heading date of an independent validation data set (88 genotypes in six location × sowing date combinations) with a root mean square error of prediction of 5 to 8.6 days, explaining 48 to 63% of the variation for heading date. The QTL-based model proposed in this study may be used for agronomic purposes and to assist breeders in suggesting locally adapted ideotypes for wheat phenology. PMID:25148833

  13. Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes

    PubMed Central

    Ferguson, Moira M.; Danzmann, Roy G.

    2013-01-01

    Osmoregulatory capabilities have played an important role in the evolution, dispersal, and diversification of vertebrates. To better understand the genetic architecture of hypo-osmoregulation in fishes and to determine which genes and biological processes affect intraspecific variation in salinity tolerance, we used mRNA sequence libraries from Arctic charr gill tissue to compare gene expression profiles in fish exhibiting divergent salinity tolerance quantitative trait locus (QTL) genotypes. We compared differentially expressed genes with QTL positions to gain insight about the nature of the underlying polymorphisms and examined gene expression within the context of genome organization to gain insight about the evolution of hypo-osmoregulation in fishes. mRNA sequencing of 18 gill tissue libraries produced 417 million reads, and the final reduced de novo transcriptome assembly consisted of 92,543 contigs. Families contained a similar number of differentially expressed contigs between high and low salinity tolerance capacity groups, and log2 expression ratios ranged from 10.4 to −8.6. We found that intraspecific variation in salinity tolerance capacity correlated with differential expression of immune response genes. Some differentially expressed genes formed clusters along linkage groups. Most clusters comprised gene pairs, though clusters of three, four, and eight genes were also observed. We postulated that conserved synteny of gene clusters on multiple ancestral and teleost chromosomes may have been preserved via purifying selection. Colocalization of QTL with differentially expressed genes suggests that polymorphisms in cis-regulatory elements are part of a majority of QTL. PMID:24368751

  14. Systems genetics, bioinformatics and eQTL mapping.

    PubMed

    Li, Hong; Deng, Hongwen

    2010-10-01

    Jansen and Nap (Trends Genet 17(7):388-391, 2001) and Jansen (Nat Rev Genet 4:145-151, 2003) first proposed the concept of genetical genomics, or genome-wide genetic analysis of gene expression data, which is also called transcriptome mapping. In this approach, microarrays are used for measuring gene expression levels across genetic mapping populations. These gene expression patterns have been used for genome-wide association analysis, an analysis referred to as expression QTL (eQTL) mapping. Recent progress in genomics and experimental biology has brought exponential growth of the biological information available for computational analysis in public genomics databases. Bioinformatics is essential to genome-wide analysis of gene expression data and used as an effective tool for eQTL mapping. The use of Plabsoft database, EcoTILLING, GNARE and FastMap allowed for dramatic reduction of time in genome analysis. Some web-based tools (e.g., Lirnet, eQTL Viewer) provide efficient and intuitive ways for biologists to explore transcriptional regulation patterns, and to generate hypotheses on the genetic basis of transcriptional regulations. Expression quantitative trait loci (eQTL) mapping concerns finding genomic variation to elucidate variation of expression traits. This problem poses significant challenges due to high dimensionality of both the gene expression and the genomic marker data. The core challenges in understanding and explaining eQTL associations are the fine mapping and the lack of mechanistic explanation. But with the development of genetical genomics and computer technology, many new approaches for eQTL mapping will emerge. The statistical methods used for the analysis of expression QTL will become mature in the future.

  15. The acetyl bromide method is faster, simpler and presents best recovery of lignin in different herbaceous tissues than Klason and thioglycolic acid methods.

    PubMed

    Moreira-Vilar, Flavia Carolina; Siqueira-Soares, Rita de Cássia; Finger-Teixeira, Aline; de Oliveira, Dyoni Matias; Ferro, Ana Paula; da Rocha, George Jackson; Ferrarese, Maria de Lourdes L; dos Santos, Wanderley Dantas; Ferrarese-Filho, Osvaldo

    2014-01-01

    We compared the amount of lignin as determined by the three most traditional methods for lignin measurement in three tissues (sugarcane bagasse, soybean roots and soybean seed coat) contrasting for lignin amount and composition. Although all methods presented high reproducibility, major inconsistencies among them were found. The amount of lignin determined by thioglycolic acid method was severely lower than that provided by the other methods (up to 95%) in all tissues analyzed. Klason method was quite similar to acetyl bromide in tissues containing higher amounts of lignin, but presented lower recovery of lignin in the less lignified tissue. To investigate the causes of the inconsistencies observed, we determined the monomer composition of all plant materials, but found no correlation. We found that the low recovery of lignin presented by the thioglycolic acid method were due losses of lignin in the residues disposed throughout the procedures. The production of furfurals by acetyl bromide method does not explain the differences observed. The acetyl bromide method is the simplest and fastest among the methods evaluated presenting similar or best recovery of lignin in all the tissues assessed.

  16. Accurate and reproducible determination of lignin molar mass by acetobromination.

    PubMed

    Asikkala, Janne; Tamminen, Tarja; Argyropoulos, Dimitris S

    2012-09-12

    The accurate and reproducible determination of lignin molar mass by using size exclusion chromatography (SEC) is challenging. The lignin association effects, known to dominate underivatized lignins, have been thoroughly addressed by reaction with acetyl bromide in an excess of glacial acetic acid. The combination of a concerted acetylation with the introduction of bromine within the lignin alkyl side chains is thought to be responsible for the observed excellent solubilization characteristics acetobromination imparts to a variety of lignin samples. The proposed methodology was compared and contrasted to traditional lignin derivatization methods. In addition, side reactions that could possibly be induced under the acetobromination conditions were explored with native softwood (milled wood lignin, MWL) and technical (kraft) lignin. These efforts lend support toward the use of room temperature acetobromination being a facile, effective, and universal lignin derivatization medium proposed to be employed prior to SEC measurements. PMID:22870925

  17. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin.

    PubMed

    Helmich, Kate E; Pereira, Jose Henrique; Gall, Daniel L; Heins, Richard A; McAndrew, Ryan P; Bingman, Craig; Deng, Kai; Holland, Keefe C; Noguera, Daniel R; Simmons, Blake A; Sale, Kenneth L; Ralph, John; Donohue, Timothy J; Adams, Paul D; Phillips, George N

    2016-03-01

    Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50-70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.

  18. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin*

    PubMed Central

    Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.; Heins, Richard A.; McAndrew, Ryan P.; Bingman, Craig; Deng, Kai; Holland, Keefe C.; Noguera, Daniel R.; Simmons, Blake A.; Sale, Kenneth L.; Ralph, John; Donohue, Timothy J.; Adams, Paul D.; Phillips, George N.

    2016-01-01

    Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin. PMID:26637355

  19. Structural basis of stereospecificity in the bacterial enzymatic cleavage of β-aryl ether bonds in lignin

    DOE PAGES

    Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.; Heins, Richard A.; McAndrew, Ryan P.; Bingman, Craig; Deng, Kai; Holland, Keefe C.; Noguera, Daniel R.; Simmons, Blake A.; et al

    2015-12-04

    Here, lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, wemore » present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.« less

  20. Structural basis of stereospecificity in the bacterial enzymatic cleavage of β-aryl ether bonds in lignin

    SciTech Connect

    Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.; Heins, Richard A.; McAndrew, Ryan P.; Bingman, Craig; Deng, Kai; Holland, Keefe C.; Noguera, Daniel R.; Simmons, Blake A.; Sale, Kenneth L.; Ralph, John; Donohue, Timothy J.; Adams, Paul D.; Phillips, George N.

    2015-12-04

    Here, lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.

  1. QTL fine mapping with Bayes C(π): a simulation study

    PubMed Central

    2013-01-01

    Background Accurate QTL mapping is a prerequisite in the search for causative mutations. Bayesian genomic selection models that analyse many markers simultaneously should provide more accurate QTL detection results than single-marker models. Our objectives were to (a) evaluate by simulation the influence of heritability, number of QTL and number of records on the accuracy of QTL mapping with Bayes Cπ and Bayes C; (b) estimate the QTL status (homozygous vs. heterozygous) of the individuals analysed. This study focussed on the ten largest detected QTL, assuming they are candidates for further characterization. Methods Our simulations were based on a true dairy cattle population genotyped for 38 277 phased markers. Some of these markers were considered biallelic QTL and used to generate corresponding phenotypes. Different numbers of records (4387 and 1500), heritability values (0.1, 0.4 and 0.7) and numbers of QTL (10, 100 and 1000) were studied. QTL detection was based on the posterior inclusion probability for individual markers, or on the sum of the posterior inclusion probabilities for consecutive markers, estimated using Bayes C or Bayes Cπ. The QTL status of the individuals was derived from the contrast between the sums of the SNP allelic effects of their chromosomal segments. Results The proportion of markers with null effect (π) frequently did not reach convergence, leading to poor results for Bayes Cπ in QTL detection. Fixing π led to better results. Detection of the largest QTL was most accurate for medium to high heritability, for low to moderate numbers of QTL, and with a large number of records. The QTL status was accurately inferred when the distribution of the contrast between chromosomal segment effects was bimodal. Conclusions QTL detection is feasible with Bayes C. For QTL detection, it is recommended to use a large dataset and to focus on highly heritable traits and on the largest QTL. QTL statuses were inferred based on the distribution of the

  2. Genetic control of soybean seed oil: I. QTL and genes associated with seed oil concentration in RIL populations derived from crossing moderately high-oil parents.

    PubMed

    Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

    2013-02-01

    Soybean seed is a major source of oil for human consumption worldwide and the main renewable feedstock for biodiesel production in North America. Increasing seed oil concentration in soybean [Glycine max (L.) Merrill] with no or minimal impact on protein concentration could be accelerated by exploiting quantitative trait loci (QTL) or gene-specific markers. Oil concentration in soybean is a polygenic trait regulated by many genes with mostly small effects and which is negatively associated with protein concentration. The objectives of this study were to discover and validate oil QTL in two recombinant inbred line (RIL) populations derived from crosses between three moderately high-oil soybean cultivars, OAC Wallace, OAC Glencoe, and RCAT Angora. The RIL populations were grown across several environments over 2 years in Ontario, Canada. In a population of 203 F(3:6) RILs from a cross of OAC Wallace and OAC Glencoe, a total of 11 genomic regions on nine different chromosomes were identified as associated with oil concentration using multiple QTL mapping and single-factor ANOVA. The percentage of the phenotypic variation accounted for by each QTL ranged from 4 to 11 %. Of the five QTL that were tested in a population of 211 F(3:5) RILs from the cross RCAT Angora × OAC Wallace, a "trait-based" bidirectional selective genotyping analysis validated four QTL (80 %). In addition, a total of seven two-way epistatic interactions were identified for oil concentration in this study. The QTL and epistatic interactions identified in this study could be used in marker-assisted introgression aimed at pyramiding high-oil alleles in soybean cultivars to increase oil concentration for biodiesel as well as edible oil applications.

  3. Characterization of electrospun lignin based carbon fibers

    SciTech Connect

    Poursorkhabi, Vida; Mohanty, Amar; Misra, Manjusri

    2015-05-22

    The production of lignin fibers has been studied in order to replace the need for petroleum based precursors for carbon fiber production. In addition to its positive environmental effects, it also benefits the economics of the industries which cannot take advantage of carbon fiber properties because of their high price. A large amount of lignin is annually produced as the byproduct of paper and growing cellulosic ethanol industry. Therefore, finding high value applications for this low cost, highly available material is getting more attention. Lignin is a biopolymer making about 15 – 30 % of the plant cell walls and has a high carbon yield upon carbonization. However, its processing is challenging due to its low molecular weight and also variations based on its origin and the method of separation from cellulose. In this study, alkali solutions of organosolv lignin with less than 1 wt/v% of poly (ethylene oxide) and two types of lignin (hardwood and softwood) were electrospun followed by carbonization. Different heating programs for carbonization were tested. The carbonized fibers had a smooth surface with an average diameter of less than 5 µm and the diameter could be controlled by the carbonization process and lignin type. Scanning electron microscopy (SEM) was used to study morphology of the fibers before and after carbonization. Thermal conductivity of a sample with amorphous carbon was 2.31 W/m.K. The electrospun lignin carbon fibers potentially have a large range of application such as in energy storage devices and water or gas purification systems.

  4. Effect of replacing polyol by organosolv and kraft lignin on the property and structure of rigid polyurethane foam

    PubMed Central

    2013-01-01

    Background Lignin is one of the three major components in plant cell walls, and it can be isolated (dissolved) from the cell wall in pretreatment or chemical pulping. However, there is a lack of high-value applications for lignin, and the commonest proposal for lignin is power and steam generation through combustion. Organosolv ethanol process is one of the effective pretreatment methods for woody biomass for cellulosic ethanol production, and kraft process is a dominant chemical pulping method in paper industry. In the present research, the lignins from organosolv pretreatment and kraft pulping were evaluated to replace polyol for producing rigid polyurethane foams (RPFs). Results Petroleum-based polyol was replaced with hardwood ethanol organosolv lignin (HEL) or hardwood kraft lignin (HKL) from 25% to 70% (molar percentage) in preparing rigid polyurethane foam. The prepared foams contained 12-36% (w/w) HEL or 9-28% (w/w) HKL. The density, compressive strength, and cellular structure of the prepared foams were investigated and compared. Chain extenders were used to improve the properties of the RPFs. Conclusions It was found that lignin was chemically crosslinked not just physically trapped in the rigid polyurethane foams. The lignin-containing foams had comparable structure and strength up to 25-30% (w/w) HEL or 19-23% (w/w) HKL addition. The results indicated that HEL performed much better in RPFs and could replace more polyol at the same strength than HKL because the former had a better miscibility with the polyol than the latter. Chain extender such as butanediol could improve the strength of lignin-containing RPFs. PMID:23356502

  5. Effect and mode of action of the Texel muscling QTL (TM-QTL) on carcass traits in purebred Texel lambs.

    PubMed

    Macfarlane, J M; Lambe, N R; Matika, O; Johnson, P L; Wolf, B T; Haresign, W; Bishop, S C; Bünger, L

    2014-07-01

    TM-QTL is a quantitative trait locus (QTL) on ovine chromosome 18 (OAR18) known to affect loin muscling in Texel sheep. Previous work suggested that its mode of inheritance is consistent with paternal polar overdominance, but this has yet to be formally demonstrated. This study used purebred Texel sheep segregating for TM-QTL to confirm its presence in the chromosomal region in which it was first reported and to determine its pattern of inheritance. To do so, this study used the first available data from a Texel flock, which included homozygote TM-QTL carriers (TM/TM; n=34) in addition to homozygote non-carriers (+/+; n=40 and, heterozygote TM-QTL-carriers inheriting TM-QTL from their sire (TM/+; n=53) or their dam (+/TM; n=17). Phenotypes included a wide range of loin muscling, carcass composition and tissue distribution traits. The presence of a QTL affecting ultrasound muscle depth on OAR18 was confirmed with a paternal QTL effect ranging from +0.54 to +2.82 mm UMD (s.e. 0.37 to 0.57 mm) across the sires segregating for TM-QTL. Loin muscle width, depth and area, loin muscle volume and dissected M. longissimus lumborum weight were significantly greater for TM/+ than +/+ lambs (+2.9% to +7.9%; P<0.05). There was significant evidence that the effect of TM-QTL on the various loin muscling traits measured was paternally polar overdominant (P<0.05). In contrast, there was an additive effect of TM-QTL on both live weight at 20 weeks and carcass weight; TM/TM animals were significantly (P<0.05) heavier than +/+ (+11.1% and +7.3%, respectively) and +/TM animals (+11.9% and +11.7%, respectively), with TM/+ intermediate. Weights of the leg, saddle and shoulder region (corrected for carcass weight) were similar in the genotypic groups. There was a tendency for lambs inheriting TM-QTL from their sire to be less fat with slightly more muscle than non-carriers. For example, carcass muscle weight measured by live animal CT-scanning was 2.8% higher in TM/TM than +/+ lambs (P<0

  6. Detection of quantitative trait loci (QTL) related to grilsing and late sexual maturation in Atlantic salmon (Salmo salar).

    PubMed

    Gutierrez, Alejandro P; Lubieniecki, Krzysztof P; Fukui, Steve; Withler, Ruth E; Swift, Bruce; Davidson, William S

    2014-02-01

    In Atlantic salmon aquaculture, early sexual maturation represents a major problem for producers. This is especially true for grilse, which mature after one sea winter before reaching a desirable harvest weight, rather than after two sea winters. Salmon maturing as grilse have a much lower market value than later maturing individuals. For this reason, most companies desire fish that grow fast and mature late. Marker-assisted selection has the potential to improve the efficiency of selection against early maturation and for late sexual maturation; however, studies identifying age of sexual maturation-related genetic markers are lacking for Atlantic salmon. Therefore, we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype five families from the Mainstream Canada broodstock program and search for SNPs associated with early (grilsing) or late sexual maturation. There were 529 SNP loci that were variable across all five families, and this was the set that was used for quantitative trait loci (QTL) analysis. GridQTL identified two chromosomes, Ssa10 and Ssa21, containing QTL related to grilsing. In contrast, only one QTL, on Ssa18, was found linked to late maturation in Atlantic salmon. Our previous work on these five families did not identify genome-wide significant growth-related QTL on Ssa10, Ssa21, or Ssa18. Therefore, taken together, these results suggest that both grilsing and late sexual maturation are controlled independently of one another and also from growth-related traits. The identification of genomic regions associated with grilsing or late sexual maturation provide an opportunity to incorporate this information into selective breeding programs that will enhance Atlantic salmon farming. PMID:23912817

  7. Genetic analysis of QTL for eye cross and eye diameter in common carp (Cyprinus carpio L.) using microsatellites and SNPs.

    PubMed

    Jin, S B; Zhang, X F; Lu, J G; Fu, H T; Jia, Z Y; Sun, X W

    2015-04-17

    A group of 107 F1 hybrid common carp was used to construct a linkage map using JoinMap 4.0. A total of 4877 microsatellite and single nucleotide polymorphism (SNP) markers isolated from a genomic library (978 microsatellite and 3899 SNP markers) were assigned to construct the genetic map, which comprised 50 linkage groups. The total length of the linkage map for the common carp was 4775.90 cM with an average distance between markers of 0.98 cM. Ten quantitative trait loci (QTL) were associated with eye diameter, corresponding to 10.5-57.2% of the total phenotypic variation. Twenty QTL were related to eye cross, contributing to 10.8-36.9% of the total phenotypic variation. Two QTL for eye diameter and four QTL for eye cross each accounted for more than 20% of the total phenotypic variation and were considered to be major QTL. One growth factor related to eye diameter was observed on LG10 of the common carp genome, and three growth factors related to eye cross were observed on LG10, LG35, and LG44 of the common carp genome. The significant positive relationship of eye cross and eye diameter with other commercial traits suggests that eye diameter and eye cross can be used to assist in indirect selection for many commercial traits, particularly body weight. Thus, the growth factor for eye cross may also contribute to the growth of body weight, implying that aggregate breeding could have multiple effects. These findings provide information for future genetic studies and breeding of common carp.

  8. Lignin composition in cambial tissues of poplar.

    PubMed

    Christiernin, M

    2006-01-01

    The cambial tissues of a Populus balsamifera, Balsam poplar clone were studied during a growth season. The Klason and acid-soluble lignin contents were determined as well as the carbohydrate monomer distribution and the protein content. Both the phloem and the xylem sides of the cambial region were examined. The samples were analyzed by thioacidolysis and structures of dimeric products were determined by mass spectrometry after desulphuration. Chemical analysis of samples during the growth season was combined with microscopy of embedded specimens that showed the state of cell differentiation at the time of sampling. In spring and early summer, growth is very rapid and the intention was to collect tissue in which exclusively the middle lamella/primary cell wall had begun to lignify. The Klason lignin, protein content and carbohydrate monomer distribution showed that all the specimens from the cambial tissues sampled during a growth season contained predominantly middle lamella and primary walls; except for the developing xylem sampled in August where the carbohydrate composition showed that secondary walls were present. Thioacidolysis showed that the lignin from the cambial tissues had more condensed structures than the lignin from the reference balsam poplar clone wood. More guaiacyl than syringyl units were detected and mass spectrometry showed that the cambial tissues contained more lignin structures with end-groups than the reference sample. These results suggest that lignification in the cambial layer and early developing xylem may take place predominantly in a bulk fashion during the summer.

  9. New perspective on glycoside hydrolase binding to lignin from pretreated corn stover

    DOE PAGES

    Yarbrough, John M.; Mittal, Ashutosh; Mansfield, Elisabeth; Taylor, II, Larry E.; Hobdey, Sarah E.; Sammond, Deanne W.; Bomble, Yannick J.; Crowley, Michael F.; Decker, Stephen R.; Himmel, Michael E.; et al

    2015-12-18

    In this study, non-specific binding of cellulases to lignin has been implicated as a major factor in the loss of cellulase activity during biomass conversion to sugars. It is believed that this binding may strongly impact process economics through loss of enzyme activities during hydrolysis and enzyme recycling scenarios. The current model suggests glycoside hydrolase activities are lost though non-specific/non-productive binding of carbohydrate-binding domains to lignin, limiting catalytic site access to the carbohydrate components of the cell wall.

  10. Combinatorial modification of multiple lignin traits in trees through multigene cotransformation

    PubMed Central

    Li, Laigeng; Zhou, Yihua; Cheng, Xiaofei; Sun, Jiayan; Marita, Jane M.; Ralph, John; Chiang, Vincent L.

    2003-01-01

    Lignin quantity and reactivity [which is associated with its syringyl/guaiacyl (S/G) constituent ratio] are two major barriers to wood-pulp production. To verify our contention that these traits are regulated by distinct monolignol biosynthesis genes, encoding 4-coumarate–CoA ligase (4CL) and coniferaldehyde 5-hydroxylase (CAld5H), we used Agrobacterium to cotransfer antisense 4CL and sense CAld5H genes into aspen (Populus tremuloides). Trees expressing each one and both of the transgenes were produced with high efficiency. Lignin reduction by as much as 40% with 14% cellulose augmentation was achieved in antisense 4CL plants; S/G-ratio increases as much as 3-fold were observed without lignin quantity change in sense CAld5H plants. Consistent with our contention, these effects were independent but additive, with plants expressing both transgenes having up to 52% less lignin, a 64% higher S/G ratio, and 30% more cellulose. An S/G-ratio increase also accelerated cell maturation in stem secondary xylem, pointing to a role for syringyl lignin moieties in coordinating xylem secondary wall biosynthesis. The results suggest that this multigene cotransfer system should be broadly useful for plant genetic engineering and functional genomics. PMID:12668766

  11. Large-Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content.

    PubMed

    Vicentini, Renato; Bottcher, Alexandra; Brito, Michael Dos Santos; Dos Santos, Adriana Brombini; Creste, Silvana; Landell, Marcos Guimarães de Andrade; Cesarino, Igor; Mazzafera, Paulo

    2015-01-01

    Sugarcane is an important crop worldwide for sugar and first generation ethanol production. Recently, the residue of sugarcane mills, named bagasse, has been considered a promising lignocellulosic biomass to produce the second-generation ethanol. Lignin is a major factor limiting the use of bagasse and other plant lignocellulosic materials to produce second-generation ethanol. Lignin biosynthesis pathway is a complex network and changes in the expression of genes of this pathway have in general led to diverse and undesirable impacts on plant structure and physiology. Despite its economic importance, sugarcane genome was still not sequenced. In this study a high-throughput transcriptome evaluation of two sugarcane genotypes contrasting for lignin content was carried out. We generated a set of 85,151 transcripts of sugarcane using RNA-seq and de novo assembling. More than 2,000 transcripts showed differential expression between the genotypes, including several genes involved in the lignin biosynthetic pathway. This information can give valuable knowledge on the lignin biosynthesis and its interactions with other metabolic pathways in the complex sugarcane genome.

  12. Leucaena leucocephala (Lam.) de Wit., "subabul" stem lignin: Isolation, structural characterization and thermal properties.

    PubMed

    Yearla, Srinivasa Rao; Padmasree, Kollipara

    2016-06-01

    Lignin is the second most abundant renewable biopolymer on earth after cellulose. It is being used in many industrial applications due to its abundance. In the present study, lignin was isolated from the stems of Leucaena leucocephala (Lam.) de Wit., a high biomass yielding plant using acidic dioxane under N2 atmosphere. Structural characterization of isolated dioxane lignin (DL) was performed by analytical techniques: UV, FT-IR, ¹H NMR and ¹³C NMR. Their monolignol content was determined by nitrobenzene oxidation followed by HPLC-MS/MS analysis. The data was compared with commercial alkali lignin (AL). The results showed that DL is of hardwood guaiacyl-syringyl (GS) type, whereas AL is softwood type with more guaiacyl units and trace amounts of p-hydroxyphenyl units (H). Thermogravimetric analysis (TGA) of DL showed two stage thermal degradation profile similar to AL. The DTGmax for DL and AL were found in the second major loss event of second stage of TGA at 424°C and 404°C, respectively. Differential scanning calorimetry (DSC) study exhibited the glass transition temperatures (Tg) at 132°C and 122°C for DL and AL, respectively. The results from thermal stability studies suggest that dioxane lignin isolated from the "miracle tree" (subabul) can be exploited in various thermoplastic industrial applications. PMID:27468468

  13. Large-Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content

    PubMed Central

    Vicentini, Renato; Bottcher, Alexandra; Brito, Michael dos Santos; dos Santos, Adriana Brombini; Creste, Silvana; Landell, Marcos Guimarães de Andrade; Cesarino, Igor; Mazzafera, Paulo

    2015-01-01

    Sugarcane is an important crop worldwide for sugar and first generation ethanol production. Recently, the residue of sugarcane mills, named bagasse, has been considered a promising lignocellulosic biomass to produce the second-generation ethanol. Lignin is a major factor limiting the use of bagasse and other plant lignocellulosic materials to produce second-generation ethanol. Lignin biosynthesis pathway is a complex network and changes in the expression of genes of this pathway have in general led to diverse and undesirable impacts on plant structure and physiology. Despite its economic importance, sugarcane genome was still not sequenced. In this study a high-throughput transcriptome evaluation of two sugarcane genotypes contrasting for lignin content was carried out. We generated a set of 85,151 transcripts of sugarcane using RNA-seq and de novo assembling. More than 2,000 transcripts showed differential expression between the genotypes, including several genes involved in the lignin biosynthetic pathway. This information can give valuable knowledge on the lignin biosynthesis and its interactions with other metabolic pathways in the complex sugarcane genome. PMID:26241317

  14. Effects of N-ammonoxidized lignins amendment on N availability and soil fertility: An incubation study

    NASA Astrophysics Data System (ADS)

    María De la Rosa, José; López-Martín, María; Liebner, Falk; Knicker, Heike

    2013-04-01

    The shift towards a biobased economy will probably generate the application of bioenergy by-products and charred residues to the soil as either amendments or fertilizers. The process of ammonoxidation (application of gaseous oxygen and aqueous ammonia under ambient pressure breaks down aromatic lignin moieties and introduces N in the form of urea, amides and amines), converts lignin, a major by-product of the pulp and paper industry, or other ligneous materials into artificial humic matter (N-lignin). The use of N-ammonoxidized lignin as soil improvers is in theory an economically viable solution, especially interesting for agricultural areas of Mediterranean countries, in which additional factors such as water shortage and fires contribute to declining N availability by lowering nutrient diffusion, litter input or sequestration of N in charred structures. However, limited research has been done to determine how this will influence C and N dynamics and soil fertility. Therefore we performed pot experiments in which a perennial ryegrass (Lolium perenne L.) was grown on a typical Andalusian soil (chromic Luvisol) after amendment of N-lignins highly enriched in 15N (Sarkanda and Indulin ammonoxidized lignins) for 75 days. For comparison, the incubation was also carried out on soils fertilized with 15NO3 and unfertilized (control). The application of ammonoxidized lignins altered the pH and electrical conductivity of the soil. At higher concentrations a retardation of seed germination was evidenced, an observation that needs further considerations before N-enriched technical lignins can be applied in agriculture. After 75 days, the plant shoots from the pots amended with15N-Indulin and 15N-Sarkanda accumulated 8% and 20%, respectively of the initial 15N (15N0). The N was efficiently sequestered from fast release or leaching and most of 15N0 remained in the soil (64%) in the 15N-Indulin pots. In contrast, the 15N-Sarkanda pots showed a lower efficiency in the N

  15. Quantitative trait loci (QTL) associated with resistance to a monogenean parasite (Benedenia seriolae) in yellowtail (Seriola quinqueradiata) through genome wide analysis.

    PubMed

    Ozaki, Akiyuki; Yoshida, Kazunori; Fuji, Kanako; Kubota, Satoshi; Kai, Wataru; Aoki, Jun-ya; Kawabata, Yumi; Suzuki, Junpei; Akita, Kazuki; Koyama, Takashi; Nakagawa, Masahiro; Hotta, Takurou; Tsuzaki, Tatsuo; Okamoto, Nobuaki; Araki, Kazuo; Sakamoto, Takashi

    2013-01-01

    Benedenia infections caused by the monogenean fluke ectoparasite Benedenia seriolae seriously impact marine finfish aquaculture. Genetic variation has been inferred to play a significant role in determining the susceptibility to this parasitic disease. To evaluate the genetic basis of Benedenia disease resistance in yellowtail (Seriola quinqueradiata), a genome-wide and chromosome-wide linkage analyses were initiated using F1 yellowtail families (n = 90 per family) based on a high-density linkage map with 860 microsatellite and 142 single nucleotide polymorphism (SNP) markers. Two major quantitative trait loci (QTL) regions on linkage groups Squ2 (BDR-1) and Squ20 (BDR-2) were identified. These QTL regions explained 32.9-35.5% of the phenotypic variance. On the other hand, we investigated the relationship between QTL for susceptibility to B. seriolae and QTL for fish body size. The QTL related to growth was found on another linkage group (Squ7). As a result, this is the first genetic evidence that contributes to detailing phenotypic resistance to Benedenia disease, and the results will help resolve the mechanism of resistance to this important parasitic infection of yellowtail. PMID:23750223

  16. Fate of Carbohydrates and Lignin during Composting and Mycelium Growth of Agaricus bisporus on Wheat Straw Based Compost.

    PubMed

    Jurak, Edita; Punt, Arjen M; Arts, Wim; Kabel, Mirjam A; Gruppen, Harry

    2015-01-01

    In wheat straw based composting, enabling growth of Agaricus bisporus mushrooms, it is unknown to which extent the carbohydrate-lignin matrix changes and how much is metabolized. In this paper we report yields and remaining structures of the major components. During the Phase II of composting 50% of both xylan and cellulose were metabolized by microbial activity, while lignin structures were unaltered. During A. bisporus' mycelium growth (Phase III) carbohydrates were only slightly consumed and xylan was found to be partially degraded. At the same time, lignin was metabolized for 45% based on pyrolysis GC/MS. Remaining lignin was found to be modified by an increase in the ratio of syringyl (S) to guaiacyl (G) units from 0.5 to 0.7 during mycelium growth, while fewer decorations on the phenolic skeleton of both S and G units remained.

  17. Fate of Carbohydrates and Lignin during Composting and Mycelium Growth of Agaricus bisporus on Wheat Straw Based Compost

    PubMed Central

    Jurak, Edita; Punt, Arjen M.; Arts, Wim; Kabel, Mirjam A.; Gruppen, Harry

    2015-01-01

    In wheat straw based composting, enabling growth of Agaricus bisporus mushrooms, it is unknown to which extent the carbohydrate-lignin matrix changes and how much is metabolized. In this paper we report yields and remaining structures of the major components. During the Phase II of composting 50% of both xylan and cellulose were metabolized by microbial activity, while lignin structures were unaltered. During A. bisporus’ mycelium growth (Phase III) carbohydrates were only slightly consumed and xylan was found to be partially degraded. At the same time, lignin was metabolized for 45% based on pyrolysis GC/MS. Remaining lignin was found to be modified by an increase in the ratio of syringyl (S) to guaiacyl (G) units from 0.5 to 0.7 during mycelium growth, while fewer decorations on the phenolic skeleton of both S and G units remained. PMID:26436656

  18. Incorporation of Epicatechin Esters into Lignin Enhances Cell Wall Fermentability

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Polyphenolic catechin esters are potentially attractive targets for lignin bioengineering because their copolymerization with monolignols could reduce lignin hydrophobicity and cross-linking to polysaccharides, or facilitate delignification by biomass pretreatments. To test this hypothesis, we biomi...

  19. Deconstruction of Lignin Model Compounds and Biomass-Derived Lignin using Layered Double Hydroxide Catalysts

    SciTech Connect

    Chmely, S. C.; McKinney, K. A.; Lawrence, K. R.; Sturgeon, M.; Katahira, R.; Beckham, G. T.

    2013-01-01

    Lignin is an underutilized value stream in current biomass conversion technologies because there exist no economic and technically feasible routes for lignin depolymerization and upgrading. Base-catalyzed deconstruction (BCD) has been applied for lignin depolymerization (e.g., the Kraft process) in the pulp and paper industry for more than a century using aqueous-phase media. However, these efforts require treatment to neutralize the resulting streams, which adds significantly to the cost of lignin deconstruction. To circumvent the need for downstream treatment, here we report recent advances in the synthesis of layered double hydroxide and metal oxide catalysts to be applied to the BCD of lignin. These catalysts may prove more cost-effective than liquid-phase, non-recyclable base, and their use obviates downstream processing steps such as neutralization. Synthetic procedures for various transition-metal containing catalysts, detailed kinetics measurements using lignin model compounds, and results of the application of these catalysts to biomass-derived lignin will be presented.

  20. Fungal biodegradation and enzymatic modification of lignin

    PubMed Central

    Dashtban, Mehdi; Schraft, Heidi; Syed, Tarannum A.; Qin, Wensheng

    2010-01-01

    Lignin, the most abundant aromatic biopolymer on Earth, is extremely recalcitrant to degradation. By linking to both hemicellulose and cellulose, it creates a barrier to any solutions or enzymes and prevents the penetration of lignocellulolytic enzymes into the interior lignocellulosic structure. Some basidiomycetes white-rot fungi are able to degrade lignin efficiently using a combination of extracellular ligninolytic enzymes, organic acids, mediators and accessory enzymes. This review describes ligninolytic enzyme families produced by these fungi that are involved in wood decay processes, their molecular structures, biochemical properties and the mechanisms of action which render them attractive candidates in biotechnological applications. These enzymes include phenol oxidase (laccase) and heme peroxidases [lignin peroxidase (LiP), manganese peroxidase (MnP) and versatile peroxidase (VP)]. Accessory enzymes such as H2O2-generating oxidases and degradation mechanisms of plant cell-wall components in a non-enzymatic manner by production of free hydroxyl radicals (·OH) are also discussed. PMID:21968746

  1. Anaerobic biodegradation of the lignin and polysaccharide components of lignocellulose and synthetic lignin by sediment microflora

    SciTech Connect

    Benner, R.; Maccubbin, A.E.; Hodson, R.E.

    1984-05-01

    Specifically radiolabeled (/sup 14/C-lignin)lignocelluloses and (/sup 14/C-polysaccharide)lignocelluloses were prepared from a variety of marine and freshwater wetland plants including a grass, a sedge, a rush, and a hardwood. These (/sup 14/C)lignocellulose preparations and synthetic (/sup 14/C)lignin were incubated anaerobically with anoxic sediments collected from a salt marsh, a freshwater marsh, and a mangrove swamp. During long-term incubations lasting up to 300 days, the lignin and polysaccharide components of the lignocelluloses were slowly degraded anaerobically to /sup 14/CO/sub 2/ and /sup 14/CH/sub 4/. Lignocelluloses derived from herbaceous plants were degraded more rapidly than lignocellulose derived from the hardwood. After 294 days, 16.9% of the lignin component and 30.0% of the polysaccharide component of lignocellulose derived from the grass used (Spartina alterniflora) were degraded to gaseous end products. In contrast, after 246 days, only 1.5% of the lignin component and 4.1% of the polysaccharide component of lignocellulose derived from the hardwood used (Rhizophora mangle) were degraded to gaseous end products. Synthetic (/sup 14/C) lignin was degraded anaerobically faster than the lignin component of the hardwood lignocellulose; after 276 days 3.7% of the synthetic lignin was degraded to gaseous end products. Contrary to previous reports, these results demonstrate that lignin and lignified plant tissues are biodegradable in the absence of oxygen. Although lignocelluloses are recalcitrant to anaerobic biodegradation, rates of degradation measured in aquatic sediments are significant and have important implications for the biospheric cycling of carbon from these abundant biopolymers. 31 references.

  2. Influence of Lignin modification on PAN-Lignin copolymers as potential carbon fiber precursors

    NASA Astrophysics Data System (ADS)

    Ramasubramanian, Gauri

    Carbon fiber based polymer composites have been recognized as advanced materials for structural applications. The unique reinforcing abilities of carbon fibers with their combination of high strength-to-weight ratio and excellent fatigue resistance have made carbon fiber based composites exceptional compared to other fiber reinforced composites. However, the high cost involved in current precursor materials for carbon fibers has limited the widespread applicability of carbon fibers. Hence, intensification of research efforts towards cheaper and easily available raw material for fabrication of carbon fibers is justified. The growing demand for low cost carbon fibers for mainstream composite applications has driven recent interests in using lignin as alternative choice of material for carbon fiber precursor. Lignin is a highly aromatic, plant-derived amorphous polymer and has been considered as potential low-cost, bio-based carbon fiber precursor. Copolymers of polyacrylonitrile/lignin were developed as alternative precursors for fabrication of raw fibers using conventional solution spinning techniques. Lignin/polyacrylonitrile copolymers were successfully synthesized and characterized using FT-IR and NMR techniques. The thermal properties of the copolymers were studied by DSC and TGA analysis. The effect of chemical modification on the morphology and stability of the carbon fibers from PAN-Lignin copolymers has been studied using Raman Spectroscopy, X-ray Diffraction and Scanning Electron Microscopy. Modification of lignin prior to copolymerization provided a significant advantage in the improvement of precursor processability using solution spinning. Additionally, carbon fibers obtained from copolymers containing different varieties of lignins were examined. Carbon fibers produced from organosolv lignin/polyacrylonitrile copolymers exhibit promising carbon fiber structure when compared to softwood/lignin polyacrylonitrile copolymers.

  3. The use of natural abundance stable isotopic ratios to indicate the presence of oxygen-containing chemical linkages between cellulose and lignin in plant cell walls.

    PubMed

    Zhou, Youping; Stuart-Williams, Hilary; Farquhar, Graham D; Hocart, Charles H

    2010-06-01

    Qualitative and quantitative understanding of the chemical linkages between the three major biochemical components (cellulose, hemicellulose and lignin) of plant cell walls is crucial to the understanding of cell wall structure. Although there is convincing evidence for chemical bonds between hemicellulose and lignin and the absence of chemical bonds between hemicellulose and cellulose, there is no conclusive evidence for the presence of covalent bonds between cellulose and lignin. This is caused by the lack of selectivity of current GC/MS-, NMR- and IR-based methods for lignin characterisation as none of these techniques directly targets the possible ester and ether linkages between lignin and cellulose. We modified the widely-accepted "standard" three-step extraction method for isolating cellulose from plants by changing the order of the steps for hemicellulose and lignin removal (solubilisation with concentrated NaOH and oxidation with acetic acid-containing NaClO(2), respectively) so that cellulose and lignin could be isolated with the possible chemical bonds between them intact. These linkages were then cleaved with NaClO(2) reagent in aqueous media of contrasting (18)O/(16)O ratios. We produced cellulose with higher purity (a lower level of residual hemicellulose and no detectable lignin) than that produced by the "standard" method. Oxidative artefacts may potentially be introduced at the lignin removal stage; but testing showed this to be minimal. Cellulose samples isolated from processing plant-derived cellulose-lignin mixtures in media of contrasting (18)O/(16)O ratios were compared to provide the first quantitative evidence for the presence of oxygen-containing ester and ether bonds between cellulose and lignin in Zea mays leaves. However, no conclusive evidence for the presence or lack of similar bonds in Araucaria cunninghamii wood was obtained.

  4. Selective conversion of biorefinery lignin into dicarboxylic acids.

    PubMed

    Ma, Ruoshui; Guo, Mond; Zhang, Xiao

    2014-02-01

    The emerging biomass-to-biofuel conversion industry has created an urgent need for identifying new applications for biorefinery lignin. This paper demonstrates a new route to producing dicarboxylic acids from biorefinery lignin through chalcopyrite-catalyzed oxidation in a highly selective process. Up to 95 % selectivity towards stable dicarboxylic acids was obtained for several types of biorefinery lignin and model compounds under mild, environmentally friendly reaction conditions. The findings from this study paved a new avenue to biorefinery lignin conversions and applications.

  5. Selective Conversion of Biorefinery Lignin into Dicarboxylic Acids

    SciTech Connect

    Ma, Ruoshui; Guo, Mond; Zhang, Xiao

    2014-02-01

    The emerging biomass-to-biofuel conversion industry has created an urgent need for identifying new applications for biorefinery lignin. This paper demonstrates a new route to producing dicarboxylic acids from biorefinery lignin through chalcopyrite-catalyzed oxidation in a highly selective process. Up to 95 % selectivity towards stable dicarboxylic acids was obtained for several types of biorefinery lignin and model compounds under mild, environmentally friendly reaction conditions. The findings from this study paved a new avenue to biorefinery lignin conversions and applications.

  6. Chemical linkage of pine polysaccharides to lignin

    SciTech Connect

    Minor, J.L.

    1982-01-01

    Methylation analysis was used to investigate the bonds to lignin of the carbohydrates remaining after enzymatic hydrolysis and alkaline reduction of ball-milled loblolly pine wood and red pine compression wood. The carbohydrates exist as oligomeric chains with degrees of polymerization of 7-14. Approximately one sugar unit per oligomer chain is bonded to lignin. Bonding at C-6 of the hexose units if favored, and the arabinose is bonded exclusively at C-5. Galactan and arabinan are structurally of the so-called ''pectin group substances''. 16 references.

  7. Process for producing phenolic compounds from lignins

    DOEpatents

    Agblevor, Foster A.

    1998-01-01

    A process for the production of low molecular weight phenolic compounds from lignins through the pyrolysis of the lignins in the presence of a strong base. In a preferred embodiment, potassium hydroxide is present in an amount of from about 0.1% to about 5% by weight, the pyrolysis temperature is from about 400.degree. C. to about 600.degree. C. at atmospheric pressure, and the time period for substantial completion of the reaction is from about 1-3 minutes. Examples of low molecular weight phenolic compounds produced include methoxyphenols, non-methoxylated phenols, and mixtures thereof.

  8. Process for producing phenolic compounds from lignins

    DOEpatents

    Agblevor, F.A.

    1998-09-15

    A process is described for the production of low molecular weight phenolic compounds from lignins through the pyrolysis of the lignins in the presence of a strong base. In a preferred embodiment, potassium hydroxide is present in an amount of from about 0.1% to about 5% by weight, the pyrolysis temperature is from about 400 C to about 600 C at atmospheric pressure, and the time period for substantial completion of the reaction is from about 1--3 minutes. Examples of low molecular weight phenolic compounds produced include methoxyphenols, non-methoxylated phenols, and mixtures thereof. 16 figs.

  9. Controlling false positives in the mapping of epistatic QTL.

    PubMed

    Wei, W-H; Knott, S; Haley, C S; de Koning, D-J

    2010-04-01

    This study addresses the poorly explored issue of the control of false positive rate (FPR) in the mapping of pair-wise epistatic quantitative trait loci (QTL). A nested test framework was developed to (1) allow pre-identified QTL to be used directly to detect epistasis in one-dimensional genome scans, (2) to detect novel epistatic QTL pairs in two-dimensional genome scans and (3) to derive genome-wide thresholds through permutation and handle multiple testing. We used large-scale simulations to evaluate the performance of both the one- and two-dimensional approaches in mapping different forms and levels of epistasis and to generate profiles of FPR, power and accuracy to inform epistasis mapping studies. We showed that the nested test framework and genome-wide thresholds were essential to control FPR at the 5% level. The one-dimensional approach was generally more powerful than the two-dimensional approach in detecting QTL-associated epistasis and identified nearly all epistatic pairs detected from the two-dimensional approach. However, only the two-dimensional approach could detect epistatic QTL with weak main effects. Combining the two approaches allowed effective mapping of different forms of epistasis, whereas using the nested test framework kept the FPR under control. This approach provides a good search engine for high-throughput epistasis analyses.

  10. Structure and radical scavenging activity relationships of pyrolytic lignins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This work deals with antioxidant properties of pyrolytic lignins against two free radicals, the 1,1-diphenyl-2-picrylhydrazyl and the 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid). Pyrolytic lignins produced by the thermal pyrolysis of the Etek lignin were extracted from the liquid pyrolysi...

  11. Caterpillar feeding responses to sorghum leaves with altered lignin levels

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Production of liquid fuels from biomass is impeded by the presence of lignin. Plants with lower or altered lignin are more amenable to lignocellulosic conversion to ethanol and other biofuels, but may be more susceptible to insect damage where lignin is an important resistance factor. Sorghum, Sorg...

  12. Genetics and chemistry of lignin degradation by Streptomyces

    SciTech Connect

    Crawford, D.L.

    1992-01-01

    Our research goal was to define the involvement of lignin peroxidases and other extracellular enzymes in lignin degradation by Streptomyces. We examined the biochemistry and genetics of lignin degrading enzyme production by several strains of Streptomyces. The lignin peroxidase ALiP-P3 of S. viridosporus was characterized kinetically and its activity optimized for oxidation of 2,4-dichlorophenol and vanillyl-acetone. Sensitive spectrophotometric assays were developed for monitoring oxidation of these substrates. ALiP-P3 reaction chemistry was examined using both spectrophotometric assays and gas chromatography/mass spectroscopy. Results showed that the enzyme oxidizes phenolic lignin substructure models in strong preference to nonphenolic ones. The peroxidase was also shown to depolymerize native lignin. We also cloned the ALip-P3 gene S. lividans in plasmid vector pIJ702. The cloned gene was partially sequenced, We also immunologically characterized the lignin peroxidase of S. viridosporus T7A and showed it to be structurally related to peroxidases produced by other lignin-solubilizing Streptomyces, but not the the H8 lignin peroxidase of P. chrysosporium. Studies with peroxidase deficient mutants of strain T7A showed that lignin peroxidases of S. viridosporus are directly involved in the solubilization of lignin. Additional research showed that other enzymes are also probably involved in lignin solubilization, possibly including extracellular esterases.

  13. Genetic engineering of syringyl-enriched lignin in plants

    DOEpatents

    Chiang, Vincent Lee; Li, Laigeng

    2004-11-02

    The present invention relates to a novel DNA sequence, which encodes a previously unidentified lignin biosynthetic pathway enzyme, sinapyl alcohol dehydrogenase (SAD) that regulates the biosynthesis of syringyl lignin in plants. Also provided are methods for incorporating this novel SAD gene sequence or substantially similar sequences into a plant genome for genetic engineering of syringyl-enriched lignin in plants.

  14. Flocculation of high purity wheat straw soda lignin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flocculant action on lignocellulose mixtures has been studied, but flocculant action on purified sulfur-free lignin has not been reported. In the last step of the industrial process, the purified lignin solution is acidified with sulfuric acid which causes the lignin to become insoluble. The feasi...

  15. ReaxFF Study of the Oxidation of Lignin Model Compounds for the Most Common Linkages in Softwood in View of Carbon Fiber Production

    SciTech Connect

    Beste, Ariana

    2014-01-01

    Lignin is an underused but major component of biomass. One possible area of utilization is the production of carbon fiber. A necessary processing step is the stabilization of lignin fiber (typically in an oxygen environment) before high temperature treatment. We investigate oxidative, thermal conversion of lignin using computational methods. Dilignol model compounds for the most common (seven) linkages in softwood are chosen to represent the diverse structure of lignin. We perform molecular dynamics simulation where the potential energy surface is described by a reactive force field (ReaxFF). We calculate overall activation energies for model conversion and reveal initial mechanisms of formaldehyde formation. We record fragmentation patterns and average carbon oxidation numbers at various temperatures. Most importantly, we identify mechanisms for stabilizing reactions that result in cyclic, and rigid connections in softwood lignin fibers that are necessary for further processing into carbon fibers.

  16. ReaxFF study of the oxidation of lignin model compounds for the most common linkages in softwood in view of carbon fiber production.

    PubMed

    Beste, Ariana

    2014-02-01

    Lignin is an underused but major component of biomass. One possible area of utilization is the production of carbon fiber. A necessary processing step is the stabilization of lignin fiber (typically in an oxygen environment) before high temperature treatment. We investigate oxidative, thermal conversion of lignin using computational methods. Dilignol model compounds for the most common (seven) linkages in softwood are chosen to represent the diverse structure of lignin. We perform molecular dynamics simulation where the potential energy surface is described by a reactive force field (ReaxFF). We calculate overall activation energies for model conversion and reveal initial mechanisms of formaldehyde formation. We record fragmentation patterns and average carbon oxidation numbers at various temperatures. Most importantly, we identify mechanisms for stabilizing reactions that result in cyclic and rigid connections in softwood lignin fibers that are necessary for further processing into carbon fibers.

  17. Exploitation of hemicellulose, cellulose and lignin from Hesperaloe funifera.

    PubMed

    Sánchez, R; Rodríguez, A; García, J C; Rosal, A; Jiménez, L

    2011-01-01

    This work seeks the integral use of all major components of Hesperaloe funifera, separating hemicelluose by hydrothermal treatments; cellulose by pulping processes; and exploitation of lignin of pulping liquor by pyrolysis and gasification processes. By using sulfuric acid in the hydrothermal treatment (150-190 °C, 0-20 min after reaching operating temperature, 6-10 liquid/solid ratio, 0.1-0.5% sulfuric acid), the glucose and xylose of liquid fraction increase from 1.5% to 5.9%, and 4.0% to 12.4%, respectively; the yields of solid fraction decrease from 91.6% to 79.5%, and the lignin content increase from 23% to 32%. Pulps and paper sheets obtained from solid fractions hydrothermal treatments and from raw material pulped with diethanolamine, are worse than those obtained with soda-anthraquinone (Yield 57.8%; kappa number 24.9; Viscosity 711 mL/g; Brightness 54.8%; Tensile index 73.6 Nm/g; Stretch 2.84%; Burst index 6.13 kN/g and Tear index 1.69 mNm2/g). By acidification (pH 6) of soda pulping liquor it separate lignin-rich solids, which by pyrolysis gave a gas containing 1.13% H2, 31.79% CO and 1.86% CH4 by weight. Gasification of the same sample provided a gas containing 0.18% H2, 24.50% CO and 17.75% CH4.

  18. Comparison of the acetyl bromide spectrophotometric method with other analytical lignin methods for determining lignin concentration in forage samples.

    PubMed

    Fukushima, Romualdo S; Hatfield, Ronald D

    2004-06-16

    Present analytical methods to quantify lignin in herbaceous plants are not totally satisfactory. A spectrophotometric method, acetyl bromide soluble lignin (ABSL), has been employed to determine lignin concentration in a range of plant materials. In this work, lignin extracted with acidic dioxane was used to develop standard curves and to calculate the derived linear regression equation (slope equals absorptivity value or extinction coefficient) for determining the lignin concentration of respective cell wall samples. This procedure yielded lignin values that were different from those obtained with Klason lignin, acid detergent acid insoluble lignin, or permanganate lignin procedures. Correlations with in vitro dry matter or cell wall digestibility of samples were highest with data from the spectrophotometric technique. The ABSL method employing as standard lignin extracted with acidic dioxane has the potential to be employed as an analytical method to determine lignin concentration in a range of forage materials. It may be useful in developing a quick and easy method to predict in vitro digestibility on the basis of the total lignin content of a sample.

  19. Propensity of lignin to associate: light scattering photometry study with native lignins.

    PubMed

    Contreras, Sofía; Gaspar, Armindo R; Guerra, Anderson; Lucia, Lucian A; Argyropoulos, Dimitris S

    2008-12-01

    Many studies of lignins in solution invoke association and aggregation phenomena to explain their solution behavior (e.g., reprecipitation onto pulp fibers, condensation, etc.). Following their colloidal (apparent) molecular weights in solution as a function of time allows us to explore observable dissociation phenomena. These measurements were carried out using multiple angle laser light scattering (MALLS) photometry in the static mode. The challenges and opportunities of measuring the specific refractive index increment (dn/dC) of lignin solutions and determining the kinetics of the dissociation process were thus investigated. Hardwood and softwood representative lignins were isolated, and method for their full dissolution in THF was further developed, which then lead to accurate dn/dC values being obtained as a function of time. When coupled to additional work using light scattering static measurements and Zimm plots for the same solutions, this effort offers insight into the aggregation and ensuing dissociative events that operate within the lignin macromolecules.

  20. Identifying New Lignin Bioengineering Targets: 1. Monolignol Substitute Impacts on Lignin Formation and Cell Wall Fermentability

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Recent discoveries highlighting the metabolic malleability of plant lignification indicate that lignin can be engineered to dramatically alter its composition and properties. Current plant engineering efforts are primarily aimed at manipulating the biosynthesis of normal monolignols but,...

  1. Identifying New Lignin Bioengineering Targets: Monolignol Substitute Impacts on Lignin Formation and Cell Wall Utilization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent discoveries highlighting the metabolic malleability of plant lignification indicate that lignin can be engineered to dramatically alter its composition and properties. Current plant engineering efforts are primarily aimed at manipulating the biosynthesis of normal monolignols, but in the futu...

  2. Lignin-blocking treatment of biomass and uses thereof

    DOEpatents

    Yang, Bin; Wyman, Charles E.

    2009-10-20

    Disclosed is a method for converting cellulose in a lignocellulosic biomass. The method provides for a lignin-blocking polypeptide and/or protein treatment of high lignin solids. The treatment enhances cellulase availability in cellulose conversion. Cellulase efficiencies are improved by the protein or polypeptide treatment. The treatment may be used in combination with steam explosion and acid prehydrolysis techniques. Hydrolysis yields from lignin containing biomass are enhanced 5-20%, and enzyme utilization is increased from 10% to 50%. Thus, a more efficient and economical method of processing lignin containing biomass materials utilizes a polypeptide/protein treatment step that effectively blocks lignin binding of cellulase.

  3. 21 CFR 573.600 - Lignin sulfonates.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... DRUGS, FEEDS, AND RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food... accordance with the following prescribed conditions: (a) For the purpose of this section, the food additive... 21 Food and Drugs 6 2014-04-01 2014-04-01 false Lignin sulfonates. 573.600 Section 573.600...

  4. 21 CFR 573.600 - Lignin sulfonates.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... DRUGS, FEEDS, AND RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food... accordance with the following prescribed conditions: (a) For the purpose of this section, the food additive... 21 Food and Drugs 6 2013-04-01 2013-04-01 false Lignin sulfonates. 573.600 Section 573.600...

  5. 21 CFR 573.600 - Lignin sulfonates.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... DRUGS, FEEDS, AND RELATED PRODUCTS FOOD ADDITIVES PERMITTED IN FEED AND DRINKING WATER OF ANIMALS Food... accordance with the following prescribed conditions: (a) For the purpose of this section, the food additive... 21 Food and Drugs 6 2012-04-01 2012-04-01 false Lignin sulfonates. 573.600 Section 573.600...

  6. Kinetic Model Development for Lignin Pyrolysis

    SciTech Connect

    Clark, J.; Robichaud, D.; Nimlos, M.

    2012-01-01

    Lignin pyrolysis poses a significant barrier to the formation of liquid fuel products from biomass. Lignin pyrolyzes at higher temperatures than other biomass components (e.g. cellulose and hemi-cellulose) and tends to form radicals species that lead to cross-linking and ultimately char formation. A first step in the advancement of biomass-to-fuel technology is to discover the underlying mechanisms that lead to the breakdown of lignin at lower temperatures into more stable and usable products. We have investigated the thermochemistry of the various inter-linkage units found in lignin (B-O4, a-O4, B-B, B-O5, etc) using electronic structure calculations at the M06-2x/6-311++G(d,p) on a series of dimer model compounds. In addition to bond homolysis reactions, a variety of concerted elimination pathways are under investigation that tend to produce closed-shell stable products. Such a bottom-up approach could aid in the targeted development of catalysts that produce more desirable products under less severe reactor conditions.

  7. Flash vacuum pyrolysis of lignin model compounds

    SciTech Connect

    Cooney, M.J.; Britt, P.F.; Buchanan, A.C. III

    1997-03-01

    Despite the extensive research into the pyrolysis of lignin, the underlying chemical reactions that lead to product formation are poorly understood. Detailed mechanistic studies on the pyrolysis of biomass and lignin under conditions relevant to current process conditions could provide insight into utilizing this renewable resource for the production of chemicals and fuel. Currently, flash or fast pyrolysis is the most promising process to maximize the yields of liquid products (up to 80 wt %) from biomass by rapidly heating the substrate to moderate temperatures, typically 500{degrees}C, for short residence times, typically less than two seconds. To provide mechanistic insight into the primary reaction pathways under process relevant conditions, we are investigating the flash vacuum pyrolysis (FVP) of lignin model compounds that contain a {beta}-ether. linkage and {alpha}- or {gamma}-alcohol, which are key structural elements in lignin. The dominant products from the FVP of PhCH{sub 2}CH{sub 2}OPh (PPE), PhC(OH)HCH{sub 2}OPh, and PhCH{sub 2}CH(CH{sub 2}OH)OPh at 500{degrees}C can be attributed to homolysis of the weakest bond in the molecule (C-O bond) or 1,2-elimination. Surprisingly, the hydroxy-substituent dramatically increases the decomposition of PPE. It is proposed that internal hydrogen bonding is accelerating the reaction.

  8. Three-dimensional model of lignin structure

    SciTech Connect

    Jurasek, L.

    1995-12-01

    An attempt to build a three-dimensional model of lignin structure using a computer program is described. The program simulates the biosynthesis of spruce lignin by allowing coniferyl alcohol subunits to be added randomly by six different types of linkages, assumed to be most common. The simulated biosynthesis starts from a number of seed points within restricted space, corresponding to 50 mM initial concentration of coniferyl alcohol. Rules of three-dimensional packing of the subunits within the lignin macro-molecule are observed during the simulated biosynthetic process. Branched oligomeric structures thus generated form crosslinks at those positions where the chains grow close enough to form a link. Inter-chain crosslinking usually joins the oligomers into one macromolecule. Intra-chain crosslinks are also formed and result in closed loops. Typically, a macromolecule with molecular weight of approx. 2 x 105 is formed, with internal density of 1.35g/cm3. Various characteristics of the internal structure, such as branching, crosslinking, bond frequencies, and chain length distribution are described. Breakdown of the polymer was also simulated and the effect of closed loops on the weight average molecular weight is shown. The effect of the shape of the biosynthetic space on the degree of crosslinking is discussed and predictions of the overall molecular shape of lignin particles are made.

  9. Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin.

    PubMed

    Eudes, Aymerick; Pereira, Jose H; Yogiswara, Sasha; Wang, George; Teixeira Benites, Veronica; Baidoo, Edward E K; Lee, Taek Soon; Adams, Paul D; Keasling, Jay D; Loqué, Dominique

    2016-03-01

    Lignin poses a major challenge in the processing of plant biomass for agro-industrial applications. For bioengineering purposes, there is a pressing interest in identifying and characterizing the enzymes responsible for the biosynthesis of lignin. Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase (HCT; EC 2.3.1.133) is a key metabolic entry point for the synthesis of the most important lignin monomers: coniferyl and sinapyl alcohols. In this study, we investigated the substrate promiscuity of HCT from a bryophyte (Physcomitrella) and from five representatives of vascular plants (Arabidopsis, poplar, switchgrass, pine and Selaginella) using a yeast expression system. We demonstrate for these HCTs a conserved capacity to acylate with p-coumaroyl-CoA several phenolic compounds in addition to the canonical acceptor shikimate normally used during lignin biosynthesis. Using either recombinant HCT from switchgrass (PvHCT2a) or an Arabidopsis stem protein extract, we show evidence of the inhibitory effect of these phenolics on the synthesis of p-coumaroyl shikimate in vitro, which presumably occurs via a mechanism of competitive inhibition. A structural study of PvHCT2a confirmed the binding of a non-canonical acceptor in a similar manner to shikimate in the active site of the enzyme. Finally, we exploited in Arabidopsis the substrate flexibility of HCT to reduce lignin content and improve biomass saccharification by engineering transgenic lines that overproduce one of the HCT non-canonical acceptors. Our results demonstrate conservation of HCT substrate promiscuity and provide support for a new strategy for lignin reduction in the effort to improve the quality of plant biomass for forage and cellulosic biofuels. PMID:26858288

  10. Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin

    PubMed Central

    Eudes, Aymerick; Pereira, Jose H.; Yogiswara, Sasha; Wang, George; Teixeira Benites, Veronica; Baidoo, Edward E.K.; Lee, Taek Soon; Adams, Paul D.; Keasling, Jay D.; Loqué, Dominique

    2016-01-01

    Lignin poses a major challenge in the processing of plant biomass for agro-industrial applications. For bioengineering purposes, there is a pressing interest in identifying and characterizing the enzymes responsible for the biosynthesis of lignin. Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase (HCT; EC 2.3.1.133) is a key metabolic entry point for the synthesis of the most important lignin monomers: coniferyl and sinapyl alcohols. In this study, we investigated the substrate promiscuity of HCT from a bryophyte (Physcomitrella) and from five representatives of vascular plants (Arabidopsis, poplar, switchgrass, pine and Selaginella) using a yeast expression system. We demonstrate for these HCTs a conserved capacity to acylate with p-coumaroyl-CoA several phenolic compounds in addition to the canonical acceptor shikimate normally used during lignin biosynthesis. Using either recombinant HCT from switchgrass (PvHCT2a) or an Arabidopsis stem protein extract, we show evidence of the inhibitory effect of these phenolics on the synthesis of p-coumaroyl shikimate in vitro, which presumably occurs via a mechanism of competitive inhibition. A structural study of PvHCT2a confirmed the binding of a non-canonical acceptor in a similar manner to shikimate in the active site of the enzyme. Finally, we exploited in Arabidopsis the substrate flexibility of HCT to reduce lignin content and improve biomass saccharification by engineering transgenic lines that overproduce one of the HCT non-canonical acceptors. Our results demonstrate conservation of HCT substrate promiscuity and provide support for a new strategy for lignin reduction in the effort to improve the quality of plant biomass for forage and cellulosic biofuels. PMID:26858288

  11. Supramolecular Interactions in Secondary Plant Cell Walls: Effect of Lignin Chemical Composition Revealed with the Molecular Theory of Solvation.

    PubMed

    Silveira, Rodrigo L; Stoyanov, Stanislav R; Gusarov, Sergey; Skaf, Munir S; Kovalenko, Andriy

    2015-01-01

    Plant biomass recalcitrance, a major obstacle to achieving sustainable production of second generation biofuels, arises mainly from the amorphous cell-wall matrix containing lignin and hemicellulose assembled into a complex supramolecular network that coats the cellulose fibrils. We employed the statistical-mechanical, 3D reference interaction site model with the Kovalenko-Hirata closure approximation (or 3D-RISM-KH molecular theory of solvation) to reveal the supramolecular interactions in this network and provide molecular-level insight into the effective lignin-lignin and lignin-hemicellulose thermodynamic interactions. We found that such interactions are hydrophobic and entropy-driven, and arise from the expelling of water from the mutual interaction surfaces. The molecular origin of these interactions is carbohydrate-π and π-π stacking forces, whose strengths are dependent on the lignin chemical composition. Methoxy substituents in the phenyl groups of lignin promote substantial entropic stabilization of the ligno-hemicellulosic matrix. Our results provide a detailed molecular view of the fundamental interactions within the secondary plant cell walls that lead to recalcitrance.

  12. Supramolecular Interactions in Secondary Plant Cell Walls: Effect of Lignin Chemical Composition Revealed with the Molecular Theory of Solvation.

    PubMed

    Silveira, Rodrigo L; Stoyanov, Stanislav R; Gusarov, Sergey; Skaf, Munir S; Kovalenko, Andriy

    2015-01-01

    Plant biomass recalcitrance, a major obstacle to achieving sustainable production of second generation biofuels, arises mainly from the amorphous cell-wall matrix containing lignin and hemicellulose assembled into a complex supramolecular network that coats the cellulose fibrils. We employed the statistical-mechanical, 3D reference interaction site model with the Kovalenko-Hirata closure approximation (or 3D-RISM-KH molecular theory of solvation) to reveal the supramolecular interactions in this network and provide molecular-level insight into the effective lignin-lignin and lignin-hemicellulose thermodynamic interactions. We found that such interactions are hydrophobic and entropy-driven, and arise from the expelling of water from the mutual interaction surfaces. The molecular origin of these interactions is carbohydrate-π and π-π stacking forces, whose strengths are dependent on the lignin chemical composition. Methoxy substituents in the phenyl groups of lignin promote substantial entropic stabilization of the ligno-hemicellulosic matrix. Our results provide a detailed molecular view of the fundamental interactions within the secondary plant cell walls that lead to recalcitrance. PMID:26263115

  13. Phoma herbarum, a soil fungus able to grow on natural lignin and synthetic lignin (DHP) as sole carbon source and cause lignin degradation.

    PubMed

    Bi, Ran; Lawoko, Martin; Henriksson, Gunnar

    2016-08-01

    The fungus Phoma herbarum isolated from soil showed growth on highly pure lignin extracted from spruce wood and on synthetic lignin (DHP). The lignin remaining after cultivation was shown to have a lower molecular weight. The reduction in the numbers of ether linkages of the extracted lignins was also observed by derivatization followed by reductive cleavage (DFRC) in combination with (31)P NMR studies. The fungal strain showed an ability to degrade synthetic lignin by extracellular catalysts. GC-MS was applied to study the evolution of low molar mass adducts, e.g., monolignols and it was shown that a reduced coniferyl alcohol product was produced from DHP in a cell-free environment. The work has demonstrated the ability of soil microbes to grow on lignin as sole carbon source. The potential impact is in the production of low molar mass renewable phenols for material application. PMID:27260523

  14. Discovery of 12-mer peptides that bind to wood lignin.

    PubMed

    Yamaguchi, Asako; Isozaki, Katsuhiro; Nakamura, Masaharu; Takaya, Hikaru; Watanabe, Takashi

    2016-01-01

    Lignin, an abundant terrestrial polymer, is the only large-volume renewable feedstock composed of an aromatic skeleton. Lignin has been used mostly as an energy source during paper production; however, recent interest in replacing fossil fuels with renewable resources has highlighted its potential value in providing aromatic chemicals. Highly selective degradation of lignin is pivotal for industrial production of paper, biofuels, chemicals, and materials. However, few studies have examined natural and synthetic molecular components recognizing the heterogeneous aromatic polymer. Here, we report the first identification of lignin-binding peptides possessing characteristic sequences using a phage display technique. The consensus sequence HFPSP was found in several lignin-binding peptides, and the outer amino acid sequence affected the binding affinity of the peptides. Substitution of phenylalanine7 with Ile in the lignin-binding peptide C416 (HFPSPIFQRHSH) decreased the affinity of the peptide for softwood lignin without changing its affinity for hardwood lignin, indicating that C416 recognised structural differences between the lignins. Circular dichroism spectroscopy demonstrated that this peptide adopted a highly flexible random coil structure, allowing key residues to be appropriately arranged in relation to the binding site in lignin. These results provide a useful platform for designing synthetic and biological catalysts selectively bind to lignin. PMID:26903196

  15. Discovery of 12-mer peptides that bind to wood lignin

    PubMed Central

    Yamaguchi, Asako; Isozaki, Katsuhiro; Nakamura, Masaharu; Takaya, Hikaru; Watanabe, Takashi

    2016-01-01

    Lignin, an abundant terrestrial polymer, is the only large-volume renewable feedstock composed of an aromatic skeleton. Lignin has been used mostly as an energy source during paper production; however, recent interest in replacing fossil fuels with renewable resources has highlighted its potential value in providing aromatic chemicals. Highly selective degradation of lignin is pivotal for industrial production of paper, biofuels, chemicals, and materials. However, few studies have examined natural and synthetic molecular components recognizing the heterogeneous aromatic polymer. Here, we report the first identification of lignin-binding peptides possessing characteristic sequences using a phage display technique. The consensus sequence HFPSP was found in several lignin-binding peptides, and the outer amino acid sequence affected the binding affinity of the peptides. Substitution of phenylalanine7 with Ile in the lignin-binding peptide C416 (HFPSPIFQRHSH) decreased the affinity of the peptide for softwood lignin without changing its affinity for hardwood lignin, indicating that C416 recognised structural differences between the lignins. Circular dichroism spectroscopy demonstrated that this peptide adopted a highly flexible random coil structure, allowing key residues to be appropriately arranged in relation to the binding site in lignin. These results provide a useful platform for designing synthetic and biological catalysts selectively bind to lignin. PMID:26903196

  16. Method for recovering and using lignin in adhesive resins

    DOEpatents

    Schroeder, Herbert A.

    1993-01-01

    Lignin, or a lignin derived material, which has been significantly demethylated (e.g., the demethylated lignin found in the raffinate produced as a by-product of dimethyl sulfide production which can be carried out using the spent liquor from wood pulping operations) can be isolated by a process wherein an organic solvent is added to a lignin-containing aqueous solution. The organic solvent is typically a polar, and at least a partially water-immiscible substance such as, for example, ethyl acetate. The resulting lignin-containing aqueous solution/organic solvent mixture is acidified to produce a water layer which is discarded and an organic solvent layer which contains the demethylated lignin. Upon its recovery, the demethylated lignin is dissolved in an alkaline solution to which an aldehyde source is added to produce a resol-type resin. The aldehyde source may be formaldehyde in solution, paraformaldehyde, hexamethylenetetramine, or other aldehydes including acetaldehyde, furfural, and their derivatives.

  17. Isolation of a Bacterium Capable of Degrading Peanut Hull Lignin

    PubMed Central

    Kerr, Thomas J.; Kerr, Robert D.; Benner, Ronald

    1983-01-01

    Thirty-seven bacterial strains capable of degrading peanut hull lignin were isolated by using four types of lignin preparations and hot-water-extracted peanut hulls. One of the isolates, tentatively identified as Arthrobacter sp., was capable of utilizing all four lignin preparations as well as extracted peanut hulls as a sole source of carbon. The bacterium was also capable of degrading specifically labeled [14C]lignin-labeled lignocellulose and [14C]cellulose-labeled lignocellulose from the cordgrass Spartina alterniflora and could also degrade [14C]Kraft lignin from slash pine. After 10 days of incubation with [14C]cellulose-labeled lignocellulose or [14C]lignin-labeled lignocellulose from S. alterniflora, the bacterium mineralized 6.5% of the polysaccharide component and 2.9% of the lignin component. Images PMID:16346424

  18. Isolation of a bacterium capable of degrading peanut hull lignin

    SciTech Connect

    Kerr, T.A.; Kerr, R.D.; Benner, R.

    1983-11-01

    Thirty-seven bacterial strains capable of degrading peanut hull lignin were isolated by using four types of lignin preparations and hot-water-extracted peanut hulls. One of the isolates, tentatively identified as Arthrobacter species, was capable of utilizing all four lignin preparations as well as extracted peanut hulls as a sole source of carbon. The bacterium was also capable of degrading specifically labeled (/sup 14/C) lignin-labeled lignocellulose and (/sup 14/C)cellulose-labeled lignocellulose from the cordgrass Spartina alterniflora and could also degrade (/sup 14/C) Kraft lignin from slash pine. After 10 days of incubation with (/sup 14/C) cellulose-labeled lignocellulose or (/sup 14/C) lignin-labeled lignocellulose from S. alterniflora, the bacterium mineralized 6.5% of the polysaccharide component and 2.9% of the lignin component. (Refs. 24).

  19. Reactions of Lignin Model Compounds in Ionic Liquids

    SciTech Connect

    Holladay, John E.; Binder, Joseph B.; Gray, Michel J.; White, James F.; Zhang, Z. Conrad

    2009-09-15

    Lignin, a readily available form of biomass, awaits novel chemistry for converting it to valuable aromatic chemicals. Recent work has demonstrated that ionic liquids are excellent solvents for processing woody biomass and lignin. Seeking to exploit ionic liquids as media for depolymerization of lignin, we investigated reactions of lignin model compounds in these solvents. Using Brønsted acid catalysts in 1-ethyl-3-methylimidazolium triflate at moderate temperatures, we obtained up to 11.6% yield of the dealkylation product guaiacol from the model compound eugenol and cleaved phenethyl phenyl ether, a model for lignin ethers. Despite these successes, acid catalysis failed in dealkylation of the unsaturated model compound 4-ethylguaiacol and did not produce monomeric products from organosolv lignin, demonstrating that further work is required to understand the complex chemistry of lignin depolymerization.

  20. Specific lignin accumulation in granulated juice sacs of Citrus maxima.

    PubMed

    Wu, Jia-Ling; Pan, Teng-Fei; Guo, Zhi-Xiong; Pan, Dong-Ming

    2014-12-17

    Juice sac granulation occurring in pummelo fruits [Citrus maxima (Burm.) Merr.] is an undesirable trait, and the underlying mechanism remains unresolved. Previous studies have shown that lignin metabolism is closely associated with the process of juice sac granulation. Here, a method suitable for lignin isolation from pummelo tissues is established. Acetylated lignins from different pummelo tissues and cultivars were analyzed by HSQC NMR. The results showed that lignins in granulated juice sacs were characterized by an extremely high abundance of guaiacyl units (91.13-96.82%), in contrast to lignins from other tissues, including leaves, stems, and segment membranes. The abnormally accumulated lignins in granulated juice sacs were specific and mainly polymerized from coniferyl alcohol. No significant difference was found in lignin types among various cultivars. These findings indicated that the mechanism of juice sac granulation might be similar among various cultivars, although very different degrees of juice sac granulation can be observed.

  1. Identification of Quantitative Trait Loci (QTL) and Candidate Genes for Cadmium Tolerance in Populus

    SciTech Connect

    Induri, Brahma R; Ellis, Danielle R; Slavov, Gancho; Yin, Tongming; Muchero, Wellington; Tuskan, Gerald A; DiFazio, Stephen P

    2012-01-01

    Knowledge of genetic variation in response of Populus to heavy metals like cadmium (Cd) is an important step in understanding the underlying mechanisms of tolerance. In this study, a pseudo-backcross pedigree of Populus trichocarpa and Populus deltoides was characterized for Cd exposure. The pedigree showed significant variation for Cd tolerance thus enabling the identification of relatively tolerant and susceptible genotypes for intensive characterization. A total of 16 QTLs at logarithm of odds (LOD) ratio > 2.5, were found to be associated with total dry weight, its components, and root volume. Four major QTLs for total dry weight were mapped to different linkage groups in control (LG III) and Cd conditions (LG XVI) and had opposite allelic effects on Cd tolerance, suggesting that these genomic regions were differentially controlled. The phenotypic variation explained by Cd QTL for all traits under study varied from 5.9% to 11.6% and averaged 8.2% across all QTL. Leaf Cd contents also showed significant variation suggesting the phytoextraction potential of Populus genotypes, though heritability of this trait was low (0.22). A whole-genome microarray study was conducted by using two genotypes with extreme responses for Cd tolerance in the above study and differentially expressed genes were identified. Candidate genes including CAD2 (CADMIUM SENSITIVE 2), HMA5 (HEAVY METAL ATPase5), ATGTST1 (Arabidopsis thaliana Glutathione S-Transferase1), ATGPX6 (Glutathione peroxidase 6), and ATMRP 14 (Arabidopsis thaliana Multidrug Resistance associated Protein 14) were identified from QTL intervals and microarray study. Functional characterization of these candidate genes could enhance phytoremediation capabilities of Populus.

  2. Joint QTL analyses for partial resistance to Phytophthora sojae using six nested inbred populations with heterogeneous conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Partial resistance to Phytophthora sojae in soybean is controlled by multiple quantitative trait loci (QTL). With traditional QTL mapping approaches, power to detect these QTL, frequently of small effect, can be limited by population size. Joint linkage QTL analysis of nested recombinant inbred li...

  3. BrFLC2 (FLOWERING LOCUS C) as a candidate gene for a vernalization response QTL in Brassica rapa.

    PubMed

    Zhao, Jianjun; Kulkarni, Vani; Liu, Nini; Del Carpio, Dunia Pino; Bucher, Johan; Bonnema, Guusje

    2010-06-01

    Flowering time is an important agronomic trait, and wide variation exists among Brassica rapa. In Arabidopsis, FLOWERING LOCUS C (FLC) plays an important role in modulating flowering time and the response to vernalization. Brassica rapa contains several paralogues of FLC at syntenic regions. BrFLC2 maps under a major flowering time and vernalization response quantitative trait locus (QTL) at the top of A02. Here the effects of vernalization on flowering time in a double haploid (DH) population and on BrFLC2 expression in selected lines of a DH population in B. rapa are descibed. The effect of the major flowering time QTL on the top of A02 where BrFLC2 maps clearly decreases upon vernalization, which points to a role for BrFLC2 underlying the QTL. In all developmental stages and tissues (seedlings, cotyledons, and leaves), BrFLC2 transcript levels are higher in late flowering pools of DH lines than in pools of early flowering DH lines. BrFLC2 expression diminished after different durations of seedling vernalization in both early and late DH lines. The reduction of BrFLC2 expression upon seedling vernalization of both early and late flowering DH lines was strongest at the seedling stage and diminished in subsequent growth stages, which suggests that the commitment to flowering is already set at very early developmental stages. Taken together, these data support the hypothesis that BrFLC2 is a candidate gene for the flowering time and vernalization response QTL in B. rapa.

  4. Novel seed coat lignins in the Cactaceae: structure, distribution and implications for the evolution of lignin diversity.

    PubMed

    Chen, Fang; Tobimatsu, Yuki; Jackson, Lisa; Nakashima, Jin; Ralph, John; Dixon, Richard A

    2013-01-01

    We have recently described a hitherto unsuspected catechyl lignin polymer (C-lignin) in the seed coats of Vanilla orchid and in cacti of one genus, Melocactus (Chen et al., Proc. Natl. Acad. Sci. USA. 2012, 109, 1772-1777.). We have now determined the lignin types in the seed coats of 130 different cactus species. Lignin in the vegetative tissues of cacti is of the normal guaiacyl/syringyl (G/S) type, but members of most genera within the subfamily Cactoidae possess seed coat lignin of the novel C-type only, which we show is a homopolymer formed by endwise β-O-4-coupling of caffeyl alcohol monomers onto the growing polymer resulting in benzodioxane units. However, the species examined within the genera Coryphantha, Cumarinia, Escobaria and Mammillaria (Cactoideae) mostly had normal G/S lignin in their seeds, as did all six species in the subfamily Opuntioidae that were examined. Seed coat lignin composition is still evolving in the Cactaceae, as seeds of one Mammillaria species (M. lasiacantha) possess only C-lignin, three Escobaria species (E. dasyacantha, E. lloydii and E. zilziana) contain an unusual lignin composed of 5-hydroxyguaiacyl units, the first report of such a polymer that occurs naturally in plants, and seeds of some species contain no lignin at all. We discuss the implications of these findings for the mechanisms that underlie the biosynthesis of these newly discovered lignin types.

  5. Dissecting the Genetic Architecture of Leaf Rust Resistance in Wheat by QTL Meta-Analysis.

    PubMed

    Soriano, Jose Miguel; Royo, Conxita

    2015-12-01

    Leaf rust is an important disease that causes significant yield losses in wheat. Many studies have reported the identification of quantitative trait loci (QTL) controlling leaf rust resistance; therefore, QTL meta-analysis has become a useful tool for identifying consensus QTL and refining QTL positions among them. In this study, QTL meta-analysis was conducted using reported results on the number, position, and effects of QTL for leaf rust resistance in bread and durum wheat. Investigation of 14 leaf rust resistance traits from 19 studies involving 20 mapping populations and 33 different parental lines provided information for 144 unique QTL that were projected onto the Wheat Composite 2004 reference map. In total, 35 meta-QTL for leaf rust resistance traits were identified in 17 wheat chromosomes and 13 QTL remained as unique QTL. The results will facilitate further work on the cloning of QTL for pyramiding minor- and partial-effect resistance genes to develop varieties with durable resistance to leaf rust.

  6. Dissecting the Genetic Architecture of Leaf Rust Resistance in Wheat by QTL Meta-Analysis.

    PubMed

    Soriano, Jose Miguel; Royo, Conxita

    2015-12-01

    Leaf rust is an important disease that causes significant yield losses in wheat. Many studies have reported the identification of quantitative trait loci (QTL) controlling leaf rust resistance; therefore, QTL meta-analysis has become a useful tool for identifying consensus QTL and refining QTL positions among them. In this study, QTL meta-analysis was conducted using reported results on the number, position, and effects of QTL for leaf rust resistance in bread and durum wheat. Investigation of 14 leaf rust resistance traits from 19 studies involving 20 mapping populations and 33 different parental lines provided information for 144 unique QTL that were projected onto the Wheat Composite 2004 reference map. In total, 35 meta-QTL for leaf rust resistance traits were identified in 17 wheat chromosomes and 13 QTL remained as unique QTL. The results will facilitate further work on the cloning of QTL for pyramiding minor- and partial-effect resistance genes to develop varieties with durable resistance to leaf rust. PMID:26571424

  7. Confirmation of a seed yield QTL in soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Exotic germplasm can be an important source of genetic diversity for soybean [Glycine max (L.) Merr.] improvement. Previously, four yield quantitative trait loci (QTL) had been identified in a cross between the exotic soybean plant introduction (PI) 68658 and the U.S. cultivar Lawrence. The confirma...

  8. QTL architecture of reproductive fitness characters in Brassica rapa

    PubMed Central

    2014-01-01

    Background Reproductive output is critical to both agronomists seeking to increase seed yield and to evolutionary biologists interested in understanding natural selection. We examine the genetic architecture of diverse reproductive fitness traits in recombinant inbred lines (RILs) developed from a crop (seed oil) × wild-like (rapid cycling) genotype of Brassica rapa in field and greenhouse environments. Results Several fitness traits showed strong correlations and QTL-colocalization across environments (days to bolting, fruit length and seed color). Total fruit number was uncorrelated across environments and most QTL affecting this trait were correspondingly environment-specific. Most fitness components were positively correlated, consistent with life-history theory that genotypic variation in resource acquisition masks tradeoffs. Finally, we detected evidence of transgenerational pleiotropy, that is, maternal days to bolting was negatively correlated with days to offspring germination. A QTL for this transgenerational correlation was mapped to a genomic region harboring one copy of FLOWERING LOCUS C, a genetic locus known to affect both days to flowering as well as germination phenotypes. Conclusions This study characterizes the genetic structure of important fitness/yield traits within and between generations in B. rapa. Several identified QTL are suitable candidates for fine-mapping for the improvement of yield in crop Brassicas. Specifically, brFLC1, warrants further investigation as a potential regulator of phenology between generations. PMID:24641198

  9. Ensemble learning of QTL models improves prediction of complex traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative trait locus (QTL) models can provide useful insights into trait genetic architecture because of their straightforward interpretability, but are less useful for genetic prediction due to difficulty in including the effects of numerous small effect loci without overfitting. Tight linkage ...

  10. Modulation of mutagenicity of various mutagens by lignin derivatives.

    PubMed

    Mikulásová, Mária; Kosíková, Bozena

    2003-03-01

    The effect of lignin on cytotoxicity, mutagenicity and SOS response induced by 4-nitroquinoline-N-oxide (4NQO), 3-(5-nitro-2-furyl)acrylic acid (5NFAA), 2-nitrofluorene (2NF) as well as hydrogen peroxide was investigated in bacterial assay systems, i.e. the Ames test with Salmonella typhimurium TA98, TA100, TA102 and the SOS chromotest with Escherichia coli PQ37. Lignin preparations obtained from beech wood significantly decreased the mutagenicity induced by 4NQO, 2NF and H(2)O(2). In the case of mutagenicity induced by 5NFAA the effect was lower. Antimutagenic properties of lignin samples tested were shown also by SOS chromotest where lignin inhibited the ability of both 4NQO and H(2)O(2) to induce the SOS response. Derivatives of lignin including those from soft and hard wood, as well as from annual plants differ in their efficiency to inhibit the induction of the SOS response. The modified lignins isolated from beech and spruce wood exhibit a high level of protection. Lignins from annual plants-corn cobs and straw-only marginally evoked an antimutagenic response, but their effect was increased by hydrothermic treatment of both annual plants. The results obtained indicate the prospective utilization of lignin preparations as additive in chemo-prevention. The antimutagenic effect of lignin samples varies with the method of isolation and modification, as well as with the genetic origin of the lignin. PMID:12581535

  11. Dynamics and turnover of lignins in soils: a review

    NASA Astrophysics Data System (ADS)

    Thevenot, M.; Rumpel, C.; Dignac, M.-F.

    2009-04-01

    Lignins are amongst the most studied bio-macromolecules in natural environments, for their properties as biomarkers and their suggested influence on soil organic carbon dynamics. A large number of methods exists to characterize lignins, but the alkaline CuO oxidation is the most used for determining lignin fate in soils. The CuO oxidation products of lignins yield quantitative information (sum of V, S and C monomers) as well as qualitative information on the degradation of lignins (S/V, C/V, (Ad/Al)V,S…). The CuO-lignin products provide information on lignins but also on the environment and particularly on the present and past vegetation. Data from several studies were compiled in order to evaluate the relations between lignins in soils and various environmental parameters. The results of the multiple correspondence analysis (MCA) performed suggest that the lignin content in soils is directly related to the C and N contents, confirming its contribution to the pool of organic carbon. The lignin distribution appears also related to the climate and to the soil texture, which suggests the impact of these parameters on the lignin degradation and retention in soils, as observed for organic carbon (Burke et al., 1989). The total lignin content generally decreases with the soil depth and with the decreasing size of the granulometric fractions. Hence, the more lignins are degraded, the more they are associated with the finest fractions. In addition, it appears that lignin contents are linked to land-use. Thus, in accordance with the land cover, management type and amount of annual input, the forest soils are described by high contents of VSC, C and N, in contrast with the arable land. Lignins were often considered to greatly participate to the stock of slowly degradable and stable carbon in soils. However, several studies suggest that lignin turnover can be more rapid than that of the bulk soil organic carbon (SOC), suggesting that they are not stabilized in soil. On the

  12. Three QTL in the honey bee Apis mellifera L. suppress reproduction of the parasitic mite Varroa destructor.

    PubMed

    Behrens, Dieter; Huang, Qiang; Geßner, Cornelia; Rosenkranz, Peter; Frey, Eva; Locke, Barbara; Moritz, Robin F A; Kraus, F B

    2011-12-01

    Varroa destructor is a highly virulent ectoparasitic mite of the honey bee Apis mellifera and a major cause of colony losses for global apiculture. Typically, chemical treatment is essential to control the parasite population in the honey bee colony. Nevertheless a few honey bee populations survive mite infestation without any treatment. We used one such Varroa mite tolerant honey bee lineage from the island of Gotland, Sweden, to identify quantitative trait loci (QTL) controlling reduced mite reproduction. We crossed a queen from this tolerant population with drones from susceptible colonies to rear hybrid queens. Two hybrid queens were used to produce a mapping population of haploid drones. We discriminated drone pupae with and without mite reproduction, and screened the genome for potential QTL using a total of 216 heterozygous microsatellite markers in a bulk segregant analysis. Subsequently, we fine mapped three candidate target regions on chromosomes 4, 7, and 9. Although the individual effect of these three QTL was found to be relatively small, the set of all three had significant impact on suppression of V. destructor reproduction by epistasis. Although it is in principle possible to use these loci for marker-assisted selection, the strong epistatic effects between the three loci complicate selective breeding programs with the Gotland Varroa tolerant honey bee stock.

  13. An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum)

    PubMed Central

    Han, Koeun; Jeong, Hee-Jin; Yang, Hee-Bum; Kang, Sung-Min; Kwon, Jin-Kyung; Kim, Seungill; Choi, Doil; Kang, Byoung-Cheorl

    2016-01-01

    Most agricultural traits are controlled by quantitative trait loci (QTLs); however, there are few studies on QTL mapping of horticultural traits in pepper (Capsicum spp.) due to the lack of high-density molecular maps and the sequence information. In this study, an ultra-high-density map and 120 recombinant inbred lines (RILs) derived from a cross between C. annuum ‘Perennial’ and C. annuum ‘Dempsey’ were used for QTL mapping of horticultural traits. Parental lines and RILs were resequenced at 18× and 1× coverage, respectively. Using a sliding window approach, an ultra-high-density bin map containing 2,578 bins was constructed. The total map length of the map was 1,372 cM, and the average interval between bins was 0.53 cM. A total of 86 significant QTLs controlling 17 horticultural traits were detected. Among these, 32 QTLs controlling 13 traits were major QTLs. Our research shows that the construction of bin maps using low-coverage sequence is a powerful method for QTL mapping, and that the short intervals between bins are helpful for fine-mapping of QTLs. Furthermore, bin maps can be used to improve the quality of reference genomes by elucidating the genetic order of unordered regions and anchoring unassigned scaffolds to linkage groups. PMID:26744365

  14. First evidence for family-specific QTL for temperature-dependent sex reversal in Nile tilapia (Oreochromis niloticus).

    PubMed

    Lühmann, L M; Knorr, C; Hörstgen-Schwark, G; Wessels, S

    2012-01-01

    This study for the first time screens microsatellite markers for associations with the temperature-dependent sex of Oreochromis niloticus. Previous studies revealed markers on linkage groups (LG) 1, 3, and 23 to be linked to the phenotypic sex of Oreochromis spp. at normal rearing temperatures. Moreover, candidate genes for sex determination and differentiation have been mapped to these linkage groups. Here, 6 families of a temperature-treated genetically all-female (XX) F(1)-population were genotyped for 21 microsatellites on the 3 LGs. No population-wide QTL (quantitative trait loci) or marker trait associations could be detected. However, family-specific QTL were found on LG 1 flanked by UNH995 and UNH104, on LG 3 at the position of GM213, and on LG 23 next to GM283. Moreover, family-specific single marker associations for UNH995 and UNH104 on LG 1, GM213 on LG 3, as well as for UNH898 and GM283 on LG 23 were detected. Yet, marker trait associations could not explain the temperature-dependent sex of all fish in the respective families. The molecular cue for the temperature-dependent sex in Nile tilapia might partially coincide with allelic variants at major and minor genetic sex determining factors. Moreover, additional QTL contributing to variable liabilities towards temperature might persist on other LGs. PMID:22797471

  15. Three QTL in the honey bee Apis mellifera L. suppress reproduction of the parasitic mite Varroa destructor

    PubMed Central

    Behrens, Dieter; Huang, Qiang; Geßner, Cornelia; Rosenkranz, Peter; Frey, Eva; Locke, Barbara; Moritz, Robin F A; Kraus, F B

    2011-01-01

    Varroa destructor is a highly virulent ectoparasitic mite of the honey bee Apis mellifera and a major cause of colony losses for global apiculture. Typically, chemical treatment is essential to control the parasite population in the honey bee colony. Nevertheless a few honey bee populations survive mite infestation without any treatment. We used one such Varroa mite tolerant honey bee lineage from the island of Gotland, Sweden, to identify quantitative trait loci (QTL) controlling reduced mite reproduction. We crossed a queen from this tolerant population with drones from susceptible colonies to rear hybrid queens. Two hybrid queens were used to produce a mapping population of haploid drones. We discriminated drone pupae with and without mite reproduction, and screened the genome for potential QTL using a total of 216 heterozygous microsatellite markers in a bulk segregant analysis. Subsequently, we fine mapped three candidate target regions on chromosomes 4, 7, and 9. Although the individual effect of these three QTL was found to be relatively small, the set of all three had significant impact on suppression of V. destructor reproduction by epistasis. Although it is in principle possible to use these loci for marker-assisted selection, the strong epistatic effects between the three loci complicate selective breeding programs with the Gotland Varroa tolerant honey bee stock. PMID:22393513

  16. Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL.

    PubMed

    Dixit, Shalabh; Kumar Biswal, Akshaya; Min, Aye; Henry, Amelia; Oane, Rowena H; Raorane, Manish L; Longkumer, Toshisangba; Pabuayon, Isaiah M; Mutte, Sumanth K; Vardarajan, Adithi R; Miro, Berta; Govindan, Ganesan; Albano-Enriquez, Blesilda; Pueffeld, Mandy; Sreenivasulu, Nese; Slamet-Loedin, Inez; Sundarvelpandian, Kalaipandian; Tsai, Yuan-Ching; Raghuvanshi, Saurabh; Hsing, Yue-Ie C; Kumar, Arvind; Kohli, Ajay

    2015-01-01

    Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor 'no apical meristem' (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security. PMID:26507552

  17. Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL

    PubMed Central

    Dixit, Shalabh; Kumar Biswal, Akshaya; Min, Aye; Henry, Amelia; Oane, Rowena H.; Raorane, Manish L.; Longkumer, Toshisangba; Pabuayon, Isaiah M.; Mutte, Sumanth K.; Vardarajan, Adithi R.; Miro, Berta; Govindan, Ganesan; Albano-Enriquez, Blesilda; Pueffeld, Mandy; Sreenivasulu, Nese; Slamet-Loedin, Inez; Sundarvelpandian, Kalaipandian; Tsai, Yuan-Ching; Raghuvanshi, Saurabh; Hsing, Yue-Ie C.; Kumar, Arvind; Kohli, Ajay

    2015-01-01

    Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor ‘no apical meristem’ (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security. PMID:26507552

  18. Microbial utilization of lignin: available biotechnologies for its degradation and valorization.

    PubMed

    Palazzolo, Martín A; Kurina-Sanz, Marcela

    2016-10-01

    Lignocellulosic biomasses, either from non-edible plants or from agricultural residues, stock biomacromolecules that can be processed to produce both energy and bioproducts. Therefore, they become major candidates to replace petroleum as the main source of energy. However, to shift the fossil-based economy to a bio-based one, it is imperative to develop robust biotechnologies to efficiently convert lignocellulosic streams in power and platform chemicals. Although most of the biomass processing facilities use celluloses and hemicelluloses to produce bioethanol and paper, there is no consolidated bioprocess to produce valuable compounds out of lignin at industrial scale available currently. Usually, lignin is burned to provide heat or it remains as a by-product in different streams, thus arising environmental concerns. In this way, the biorefinery concept is not extended to completion. Due to Nature offers an arsenal of biotechnological tools through microorganisms to accomplish lignin valorization or degradation, an increasing number of projects dealing with these tasks have been described recently. In this review, outstanding reports over the last 6 years are described, comprising the microbial utilization of lignin to produce a variety of valuable compounds as well as to diminish its ecological impact. Furthermore, perspectives on these topics are given. PMID:27565783

  19. Microbial utilization of lignin: available biotechnologies for its degradation and valorization.

    PubMed

    Palazzolo, Martín A; Kurina-Sanz, Marcela

    2016-10-01

    Lignocellulosic biomasses, either from non-edible plants or from agricultural residues, stock biomacromolecules that can be processed to produce both energy and bioproducts. Therefore, they become major candidates to replace petroleum as the main source of energy. However, to shift the fossil-based economy to a bio-based one, it is imperative to develop robust biotechnologies to efficiently convert lignocellulosic streams in power and platform chemicals. Although most of the biomass processing facilities use celluloses and hemicelluloses to produce bioethanol and paper, there is no consolidated bioprocess to produce valuable compounds out of lignin at industrial scale available currently. Usually, lignin is burned to provide heat or it remains as a by-product in different streams, thus arising environmental concerns. In this way, the biorefinery concept is not extended to completion. Due to Nature offers an arsenal of biotechnological tools through microorganisms to accomplish lignin valorization or degradation, an increasing number of projects dealing with these tasks have been described recently. In this review, outstanding reports over the last 6 years are described, comprising the microbial utilization of lignin to produce a variety of valuable compounds as well as to diminish its ecological impact. Furthermore, perspectives on these topics are given.

  20. Increased cuticular carbon sequestration and lignin oxidation in response to soil warming

    NASA Astrophysics Data System (ADS)

    Feng, Xiaojuan; Simpson, André J.; Wilson, Kevin P.; Dudley Williams, D.; Simpson, Myrna J.

    2008-12-01

    Rising temperatures are predicted to accelerate the decomposition of labile soil organic compounds such as proteins and carbohydrates, whereas biochemically resistant compounds, such as lipids from leaf cuticles and roots and lignin from woody tissues, are expected to remain stable on decadal to centennial timescales. However, the extent to which soil warming changes the molecular composition of soil organic matter is poorly understood. Here we examine the impact of soil warming in a mixed temperate forest on the molecular make-up of soil organic matter. We show that the abundance of leaf-cuticle-derived compounds is increased following 14 months of soil warming; we confirm this with nuclear magnetic resonance spectra of soil organic matter extracts. In contrast, we find that the abundance of lignin-derived compounds is decreased after the same treatment, while soil fungi, the primary decomposers of lignin in soil, increase in abundance. We conclude that future warming could alter the composition of soil organic matter at the molecular level, accelerating lignin degradation and increasing leaf-cuticle-derived carbon sequestration. With annual litterfall predicted to increase in the world's major forests with a 3∘C warming, we suggest that future warming may enhance the sequestration of cuticular carbon in soil.

  1. QTL for seed iron and zinc concentration and content in a Mesoamerican common bean (Phaseolus vulgaris L.) population.

    PubMed

    Blair, Matthew W; Medina, Juliana I; Astudillo, Carolina; Rengifo, Judith; Beebe, Steve E; Machado, Gloria; Graham, Robin

    2010-10-01

    Iron and zinc deficiencies are human health problems found throughout the world and biofortification is a plant breeding-based strategy to improve the staple crops that could address these dietary constraints. Common bean is an important legume crop with two major genepools that has been the focus of genetic improvement for seed micronutrient levels. The objective of this study was to evaluate the inheritance of seed iron and zinc concentrations and contents in an intra-genepool Mesoamerican × Mesoamerican recombinant inbred line population grown over three sites in Colombia and to identify quantitative trait loci (QTL) for each mineral. The population had 110 lines and was derived from a high-seed iron and zinc climbing bean genotype (G14519) crossed with a low-mineral Carioca-type, prostrate bush bean genotype (G4825). The genetic map for QTL analysis was created from SSR and RAPD markers covering all 11 chromosomes of the common bean genome. A set of across-site, overlapping iron and zinc QTL was discovered on linkage group b06 suggesting a possibly pleiotropic locus and common physiology for mineral uptake or loading. Other QTL for mineral concentration or content were found on linkage groups b02, b03, b04, b07, b08 and b11 and together with the b06 cluster were mostly novel compared to loci found in previous studies of the Andean genepool or inter-genepool crosses. The discovery of an important new locus for seed iron and zinc concentrations may facilitate crop improvement and biofortification using the high-mineral genotype especially within the Mesoamerican genepool.

  2. Advanced Model Compounds for Understanding Acid-Catalyzed Lignin Depolymerization: Identification of Renewable Aromatics and a Lignin-Derived Solvent.

    PubMed

    Lahive, Ciaran W; Deuss, Peter J; Lancefield, Christopher S; Sun, Zhuohua; Cordes, David B; Young, Claire M; Tran, Fanny; Slawin, Alexandra M Z; de Vries, Johannes G; Kamer, Paul C J; Westwood, Nicholas J; Barta, Katalin

    2016-07-20

    The development of fundamentally new approaches for lignin depolymerization is challenged by the complexity of this aromatic biopolymer. While overly simplified model compounds often lack relevance to the chemistry of lignin, the direct use of lignin streams poses significant analytical challenges to methodology development. Ideally, new methods should be tested on model compounds that are complex enough to mirror the structural diversity in lignin but still of sufficiently low molecular weight to enable facile analysis. In this contribution, we present a new class of advanced (β-O-4)-(β-5) dilinkage models that are highly realistic representations of a lignin fragment. Together with selected β-O-4, β-5, and β-β structures, these compounds provide a detailed understanding of the reactivity of various types of lignin linkages in acid catalysis in conjunction with stabilization of reactive intermediates using ethylene glycol. The use of these new models has allowed for identification of novel reaction pathways and intermediates and led to the characterization of new dimeric products in subsequent lignin depolymerization studies. The excellent correlation between model and lignin experiments highlights the relevance of this new class of model compounds for broader use in catalysis studies. Only by understanding the reactivity of the linkages in lignin at this level of detail can fully optimized lignin depolymerization strategies be developed.

  3. De novo assembly, transcriptome characterization, lignin accumulation, and anatomic characteristics: novel insights into lignin biosynthesis during celery leaf development.

    PubMed

    Jia, Xiao-Ling; Wang, Guang-Long; Xiong, Fei; Yu, Xu-Run; Xu, Zhi-Sheng; Wang, Feng; Xiong, Ai-Sheng

    2015-01-01

    Celery of the family Apiaceae is a biennial herb that is cultivated and consumed worldwide. Lignin is essential for cell wall structural integrity, stem strength, water transport, mechanical support, and plant pathogen defense. This study discussed the mechanism of lignin formation at different stages of celery development. The transcriptome profile, lignin distribution, anatomical characteristics, and expression profile of leaves at three stages were analyzed. Regulating lignin synthesis in celery growth development has a significant economic value. Celery leaves at three stages were collected, and Illumina paired-end sequencing technology was used to analyze large-scale transcriptome sequences. From Stage 1 to 3, the collenchyma and vascular bundles in the petioles and leaf blades thickened and expanded, whereas the phloem and the xylem extensively developed. Spongy and palisade mesophyll tissues further developed and were tightly arranged. Lignin accumulation increased in the petioles and the mesophyll (palisade and spongy), and the xylem showed strong lignification. Lignin accumulation in different tissues and at different stages of celery development coincides with the anatomic characteristics and transcript levels of genes involved in lignin biosynthesis. Identifying the genes that encode lignin biosynthesis-related enzymes accompanied by lignin distribution may help elucidate the regulatory mechanisms of lignin biosynthesis in celery. PMID:25651889

  4. De novo assembly, transcriptome characterization, lignin accumulation, and anatomic characteristics: novel insights into lignin biosynthesis during celery leaf development

    PubMed Central

    Jia, Xiao-Ling; Wang, Guang-Long; Xiong, Fei; Yu, Xu-Run; Xu, Zhi-Sheng; Wang, Feng; Xiong, Ai-Sheng

    2015-01-01

    Celery of the family Apiaceae is a biennial herb that is cultivated and consumed worldwide. Lignin is essential for cell wall structural integrity, stem strength, water transport, mechanical support, and plant pathogen defense. This study discussed the mechanism of lignin formation at different stages of celery development. The transcriptome profile, lignin distribution, anatomical characteristics, and expression profile of leaves at three stages were analyzed. Regulating lignin synthesis in celery growth development has a significant economic value. Celery leaves at three stages were collected, and Illumina paired-end sequencing technology was used to analyze large-scale transcriptome sequences. From Stage 1 to 3, the collenchyma and vascular bundles in the petioles and leaf blades thickened and expanded, whereas the phloem and the xylem extensively developed. Spongy and palisade mesophyll tissues further developed and were tightly arranged. Lignin accumulation increased in the petioles and the mesophyll (palisade and spongy), and the xylem showed strong lignification. Lignin accumulation in different tissues and at different stages of celery development coincides with the anatomic characteristics and transcript levels of genes involved in lignin biosynthesis. Identifying the genes that encode lignin biosynthesis-related enzymes accompanied by lignin distribution may help elucidate the regulatory mechanisms of lignin biosynthesis in celery. PMID:25651889

  5. A facile method for processing lignin reinforced chitosan biopolymer microfibres: optimising the fibre mechanical properties through lignin type and concentration

    NASA Astrophysics Data System (ADS)

    Wang, K.; Loo, L. S.; Goh, K. L.

    2016-03-01

    A chitosan biopolymer microfibre—reinforced by lignin—has been processed by a wet-spinning method. To optimise the fibre mechanical and structural properties two types of lignin, with molecular weights 28 000 g mol-1 and 60 000 g mol-1, were examined and the chitosan fibre was blended with the respective lignin type at 1, 3, 5, 7 and 8 wt% lignin concentrations. The main effects of lignin type and concentration, as well as the interaction between the two parameters, on the fibre tensile stiffness, extensibility, strength and toughness were evaluated using the two-factor analysis of variance. Significant variations in the respective mechanical properties were observed with varying lignin concentrations (P < 0.05). The magnitude of the respective mechanical properties is low at 1 wt% but peaks at 3 wt% before decreasing steadily with increasing lignin concentration. Except for extensibility, significant variations in the strength and toughness were observed with respect to lignin type (P < 0.05) variations in the stiffness were masked by interactions between lignin type and concentration. These results were related to the dispersion of lignin in the fibre and the nature of the bonds between lignin and chitosan, based on findings from scanning electron microscopy and Fourier transform infrared spectroscopy. This new method for the fabrication of chitosan biopolymer microfibre is inexpensive and versatile and could lend itself to the production of high performance biocomposite structures.

  6. Effect of lignin on water vapor barrier, mechanical, and structural properties of agar/lignin composite films.

    PubMed

    Shankar, Shiv; Reddy, Jeevan Prasad; Rhim, Jong-Whan

    2015-11-01

    Biodegradable composite films were prepared using two renewable resources based biopolymers, agar and lignin alkali. The lignin was used as a reinforcing material and agar as a biopolymer matrix. The effect of lignin concentration (1, 3, 5, and 10wt%) on the performance of the composite films was studied. In addition, the mechanical, water vapor barrier, UV light barrier properties, FE-SEM, and TGA of the films were analyzed. The agar/lignin films exhibited higher mechanical and UV barrier properties along with lower water vapor permeability compared to the neat agar film. The FTIR and SEM results showed the compatibility of lignin with agar polymer. The swelling ratio and moisture content of agar/lignin composite films were decreased with increase in lignin content. The thermostability and char content of agar/lignin composite films increased with increased lignin content. The results suggested that agar/lignin films have a potential to be used as a UV barrier food packaging material for maintaining food safety and extending the shelf-life of the packaged food.

  7. De novo assembly, transcriptome characterization, lignin accumulation, and anatomic characteristics: novel insights into lignin biosynthesis during celery leaf development.

    PubMed

    Jia, Xiao-Ling; Wang, Guang-Long; Xiong, Fei; Yu, Xu-Run; Xu, Zhi-Sheng; Wang, Feng; Xiong, Ai-Sheng

    2015-02-05

    Celery of the family Apiaceae is a biennial herb that is cultivated and consumed worldwide. Lignin is essential for cell wall structural integrity, stem strength, water transport, mechanical support, and plant pathogen defense. This study discussed the mechanism of lignin formation at different stages of celery development. The transcriptome profile, lignin distribution, anatomical characteristics, and expression profile of leaves at three stages were analyzed. Regulating lignin synthesis in celery growth development has a significant economic value. Celery leaves at three stages were collected, and Illumina paired-end sequencing technology was used to analyze large-scale transcriptome sequences. From Stage 1 to 3, the collenchyma and vascular bundles in the petioles and leaf blades thickened and expanded, whereas the phloem and the xylem extensively developed. Spongy and palisade mesophyll tissues further developed and were tightly arranged. Lignin accumulation increased in the petioles and the mesophyll (palisade and spongy), and the xylem showed strong lignification. Lignin accumulation in different tissues and at different stages of celery development coincides with the anatomic characteristics and transcript levels of genes involved in lignin biosynthesis. Identifying the genes that encode lignin biosynthesis-related enzymes accompanied by lignin distribution may help elucidate the regulatory mechanisms of lignin biosynthesis in celery.

  8. Advanced Model Compounds for Understanding Acid-Catalyzed Lignin Depolymerization: Identification of Renewable Aromatics and a Lignin-Derived Solvent.

    PubMed

    Lahive, Ciaran W; Deuss, Peter J; Lancefield, Christopher S; Sun, Zhuohua; Cordes, David B; Young, Claire M; Tran, Fanny; Slawin, Alexandra M Z; de Vries, Johannes G; Kamer, Paul C J; Westwood, Nicholas J; Barta, Katalin

    2016-07-20

    The development of fundamentally new approaches for lignin depolymerization is challenged by the complexity of this aromatic biopolymer. While overly simplified model compounds often lack relevance to the chemistry of lignin, the direct use of lignin streams poses significant analytical challenges to methodology development. Ideally, new methods should be tested on model compounds that are complex enough to mirror the structural diversity in lignin but still of sufficiently low molecular weight to enable facile analysis. In this contribution, we present a new class of advanced (β-O-4)-(β-5) dilinkage models that are highly realistic representations of a lignin fragment. Together with selected β-O-4, β-5, and β-β structures, these compounds provide a detailed understanding of the reactivity of various types of lignin linkages in acid catalysis in conjunction with stabilization of reactive intermediates using ethylene glycol. The use of these new models has allowed for identification of novel reaction pathways and intermediates and led to the characterization of new dimeric products in subsequent lignin depolymerization studies. The excellent correlation between model and lignin experiments highlights the relevance of this new class of model compounds for broader use in catalysis studies. Only by understanding the reactivity of the linkages in lignin at this level of detail can fully optimized lignin depolymerization strategies be developed. PMID:27310182

  9. Enzymatic synthesis of lignin-siloxane hybrid functional polymers.

    PubMed

    Prasetyo, Endry Nugroho; Kudanga, Tukayi; Fischer, Roman; Eichinger, Reinhard; Nyanhongo, Gibson S; Guebitz, Georg M

    2012-02-01

    This study combines the properties of siloxanes and lignin polymers to produce hybrid functional polymers that can be used as adhesives, coating materials, and/or multifunctionalized thin-coating films. Lignin-silica hybrid copolymers were synthesized by using a sol-gel process. Laccases from Trametes hirsuta were used to oxidize lignosulphonates to enhance their reactivity towards siloxanes and then were incorporated into siloxane precursors undergoing a sol-gel process. In vitro copolymerization studies using pure lignin monomers with aminosilanes or ethoxytrimethylsilane and analysis by ²⁹Si NMR spectroscopy revealed hybrid products. Except for kraft lignin, an increase in lignin concentration positively affected the tensile strength in all samples. Similarly, the viscosity generally increased in all samples with increasing lignin concentration and also affected the curing time.

  10. Lignin profiling in extracted xylans by size-exclusion chromatography.

    PubMed

    Hutterer, Christian; Schild, Gabriele; Kliba, Gerhard; Potthast, Antje

    2016-10-20

    Utilization of the polymeric parts of lignocellulose is expected to gain increasing importance in future biorefinery scenarios. In that respect, a particular focus is placed on hemicelluloses from different wood species gained from an industrially feasible upgrading step in the production of dissolving pulps from paper pulps. During alkaline post-extractions for hemicellulose removal, residual lignins are extracted as well. They are either covalently linked to the extracted hardwood xylans or simply co-dissolved in the alkaline lye. In order to better describe the lignin in xylan containing lyes, a method for lignin profiling was set up by hyphenating size-exclusion chromatography of xylans with UV detection which facilitates visualization of the residual lignin distribution. Simultaneous lignin quantification was achieved with lignin standards prepared from Kraft cooking liquors. The setup presented may serve as advanced characterization for novel xylan products. PMID:27474629

  11. Mechanism of lignin inhibition of enzymatic biomass deconstruction

    DOE PAGES

    Vermaas, Josh V.; Petridis, Loukas; Qi, Xianghong; Schulz, Roland; Lindner, Benjamin; Smith, Jeremy. C.

    2015-12-01

    The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route to biofuel production. However, the inhibition of enzymatic activity in pretreated biomass by lignin severely limits the efficiency of this process. By performing atomic-detail molecular dynamics simulation of a biomass model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed lignin inhibition mechanisms. We find that lignin binds preferentially both to the elements of cellulose to which the cellulases also preferentially bind (the hydrophobic faces) and also to the specific residues on the cellulose-binding module of the cellulase that are critical for cellulose bindingmore » of TrCel7A (Y466, Y492, and Y493). In conclusion, lignin thus binds exactly where for industrial purposes it is least desired, providing a simple explanation of why hydrolysis yields increase with lignin removal.« less

  12. Directional synthesis of ethylbenzene through catalytic transformation of lignin.

    PubMed

    Fan, Minghui; Jiang, Peiwen; Bi, Peiyan; Deng, Shumei; Yan, Lifeng; Zhai, Qi; Wang, Tiejun; Li, Quanxin

    2013-09-01

    Transformation of lignin to ethylbenzene can provide an important bulk raw material for the petrochemical industry. This work explored the production of ethylbenzene from lignin through the directional catalytic depolymerization of lignin into the aromatic monomers followed by the selective alkylation of the aromatic monomers. For the first step, the aromatics selectivity of benzene derived from the catalytic depolymerization of lignin reached about 90.2 C-mol% over the composite catalyst of Re-Y/HZSM-5 (25). For the alkylation of the aromatic monomers in the second step, the highest selectivity of ethylbenzene was about 72.3 C-mol% over the HZSM-5 (25) catalyst. The reaction pathway for the transformation of lignin to ethylbenzene was also addressed. Present transformation potentially provides a useful approach for the production of the basic petrochemical material and development of high-end chemicals utilizing lignin as the abundant natural aromatic resource.

  13. Creation of degenerative copolymers and plastics of lignin

    SciTech Connect

    Meister, J.J.; Chen, M.J.; McNichols, W.

    1995-12-01

    Polymers and plastics which degrade under environmental conditions can be made by graft copolymerization on lignin. The reaction can be run by solution, bulk, and precipitation polymerization. Poly(lignin-g-(1-phenylethylene)) and poly(lignin-g-(1-methyl-l-(1-oxo-2-oxypropyl)ethylene)) can be made by combining lignin, monomer, calcium chloride, and a hydroperoxide in such solvents as 1-methyl-2-pyrrolidinone, dimethylsulfoxide, dimethylacetamide, dimethylformamide, pyridine, or water-polar organic solvent mixtures. The products contain 4 to 50 wt. percent lignin with the rest of the material being polymeric sidechain if the copolymer is properly purified. Properties of the products depend on and are controlled by the sidechain attached to the lignin. Properties such as solubility, tensile strength, surface activity, glass transition temperature, and modulus can be altered by altering the sidechain structure and length.

  14. Comparison of lignin extraction processes: Economic and environmental assessment.

    PubMed

    Carvajal, Juan C; Gómez, Álvaro; Cardona, Carlos A

    2016-08-01

    This paper presents the technical-economic and environmental assessment of four lignin extraction processes from two different raw materials (sugarcane bagasse and rice husks). The processes are divided into two categories, the first processes evaluates lignin extraction with prior acid hydrolysis step, while in the second case the extraction processes are evaluated standalone for a total analysis of 16 scenarios. Profitability indicators as the net present value (NPV) and environmental indicators as the potential environmental impact (PEI) are used through a process engineering approach to understand and select the best lignin extraction process. The results show that both economically and environmentally process with sulfites and soda from rice husk presents the best results; however the quality of lignin obtained with sulfites is not suitable for high value-added products. Then, the soda is an interesting option for the extraction of lignin if high quality lignin is required for high value-added products at low costs.

  15. Redistribution of Lignin Caused by Dilute Acid Pretreatment of Biomass

    SciTech Connect

    Johnson, D. K.; Donohoe, B. S.; Katahira, R.; Tucker, M. P.; Vinzant, T. B.; Himmel, M. E.

    2012-01-01

    Research conducted at NREL has shown that lignin undergoes a phase transition during thermochemical pretreatments conducted above its glass transition temperature. The lignin coalesces within the plant cell wall and appears as microscopic droplets on cell surfaces. It is clear that pretreatment causes significant changes in lignin distribution in pretreatments at all scales from small laboratory reactors to pilot scale reactors. A method for selectively extracting lignin droplets from the surfaces of pretreated cell walls has allowed us to characterize the chemical nature and molecular weight distribution of this fraction. The effect of lignin redistribution on the digestibility of pretreated solids has also been tested. It is clear that removal of the droplets increases the digestibility of pretreated corn stover. The improved digestibility could be due to decreased non-specific binding of enzymes to lignin in the droplets, or because the droplets no longer block access to cellulose.

  16. Mechanism of lignin inhibition of enzymatic biomass deconstruction

    SciTech Connect

    Vermaas, Josh V.; Petridis, Loukas; Qi, Xianghong; Schulz, Roland; Lindner, Benjamin; Smith, Jeremy. C.

    2015-12-01

    The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route to biofuel production. However, the inhibition of enzymatic activity in pretreated biomass by lignin severely limits the efficiency of this process. By performing atomic-detail molecular dynamics simulation of a biomass model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed lignin inhibition mechanisms. We find that lignin binds preferentially both to the elements of cellulose to which the cellulases also preferentially bind (the hydrophobic faces) and also to the specific residues on the cellulose-binding module of the cellulase that are critical for cellulose binding of TrCel7A (Y466, Y492, and Y493). In conclusion, lignin thus binds exactly where for industrial purposes it is least desired, providing a simple explanation of why hydrolysis yields increase with lignin removal.

  17. Comparison of lignin extraction processes: Economic and environmental assessment.

    PubMed

    Carvajal, Juan C; Gómez, Álvaro; Cardona, Carlos A

    2016-08-01

    This paper presents the technical-economic and environmental assessment of four lignin extraction processes from two different raw materials (sugarcane bagasse and rice husks). The processes are divided into two categories, the first processes evaluates lignin extraction with prior acid hydrolysis step, while in the second case the extraction processes are evaluated standalone for a total analysis of 16 scenarios. Profitability indicators as the net present value (NPV) and environmental indicators as the potential environmental impact (PEI) are used through a process engineering approach to understand and select the best lignin extraction process. The results show that both economically and environmentally process with sulfites and soda from rice husk presents the best results; however the quality of lignin obtained with sulfites is not suitable for high value-added products. Then, the soda is an interesting option for the extraction of lignin if high quality lignin is required for high value-added products at low costs. PMID:27174614

  18. Green Diesel from Kraft Lignin in Three Steps.

    PubMed

    Löfstedt, Joakim; Dahlstrand, Christian; Orebom, Alexander; Meuzelaar, Gerrit; Sawadjoon, Supaporn; Galkin, Maxim V; Agback, Peter; Wimby, Martin; Corresa, Elena; Mathieu, Yannick; Sauvanaud, Laurent; Eriksson, Sören; Corma, Avelino; Samec, Joseph S M

    2016-06-22

    Precipitated kraft lignin from black liquor was converted into green diesel in three steps. A mild Ni-catalyzed transfer hydrogenation/hydrogenolysis using 2-propanol generated a lignin residue in which the ethers, carbonyls, and olefins were reduced. An organocatalyzed esterification of the lignin residue with an in situ prepared tall oil fatty acid anhydride gave an esterified lignin residue that was soluble in light gas oil. The esterified lignin residue was coprocessed with light gas oil in a continous hydrotreater to produce a green diesel. This approach will enable the development of new techniques to process commercial lignin in existing oil refinery infrastructures to standardized transportation fuels in the future. PMID:27246391

  19. Mendelizing all Components of a Pyramid of Three Yield QTL in Tomato.

    PubMed

    Gur, Amit; Zamir, Dani

    2015-01-01

    Molecular markers allowed breeders to mendelize quantitative trait loci (QTL) providing another demonstration that quantitative traits are governed by the same principles as single qualitative genes. This research extends the QTL analysis to two and three QTL and tests our ability to mendelize an oligogenic trait. In tomato, agricultural yield is determined by the weight of the fruits harvested per unit area and the total soluble solids (% Brix)-sugars and acids. The current study explores the segregation of multiple independent yield-related QTL that were identified and mapped using introgression lines (IL) of Solanum pennellii in cultivated processing tomato (S. lycopersicum). We screened 45 different double and triple IL-QTL combinations for agricultural yield, to identify QTL pyramids that behaved in an additive manner and were suitable substrate for mendelizing an oligogenic trait. A pyramid of three independent QTL that significantly improved Brix(∗)Yield (BXY - the soluble solids output per unit area) compared to M82 was selected. In the progenies of the tri-hybrid we bred using markers a nearly isogenic 'immortalized F2.' While the common mode of QTL-QTL interactions across the 45 IL-QTLs combinations was less than additive, the three QTLs in the selected triple-stack performed in an additive manner which made it an exceptional material for breeding. This study demonstrates that using the phenotypic effect of all 27 possible QTL-alleles combinations it is possible to make reliable predictions about the genotypes that will maximize the yield.

  20. Mendelizing all Components of a Pyramid of Three Yield QTL in Tomato.

    PubMed

    Gur, Amit; Zamir, Dani

    2015-01-01

    Molecular markers allowed breeders to mendelize quantitative trait loci (QTL) providing another demonstration that quantitative traits are governed by the same principles as single qualitative genes. This research extends the QTL analysis to two and three QTL and tests our ability to mendelize an oligogenic trait. In tomato, agricultural yield is determined by the weight of the fruits harvested per unit area and the total soluble solids (% Brix)-sugars and acids. The current study explores the segregation of multiple independent yield-related QTL that were identified and mapped using introgression lines (IL) of Solanum pennellii in cultivated processing tomato (S. lycopersicum). We screened 45 different double and triple IL-QTL combinations for agricultural yield, to identify QTL pyramids that behaved in an additive manner and were suitable substrate for mendelizing an oligogenic trait. A pyramid of three independent QTL that significantly improved Brix(∗)Yield (BXY - the soluble solids output per unit area) compared to M82 was selected. In the progenies of the tri-hybrid we bred using markers a nearly isogenic 'immortalized F2.' While the common mode of QTL-QTL interactions across the 45 IL-QTLs combinations was less than additive, the three QTLs in the selected triple-stack performed in an additive manner which made it an exceptional material for breeding. This study demonstrates that using the phenotypic effect of all 27 possible QTL-alleles combinations it is possible to make reliable predictions about the genotypes that will maximize the yield. PMID:26697048

  1. Modeling lignin liquefaction: 1. Catalytic hydroprocessing of lignin-related methoxyphenols and interaromatic unit linkages

    SciTech Connect

    Petrocelli, F.P.; Klein, M.T.

    1987-01-01

    The reactions of two sets of lignin model compounds over a sulfided CoOMoO/sub 3//..gamma..-Al/sub 2/O/sub 3/ catalyst were studied. The first set mimicked lignin methoxyphenol residues and comprised 4-methyl-guaiacol, 4-methylcatechol, eugenol and vanillin. Deoxygenation and hydrogenation were facile and led to ultimate molar yields of single-ring products as high as 0.70. The selectivity to single-ring products increased with increases in temperature. o-hydroxydiphenylmethane, phenyl ether and o,o'-biphenol constituted the second set that mimicked thermally stable lignin bonds. Fragmentation of o-hydroxydiphenylmethane and phenyl ether occurred readily; o,o'-biphenol reacted to dibenzofuran.

  2. Evidence for lignin oxidation by the giant panda fecal microbiome.

    PubMed

    Fang, Wei; Fang, Zemin; Zhou, Peng; Chang, Fei; Hong, Yuzhi; Zhang, Xuecheng; Peng, Hui; Xiao, Yazhong

    2012-01-01

    The digestion of lignin and lignin-related phenolic compounds from bamboo by giant pandas has puzzled scientists because of the lack of lignin-degrading genes in the genome of the bamboo-feeding animals. We constructed a 16S rRNA gene library from the microorganisms derived from the giant panda feces to identify the possibility for the presence of potential lignin-degrading bacteria. Phylogenetic analysis showed that the phylotypes of the intestinal bacteria were affiliated with the phyla Proteobacteria (53%) and Firmicutes (47%). Two phylotypes were affiliated with the known lignin-degrading bacterium Pseudomonas putida and the mangrove forest bacteria. To test the hypothesis that microbes in the giant panda gut help degrade lignin, a metagenomic library of the intestinal bacteria was constructed and screened for clones that contained genes encoding laccase, a lignin-degrading related enzyme. A multicopper oxidase gene, designated as lac51, was identified from a metagenomic clone. Sequence analysis and copper content determination indicated that Lac51 is a laccase rather than a metallo-oxidase and may work outside its original host cell because it has a TAT-type signal peptide and a transmembrane segment at its N-terminus. Lac51 oxidizes a variety of lignin-related phenolic compounds, including syringaldazine, 2,6-dimethoxyphenol, ferulic acid, veratryl alcohol, guaiacol, and sinapinic acid at conditions that simulate the physiologic environment in giant panda intestines. Furthermore, in the presence of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), syringic acid, or ferulic acid as mediators, the oxidative ability of Lac51 on lignin was promoted. The absorbance of lignin at 445 nm decreased to 36% for ABTS, 51% for syringic acid, and 51% for ferulic acid after incubation for 10 h. Our findings demonstrate that the intestinal bacteria of giant pandas may facilitate the oxidation of lignin moieties, thereby clarifying the digestion of bamboo lignin

  3. Lignin transformations and reactivity upon ozonation in aqueous media

    NASA Astrophysics Data System (ADS)

    Khudoshin, A. G.; Mitrofanova, A. N.; Lunin, V. V.

    2012-03-01

    The reaction of ozone with lignin in aqueous acidic solutions is investigated. The Danckwerst model is used to describe the kinetics of gas/liquid processes occurring in a bubble reactor. The efficient ozonation rate of a soluble lignin analog, sodium lignosulfate, is determined. The main lines of the reaction between ozone and lignin are revealed on the basis of kinetic analysis results and IR and UV spectroscopy data.

  4. Evidence for Lignin Oxidation by the Giant Panda Fecal Microbiome

    PubMed Central

    Zhou, Peng; Chang, Fei; Hong, Yuzhi; Zhang, Xuecheng; Peng, Hui; Xiao, Yazhong

    2012-01-01

    The digestion of lignin and lignin-related phenolic compounds from bamboo by giant pandas has puzzled scientists because of the lack of lignin-degrading genes in the genome of the bamboo-feeding animals. We constructed a 16S rRNA gene library from the microorganisms derived from the giant panda feces to identify the possibility for the presence of potential lignin-degrading bacteria. Phylogenetic analysis showed that the phylotypes of the intestinal bacteria were affiliated with the phyla Proteobacteria (53%) and Firmicutes (47%). Two phylotypes were affiliated with the known lignin-degrading bacterium Pseudomonas putida and the mangrove forest bacteria. To test the hypothesis that microbes in the giant panda gut help degrade lignin, a metagenomic library of the intestinal bacteria was constructed and screened for clones that contained genes encoding laccase, a lignin-degrading related enzyme. A multicopper oxidase gene, designated as lac51, was identified from a metagenomic clone. Sequence analysis and copper content determination indicated that Lac51 is a laccase rather than a metallo-oxidase and may work outside its original host cell because it has a TAT-type signal peptide and a transmembrane segment at its N-terminus. Lac51 oxidizes a variety of lignin-related phenolic compounds, including syringaldazine, 2,6-dimethoxyphenol, ferulic acid, veratryl alcohol, guaiacol, and sinapinic acid at conditions that simulate the physiologic environment in giant panda intestines. Furthermore, in the presence of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), syringic acid, or ferulic acid as mediators, the oxidative ability of Lac51 on lignin was promoted. The absorbance of lignin at 445 nm decreased to 36% for ABTS, 51% for syringic acid, and 51% for ferulic acid after incubation for 10 h. Our findings demonstrate that the intestinal bacteria of giant pandas may facilitate the oxidation of lignin moieties, thereby clarifying the digestion of bamboo

  5. Helicoverpa zea (Lepidoptera: Noctuidae) and Spodoptera frugiperda (Lepidoptera: Noctuidae) Responses to Sorghum bicolor (Poales: Poaceae) Tissues From Lowered Lignin Lines

    PubMed Central

    Dowd, Patrick F.; Sattler, Scott E.

    2015-01-01

    The presence of lignin within biomass impedes the production of liquid fuels. Plants with altered lignin content and composition are more amenable to lignocellulosic conversion to ethanol and other biofuels but may be more susceptible to insect damage where lignin is an important resistance factor. However, reduced lignin lines of switchgrasses still retained insect resistance in prior studies. Therefore, we hypothesized that sorghum lines with lowered lignin content will also retain insect resistance. Sorghum excised leaves and stalk pith Sorghum bicolor (L.) Moench (Poales: Poaceae) from near isogenic brown midrib (bmr) 6 and 12 mutants lines, which have lowered lignin content and increased lignocellulosic ethanol conversion efficiency, were examined for insect resistance relative to wild-type (normal BTx623). Greenhouse and growth chamber grown plant tissues were fed to first-instar larvae of corn earworms, Helicoverpa zea (Boddie) and fall armyworms Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), two sorghum major pests. Younger bmr leaves had significantly greater feeding damage in some assays than wild-type leaves, but older bmr6 leaves generally had significantly less damage than wild-type leaves. Caterpillars feeding on the bmr6 leaves often weighed significantly less than those feeding on wild-type leaves, especially in the S. frugiperda assays. Larvae fed the pith from bmr stalks had significantly higher mortality compared with those larvae fed on wild-type pith, which suggested that bmr pith was more toxic. Thus, reducing lignin content or changing subunit composition of bioenergy grasses does not necessarily increase their susceptibility to insects and may result in increased resistance, which would contribute to sustainable production. PMID:25601946

  6. Genetic control of soybean seed oil: II. QTL and genes that increase oil concentration without decreasing protein or with increased seed yield.

    PubMed

    Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

    2013-06-01

    Soybean [Glycine max (L.) Merrill] seed oil is the primary global source of edible oil and a major renewable and sustainable feedstock for biodiesel production. Therefore, increasing the relative oil concentration in soybean is desirable; however, that goal is complex due to the quantitative nature of the oil concentration trait and possible effects on major agronomic traits such as seed yield or protein concentration. The objectives of the present study were to study the relationship between seed oil concentration and important agronomic and seed quality traits, including seed yield, 100-seed weight, protein concentration, plant height, and days to maturity, and to identify oil quantitative trait loci (QTL) that are co-localized with the traits evaluated. A population of 203 F4:6 recombinant inbred lines, derived from a cross between moderately high oil soybean genotypes OAC Wallace and OAC Glencoe, was developed and grown across multiple environments in Ontario, Canada, in 2009 and 2010. Among the 11 QTL associated with seed oil concentration in the population, which were detected using either single-factor ANOVA or multiple QTL mapping methods, the number of QTL that were co-localized with other important traits QTL were six for protein concentration, four for seed yield, two for 100-seed weight, one for days to maturity, and one for plant height. The oil-beneficial allele of the QTL tagged by marker Sat_020 was positively associated with seed protein concentration. The oil favorable alleles of markers Satt001 and GmDGAT2B were positively correlated with seed yield. In addition, significant two-way epistatic interactions, where one of the interacting markers was solely associated with seed oil concentration, were identified for the selected traits in this study. The number of significant epistatic interactions was seven for yield, four for days to maturity, two for 100-seed weight, one for protein concentration, and one for plant height. The identified molecular

  7. Identification of QTL in soybean underlying resistance to herbivory by Japanese beetles (Popillia japonica, Newman).

    PubMed

    Yesudas, C R; Sharma, H; Lightfoot, D A

    2010-07-01

    Soybean [Glycine max (L.) Merr.] was one of the most important legume crops in the world in 2010. Japanese beetles (JB; Popillia japonica, Newman) in the US were an introduced and potentially damaging insect pest for soybean. JBs are likely to spread across the US if global warming occurs. Resistance to JB in soybean was previously reported only in plant introductions. The aims here were to identify loci underlying resistance to JB herbivory in recombinant inbred lines (RILs) derived from the cross of Essex x Forrest cultivars (EF94) and to correlate those with loci with factors that confer insect resistance in soybean cultivars. The RIL population was used to map 413 markers, 238 satellite markers and 177 other DNA markers. Field data were from two environments over 2 years. Pest severity (PS) measured defoliation on a 0-9 scale. Pest incidence (PI) was the percentage of plants within each RIL with beetles on them. Antibiosis and antixenosis data were from feeding assays with detached leaves in petri plates. Five QTL were detected for the mean PS field trait (16% < R (2) < 27%). The loci were within the intervals Satt632-A2D8 on linkage group (LG) A2 (chromosome 8); Satt583-Satt415 on LG B1 (11); Satt009-Satt530 on LG N (3); and close to two markers OB02_140 (LG E; 20 cM from Satt572) and OZ15_150 LG (19 cM from Satt291 C2). Two QTL were detected for the mean PI field trait (16% < R (2) < 18%) close to Satt385 on LG A1 and Satt440 on LG I. The no choice feeding studies detected three QTL that were significant; two for antixenosis (22% < R (2) < 24%) between Satt632-A2D8 on LG A2 (8) and Sat_039-Satt160 on LG F (13); and a major locus effect (R (2) = 54%) for antibiosis on LG D2 (17) between Satt464-Satt488. Therefore, loci underlying resistance to JB herbivory were a mixture of major and minor gene effects. Some loci were within regions underlying resistance to soybean cyst nematode (LGs A2 and I) and root knot nematode (LG F) but not other major loci underlying

  8. Uv Photofragmentation Spectroscopy of Model Lignin-Alkali Ion Complexes: Extending Lignomics Into the Spectroscopic Regime

    NASA Astrophysics Data System (ADS)

    Dean, Jacob C.; Burke, Nicole L.; Hopkins, John R.; Redwine, James; Biswas, Bidyut; Ramachandran, P. V.; McLuckey, Scott A.; Zwier, Timothy S.

    2014-06-01

    Lignin is a heteroaromatic biopolymer that is an essential component in the cell wall of plants. The structural and chemical properties of lignin provide plants with macroscopic structural rigidity, and protection against microbial invasion leading to subsequent cell wall degradation. For this reason, lignin presents a major inhibition to the efficient harvesting of biomass. Given the variability of lignin composition and structure among species, environment, etc., the field of "lignomics" seeks to "sequence" lignin oligomers into constituent unit types (H, G, S) and linkages. This is predominantly done by means of tandem mass-spectrometry, by first generating a library of characteristic fragmentation pathways built from collision-induced dissociation of model dilignol ions, and applying them to the interpretation of fragmentation in larger ions. While these methods have proven powerful, UV photofragmentation spectroscopy of lignin ions cooled in a 22-pole cold ion trap provides an alternative approach to lignomics based on fragmentation following resonant UV excitation. This approach serves as a complimentary method to pure MSn-based methods with the potential for unveiling dissociation pathways only accessed by UV excitation. Further, the multichromophoric nature of lignin enables site-selectivity for the energy imparted into the molecule/ion when differentiation of the site absorptions may be possible. IR spectroscopy of the cold ions can be used for detailed analysis of the preferred conformations and binding sites of metal cations. UV spectroscopy and photofragmentation mass spectrometry has been carried out on the model (G-type) β-O-4 and β-β dilignol linkages complexed with Li+ and Na+. The UV spectral signatures were found to vary between dilignols and metal complexes, and unique photofragmentation pathways were observed among the four complexes. IR spectroscopy in the OH stretch region was used as a probe of the conformation and binding preferences. In

  9. Identification of expression QTL (eQTL) of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits

    PubMed Central

    2010-01-01

    Background Genetic analysis of transcriptional profiles is a promising approach for identifying and dissecting the genetics of complex traits like meat performance. Accordingly, expression levels obtained by microarray analysis were taken as phenotypes in a linkage analysis to map eQTL. Moreover, expression levels were correlated with traits related to meat quality and principle components with high loadings of these traits. By using an up-to-date annotation and localization of the respective probe-sets, the integration of eQTL mapping data and information of trait correlated expression finally served to point to candidate genes for meat quality traits. Results Genome-wide transcriptional profiles of M. longissimus dorsi RNAs samples of 74 F2 animals of a pig resource population revealed 11,457 probe-sets representing genes expressed in the muscle. Linkage analysis of expression levels of these probe-sets provided 9,180 eQTL at the suggestive significance threshold of LOD > 2. We mapped 653 eQTL on the same chromosome as the corresponding gene and these were designated as 'putative cis-eQTL'. In order to link eQTL to the traits of interest, probe-sets were addressed with relative transcript abundances that showed correlation with meat quality traits at p ≤ 0.05. Out of the 653 'putative cis-eQTL', 262 transcripts were correlated with at least one meat quality trait. Furthermore, association of expression levels with composite traits with high loadings for meat quality traits generated by principle component analysis were taken into account leading to a list of 85 genes exhibiting cis-eQTL and trait dependent expression. Conclusion Holistic expression profiling was integrated with QTL analysis for meat quality traits. Correlations between transcript abundance and meat quality traits, combined with genetic positional information of eQTL allowed us to prioritise candidate genes for further study. PMID:20950486

  10. QTL mapping in outbred half-sib families using Bayesian model selection.

    PubMed

    Fang, M; Liu, J; Sun, D; Zhang, Y; Zhang, Q; Zhang, Y; Zhang, S

    2011-09-01

    In this article, we propose a model selection method, the Bayesian composite model space approach, to map quantitative trait loci (QTL) in a half-sib population for continuous and binary traits. In our method, the identity-by-descent-based variance component model is used. To demonstrate the performance of this model, the method was applied to map QTL underlying production traits on BTA6 in a Chinese half-sib dairy cattle population. A total of four QTLs were detected, whereas only one QTL was identified using the traditional least square (LS) method. We also conducted two simulation experiments to validate the efficiency of our method. The results suggest that the proposed method based on a multiple-QTL model is efficient in mapping multiple QTL for an outbred half-sib population and is more powerful than the LS method based on a single-QTL model.

  11. Cell Specific eQTL Analysis without Sorting Cells

    PubMed Central

    Esko, Tõnu; Peters, Marjolein J.; Schurmann, Claudia; Schramm, Katharina; Kettunen, Johannes; Yaghootkar, Hanieh; Fairfax, Benjamin P.; Andiappan, Anand Kumar; Li, Yang; Fu, Jingyuan; Karjalainen, Juha; Platteel, Mathieu; Visschedijk, Marijn; Weersma, Rinse K.; Kasela, Silva; Milani, Lili; Tserel, Liina; Peterson, Pärt; Reinmaa, Eva; Hofman, Albert; Uitterlinden, André G.; Rivadeneira, Fernando; Homuth, Georg; Petersmann, Astrid; Lorbeer, Roberto; Prokisch, Holger; Meitinger, Thomas; Herder, Christian; Roden, Michael; Grallert, Harald; Ripatti, Samuli; Perola, Markus; Wood, Andrew R.; Melzer, David; Ferrucci, Luigi; Singleton, Andrew B.; Hernandez, Dena G.; Knight, Julian C.; Melchiotti, Rossella; Lee, Bernett; Poidinger, Michael; Zolezzi, Francesca; Larbi, Anis; Wang, De Yun; van den Berg, Leonard H.; Veldink, Jan H.; Rotzschke, Olaf; Makino, Seiko; Salomaa, Veikko; Strauch, Konstantin; Völker, Uwe; van Meurs, Joyce B. J.; Metspalu, Andres; Wijmenga, Cisca; Jansen, Ritsert C.; Franke, Lude

    2015-01-01

    The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn’s disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus. PMID:25955312

  12. Cell Specific eQTL Analysis without Sorting Cells.

    PubMed

    Westra, Harm-Jan; Arends, Danny; Esko, Tõnu; Peters, Marjolein J; Schurmann, Claudia; Schramm, Katharina; Kettunen, Johannes; Yaghootkar, Hanieh; Fairfax, Benjamin P; Andiappan, Anand Kumar; Li, Yang; Fu, Jingyuan; Karjalainen, Juha; Platteel, Mathieu; Visschedijk, Marijn; Weersma, Rinse K; Kasela, Silva; Milani, Lili; Tserel, Liina; Peterson, Pärt; Reinmaa, Eva; Hofman, Albert; Uitterlinden, André G; Rivadeneira, Fernando; Homuth, Georg; Petersmann, Astrid; Lorbeer, Roberto; Prokisch, Holger; Meitinger, Thomas; Herder, Christian; Roden, Michael; Grallert, Harald; Ripatti, Samuli; Perola, Markus; Wood, Andrew R; Melzer, David; Ferrucci, Luigi; Singleton, Andrew B; Hernandez, Dena G; Knight, Julian C; Melchiotti, Rossella; Lee, Bernett; Poidinger, Michael; Zolezzi, Francesca; Larbi, Anis; Wang, De Yun; van den Berg, Leonard H; Veldink, Jan H; Rotzschke, Olaf; Makino, Seiko; Salomaa, Veikko; Strauch, Konstantin; Völker, Uwe; van Meurs, Joyce B J; Metspalu, Andres; Wijmenga, Cisca; Jansen, Ritsert C; Franke, Lude

    2015-05-01

    The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn's disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus. PMID:25955312

  13. Restricting lignin and enhancing sugar deposition in secondary cell walls enhances monomeric sugar release after low temperature ionic liquid pretreatment

    DOE PAGES

    Scullin, Chessa; Cruz, Alejandro G.; Chuang, Yi -De; Simmons, Blake A.; Loque, Dominique; Singh, Seema

    2015-07-04

    Lignocellulosic biomass has the potential to be a major source of renewable sugar for biofuel production. Before enzymatic hydrolysis, biomass must first undergo a pretreatment step in order to be more susceptible to saccharification and generate high yields of fermentable sugars. Lignin, a complex, interlinked, phenolic polymer, associates with secondary cell wall polysaccharides, rendering them less accessible to enzymatic hydrolysis. Herein, we describe the analysis of engineered Arabidopsis lines where lignin biosynthesis was repressed in fiber tissues but retained in the vessels, and polysaccharide deposition was enhanced in fiber cells with little to no apparent negative impact on growth phenotype.

  14. Restricting lignin and enhancing sugar deposition in secondary cell walls enhances monomeric sugar release after low temperature ionic liquid pretreatment

    SciTech Connect

    Scullin, Chessa; Cruz, Alejandro G.; Chuang, Yi -De; Simmons, Blake A.; Loque, Dominique; Singh, Seema

    2015-07-04

    Lignocellulosic biomass has the potential to be a major source of renewable sugar for biofuel production. Before enzymatic hydrolysis, biomass must first undergo a pretreatment step in order to be more susceptible to saccharification and generate high yields of fermentable sugars. Lignin, a complex, interlinked, phenolic polymer, associates with secondary cell wall polysaccharides, rendering them less accessible to enzymatic hydrolysis. Herein, we describe the analysis of engineered Arabidopsis lines where lignin biosynthesis was repressed in fiber tissues but retained in the vessels, and polysaccharide deposition was enhanced in fiber cells with little to no apparent negative impact on growth phenotype.

  15. Highly selective generation of vanillin by anodic degradation of lignin: a combined approach of electrochemistry and product isolation by adsorption

    PubMed Central

    Schmitt, Dominik; Regenbrecht, Carolin; Hartmer, Marius; Stecker, Florian

    2015-01-01

    Summary The oxidative degradation of lignin into a variety of valuable products has been under investigation since the first half of the last century. Especially, the chance to claim this cheap, abundant and renewable source for the production of the important aroma chemical vanillin (1) was one of the major driving forces of lignin research. So far most of the developed methods fail in technical application since no viable concept for work-up is included. This work represents a combined approach of electrochemical conversion of Kraft lignin and product recovery by adsorption on a strongly basic anion exchange resin. Electrolysis conditions are optimized regarding reaction temperatures below 100 °C allowing operation of aqueous electrolytes in simple experimental set-up. Employing ion exchange resins gives rise to a selective removal of low molecular weight phenols from the strongly alkaline electrolyte without acidification and precipitation of remaining lignin. The latter represents a significant advantage compared with conventional work-up protocols of lignin solutions. PMID:25977721

  16. Biomarker signature in tropical wetland: lignin phenol vegetation index (LPVI) and its implications for reconstructing the paleoenvironment.

    PubMed

    Tareq, Shafi M; Tanaka, Noriyuki; Ohta, Keiichi

    2004-05-25

    Organic matter of a peat core (3.60 m, 7428 years BP) collected from Rawa Danau, west Java, Indonesia, was analyzed to evaluate the early diagenetic fates of lignin in a tropical wetland and to reconstruct past vegetation and climate changes. Vertical profiles of (Ad/Al)v, (Ad/Al)s, and lambda(8) show that the lignin composition is well preserved in a sub-aqueous environment under reducing conditions. The sedimentary terrigenous plant material at Rawa Danau is comprised predominantly of angiosperm wood. For this kind of tropical, diverse, and dynamic ecosystem, a new vegetation change index called lignin phenol vegetation index (LPVI): LPVI is defined using the lignin phenol composition. This index can sensitively detect terrestrial vegetation changes as well as environmental conditions forcing such changes. The LPVI of the Rawa Danau peat core provides better resolution than other lignin parameters used previously, and reveals four major vegetation change events since the mid-late Holocene. In comparison to other geochemical data (i.e. elemental carbon, isotopes, and hydrocarbons), the LPVI is more sensitive and is able to trace even minor vegetation and climate changes and thus could improve biogeochemical interpretations of peat records. PMID:15081699

  17. Ultra-high performance supercritical fluid chromatography of lignin-derived phenols from alkaline cupric oxide oxidation.

    PubMed

    Sun, Mingzhe; Lidén, Gunnar; Sandahl, Margareta; Turner, Charlotta

    2016-08-01

    Traditional chromatographic methods for the analysis of lignin-derived phenolic compounds in environmental samples are generally time consuming. In this work, an ultra-high performance supercritical fluid chromatography method with a diode array detector for the analysis of major lignin-derived phenolic compounds produced by alkaline cupric oxide oxidation was developed. In an analysis of a collection of 11 representative monomeric lignin phenolic compounds, all compounds were clearly separated within 6 min with excellent peak shapes, with a limit of detection of 0.5-2.5 μM, a limit of quantification of 2.5-5.0 μM, and a dynamic range of 5.0-2.0 mM (R(2) > 0.997). The new ultra-high performance supercritical fluid chromatography method was also applied for the qualitative and quantitative analysis of lignin-derived phenolic compounds obtained upon alkaline cupric oxide oxidation of a commercial humic acid. Ten out of the previous eleven model compounds could be quantified in the oxidized humic acid sample. The high separation power and short analysis time obtained demonstrate for the first time that supercritical fluid chromatography is a fast and reliable technique for the analysis of lignin-derived phenols in complex environmental samples. PMID:27452148

  18. Formic-acid-induced depolymerization of oxidized lignin to aromatics.

    PubMed

    Rahimi, Alireza; Ulbrich, Arne; Coon, Joshua J; Stahl, Shannon S

    2014-11-13

    Lignin is a heterogeneous aromatic biopolymer that accounts for nearly 30% of the organic carbon on Earth and is one of the few renewable sources of aromatic chemicals. As the most recalcitrant of the three components of lignocellulosic biomass (cellulose, hemicellulose and lignin), lignin has been treated as a waste product in the pulp and paper industry, where it is burned to supply energy and recover pulping chemicals in the operation of paper mills. Extraction of higher value from lignin is increasingly recognized as being crucial to the economic viability of integrated biorefineries. Depolymerization is an important starting point for many lignin valorization strategies, because it could generate valuable aromatic chemicals and/or provide a source of low-molecular-mass feedstocks suitable for downstream processing. Commercial precedents show that certain types of lignin (lignosulphonates) may be converted into vanillin and other marketable products, but new technologies are needed to enhance the lignin value chain. The complex, irregular structure of lignin complicates chemical conversion efforts, and known depolymerization methods typically afford ill-defined products in low yields (that is, less than 10-20wt%). Here we describe a method for the depolymerization of oxidized lignin under mild conditions in aqueous formic acid that results in more than 60wt% yield of low-molecular-mass aromatics. We present the discovery of this facile C-O cleavage method, its application to aspen lignin depolymerization, and mechanistic insights into the reaction. The broader implications of these results for lignin conversion and biomass refining are also considered.

  19. Pathways for Biomass-Derived Lignin to Hydrocarbon Fuels

    SciTech Connect

    Laskar, Dhrubojyoti; Yang, Bin; Wang, Huamin; Lee, Guo-Shuh J.

    2013-09-01

    Production of hydrocarbon fuel from biomass-derived lignin sources with current version of biorefinery infrastructure would significantly improve the total carbon use in biomass and make biomass conversion more economically viable. Thus, developing specialty and commodity products from biomass derived-lignin has been an important industrial and scientific endeavor for several decades. However, deconstruction of lignin’s complex polymeric framework into low molecular weight reactive moieties amenable for deoxygenation and subsequent processing into hydrocarbons has been proven challenging. This review offers a comprehensive outlook on the existing body of work that has been devoted to catalytic processing of lignin derivatives into hydrocarbon fuels, focusing on: (1) The intrinsic complexity and characteristic structural features of biomass-derived lignin; (2) Existing processing technologies for the isolation and depolymerization of bulk lignin (including detailed mechanistic considerations); (3) Approaches aimed at significantly improving the yields of depolymerized lignin species amenable to catalytic upgrading, and; (4) Catalytic upgrading, using aqueous phase processes for transforming depolymerized lignin to hydrocarbon derivatives. Technical barriers and challenges to the valorization of lignin are highlighted throughout. The central goal of this review is to present an array of strategies that have been reported to obtain lignin, deconstruct it to reactive intermediates, and reduce its substantial oxygen content to yield hydrocarbon liquids. In this regard, reaction networks with reference to studies of lignin model compounds are exclusively surveyed. Special attention is paid to catalytic hydrodeoxygenation, hydrogenolyis and hydrogenation. Finally, this review addresses important features of lignin that are vital to economic success of hydrocarbon production.

  20. Formic-acid-induced depolymerization of oxidized lignin to aromatics

    NASA Astrophysics Data System (ADS)

    Rahimi, Alireza; Ulbrich, Arne; Coon, Joshua J.; Stahl, Shannon S.

    2014-11-01

    Lignin is a heterogeneous aromatic biopolymer that accounts for nearly 30% of the organic carbon on Earth and is one of the few renewable sources of aromatic chemicals. As the most recalcitrant of the three components of lignocellulosic biomass (cellulose, hemicellulose and lignin), lignin has been treated as a waste product in the pulp and paper industry, where it is burned to supply energy and recover pulping chemicals in the operation of paper mills. Extraction of higher value from lignin is increasingly recognized as being crucial to the economic viability of integrated biorefineries. Depolymerization is an important starting point for many lignin valorization strategies, because it could generate valuable aromatic chemicals and/or provide a source of low-molecular-mass feedstocks suitable for downstream processing. Commercial precedents show that certain types of lignin (lignosulphonates) may be converted into vanillin and other marketable products, but new technologies are needed to enhance the lignin value chain. The complex, irregular structure of lignin complicates chemical conversion efforts, and known depolymerization methods typically afford ill-defined products in low yields (that is, less than 10-20wt%). Here we describe a method for the depolymerization of oxidized lignin under mild conditions in aqueous formic acid that results in more than 60wt% yield of low-molecular-mass aromatics. We present the discovery of this facile C-O cleavage method, its application to aspen lignin depolymerization, and mechanistic insights into the reaction. The broader implications of these results for lignin conversion and biomass refining are also considered.

  1. Analysis of morphine responses in mice reveals a QTL on Chromosome 7

    PubMed Central

    Crusio, Wim E.; Dhawan, Esha; Chesler, Elissa J.; Delprato, Anna

    2016-01-01

    In this study we identified a quantitative trait locus (QTL) on mouse Chromosome 7 associated with locomotor activity and rearing post morphine treatment. This QTL was revealed after correcting for the effects of another QTL peak on Chromosome 10 using composite interval mapping. The positional candidate genes are Syt9 and Ppfibp2. Several other genes within the interval are linked to neural processes, locomotor activity, and the defensive response to harmful stimuli. PMID:27746909

  2. Lignin decomposition and microbial community in paddy soils: effects of alternating redox conditions

    NASA Astrophysics Data System (ADS)

    Cerli, Chiara; Liu, Qin; Hanke, Alexander; Kaiser, Klaus; Kalbitz, Karsten

    2013-04-01

    Paddy soils are characterised by interchanging cycles of anaerobic and aerobic conditions. Such fluctuations cause continuous changes in soil solution chemistry as well as in the composition and physiological responses of the microbial community. Temporary deficiency in oxygen creates conditions favourable to facultative or obligates anaerobic bacteria, while aerobic communities can thrive in the period of water absence. These alterations can strongly affect soil processes, in particular organic matter (OM) accumulation and mineralization. In submerged soils, lignin generally constitutes a major portion of the total OM because of hampered degradation under anoxic conditions. The alternating redox cycles resulting from paddy soil management might promote both degradation and preservation of lignin, affecting the overall composition and reactivity of total and dissolved OM. We sampled soils subjected to cycles of anoxic (rice growing period) and oxic (harvest and growth of other crops) conditions since 700 and 2000 years. We incubated suspended Ap material, sampled from the two paddy plus two corresponding non-paddy control soils under oxic and anoxic condition, for 3 months, interrupted by a short period of three weeks (from day 21 to day 43) with reversed redox conditions. At each sampling time (day 2, 21, 42, 63, 84), we determined lignin-derived phenols (by CuO oxidation) as well as phospholipids fatty acids contents and composition. We aimed to highlight changes in lignin decomposition as related to the potential rapid changes in microbial community composition. Since the studied paddy soils had a long history of wet rice cultivation, the microbial community should be well adapted to interchanging oxic and anoxic cycles, therefore fully expressing its activity at both conditions. In non-paddy soil changes in redox conditions caused modification of quantity and composition of the microbial community. On the contrary, in well-established paddy soils the microbial

  3. Obtainment of chelating agents through the enzymatic oxidation of lignins by phenol oxidase.

    PubMed

    Calabria, Gabriela M M; Gonçalves, Adilson R

    2006-01-01

    Oxidation of lignin obtained from acetosolv and ethanol/water pulping of sugarcane bagasse was performed by phenol oxidases: tyrosinase (TYR) and laccase (LAC), to increase the number of carbonyl and hydroxyl groups in lignin, and to improve its chelating capacity. The chelating properties of the original and oxidized lignins were compared by monitoring the amount of Cu2+ bound to lignin by gel permeation chromatography. The Acetosolv lignin oxidized with TYR was 16.8% and with LAC 21% higher than that of the original lignin. For ethanol/water lignin oxidized with TYR was 17.2% and with LAC 18% higher than that of the original lignin. PMID:16915650

  4. Selective aerobic alcohol oxidation method for conversion of lignin into simple aromatic compounds

    DOEpatents

    Stahl, Shannon S; Rahimi, Alireza

    2015-03-03

    Described is a method to oxidize lignin or lignin sub-units. The method includes oxidation of secondary benzylic alcohol in the lignin or lignin sub-unit to a corresponding ketone in the presence of unprotected primarily aliphatic alcohol in the lignin or lignin sub-unit. The optimal catalyst system consists of HNO.sub.3 in combination with another Bronsted acid, in the absence of a metal-containing catalyst, thereby yielding a selectively oxidized lignin or lignin sub-unit. The method may be carried out in the presence or absence of additional reagents including TEMPO and TEMPO derivatives.

  5. Pathways associated with lignin biosynthesis in lignomaniac jute fibres.

    PubMed

    Chakraborty, Avrajit; Sarkar, Debabrata; Satya, Pratik; Karmakar, Pran Gobinda; Singh, Nagendra Kumar

    2015-08-01

    We generated the bast transcriptomes of a deficient lignified phloem fibre mutant and its wild-type jute (Corchorus capsularis) using Illumina paired-end sequencing. A total of 34,163 wild-type and 29,463 mutant unigenes, with average lengths of 1442 and 1136 bp, respectively, were assembled de novo, ~77-79 % of which were functionally annotated. These annotated unigenes were assigned to COG (~37-40 %) and GO (~22-28 %) classifications and mapped to 189 KEGG pathways (~19-21 %). We discovered 38 and 43 isoforms of 16 and 10 genes of the upstream shikimate-aromatic amino acid and downstream monolignol biosynthetic pathways, respectively, rendered their sequence similarities, confirmed the identities of 22 of these candidate gene families by phylogenetic analyses and reconstructed the pathway leading to lignin biosynthesis in jute fibres. We also identified major genes and bast-related transcription factors involved in secondary cell wall (SCW) formation. The quantitative RT-PCRs revealed that phenylalanine ammonia-lyase 1 (CcPAL1) was co-down-regulated with several genes of the upstream shikimate pathway in mutant bast tissues at an early growth stage, although its expression relapsed to the normal level at the later growth stage. However, cinnamyl alcohol dehydrogenase 7 (CcCAD7) was strongly down-regulated in mutant bast tissues irrespective of growth stages. CcCAD7 disruption at an early growth stage was accompanied by co-up-regulation of SCW-specific genes cellulose synthase A7 (CcCesA7) and fasciclin-like arabinogalactan 6 (CcFLA6), which was predicted to be involved in coordinating the S-layers' deposition in the xylan-type jute fibres. Our results identified CAD as a promising target for developing low-lignin jute fibres using genomics-assisted molecular approaches.

  6. Pathways associated with lignin biosynthesis in lignomaniac jute fibres.

    PubMed

    Chakraborty, Avrajit; Sarkar, Debabrata; Satya, Pratik; Karmakar, Pran Gobinda; Singh, Nagendra Kumar

    2015-08-01

    We generated the bast transcriptomes of a deficient lignified phloem fibre mutant and its wild-type jute (Corchorus capsularis) using Illumina paired-end sequencing. A total of 34,163 wild-type and 29,463 mutant unigenes, with average lengths of 1442 and 1136 bp, respectively, were assembled de novo, ~77-79 % of which were functionally annotated. These annotated unigenes were assigned to COG (~37-40 %) and GO (~22-28 %) classifications and mapped to 189 KEGG pathways (~19-21 %). We discovered 38 and 43 isoforms of 16 and 10 genes of the upstream shikimate-aromatic amino acid and downstream monolignol biosynthetic pathways, respectively, rendered their sequence similarities, confirmed the identities of 22 of these candidate gene families by phylogenetic analyses and reconstructed the pathway leading to lignin biosynthesis in jute fibres. We also identified major genes and bast-related transcription factors involved in secondary cell wall (SCW) formation. The quantitative RT-PCRs revealed that phenylalanine ammonia-lyase 1 (CcPAL1) was co-down-regulated with several genes of the upstream shikimate pathway in mutant bast tissues at an early growth stage, although its expression relapsed to the normal level at the later growth stage. However, cinnamyl alcohol dehydrogenase 7 (CcCAD7) was strongly down-regulated in mutant bast tissues irrespective of growth stages. CcCAD7 disruption at an early growth stage was accompanied by co-up-regulation of SCW-specific genes cellulose synthase A7 (CcCesA7) and fasciclin-like arabinogalactan 6 (CcFLA6), which was predicted to be involved in coordinating the S-layers' deposition in the xylan-type jute fibres. Our results identified CAD as a promising target for developing low-lignin jute fibres using genomics-assisted molecular approaches. PMID:25724692

  7. QTL analysis of soft scald in two apple populations

    PubMed Central

    McClure, Kendra A; Gardner, Kyle M; Toivonen, Peter MA; Hampson, Cheryl R; Song, Jun; Forney, Charles F; DeLong, John; Rajcan, Istvan; Myles, Sean

    2016-01-01

    The apple (Malus×domestica Borkh.) is one of the world’s most widely grown and valuable fruit crops. With demand for apples year round, storability has emerged as an important consideration for apple breeding programs. Soft scald is a cold storage-related disorder that results in sunken, darkened tissue on the fruit surface. Apple breeders are keen to generate new cultivars that do not suffer from soft scald and can thus be marketed year round. Traditional breeding approaches are protracted and labor intensive, and therefore marker-assisted selection (MAS) is a valuable tool for breeders. To advance MAS for storage disorders in apple, we used genotyping-by-sequencing (GBS) to generate high-density genetic maps in two F1 apple populations, which were then used for quantitative trait locus (QTL) mapping of soft scald. In total, 900 million DNA sequence reads were generated, but after several data filtering steps, only 2% of reads were ultimately used to create two genetic maps that included 1918 and 2818 single-nucleotide polymorphisms. Two QTL associated with soft scald were identified in one of the bi-parental populations originating from parent 11W-12-11, an advanced breeding line. This study demonstrates the utility of next-generation DNA sequencing technologies for QTL mapping in F1 populations, and provides a basis for the advancement of MAS to improve storability of apples. PMID:27651916

  8. QTL analysis of soft scald in two apple populations.

    PubMed

    McClure, Kendra A; Gardner, Kyle M; Toivonen, Peter Ma; Hampson, Cheryl R; Song, Jun; Forney, Charles F; DeLong, John; Rajcan, Istvan; Myles, Sean

    2016-01-01

    The apple (Malus×domestica Borkh.) is one of the world's most widely grown and valuable fruit crops. With demand for apples year round, storability has emerged as an important consideration for apple breeding programs. Soft scald is a cold storage-related disorder that results in sunken, darkened tissue on the fruit surface. Apple breeders are keen to generate new cultivars that do not suffer from soft scald and can thus be marketed year round. Traditional breeding approaches are protracted and labor intensive, and therefore marker-assisted selection (MAS) is a valuable tool for breeders. To advance MAS for storage disorders in apple, we used genotyping-by-sequencing (GBS) to generate high-density genetic maps in two F1 apple populations, which were then used for quantitative trait locus (QTL) mapping of soft scald. In total, 900 million DNA sequence reads were generated, but after several data filtering steps, only 2% of reads were ultimately used to create two genetic maps that included 1918 and 2818 single-nucleotide polymorphisms. Two QTL associated with soft scald were identified in one of the bi-parental populations originating from parent 11W-12-11, an advanced breeding line. This study demonstrates the utility of next-generation DNA sequencing technologies for QTL mapping in F1 populations, and provides a basis for the advancement of MAS to improve storability of apples. PMID:27651916

  9. QTL analysis of soft scald in two apple populations

    PubMed Central

    McClure, Kendra A; Gardner, Kyle M; Toivonen, Peter MA; Hampson, Cheryl R; Song, Jun; Forney, Charles F; DeLong, John; Rajcan, Istvan; Myles, Sean

    2016-01-01

    The apple (Malus×domestica Borkh.) is one of the world’s most widely grown and valuable fruit crops. With demand for apples year round, storability has emerged as an important consideration for apple breeding programs. Soft scald is a cold storage-related disorder that results in sunken, darkened tissue on the fruit surface. Apple breeders are keen to generate new cultivars that do not suffer from soft scald and can thus be marketed year round. Traditional breeding approaches are protracted and labor intensive, and therefore marker-assisted selection (MAS) is a valuable tool for breeders. To advance MAS for storage disorders in apple, we used genotyping-by-sequencing (GBS) to generate high-density genetic maps in two F1 apple populations, which were then used for quantitative trait locus (QTL) mapping of soft scald. In total, 900 million DNA sequence reads were generated, but after several data filtering steps, only 2% of reads were ultimately used to create two genetic maps that included 1918 and 2818 single-nucleotide polymorphisms. Two QTL associated with soft scald were identified in one of the bi-parental populations originating from parent 11W-12-11, an advanced breeding line. This study demonstrates the utility of next-generation DNA sequencing technologies for QTL mapping in F1 populations, and provides a basis for the advancement of MAS to improve storability of apples.

  10. Mapping QTL conferring resistance in maize to gray leaf spot disease caused by Cercospora zeina

    PubMed Central

    2014-01-01

    Background Gray leaf spot (GLS) is a globally important foliar disease of maize. Cercospora zeina, one of the two fungal species that cause the disease, is prevalent in southern Africa, China, Brazil and the eastern corn belt of the USA. Identification of QTL for GLS resistance in subtropical germplasm is important to support breeding programmes in developing countries where C. zeina limits production of this staple food crop. Results A maize RIL population (F7:S6) from a cross between CML444 and SC Malawi was field-tested under GLS disease pressure at five field sites over three seasons in KwaZulu-Natal, South Africa. Thirty QTL identified from eleven field trials (environments) were consolidated to seven QTL for GLS resistance based on their expression in at least two environments and location in the same core maize bins. Four GLS resistance alleles were derived from the more resistant parent CML444 (bin 1.10, 4.08, 9.04/9.05, 10.06/10.07), whereas the remainder were from SC Malawi (bin 6.06/6.07, 7.02/7.03, 9.06). QTLs in bin 4.08 and bin 6.06/6.07 were also detected as joint QTLs, each explained more than 11% of the phenotypic variation, and were identified in four and seven environments, respectively. Common markers were used to allocate GLS QTL from eleven previous studies to bins on the IBM2005 map, and GLS QTL “hotspots” were noted. Bin 4.08 and 7.02/7.03 GLS QTL from this study overlapped with hotspots, whereas the bin 6.06/6.07 and bin 9.06 QTLs appeared to be unique. QTL for flowering time (bin 1.07, 4.09) in this population did not correspond to QTL for GLS resistance. Conclusions QTL mapping of a RIL population from the subtropical maize parents CML444 and SC Malawi identified seven QTL for resistance to gray leaf spot disease caused by C. zeina. These QTL together with QTL from eleven studies were allocated to bins on the IBM2005 map to provide a basis for comparison. Hotspots of GLS QTL were identified on chromosomes one, two, four, five and

  11. SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach.

    PubMed

    Mora, Freddy; Quitral, Yerko A; Matus, Ivan; Russell, Joanne; Waugh, Robbie; Del Pozo, Alejandro

    2016-01-01

    This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5-22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5-35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint. PMID:27446139

  12. SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach.

    PubMed

    Mora, Freddy; Quitral, Yerko A; Matus, Ivan; Russell, Joanne; Waugh, Robbie; Del Pozo, Alejandro

    2016-01-01

    This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5-22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5-35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint.

  13. SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach

    PubMed Central

    Mora, Freddy; Quitral, Yerko A.; Matus, Ivan; Russell, Joanne; Waugh, Robbie; del Pozo, Alejandro

    2016-01-01

    This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5–22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5–35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint. PMID:27446139

  14. QTL for yield and associated traits in the Seri/Babax population grown across several environments in Mexico, in the West Asia, North Africa, and South Asia regions.

    PubMed

    Lopes, Marta S; Reynolds, Matthew P; McIntyre, C Lynne; Mathews, Ky L; Jalal Kamali, M R; Mossad, Moussa; Feltaous, Yousef; Tahir, Izzat S A; Chatrath, Ravish; Ogbonnaya, Francis; Baum, Michael

    2013-04-01

    Heat and drought adaptive quantitative trait loci (QTL) in a spring bread wheat population resulting from the Seri/Babax cross designed to minimize confounding agronomic traits have been identified previously in trials conducted in Mexico. The same population was grown across a wide range of environments where heat and drought stress are naturally experienced including environments in Mexico, West Asia, North Africa (WANA), and South Asia regions. A molecular genetic linkage map including 475 marker loci associated to 29 linkage groups was used for QTL analysis of yield, days to heading (DH) and to maturity (DM), grain number (GM2), thousand kernel weight (TKW), plant height (PH), canopy temperature at the vegetative and grain filling stages (CTvg and CTgf), and early ground cover. A QTL for yield on chromosome 4A was confirmed across several environments, in subsets of lines with uniform allelic expression of a major phenology QTL, but not independently from PH. With terminal stress, TKW QTL was linked or pleiotropic to DH and DM. The link between phenology and TKW suggested that early maturity would favor the post-anthesis grain growth periods resulting in increased grain size and yields under terminal stress. GM2 and TKW were partially associated with markers at different positions suggesting different genetic regulation and room for improvement of both traits. Prediction accuracy of yield was improved by 5 % when using marker scores of component traits (GM2 and DH) together with yield in multiple regression. This procedure may provide accumulation of more favorable alleles during selection. PMID:23269228

  15. [Characterization of lignin and Mn peroxidases from Phanerochaete chrysosporium

    SciTech Connect

    Not Available

    1992-01-01

    Lignin peroxidases were investigated with respect to enzyme kinetics and NMR spectroscopy of the heme domain. MN peroxidases were studied with respect to the role of oxalate in enzyme activity, the NMR spectroscopy of the heme domain. Gene expression of both lignin and MN peroxidases were examined as well as expression of site-directed mutants aimed at scale up production of these enzymes.

  16. Modification of lignin content and composition in plants

    DOEpatents

    Ye, Zheng-Hua

    2002-01-01

    Plants and methods of preparing plants having reduced lignin content and/or altered lignin composition are provided. The activities of caffeoyl-CoA O-methyltransferase and/or caffeic acid O-methyltransferase enzymes in the modified plants are reduced.

  17. Flocculation of high purity wheat straw soda lignin.

    PubMed

    Piazza, G J; Lora, J H; Garcia, R A

    2014-01-01

    In industrial process, acidification causes non-sulfonated lignin insolubility. The flocculants poly(diallyldimethylammonium chloride) (pDADMAC) and bovine blood (BB) also caused lignin insolubility while cationic polyacrylamide, chitosan, and soy protein PF 974 were ineffective. Turbidity determined optimal flocculant, but turbidity magnitude with BB was greater than expected. pDADMAC caused negative lignin Zeta potential to became positive, but BB-lignin Zeta potential was always negative. Insoluble lignin did not gravity sediment, and flocculant-lignin mixtures were centrifuged. Pellet and supernatant dry mass and corrected spectroscopic results were in good agreement for optimal pDADMAC and BB. Spectroscopy showed 87-92% loss of supernatant lignin. Nitrogen analysis showed BB concentrated in the pellet until the pellet became saturated with BB. Subtracting ash and BB mass from pellet and supernatant mass confirmed optimal BB. Low levels of alum caused increased lignin flocculation at lower levels of pDADMAC and BB, but alum did not affect optimal flocculant.

  18. Structural characterization of lignin from grape stalks (Vitis vinifera L.).

    PubMed

    Prozil, Sónia O; Evtuguin, Dmitry V; Silva, Artur M S; Lopes, Luísa P C

    2014-06-18

    The chemical structure of lignin from grape stalks, an abundant waste of winemaking, has been studied. The dioxane lignin was isolated from extractive- and protein-free grape stalks (Vitis vinifera L.) by modified acidolytic procedure and submitted to a structural analysis by wet chemistry (nitrobenzene and permanganate oxidation (PO)) and spectroscopic techniques. The results obtained suggest that grape stalk lignin is an HGS type with molar proportions of p-hydroxyphenyl (H), guaiacyl (G) and syringyl (S) units of 3:71:26. Structural analysis by (1)H and (13)C NMR spectroscopy and PO indicates the predominance of β-O-4' structures (39% mol) in grape stalk lignin together with moderate amounts of β-5', β-β, β-1', 5-5', and 4-O-5' structures. NMR studies also revealed that grape lignin should be structurally associated with tannins. The condensation degree of grape stalks lignin is higher than that of conventional wood lignins and lignins from other agricultural residues.

  19. Partial Dominance, Overdominance, Epistasis and QTL by Environment Interactions Contribute to Heterosis in Two Upland Cotton Hybrids

    PubMed Central

    Shang, Lianguang; Wang, Yumei; Cai, Shihu; Wang, Xiaocui; Li, Yuhua; Abduweli, Abdugheni; Hua, Jinping

    2015-01-01

    Based on two recombinant inbred line (RIL) populations, two corresponding backcross (BC) populations were constructed to elucidate the genetic basis of heterosis in Upland cotton (Gossypium hirsutum L.). The yield, and yield components, of these populations were evaluated in three environments. At the single-locus level, 78 and 66 quantitative trait loci (QTL) were detected using composite interval mapping in RIL and BC populations, respectively, and 29 QTL were identified based on mid-parental heterosis (MPH) data of two hybrids. Considering all traits together, a total of 50 (64.9%) QTL with partial dominance effect, and 27 (35.1%) QTL for overdominance effect were identified in two BC populations. At the two-locus level, 120 and 88 QTL with main effects (M-QTL), and 335 and 99 QTL involved in digenic interactions (E-QTL), were detected by inclusive composite interval mapping in RIL and BC populations, respectively. A large number of QTL by environment interactions (QEs) for M-QTL and E-QTL were detected in three environments. For most traits, average E-QTL explained a larger proportion of phenotypic variation than did M-QTL in two RIL populations and two BC populations. It was concluded that partial dominance, overdominance, epistasis, and QEs all contribute to heterosis in Upland cotton, and that partial dominance resulting from single loci and epistasis play a relatively more important role than other genetic effects in heterosis in Upland cotton. PMID:26715091

  20. Partial Dominance, Overdominance, Epistasis and QTL by Environment Interactions Contribute to Heterosis in Two Upland Cotton Hybrids.

    PubMed

    Shang, Lianguang; Wang, Yumei; Cai, Shihu; Wang, Xiaocui; Li, Yuhua; Abduweli, Abdugheni; Hua, Jinping

    2016-03-01

    Based on two recombinant inbred line (RIL) populations, two corresponding backcross (BC) populations were constructed to elucidate the genetic basis of heterosis in Upland cotton (Gossypium hirsutum L.). The yield, and yield components, of these populations were evaluated in three environments. At the single-locus level, 78 and 66 quantitative trait loci (QTL) were detected using composite interval mapping in RIL and BC populations, respectively, and 29 QTL were identified based on mid-parental heterosis (MPH) data of two hybrids. Considering all traits together, a total of 50 (64.9%) QTL with partial dominance effect, and 27 (35.1%) QTL for overdominance effect were identified in two BC populations. At the two-locus level, 120 and 88 QTL with main effects (M-QTL), and 335 and 99 QTL involved in digenic interactions (E-QTL), were detected by inclusive composite interval mapping in RIL and BC populations, respectively. A large number of QTL by environment interactions (QEs) for M-QTL and E-QTL were detected in three environments. For most traits, average E-QTL explained a larger proportion of phenotypic variation than did M-QTL in two RIL populations and two BC populations. It was concluded that partial dominance, overdominance, epistasis, and QEs all contribute to heterosis in Upland cotton, and that partial dominance resulting from single loci and epistasis play a relatively more important role than other genetic effects in heterosis in Upland cotton. PMID:26715091

  1. Bioelectrocatalytic properties of lignin peroxidase from Phanerochaete chrysosporium in reactions with phenols, catechols and lignin-model compounds.

    PubMed

    Ferapontova, Elena E; Castillo, John; Gorton, Lo

    2006-09-01

    Bioelectrocatalytic reduction of H(2)O(2) catalysed by lignin peroxidase from Phanerochaete chrysosporium (LiP) was studied with LiP-modified graphite electrodes to elucidate the ability of LiP to electro-enzymatically oxidise phenols, catechols, as well as veratryl alcohol (VA) and some other high-redox-potential lignin model compounds (LMC). Flow-through amperometric experiments performed at +0.1 V vs. Ag|AgCl demonstrated that LiP displayed significant bioelectrocatalytic activity for the reduction of H(2)O(2) both directly (i.e., in direct electron transfer (ET) reaction between LiP and the electrode) and using most of studied compounds acting as redox mediators in the LiP bioelectrocatalytic cycle, with a pH optimum of 3.0. The bioelectrocatalytic reduction of H(2)O(2) mediated by VA and effects of VA on the efficiency of bioelectrocatalytic oxidation of other co-substrates acting as mediators were investigated. The bioelectrocatalytic oxidation of phenol- and catechol derivatives and 2,2'-azino-bis(3-ethyl-benzothiazoline-6-sulphonate) by LiP was independent of the presence of VA, whereas the efficiency of the LiP bioelectrocatalysis with the majority of other LMC acting as mediators increased upon addition of VA. Special cases were phenol and 4-methoxymandelic acid (4-MMA). Both phenol and 4-MMA suppressed the bioelectrocatalytic activity of LiP below the direct ET level, which was, however, restored and increased in the presence of VA mediating the ET between LiP and these two compounds. The obtained results suggest different mechanisms for the bioelectrocatalysis of LiP depending on the chemical nature of the mediators and are of a special interest both for fundamental science and for application of LiP in biotechnological processes as solid-phase bio(electro)catalyst for decomposition/detection of recalcitrant aromatic compounds.

  2. Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity

    NASA Technical Reports Server (NTRS)

    Anterola, Aldwin M.; Lewis, Norman G.

    2002-01-01

    both sophisticated and differential control of monolignol biosynthetic networks in different cell types, which serve to underscore the fact that complexity of assembly need not be confused any further with random formation. Moreover, this analysis revealed another factor which continues to cloud interpretations of lignin downregulation/mutational analyses, namely the serious technical problems associated with all aspects of lignin characterization, whether for lignin quantification, isolation of lignin-enriched preparations and/or in determining monomeric compositions. For example, in the latter analyses, some 50-90% of the lignin components still cannot be detected using current methodologies, e.g. by thioacidolysis cleavage and nitrobenzene oxidative cleavage. This deficiency in lignin characterization thus represents one of the major hurdles remaining in delineating how lignin assembly (in distinct cell types) and their configuration actually occurs.

  3. Meloidogyne incognita nematode resistance QTL in carrot

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Root-knot nematodes (Meloidogyne spp.) are major pests attacking carrots (Daucus carota) worldwide, causing galling and forking of the storage roots, rendering them unacceptable for market. Genetic resistance could significantly reduce the need for broad-spectrum soil fumigants in carrot production....

  4. Catalytic Hydrolytic Cleavage and Oxy-Cleavage of Lignin Linkages

    SciTech Connect

    Xia, Guanguang; Chen, Baowei; Zhang, Rui; Zhang, Z. Conrad

    2014-07-26

    In this work, new strategies involving organic bases were evaluated to depolymerize lignin to reduced molecular fragments in aqueous medium. NaOH as an inorganic base was also investigated as a reference. Full nature lignin samples are used for the study. As research tools to unravel the complexity of the macro lignin structure and bulky molecular size under this study, size exclusion chromatography and high resolution mass spectrometric analysis, typically used for protein characterizations, were used to follow the progress of lignin depolymerisation by measuring the molecular weight distribution of the products and determining the key molecular fingerprints, respectively. The results show that sodium phenoxide and guanidine carbonate are effective catalysts for lignin depolymerization. It is observed that there exists a synergism between H2O2 and the organic base, which is strongest with guanidine carbonate.

  5. Altered lignin biosynthesis using biotechnology to improve lignocellulosic biofuel feedstocks.

    PubMed

    Poovaiah, Charleson R; Nageswara-Rao, Madhugiri; Soneji, Jaya R; Baxter, Holly L; Stewart, Charles N

    2014-12-01

    Lignocellulosic feedstocks can be converted to biofuels, which can conceivably replace a large fraction of fossil fuels currently used for transformation. However, lignin, a prominent constituent of secondary cell walls, is an impediment to the conversion of cell walls to fuel: the recalcitrance problem. Biomass pretreatment for removing lignin is the most expensive step in the production of lignocellulosic biofuels. Even though we have learned a great deal about the biosynthesis of lignin, we do not fully understand its role in plant biology, which is needed for the rational design of engineered cell walls for lignocellulosic feedstocks. This review will recapitulate our knowledge of lignin biosynthesis and discuss how lignin has been modified and the consequences for the host plant.

  6. Lignin oxidation and pulp delignification by laccase and mediators

    SciTech Connect

    Bourbonnais, R.; Paice, M.G.; Reid, I.D.

    1996-10-01

    The phenol oxidizing enzyme laccase is produced abundantly by the lignin-degrading fungus Trametes versicolor. We found previously that laccase can oxidize veratryl alcohol and other non-phenolic lignin model compounds when a mediator such as 2,2{prime}-azinobis(3-ethylbenzthiazoline-5-sulphonate) (ABTS) was present. The laccase/mediator couple was also shown to be effective for delignification of kraft pulps. Two different isozymes of laccase produced by this fungus were purified and their reactivities towards lignins and kraft pulps were studied. The mediator ABTS was shown to be essential for pulp delignification and to reverse the polymerization of kraft lignin by either laccase. Pulp delignification with laccase and ABTS was also optimized. resulting in up to 55% lignin removal from kraft pulp following sequential enzyme treatments and alkaline extractions. Several variables were surveyed including enzyme and mediator dosage, oxygen pressure, temperature, reaction time, and pH.

  7. Process for conversion of lignin to reformulated hydrocarbon gasoline

    DOEpatents

    Shabtai, Joseph S.; Zmierczak, Wlodzimierz W.; Chornet, Esteban

    1999-09-28

    A process for converting lignin into high-quality reformulated hydrocarbon gasoline compositions in high yields is disclosed. The process is a two-stage, catalytic reaction process that produces a reformulated hydrocarbon gasoline product with a controlled amount of aromatics. In the first stage, a lignin material is subjected to a base-catalyzed depolymerization reaction in the presence of a supercritical alcohol as a reaction medium, to thereby produce a depolymerized lignin product. In the second stage, the depolymerized lignin product is subjected to a sequential two-step hydroprocessing reaction to produce a reformulated hydrocarbon gasoline product. In the first hydroprocessing step, the depolymerized lignin is contacted with a hydrodeoxygenation catalyst to produce a hydrodeoxygenated intermediate product. In the second hydroprocessing step, the hydrodeoxygenated intermediate product is contacted with a hydrocracking/ring hydrogenation catalyst to produce the reformulated hydrocarbon gasoline product which includes various desirable naphthenic and paraffinic compounds.

  8. Conformations of Low-Molecular-Weight Lignin Polymers in Water.

    PubMed

    Petridis, Loukas; Smith, Jeremy C

    2016-02-01

    Low-molecular-weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a critical degree of polymerization, Nc =15, the polymer adopts less spherical conformations than above Nc. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. An implication relevant to cellulosic biofuel production is that lignin will self-aggregate even at high pretreatment temperatures.

  9. Conformations of low-molecular-weight lignin polymers in water

    DOE PAGES

    Petridis, Loukas; Smith, Jeremy C.

    2016-01-13

    Low-molecular-weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a criticalmore » degree of polymerization, Nc=15, the polymer adopts less spherical conformations than above Nc. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. As a result, an implication relevant to cellulosic biofuel production is that lignin will self-aggregate even at high pretreatment temperatures.« less

  10. Comparative genetic and QTL mapping in sorghum and maize.

    PubMed

    Lee, M

    1996-01-01

    DNA markers and genetic maps will be important tools for direct investigations of several facets of crop improvement and will provide vital links between plant breeding and basic plant biology. The markers and maps will become more important for increased crop production because plant genetics will be required to extend or replace extant management practices such as chemical fertilizers, pesticides, and irrigation (Lee, 1995). Despite the importance of the sorghum crop, comprehensive genetic characterization has been limited. Therefore, the primary goal of this research program was to develop basic genetic tools to facilitate research in the genetics and breeding of sorghum. The first phase of this project consisted of constructing a genetic map based on restriction fragment length polymorphisms (RFLPs). The ISU sorghum map was created through linkage analysis of 78 F2 plants of an intraspecific cross between inbred CK60 and accession P1229828 (Pereira et al., 1994). The map consists of 201 loci distributed among 10 linkage groups covering 1,299 cM. Comparison of sorghum and maize RFLP maps on the basis of common sets of DNA probes revealed a high degree of conservation as reflected by homology, copy number, and collinearity. Examples of conserved and rearranged locus orders were observed. The same sorghum population was used to map genetic factors (mutants and QTL) for several traits including vegetative and reproductive morphology, maturity, insect, and disease resistance. This presentation will emphasize analysis of genetic factors affecting plant height, an important character for sorghum adaptation in temperate latitudes for grain production. Four QTL for plant height were identified in a sample of 152 F2 plants (Pereira and Lee, 1995) whereas 6 QTL were detected among their F3 progeny. These observations and assessments of other traits at 4 QTL common to F2 plants and their F3 progeny indicate some of these regions correspond to loci (dw) previously

  11. Development of a prototype lignin concentration sensor

    SciTech Connect

    Malito, M.L.; Jeffers, L.A.

    1993-01-01

    The US Department of Energy, Office of Industrial Technologies, is sponsoring a research and development program for the development of a real-time, in-situ sensor to measure the concentration of lignin in wood pulp. The program is composed of phase I showing feasibility which is now complete, phase II for development and testing of a Field Prototype, in progress, Phase III commercialization. Phase I work (funded entirely by B W) demonstrated a correlation between the fluorescence intensity and lignin concentration (as measured by TAPPI procedure, T 236 hm-85 Kappa Number of Pulp) for undiluted wood pulp samples. In Phase II, a laboratory test program directed at characterizing the fluorescence of wood pulp has been conducted as a prelude to the design of a prototype sensor. The current report summarizes the testing completed in Phase I and documents the Phase II laboratory testing completed through December 1991. Future Phase II efforts include additional laboratory testing, design and fabrication of a prototype sensor, and field testing of the prototype sensor. Phase III of the program will concentrate on the incorporation of the sensor into a control system and commercialization of the sensor.

  12. Development of a prototype lignin concentration sensor

    SciTech Connect

    Malito, M.L.; Jeffers, L.A.

    1993-01-01

    The US Department of Energy, Office of Industrial Technologies, is sponsoring a research and development program for the development of a real-time, in-situ sensor to measure the concentration of lignin in wood pulp. The program is composed of phase I showing feasibility which is now complete, phase II for development and testing of a Field Prototype, in progress, Phase III commercialization. Phase I work (funded entirely by B&W) demonstrated a correlation between the fluorescence intensity and lignin concentration (as measured by TAPPI procedure, T 236 hm-85 Kappa Number of Pulp) for undiluted wood pulp samples. In Phase II, a laboratory test program directed at characterizing the fluorescence of wood pulp has been conducted as a prelude to the design of a prototype sensor. The current report summarizes the testing completed in Phase I and documents the Phase II laboratory testing completed through December 1991. Future Phase II efforts include additional laboratory testing, design and fabrication of a prototype sensor, and field testing of the prototype sensor. Phase III of the program will concentrate on the incorporation of the sensor into a control system and commercialization of the sensor.

  13. Lignin biodegradation and the production of ethyl alcohol from cellulose

    SciTech Connect

    Rosenberg, S.L.; Wilke, C.R.

    1981-02-01

    During the last few years our group has been engaged in developing a biochemical process for the conversion of lignocellulosic materials to ethyl alcohol. Lignin is a barrier to complete cellulose saccharification in this process, but chemical and physical delignification steps are too expensive to be used at the present time. An enzymatic delignification process might be attractive for several reasons: little energy would be expected to be needed, enzymes could be recovered and reused, and useful chemicals might be produced from dissolved lignin. A number of thermophilic and thermotolerant fungi were examined for the ability to rapidly degrade lignocellulose in order to find an organism whcih produced an active lignin-degrading enzyme system. Chryosporium pruinosum and Sporotrichum pulverulentum were found to be active lignocellulose degraders, and C. pruinosum was chosen for further study. Lignin and carbohydrate were degraded when the substrate remained moistened by, but not submerged in, the liquid medium. Attempts were made to demonstrate a cell-free lignin degrading system by both extraction and pressing of cultures grown on moist lignocellulose. Carbohydrate-degrading activity was found but not lignin-degrading activity. This led us to ask whether diffusible lignin-degrading activity could be demonstrated in this organism. The data indicate that the lignin degradation system, or one or more of its components, produced by this organism is either unstable, non-diffusible, or inactive at small distances (about 1 mm) from growing hyphae. At present, studies are being conducted using diffusion cultures to select mutants of C. pruinosum that do produce a diffusible lignin degradation system. We are also examining a number of mesophilic lignin-degrading molds for this ability.

  14. Lignin Valorization through Catalytic Lignocellulose Fractionation: A Fundamental Platform for the Future Biorefinery.

    PubMed

    Galkin, Maxim V; Samec, Joseph S M

    2016-07-01

    Current processes for the fractionation of lignocellulosic biomass focus on the production of high-quality cellulosic fibers for paper, board, and viscose production. The other fractions that constitute a major part of lignocellulose are treated as waste or used for energy production. The transformation of lignocellulose beyond paper pulp to a commodity (e.g., fine chemicals, polymer precursors, and fuels) is the only feasible alternative to current refining of fossil fuels as a carbon feedstock. Inspired by this challenge, scientists and engineers have developed a plethora of methods for the valorization of biomass. However, most studies have focused on using one single purified component from lignocellulose that is not currently generated by the existing biomass fractionation processes. A lot of effort has been made to develop efficient methods for lignin depolymerization. The step to take this fundamental research to industrial applications is still a major challenge. This review covers an alternative approach, in which the lignin valorization is performed in concert with the pulping process. This enables the fractionation of all components of the lignocellulosic biomass into valorizable streams. Lignocellulose fractions obtained this way (e.g., lignin oil and glucose) can be utilized in a number of existing procedures. The review covers historic, current, and future perspectives, with respect to catalytic lignocellulose fractionation processes.

  15. Lignin Valorization through Catalytic Lignocellulose Fractionation: A Fundamental Platform for the Future Biorefinery.

    PubMed

    Galkin, Maxim V; Samec, Joseph S M

    2016-07-01

    Current processes for the fractionation of lignocellulosic biomass focus on the production of high-quality cellulosic fibers for paper, board, and viscose production. The other fractions that constitute a major part of lignocellulose are treated as waste or used for energy production. The transformation of lignocellulose beyond paper pulp to a commodity (e.g., fine chemicals, polymer precursors, and fuels) is the only feasible alternative to current refining of fossil fuels as a carbon feedstock. Inspired by this challenge, scientists and engineers have developed a plethora of methods for the valorization of biomass. However, most studies have focused on using one single purified component from lignocellulose that is not currently generated by the existing biomass fractionation processes. A lot of effort has been made to develop efficient methods for lignin depolymerization. The step to take this fundamental research to industrial applications is still a major challenge. This review covers an alternative approach, in which the lignin valorization is performed in concert with the pulping process. This enables the fractionation of all components of the lignocellulosic biomass into valorizable streams. Lignocellulose fractions obtained this way (e.g., lignin oil and glucose) can be utilized in a number of existing procedures. The review covers historic, current, and future perspectives, with respect to catalytic lignocellulose fractionation processes. PMID:27273230

  16. Catalytic Reforming of Lignin-Derived Bio-Oil Over a Nanoporous Molecular Sieve Silicoaluminophosphate-11.

    PubMed

    Park, Y K; Kang, Hyeon Koo; Jang, Hansaem; Suh, Dong Jin; Park, Sung Hoon

    2016-05-01

    Catalytic pyrolysis of lignin, a major constituent of biomass, was performed. A nanoporous molecular sieve silicoaluminophosphate-11 (SAPO-11) was selected as catalyst. Thermogravimetric analysis showed that 500 degrees C was the optimal pyrolysis temperature. Pyrolyzer-gas chromatography/mass spectroscopy was used to investigate the pyrolysis product distribution. Production of phenolics, the dominant product from the pyrolysis of lignin, was promoted by the increase in the catalyst dose. In particular, low-molecular-mass phenolics were produced more over SAPO-11, while high-molecular-mass phenolics and double-bond-containing phenolics were produced less. The fraction of aromatic compounds, including benzene, toluene, xylene, and ethylbenzene, was also increased by catalytic reforming. The catalytic effects were more pronounced when the catalyst/biomass ratio was increased. The enhanced production of aromatic compounds by an acidic catalyst obtained in this study is in good agreement with the results of previous studies.

  17. Catalytic Reforming of Lignin-Derived Bio-Oil Over a Nanoporous Molecular Sieve Silicoaluminophosphate-11.

    PubMed

    Park, Y K; Kang, Hyeon Koo; Jang, Hansaem; Suh, Dong Jin; Park, Sung Hoon

    2016-05-01

    Catalytic pyrolysis of lignin, a major constituent of biomass, was performed. A nanoporous molecular sieve silicoaluminophosphate-11 (SAPO-11) was selected as catalyst. Thermogravimetric analysis showed that 500 degrees C was the optimal pyrolysis temperature. Pyrolyzer-gas chromatography/mass spectroscopy was used to investigate the pyrolysis product distribution. Production of phenolics, the dominant product from the pyrolysis of lignin, was promoted by the increase in the catalyst dose. In particular, low-molecular-mass phenolics were produced more over SAPO-11, while high-molecular-mass phenolics and double-bond-containing phenolics were produced less. The fraction of aromatic compounds, including benzene, toluene, xylene, and ethylbenzene, was also increased by catalytic reforming. The catalytic effects were more pronounced when the catalyst/biomass ratio was increased. The enhanced production of aromatic compounds by an acidic catalyst obtained in this study is in good agreement with the results of previous studies. PMID:27483769

  18. Investigation of the genetic architecture of a bone carcass weight QTL on BTA6.

    PubMed

    Gutiérrez-Gil, B; Wiener, P; Williams, J L; Haley, C S

    2012-12-01

    A previous analysis of an F(2) /Backcross Charolais × Holstein cross population identified the presence of a highly significant QTL on chromosome 6 (BTA6) affecting the proportion of bone in the carcass. Two closely linked QTL affected birth weight (BW) and body length at birth (BBL). In this report, the marker density around the QTL on BTA6 was increased, adding four additional microsatellite markers across the chromosome and 46 SNPs within the target QTL confidence interval. Of the SNPs, 26 were in positional candidate genes and the remaining 20 provided an even distribution of markers in the target QTL region. As a bone-related trait, the sum of the bone weight for all the left fore- and hindquarter joints of the carcass was analysed. We also studied the BW and BBL. Analyses of the data substantially reduced the QTL confidence interval. No strong evidence was found that the QTL for the three traits studied are different, and we conclude that the results are consistent with a single pleiotropic QTL influencing the three traits, with the largest effects on the proportion of bone in the carcass. The analyses also suggest that none of the SNPs tested is the sole causative variant of the QTL effects. Specifically, the SNP in the NCAPG gene previously reported as a causal mutation for foetal growth and carcass traits in other cattle populations was excluded as the causal mutation for the QTL reported here. Polymorphisms located in other previously identified candidate genes including SPP1, ABCG2, IBSP, MEPE and PPARGC1A were also excluded. The results suggest that SNP51_BTA-119876 is the polymorphism in strongest linkage disequilibrium with the causal mutation(s). Further research is required to identify the causal variant(s) associated with this bone-related QTL.

  19. QTL associated with horizontal resistance to soybean cyst nematode in Glycine soja PI464925B.

    PubMed

    Winter, Shawn M J; Shelp, Barry J; Anderson, Terry R; Welacky, Tom W; Rajcan, Istvan

    2007-02-01

    the novel resistance QTL from G. soja could increase the durability of SCN-resistance in soybean cultivars, especially if major gene resistance breaks down.

  20. Genome-wide association studies identifies seven major regions responsible for iron deficiency chlorosis in soybean (Glycine max).

    PubMed

    Mamidi, Sujan; Lee, Rian K; Goos, Jay R; McClean, Phillip E

    2014-01-01

    Iron deficiency chlorosis (IDC) is a yield limiting problem in soybean (Glycine max (L.) Merr) production regions with calcareous soils. Genome-wide association study (GWAS) was performed using a high density SNP map to discover significant markers, QTL and candidate genes associated with IDC trait variation. A stepwise regression model included eight markers after considering LD between markers, and identified seven major effect QTL on seven chromosomes. Twelve candidate genes known to be associated with iron metabolism mapped near these QTL supporting the polygenic nature of IDC. A non-synonymous substitution with the highest significance in a major QTL region suggests soybean orthologs of FRE1 on Gm03 is a major gene responsible for trait variation. NAS3, a gene that encodes the enzyme nicotianamine synthase which synthesizes the iron chelator nicotianamine also maps to the same QTL region. Disease resistant genes also map to the major QTL, supporting the hypothesis that pathogens compete with the plant for Fe and increase iron deficiency. The markers and the allelic combinations identified here can be further used for marker assisted selection.

  1. Genome-Wide Association Studies Identifies Seven Major Regions Responsible for Iron Deficiency Chlorosis in Soybean (Glycine max)

    PubMed Central

    Mamidi, Sujan; Lee, Rian K.; Goos, Jay R.; McClean, Phillip E.

    2014-01-01

    Iron deficiency chlorosis (IDC) is a yield limiting problem in soybean (Glycine max (L.) Merr) production regions with calcareous soils. Genome-wide association study (GWAS) was performed using a high density SNP map to discover significant markers, QTL and candidate genes associated with IDC trait variation. A stepwise regression model included eight markers after considering LD between markers, and identified seven major effect QTL on seven chromosomes. Twelve candidate genes known to be associated with iron metabolism mapped near these QTL supporting the polygenic nature of IDC. A non-synonymous substitution with the highest significance in a major QTL region suggests soybean orthologs of FRE1 on Gm03 is a major gene responsible for trait variation. NAS3, a gene that encodes the enzyme nicotianamine synthase which synthesizes the iron chelator nicotianamine also maps to the same QTL region. Disease resistant genes also map to the major QTL, supporting the hypothesis that pathogens compete with the plant for Fe and increase iron deficiency. The markers and the allelic combinations identified here can be further used for marker assisted selection. PMID:25225893

  2. CONCEPTUAL DESIGN ASSESSMENT FOR THE CO-FIRING OF BIO-REFINERY SUPPLIED LIGNIN PROJECT

    SciTech Connect

    Ted Berglund; Jeffrey T. Ranney; Carol L. Babb; Jacqueline G. Broder

    2001-01-01

    The major aspects of this project are proceeding toward completion. Prior to this quarter, design criteria, tentative site selection, facility layout, and preliminary facility cost estimates have been completed and issued for review. Processing of bio-solids was completed, providing material for the pilot operations. Pilot facility design, equipment selection, and modification were completed during the fourth quarter. Initial pilot facility shakedown was completed during the fourth quarter. During pilot plant shakedown operations, several production batch test runs were performed. These pilot tests were coupled with laboratory testing to confirm pilot results. In initial batches of operations, cellulose to glucose conversions of 62.5% and 64.8% were observed in laboratory hydrolysis. As part of this testing, lignin dewatering was tested using laboratory and vendor-supplied filtration equipment. Dewatering tests reported moisture contents in the lignin of between 50% and 60%. Dewatering parameters and options will continue to be investigated during lignin production. After some unavoidable delays, a suitable representative supply of MSW feed material was procured. Shredding of the feed material was completed and final drying of the feed is expected to be completed by late January. Once feed drying is completed, pilot facility production will begin to produce lignin for co-fire testing. Facility modifications are expected to continue to improve facility operations and performance during the first quarter of 2001. The TVA-Colbert facility continues to make progress in evaluating the co-location of the Masada facility on the operation of the power generation facility. The TVA-Colbert fossil plant is fully capable of providing a reliable steam supply. The preferred steam supply connection points and steam pipeline routing have been identified. The environmental review of the pipeline routing has been completed and no major impacts have been identified. Detailed

  3. CONCEPTUAL DESIGN ASSESSMENT FOR THE COFIRING OF BIOREFINERY SUPPLIED LIGNIN PROJECT

    SciTech Connect

    David J. Webster; Jeffrey T. Ranney; Jacqueline G. Broder

    2002-07-01

    The major aspects of this project are proceeding toward completion. Prior to this quarter, design criteria, tentative site selection, facility layout, and preliminary facility cost estimates were completed. Processing of biosolids and pilot facility hydrolysis production have been completed to produce lignin for cofire testing. EERC had received all the biomass and baseline coal fuels for use in testing. All the combustion and fuel handling tests at EERC have been completed. During fuel preparation EERC reported no difficulties in fuel blending and handling. Preliminary cofire test results indicate that the blending of lignin and biosolids with the Colbert coal blend generally reduces NOx emissions, increases the reactivity of the coal, and increases the ash deposition rate on superheater surfaces. Deposits produced from the fuel blends, however, are more friable and hence easier to remove from tube surfaces relative to those produced from the baseline Colbert coal blend. A draft of the final cofire technical report entitled ''Effects of Cofiring Lignin and Biosolids with Coal on Fireside Performance and Combustion Products'' has been prepared and is currently being reviewed by project team members. A final report is expected by mid-third quarter 2002. The TVA-Colbert facility has neared completion of the task to evaluate co-location of the Masada facility on the operation of the power generation facility. The TVA-Colbert fossil plant is fully capable of providing a reliable steam supply. The environmental review, preferred steam supply connection points and steam pipeline routing, and assessment of steam export impacts have been completed without major issue. A cost estimate for the steam supply system was also completed. TVA is further evaluating the impacts of adding lignin to the coal fuel blend and how the steam cost is impacted by proximity of the Masada biomass facility. TVA has provided a draft final report that is under review by team members.

  4. Adsorption of β-glucosidases in two commercial preparations onto pretreated biomass and lignin

    PubMed Central

    2013-01-01

    Background Enzyme recycling is a method to reduce the production costs for advanced bioethanol by lowering the overall use of enzymes. Commercial cellulase preparations consist of many different enzymes that are important for efficient and complete cellulose (and hemicellulose) hydrolysis. This abundance of different activities complicates enzyme recycling since the individual enzymes behave differently in the process. Previously, the general perception was that β-glucosidases could easily be recycled via the liquid phase, as they have mostly been observed not to adsorb to pretreated biomass or only adsorb to a minor extent. Results The results from this study with Cellic® CTec2 revealed that the vast majority of the β-glucosidase activity was lost from the liquid phase and was adsorbed to the residual biomass during hydrolysis and fermentation. Adsorption studies with β-glucosidases in two commercial preparations (Novozym 188 and Cellic® CTec2) to substrates mimicking the components in pretreated wheat straw revealed that the Aspergillus niger β-glucosidase in Novozym 188 did not adsorb significantly to any of the components in pretreated wheat straw, whereas the β-glucosidase in Cellic® CTec2 adsorbed strongly to lignin. The extent of adsorption of β-glucosidase from Cellic® CTec2 was affected by both type of biomass and pretreatment method. With approximately 65% of the β-glucosidases from Cellic® CTec2 adsorbed onto lignin from pretreated wheat straw, the activity of the β-glucosidases in the slurry decreased by only 15%. This demonstrated that some enzyme remained active despite being bound. It was possible to reduce the adsorption of Cellic® CTec2 β-glucosidase to lignin from pretreated wheat straw by addition of bovine serum albumin or poly(ethylene glycol). Conclusions Contrary to the β-glucosidases in Novozym 188, the β-glucosidases in Cellic® CTec2 adsorb significantly to lignin. The lignin adsorption observed for Cellic® CTec2 is

  5. Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum

    DOE PAGES

    Faraji, Mojdeh; Fonseca, Luis L.; Escamilla-Treviño, Luis; Dixon, Richard A.; Voit, Eberhard O.

    2015-09-17

    Switchgrass is a prime target for biofuel production from inedible plant parts and has been the subject of numerous investigations in recent years. Yet, one of the main obstacles to effective biofuel production remains to be the major problem of recalcitrance. Recalcitrance emerges in part from the 3-D structure of lignin as a polymer in the secondary cell wall. Lignin limits accessibility of the sugars in the cellulose and hemicellulose polymers to enzymes and ultimately decreases ethanol yield. Monolignols, the building blocks of lignin polymers, are synthesized in the cytosol and translocated to the plant cell wall, where they undergomore » polymerization. The biosynthetic pathway leading to monolignols in switchgrass is not completely known, and difficulties associated with in vivo measurements of these intermediates pose a challenge for a true understanding of the functioning of the pathway. In this study, a systems biological modeling approach is used to address this challenge and to elucidate the structure and regulation of the lignin pathway through a computational characterization of alternate candidate topologies. The analysis is based on experimental data characterizing stem and tiller tissue of four transgenic lines (knock-downs of genes coding for key enzymes in the pathway) as well as wild-type switchgrass plants. These data consist of the observed content and composition of monolignols. The possibility of a G-lignin specific metabolic channel associated with the production and degradation of coniferaldehyde is examined, and the results support previous findings from another plant species. The computational analysis suggests regulatory mechanisms of product inhibition and enzyme competition, which are well known in biochemistry, but so far had not been reported in switchgrass. By including these mechanisms, the pathway model is able to represent all observations. In conclusion, the results show that the presence of the coniferaldehyde channel is

  6. Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum

    SciTech Connect

    Faraji, Mojdeh; Fonseca, Luis L.; Escamilla-Treviño, Luis; Dixon, Richard A.; Voit, Eberhard O.

    2015-09-17

    Switchgrass is a prime target for biofuel production from inedible plant parts and has been the subject of numerous investigations in recent years. Yet, one of the main obstacles to effective biofuel production remains to be the major problem of recalcitrance. Recalcitrance emerges in part from the 3-D structure of lignin as a polymer in the secondary cell wall. Lignin limits accessibility of the sugars in the cellulose and hemicellulose polymers to enzymes and ultimately decreases ethanol yield. Monolignols, the building blocks of lignin polymers, are synthesized in the cytosol and translocated to the plant cell wall, where they undergo polymerization. The biosynthetic pathway leading to monolignols in switchgrass is not completely known, and difficulties associated with in vivo measurements of these intermediates pose a challenge for a true understanding of the functioning of the pathway. In this study, a systems biological modeling approach is used to address this challenge and to elucidate the structure and regulation of the lignin pathway through a computational characterization of alternate candidate topologies. The analysis is based on experimental data characterizing stem and tiller tissue of four transgenic lines (knock-downs of genes coding for key enzymes in the pathway) as well as wild-type switchgrass plants. These data consist of the observed content and composition of monolignols. The possibility of a G-lignin specific metabolic channel associated with the production and degradation of coniferaldehyde is examined, and the results support previous findings from another plant species. The computational analysis suggests regulatory mechanisms of product inhibition and enzyme competition, which are well known in biochemistry, but so far had not been reported in switchgrass. By including these mechanisms, the pathway model is able to represent all observations. In conclusion, the results show that the presence of the coniferaldehyde channel is necessary

  7. Floral genetic architecture: an examination of QTL architecture underlying floral (co)variation across environments.

    PubMed

    Brock, Marcus T; Dechaine, Jennifer M; Iniguez-Luy, Federico L; Maloof, Julin N; Stinchcombe, John R; Weinig, Cynthia

    2010-12-01

    Genetic correlations are expected to be high among functionally related traits and lower between groups of traits with distinct functions (e.g., reproductive vs. resource-acquisition traits). Here, we explore the quantitative-genetic and QTL architecture of floral organ sizes, vegetative traits, and life history in a set of Brassica rapa recombinant inbred lines within and across field and greenhouse environments. Floral organ lengths were strongly positively correlated within both environments, and analysis of standardized G-matrices indicates that the structure of genetic correlations is ∼80% conserved across environments. Consistent with these correlations, we detected a total of 19 and 21 additive-effect floral QTL in the field and the greenhouse, respectively, and individual QTL typically affected multiple organ types. Interestingly, QTL×QTL epistasis also appeared to contribute to observed genetic correlations; i.e., interactions between two QTL had similar effects on filament length and two estimates of petal size. Although floral and nonfloral traits are hypothesized to be genetically decoupled, correlations between floral organ size and both vegetative and life-history traits were highly significant in the greenhouse; G-matrices of floral and vegetative traits as well as floral and life-history traits differed across environments. Correspondingly, many QTL (45% of those mapped in the greenhouse) showed environmental interactions, including approximately even numbers of floral and nonfloral QTL. Most instances of QTL×QTL epistasis for floral traits were environment dependent.

  8. Dynamic QTL and epistasis analysis on seedling root traits in upland cotton.

    PubMed

    Liang, Qingzhi; Li, Pengbo; Hu, Cheng; Hua, Hua; Li, Zhaohu; Rong, Yihua; Wang, Kunbo; Hua, Jinping

    2014-04-01

    Roots are involved in acquisition of water and nutrients, as well as in providing structural support to plant. The root system provides a dynamic model for developmental analysis. Here, we investigated quantitative trait loci (QTL), dynamic conditional QTL and epistatic interactions for seedling root traits using an upland cotton F2 population and a constructed genetic map. Totally, 37 QTLs for root traits, 35 dynamic conditional QTLs based on the net increased amount of root traits (root tips, forks, length, surface area and volume) (i) after transplanting 10 days compared to 5 days, and (ii) after transplanting 15 days to 10 days were detected. Obvious dynamic characteristic of QTL and dynamic conditional QTL existed at different developmental stages of root because QTL and dynamic conditional QTL had not been detected simultaneously. We further confirmed that additive and dominance effects of QTL qRSA-chr1-1 in interval time 5 to 10 DAT (days after transplant) offset the effects in 10 to 15 DAT. Lots of two-locus interactions for root traits were identified unconditionally or dynamically, and a few epistatic interactions were only detected simultaneously in interval time of 5-10 DAT and 10-15 DAT, suggesting different interactive genetic mechanisms on root development at different stages. Dynamic conditional QTL and epistasis effects provide new attempts to understand the dynamics of roots and provide clues for root architecture selection in upland cotton. PMID:24840824

  9. Use of single nucleotide polymorphisms (SNP) to fine-map quantitative trait loci (QTL) in swine

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mapping quantitative trait loci (QTL) in swine at the US Meat Animal Research Center has relied heavily on linkage mapping in either F2 or Backcross families. QTL identified in the initial scans typically have very broad confidence intervals and further refinement of the QTL’s position is needed bef...

  10. QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines

    PubMed Central

    Singh, Anandita; Warthmann, Norman; Kim, Min Chul; Maloof, Julin N.; Loudet, Olivier; Trainer, Gabriel T.; Dabi, Tsegaye; Borevitz, Justin O.; Chory, Joanne; Weigel, Detlef

    2009-01-01

    Background Even when phenotypic differences are large between natural or domesticated strains, the underlying genetic basis is often complex, and causal genomic regions need to be identified by quantitative trait locus (QTL) mapping. Unfortunately, QTL positions typically have large confidence intervals, which can, for example, lead to one QTL being masked by another, when two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs). Methodology/Principal Findings We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb. The advanced intercrossing design led to expansion of the genetic map in the two populations, which contain recombination events corresponding to 50 kb/cM in an F2 population. We used the AI-RILs to map QTL for light response and flowering time, and to identify segregation distortion in one of the AI-RIL populations due to a negative epistatic interaction between two genomic regions. Conclusions/Significance The two new AI-RIL populations, EstC and KendC, derived from crosses of Columbia (Col) to Estland (Est-1) and Kendallville (Kend-L) provide an excellent resource for high precision QTL mapping. Moreover, because they have been genotyped with over 100 common markers, they are also excellent material for comparative QTL mapping. PMID:19183806

  11. Yeast growth plasticity is regulated by environment-specific multi-QTL interactions.

    PubMed

    Bhatia, Aatish; Yadav, Anupama; Zhu, Chenchen; Gagneur, Julien; Radhakrishnan, Aparna; Steinmetz, Lars M; Bhanot, Gyan; Sinha, Himanshu

    2014-01-28

    For a unicellular, nonmotile organism like Saccharomyces cerevisiae, carbon sources act as nutrients and as signaling molecules; consequently, these sources affect various fitness parameters, including growth. It is therefore advantageous for yeast strains to adapt their growth to carbon source variation. The ability of a given genotype to manifest different phenotypes in varying environments is known as phenotypic plasticity. To identify quantitative trait loci (QTL) that drive plasticity in growth, two growth parameters (growth rate and biomass) were measured for a set of meiotic recombinants of two genetically divergent yeast strains grown in different carbon sources. To identify QTL contributing to plasticity across pairs of environments, gene-environment interaction mapping was performed, which identified several QTL that have a differential effect across environments, some of which act antagonistically across pairs of environments. Multi-QTL analysis identified loci interacting with previously known growth affecting QTL as well as novel two-QTL interactions that affect growth. A QTL that had no significant independent effect was found to alter growth rate and biomass for several carbon sources through two-QTL interactions. Our study demonstrates that environment-specific epistatic interactions contribute to the growth plasticity in yeast. We propose that a targeted scan for epistatic interactions, such as the one described here, can help unravel mechanisms regulating phenotypic plasticity.

  12. The role of lignin and lignin-like materials during wood hydrolysis

    SciTech Connect

    Zaher, F.A.

    1981-01-01

    The nature of the material precipitating from the acid prehydrolysates and hydrolysates of wood upon storage has been investigated. This material was analyzed for its sugar content, ultraviolet spectra, elemental composition, molecular weight distribution, and thermogravimetric behavior. All the results indicate that this material has the same properties as lignin. The results suggest also that this material is neither a resinification product from sugar decomposition nor extraneous materials of wood (resins, tannins, etc.). It is suggested, too, that the extraction of this material along with sugar during hydrolysis and prehydrolysis causes a considerable error in the results of wood analysis using standard methods based on weight loss. The actual percentages of lignin in the wood samples tested appear to vary from two to four times their values measured by standard methods. Consequently, the actual cellulose content of these materials may be far lower than has been reported. This has serious implications for schemes based on biomass conversion.

  13. A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum interspecific populations and Gossypium hirsutum x Gossypium barbadense populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent Meta-analysis of quantitative trait loci (QTL) in tetraploid cotton (Gossypium spp.) has identified regions of the genome with high concentrations of various trait QTL called clusters, and specific trait QTL called hotspots. The Meta-analysis included all population types of Gossypium mixing ...

  14. Loss of function of cinnamyl alcohol dehydrogenase 1 leads to unconventional lignin and a temperature-sensitive growth defect in Medicago truncatula

    PubMed Central

    Zhao, Qiao; Tobimatsu, Yuki; Zhou, Rui; Pattathil, Sivakumar; Gallego-Giraldo, Lina; Fu, Chunxiang; Jackson, Lisa A.; Hahn, Michael G.; Kim, Hoon; Chen, Fang; Ralph, John; Dixon, Richard A.

    2013-01-01

    There is considerable debate over the capacity of the cell wall polymer lignin to incorporate unnatural monomer units. We have identified Tnt1 retrotransposon insertion mutants of barrel medic (Medicago truncatula) that show reduced lignin autofluorescence under UV microscopy and red coloration in interfascicular fibers. The phenotype is caused by insertion of retrotransposons into a gene annotated as encoding cinnamyl alcohol dehydrogenase, here designated M. truncatula CAD1. NMR analysis indicated that the lignin is derived almost exclusively from coniferaldehyde and sinapaldehyde and is therefore strikingly different from classical lignins, which are derived mainly from coniferyl and sinapyl alcohols. Despite such a major alteration in lignin structure, the plants appear normal under standard conditions in the greenhouse or growth chamber. However, the plants are dwarfed when grown at 30 °C. Glycome profiling revealed an increased extractability of some xylan and pectin epitopes from the cell walls of the cad1-1 mutant but decreased extractability of others, suggesting that aldehyde-dominant lignin significantly alters cell wall structure. PMID:23901113

  15. Abiotic stress induces change in Cinnamoyl CoA Reductase (CCR) protein abundance and lignin deposition in developing seedlings of Leucaena leucocephala.

    PubMed

    Srivastava, Sameer; Vishwakarma, Rishi K; Arafat, Yasir Ali; Gupta, Sushim K; Khan, Bashir M

    2015-04-01

    Aboitic stress such as drought and salinity are class of major threats, which plants undergo through their lifetime. Lignin deposition is one of the responses to such abiotic stresses. The gene encoding Cinnamoyl CoA Reductase (CCR) is a key gene for lignin biosynthesis, which has been shown to be over-expressed under stress conditions. In the present study, developing seedlings of Leucaena leucocephala (Vernacular name: Subabul, White popinac) were treated with 1 % mannitol and 200 mM NaCl to mimic drought and salinity stress conditions, respectively. Enzyme linked immunosorbant assay (ELISA) based expression pattern of CCR protein was monitored coupled with Phlorogucinol/HCl activity staining of lignin in transverse sections of developing L. leucocephala seedlings under stress. Our result suggests a differential lignification pattern in developing root and stem under stress conditions. Increase in lignification was observed in mannitol treated stems and corresponding CCR protein accumulation was also higher than control and salt stress treated samples. On the contrary CCR protein was lower in NaCl treated stems and corresponding lignin deposition was also low. Developing root tissue showed a high level of CCR content and lignin deposition than stem samples under all conditions tested. Overall result suggested that lignin accumulation was not affected much in case of developing root however developing stems were significantly affected under drought and salinity stress condition. PMID:25931776

  16. A Major Locus for Chloride Accumulation on Chromosome 5A in Bread Wheat

    PubMed Central

    Genc, Yusuf; Taylor, Julian; Rongala, Jay; Oldach, Klaus

    2014-01-01

    Chloride (Cl−) is an essential micronutrient for plant growth, but can be toxic at high concentrations resulting in reduced growth and yield. Although saline soils are generally dominated by both sodium (Na+) and Cl− ions, compared to Na+ toxicity, very little is known about physiological and genetic control mechanisms of tolerance to Cl− toxicity. In hydroponics and field studies, a bread wheat mapping population was tested to examine the relationships between physiological traits [Na+, potassium (K+) and Cl− concentration] involved in salinity tolerance (ST) and seedling growth or grain yield, and to elucidate the genetic control mechanism of plant Cl− accumulation using a quantitative trait loci (QTL) analysis approach. Plant Na+ or Cl− concentration were moderately correlated (genetically) with seedling biomass in hydroponics, but showed no correlations with grain yield in the field, indicating little value in selecting for ion concentration to improve ST. In accordance with phenotypic responses, QTL controlling Cl− accumulation differed entirely between hydroponics and field locations, and few were detected in two or more environments, demonstrating substantial QTL-by-environment interactions. The presence of several QTL for Cl− concentration indicated that uptake and accumulation was a polygenic trait. A major Cl− concentration QTL (5A; barc56/gwm186) was identified in three field environments, and accounted for 27–32% of the total genetic variance. Alignment between the 5A QTL interval and its corresponding physical genome regions in wheat and other grasses has enabled the search for candidate genes involved in Cl− transport, which is discussed. PMID:24893005

  17. Mapping and characterization of FLC homologs and QTL analysis of flowering time in Brassica oleracea.

    PubMed

    Okazaki, K; Sakamoto, K; Kikuchi, R; Saito, A; Togashi, E; Kuginuki, Y; Matsumoto, S; Hirai, M

    2007-02-01

    The FLC gene product is an inhibitor of flowering in Arabidopsis. FLC homologs in Brassica species are thought to control vernalization. We cloned four FLC homologs (BoFLCs) from Brassica oleracea. Three of these, BoFLC1, BoFLC3 and BoFLC5, have been previously characterized. The fourth novel sequence displayed 98% sequence homology to the previously identified gene BoFLC4, but also showed 91% homology to BrFLC2 from Brassica rapa. Phylogenetic analysis showed that this clone belongs to the FLC2 clade. Therefore, we designated this gene BoFLC2. Based on the segregation of RFLP, SRAP, CAPS, SSR and AFLP loci, a detailed linkage map of B. oleracea was constructed in the F(2) progeny obtained from a cross of B. oleracea cv. Green Comet (broccoli; non-vernalization type) and B. oleracea cv. Reiho (cabbage; vernalization type), which covered 540 cM, 9 major linkage groups. Six quantitative trait loci (QTL) controlling flowering time were detected. BoFLC1, BoFLC3 and BoFLC5 were not linked to the QTLs controlling flowering time. However, the largest QTL effect was located in the region where BoFLC2 was mapped. Genotyping of F(2 )plants at the BoFLC2 locus showed that most of the early flowering plants were homozygotes of BoFLC-GC, whereas most of the late- and non-flowering plants were homozygotes of BoFLC-Rei. The BoFLC2 homologs present in plants of the non-vernalization type were non-functional, due to a frameshift in exon 4. Moreover, duplications and deletions of BoFLC2 were detected in broccoli and a rapid cycling line, respectively. These results suggest that BoFLC2 contributes to the control of flowering time in B. oleracea.

  18. QTL mapping of agronomic traits in tef [Eragrostis tef (Zucc) Trotter

    PubMed Central

    Yu, Ju-Kyung; Graznak, Elizabeth; Breseghello, Flavio; Tefera, Hailu; Sorrells, Mark E

    2007-01-01

    Background Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4× = 40) and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL) using recombinant inbred lines (RIL) derived from an inter-specific cross between E. tef and E. pilosa (30-5). Results Twenty-two yield-related and morphological traits were assessed across eight different locations in Ethiopia during the growing seasons of 1999 and 2000. Using composite interval mapping and a linkage map incorporating 192 loci, 99 QTLs were identified on 15 of the 21 linkage groups for 19 traits. Twelve QTLs on nine linkage groups were identified for grain yield. Clusters of more than five QTLs for various traits were identified on seven linkage groups. The largest cluster (10 QTLs) was identified on linkage group 8; eight of these QTLs were for yield or yield components, suggesting linkage or pleotrophic effects of loci. There were 15 two-way interactions of loci to detect potential epistasis identified and 75% of the interactions were derived from yield and shoot biomass. Thirty-one percent of the QTLs were observed in multiple environments; two yield QTLs were consistent across all agro-ecology zones. For 29.3% of the QTLs, the alleles from E. pilosa (30-5) had a beneficial effect. Conclusion The extensive QTL data generated for tef in this study will provide a basis for initiating molecular breeding to improve agronomic traits in this staple food crop for the people of Ethiopia. PMID:17565675

  19. Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex

    PubMed Central

    2012-01-01

    Background The Asteraceae species Cynara cardunculus (2n = 2x = 34) includes the two fully cross-compatible domesticated taxa globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC). As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach. Results A set of 172 microsatellite (SSR) loci derived from expressed sequence tag DNA sequence were integrated into the reference C. cardunculus genetic maps, based on segregation among the F1 progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species’ haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs) assembled 694 loci, with a mean inter-marker spacing of 2.5 cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL). Together, these QTL accounted for up to 74% of the overall phenotypic variance. Conclusion The newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection. PMID:22621324

  20. Azo Dye Biodecolorization Enhanced by Echinodontium taxodii Cultured with Lignin

    PubMed Central

    Meng, Jing; Yu, Hongbo; Zhang, Xiaoyu

    2014-01-01

    Lignocellulose facilitates the fungal oxidization of recalcitrant organic pollutants through the extracellular ligninolytic enzymes induced by lignin in wood or other plant tissues. However, available information on this phenomenon is insufficient. Free radical chain reactions during lignin metabolism are important in xenobiotic removal. Thus, the effect of lignin on azo dye decolorization in vivo by Echinodontium taxodii was evaluated. In the presence of lignin, optimum decolorization percentages for Remazol Brilliant Violet 5R, Direct Red 5B, Direct Black 38, and Direct Black 22 were 91.75% (control, 65.96%), 76.89% (control, 43.78%), 43.44% (control, 17.02%), and 44.75% (control, 12.16%), respectively, in the submerged cultures. Laccase was the most important enzyme during biodecolorization. Aside from the stimulating of laccase activity, lignin might be degraded by E. taxodii, and then these degraded low-molecular-weight metabolites could act as redox mediators promoting decolorization of azo dyes. The relationship between laccase and lignin degradation was investigated through decolorization tests in vitro with purified enzyme and dozens of aromatics, which can be derivatives of lignin and can function as laccase mediators or inducers. Dyes were decolorized at triple or even higher rates in certain laccase–aromatic systems at chemical concentrations as low as 10 µM. PMID:25285777

  1. Producing a True Lignin Depolymerase for Biobleaching Softwood Kraft Pulp

    SciTech Connect

    Simo Sarkanen

    2002-02-04

    This project constituted an intensive effort devoted to producing, from the white-rot fungus Tramets Cingulata, a lignin degrading enzyme (lignin depolymerase) that is directly able to biobleach or delignify softwood kraft pulp brownstock. To this end, the solutions in which T. cingulata was grown contained dissolved kraft lignin which fulfilled two functions; it behaved as a lignin deploymerase substrate and it also appeared to act as an inducer of enzyme expression. However, the lignin depolymerase isoenzymes (and other extracellular T. cingulata enzymes) interacted very strongly with both the kraft lignin components and the fungal hypae, so the isolating these proteins from the culture solutions proved to be unexpectedly difficult. Even after extensive experimentation with a variety of protein purification techniques, only one approach appeared to be capable of purifying lignin depolymerases to homogeneity. Unfortunately the procedure was extremely laborious; it involved the iso electric focusing of concentrated buffer-exchanged culture solutions followed by electro-elution of the desired protein bands from the appropriate polyacrylamide gel segments

  2. Recent advances in green hydrogels from lignin: a review.

    PubMed

    Thakur, Vijay Kumar; Thakur, Manju Kumari

    2015-01-01

    Recently, biorenewable polymers from different natural resources have attracted a greater attention of the research community for different applications starting from biomedical to automotive. Lignin is the second most abundant non-food biomass next to cellulose in the category of biorenewable polymers and is abundantly available as byproduct of several industries involved in paper making, ethanol production, etc. The development of various green materials from lignin, which is most often considered as waste, is therefore of prime interest from environmental and economic points of view. Over the last few years, little studies have been made into the use of lignin as an indispensable component in the hydrogels. This article provides an overview of the research work carried out in the last few years on lignin based hydrogels. This article comprehensively reviews the potential efficacy of lignin in biopolymer based green hydrogels with particular emphasis on synthesis, characterization and applications. In this article, several examples of hydrogels synthesized using different types of lignin are discussed to illustrate the state of the art in the use of lignin.

  3. Oxidation in Acidic Medium of Lignins from Agricultural Residues

    NASA Astrophysics Data System (ADS)

    Labat, Gisele Aparecida Amaral; Gonçalves, Adilson Roberto

    Agricultural residues as sugarcane straw and bagasse are burned in boilers for generation of energy in sugar and alcohol industries. However, excess of those by-products could be used to obtain products with higher value. Pulping process generates cellulosic pulps and lignin. The lignin could be oxidized and applied in effluent treatments for heavy metal removal. Oxidized lignin presents very strong chelating properties. Lignins from sugarcane straw and bagasse were obtained by ethanol-water pulping. Oxidation of lignins was carried out using acetic acid and Co/Mn/Br catalytical system at 50, 80, and 115 °C for 5 h. Kinetics of the reaction was accomplished by measuring the UV-visible region. Activation energy was calculated for lignins from sugarcane straw and bagasse (34.2 and 23.4 kJ mol-1, respectively). The first value indicates higher cross-linked formation. Fourier-transformed infrared spectroscopy data of samples collected during oxidation are very similar. Principal component analysis applied to spectra shows only slight structure modifications in lignins after oxidation reaction.

  4. Phenolic mediators enhance the manganese peroxidase catalyzed oxidation of recalcitrant lignin model compounds and synthetic lignin.

    PubMed

    Nousiainen, Paula; Kontro, Jussi; Manner, Helmiina; Hatakka, Annele; Sipilä, Jussi

    2014-11-01

    Fungal oxidative enzymes, such as peroxidases and laccases, are the key catalysts in lignin biodegradation in vivo, and consequently provide an important source for industrial ligninolytic biocatalysts. Recently, it has been shown that some syringyl-type phenolics have potential as industrial co-oxidants or mediators, in laccase-catalyzed modification of lignocellulosic material. We have now studied the effect of such mediators with ligninolytic peroxidases on oxidation of the most recalcitrant lignin model compounds. We found that they are able to enhance the manganese peroxidase (MnP) catalyzed oxidation reactions of small non-phenolic compounds, veratryl alcohol and veratrylglycerol β-guaiacyl ether (adlerol), which are not usually oxidized by manganese peroxidases alone. In these experiments we compared two peroxidases from white-rot fungi, MnP from Phlebia sp. Nf b19 and versatile peroxidase (VP) from Bjerkandera adusta under two oxidation conditions: (i) the Mn(III) initiated mediated oxidation by syringyl compounds and (ii) the system involving MnP-dependent lipid peroxidation, both with production of (hydrogen) peroxides in situ to maintain the peroxidase catalytic cycle. It was found that both peroxidases produced α-carbonyl oxidation product of veratryl alcohol in clearly higher yields in reactions mediated by phenoxy radicals than in lipid-peroxyl radical system. The oxidation of adlerol, on the other hand, was more efficient in lipid-peroxidation-system. VP was more efficient than MnP in the oxidation of veratryl alcohol and showed its lignin peroxidase type activity in the reaction conditions indicated by some cleavage of Cα-Cβ-bond of adlerol. Finally, the mediator assisted oxidation conditions were applied in the oxidation of synthetic lignin (DHP) and the structural analysis of the oxidized polymers showed clear modifications in the polymer outcome, e.g. the oxidation resulted in reduced amount of aliphatic hydroxyls indicated by (31)P NMR.

  5. Phenolic mediators enhance the manganese peroxidase catalyzed oxidation of recalcitrant lignin model compounds and synthetic lignin.

    PubMed

    Nousiainen, Paula; Kontro, Jussi; Manner, Helmiina; Hatakka, Annele; Sipilä, Jussi

    2014-11-01

    Fungal oxidative enzymes, such as peroxidases and laccases, are the key catalysts in lignin biodegradation in vivo, and consequently provide an important source for industrial ligninolytic biocatalysts. Recently, it has been shown that some syringyl-type phenolics have potential as industrial co-oxidants or mediators, in laccase-catalyzed modification of lignocellulosic material. We have now studied the effect of such mediators with ligninolytic peroxidases on oxidation of the most recalcitrant lignin model compounds. We found that they are able to enhance the manganese peroxidase (MnP) catalyzed oxidation reactions of small non-phenolic compounds, veratryl alcohol and veratrylglycerol β-guaiacyl ether (adlerol), which are not usually oxidized by manganese peroxidases alone. In these experiments we compared two peroxidases from white-rot fungi, MnP from Phlebia sp. Nf b19 and versatile peroxidase (VP) from Bjerkandera adusta under two oxidation conditions: (i) the Mn(III) initiated mediated oxidation by syringyl compounds and (ii) the system involving MnP-dependent lipid peroxidation, both with production of (hydrogen) peroxides in situ to maintain the peroxidase catalytic cycle. It was found that both peroxidases produced α-carbonyl oxidation product of veratryl alcohol in clearly higher yields in reactions mediated by phenoxy radicals than in lipid-peroxyl radical system. The oxidation of adlerol, on the other hand, was more efficient in lipid-peroxidation-system. VP was more efficient than MnP in the oxidation of veratryl alcohol and showed its lignin peroxidase type activity in the reaction conditions indicated by some cleavage of Cα-Cβ-bond of adlerol. Finally, the mediator assisted oxidation conditions were applied in the oxidation of synthetic lignin (DHP) and the structural analysis of the oxidized polymers showed clear modifications in the polymer outcome, e.g. the oxidation resulted in reduced amount of aliphatic hydroxyls indicated by (31)P NMR. PMID

  6. Tunable Pickering emulsions with polymer-grafted lignin nanoparticles (PGLNs).

    PubMed

    Silmore, Kevin S; Gupta, Chetali; Washburn, Newell R

    2016-03-15

    Lignin is an abundant biopolymer that has native interfacial functions but aggregates strongly in aqueous media. Polyacrylamide was grafted onto kraft lignin nanoparticles using reversible addition-fragmentation chain transfer (RAFT) chemistry to form polymer-grafted lignin nanoparticles (PGLNs) that tune aggregation strength while retaining interfacial activities in forming Pickering emulsions. Polymer graft density on the particle surface, ionic strength, and initial water and cyclohexane volume fractions were varied and found to have profound effects on emulsion characteristics, including emulsion volume fraction, droplet size, and particle interfacial concentration that were attributed to changes in lignin aggregation and hydrophobic interactions. In particular, salt concentration was found to have a significant effect on aggregation, zeta potential, and interfacial tension, which was attributed to changes in solubility of both the kraft lignin and the polyacrylamide grafts. Dynamic light scattering, UV-vis spectroscopy, optical microscopy, and tensiometry were used to quantify emulsion properties and nanoparticle behavior. Under all conditions, the emulsions exhibited relatively fast creaming but were stable against coalescence and Ostwald ripening for a period of months. All emulsions were also oil-in-water (o/w) emulsions, as predicted by the Bancroft rule, and no catastrophic phase inversions were observed for any nanoparticle compositions. We conclude that lower grafting density of polyacrylamide on a lignin core resulted in high levels of interfacial activity, as characterized by higher concentration at the water-cyclohexane interface with a corresponding decrease in interfacial tension. These results indicate that the interfacial properties of polymer-grafted lignin nanoparticles are primarily due to the native hydrophobic interactions of the lignin core. These results suggest that the forces that drive aggregation are also correlated with interfacial

  7. Functional screening of an asthma QTL in YAC transgenic mice

    SciTech Connect

    Symula, Derek J.; Frazer, Kelly A.; Ueda, Yukihiko; Denefle, Patrice; Stevens, Mary E.; Wang, Zhi-En; Locksley, Richard; Rubin, Edward M.

    1999-07-02

    While large numbers of quantitative trait loci (QTLs) contributing to genetically complex conditions have been discovered, few causative genes have been identified. This is mainly due to the large size of QTLs and the subtle connection between genotype and quantitative phenotype associated with these conditions. While large numbers of quantitative trait loci (QTLs) contributing to genetically complex conditions have been discovered, few causative genes have been identified. This is mainly due to the large size of QTLs and the subtle connection between genotype and quantitative phenotype associated with these conditions. To screen for genes contributing to an asthma QTL mapped to human chromosome 5q33, the authors characterized a panel of large-insert 5q31 transgenics based on studies demonstrating that altering gene dosage frequently affects quantitative phenotypes normally influenced by that gene. This panel of human YAC transgenics, propagating a one megabase interva2048 chromosome 5q31 containing 23 genes, was screened for quantitative changes in several asthma-associated phenotypes. Multiple independent transgenic lines with altered IgE response to antigen treatment shared a 180 kb region containing 5 genes, including human interleukin 4 (IL4) and interleukin 13 (IL13), which induce IgE class switching in B cells5. Further analysis of these mice and mice transgenic for only murine Il4 and Il13 demonstrated that moderate changes in murine Il4 and Il13 expression affect asthma-associated phenotypes in vivo. This functional screen of large-insert transgenics enabled them to sift through multiple genes in the 5q3 asthma QTL without prior consideration of assumed individual gene function and identify genes that influence the QTL phenotype in vivo.

  8. Biphasic survival analysis of trypanotolerance QTL in mice.

    PubMed

    Koudandé, O D; Thomson, P C; Bovenhuis, H; Iraqi, F; Gibson, J P; van Arendonk, J A M

    2008-04-01

    A marker-assisted introgression (MAI) experiment was conducted to transfer trypanotolerance quantitative trait loci (QTL) from a donor mouse strain, C57BL/6, into a recipient mouse strain, A/J. The objective was to assess the effect of three previously identified chromosomal regions on mouse chromosomes 1 (MMU1), 5 (MMU5) and 17 (MMU17) in different genetic backgrounds on the survival pattern following infection with Trypanosoma congolense. An exploratory data analysis revealed a biphasic pattern of time to death, with highly distinct early and late mortality phases. In this paper, we present survival analysis methods that account for the biphasic mortality pattern and results of reanalyzing the data from the MAI experiment. The analysis with a Weibull mixture model confirmed the biphasic pattern of time to death. Mortality phase, an unobserved variable, appears to be an important factor influencing survival time and is modeled as a binary outcome variable using logistic regression analysis. Accounting for this biphasic pattern in the analysis reveals that a previously observed sex effect on average survival is rather an effect on proportion of mice in the two mortality phases. The C57BL/6 (donor) QTL alleles on MMU1 and MMU17 act dominantly in the late mortality phase while the A/J (recipient) QTL allele on MMU17 acts dominantly in the early mortality phase. From this study, we found clear evidence for a biphasic survival pattern and provided models for its analysis. These models can also be used when studying defense mechanisms against other pathogens. Finally, these approaches provide further information on the nature of gene actions. PMID:18253157

  9. The effect of conditioning period on loin muscle tenderness in crossbred lambs with or without the Texel muscling QTL (TM-QTL).

    PubMed

    Lambe, N R; Haresign, W; Macfarlane, J; Richardson, R I; Matika, O; Bünger, L

    2010-08-01

    A Texel muscling quantitative trait locus (TM-QTL) has been identified on chromosome 18, which increases loin muscling, but may also have a negative impact on mechanically-measured loin tenderness in crossbred lambs, depending on conditioning time. This study investigated the influence of a range of conditioning times (3, 5, 7 or 9 days) on the effect of TM-QTL on loin muscle tenderness. Using Texel rams heterozygous for TM-QTL, mated to non-carrier Mule ewes, heterozygous (n=45) and wild-type (n=50) crossbred lambs were produced. Weight of the valuable Longissimus lumborum muscle was higher in TM-QTL carriers than non-carriers, when compared at a fixed age (+11.5%; P=0.038), with the same trend at a fixed carcass weight (+10.2%; P=0.064). Toughness, measured by shear force, was significantly higher in samples from TM-QTL carriers than non-carriers, after conditioning for 3 days (P=0.002), 5 days (P=0.003) or 7 days (P=0.03), but was not significantly different after 9 days of conditioning (P=0.32). Compared to non-carrier lambs, the proportion of samples above consumer acceptability thresholds for toughness was greater in the TM-QTL carrier lambs after 3 and 5 days of conditioning, similar at 7 days, but lower at 9 days. The results suggest that the negative effect of TM-QTL on loin tenderness in crossbred lambs can be overcome by conditioning for more than 7 days. Marketing of TM-QTL carrier lambs through companies that use enhanced processing protocols could be beneficial, due to higher loin muscle weights, without negative effects on meat quality. PMID:20416792

  10. Genome-Wide Identification of QTL for Seed Yield and Yield-Related Traits and Construction of a High-Density Consensus Map for QTL Comparison in Brassica napus

    PubMed Central

    Zhao, Weiguo; Wang, Xiaodong; Wang, Hao; Tian, Jianhua; Li, Baojun; Chen, Li; Chao, Hongbo; Long, Yan; Xiang, Jun; Gan, Jianping; Liang, Wusheng; Li, Maoteng

    2016-01-01

    Seed yield (SY) is the most important trait in rapeseed, is determined by multiple seed yield-related traits (SYRTs) and is also easily subject to environmental influence. Many quantitative trait loci (QTLs) for SY and SYRTs have been reported in Brassica napus; however, no studies have focused on seven agronomic traits simultaneously affecting SY. Genome-wide QTL analysis for SY and seven SYRTs in eight environments was conducted in a doubled haploid population containing 348 lines. Totally, 18 and 208 QTLs for SY and SYRTs were observed, respectively, and then these QTLs were integrated into 144 consensus QTLs using a meta-analysis. Three major QTLs for SY were observed, including cqSY-C6-2 and cqSY-C6-3 that were expressed stably in winter cultivation area for 3 years and cqSY-A2-2 only expressed in spring rapeseed area. Trait-by-trait meta-analysis revealed that the 144 consensus QTLs were integrated into 72 pleiotropic unique QTLs. Among them, all the unique QTLs affected SY, except for uq.A6-1, including uq.A2-3, uq.C1-2, uq.C1-3, uq.C6-1, uq.C6-5, and uq.C6-6 could also affect more than two SYRTs. According to the constructed high-density consensus map and QTL comparison from literatures, 36 QTLs from five populations were co-localized with QTLs identified in this study. In addition, 13 orthologous genes were observed, including five each gene for SY and thousand seed weight, and one gene each for biomass yield, branch height, and plant height. The genomic information of these QTLs will be valuable in hybrid cultivar breeding and in analyzing QTL expression in different environments. PMID:26858737

  11. Preparation of different carbon materials by thermochemical conversion of Lignin

    NASA Astrophysics Data System (ADS)

    Rosas, Juana; Berenguer, Raul; Valero-Romero, Maria; Rodriguez-Mirasol, Jose; Cordero, Tomás

    2014-12-01

    Lignin valorization plays a crucial role within the modern biorefinery scheme from both the economic and environmental points of view; and the structure and composition of lignin becomes it an ideal precursor for the preparation of advanced carbon materials with high added-value. This review provides an overview of the different carbonaceous materials obtained by thermochemical conversion of lignin, such as activated carbons, carbon fibers, template carbons; high ordered carbons; giving information about the new strategies in terms of the preparation method and their possible applications.

  12. Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress

    PubMed Central

    2014-01-01

    Background Drought is one of the most important abiotic stresses that cause drastic reduction in rice grain yield (GY) in rainfed environments. The identification and introgression of QTL leading to high GY under drought have been advocated to be the preferred breeding strategy to improve drought tolerance of popular rice varieties. Genetic control of GY under reproductive-stage drought stress (RS) was studied in two BC1F4 mapping populations derived from crosses of Kali Aus, a drought-tolerant aus cultivar, with high-yielding popular varieties MTU1010 and IR64. The aim was to identify QTL for GY under RS that show a large and consistent effect for the trait. Bulk segregant analysis (BSA) was used to identify significant markers putatively linked with high GY under drought. Results QTL analysis revealed major-effect GY QTL: qDTY 1.2 , qDTY 2.2 and qDTY 1.3 , qDTY 2.3 (DTY; Drought grain yield) under drought consistently over two seasons in Kali Aus/2*MTU1010 and Kali Aus/2*IR64 populations, respectively. qDTY 1.2 and qDTY 2.2 explained an additive effect of 288 kg ha−1 and 567 kg ha−1 in Kali Aus/2*MTU1010, whereas qDTY 1.3 and qDTY 2.3 explained an additive effect of 198 kg ha−1 and 147 kg ha−1 in Kali Aus/2*IR64 populations, respectively. Epistatic interaction was observed for DTF (days to flowering) between regions on chromosome 2 flanked by markers RM154–RM324 and RM263–RM573 and major epistatic QTL for GY showing interaction between genomic locations on chromosome 1 at marker interval RM488–RM315 and chromosome 2 at RM324–RM263 in 2012 DS and 2013 DS RS in Kali Aus/2*IR64 mapping populations. Conclusion The QTL, qDTY 1.2 , qDTY 1.3 , qDTY 2.2 , and qDTY 2.3, identified in this study can be used to improve GY of mega varieties MTU1010 and IR64 under different degrees of severity of drought stress through marker-aided backcrossing and provide farmers with improved varieties that effectively combine high yield potential with good yield

  13. Functional Multi-Locus QTL Mapping of Temporal Trends in Scots Pine Wood Traits

    PubMed Central

    Li, Zitong; Hallingbäck, Henrik R.; Abrahamsson, Sara; Fries, Anders; Gull, Bengt Andersson; Sillanpää, Mikko J.; García-Gil, M. Rosario

    2014-01-01

    Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals. PMID:25305041

  14. Radical coupling reactions in lignin synthesis: a density functional theory study.

    PubMed

    Sangha, Amandeep K; Parks, Jerry M; Standaert, Robert F; Ziebell, Angela; Davis, Mark; Smith, Jeremy C

    2012-04-26

    Lignin is a complex, heterogeneous polymer in plant cell walls that provides mechanical strength to the plant stem and confers resistance to degrading microbes, enzymes, and chemicals. Lignin synthesis initiates through oxidative radical-radical coupling of monolignols, the most common of which are p-coumaryl, coniferyl, and sinapyl alcohols. Here, we use density functional theory to characterize radical-radical coupling reactions involved in monolignol dimerization. We compute reaction enthalpies for the initial self- and cross-coupling reactions of these monolignol radicals to form dimeric intermediates via six major linkages observed in natural lignin. The 8-O-4, 8-8, and 8-5 coupling are computed to be the most favorable, whereas the 5-O-4, 5-5, and 8-1 linkages are less favorable. Overall, p-coumaryl self- and cross-coupling reactions are calculated to be the most favorable. For cross-coupling reactions, in which each radical can couple via either of the two sites involved in dimer formation, the more reactive of the two radicals is found to undergo coupling at its site with the highest spin density.

  15. Characterization of Transport Proteins for Aromatic Compounds Derived from Lignin: Benzoate Derivative Binding Proteins

    PubMed Central

    Michalska, Karolina; Chang, Changsoo; Mack, Jamey C.; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R.

    2013-01-01

    In vitro growth experiments have demonstrated that aromatic compounds derived from lignin can be metabolized and represent a major carbon resource for many soil bacteria. However, the proteins that mediate the movement of these metabolites across the cell membrane have not been thoroughly characterized. To address this deficiency, we used a library representative of lignin degradation products and a thermal stability screen to determine ligand specificity for a set of solute-binding proteins (SBPs) from ATP-binding cassette (ABC) transporters. The ligand mapping process identified a set of proteins from Alphaproteobacteria that recognize various benzoate derivatives. Seven high-resolution crystal structures of these proteins in complex with four different aromatic compounds were obtained. The protein–ligand complexes provide details of molecular recognition that can be used to infer binding specificity. This structure–function characterization provides new insight for the biological roles of these ABC transporters and their SBPs, which had been previously annotated as branched-chain amino-acid-binding proteins. The knowledge derived from the crystal structures provides a foundation for development of sequencebased methods to predict the ligand specificity of other uncharacterized transporters. These results also demonstrate that Alphaproteobacteria possess a diverse set of transport capabilities for lignin-derived compounds. Characterization of this new class of transporters improves genomic annotation projects and provides insight into the metabolic potential of soil bacteria. PMID:22925578

  16. Lignin engineering through laccase modification: a promising field for energy plant improvement.

    PubMed

    Wang, Jinhui; Feng, Juanjuan; Jia, Weitao; Chang, Sandra; Li, Shizhong; Li, Yinxin

    2015-01-01

    Laccase (p-diphenol:dioxygen oxidoreductase, EC 1.10.3.2) is a member of the multicopper oxidases and catalyzes the one-electron oxidation of a wide range of substrates, coupled with the reduction of oxygen to water. It is widely distributed in bacteria, fungi, plants and insects. Laccases are encoded by multigene family, and have been characterized mostly from fungi till now, with abundant industrial applications in pulp and paper, textile, food industries, organic synthesis, bioremediation and nanobiotechnology, while limited researches have been performed in plants, and no application has been reported. Plant laccases share the common molecular architecture and reaction mechanism with fungal ones, despite of difference in redox potential and pH optima. Plant laccases are implicated in lignin biosynthesis since genetic evidence was derived from the Arabidopsis LAC4 and LAC17. Manipulation of plant laccases has been considered as a promising and innovative strategy in plant biomass engineering for desirable lignin content and/or composition, since lignin is the major recalcitrant component to saccharification in biofuel production from lignocellulose, and therefore directly limits the fermentation yields. Moreover, plant laccases have been reported to be involved in wound healing, maintenance of cell wall structure and integrity, and plant responses to environmental stresses. Here, we summarize the properties and functions of plant laccase, and discuss the potential of biotechnological application, thus providing a new insight into plant laccase, an old enzyme with a promising beginning in lignocellulose biofuel production. PMID:26379777

  17. Novel Bioactive Antimicrobial Lignin Containing Coatings on Titanium Obtained by Electrophoretic Deposition

    PubMed Central

    Erakovic, Sanja; Jankovic, Ana; Tsui, Gary C. P.; Tang, Chak-Yin; Miskovic-Stankovic, Vesna; Stevanovic, Tatjana

    2014-01-01

    Hydroxyapatite (HAP) is the most suitable biocompatible material for bone implant coatings; its brittleness, however, is a major obstacle, and the reason why research focuses on creating composites with biopolymers. Organosolv lignin (Lig) is used for the production of composite coatings, and these composites were examined in this study. Titanium substrate is a key biomedical material due to its well-known properties, but infections of the implantation site still impose a serious threat. One approach to prevent infection is to improve antimicrobial properties of the coating material. Silver doped hydroxyapatite (Ag/HAP) and HAP coatings on titanium were obtained by an electrophoretic deposition method in order to control deposited coating mass and morphology by varying applied voltage and deposition time. The effect of lignin on microstructure, morphology and thermal behavior of biocomposite coatings was investigated. The results showed that higher lignin concentrations protect the HAP lattice during sintering, improving coating stability. The corrosion stability was evaluated in simulated body fluid (SBF) at 37 °C. Newly formed plate-shaped carbonate-HAP was detected, indicating enhanced bioactive performance. The antimicrobial efficiency of Ag/HAP/Lig was confirmed by its higher reduction of bacteria Staphylococcus aureus TL (S. aureus TL) than of HAP/Lig coating. Cytotoxicity assay revealed that both coatings can be classified as non-toxic against healthy immunocompetent peripheral blood mononuclear cells (PBMC). PMID:25019343

  18. Peroxidases Bound to the Growing Lignin Polymer Produce Natural Like Extracellular Lignin in a Cell Culture of Norway Spruce

    PubMed Central

    Warinowski, Tino; Koutaniemi, Sanna; Kärkönen, Anna; Sundberg, Ilari; Toikka, Merja; Simola, Liisa Kaarina; Kilpeläinen, Ilkka; Teeri, Teemu H.

    2016-01-01

    Lignin, an important component of plant cell walls, is a polymer of monolignols derived from the phenylpropanoid pathway. Monolignols are oxidized in the cell wall by oxidative enzymes (peroxidases and/or laccases) to radicals, which then couple with the growing lignin polymer. We have investigated the characteristics of the polymerization reaction by producing lignin polymers in vitro using different oxidative enzymes and analyzing the structures formed with NMR. The ability of the enzymes to oxidize high-molecular-weight compounds was tested using cytochrome c as a substrate. The results support an idea that lignin structure is largely determined by the concentration ratios of the monolignol (coniferyl alcohol) and polymer radicals involved in the coupling reaction. High rate of the lignin polymer oxidation compared to monolignol oxidation leads to a natural-like structure. The high relative rate can be achieved by an open active site of the oxidative enzyme, close proximity of the enzyme with the polymeric substrate or simply by high enzymatic activity that consumes monolignols rapidly. Monolignols, which are oxidized efficiently, can be seen as competitive inhibitors of polymer oxidation. Our results indicate that, at least in a Norway spruce (Picea abies L. Karst.) cell culture, a group of apoplastic, polymer-oxidizing peroxidases bind to the lignin polymer and are responsible for production of natural-like lignin in cell suspension cultures in vivo, and also in vitro. The peroxidases bound to the extracellular lignin had the highest ability to bind to various cell wall polymers in vitro. Extracellular lignin contains pectin-type sugars, making them possible attachment points for these cationic peroxidases. PMID:27803704

  19. Identification of genome regions controlling cotyledon, pod wall/seed coat and pod wall resistance to pea weevil through QTL mapping.

    PubMed

    Aryamanesh, N; Zeng, Y; Byrne, O; Hardie, D C; Al-Subhi, A M; Khan, T; Siddique, K H M; Yan, G

    2013-11-15

    Pea weevil, Bruchus pisorum, is one of the limiting factors for field pea (Pisum sativum) cultivation in the world with pesticide application the only available method for its control. Resistance to pea weevil has been found in an accession of Pisum fulvum but transfer of this resistance to cultivated pea (P. sativum) is limited due to a lack of easy-to-use techniques for screening interspecific breeding populations. To address this problem, an interspecific population was created from a cross between cultivated field pea and P. fulvum (resistance source). Quantitative trait locus (QTL) mapping was performed to discover the regions associated with resistance to cotyledon, pod wall/seed coat and pod wall resistance. Three major QTLs, located on linkage groups LG2, LG4 and LG5 were found for cotyledon resistance explaining approximately 80 % of the phenotypic variation. Two major QTLs were found for pod wall/seed coat resistance on LG2 and LG5 explaining approximately 70 % of the phenotypic variation. Co-linearity of QTLs for cotyledon and pod wall/seed coat resistance suggested that the mechanism of resistance for these two traits might act through the same pathways. Only one QTL was found for pod wall resistance on LG7 explaining approximately 9 % of the phenotypic variation. This is the first report on the development of QTL markers to probe Pisum germplasm for pea weevil resistance genes. These flanking markers will be useful in accelerating the process of screening when breeding for pea weevil resistance.

  20. A clinical pilot study of lignin--ascorbic acid combination treatment of herpes simplex virus.

    PubMed

    Lopez, Blanca Silvia Gonzalez; Yamamoto, Masaji; Utsumi, Katsuaki; Aratsu, Chiaki; Sakagami, Hiroshi

    2009-01-01

    Antiviral drugs as well as natural remedies have been used to reduce symptoms and the rate of recurrences of herpes simplex virus type 1 (HSV-1) infection, a common disease. To evaluate anti-HSV-1 activity of a pine cone lignin and ascorbic acid treatment, a clinical pilot study was carried out. Forty-eight healthy patients of both genders between 4 and 61 years old (mean: 31+/-16 years), with active lesions of HSV-1, took part in the study. According to the HSV-1 stage at the presentation, the patients were classified into the prodromic (16 patients), erythema (11 patients), papule edema (1 patient), vesicle/pustule (13 patients) and ulcer stages (7 patients). One mg of lignin-ascorbic acid tablet or solution was orally administered three times daily for a month. Clinical evaluations were made daily the first week and at least three times a week during the second week after the onset and every six months during the subsequent year to identify recurrence episodes. The patients who began the lignin-ascorbic acid treatment within the first 48 hours of symptom onset did not develop HSV-1 characteristic lesions, whereas those patients who began the treatment later experienced a shorter duration of cold sore lesions and a decrease in the symptoms compared with previous episodes. The majority of the patients reported the reduction in the severity of symptoms and the reduction in the recurrence episodes after the lignin-ascorbic acid treatment compared with previous episodes, suggesting its possible applicability for the prevention and treatment of HSV-1 infection. PMID:20023248

  1. Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.).

    PubMed

    Escamilla-Treviño, Luis L; Shen, Hui; Hernandez, Timothy; Yin, Yanbin; Xu, Ying; Dixon, Richard A

    2014-03-01

    Studying lignin biosynthesis in Panicum virgatum (switchgrass) has provided a basis for generating plants with reduced lignin content and increased saccharification efficiency. Chlorogenic acid (CGA, caffeoyl quinate) is the major soluble phenolic compound in switchgrass, and the lignin and CGA biosynthetic pathways potentially share intermediates and enzymes. The enzyme hydroxycinnamoyl-CoA: quinate hydroxycinnamoyltransferase (HQT) is responsible for CGA biosynthesis in tobacco, tomato and globe artichoke, but there are no close orthologs of HQT in switchgrass or in other monocotyledonous plants with complete genome sequences. We examined available transcriptomic databases for genes encoding enzymes potentially involved in CGA biosynthesis in switchgrass. The protein products of two hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT) genes (PvHCT1a and PvHCT2a), closely related to lignin pathway HCTs from other species, were characterized biochemically and exhibited the expected HCT activity, preferring shikimic acid as acyl acceptor. We also characterized two switchgrass coumaroyl shikimate 3'-hydroxylase (C3'H) enzymes (PvC3'H1 and PvC3'H2); both of these cytochrome P450s had the capacity to hydroxylate 4-coumaroyl shikimate or 4-coumaroyl quinate to generate caffeoyl shikimate or CGA. Another switchgrass hydroxycinnamoyl transferase, PvHCT-Like1, is phylogenetically distant from HCTs or HQTs, but exhibits HQT activity, preferring quinic acid as acyl acceptor, and could therefore function in CGA biosynthesis. The biochemical features of the recombinant enzymes, the presence of the corresponding activities in plant protein extracts, and the expression patterns of the corresponding genes, suggest preferred routes to CGA in switchgrass.

  2. Lignin-modifying enzymes of the white rot basidiomycete Ganoderma lucidum

    SciTech Connect

    D Merritt, C.S.; Reddy, C.A.

    1999-12-01

    Ganoderma lucidum, a white rot basidiomycete widely distributed worldwide, was studied for the production of the lignin-modifying enzymes laccase, manganese-dependent peroxidase (MnP), and lignin peroxidase (LiP). Laccase levels observed in high-nitrogen shaken cultures were much greater than those seen in low-nitrogen, malt extract, or wool-grown cultures and those reported for most other white rot fungi to date. Laccase production was readily seen in cultures grown with pine or poplar as the sole carbon and energy source. Cultures containing both pine and poplar showed 5- to 10-fold-higher levels of laccase than cultures containing pine or poplar alone. Since syringyl units are structural components important in poplar lignin and other hardwoods but much less so in pine lignin and other softwoods, pine cultures were supplemented with syringic acid, and this resulted in laccase levels comparable to those seen in pine-plus-poplar cultures. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of concentrated extracellular culture fluid from HM cultures showed two laccase activity bands, where as isoelectric focusing revealed five major laccase activity bands with estimated pIs of 3.0, 4.25, 4.5, and 5.1. Low levels of MnP activity were detected in poplar-grown cultures but not in cultures grown with pine, with pine plus syringic acid, or in HN medium. No LiP activity was seen in any of the media tested; however, probing the genomic DNA with the LiP cDNA (CLG4) from the white rot fungus Phanerochaete chrysosporium showed distinct hybridization bands suggesting the presence of lip-like sequences in G. lucidum.

  3. Lignin-Modifying Enzymes of the White Rot Basidiomycete Ganoderma lucidum

    PubMed Central

    D’Souza, Trevor M.; Merritt, Carlos S.; Reddy, C. Adinarayana

    1999-01-01

    Ganoderma lucidum, a white rot basidiomycete widely distributed worldwide, was studied for the production of the lignin-modifying enzymes laccase, manganese-dependent peroxidase (MnP), and lignin peroxidase (LiP). Laccase levels observed in high-nitrogen (HN; 24 mM N) shaken cultures were much greater than those seen in low-nitrogen (2.4 mM N), malt extract, or wood-grown cultures and those reported for most other white rot fungi to date. Laccase production was readily seen in cultures grown with pine or poplar (100-mesh-size ground wood) as the sole carbon and energy source. Cultures containing both pine and poplar showed 5- to 10-fold-higher levels of laccase than cultures containing pine or poplar alone. Since syringyl units are structural components important in poplar lignin and other hardwoods but much less so in pine lignin and other softwoods, pine cultures were supplemented with syringic acid, and this resulted in laccase levels comparable to those seen in pine-plus-poplar cultures. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of concentrated extracellular culture fluid from HN cultures showed two laccase activity bands (Mr of 40,000 and 66,000), whereas isoelectric focusing revealed five major laccase activity bands with estimated pIs of 3.0, 4.25, 4.5, 4.8, and 5.1. Low levels of MnP activity (∼100 U/liter) were detected in poplar-grown cultures but not in cultures grown with pine, with pine plus syringic acid, or in HN medium. No LiP activity was seen in any of the media tested; however, probing the genomic DNA with the LiP cDNA (CLG4) from the white rot fungus Phanerochaete chrysosporium showed distinct hybridization bands suggesting the presence of lip-like sequences in G. lucidum. PMID:10583981

  4. A clinical pilot study of lignin--ascorbic acid combination treatment of herpes simplex virus.

    PubMed

    Lopez, Blanca Silvia Gonzalez; Yamamoto, Masaji; Utsumi, Katsuaki; Aratsu, Chiaki; Sakagami, Hiroshi

    2009-01-01

    Antiviral drugs as well as natural remedies have been used to reduce symptoms and the rate of recurrences of herpes simplex virus type 1 (HSV-1) infection, a common disease. To evaluate anti-HSV-1 activity of a pine cone lignin and ascorbic acid treatment, a clinical pilot study was carried out. Forty-eight healthy patients of both genders between 4 and 61 years old (mean: 31+/-16 years), with active lesions of HSV-1, took part in the study. According to the HSV-1 stage at the presentation, the patients were classified into the prodromic (16 patients), erythema (11 patients), papule edema (1 patient), vesicle/pustule (13 patients) and ulcer stages (7 patients). One mg of lignin-ascorbic acid tablet or solution was orally administered three times daily for a month. Clinical evaluations were made daily the first week and at least three times a week during the second week after the onset and every six months during the subsequent year to identify recurrence episodes. The patients who began the lignin-ascorbic acid treatment within the first 48 hours of symptom onset did not develop HSV-1 characteristic lesions, whereas those patients who began the treatment later experienced a shorter duration of cold sore lesions and a decrease in the symptoms compared with previous episodes. The majority of the patients reported the reduction in the severity of symptoms and the reduction in the recurrence episodes after the lignin-ascorbic acid treatment compared with previous episodes, suggesting its possible applicability for the prevention and treatment of HSV-1 infection.

  5. Whole-Genome Mapping Reveals Novel QTL Clusters Associated with Main Agronomic Traits of Cabbage (Brassica oleracea var. capitata L.)

    PubMed Central

    Lv, Honghao; Wang, Qingbiao; Liu, Xing; Han, Fengqing; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Liu, Yumei; Li, Zhansheng; Zhang, Yangyong

    2016-01-01

    We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0–55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R2 = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R2 = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R2 = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481–scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64–scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782–Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353–Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits. PMID:27458471

  6. Whole-Genome Mapping Reveals Novel QTL Clusters Associated with Main Agronomic Traits of Cabbage (Brassica oleracea var. capitata L.).

    PubMed

    Lv, Honghao; Wang, Qingbiao; Liu, Xing; Han, Fengqing; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Liu, Yumei; Li, Zhansheng; Zhang, Yangyong

    2016-01-01

    We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0-55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R (2) = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R (2) = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R (2) = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481-scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64-scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782-Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353-Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits.

  7. Whole-Genome Mapping Reveals Novel QTL Clusters Associated with Main Agronomic Traits of Cabbage (Brassica oleracea var. capitata L.).

    PubMed

    Lv, Honghao; Wang, Qingbiao; Liu, Xing; Han, Fengqing; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Liu, Yumei; Li, Zhansheng; Zhang, Yangyong

    2016-01-01

    We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0-55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R (2) = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R (2) = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R (2) = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481-scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64-scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782-Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353-Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits. PMID:27458471

  8. Preparation of lignopolyols from wheat straw soda lignin.

    PubMed

    Ahvazi, Behzad; Wojciechowicz, Olivia; Ton-That, Tan-Minh; Hawari, Jalal

    2011-10-12

    Wheat straw soda lignin was modified and characterized by several qualitative and quantitative methods such as (31)P NMR spectroscopy to evaluate its potential as a substitute for polyols in view of polyurethane applications. Chemical modification of the lignin was achieved with propylene oxide to form lignopolyol derivatives. This was performed by a two-step reaction of lignin with maleic anhydride followed by propylene oxide and by direct oxyalkylation under acidic and alkaline conditions. The physical and chemical properties of lignopolyols from each method and the subsequent chain-extended hydroxyl groups were evaluated. Direct oxyalkylation of lignin under alkaline conditions was found to be more efficient than acidic conditions and more effective than the two-step process for preparing lignopolyol with higher aliphatic hydroxyl contents. PMID:21854019

  9. Hydrothermal fractionation of woody biomass: Lignin effect on sugars recovery.

    PubMed

    Yedro, Florencia M; Cantero, Danilo A; Pascual, Marcos; García-Serna, Juan; Cocero, M José

    2015-09-01

    Subcritical water was employed to fractionate woody biomass into carbohydrates and lignin. Nine urban trees species (hardwood and softwood) from Spain were studied. The experiments were carried out in a semi-continuous reactor at 250 °C for 64 min. The hemicellulose and cellulose recovery yields were between 30%wt. and 80%wt. while the lignin content in the solid product ranged between 32%wt. and 92%wt. It was observed that an increment of solubilized lignin disfavored the hydrolysis of hemicelluloses. It was determined that the maximum extraction of hemicellulose was achieved at 20 min of solid reaction time while the extraction of celluloses not exhibited a maximum value. The hydrolysis of hemicellulose and cellulose would be governed by the hydrolysis kinetic and the polymers accessibility. In addition, the extraction of hemicellulose was negatively affected by the lignin content in the raw material while cellulose hydrolysis was not affected by this parameter. PMID:25985415

  10. Molecular simulation as a tool for studying lignin

    SciTech Connect

    Sangha, Amandeep K; Petridis, Loukas; Smith, Jeremy C; Ziebell, Angela L; Parks, Jerry M

    2012-01-01

    Lignocellulosic biomass provides a sustainable source of sugars for biofuel and biomaterial production. However, biomass resistance to degradation imposes difficulties for economical conversion of plant carbohydrates to fermentable sugars. One of the key contributors to recalcitrance is lignin. Understanding the properties of lignin macromolecules in the cell wall matrix is useful for manipulating biomass structure to generate more easily degradable biomass. Along with experimental techniques such as 2D-NMR and mass spectrometry, computational techniques can be useful for characterizing the structural and energetic properties of the biomass assembly and its individual constituents. Here, we provide a brief introduction to lignin, review some of the recent, relevant scientific literature, and give our perspectives on the role of molecular simulation in understanding lignin structure.

  11. Hydrothermal fractionation of woody biomass: Lignin effect on sugars recovery.

    PubMed

    Yedro, Florencia M; Cantero, Danilo A; Pascual, Marcos; García-Serna, Juan; Cocero, M José

    2015-09-01

    Subcritical water was employed to fractionate woody biomass into carbohydrates and lignin. Nine urban trees species (hardwood and softwood) from Spain were studied. The experiments were carried out in a semi-continuous reactor at 250 °C for 64 min. The hemicellulose and cellulose recovery yields were between 30%wt. and 80%wt. while the lignin content in the solid product ranged between 32%wt. and 92%wt. It was observed that an increment of solubilized lignin disfavored the hydrolysis of hemicelluloses. It was determined that the maximum extraction of hemicellulose was achieved at 20 min of solid reaction time while the extraction of celluloses not exhibited a maximum value. The hydrolysis of hemicellulose and cellulose would be governed by the hydrolysis kinetic and the polymers accessibility. In addition, the extraction of hemicellulose was negatively affected by the lignin content in the raw material while cellulose hydrolysis was not affected by this parameter.

  12. Lignin in marine environment and its analysis—A review

    NASA Astrophysics Data System (ADS)

    Li, Xianguo; Zhang, Ting; Sun, Shuwen; Lan, Haiqing; Yu, Tao

    2012-12-01

    Lignin is a group of phenolic polymers which is abundant in the woody tissues of vascular plants, and is essentially absent from all other living organisms. It has therefore been accepted as a tracer for terrestrial organic carbon (TOC) in marine environment since the 1970s. Lignin polymers are not amenable to direct chemical analysis without prior isolation. This review focused on the methods of chemical decomposition, extraction, derivatization and detection of lignin in marine environment. We described and compared several chemical decomposition methods, including nitrobenzene oxidation, alkaline cupric oxide (CuO) oxidation and thermochemolysis, and detection methods such as gas chromatography (GC), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC) and so on. Possible improvement of lignin analysis and the application prospects of this tracer were also discussed.

  13. Membrane Technology for the Recovery of Lignin: A Review

    PubMed Central

    Humpert, Daniel; Ebrahimi, Mehrdad; Czermak, Peter

    2016-01-01

    Utilization of renewable resources is becoming increasingly important, and only sustainable processes that convert such resources into useful products can achieve environmentally beneficial economic growth. Wastewater from the pulp and paper industry is an unutilized resource offering the potential to recover valuable products such as lignin, pigments, and water [1]. The recovery of lignin is particularly important because it has many applications, and membrane technology has been investigated as the basis of innovative recovery solutions. The concentration of lignin can be increased from 62 to 285 g∙L−1 using membranes and the recovered lignin is extremely pure. Membrane technology is also scalable and adaptable to different waste liquors from the pulp and paper industry. PMID:27608047

  14. Membrane Technology for the Recovery of Lignin: A Review.

    PubMed

    Humpert, Daniel; Ebrahimi, Mehrdad; Czermak, Peter

    2016-01-01

    Utilization of renewable resources is becoming increasingly important, and only sustainable processes that convert such resources into useful products can achieve environmentally beneficial economic growth. Wastewater from the pulp and paper industry is an unutilized resource offering the potential to recover valuable products such as lignin, pigments, and water [1]. The recovery of lignin is particularly important because it has many applications, and membrane technology has been investigated as the basis of innovative recovery solutions. The concentration of lignin can be increased from 62 to 285 g∙L(-1) using membranes and the recovered lignin is extremely pure. Membrane technology is also scalable and adaptable to different waste liquors from the pulp and paper industry. PMID:27608047

  15. Mapping eQTL Networks with Mixed Graphical Markov Models

    PubMed Central

    Tur, Inma; Roverato, Alberto; Castelo, Robert

    2014-01-01

    Expression quantitative trait loci (eQTL) mapping constitutes a challenging problem due to, among other reasons, the high-dimensional multivariate nature of gene-expression traits. Next to the expression heterogeneity produced by confounding factors and other sources of unwanted variation, indirect effects spread throughout genes as a result of genetic, molecular, and environmental perturbations. From a multivariate perspective one would like to adjust for the effect of all of these factors to end up with a network of direct associations connecting the path from genotype to phenotype. In this article we approach this challenge with mixed graphical Markov models, higher-order conditional independences, and q-order correlation graphs. These models show that additive genetic effects propagate through the network as function of gene–gene correlations. Our estimation of the eQTL network underlying a well-studied yeast data set leads to a sparse structure with more direct genetic and regulatory associations that enable a straightforward comparison of the genetic control of gene expression across chromosomes. Interestingly, it also reveals that eQTLs explain most of the expression variability of network hub genes. PMID:25271303

  16. Mapping of QTL for downy mildew resistance in maize.

    PubMed

    Agrama, H A; Moussa, M E; Naser, M E; Tarek, M A; Ibrahim, A H

    1999-08-01

    Quantitative trait loci (QTLs) of maize involved in mediating resistance to Peronosclerospora sorghi, the causative agent of sorghum downy mildew (SDM), were detected in a population of recombinant inbred lines (RILs) derived from the Zea mays L. cross between resistant (G62) and susceptible (G58) inbred lines. Field tests of 94 RILs were conducted over two growing seasons using artificial inoculation. Heritability of the disease reaction was high (around 70%). The mapping population of the RILs was also scored for restriction fragment length polymorphic (RFLP) markers. One hundred and six polymorphic RFLP markers were assigned to ten chromosomes covering 1648 cM. Three QTLs were detected that significantly affected resistance to SDM combined across seasons. Two of these mapped quite close together on chromosome 1, while the third one was on chromosome 9. The percentage of phenotypic variance explained by each QTL ranged from 12.4% to 23.8%. Collectively, the three QTLs identified in this study explained 53.6% of the phenotypic variation in susceptibility to the infection. The three resistant QTLs appeared to have additive effects. Increased susceptibility was contributed by the alleles of the susceptible parent. The detection of more than one QTL supports the hypothesis that several qualitative and quantitative genes control resistance to P. sorghi.

  17. QTL mapping of clubroot resistance in radish (Raphanus sativus L.).

    PubMed

    Kamei, Akito; Tsuro, Masato; Kubo, Nakao; Hayashi, Takeshi; Wang, Ning; Fujimura, Tatsuhito; Hirai, Masashi

    2010-03-01

    A QTL analysis for clubroot resistance (CR) of radish was performed using an F(2) population derived from a crossing of a CR Japanese radish and a clubroot-susceptible (CS) Chinese radish. F(3) plants obtained by selfing of F(2) plants were used for the CR tests. The potted seedlings were inoculated and the symptom was evaluated 6 weeks thereafter. The mean disease indexes of the F(3) plants were used for the phenotype of the F(2). The results of two CR tests were analyzed for the presence of QTL. A linkage map was constructed using AFLP and SSR markers; it spanned 554 cM and contained 18 linkage groups. A CR locus was observed in the top region of linkage group 1 in two tests. Therefore, the present results suggest that a large part of radish CR is controlled by a single gene or closely linked genes in this radish population, although minor effects of other genomic areas cannot be ruled out. The CR locus was named Crs1. Markers linked to Crs1 showed sequence homology to the genomic region of the top of chromosome 3 of Arabidopsis, as in the case of Crr3, a CR locus in Brassica rapa. These markers should be useful for breeding CR cultivars of radish. As Japanese radishes are known to be highly resistant or immune to clubroot, these markers may also be useful in the introgression of this CR gene to Brassica crops.

  18. Improvement of Rice Biomass Yield through QTL-Based Selection.

    PubMed

    Matsubara, Kazuki; Y