Captive breeding of pangolins: current status, problems and future prospects

PubMed Central

Hua, Liushuai; Gong, Shiping; Wang, Fumin; Li, Weiye; Ge, Yan; Li, Xiaonan; Hou, Fanghui

2015-01-01

Abstract Pangolins are unique placental mammals with eight species existing in the world, which have adapted to a highly specialized diet of ants and termites, and are of significance in the control of forest termite disaster. Besides their ecological value, pangolins are extremely important economic animals with the value as medicine and food. At present, illegal hunting and habitat destruction have drastically decreased the wild population of pangolins, pushing them to the edge of extinction. Captive breeding is an important way to protect these species, but because of pangolin’s specialized behaviors and high dependence on natural ecosystem, there still exist many technical barriers to successful captive breeding programs. In this paper, based on the literatures and our practical experience, we reviewed the status and existing problems in captive breeding of pangolins, including four aspects, the naturalistic habitat, dietary husbandry, reproduction and disease control. Some recommendations are presented for effective captive breeding and protection of pangolins. PMID:26155072

Evaluation of mechanical cotton seed delinter for breeders

USDA-ARS?s Scientific Manuscript database

Delinting seed is common practice in cotton breeding programs. The predominant method of delinting cotton seed is acid delinting. Acid delinting can be dangerous and effluent disposal is difficult and costly. Current research on mechanical delinting proposes an alternative to acid delinting. A pr...

Mating practices and the dissemination of genetic disorders in domestic animals, based on the example of dog breeding.

PubMed

Leroy, G; Baumung, R

2011-02-01

On the basis of simulations and genealogical data of ten dog breeds, three popular mating practices (popular sire effect, line breeding, close breeding) were investigated along with their effects on the dissemination of genetic disorders. Our results showed that the use of sires in these ten breeds is clearly unbalanced. Depending on the breed, the effective number of sires represented between 33% and 70% of the total number of sires. Mating between close relatives was also found to be quite common, and the percentage of dogs inbred after two generations ranged from 1% to about 8%. A more or less long-term genetic differentiation, linked to line breeding practices, was also emphasized in most breeds. F(IT) index based on gene dropping proved to be efficient in differentiating the effects of the different mating practices, and it ranged from -1.3% to 3.2% when real founders were used to begin a gene dropping process. Simulation results confirmed that the popular sire practice leads to a dissemination of genetic disorders. Under a realistic scenario, regarding the imbalance in the use of sires, the dissemination risk was indeed 4.4 times higher than under random mating conditions. In contrast, line breeding and close breeding practices tend to decrease the risk of the dissemination of genetic disorders. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

Will genomic selection be a practical method for plant breeding?

PubMed Central

Nakaya, Akihiro; Isobe, Sachiko N.

2012-01-01

Background Genomic selection or genome-wide selection (GS) has been highlighted as a new approach for marker-assisted selection (MAS) in recent years. GS is a form of MAS that selects favourable individuals based on genomic estimated breeding values. Previous studies have suggested the utility of GS, especially for capturing small-effect quantitative trait loci, but GS has not become a popular methodology in the field of plant breeding, possibly because there is insufficient information available on GS for practical use. Scope In this review, GS is discussed from a practical breeding viewpoint. Statistical approaches employed in GS are briefly described, before the recent progress in GS studies is surveyed. GS practices in plant breeding are then reviewed before future prospects are discussed. Conclusions Statistical concepts used in GS are discussed with genetic models and variance decomposition, heritability, breeding value and linear model. Recent progress in GS studies is reviewed with a focus on empirical studies. For the practice of GS in plant breeding, several specific points are discussed including linkage disequilibrium, feature of populations and genotyped markers and breeding scheme. Currently, GS is not perfect, but it is a potent, attractive and valuable approach for plant breeding. This method will be integrated into many practical breeding programmes in the near future with further advances and the maturing of its theory. PMID:22645117

Genetic Factors Involved in Fumonisin Accumulation in Maize Kernels and Their Implications in Maize Agronomic Management and Breeding

PubMed Central

Santiago, Rogelio; Cao, Ana; Butrón, Ana

2015-01-01

Contamination of maize with fumonisins depends on the environmental conditions; the maize resistance to contamination and the interaction between both factors. Although the effect of environmental factors is a determinant for establishing the risk of kernel contamination in a region, there is sufficient genetic variability among maize to develop resistance to fumonisin contamination and to breed varieties with contamination at safe levels. In addition, ascertaining which environmental factors are the most important in a region will allow the implementation of risk monitoring programs and suitable cultural practices to reduce the impact of such environmental variables. The current paper reviews all works done to address the influence of environmental variables on fumonisin accumulation, the genetics of maize resistance to fumonisin accumulation, and the search for the biochemical and/or structural mechanisms of the maize plant that could be involved in resistance to fumonisin contamination. We also explore the outcomes of breeding programs and risk monitoring of undertaken projects. PMID:26308050

Genetic Factors Involved in Fumonisin Accumulation in Maize Kernels and Their Implications in Maize Agronomic Management and Breeding.

PubMed

Santiago, Rogelio; Cao, Ana; Butrón, Ana

2015-08-20

Contamination of maize with fumonisins depends on the environmental conditions; the maize resistance to contamination and the interaction between both factors. Although the effect of environmental factors is a determinant for establishing the risk of kernel contamination in a region, there is sufficient genetic variability among maize to develop resistance to fumonisin contamination and to breed varieties with contamination at safe levels. In addition, ascertaining which environmental factors are the most important in a region will allow the implementation of risk monitoring programs and suitable cultural practices to reduce the impact of such environmental variables. The current paper reviews all works done to address the influence of environmental variables on fumonisin accumulation, the genetics of maize resistance to fumonisin accumulation, and the search for the biochemical and/or structural mechanisms of the maize plant that could be involved in resistance to fumonisin contamination. We also explore the outcomes of breeding programs and risk monitoring of undertaken projects.

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2011 CFR

2011-10-01

... WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.26 Approval of cooperative breeding programs. Upon receipt of a complete application, the Director... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Approval of cooperative breeding programs...

Current knowledge and practices related to seed transmission of sugarcane pathogens and movement of seed

USDA-ARS?s Scientific Manuscript database

Sugarcane breeding programs benefit from sharing genetic resources. Traditionally, this has been accomplished by exchanging vegetative planting material of clones of interest. Diseases can spread during this process, and quarantines were established to enable continued sharing of germplasm while min...

Analysis of genotype by environment interaction in Louisiana sugarcane research plots by GGE biplots

USDA-ARS?s Scientific Manuscript database

Genotype by environment (G x E) interactions complicate genotype selection in breeding programs. In south Louisiana, sugarcane is cultivated under a wide range of environments including soil types and cultural management practices. To evaluate experimental genotypes in different environments, the va...

Sequencing consolidates molecular markers with plant breeding practice.

PubMed

Yang, Huaan; Li, Chengdao; Lam, Hon-Ming; Clements, Jonathan; Yan, Guijun; Zhao, Shancen

2015-05-01

Plenty of molecular markers have been developed by contemporary sequencing technologies, whereas few of them are successfully applied in breeding, thus we present a review on how sequencing can facilitate marker-assisted selection in plant breeding. The growing global population and shrinking arable land area require efficient plant breeding. Novel strategies assisted by certain markers have proven effective for genetic gains. Fortunately, cutting-edge sequencing technologies bring us a deluge of genomes and genetic variations, enlightening the potential of marker development. However, a large gap still exists between the potential of molecular markers and actual plant breeding practices. In this review, we discuss marker-assisted breeding from a historical perspective, describe the road from crop sequencing to breeding, and highlight how sequencing facilitates the application of markers in breeding practice.

50 CFR 15.23 - Permits for zoological breeding or display programs.

Code of Federal Regulations, 2011 CFR

2011-10-01

... OF WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.23 Permits for zoological breeding or display programs. (a) Application requirements for... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Permits for zoological breeding or display...

50 CFR 15.23 - Permits for zoological breeding or display programs.

Code of Federal Regulations, 2010 CFR

2010-10-01

... OF WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.23 Permits for zoological breeding or display programs. (a) Application requirements for... 50 Wildlife and Fisheries 1 2010-10-01 2010-10-01 false Permits for zoological breeding or display...

Feasibility of pedigree recording and genetic selection in village sheep flocks of smallholder farmers.

PubMed

Gizaw, Solomon; Goshme, Shenkute; Getachew, Tesfaye; Haile, Aynalem; Rischkowsky, Barbara; van Arendonk, Johan; Valle-Zárate, Anne; Dessie, Tadelle; Mwai, Ally Okeyo

2014-06-01

Pedigree recording and genetic selection in village flocks of smallholder farmers have been deemed infeasible by researchers and development workers. This is mainly due to the difficulty of sire identification under uncontrolled village breeding practices. A cooperative village sheep-breeding scheme was designed to achieve controlled breeding and implemented for Menz sheep of Ethiopia in 2009. In this paper, we evaluated the reliability of pedigree recording in village flocks by comparing genetic parameters estimated from data sets collected in the cooperative village and in a nucleus flock maintained under controlled breeding. Effectiveness of selection in the cooperative village was evaluated based on trends in breeding values over generations. Heritability estimates for 6-month weight recorded in the village and the nucleus flock were very similar. There was an increasing trend over generations in average estimated breeding values for 6-month weight in the village flocks. These results have a number of implications: the pedigree recorded in the village flocks was reliable; genetic parameters, which have so far been estimated based on nucleus data sets, can be estimated based on village recording; and appreciable genetic improvement could be achieved in village sheep selection programs under low-input smallholder farming systems.

Advocating a need for suitable breeding approaches to boost integrated pest management: a European perspective.

PubMed

Lamichhane, Jay Ram; Arseniuk, Edward; Boonekamp, Piet; Czembor, Jerzy; Decroocq, Veronique; Enjalbert, Jérome; Finckh, Maria R; Korbin, Małgorzata; Koppel, Mati; Kudsk, Per; Mesterhazy, Akos; Sosnowska, Danuta; Zimnoch-Guzowska, Ewa; Messéan, Antoine

2018-06-01

Currently, European farmers do not have access to sufficient numbers and diversity of crop species/varieties. This prevents them from designing cropping systems more resilient to abiotic and biotic stresses. Crop diversification is a key lever to reduce pest (pathogens, animal pests and weeds) pressures at all spatial levels from fields to landscapes. In this context, plant breeding should consist of: (1) increased efforts in the development of new or minor crop varieties to foster diversity in cropping systems, and (2) focus on more resilient varieties showing local adaptation. This new breeding paradigm, called here 'breeding for integrated pest management (IPM)', may boost IPM through the development of cultivars with tolerance or resistance to key pests, with the goal of reducing reliance on conventional pesticides. At the same time, this paradigm has legal and practical implications for future breeding programs, including those targeting sustainable agricultural systems. By putting these issues into the context, this article presents the key outcomes of a questionnaire survey and experts' views expressed during an EU workshop entitled 'Breeding for IPM in sustainable agricultural systems'. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

The importance of reproductive barriers and the effect of allopolyploidization on crop breeding

PubMed Central

Tonosaki, Kaoru; Osabe, Kenji; Kawanabe, Takahiro; Fujimoto, Ryo

2016-01-01

Inter-specific hybrids are a useful source for increasing genetic diversity. Some reproductive barriers before and/or after fertilization prevent production of hybrid plants by inter-specific crossing. Therefore, techniques to overcome the reproductive barrier have been developed, and have contributed to hybridization breeding. In recent studies, identification of molecules involved in plant reproduction has been studied to understand the mechanisms of reproductive barriers. Revealing the molecular mechanisms of reproductive barriers may allow us to overcome reproductive barriers in inter-specific crossing, and to efficiently produce inter-specific hybrids in cross-combinations that cannot be produced through artificial techniques. Inter-specific hybrid plants can potentially serve as an elite material for plant breeding, produced through the merging of genomes of parental species by allopolyploidization. Allopolyploidization provides some benefits, such as heterosis, increased genetic diversity and phenotypic variability, which are caused by dynamic changes of the genome and epigenome. Understanding of allopolyploidization mechanisms is important for practical utilization of inter-specific hybrids as a breeding material. This review discusses the importance of reproductive barriers and the effect of allopolyploidization in crop breeding programs. PMID:27436943

Identification of unknown apple cultivars demonstrates the impact of local breeding program on cultivar diversity

USDA-ARS?s Scientific Manuscript database

Apple trees, either abandoned or cared for, are common on the North American landscape. These trees can live for decades, and therefore represent a record of large- and small-scale agricultural practices through time. Here, we assessed the genetic diversity and identity of 330 unknown apple trees in...

Breeding Resistant Sugarcane for Managing the Stem Borer Diatraea saccharalis: Progress and Prospects for Louisiana

USDA-ARS?s Scientific Manuscript database

The stem borer, Diatraea saccharalis (F.), is an important insect pest of sugarcane in Louisiana. Growing resistant varieties is a component of the Integrated Pest Management Program as practiced in Louisiana for managing this insect; however, the release of stem borer resistant varieties is intermi...

Training Program for Teachers of Technical Mathematics in Two-Year Curricula.

ERIC Educational Resources Information Center

Queensborough Community Coll., Bayside, NY.

This handbook is designed to assist teachers of technical mathematics in developing practically-oriented curricula for their students. The underlying assumption is that, while technology students are not a breed apart, their needs and orientation are to the concrete, rather than the abstract. It describes the nature, scope, and content of…

Training Engineers for the Ambient Intelligence Challenge

ERIC Educational Resources Information Center

Corno, Fulvio; De Russis, Luigi

2017-01-01

The increasing complexity of the new breed of distributed intelligent systems, such as the Internet of Things, which require a diversity of languages and protocols, can only be tamed with design and programming best practices. Interest is also growing for including the human factor, as advocated by the "ambient intelligence" (AmI)…

Applications of population genetics to animal breeding, from wright, fisher and lush to genomic prediction.

PubMed

Hill, William G

2014-01-01

Although animal breeding was practiced long before the science of genetics and the relevant disciplines of population and quantitative genetics were known, breeding programs have mainly relied on simply selecting and mating the best individuals on their own or relatives' performance. This is based on sound quantitative genetic principles, developed and expounded by Lush, who attributed much of his understanding to Wright, and formalized in Fisher's infinitesimal model. Analysis at the level of individual loci and gene frequency distributions has had relatively little impact. Now with access to genomic data, a revolution in which molecular information is being used to enhance response with "genomic selection" is occurring. The predictions of breeding value still utilize multiple loci throughout the genome and, indeed, are largely compatible with additive and specifically infinitesimal model assumptions. I discuss some of the history and genetic issues as applied to the science of livestock improvement, which has had and continues to have major spin-offs into ideas and applications in other areas.

Schemes for Oestrus Synchronization Protocols and Controlled Breeding Programs in Cattle

NASA Astrophysics Data System (ADS)

Sabo, Y. G.; Sandabe, U. K.; Maina, V. A.; Balla, H. G.

Today prostaglandin and progesterone has been found widely used in several schemes of oestrus synchronization and controlled breeding program. Several controlled breeding program, have been developed for synchronizing groups of all open or lactating cows within a breeding group with or without ovarian palpation. Such programs are reviewed in this article which involves extending the luteal phase by treatment with exogenous progesterone such as: progesterone treatment regimes using syncro-mate-B, progesterone releasing intravaginal device, melengesterol acetate-select and melegestrol acetate plus prostaglandin. Also reviewed in the program is the termination of the luteal phase by treatment with prostaglandin or its analogues. These includes, controlled breeding without ovarian palpation such as, the 7-days program; 11-days program, target breeding, ovsynch program, Heat synch, Cosynch and pre synch-ovsynch program. In our opinion full potential of progesterone and prostaglandin for the detection of oestrus and timed artificial insemination should be utilized. This reduces the much labour input employed in previous years. The practitioner of the livestock herd health must-develop strategies for the delivery of this technology to livestock farmers, its use and limitations.

Breeding strategies for north central tree improvement programs

Treesearch

Ronald P. Overton; Hyun Kang

1985-01-01

The rationales and concepts of long-term tree breeding are discussed and compared with those for short-term breeding. A model breeding program is reviewed which maximizes short-term genetic gain for currently important traits and provides genetic resources that can be used effectively in future short-term breeding. The resources of the north-central region are examined...

Review: Sustainability of crossbreeding in developing countries; definitely not like crossing a meadow….

PubMed

Leroy, G; Baumung, R; Boettcher, P; Scherf, B; Hoffmann, I

2016-02-01

Crossbreeding, considering either terminal or rotational crossing, synthetic breed creation or breed replacement, is often promoted as an efficient strategy to increase farmers' income through the improvement of productivity of local livestock in developing countries. Sustainability of crossbreeding is however frequently challenged by constraints such as poor adaptation to the local environment or lack of logistic support. In this review, we investigate factors that may influence the long-term success or the failure of crossbreeding programs, based on the scientific literature and country reports submitted for The Second Report on the State of the World's Animal Genetic Resources for Food and Agriculture. Crossbreeding activities vary widely across species and countries. Its sustainability is dependent on different prerequisites such as continual access to adequate breeding stock (especially after the end of externally funded crossbreeding projects), the opportunity of improved livestock to express their genetic potential (e.g. through providing proper inputs) and integration within a reliable market chain. As formal crossbreeding programs are often associated with adoption of other technologies, they can be a catalyst for innovation and development for smallholders. Given the increasing global demand for animal products, as well as the potential environmental consequences of climate change, there is a need for practical research to improve the implementation of long-term crossbreeding programs in developing countries.

Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples

PubMed Central

Cornille, Amandine; Feurtey, Alice; Gélin, Uriel; Ropars, Jeanne; Misvanderbrugge, Kristine; Gladieux, Pierre; Giraud, Tatiana

2015-01-01

Gene flow is an essential component of population adaptation and species evolution. Understanding of the natural and anthropogenic factors affecting gene flow is also critical for the development of appropriate management, breeding, and conservation programs. Here, we explored the natural and anthropogenic factors impacting crop-to-wild and within wild gene flow in apples in Europe using an unprecedented dense sampling of 1889 wild apple (Malus sylvestris) from European forests and 339 apple cultivars (Malus domestica). We made use of genetic, environmental, and ecological data (microsatellite markers, apple production across landscapes and records of apple flower visitors, respectively). We provide the first evidence that both human activities, through apple production, and human disturbance, through modifications of apple flower visitor diversity, have had a significant impact on crop-to-wild interspecific introgression rates. Our analysis also revealed the impact of previous natural climate change on historical gene flow in the nonintrogressed wild apple M. sylvestris, by identifying five distinct genetic groups in Europe and a north–south gradient of genetic diversity. These findings identify human activities and climate as key drivers of gene flow in a wild temperate fruit tree and provide a practical basis for conservation, agroforestry, and breeding programs for apples in Europe. PMID:25926882

Advantages and limitations of in vitro and in vivo methods of iron and zinc bioavailability evaluation in the assessment of biofortification program effectiveness

USDA-ARS?s Scientific Manuscript database

Biofortification aims to improve the micronutrient concentration of staple food crops through the best practices of breeding and modern biotechnology. However, increased zinc and iron concentrations in food crops may not always translate into proportional increases in absorbed zinc (Zn) and iron (Fe...

Increased genetic gains in sheep, beef and dairy breeding programs from using female reproductive technologies combined with optimal contribution selection and genomic breeding values.

PubMed

Granleese, Tom; Clark, Samuel A; Swan, Andrew A; van der Werf, Julius H J

2015-09-14

Female reproductive technologies such as multiple ovulation and embryo transfer (MOET) and juvenile in vitro embryo production and embryo transfer (JIVET) can boost rates of genetic gain but they can also increase rates of inbreeding. Inbreeding can be managed using the principles of optimal contribution selection (OCS), which maximizes genetic gain while placing a penalty on the rate of inbreeding. We evaluated the potential benefits and synergies that exist between genomic selection (GS) and reproductive technologies under OCS for sheep and cattle breeding programs. Various breeding program scenarios were simulated stochastically including: (1) a sheep breeding program for the selection of a single trait that could be measured either early or late in life; (2) a beef breeding program with an early or late trait; and (3) a dairy breeding program with a sex limited trait. OCS was applied using a range of penalties (severe to no penalty) on co-ancestry of selection candidates, with the possibility of using multiple ovulation and embryo transfer (MOET) and/or juvenile in vitro embryo production and embryo transfer (JIVET) for females. Each breeding program was simulated with and without genomic selection. All breeding programs could be penalized to result in an inbreeding rate of 1 % increase per generation. The addition of MOET to artificial insemination or natural breeding (AI/N), without the use of GS yielded an extra 25 to 60 % genetic gain. The further addition of JIVET did not yield an extra genetic gain. When GS was used, MOET and MOET + JIVET programs increased rates of genetic gain by 38 to 76 % and 51 to 81 % compared to AI/N, respectively. Large increases in genetic gain were found across species when female reproductive technologies combined with genomic selection were applied and inbreeding was managed, especially for breeding programs that focus on the selection of traits measured late in life or that are sex-limited. Optimal contribution selection was an effective tool to optimally allocate different combinations of reproductive technologies. Applying a range of penalties to co-ancestry of selection candidates allows a comprehensive exploration of the inbreeding vs. genetic gain space.

Breed and trait preferences of Sheko cattle keepers in southwestern Ethiopia.

PubMed

Desta, Takele Taye; Ayalew, Workneh; Hegde, B P

2011-04-01

Like their smallholder subsistence counterparts in developing countries, breed and trait preferences of Sheko cattle keepers have broad perspectives. Our study has documented breed and trait preferences of Sheko cattle keepers in southwestern Ethiopia--the natural breeding tract of Sheko cattle. Our results showed that due to their multifunctionality, cattle are the most preferred livestock species. Overall, farmers showed slightly more preference to local Zebus over Sheko breed. This is due to voracious feeding behavior of Sheko cattle, which make them less preferable in the face of worsening feed shortage, and due to aggressive temperament of Sheko cattle. This is despite Sheko's outperforming potential over local Zebus in their milk production, draft power, and hardiness. At trait level, overall milk production was consistently reported as the most preferred trait followed by fertility and traction. This trait preference rank has matched with the reported frequency count ranks for Sheko cattle use. However, breed preference rank has not matched with reported trait preference ranks because Sheko excels local Zebus in all the three most preferred traits, but it was ranked second. Therefore, to minimize these conflicting interests, breed management plans for Sheko cattle should target on strategies that help to solve feed shortage problem and to improve feeding practices, and on selection of less aggressive Sheko cattle. Therefore, these strategies should be considered in line with Sheko cattle conservation and genetic improvement programs.

Breeding and Selection of New Switchgrass Varieties for Increased Biomass Production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taliaferro, C.M.

2003-05-27

Switchgrass breeding and genetics research was conducted from 1992-2002 at the Oklahoma State University as part of the national DOE-Bioenergy Feedstock Development Program (BFDP) effort to develop the species as a bioenergy feedstock crop. The fundamental objective of the program was to implement and conduct a breeding program to increase biomass yield capability in switchgrass and develop cultivars for the central and southern United States. Supporting research objectives included: (1) switchgrass germplasm collection, characterization, and enhancement; (2) elucidation of cytogenetic and breeding behavior; and (3) identification of best breeding procedures.

A statistical design for testing apomictic diversification through linkage analysis.

PubMed

Zeng, Yanru; Hou, Wei; Song, Shuang; Feng, Sisi; Shen, Lin; Xia, Guohua; Wu, Rongling

2014-03-01

The capacity of apomixis to generate maternal clones through seed reproduction has made it a useful characteristic for the fixation of heterosis in plant breeding. It has been observed that apomixis displays pronounced intra- and interspecific diversification, but the genetic mechanisms underlying this diversification remains elusive, obstructing the exploitation of this phenomenon in practical breeding programs. By capitalizing on molecular information in mapping populations, we describe and assess a statistical design that deploys linkage analysis to estimate and test the pattern and extent of apomictic differences at various levels from genotypes to species. The design is based on two reciprocal crosses between two individuals each chosen from a hermaphrodite or monoecious species. A multinomial distribution likelihood is constructed by combining marker information from two crosses. The EM algorithm is implemented to estimate the rate of apomixis and test its difference between two plant populations or species as the parents. The design is validated by computer simulation. A real data analysis of two reciprocal crosses between hickory (Carya cathayensis) and pecan (C. illinoensis) demonstrates the utilization and usefulness of the design in practice. The design provides a tool to address fundamental and applied questions related to the evolution and breeding of apomixis.

Root Traits and Phenotyping Strategies for Plant Improvement

PubMed Central

Paez-Garcia, Ana; Motes, Christy M.; Scheible, Wolf-Rüdiger; Chen, Rujin; Blancaflor, Elison B.; Monteros, Maria J.

2015-01-01

Roots are crucial for nutrient and water acquisition and can be targeted to enhance plant productivity under a broad range of growing conditions. A current challenge for plant breeding is the limited ability to phenotype and select for desirable root characteristics due to their underground location. Plant breeding efforts aimed at modifying root traits can result in novel, more stress-tolerant crops and increased yield by enhancing the capacity of the plant for soil exploration and, thus, water and nutrient acquisition. Available approaches for root phenotyping in laboratory, greenhouse and field encompass simple agar plates to labor-intensive root digging (i.e., shovelomics) and soil boring methods, the construction of underground root observation stations and sophisticated computer-assisted root imaging. Here, we summarize root architectural traits relevant to crop productivity, survey root phenotyping strategies and describe their advantages, limitations and practical value for crop and forage breeding programs. PMID:27135332

Root Traits and Phenotyping Strategies for Plant Improvement.

PubMed

Paez-Garcia, Ana; Motes, Christy M; Scheible, Wolf-Rüdiger; Chen, Rujin; Blancaflor, Elison B; Monteros, Maria J

2015-06-15

Roots are crucial for nutrient and water acquisition and can be targeted to enhance plant productivity under a broad range of growing conditions. A current challenge for plant breeding is the limited ability to phenotype and select for desirable root characteristics due to their underground location. Plant breeding efforts aimed at modifying root traits can result in novel, more stress-tolerant crops and increased yield by enhancing the capacity of the plant for soil exploration and, thus, water and nutrient acquisition. Available approaches for root phenotyping in laboratory, greenhouse and field encompass simple agar plates to labor-intensive root digging (i.e., shovelomics) and soil boring methods, the construction of underground root observation stations and sophisticated computer-assisted root imaging. Here, we summarize root architectural traits relevant to crop productivity, survey root phenotyping strategies and describe their advantages, limitations and practical value for crop and forage breeding programs.

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 1 2014-10-01 2014-10-01 false Approval of cooperative breeding programs. 15.26 Section 15.26 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE... program requested for the exotic bird species, including: (i) A breeding protocol, including a genetic...

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 1 2013-10-01 2013-10-01 false Approval of cooperative breeding programs. 15.26 Section 15.26 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE... program requested for the exotic bird species, including: (i) A breeding protocol, including a genetic...

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 1 2012-10-01 2012-10-01 false Approval of cooperative breeding programs. 15.26 Section 15.26 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE... program requested for the exotic bird species, including: (i) A breeding protocol, including a genetic...

Persian walnut breeding in California

Treesearch

Charles A. Leslie; Gale H. McGranahan

2004-01-01

For over 50 years the University of California Davis Walnut Breeding Program has worked to address the needs of California walnut growers by identifying genetic approaches to problems and developing improved cultivars. The breeding program is a cooperative endeavor that draws on the efforts and resources of university researchers and facilities, USDA germplasm programs...

Global impact of accelerated plant breeding: Evidence from a meta-analysis on rice breeding.

PubMed

Lenaerts, Bert; de Mey, Yann; Demont, Matty

2018-01-01

Rice breeders in Asia and elsewhere in the world have long overlooked trying to shorten the time it takes to develop new varieties. Plant breeders have proposed a technique called Rapid Generation Advance (RGA) as a way to accelerate the results of public rice breeding programs. However, little is known about RGA's potential impact. Here, we present the first results of a global impact study of RGA. More specifically, we calculated the multiplicator effects of RGA on the research benefits generated by conventional rice breeding programs and applied them to a meta-analysis of selected impact studies in the literature. These insights are a first crucial step in developing a targeted approach for disseminating RGA technology among rice breeders to accelerate the impact of their public rice breeding programs around the world. We show that the additional benefits due to time savings are considerable and offer some insights into the economics of breeding. Our results confirm that the adoption of accelerated breeding would lead to substantial advantages to rice breeding programs and the earlier variety release leads to significant economic benefits to society. This can be important to policy makers when reshaping their public breeding methods and optimising their return on research investments in breeding.

Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs

PubMed Central

Jonas, Elisabeth; de Koning, Dirk-Jan

2015-01-01

Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios. PMID:25750652

Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs.

PubMed

Jonas, Elisabeth; de Koning, Dirk-Jan

2015-01-01

Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios.

Hybrid maize breeding with doubled haploids: II. Optimum type and number of testers in two-stage selection for general combining ability.

PubMed

Longin, C Friedrich H; Utz, H Friedrich; Melchinger, Albrecht E; Reif, Jochen C

2007-02-01

Optimum allocation of test resources is of crucial importance for the efficiency of breeding programs. Our objectives were to (1) determine the optimum allocation of the number of lines, test locations, as well as number and type of testers in hybrid maize breeding using doubled haploids with two breeding strategies for improvement of general combining ability (GCA), (2) compare the maximum selection gain (DeltaG) achievable under both strategies, and (3) give recommendations for the optimum implementation of doubled haploids in commercial hybrid maize breeding. We calculated DeltaG by numerical integration for two two-stage selection strategies with evaluation of (1) testcross performance in both stages (BS1) or (2) line per se performance in the first stage followed by testcross performance in the second stage (BS2). Different assumptions were made regarding the budget, variance components (VCs), and the correlation between line per se performance and GCA. Selection gain for GCA increased with a broader genetic base of the tester. Hence, testers combining a large number of divergent lines are advantageous. However, in applied breeding programs, the use of single- or double-cross testers in the first and inbred testers in the second selection stage may be a good compromise between theoretical and practical requirements. With a correlation between line per se performance and GCA of 0.50, DeltaG for BS1 is about 5% higher than for BS2, if an economic weight of line per se performance is neglected. With increasing economic weight of line per se performance, relative efficiency of BS2 increased rapidly resulting in a superiority of BS2 over BS1 already for an economic weight for line per se performance larger than 0.1. Considering the importance of an economic seed production, an economic weight larger than 0.1 seems realistic indicating the necessity of separate breeding strategies for seed and pollen parent heterotic groups.

Perceptions of households on purpose of keeping, trait preference, and production constraints for selected goat types in Ethiopia.

PubMed

Tadesse, Dereje; Urge, Mengistu; Animut, Getachew; Mekasha, Yoseph

2014-02-01

A study was carried out to understand the needs and perception of goat keepers in selected areas of Ethiopia in order to identify the breeding objectives, traits of preference, and production constraints that may be required in designing improvement programs. The study was conducted in three districts (Bati, Meta, and Kebri-Beyah) representing the lowland crop-livestock (LLCL), highland cereal-livestock (HLCL), and pastoral/agropastoral (P/AP) systems, respectively. The study targeted the three goat types (Bati, Hararghe Highland, and Short-eared Somali) found in Ethiopia. Households in all systems considered meat production, milk production, and income generation as major purpose of keeping goats. However, those in the low rainfall and arid environments of P/AP systems gave high ranking to adaptability to harsh environments and also to building social and religious values. In LLCL and HLCL systems, goat skin and manure were more valued than in P/AP systems. Principally, in P/AP systems, the awareness of households to skin utilization and marketing was very low. Despite diverse multiple breeding objectives identified, household breeding practices were affected by constraints related to disease prevalence, feed shortage and water scarcity, and lack of awareness on skin management, utilization, and marketing. Thus, designing and implementing of sustainable goat improvement programs is an overriding priority and should take into account the breeding objectives and knowledge of goat keepers in all production systems. Along with the breed improvement, a strategy should also be devised to enhance the utilization and marketing of goat skin at all levels of production.

Simulated selection responses for breeding programs including resistance and resilience to parasites in Creole goats.

PubMed

Gunia, M; Phocas, F; Gourdine, J-L; Bijma, P; Mandonnet, N

2013-02-01

The Creole goat is a local breed used for meat production in Guadeloupe (French West Indies). As in other tropical countries, improvement of parasite resistance is needed. In this study, we compared predicted selection responses for alternative breeding programs with or without parasite resistance and resilience traits. The overall breeding goal included traits for production, reproduction, and parasite resilience and resistance to ensure a balanced selection outcome. The production traits were BW and dressing percentage (DP). The reproduction trait was fertility (FER), which was the number of doe kiddings per mating. The resistance trait was worm fecal egg count (FEC), which is a measurement of the number of gastro-intestinal parasite eggs found in the feces. The resilience trait was the packed cell volume (PCV), which is a measurement of the volume of red blood cells in the blood. Dressing percentage, BW, and FEC were measured at 11 mo of age, which is the mating or selling age. Fertility and PCV were measured on females at each kidding period. The breeding program accounting for the overall breeding goal and a selection index including all traits gave annual selection responses of 800 g for BW, 3.75% for FER, 0.08% for DP, -0.005 ln(eggs/g) for FEC, and 0.28% for PCV. The expected selection responses for BW and DP in this breeding program were reduced by 2% and 6%, respectively, compared with a breeding program not accounting for FEC and PCV. The overall breeding program, proposed for the Creole breed, offers the best breeding strategy in terms of expected selection responses, making it possible to improve all traits together. It offers a good balance between production and adaptation traits and may present some interest for the selection of other goat breeds in the tropics.

[A review of the genomic and gene cloning studies in trees].

PubMed

Yin, Tong-Ming

2010-07-01

Supported by the Department of Energy (DOE) of U.S., the first tree genome, black cottonwood (Populus trichocarpa), has been completely sequenced and publicly release. This is the milestone that indicates the beginning of post-genome era for forest trees. Identification and cloning genes underlying important traits are one of the main tasks for the post-genome-era tree genomic studies. Recently, great achievements have been made in cloning genes coordinating important domestication traits in some crops, such as rice, tomato, maize and so on. Molecular breeding has been applied in the practical breeding programs for many crops. By contrast, molecular studies in trees are lagging behind. Trees possess some characteristics that make them as difficult organisms for studying on locating and cloning of genes. With the advances in techniques, given also the fast growth of tree genomic resources, great achievements are desirable in cloning unknown genes from trees, which will facilitate tree improvement programs by means of molecular breeding. In this paper, the author reviewed the progress in tree genomic and gene cloning studies, and prospected the future achievements in order to provide a useful reference for researchers working in this area.

Archive eggs: a research and management tool for avian conservation breeding

USGS Publications Warehouse

Smith, Des H.V.; Moehrenschlager, Axel; Christensen, Nancy; Knapik, Dwight; Gibson, Keith; Converse, Sarah J.

2012-01-01

Worldwide, approximately 168 bird species are captive-bred for reintroduction into the wild. Programs tend to be initiated for species with a high level of endangerment. Depressed hatching success can be a problem for such programs and has been linked to artificial incubation. The need for artificial incubation is driven by the practice of multiclutching to increase egg production or by uncertainty over the incubation abilities of captive birds. There has been little attempt to determine how artificial incubation differs from bird-contact incubation. We describe a novel archive (data-logger) egg and use it to compare temperature, humidity, and egg-turning in 5 whooping crane (Grus americana) nests, 4 sandhill crane (G. canadensis) nests, and 3 models of artificial incubator; each of which are used to incubate eggs in whooping crane captive-breeding programs. Mean incubation temperature was 31.7° C for whooping cranes and 32.83° C for sandhill cranes. This is well below that of the artificial incubators (which were set based on a protocol of 37.6° C). Humidity in crane nests varied considerably, but median humidity in all 3 artificial incubators was substantially different from that in the crane nests. Two artificial incubators failed to turn the eggs in a way that mimicked crane egg-turning. Archive eggs are an effective tool for guiding the management of avian conservation breeding programs, and can be custom-made for other species. They also have potential to be applied to research on wild populations.

Prediction of genetic values of quantitative traits with epistatic effects in plant breeding populations.

PubMed

Wang, D; Salah El-Basyoni, I; Stephen Baenziger, P; Crossa, J; Eskridge, K M; Dweikat, I

2012-11-01

Though epistasis has long been postulated to have a critical role in genetic regulation of important pathways as well as provide a major source of variation in the process of speciation, the importance of epistasis for genomic selection in the context of plant breeding is still being debated. In this paper, we report the results on the prediction of genetic values with epistatic effects for 280 accessions in the Nebraska Wheat Breeding Program using adaptive mixed least absolute shrinkage and selection operator (LASSO). The development of adaptive mixed LASSO, originally designed for association mapping, for the context of genomic selection is reported. The results show that adaptive mixed LASSO can be successfully applied to the prediction of genetic values while incorporating both marker main effects and epistatic effects. Especially, the prediction accuracy is substantially improved by the inclusion of two-locus epistatic effects (more than onefold in some cases as measured by cross-validation correlation coefficient), which is observed for multiple traits and planting locations. This points to significant potential in using non-additive genetic effects for genomic selection in crop breeding practices.

Applications of Population Genetics to Animal Breeding, from Wright, Fisher and Lush to Genomic Prediction

PubMed Central

Hill, William G.

2014-01-01

Although animal breeding was practiced long before the science of genetics and the relevant disciplines of population and quantitative genetics were known, breeding programs have mainly relied on simply selecting and mating the best individuals on their own or relatives’ performance. This is based on sound quantitative genetic principles, developed and expounded by Lush, who attributed much of his understanding to Wright, and formalized in Fisher’s infinitesimal model. Analysis at the level of individual loci and gene frequency distributions has had relatively little impact. Now with access to genomic data, a revolution in which molecular information is being used to enhance response with “genomic selection” is occurring. The predictions of breeding value still utilize multiple loci throughout the genome and, indeed, are largely compatible with additive and specifically infinitesimal model assumptions. I discuss some of the history and genetic issues as applied to the science of livestock improvement, which has had and continues to have major spin-offs into ideas and applications in other areas. PMID:24395822

The chapter breeding program of the American Chestnut Foundation

Treesearch

Sara Fitzsimmons; Kendra Gurney; William White; Katy McCune

2012-01-01

A unique feature of the American Chestnut Foundation breeding program is the use of volunteers to conduct most of the regional breeding that will help increase genetic diversity and preserve local adaptation in the products of our program. This effort is coordinated by the four authors of this abstract, who are employees of the Foundation. The Foundation has...

Tree improvement in the Pacific Northwest.

Treesearch

R. Johnson

2000-01-01

Advanced-generation tree breeding programs are underway for Douglas-fir and coastal western hemlock. These programs will continue to improve growth rates and other traits. Regardless of whether seeds is from a seed orchard or natural collection, it must be used in its appropriated breeding zone or seed zone. These zones vary by species. Breeding programs are underway...

Optimum allocation of conservation funds and choice of conservation programs for a set of African cattle breeds

PubMed Central

Reist-Marti, Sabine B; Abdulai, Awudu; Simianer, Henner

2006-01-01

Although funds for livestock conservation are limited there is little known about the optimal allocation of conservation funds. A new algorithm was used to allocate Mio US$ 1, 2, 3, 5 or unlimited funds, discounted over 50 years, on 23 African cattle breeds conserved with four different possible conservation programs. Additionally, Mio US$ 1 was preferably allocated to breeds with special traits. The conceptional in situ conservation programs strongly involve breeders and give them part of the responsibility for the conservation of the breed. Therefore, the pure in situ conservation was more efficient than cryoconservation or combined in situ and cryoconservation. The average annual discounted conservation cost for a breed can be as low as US$ 1000 to US$ 4400 depending on the design of the conservation program and the economic situation of the country of conservation. The choice of the breeds and the optimal conservation program and the amount of money allocated to each breed depend on many factors such as the amount of funds available, the conservation potential of each breed, the effects of the conservation program as well as its cost. With Mio US$ 1, 64% of the present diversity could be maintained over 50 years, which is 13% more than would be maintained if no conservation measures were implemented. Special traits could be conserved with a rather small amount of the total funds. Diversity can not be conserved completely, not even with unlimited funds. A maximum of 92% of the present diversity could be conserved with Mio US$ 10, leaving 8% of the diversity to unpredictable happenings. The suggested algorithm proved to be useful for optimal allocation of conservation funds. It allocated the funds optimally among breeds by identifying the most suited conservation program for each breed, also accounting for differences in currency exchange rates between the different countries. PMID:16451794

Potential benefits of genomic selection on genetic gain of small ruminant breeding programs.

PubMed

Shumbusho, F; Raoul, J; Astruc, J M; Palhiere, I; Elsen, J M

2013-08-01

In conventional small ruminant breeding programs, only pedigree and phenotype records are used to make selection decisions but prospects of including genomic information are now under consideration. The objective of this study was to assess the potential benefits of genomic selection on the genetic gain in French sheep and goat breeding designs of today. Traditional and genomic scenarios were modeled with deterministic methods for 3 breeding programs. The models included decisional variables related to male selection candidates, progeny testing capacity, and economic weights that were optimized to maximize annual genetic gain (AGG) of i) a meat sheep breeding program that improved a meat trait of heritability (h(2)) = 0.30 and a maternal trait of h(2) = 0.09 and ii) dairy sheep and goat breeding programs that improved a milk trait of h(2) = 0.30. Values of ±0.20 of genetic correlation between meat and maternal traits were considered to study their effects on AGG. The Bulmer effect was accounted for and the results presented here are the averages of AGG after 10 generations of selection. Results showed that current traditional breeding programs provide an AGG of 0.095 genetic standard deviation (σa) for meat and 0.061 σa for maternal trait in meat breed and 0.147 σa and 0.120 σa in sheep and goat dairy breeds, respectively. By optimizing decisional variables, the AGG with traditional selection methods increased to 0.139 σa for meat and 0.096 σa for maternal traits in meat breeding programs and to 0.174 σa and 0.183 σa in dairy sheep and goat breeding programs, respectively. With a medium-sized reference population (nref) of 2,000 individuals, the best genomic scenarios gave an AGG that was 17.9% greater than with traditional selection methods with optimized values of decisional variables for combined meat and maternal traits in meat sheep, 51.7% in dairy sheep, and 26.2% in dairy goats. The superiority of genomic schemes increased with the size of the reference population and genomic selection gave the best results when nref > 1,000 individuals for dairy breeds and nref > 2,000 individuals for meat breed. Genetic correlation between meat and maternal traits had a large impact on the genetic gain of both traits. Changes in AGG due to correlation were greatest for low heritable maternal traits. As a general rule, AGG was increased both by optimizing selection designs and including genomic information.

Long-term selection strategies for complex traits using high-density genetic markers.

PubMed

Kemper, K E; Bowman, P J; Pryce, J E; Hayes, B J; Goddard, M E

2012-08-01

Selection of animals for breeding ranked on estimated breeding value maximizes genetic gain in the next generation but does not necessarily maximize long-term response. An alternative method, as practiced by plant breeders, is to build a desired genotype by selection on specific loci. Maximal long-term response in animal breeding requires selection on estimated breeding values with constraints on coancestry. In this paper, we compared long-term genetic response using either a genotype building or a genomic estimated breeding value (GEBV) strategy for the Australian Selection Index (ASI), a measure of profit. First, we used real marker effects from the Australian Dairy Herd Improvement Scheme to estimate breeding values for chromosome segments (approximately 25 cM long) for 2,650 Holstein bulls. Second, we selected 16 animals to be founders for a simulated breeding program where, between them, founders contain the best possible combination of 2 segments from 2 animals at each position in the genome. Third, we mated founder animals and their descendants over 30 generations with 2 breeding objectives: (1) to create a population with the "ideal genotype," where the best 2 segments from the founders segregate at each position, or (2) obtain the highest possible response in ASI with coancestry lower than that achieved under breeding objective 1. Results show that genotype building achieved the ideal genotype for breeding objective 1 and obtained a large gain in ASI over the current population (+A$864.99). However, selection on overall GEBV had greater short-term response and almost as much long-term gain (+A$820.42). When coancestry was lowered under breeding objective 2, selection on overall GEBV achieved a higher response in ASI than the genotype building strategy. Selection on overall GEBV seems more flexible in its selection decisions and was therefore better able to precisely control coancestry while maximizing ASI. We conclude that selection on overall GEBV while minimizing average coancestry is the more practical strategy for dairy cattle where selection is for highly polygenic traits, the reproductive rate is relatively low, and there is low tolerance of coancestry. The outcome may be different for traits controlled by few loci of relatively large effects or for different species. In contrast to other simulations, our results indicate that response to selection on overall GEBV may continue for several generations. This is because long-term genetic change in complex traits requires favorable changes to allele frequencies for many loci located throughout the genome. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Identification of key ancestors of modern germplasm in a breeding program of maize.

PubMed

Technow, F; Schrag, T A; Schipprack, W; Melchinger, A E

2014-12-01

Probabilities of gene origin computed from the genomic kinships matrix can accurately identify key ancestors of modern germplasms Identifying the key ancestors of modern plant breeding populations can provide valuable insights into the history of a breeding program and provide reference genomes for next generation whole genome sequencing. In an animal breeding context, a method was developed that employs probabilities of gene origin, computed from the pedigree-based additive kinship matrix, for identifying key ancestors. Because reliable and complete pedigree information is often not available in plant breeding, we replaced the additive kinship matrix with the genomic kinship matrix. As a proof-of-concept, we applied this approach to simulated data sets with known ancestries. The relative contribution of the ancestral lines to later generations could be determined with high accuracy, with and without selection. Our method was subsequently used for identifying the key ancestors of the modern Dent germplasm of the public maize breeding program of the University of Hohenheim. We found that the modern germplasm can be traced back to six or seven key ancestors, with one or two of them having a disproportionately large contribution. These results largely corroborated conjectures based on early records of the breeding program. We conclude that probabilities of gene origin computed from the genomic kinships matrix can be used for identifying key ancestors in breeding programs and estimating the proportion of genes contributed by them.

Current status for gastrointestinal nematode diagnosis in small ruminants: where are we and where are we going?

PubMed

Preston, Sarah Jane Margaret; Sandeman, Mark; Gonzalez, Jorge; Piedrafita, David

2014-01-01

Gastrointestinal nematode (GIN) parasites pose a significant economic burden particularly in small ruminant production systems. Anthelmintic resistance is a serious concern to the effective control of GIN parasites and has fuelled the focus to design and promote sustainable control of practices of parasite control. Many facets of sustainable GIN parasite control programs rely on the ability to diagnose infection both qualitatively and quantitatively. Diagnostics are required to determine anthelmintic efficacies, for targeted treatment programs and selection of animals for parasite resistant breeding. This review describes much of the research investigated to date to improve the current diagnostic for the above practices which is based on counting the number of parasite eggs in faeces.

Selective breeding of food sized rainbow trout against Flavobacteriosis

USDA-ARS?s Scientific Manuscript database

Selective breeding of rainbow trout is an important component of an integrated fish health management program. The current goals of our selective breeding program are to improve disease resistance, growth and survival in a reuse water environment. To improve these traits, data are recorded on thousa...

Selective breeding of food size rainbow trout against Flavobacteriosis

USDA-ARS?s Scientific Manuscript database

Selective breeding of rainbow trout is an important component of an integrated fish health management program. The current goals of our selective breeding program are to improve disease resistance, growth and survival in a reuse water environment. To improve these traits, data are recorded on thousa...

Leaf physiology and morphology of Castanea dentata (Marsh) Borkh., Castanea mollissima Blume, and three backcross breeding generations planted in the southern Appalachians, USA

Treesearch

Benjamin O. Knapp; G. Geoff Wang; Stacy L Clark; Lauren S. Pile; Scott E. Schlarbaum

2014-01-01

Backcross breeding programs have been used to transfer disease resistance and other traits from one forest tree species to another in order to meet restoration objectives. Evaluating the field performance of such material is critical for determining the success of breeding programs. In eastern North America, The American Chestnut Foundation has a backcross breeding...

A simple language to script and simulate breeding schemes: the breeding scheme language

USDA-ARS?s Scientific Manuscript database

It is difficult for plant breeders to determine an optimal breeding strategy given that the problem involves many factors, such as target trait genetic architecture and breeding resource availability. There are many possible breeding schemes for each breeding program. Although simulation study may b...

Ecohealth System Dynamic Model as a Planning Tool for the Reduction of Breeding Sites

NASA Astrophysics Data System (ADS)

Respati, T.; Raksanagara, A.; Djuhaeni, H.; Sofyan, A.; Shandriasti, A.

2017-03-01

Dengue is still one of major health problem in Indonesia. Dengue transmission is influenced by dengue prevention and eradication program, community participation, housing environment and climate. The complexity of the disease coupled with limited resources necessitates different approach for prevention methods that include factors contribute to the transmission. One way to prevent the dengue transmission is by reducing the mosquito’s breeding sites. Four factors suspected to influence breeding sites are dengue prevention and eradication program, community participation, housing environment, and weather condition. In order to have an effective program in reducing the breeding site it is needed to have a model which can predict existence of the breeding sites while the four factors under study are controlled. The objective of this study is to develop an Ecohealth model using system dynamic as a planning tool for the reduction of breeding sites to prevent dengue transmission with regard to dengue prevention and eradication program, community participation, housing environment, and weather condition. The methodology is a mixed method study using sequential exploratory design. The study comprised of 3 stages: first a qualitative study to 14 respondents using in-depth interview and 6 respondents for focus group discussion. The results from the first stage was used to develop entomology and household survey questionnaires for second stage conducted in 2036 households across 12 sub districts in Bandung City. Ecohealth system dynamic model was developed using data from first and second stages. Analyses used are thematic analysis for qualitative data; spatial, generalized estimating equation (GEE) and structural equation modeling for quantitative data; also average mean error (AME) and average variance error (AVE) for dynamic system model validation. System dynamic model showed that the most effective approach to eliminate breeding places was by ensuring the availability of basic sanitation for all houses. Weather factors such as precipitation can be compensated with the eradication of breeding sites activities which is conducted as scheduled and at the same time for the whole areas. Conclusion of this study is that dengue prevention and eradication program, community participation, and housing environment contributed to breeding places elimination influenced the existence of the breeding sites. The availability of basic sanitation and breeding places eradication program done timely and collectively are the most effective approach to eradicate breeding sites. Ecohealth dynamic system model can be used as a tool for the planning of breeding sites eradication program to prevent disease transmissions at city level.

Fasciola hepatica in goats from north-western Spain: Risk factor analysis using a capture ELISA.

PubMed

Pérez-Creo, Ana; Díaz, Pablo; López, Ceferino; Béjar, Juan Pablo; Martínez-Sernández, Victoria; Panadero, Rosario; Díez-Baños, Pablo; Ubeira, Florencio M; Morrondo, Patrocinio

2016-02-01

In order to study the seroprevalence of Fasciola hepatica infection in goats from north-western Spain, a total of 603 serum samples from 47 herds were tested using a capture ELISA (MM3-SERO). The identification of risk factors was assessed by a mixed-effects logistic regression analysis. The results showed that F. hepatica is widespread in this area with 57.4% of the herds and 22.7% of the animals testing positive. Breed and age were identified as determining factors for caprine F. hepatica infection. Seroprevalence in cross-bred animals was significantly higher than in the autochthonous Cabra Galega breed. A significantly higher seroprevalence was observed in older animals. The use of locally adapted breeds and the implementation of suitable management practices could provide a substantial improvement over the current F. hepatica control measures carried out in goat herds and should be considered when designing new F. hepatica control programs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Disease burden in four populations of dog and cat breeds compared to mixed-breed dogs and European shorthair cats.

PubMed

Keijser, S F A; Meijndert, L E; Fieten, H; Carrière, B J; van Steenbeek, F G; Leegwater, P A J; Rothuizen, J; Nielen, M

2017-05-01

Current public and professional opinion is that many dog breeds suffer from health issues related to inherited diseases or extreme phenotypes. The aim of this historical comparative observational study was to evaluate the breed-related disease burden in three purebred dog populations (Chihuahua, French bulldog, Labrador retriever) and one purebred cat breed (Persian cats) in the Netherlands by comparison to a control population of mixed-breed dogs and European Shorthair cats. A qualitative query was performed, consisting of a literature review and collecting the expert opinions of University veterinary specialists, to gather insight into potential diseases of the study population. Next, a referral clinic case control study of the patients referred to specific medical disciplines in the University Clinic was performed. The odds ratio (OR) was calculated to determine the likelihood of a patient referred to a particular medical discipline being a certain breed. Together, the qualitative query and the case control study resulted in a list of potentially relevant diseases limited to five organ systems per breed. These were analysed in data from primary practices. Patient files from ten primary practices over a period of two years were manually extracted and examined. Four-hundred individual patient records per breed as well as 1000 non-breed records were randomly selected from the 10 practices, weighted per practice size. Records were then examined and the presence or absence of certain diseases was identified. To evaluate the disease burden per breed, proportional difference (PD) was estimated, as well as the animal's age at presentation in months. The results of the referral clinic case control study showed an overrepresentation (Odds Ratio>1.5) of the selected breeds in several medical specialties, while median age at presentation was in some cases significantly lower than in the non-breed animals. Results of the practice-based extended cross-sectional study showed that only a few of the selected diseases contribute to the disease burden in these purebred populations, which was different from the expectations derived from the literature or expert opinion. Additional results included age difference at presentation, which may be interpreted as age of onset, and could indicate a higher disease burden for the individual animal. Also, only a small percentage of purebred dogs was registered with the national kennel club. Our final recommendation is that population-based data mining is needed to evaluate country-specific companion animal health and welfare. Copyright © 2017 Elsevier B.V. All rights reserved.

A genealogical survey of Australian registered dog breeds.

PubMed

Shariflou, Mohammad R; James, John W; Nicholas, Frank W; Wade, Claire M

2011-08-01

Breeding practices were analysed for 32 registered dog breeds representing very small registries (120 Central Asian shepherd dogs) through to very large registries (252,521 German shepherd dogs) in Australia. The vast majority (91%) of registered kennels in Australia that were sampled did not regularly employ either close breeding or popular sire usage in their kennels and the weighted mean inbreeding coefficient of Australian pedigree dogs was <5%. Australian breed mean inbreeding coefficients ranged from 0% (Central Asian shepherd dog) to 10.1% (Bichon Frise). Breed effective population sizes ranged from 26 (Ibizan hound) to 1090 (Golden retriever), comparable with other species of domesticated animals. The relatively low levels of inbreeding suggest that pedigree dog disorders are unlikely to arise frequently from the use of popular sires or close breeding in Australian registered dog breeds. It is possible that deleterious allele fixation might be driven by founder effects, genetic drift or adverse selection practices, which were not assessed in this analysis. European popular sire definitions should be revisited for rare breeds. Copyright © 2011. Published by Elsevier Ltd.

Review of recent transgenic studies on abiotic stress tolerance and future molecular breeding in potato.

PubMed

Kikuchi, Akira; Huynh, Huu Duc; Endo, Tsukasa; Watanabe, Kazuo

2015-03-01

Global warming has become a major issue within the last decade. Traditional breeding programs for potato have focused on increasing productivity and quality and disease resistance, thus, modern cultivars have limited tolerance of abiotic stresses. The introgression of abiotic stress tolerance into modern cultivars is essential work for the future. Recently, many studies have investigated abiotic stress using transgenic techniques. This manuscript focuses on the study of abiotic stress, in particular drought, salinity and low temperature, during this century. Dividing studies into these three stress categories for this review was difficult. Thus, based on the study title and the transgene property, transgenic studies were classified into five categories in this review; oxidative scavengers, transcriptional factors, and above three abiotic categories. The review focuses on studies that investigate confer of stress tolerance and the identification of responsible factors, including wild relatives. From a practical application perspective, further evaluation of transgenic potato with abiotic stress tolerance is required. Although potato plants, including wild species, have a large potential for abiotic stress tolerance, exploration of the factors responsible for conferring this tolerance is still developing. Molecular breeding, including genetic engineering and conventional breeding using DNA markers, is expected to develop in the future.

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2010 CFR

2010-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding. Each... 50 Wildlife and Fisheries 1 2010-10-01 2010-10-01 false Permits for cooperative breeding. 15.24...

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2011 CFR

2011-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding. Each... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Permits for cooperative breeding. 15.24...

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2012 CFR

2012-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding. Each... 50 Wildlife and Fisheries 1 2012-10-01 2012-10-01 false Permits for cooperative breeding. 15.24...

50 CFR 15.21 - General application procedures.

Code of Federal Regulations, 2013 CFR

2013-10-01

... purposes only: Scientific research; zoological breeding or display programs; cooperative breeding programs...: Office of Management Authority), 4401 N. Fairfax Drive, Room 700, Arlington, VA 22203. Each application...

50 CFR 15.21 - General application procedures.

Code of Federal Regulations, 2012 CFR

2012-10-01

... purposes only: Scientific research; zoological breeding or display programs; cooperative breeding programs...: Office of Management Authority), 4401 N. Fairfax Drive, Room 700, Arlington, VA 22203. Each application...

Population genetics of commercial and feral honey bees in Western Australia.

PubMed

Chapman, Nadine C; Lim, Julianne; Oldroyd, Benjamin P

2008-04-01

Due to the introduction of exotic honey bee (Apis mellifera L.) diseases in the eastern states, the borders of the state of Western Australia were closed to the import of bees for breeding and other purposes > 25 yr ago. To provide genetically improved stock for the industry, a closed population breeding program was established that now provides stock for the majority of Western Australian beekeepers. Given concerns that inbreeding may have resulted from the closed population breeding structure, we assessed the genetic diversity within and between the breeding lines by using microsatellite and mitochondrial markers. We found that the breeding population still maintains considerable genetic diversity, despite 25 yr of selective breeding. We also investigated the genetic distance of the closed population breeding program to that of beekeepers outside of the program, and the feral Western Australian honey bee population. The feral population is genetically distinct from the closed population, but not from the genetic stock maintained by beekeepers outside of the program. The honey bees of Western Australia show three mitotypes, originating from two subspecies: Apis mellifera ligustica (mitotypes C1 and M7b) and Apis mellifera iberica (mitotype M6). Only mitotypes C1 and M6 are present in the commercial populations. The feral population contains all three mitotypes.

Accuracies of univariate and multivariate genomic prediction models in African cassava.

PubMed

Okeke, Uche Godfrey; Akdemir, Deniz; Rabbi, Ismail; Kulakow, Peter; Jannink, Jean-Luc

2017-12-04

Genomic selection (GS) promises to accelerate genetic gain in plant breeding programs especially for crop species such as cassava that have long breeding cycles. Practically, to implement GS in cassava breeding, it is necessary to evaluate different GS models and to develop suitable models for an optimized breeding pipeline. In this paper, we compared (1) prediction accuracies from a single-trait (uT) and a multi-trait (MT) mixed model for a single-environment genetic evaluation (Scenario 1), and (2) accuracies from a compound symmetric multi-environment model (uE) parameterized as a univariate multi-kernel model to a multivariate (ME) multi-environment mixed model that accounts for genotype-by-environment interaction for multi-environment genetic evaluation (Scenario 2). For these analyses, we used 16 years of public cassava breeding data for six target cassava traits and a fivefold cross-validation scheme with 10-repeat cycles to assess model prediction accuracies. In Scenario 1, the MT models had higher prediction accuracies than the uT models for all traits and locations analyzed, which amounted to on average a 40% improved prediction accuracy. For Scenario 2, we observed that the ME model had on average (across all locations and traits) a 12% improved prediction accuracy compared to the uE model. We recommend the use of multivariate mixed models (MT and ME) for cassava genetic evaluation. These models may be useful for other plant species.

Selecting loblolly pine parents for seed orchards to minimize the cost of producing pulp

Treesearch

W.J. Lowe; T.D. Byram; F.E. Bridgwater

1999-01-01

Southern pine cooperative breeding programs currently emphasize genetic improvement of growth rates. When a deployment population, typically a seed orchard, is established, there is an opportunity to emphasize traits other than growth rate to maximize the profit of individual cooperators in the breeding program. The authors studied a southeast Texas breeding population...

Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015.

PubMed

Doekes, Harmen P; Veerkamp, Roel F; Bijma, Piter; Hiemstra, Sipke J; Windig, Jack J

2018-04-11

In recent decades, Holstein-Friesian (HF) selection schemes have undergone profound changes, including the introduction of optimal contribution selection (OCS; around 2000), a major shift in breeding goal composition (around 2000) and the implementation of genomic selection (GS; around 2010). These changes are expected to have influenced genetic diversity trends. Our aim was to evaluate genome-wide and region-specific diversity in HF artificial insemination (AI) bulls in the Dutch-Flemish breeding program from 1986 to 2015. Pedigree and genotype data (~ 75.5 k) of 6280 AI-bulls were used to estimate rates of genome-wide inbreeding and kinship and corresponding effective population sizes. Region-specific inbreeding trends were evaluated using regions of homozygosity (ROH). Changes in observed allele frequencies were compared to those expected under pure drift to identify putative regions under selection. We also investigated the direction of changes in allele frequency over time. Effective population size estimates for the 1986-2015 period ranged from 69 to 102. Two major breakpoints were observed in genome-wide inbreeding and kinship trends. Around 2000, inbreeding and kinship levels temporarily dropped. From 2010 onwards, they steeply increased, with pedigree-based, ROH-based and marker-based inbreeding rates as high as 1.8, 2.1 and 2.8% per generation, respectively. Accumulation of inbreeding varied substantially across the genome. A considerable fraction of markers showed changes in allele frequency that were greater than expected under pure drift. Putative selected regions harboured many quantitative trait loci (QTL) associated to a wide range of traits. In consecutive 5-year periods, allele frequencies changed more often in the same direction than in opposite directions, except when comparing the 1996-2000 and 2001-2005 periods. Genome-wide and region-specific diversity trends reflect major changes in the Dutch-Flemish HF breeding program. Introduction of OCS and the shift in breeding goal were followed by a drop in inbreeding and kinship and a shift in the direction of changes in allele frequency. After introduction of GS, rates of inbreeding and kinship increased substantially while allele frequencies continued to change in the same direction as before GS. These results provide insight in the effect of breeding practices on genomic diversity and emphasize the need for efficient management of genetic diversity in GS schemes.

Flock composition, breeding strategies and farmers' traits of interest evaluation of Wollo highland sheep and their F1 crosses.

PubMed

Amare, Tadesse; Goshu, Gebeyehu; Tamir, Berhan

2018-01-01

Sheep production is a major component of the livestock sector in Ethiopia. The country owing to the large population of 30.70 million estimated numbers of sheep in the country and out of which about 72.14% are females, and 27.86% are males with diverse genetic resources. The real value of indigenous breeds was often under-estimated mostly due to their poor appearance and relatively low productivity. Developing countries in most cases opt for exotic breeds to increase animal productivity through crossbreeding or breed substitution without properly investigating the production potential of the indigenous breeds. The main objective of the research was to identify sheep flock composition and structure, farmers' traits of interest and breeding objective of Wollo highland sheep, and their F 1 crossbreed progenies. Smallholder farmers' flock synthesized from breeding ewes, breeding rams, pre-weaned ewe lambs, pre-weaned ram lambs, unproductive ewes, castrated and fattened rams, with the percentage coverage of 29.2, 13.3, 15.5, 16.5, 12.4, and 12.5%, respectively. The maximum number of flock size was 289.0 sheep per flock and higher in the third stratum. The off-take rate percentage of the three strata presented as 21.9% in 1st stratum, 12% in the 2nd stratum, and 16.4% in the 3rd stratum and higher off-take rate recorded in the first stratum. Sheep producer's traits of interest ranked by growth rate (first), body size (second) and marketing value was third rank. Communal breeding (random mating), village based controlled breeding, mixed type and private ram controlled breeding practice were comprised of 39.7, 61.7, 52 and 71.3%, respectively. The percentages of ewes per flock composition were presented as 36.5, 27.1 and 25.5%, respectively in the 3rd stratum, 2nd stratum and 3rd stratum in the order of their importance's. Genetic improvement practices at smallholder sheep producers situation was showing promising outcome with indigenous Washera F 1 crossbred lambs and which designated for weaning rate, body size, marketing age, age at first lambing, good temperament and large litter size in the order of their rank. The contemporary breeding practice tendency indicated that, reduced flock size to improve flock productivity via crossbreeding practices.

Advances and Challenges in Genomic Selection for Disease Resistance.

PubMed

Poland, Jesse; Rutkoski, Jessica

2016-08-04

Breeding for disease resistance is a central focus of plant breeding programs, as any successful variety must have the complete package of high yield, disease resistance, agronomic performance, and end-use quality. With the need to accelerate the development of improved varieties, genomics-assisted breeding is becoming an important tool in breeding programs. With marker-assisted selection, there has been success in breeding for disease resistance; however, much of this work and research has focused on identifying, mapping, and selecting for major resistance genes that tend to be highly effective but vulnerable to breakdown with rapid changes in pathogen races. In contrast, breeding for minor-gene quantitative resistance tends to produce more durable varieties but is a more challenging breeding objective. As the genetic architecture of resistance shifts from single major R genes to a diffused architecture of many minor genes, the best approach for molecular breeding will shift from marker-assisted selection to genomic selection. Genomics-assisted breeding for quantitative resistance will therefore necessitate whole-genome prediction models and selection methodology as implemented for classical complex traits such as yield. Here, we examine multiple case studies testing whole-genome prediction models and genomic selection for disease resistance. In general, whole-genome models for disease resistance can produce prediction accuracy suitable for application in breeding. These models also largely outperform multiple linear regression as would be applied in marker-assisted selection. With the implementation of genomic selection for yield and other agronomic traits, whole-genome marker profiles will be available for the entire set of breeding lines, enabling genomic selection for disease at no additional direct cost. In this context, the scope of implementing genomics selection for disease resistance, and specifically for quantitative resistance and quarantined pathogens, becomes a tractable and powerful approach in breeding programs.

Exploitation of data from breeding programs supports rapid implementation of genomic selection for key agronomic traits in perennial ryegrass.

PubMed

Pembleton, Luke W; Inch, Courtney; Baillie, Rebecca C; Drayton, Michelle C; Thakur, Preeti; Ogaji, Yvonne O; Spangenberg, German C; Forster, John W; Daetwyler, Hans D; Cogan, Noel O I

2018-06-02

Exploitation of data from a ryegrass breeding program has enabled rapid development and implementation of genomic selection for sward-based biomass yield with a twofold-to-threefold increase in genetic gain. Genomic selection, which uses genome-wide sequence polymorphism data and quantitative genetics techniques to predict plant performance, has large potential for the improvement in pasture plants. Major factors influencing the accuracy of genomic selection include the size of reference populations, trait heritability values and the genetic diversity of breeding populations. Global diversity of the important forage species perennial ryegrass is high and so would require a large reference population in order to achieve moderate accuracies of genomic selection. However, diversity of germplasm within a breeding program is likely to be lower. In addition, de novo construction and characterisation of reference populations are a logistically complex process. Consequently, historical phenotypic records for seasonal biomass yield and heading date over a 18-year period within a commercial perennial ryegrass breeding program have been accessed, and target populations have been characterised with a high-density transcriptome-based genotyping-by-sequencing assay. Ability to predict observed phenotypic performance in each successive year was assessed by using all synthetic populations from previous years as a reference population. Moderate and high accuracies were achieved for the two traits, respectively, consistent with broad-sense heritability values. The present study represents the first demonstration and validation of genomic selection for seasonal biomass yield within a diverse commercial breeding program across multiple years. These results, supported by previous simulation studies, demonstrate the ability to predict sward-based phenotypic performance early in the process of individual plant selection, so shortening the breeding cycle, increasing the rate of genetic gain and allowing rapid adoption in ryegrass improvement programs.

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs.

PubMed

Marsden, Clare D; Ortega-Del Vecchyo, Diego; O'Brien, Dennis P; Taylor, Jeremy F; Ramirez, Oscar; Vilà, Carles; Marques-Bonet, Tomas; Schnabel, Robert D; Wayne, Robert K; Lohmueller, Kirk E

2016-01-05

Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2-3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants.

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

PubMed Central

Marsden, Clare D.; Ortega-Del Vecchyo, Diego; O’Brien, Dennis P.; Taylor, Jeremy F.; Ramirez, Oscar; Vilà, Carles; Marques-Bonet, Tomas; Schnabel, Robert D.; Wayne, Robert K.; Lohmueller, Kirk E.

2016-01-01

Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2–3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants. PMID:26699508

Can functional hologenomics aid tackling current challenges in plant breeding?

PubMed

Nogales, Amaia; Nobre, Tânia; Valadas, Vera; Ragonezi, Carla; Döring, Matthias; Polidoros, Alexios; Arnholdt-Schmitt, Birgit

2016-07-01

Molecular plant breeding usually overlooks the genetic variability that arises from the association of plants with endophytic microorganisms, when looking at agronomic interesting target traits. This source of variability can have crucial effects on the functionality of the organism considered as a whole (the holobiont), and therefore can be selectable in breeding programs. However, seeing the holobiont as a unit for selection and improvement in breeding programs requires novel approaches for genotyping and phenotyping. These should not focus just at the plant level, but also include the associated endophytes and their functional effects on the plant, to make effective desirable trait screenings. The present review intends to draw attention to a new research field on functional hologenomics that if associated with adequate phenotyping tools could greatly increase the efficiency of breeding programs. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

A computational approach to animal breeding.

PubMed

Berger-Wolf, Tanya Y; Moore, Cristopher; Saia, Jared

2007-02-07

We propose a computational model of mating strategies for controlled animal breeding programs. A mating strategy in a controlled breeding program is a heuristic with some optimization criteria as a goal. Thus, it is appropriate to use the computational tools available for analysis of optimization heuristics. In this paper, we propose the first discrete model of the controlled animal breeding problem and analyse heuristics for two possible objectives: (1) breeding for maximum diversity and (2) breeding a target individual. These two goals are representative of conservation biology and agricultural livestock management, respectively. We evaluate several mating strategies and provide upper and lower bounds for the expected number of matings. While the population parameters may vary and can change the actual number of matings for a particular strategy, the order of magnitude of the number of expected matings and the relative competitiveness of the mating heuristics remains the same. Thus, our simple discrete model of the animal breeding problem provides a novel viable and robust approach to designing and comparing breeding strategies in captive populations.

Improving Charging-Breeding Simulations with Space-Charge Effects

NASA Astrophysics Data System (ADS)

Bilek, Ryan; Kwiatkowski, Ania; Steinbrügge, René

2016-09-01

Rare-isotope-beam facilities use Highly Charged Ions (HCI) for accelerators accelerating heavy ions and to improve measurement precision and resolving power of certain experiments. An Electron Beam Ion Trap (EBIT) is able to create HCI through successive electron impact, charge breeding trapped ions into higher charge states. CBSIM was created to calculate successive charge breeding with an EBIT. It was augmented by transferring it into an object-oriented programming language, including additional elements, improving ion-ion collision factors, and exploring the overlap of the electron beam with the ions. The calculation is enhanced with the effects of residual background gas by computing the space charge due to charge breeding. The program assimilates background species, ionizes and charge breeds them alongside the element being studied, and allows them to interact with the desired species through charge exchange, giving fairer overview of realistic charge breeding. Calculations of charge breeding will be shown for realistic experimental conditions. We reexamined the implementation of ionization energies, cross sections, and ion-ion interactions when charge breeding.

Breeding design considerations for coastal Douglas-fir.

Treesearch

Randy Johnson

1998-01-01

The basic principles of designing forest tree breeding programs are reviewed for Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) in the Pacific Northwest. Breeding populations are discussed given current and future breeding zone sizes and seed orchard designs. Seed orchard composition is discussed for potential genetic gain and maintaining...

Non-invasive assessment of reproductive status and stress in captive Asian elephants in three south Indian zoos.

PubMed

Kumar, Vinod; Palugulla Reddy, Vivekananda; Kokkiligadda, Adiseshu; Shivaji, Sisinthy; Umapathy, Govindhaswamy

2014-05-15

Asian elephants in captivity need immediate attention to be bred so as to meet the increasing demand for captive elephants and to overcome the dependence on supplementing the captive stock with wild animals. Unfortunately, captive breeding programs across the globe have met with limited success and therefore more effort is needed to improve breeding in captivity. Endocrine profiling of reproductive hormones (progestagens and androgens) and the stress hormone (glucocorticoids) could facilitate better management and breeding strategies. In the present study, we investigated reproductive and stress physiology of 12 captive Asian elephants for 10-27 months using a non-invasive method based on steroid analysis of 1700 elephant dung samples. Most of the elephants were cycling regularly. Males during musth showed increased fecal androgen metabolite concentrations and exhibited a slight increase in fecal glucocorticoid metabolite levels. Elephants used in public festivals and processions showed significantly increased in faecal glucocorticoid metabolite levels. The results indicate that captive elephants require periodic health care, better husbandry practices and scientific management for sustainable captive population. Copyright © 2014 Elsevier Inc. All rights reserved.

Historical use of cultivars as parents in Florida and Louisiana sugarcane breeding program

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum L. spp. hybrids) growers depend on breeding programs for new, high-yielding cultivars that have resistance to abiotic and biotic stresses, so breeders continually seek out widely adapted, high yielding germplasm to be used as parents for their programs. Cultivars are sometimes u...

Genetic diversity and differentiation of exotic and American commercial cattle breeds raised in Brazil.

PubMed

Brasil, B S A F; Coelho, E G A; Drummond, M G; Oliveira, D A A

2013-11-18

The Brazilian cattle population is mainly composed of breeds of zebuine origin and their American derivatives. Comprehensive knowledge about the genetic diversity of these populations is fundamental for animal breeding programs and the conservation of genetic resources. This study aimed to assess the phylogenetic relationships, levels of genetic diversity, and patterns of taurine/zebuine admixture among 9 commercial cattle breeds raised in Brazil. Analysis of DNA polymorphisms was performed on 2965 animals using the 11 microsatellite markers recommended by the International Society of Animal Genetics. High genetic diversity was detected in all breeds, even though significant inbreeding was observed within some. Differences among the breeds accounted for 14.72% of the total genetic variability, and genetic differentiation was higher among taurine than among zebuine cattle. Of note, Nelore cattle presented with high levels of admixture, which is consistent with the history of frequent gene flow during the establishment of this breed in Brazil. Furthermore, significant genetic variability was partitioned within the commercial cattle breeds formed in America, which, therefore, comprise important resources of genetic diversity in the tropics. The genetic characterization of these important Brazilian breeds may now facilitate the development of management and breeding programs for these populations.

Genetic profile of scrapie codons 146, 211 and 222 in the PRNP gene locus in three breeds of dairy goats.

PubMed

Vouraki, Sotiria; Gelasakis, Athanasios I; Alexandri, Panoraia; Boukouvala, Evridiki; Ekateriniadou, Loukia V; Banos, Georgios; Arsenos, Georgios

2018-01-01

Polymorphisms at PRNP gene locus have been associated with resistance against classical scrapie in goats. Genetic selection on this gene within appropriate breeding programs may contribute to the control of the disease. The present study characterized the genetic profile of codons 146, 211 and 222 in three dairy goat breeds in Greece. A total of 766 dairy goats from seven farms were used. Animals belonged to two indigenous Greek, Eghoria (n = 264) and Skopelos (n = 287) and a foreign breed, Damascus (n = 215). Genomic DNA was extracted from blood samples from individual animals. Polymorphisms were detected in these codons using Real-Time PCR analysis and four different Custom TaqMan® SNP Genotyping Assays. Genotypic, allelic and haplotypic frequencies were calculated based on individual animal genotypes. Chi-square tests were used to examine Hardy-Weinberg equilibrium state and compare genotypic distribution across breeds. Genetic distances among the three breeds, and between these and 30 breeds reared in other countries were estimated based on haplotypic frequencies using fixation index FST with Arlequin v3.1 software; a Neighbor-Joining tree was created using PHYLIP package v3.695. Level of statistical significance was set at P = 0.01. All scrapie resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied population. Significant frequency differences were observed between the indigenous Greek and Damascus breeds. Alleles 222K and 146S had the highest frequency in the two indigenous and the Damascus breed, respectively (ca. 6.0%). The studied breeds shared similar haplotypic frequencies with most South Italian and Turkish breeds but differed significantly from North-Western European, Far East and some USA goat breeds. Results suggest there is adequate variation in the PRNP gene locus to support breeding programs for enhanced scrapie resistance in goats reared in Greece. Genetic comparisons among goat breeds indicate that separate breeding programs should apply to the two indigenous and the imported Damascus breeds.

A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes

PubMed Central

2012-01-01

Background Carcass fatness is an important trait in most pig breeding programs. Following market requests, breeding plans for fresh pork consumption are usually designed to reduce carcass fat content and increase lean meat deposition. However, the Italian pig industry is mainly devoted to the production of Protected Designation of Origin dry cured hams: pigs are slaughtered at around 160 kg of live weight and the breeding goal aims at maintaining fat coverage, measured as backfat thickness to avoid excessive desiccation of the hams. This objective has shaped the genetic pool of Italian heavy pig breeds for a few decades. In this study we applied a selective genotyping approach within a population of ~ 12,000 performance tested Italian Large White pigs. Within this population, we selectively genotyped 304 pigs with extreme and divergent backfat thickness estimated breeding value by the Illumina PorcineSNP60 BeadChip and performed a genome wide association study to identify loci associated to this trait. Results We identified 4 single nucleotide polymorphisms with P≤5.0E-07 and additional 119 ones with 5.0E-07

What’s in a Name? Effect of Breed Perceptions & Labeling on Attractiveness, Adoptions & Length of Stay for Pit-Bull-Type Dogs

PubMed Central

Gunter, Lisa M.; Barber, Rebecca T.; Wynne, Clive D. L.

2016-01-01

Previous research has indicated that certain breeds of dogs stay longer in shelters than others. However, exactly how breed perception and identification influences potential adopters' decisions remains unclear. Current dog breed identification practices in animal shelters are often based upon information supplied by the relinquishing owner, or staff determination based on the dog's phenotype. However, discrepancies have been found between breed identification as typically assessed by welfare agencies and the outcome of DNA analysis. In Study 1, the perceived behavioral and adoptability characteristics of a pit-bull-type dog were compared with those of a Labrador Retriever and Border Collie. How the addition of a human handler influenced those perceptions was also assessed. In Study 2, lengths of stay and perceived attractiveness of dogs that were labeled as pit bull breeds were compared to dogs that were phenotypically similar but were labeled as another breed at an animal shelter. The latter dogs were called "lookalikes." In Study 3, we compared perceived attractiveness in video recordings of pit-bull-type dogs and lookalikes with and without breed labels. Lastly, data from an animal shelter that ceased applying breed labeling on kennels were analyzed, and lengths of stay and outcomes for all dog breeds, including pit bulls, before and after the change in labeling practice were compared. In total, these findings suggest that breed labeling influences potential adopters' perceptions and decision-making. Given the inherent complexity of breed assignment based on morphology coupled with negative breed perceptions, removing breed labels is a relatively low-cost strategy that will likely improve outcomes for dogs in animal shelters. PMID:27008213

What's in a Name? Effect of Breed Perceptions & Labeling on Attractiveness, Adoptions & Length of Stay for Pit-Bull-Type Dogs.

PubMed

Gunter, Lisa M; Barber, Rebecca T; Wynne, Clive D L

2016-01-01

Previous research has indicated that certain breeds of dogs stay longer in shelters than others. However, exactly how breed perception and identification influences potential adopters' decisions remains unclear. Current dog breed identification practices in animal shelters are often based upon information supplied by the relinquishing owner, or staff determination based on the dog's phenotype. However, discrepancies have been found between breed identification as typically assessed by welfare agencies and the outcome of DNA analysis. In Study 1, the perceived behavioral and adoptability characteristics of a pit-bull-type dog were compared with those of a Labrador Retriever and Border Collie. How the addition of a human handler influenced those perceptions was also assessed. In Study 2, lengths of stay and perceived attractiveness of dogs that were labeled as pit bull breeds were compared to dogs that were phenotypically similar but were labeled as another breed at an animal shelter. The latter dogs were called "lookalikes." In Study 3, we compared perceived attractiveness in video recordings of pit-bull-type dogs and lookalikes with and without breed labels. Lastly, data from an animal shelter that ceased applying breed labeling on kennels were analyzed, and lengths of stay and outcomes for all dog breeds, including pit bulls, before and after the change in labeling practice were compared. In total, these findings suggest that breed labeling influences potential adopters' perceptions and decision-making. Given the inherent complexity of breed assignment based on morphology coupled with negative breed perceptions, removing breed labels is a relatively low-cost strategy that will likely improve outcomes for dogs in animal shelters.

Estimation of genetic diversity in Gute sheep: pedigree and microsatellite analyses of an ancient Swedish breed.

PubMed

Rochus, Christina M; Johansson, Anna M

2017-01-01

Breeds with small population size are in danger of an increased inbreeding rate and loss of genetic diversity, which puts them at risk for extinction. In Sweden there are a number of local breeds, native breeds which have adapted to specific areas in Sweden, for which efforts are being made to keep them pure and healthy over time. One example of such a breed is the Swedish Gute sheep. The objective of this study was to estimate inbreeding and genetic diversity of Swedish Gute sheep. Three datasets were analysed: pedigree information of the whole population, pedigree information for 100 animals of the population, and microsatellite genotypes for 94 of the 100 animals. The average inbreeding coefficient for lambs born during a six year time period (2007-2012) did not increase during that time period. The inbreeding calculated from the entire pedigree (0.038) and for a sample of the population (0.018) was very low. Sheep were more heterozygous at the microsatellite markers than expected (average multilocus heterozygosity and Ritland inbreeding estimates 1.01845 and -0.03931) and five of seven microsatellite markers were not in Hardy Weinberg equilibrium due to heterozygosity excess. The total effective population size estimated from the pedigree information was 155.4 and the average harmonic mean effective population size estimated from microsatellites was 88.3. Pedigree and microsatellite genotype estimations of inbreeding were consistent with a breeding program with the purpose of reducing inbreeding. Our results showed that current breeding programs of the Swedish Gute sheep are consistent with efforts of keeping this breed viable and these breeding programs are an example for other small local breeds in conserving breeds for the future.

Extending RosBREED in the Pacific Northwest for strawberry processing traits: year 1

USDA-ARS?s Scientific Manuscript database

In an effort to implement marker-assisted breeding in Rosaceae, many traits need to be characterized in diverse germplasm. The USDA-NIFA Specialty Crop Research Initiative-funded RosBREED project includes breeding programs of four Rosaceae crops (apple, peach, cherry, and strawberry). Phenotyping ea...

PALLAS BARLEY, A VARIETY PRODUCED BY IONIZING RADIATION: ITS SIGNIFICANCE FOR PLANT BREEDING AND EVOLUTION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borg, G.; Froier, K.f Gustafsson, A.

1959-10-31

Results are reported from plant breeding programs in which mutations induced in barley by irradiation resulted in the development of a variety with characteristics superior to the parents. Good results were also reported in the development of superior varieties of oil rape, white mustard, and pea plants. The usefulness of radiation-induced mutations in plant breeding programs is discussed. (C.H.)

Genetic characterization of Russian honey bee stock selected for improved resistance to Varroa destructor.

PubMed

Bourgeois, A Lelania; Rinderer, Thomas E

2009-06-01

Maintenance of genetic diversity among breeding lines is important in selective breeding and stock management. The Russian Honey Bee Breeding Program has strived to maintain high levels of heterozygosity among its breeding lines since its inception in 1997. After numerous rounds of selection for resistance to tracheal and varroa mites and improved honey production, 18 lines were selected as the core of the program. These lines were grouped into three breeding blocks that were crossbred to improve overall heterozygosity levels of the population. Microsatellite DNA data demonstrated that the program has been successful. Heterozygosity and allelic richness values are high and there are no indications of inbreeding among the three blocks. There were significant levels of genetic structure measured among the three blocks. Block C was genetically distinct from both blocks A and B (F(ST) = 0.0238), whereas blocks A and B did not differ from each other (F(ST) = 0.0074). The same pattern was seen for genic (based on numbers of alleles) differentiation. Genetic distance, as measured by chord distance, indicates that all of the 18 lines are equally distant, with minimal clustering. The data indicate that the overall design of the breeding program has been successful in maintaining high levels of diversity and avoiding problems associated with inbreeding.

Methods for shorebird surveys in the Arctic

Treesearch

Jonathan Bart; Susan L. Earnst

2005-01-01

A substantial effort is being made to develop a longterm monitoring program for shorebirds in North American (Brown et al. 2000, Donaldson et al. 2001, Bart et al. this volume). The current program, PRISM (Program for Regional and International Shorebird Monitoring), has four segments: arctic and boreal breeding surveys, temperate breeding surveys, temperate non-...

Integrating molecular tools and conventional approaches in the Oregon State University hazelnut breeding program

Treesearch

Shawn A. Mehlenbacher

2012-01-01

The Oregon State University (OSU) hazelnut breeding program, initiated in 1969, continues to develop new cultivars for the hazelnut industry that combine suitability to the blanched kernel market with resistance to eastern filbert blight (EFB) caused by Anisogramma anomala. Oregon's hazelnut growers support the program through the Oregon...

Assessing admixture by multivariate analyses of phenotypic differentiation in the Algerian goat livestock.

PubMed

Ouchene-Khelifi, Nadjet-Amina; Ouchene, Nassim; Maftah, Abderrahman; Da Silva, Anne Blondeau; Lafri, Mohamed

2015-10-01

In Algeria, goat research has been largely neglected, in spite of the economic importance of this domestic species for rural livelihoods. Goat farming is traditional and cross-breeding practices are current. The phenotypic variability of the four main native breeds (Arabia, Makatia, M'zabite and Kabyle), and of two exotic breeds (Alpine and Saanen), was investigated for the first time, using multivariate discriminant analysis. A total of 892 females were sampled in a large area, including the cradle of the native breeds, and phenotyped with 23 quantitative measures and 10 qualitative traits. Our results suggested that cross-breeding practices have ever led to critical consequences, particularly for Makatia and M'zabite. The information reported in this study has to be carefully considered in order to establish governmental plan able to prevent the genetic dilution of the Algerian goat livestock.

Possibilities in an age of genomics: The future of the breeding index

USDA-ARS?s Scientific Manuscript database

Selective breeding has been practiced since domestication, but early breeders commonly selected on appearance (e.g., coat color and pattern) rather than quantitative phenotypes (e.g., milk yield). A breeding index converts information about several traits of a cow – for example, how much she milks a...

Symposium review: Possibilities in an age of genomics: The future of the breeding index

USDA-ARS?s Scientific Manuscript database

Selective breeding has been practiced since domestication, but early breeders commonly selected on appearance (e.g., coat color) rather than quantitative phenotypes (e.g., milk yield). A breeding index converts information about several traits into 1 number used for selection and also to predict an ...

Fruit Phenolic Profiling: A New Selection Criterion in Olive Breeding Programs

PubMed Central

Pérez, Ana G.; León, Lorenzo; Sanz, Carlos; de la Rosa, Raúl

2018-01-01

Olive growing is mainly based on traditional varieties selected by the growers across the centuries. The few attempts so far reported to obtain new varieties by systematic breeding have been mainly focused on improving the olive adaptation to different growing systems, the productivity and the oil content. However, the improvement of oil quality has rarely been considered as selection criterion and only in the latter stages of the breeding programs. Due to their health promoting and organoleptic properties, phenolic compounds are one of the most important quality markers for Virgin olive oil (VOO) although they are not commonly used as quality traits in olive breeding programs. This is mainly due to the difficulties for evaluating oil phenolic composition in large number of samples and the limited knowledge on the genetic and environmental factors that may influence phenolic composition. In the present work, we propose a high throughput methodology to include the phenolic composition as a selection criterion in olive breeding programs. For that purpose, the phenolic profile has been determined in fruits and oils of several breeding selections and two varieties (“Picual” and “Arbequina”) used as control. The effect of three different environments, typical for olive growing in Andalusia, Southern Spain, was also evaluated. A high genetic effect was observed on both fruit and oil phenolic profile. In particular, the breeding selection UCI2-68 showed an optimum phenolic profile, which sums up to a good agronomic performance previously reported. A high correlation was found between fruit and oil total phenolic content as well as some individual phenols from the two different matrices. The environmental effect on phenolic compounds was also significant in both fruit and oil, although the low genotype × environment interaction allowed similar ranking of genotypes on the different environments. In summary, the high genotypic variance and the simplified procedure of the proposed methodology for fruit phenol evaluation seems to be convenient for breeding programs aiming at obtaining new cultivars with improved phenolic profile. PMID:29535752

Fruit Phenolic Profiling: A New Selection Criterion in Olive Breeding Programs.

PubMed

Pérez, Ana G; León, Lorenzo; Sanz, Carlos; de la Rosa, Raúl

2018-01-01

Olive growing is mainly based on traditional varieties selected by the growers across the centuries. The few attempts so far reported to obtain new varieties by systematic breeding have been mainly focused on improving the olive adaptation to different growing systems, the productivity and the oil content. However, the improvement of oil quality has rarely been considered as selection criterion and only in the latter stages of the breeding programs. Due to their health promoting and organoleptic properties, phenolic compounds are one of the most important quality markers for Virgin olive oil (VOO) although they are not commonly used as quality traits in olive breeding programs. This is mainly due to the difficulties for evaluating oil phenolic composition in large number of samples and the limited knowledge on the genetic and environmental factors that may influence phenolic composition. In the present work, we propose a high throughput methodology to include the phenolic composition as a selection criterion in olive breeding programs. For that purpose, the phenolic profile has been determined in fruits and oils of several breeding selections and two varieties ("Picual" and "Arbequina") used as control. The effect of three different environments, typical for olive growing in Andalusia, Southern Spain, was also evaluated. A high genetic effect was observed on both fruit and oil phenolic profile. In particular, the breeding selection UCI2-68 showed an optimum phenolic profile, which sums up to a good agronomic performance previously reported. A high correlation was found between fruit and oil total phenolic content as well as some individual phenols from the two different matrices. The environmental effect on phenolic compounds was also significant in both fruit and oil, although the low genotype × environment interaction allowed similar ranking of genotypes on the different environments. In summary, the high genotypic variance and the simplified procedure of the proposed methodology for fruit phenol evaluation seems to be convenient for breeding programs aiming at obtaining new cultivars with improved phenolic profile.

Effects of wildlife forestry on abundance of breeding birds in bottomland hardwood forests of Louisiana

USGS Publications Warehouse

Norris, Jennifer L.; Chamberlain, Michael J.; Twedt, Daniel J.

2009-01-01

Effects of silvicultural activities on birds are of increasing interest because of documented national declines in breeding bird populations for some species and the potential that these declines are in part due to changes in forest habitat. Silviculturally induced disturbances have been advocated as a means to achieve suitable forest conditions for priority wildlife species in bottomland hardwood forests. We evaluated how silvicultural activities on conservation lands in bottomland hardwood forests of Louisiana, USA, influenced species-specific densities of breeding birds. Our data were from independent studies, which used standardized point-count surveys for breeding birds in 124 bottomland hardwood forest stands on 12 management areas. We used Program DISTANCE 5.0, Release 2.0 (Thomas et al. 2006) to estimate density for 43 species with > 50 detections. For 36 of those species we compared density estimates among harvest regimes (individual selection, group selection, extensive harvest, and no harvest). We observed 10 species with similar densities in those harvest regimes compared with densities in stands not harvested. However, we observed 10 species that were negatively impacted by harvest with greater densities in stands not harvested, 9 species with greater densities in individual selection stands, 4 species with greater densities in group selection stands, and 4 species with greater densities in stands receiving an extensive harvest (e.g., > 40% canopy removal). Differences in intensity of harvest influenced densities of breeding birds. Moreover, community-wide avian conservation values of stands subjected to individual and group selection, and stands not harvested, were similar to each other and greater than that of stands subjected to extensive harvest that removed > 40% canopy cover. These results have implications for managers estimating breeding bird populations, in addition to predicting changes in bird communities as a result of prescribed and future forest management practices.

Saving genetic resources of native pigs in Occidental and Oriental countries - practical examples of the characterization and utilization of native pigs in Hungary and Laos.

PubMed

Rátky, Jozsef; Egerszegi, Istvan; Toth, Peter; Keonuchan, Soukanh; Nagai, Takashi; Kikuchi, Kazuhiro; Manabe, Noboru; Brüssow, Klaus-Peter

2013-10-01

Worldwide, only a few "fatty" pig breeds exist with different and/or regional utilization. Using the Hungarian Mangalica, which almost went extinct in Europe and the Lao Moo Lat pig, which still has a large population in South-East Asia as exemples, we wanted to demonstrate that indigenous (fatty) pig breeds may represent both national value and tremendous economic potential. Since these less prolific and less productive breeds cannot contribute to mass production, new market roles and methods should be established for them in the premium segment of pork trading. Thus their preservation and propagation needs the comprehensive collaboration of commercial, governmental actors and researchers. Briefly summarizing the history, we report the current results of reproductive physiology research. The commercial renaissance of Mangalica pigs is indebted to the enthusiastic efforts of basic scientists, pig breeding experts and dedicated Mangalica producers. Scientific achievements were applied to practical breeding and production of delicious pork and processed products, which ultimately made the economic success in the Mangalica sector possible. Both, research on and utilization of endangered (pig) breeds maintain not only breed diversities, but also may improve the livelihood of farmers worldwide.

Integration of genomic information into sport horse breeding programs for optimization of accuracy of selection.

PubMed

Haberland, A M; König von Borstel, U; Simianer, H; König, S

2012-09-01

Reliable selection criteria are required for young riding horses to increase genetic gain by increasing accuracy of selection and decreasing generation intervals. In this study, selection strategies incorporating genomic breeding values (GEBVs) were evaluated. Relevant stages of selection in sport horse breeding programs were analyzed by applying selection index theory. Results in terms of accuracies of indices (r(TI) ) and relative selection response indicated that information on single nucleotide polymorphism (SNP) genotypes considerably increases the accuracy of breeding values estimated for young horses without own or progeny performance. In a first scenario, the correlation between the breeding value estimated from the SNP genotype and the true breeding value (= accuracy of GEBV) was fixed to a relatively low value of r(mg) = 0.5. For a low heritability trait (h(2) = 0.15), and an index for a young horse based only on information from both parents, additional genomic information doubles r(TI) from 0.27 to 0.54. Including the conventional information source 'own performance' into the before mentioned index, additional SNP information increases r(TI) by 40%. Thus, particularly with regard to traits of low heritability, genomic information can provide a tool for well-founded selection decisions early in life. In a further approach, different sources of breeding values (e.g. GEBV and estimated breeding values (EBVs) from different countries) were combined into an overall index when altering accuracies of EBVs and correlations between traits. In summary, we showed that genomic selection strategies have the potential to contribute to a substantial reduction in generation intervals in horse breeding programs.

Peasant friendly plant breeding and the early years of the green revolution in Mexico.

PubMed

Harwood, Jonathan

2009-01-01

Despite their success in boosting cereals production overall, the Green Revolution programs of the 1950s and 1960s were often criticized for failing to achieve their declared aim of alleviating world hunger. Most critics argued that the programs had produced a technology unsuited to the needs of small peasant farmers. This paper explores why such inappropriate technology might have been developed, focusing on the early years of the Rockefeller Foundation's Mexican Agricultural Program (MAP). It shows that some foundation officers as well as agricultural advisors had prior experience of the problems faced by small farmers in the United States and elsewhere. Moreover, the foundation's expressed concern for rural poverty does not appear to have been mere posturing by an organization anxious to be seen as an agent of philanthropy. Furthermore, the program's early work in maize-breeding was well tailored to the conditions of Mexican agriculture. Once the MAP was up and running, however, it became apparent that the task of getting new varieties and cultivation practices to small farmers was going to be difficult. Needing to make some kind of impact quickly, MAP staff chose to concentrate upon projects that were likely to find a rapid uptake. This meant setting aside the needs of peasant farmers to develop high-yielding varieties suited to large commercial farms.

Genetic evaluation of a Great Lakes lake trout hatchery program

USGS Publications Warehouse

Page, K.S.; Scribner, K.T.; Bast, D.; Holey, M.E.; Burnham-Curtis, M. K.

2005-01-01

Efforts over several decades to restore lake trout Salvelinus namaycush in U.S. waters of the upper Great Lakes have emphasized the stocking of juveniles from each of six hatchery broodstocks. Retention of genetic diversity across all offspring life history stages throughout the hatchery system has been an important component of the restoration hatchery and stocking program. Different stages of the lake trout hatchery program were examined to determine how effective hatchery practices have been in minimizing the loss of genetic diversity in broodstock adults and in progeny stocked. Microsatellite loci were used to estimate allele frequencies, measures of genetic diversity, and relatedness for wild source populations, hatchery broodstocks, and juveniles. We also estimated the effective number of breeders for each broodstock. Hatchery records were used to track destinations of fertilized eggs from all spawning dates to determine whether adult contributions to stocking programs were proportional to reproductive effort. Overall, management goals of maintaining genetic diversity were met across all stages of the hatchery program; however, we identified key areas where changes in mating regimes and in the distribution of fertilized gametes and juveniles could be improved. Estimates of effective breeding population size (Nb) were 9-41% of the total number of adults spawned. Low estimates of Nb were primarily attributed to spawning practices, including the pooling of gametes from multiple males and females and the reuse of males. Nonrandom selection and distribution of fertilized eggs before stocking accentuated declines in effective breeding population size and increased levels of relatedness of juveniles distributed to different rearing facilities and stocking locales. Adoption of guidelines that decrease adult reproductive variance and promote more equitable reproductive contributions of broodstock adults to juveniles would further enhance management goals of maintaining genetic diversity and minimize probabilities of consanguineous matings among stocked individuals when sexually mature. ?? Copyright by the American Fisheries Society 2005.

Assessing the impact of natural service bulls and genotype by environment interactions on genetic gain and inbreeding in organic dairy cattle genomic breeding programs.

PubMed

Yin, T; Wensch-Dorendorf, M; Simianer, H; Swalve, H H; König, S

2014-06-01

The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G×E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either 'conventional' estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low (h 2=0.05) and moderate heritability (h 2=0.30). GEBV were calculated for different accuracies (r mg), and G×E interactions were considered by modifying originally simulated true breeding values in the range from r g=0.5 to 1.0. For both traits (h 2=0.05 and 0.30) and r mg⩾0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G×E interactions. Only for pronounced G×E interactions (r g=0.5), and for highly accurate GEBV for natural service bulls (r mg>0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices.

Selection of Breeding Stock among Australian Purebred Dog Breeders, with Particular Emphasis on the Dam.

PubMed

Czerwinski, Veronika; McArthur, Michelle; Smith, Bradley; Hynd, Philip; Hazel, Susan

2016-11-16

Every year, thousands of purebred domestic dogs are bred by registered dog breeders. Yet, little is known about the rearing environment of these dogs, or the attitudes and priorities surrounding breeding practices of these dog breeders. The objective of this study was to explore some of the factors that dog breeders consider important for stock selection, with a particular emphasis on issues relating to the dam. Two-hundred and seventy-four Australian purebred dog breeders, covering 91 breeds across all Australian National Kennel Club breed groups, completed an online survey relating to breeding practices. Most breeders surveyed (76%) reported specialising in one breed of dog, the median number of dogs and bitches per breeder was two and three respectively, and most breeders bred two litters or less a year. We identified four components, relating to the dam, that were considered important to breeders. These were defined as Maternal Care, Offspring Potential, Dam Temperament, and Dam Genetics and Health. Overall, differences were observed in attitudes and beliefs across these components, showing that there is variation according to breed/breed groups. In particular, the importance of Maternal Care varied according to dog breed group. Breeders of brachycephalic breeds tended to differ the most in relation to Offspring Potential and Dam Genetics and Health. The number of breeding dogs/bitches influenced breeding priority, especially in relation to Dam Temperament, however no effect was found relating to the number of puppies bred each year. Only 24% of breeders used their own sire for breeding. The finding that some breeders did not test for diseases relevant to their breed, such as hip dysplasia in Labrador Retrievers and German Shepherds, provides important information on the need to educate some breeders, and also buyers of purebred puppies, that screening for significant diseases should occur. Further research into the selection of breeding dams and sires will inform future strategies to improve the health and behaviour of our best friend.

Addition of a breeding database in the Genome Database for Rosaceae

PubMed Central

Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

2013-01-01

Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox PMID:24247530

Addition of a breeding database in the Genome Database for Rosaceae.

PubMed

Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

2013-01-01

Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox.

Genotype by environment interaction and breeding for robustness in livestock

PubMed Central

Rauw, Wendy M.; Gomez-Raya, Luis

2015-01-01

The increasing size of the human population is projected to result in an increase in meat consumption. However, at the same time, the dominant position of meat as the center of meals is on the decline. Modern objections to the consumption of meat include public concerns with animal welfare in livestock production systems. Animal breeding practices have become part of the debate since it became recognized that animals in a population that have been selected for high production efficiency are more at risk for behavioral, physiological and immunological problems. As a solution, animal breeding practices need to include selection for robustness traits, which can be implemented through the use of reaction norms analysis, or though the direct inclusion of robustness traits in the breeding objective and in the selection index. This review gives an overview of genotype × environment interactions (the influence of the environment, reaction norms, phenotypic plasticity, canalization, and genetic homeostasis), reaction norms analysis in livestock production, options for selection for increased levels of production and against environmental sensitivity, and direct inclusion of robustness traits in the selection index. Ethical considerations of breeding for improved animal welfare are discussed. The discussion on animal breeding practices has been initiated and is very alive today. This positive trend is part of the sustainable food production movement that aims at feeding 9.15 billion people not just in the near future but also beyond. PMID:26539207

Perennial plants for biofuel production: bridging genomics and field research.

PubMed

Alves, Alexandre Alonso; Laviola, Bruno G; Formighieri, Eduardo F; Carels, Nicolas

2015-04-01

Development of dedicated perennial crops has been indicated as a strategic action to meet the growing demand for biofuels. Breeding of perennial crops,however, is often time- and resource-consuming. As genomics offers a platform from which to learn more about the relationships of genes and phenotypes,its operational use in the context of breeding programs through strategies such as genomic selection promises to foster the development of perennial crops dedicated to biodiesel production by increasing the efficiency of breeding programs and by shortening the length of the breeding cycles. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selection of Breeding Stock among Australian Purebred Dog Breeders, with Particular Emphasis on the Dam

PubMed Central

Czerwinski, Veronika; McArthur, Michelle; Smith, Bradley; Hynd, Philip; Hazel, Susan

2016-01-01

Simple Summary One of the most important factors influencing the health and welfare of puppies is the decision made by the breeder on which dam and sire they will breed from. Unfortunately, our understanding of what dog breeders consider important when selecting their dogs, particularly the dam, is limited. In order to bridge this gap, we conducted an online survey of Australian purebred dog breeders. We identified four major factors that the breeder considered important in relation to the dam: Maternal Care; Offspring Potential; Dam Temperament; and Dam Genetics and Health. Overall, the priorities and practices of dog breeders surveyed were variable across breeds. Importantly, it seemed that not all breeders understood the importance of maternal care behaviour, despite the significant role it may play on future puppy behaviour. Abstract Every year, thousands of purebred domestic dogs are bred by registered dog breeders. Yet, little is known about the rearing environment of these dogs, or the attitudes and priorities surrounding breeding practices of these dog breeders. The objective of this study was to explore some of the factors that dog breeders consider important for stock selection, with a particular emphasis on issues relating to the dam. Two-hundred and seventy-four Australian purebred dog breeders, covering 91 breeds across all Australian National Kennel Club breed groups, completed an online survey relating to breeding practices. Most breeders surveyed (76%) reported specialising in one breed of dog, the median number of dogs and bitches per breeder was two and three respectively, and most breeders bred two litters or less a year. We identified four components, relating to the dam, that were considered important to breeders. These were defined as Maternal Care, Offspring Potential, Dam Temperament, and Dam Genetics and Health. Overall, differences were observed in attitudes and beliefs across these components, showing that there is variation according to breed/breed groups. In particular, the importance of Maternal Care varied according to dog breed group. Breeders of brachycephalic breeds tended to differ the most in relation to Offspring Potential and Dam Genetics and Health. The number of breeding dogs/bitches influenced breeding priority, especially in relation to Dam Temperament, however no effect was found relating to the number of puppies bred each year. Only 24% of breeders used their own sire for breeding. The finding that some breeders did not test for diseases relevant to their breed, such as hip dysplasia in Labrador Retrievers and German Shepherds, provides important information on the need to educate some breeders, and also buyers of purebred puppies, that screening for significant diseases should occur. Further research into the selection of breeding dams and sires will inform future strategies to improve the health and behaviour of our best friend. PMID:27854338

Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass.

PubMed

Lin, Zibei; Cogan, Noel O I; Pembleton, Luke W; Spangenberg, German C; Forster, John W; Hayes, Ben J; Daetwyler, Hans D

2016-03-01

Genomic selection (GS) provides an attractive option for accelerating genetic gain in perennial ryegrass () improvement given the long cycle times of most current breeding programs. The present study used simulation to investigate the level of genetic gain and inbreeding obtained from GS breeding strategies compared with traditional breeding strategies for key traits (persistency, yield, and flowering time). Base population genomes were simulated through random mating for 60,000 generations at an effective population size of 10,000. The degree of linkage disequilibrium (LD) in the resulting population was compared with that obtained from empirical studies. Initial parental varieties were simulated to match diversity of current commercial cultivars. Genomic selection was designed to fit into a company breeding program at two selection points in the breeding cycle (spaced plants and miniplot). Genomic estimated breeding values (GEBVs) for productivity traits were trained with phenotypes and genotypes from plots. Accuracy of GEBVs was 0.24 for persistency and 0.36 for yield for single plants, while for plots it was lower (0.17 and 0.19, respectively). Higher accuracy of GEBVs was obtained for flowering time (up to 0.7), partially as a result of the larger reference population size that was available from the clonal row stage. The availability of GEBVs permit a 4-yr reduction in cycle time, which led to at least a doubling and trebling genetic gain for persistency and yield, respectively, than the traditional program. However, a higher rate of inbreeding per cycle among varieties was also observed for the GS strategy. Copyright © 2016 Crop Science Society of America.

Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers

PubMed Central

2013-01-01

Background Determining the value of livestock breeds is essential to define conservation priorities, manage genetic diversity and allocate funds. Within- and between-breed genetic diversity need to be assessed to preserve the highest intra-specific variability. Information on genetic diversity and risk status is still lacking for many Creole cattle breeds from the Americas, despite their distinct evolutionary trajectories and adaptation to extreme environmental conditions. Methods A comprehensive genetic analysis of 67 Iberoamerican cattle breeds was carried out with 19 FAO-recommended microsatellites to assess conservation priorities. Contributions to global diversity were investigated using alternative methods, with different weights given to the within- and between-breed components of genetic diversity. Information on Iberoamerican plus 15 worldwide cattle breeds was used to investigate the contribution of geographical breed groups to global genetic diversity. Results Overall, Creole cattle breeds showed a high level of genetic diversity with the highest level found in breeds admixed with zebu cattle, which were clearly differentiated from all other breeds. Within-breed kinships revealed seven highly inbred Creole breeds for which measures are needed to avoid further genetic erosion. However, if contribution to heterozygosity was the only criterion considered, some of these breeds had the lowest priority for conservation decisions. The Weitzman approach prioritized highly differentiated breeds, such as Guabalá, Romosinuano, Cr. Patagonico, Siboney and Caracú, while kinship-based methods prioritized mainly zebu-related breeds. With the combined approaches, breed ranking depended on the weights given to the within- and between-breed components of diversity. Overall, the Creole groups of breeds were generally assigned a higher priority for conservation than the European groups of breeds. Conclusions Conservation priorities differed significantly according to the weight given to within- and between-breed genetic diversity. Thus, when establishing conservation programs, it is necessary to also take into account other features. Creole cattle and local isolated breeds retain a high level of genetic diversity. The development of sustainable breeding and crossbreeding programs for Creole breeds, and the added value resulting from their products should be taken into consideration to ensure their long-term survival. PMID:24079454

‘Norman’ southern highbush blueberry

USDA-ARS?s Scientific Manuscript database

‘Norman’ is the third cultivar released from the University of Arkansas blueberry breeding program, which began in the late 1970s and has involved cooperative efforts with the U.S. Department of Agriculture (USDA). Previous cultivars released from this breeding program were ‘Ozarkblue’ and ‘Summit’....

St. Paul's Pig Pack.

ERIC Educational Resources Information Center

Miller, Penny Folley

1982-01-01

Describes a guinea pig (cavy) breeding and management program developed as part of an elementary school science curriculum. Includes comments on show competitions (sponsored by the American Rabbit Breeders Association) to measure the success of the breeding program and to enable children to experience the business world. (Author/JN)

Genotype disclosure in the genomics era: roles and responsibilities.

PubMed

Denholm, L

2017-09-01

Disclosure of affected breed without disclosure of major progenitors has been the usual practice in scientific papers reporting recessive heritable disorders of cattle. Before molecular genetics, carrier identity could not be used by breeders to control causal mutations because phenotypically normal heterozygotes among genetically related animals could not be detected other than by test mating. Accurate, low-cost DNA tests fundamentally changed this situation. Genomics can provide relief from the old problem of emerging recessive disorders in cattle breeding, but greater transparency of genotype data between breeders is necessary to fully exploit the opportunities for cost-efficient genetic disease control. Effective control of several recessive disorders has been demonstrated in Angus cattle, based entirely on voluntary DNA testing by breeders but mandatory public disclosure of test results and genotype probabilities for all registered animals. When a DNA test is available, major progenitors (particularly bulls from which semen has been distributed) should be identified and disclosed concurrently with the affected breed. As a minimum, whenever possible the closest common ancestors in the pedigrees of the parents of homozygous mutants should be disclosed after confirmation of carrier status. Progenitor disclosure in scientific publications should occur in cooperation with breed societies, which should have the opportunity to advise breeders and initiate management programs before scientific publication. Unless properly managed, genomic enhancement of animal selection using SNP markers may increase inbreeding, co-ancestry and emergence of recessive disorders. The information systems and genotype disclosure policies of some breed societies will be increasingly challenged, particularly with accelerating mutation discovery using next-generation sequencing. © 2017 State of New South Wales.

Genetic fingerprinting of potato varieties from the Northwest Potato Variety Development Program

USDA-ARS?s Scientific Manuscript database

The Northwest Potato Variety Development Program using conventional breeding has successfully released more than 40 improved varieties of potato since its inception in 1983. Potato breeders rely primarily on morphological and phenotypic data for selection and breeding of potato cultivars. With the a...

Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)

NASA Astrophysics Data System (ADS)

Jin, Yuqing; Ma, Yongpeng; Wang, Shun; Hu, Xian-Ge; Huang, Li-Sha; Li, Yue; Wang, Xiao-Ru; Mao, Jian-Feng

2016-10-01

Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.

Development of new techniques of using irradiation in the genetic improvement of warm season grasses and an assessment of the genetic and cytogenetic effects. Progress report, November 1, 1977--October 31, 1978. [Pearl millet, Bermuda-grass, and coastcross

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanna, W.W.; Burton, G.W.

1978-05-01

Progress is reported on plant breeding programs for the genetic improvement of warm season grasses using irradiation as a tool. Data are included from studies on alteration of the protein quantity and quality in pearl millet grain by irradiation and mutation breeding; the effects of nitrogen and genotype on pearl millet grain; the effects of seed size on quality in pearl millet; irradiation breeding of sterile triploid turf Bermuda grasses; irradiation breeding of sterile coastcross-1, a forage grass, to increase winter hardiness; use of irradiation to induce resistance to rust disease; and an economic assessment of irradiation-induced mutants for plantmore » breeding programs.« less

Genetic and economic benefits of selection based on performance recording and genotyping in lower tiers of multi-tiered sheep breeding schemes.

PubMed

Santos, Bruno F S; van der Werf, Julius H J; Gibson, John P; Byrne, Timothy J; Amer, Peter R

2017-01-17

Performance recording and genotyping in the multiplier tier of multi-tiered sheep breeding schemes could potentially reduce the difference in the average genetic merit between nucleus and commercial flocks, and create additional economic benefits for the breeding structure. The genetic change in a multiple-trait breeding objective was predicted for various selection strategies that included performance recording, parentage testing and genomic selection. A deterministic simulation model was used to predict selection differentials and the flow of genetic superiority through the different tiers. Cumulative discounted economic benefits were calculated based on trait gains achieved in each of the tiers and considering the extra revenue and associated costs of applying recording, genotyping and selection practices in the multiplier tier of the breeding scheme. Performance recording combined with genomic or parentage information in the multiplier tier reduced the genetic lag between the nucleus and commercial flock by 2 to 3 years. The overall economic benefits of improved performance in the commercial tier offset the costs of recording the multiplier. However, it took more than 18 years before the cumulative net present value of benefits offset the costs at current test prices. Strategies in which recorded multiplier ewes were selected as replacements for the nucleus flock did modestly increase profitability when compared to a closed nucleus structure. Applying genomic selection is the most beneficial strategy if testing costs can be reduced or by genotyping only a proportion of the selection candidates. When the cost of genotyping was reduced, scenarios that combine performance recording with genomic selection were more profitable and reached breakeven point about 10 years earlier. Economic benefits can be generated in multiplier flocks by implementing performance recording in conjunction with either DNA pedigree recording or genomic technology. These recording practices reduce the long genetic lag between the nucleus and commercial flocks in multi-tiered breeding programs. Under current genotyping costs, the time to breakeven was found to be generally very long, although this varied between strategies. Strategies using either genomic selection or DNA pedigree verification were found to be economically viable provided the price paid for the tests is lower than current prices, in the long-term.

Breeding bird populations in Missouri Ozark forests with and without clearcutting

Treesearch

Frank R., III Thompson; William D. Dijak; Thomas G. Kulowiec; David A. Hamilton

1992-01-01

Concern has arisen that forest management practices that create edge (such as clearcutting) are contributing to regional declines in neotropical migrant birds that inhabit forest interiors. Consequently, we studied breeding bird populations in an extensively forested region of southern Missouri to determine if the numbers of breeding birds differed between areas (n = 9...

Practical breeding of cottonwood in the north-central region

Treesearch

Carl A. Mohn

1973-01-01

More than 20 years ago Scott Pauley (1949) designated the genus Populus as the "guinea pig of forest-tree breeding. This designation is still appropriate as evidenced by the steady, almost overwhelming, stream of publications related to the genetics and breeding of poplars. A good indication of the scope and depth of genetic work with poplars...

Characteristics of and factors associated with dengue vector breeding sites in the City of Colombo, Sri Lanka

PubMed Central

Kusumawathie, Pad; Palihawadana, Paba; Janaki, Sakoo; Wijemuni, Ruwan; Wilder-Smith, Annelies; Tissera, Hasitha A.

2016-01-01

Introduction Dengue has emerged as a major public health problem in Sri Lanka. Vector control at community level is a frequent and widespread strategy for dengue control. The aim of the study was to assess Aedes mosquito breeding sites and the prevention practices of community members in a heavily urbanized part of Colombo. Methods A cross-sectional entomological survey was conducted from April to June 2013 in 1469 premises located in a subdistrict of the City of Colombo. Types of breeding sites and, where found, their infestation with larvae or pupae were recorded. Furthermore, a questionnaire was administered to the occupants of these premises to record current practices of dengue vector control. Results The surveyed premises consisted of 1341 residential premises and 110 non-residential premises (11 schools, 99 work or public sites), 5 open lands, and 13 non-specified. In these 1469 premises, 15447 potential breeding sites suitable to host larvae of pupae were found; of these sites18.0% contained water. Among the 2775 potential breeding sites that contained water, 452 (16.3%) were positive for larvae and/or pupae. Schools were associated with the proportionally highest number of breeding sites; 85 out of 133 (63.9%) breeding sites were positive for larvae and/or pupae in schools compared with 338 out of 2288 (14.8%) in residential premises. The odds ratio (OR) for schools and work or public sites for being infested with larvae and/or pupae was 2.77 (95% CI 1.58, 4.86), when compared to residential premises. Occupants of 80.8% of the residential premises, 54.5% of the schools and 67.7% of the work or public sites reported using preventive measures. The main prevention practices were coverage of containers and elimination of mosquito breeding places. Occupants of residential premises were much more likely to practice preventive measures than were those of non-residential premises (OR 2.23; 1.49, 3.36). Conclusion Schools and working sites were associated with the highest numbers of breeding sites and lacked preventive measures for vector control. In addition to pursuing vector control measures at residential level, public health strategies should be expanded in schools and work places. PMID:27241954

Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles.

PubMed

Hoffert, Jason D; Pisitkun, Trairak; Miller, R Lance

2012-06-01

Transgenic and conditional knockout mouse models play an important role in biomedical research and their use has grown exponentially in the last 5-10 years. Generating conditional knockouts often requires breeding multiple alleles onto the background of a single mouse or group of mice. Breeding these mice depends on parental genotype, litter size, transmission frequency, and the number of breeding rounds. Therefore, a well planned breeding strategy is critical for keeping costs to a minimum. However, designing a viable breeding strategy can be challenging. With so many different variables this would be an ideal task for a computer program. To facilitate this process, we created a Java-based program called Conditional Allele Mouse Planner (CAMP). CAMP is designed to provide an estimate of the number of breeders, amount of time, and costs associated with generating mice of a particular genotype. We provide a description of CAMP, how to use it, and offer it freely as an application.

Initial experiences utilizing exotic landrace germplasm in an upland cotton breeding program

USDA-ARS?s Scientific Manuscript database

A critical objective of plant breeding programs is accessing new sources of genetic variation. In upland cotton, one of the relatively untapped sources of genetic variation is maintained in the USDA-ARS cotton germplasm collection and is the exotic landrace collection. Photoperiod sensitivity is a m...

Increased use of young bulls in dairy cattle breeding programs

USDA-ARS?s Scientific Manuscript database

Availability of genomic evaluations since 2008 has provided many benefits with regard to improving the rate of genetic gain in dairy cattle breeding programs, one of which is a greater accuracy for young animals. As a result, AI organizations have been aggressively promoting young bulls and producer...

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

USDA-ARS?s Scientific Manuscript database

Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental populations are typically unrepli...

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

USDA-ARS?s Scientific Manuscript database

Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental families are typically unreplicat...

The plant breeding industry after pure line theory: Lessons from the National Institute of Agricultural Botany.

PubMed

Berry, Dominic

2014-06-01

In the early twentieth century, Wilhelm Johannsen proposed his pure line theory and the genotype/phenotype distinction, work that is prized as one of the most important founding contributions to genetics and Mendelian plant breeding. Most historians have already concluded that pure line theory did not change breeding practices directly. Instead, breeding became more orderly as a consequence of pure line theory, which structured breeding programmes and eliminated external heritable influences. This incremental change then explains how and why the large multi-national seed companies that we know today were created; pure lines invited standardisation and economies of scale that the latter were designed to exploit. Rather than focus on breeding practice, this paper examines the plant varietal market itself. It focusses upon work conducted by the National Institute of Agricultural Botany (NIAB) during the interwar years, and in doing so demonstrates that, on the contrary, the pure line was actually only partially accepted by the industry. Moreover, claims that contradicted the logic of the pure line were not merely tolerated by the agricultural geneticists affiliated with NIAB, but were acknowledged and legitimised by them. The history of how and why the plant breeding industry was transformed remains to be written. Copyright © 2014 Elsevier Ltd. All rights reserved.

Prevalence and inheritance of and selection for hip dysplasia in seven breeds of dogs in Sweden and benefit: cost analysis of a screening and control program.

PubMed

Swenson, L; Audell, L; Hedhammar, A

1997-01-15

To determine the prevalence and changes over time in the prevalence of hip dysplasia; to ascertain whether prevalence or severity of hip dysplasia was associated with sex of the dogs, age at which coxofemoral joint status was evaluated, or ancestral background; to determine the effects of selective breeding; and to conduct an economic evaluation of the hip dysplasia program operated by the Swedish Kennel Club. Analysis of radiographic evaluations of coxofemoral joint conformity. 83,229 dogs from 7 breeds registered by the Swedish Kennel Club. All radiographs were scrutinized by a single radiologist (LA), and coxofemoral joint conformation was classified as normal or dysplastic, with the degree of dysplasia classified as 1,2,3, or 4. Decreasing prevalence of hip dysplasia corresponding to selection of breeding stock and high heritabilities was found. Sex differences were documented in 3 of the breeds. This was interpreted as breed differences in the distribution of genes related to hip dysplasia. Economic analyses showed that costs of screening and registration of coxofemoral joints was less than the value of dogs estimated to have been saved from moderate, severe, or very severe hip dysplasia in 6 of the breeds. Documented effects of age suggest that all dogs should be screened at the same age, rather than screening a few dogs at an older, more revealing age. In screening and control programs based on an open registry with access to family records, decreasing prevalence of hip dysplasia can be expected, and related to selection of breeding stock.

Mitigation of inbreeding while preserving genetic gain in genomic breeding programs for outbred plants.

PubMed

Lin, Zibei; Shi, Fan; Hayes, Ben J; Daetwyler, Hans D

2017-05-01

Heuristic genomic inbreeding controls reduce inbreeding in genomic breeding schemes without reducing genetic gain. Genomic selection is increasingly being implemented in plant breeding programs to accelerate genetic gain of economically important traits. However, it may cause significant loss of genetic diversity when compared with traditional schemes using phenotypic selection. We propose heuristic strategies to control the rate of inbreeding in outbred plants, which can be categorised into three types: controls during mate allocation, during selection, and simultaneous selection and mate allocation. The proposed mate allocation measure GminF allocates two or more parents for mating in mating groups that minimise coancestry using a genomic relationship matrix. Two types of relationship-adjusted genomic breeding values for parent selection candidates ([Formula: see text]) and potential offspring ([Formula: see text]) are devised to control inbreeding during selection and even enabling simultaneous selection and mate allocation. These strategies were tested in a case study using a simulated perennial ryegrass breeding scheme. As compared to the genomic selection scheme without controls, all proposed strategies could significantly decrease inbreeding while achieving comparable genetic gain. In particular, the scenario using [Formula: see text] in simultaneous selection and mate allocation reduced inbreeding to one-third of the original genomic selection scheme. The proposed strategies are readily applicable in any outbred plant breeding program.

Application of selection index calculations to determine selection strategies in genomic breeding programs.

PubMed

König, S; Swalve, H H

2009-10-01

The availability of genomic estimated breeding values (GEBV) allows for possible modifications to existing dairy cattle breeding programs. Selection index calculations including genomic and phenotypic observations as index sources were used to determine the optimal number of offspring per genotyped sire with a focus on functional traits and the design of cooperator herds, and to evaluate the importance of a central station test for genotyped bull dams. Evaluation criteria to compare different breeding strategies were correlations between index and aggregate genotype (r(TI)), and the relative selection response percentage (RSR) of an index without single nucleotide polymorphism information in relation to a single nucleotide polymorphism-based index. The number of required daughter records per sire to achieve a predefined r(TI) strongly depends on the accuracy of GEBV (r(mg)) and the heritability of the trait. For a desired r(TI) of 0.8, h(2) = 0.10, and r(mg) = 0.5, at least 57 additional daughters have to be included in the genetic evaluation. Daughter records of genotyped sires are not necessary for optimal scenarios where r(mg) is greater than or equal to r(TI). There still is a substantial need for phenotypic daughter records, especially for low-heritability functional traits and r(mg) < 0.7. Phenotypic records from genotyped potential bull dams have no relevance for increasing r(TI), even with a low value for r(mg) of 0.5. Hence, genomic breeding programs should focus on recording functional traits within progeny groups, preferably in cooperator herds. For low-heritability traits and with r(mg) > 0.7, the RSR of conventional breeding programs was only 10% of RSR from genomic breeding strategies. As shown in scenarios including 2 traits in the index as well as in the aggregate genotype, the availability of highly accurate GEBV for production traits and low-accuracy GEBV for functional traits increased the risk of widening the gap between selection responses in production and functionality. Counteractions are possible, such as via higher economic weights for low-heritability functional traits. Finally, an alternative selection strategy considering only 2 pathways of selection for genotyped male calves and for cow dams was evaluated. This strategy is competitive with a 4-pathway genomic breeding program if the fraction of selected male calves for the artificial insemination program is below 1% and if selection is focused on functionality, thus pointing to substantial insufficiencies caused by low reliabilities of breeding values for cows for such traits in conventional bull dam selection schemes.

Tilting at windmills: 20 years of Hippeastrum breeding

USDA-ARS?s Scientific Manuscript database

Hippeastrum Herbert, amaryllis, has yielded popular large-flowered hybrids over a 200-year breeding history, with the Netherlands and South Africa currently dominating the market. The USDA breeding program is now almost ten years old, built upon a ten-year previous history at the University of Flori...

A role for selective contraception of individuals in conservation.

PubMed

Cope, Holly R; Hogg, Carolyn J; White, Peter J; Herbert, Catherine A

2018-06-01

Contraception has an established role in managing overabundant populations and preventing undesirable breeding in zoos. We propose that it can also be used strategically and selectively in conservation to increase the genetic and behavioral quality of the animals. In captive breeding programs, it is becoming increasingly important to maximize the retention of genetic diversity by managing the reproductive contribution of each individual and preventing genetically suboptimal breeding through the use of selective contraception. Reproductive suppression of selected individuals in conservation programs has further benefits of allowing animals to be housed as a group in extensive enclosures without interfering with breeding recommendations, which reduces adaptation to captivity and facilitates the expression of wild behaviors and social structures. Before selective contraception can be incorporated into a breeding program, the most suitable method of fertility control must be selected, and this can be influenced by factors such as species life history, age, ease of treatment, potential for reversibility, and desired management outcome for the individual or population. Contraception should then be implemented in the population following a step-by-step process. In this way, it can provide crucial, flexible control over breeding to promote the physical and genetic health and sustainability of a conservation dependent species held in captivity. For Tasmanian devils (Sarcophilus harrisii), black-flanked rock wallabies (Petrogale lateralis), and burrowing bettongs (Bettongia lesueur), contraception can benefit their conservation by maximizing genetic diversity and behavioral integrity in the captive breeding program, or, in the case of the wallabies and bettongs, by reducing populations to a sustainable size when they become locally overabundant. In these examples, contraceptive duration relative to reproductive life, reversibility, and predictability of the contraceptive agent being used are important to ensure the potential for individuals to reproduce following cessation of contraception, as exemplified by the wallabies when their population crashed and needed females to resume breeding. © 2017 Society for Conservation Biology.

Biochemical identification of mallard-black duck hybrids through a breeding program and in nature

USGS Publications Warehouse

Morgan, R.P.; Meritt, D.W.; Block, S.B.; Cole, M.

1978-01-01

From 1974 to 1976, a breeding program was used to produce black duck-mallard hybrids for the evaluation of inheritance patterns of serum proteins and esterases. In addition to the initial crosses, a series of matings in 1975 and 1976 were designed to evaluate inheritance patterns in hybrid matings with either black duck or mallards. At the F1 level, hybrids were easily distinguished. However, mallard or black duck crosses with hybrids were detectable as hybrids in only 11.5 - 22.6% of the progeny using serum proteins, and 22.6 - 38.8% using serum esterases. Concurrent with the breeding program, a field survey indicated hybrid frequencies ranging from 4% to 28%.

BREEDING AND GENETICS SYMPOSIUM: Climate change and selective breeding in aquaculture.

PubMed

Sae-Lim, P; Kause, A; Mulder, H A; Olesen, I

2017-04-01

Aquaculture is the fastest growing food production sector and it contributes significantly to global food security. Based on Food and Agriculture Organization (FAO) of the United Nations, aquaculture production must increase significantly to meet the future global demand for aquatic foods in 2050. According to Intergovernmental Panel on Climate Change (IPCC) and FAO, climate change may result in global warming, sea level rise, changes of ocean productivity, freshwater shortage, and more frequent extreme climate events. Consequently, climate change may affect aquaculture to various extents depending on climatic zones, geographical areas, rearing systems, and species farmed. There are 2 major challenges for aquaculture caused by climate change. First, the current fish, adapted to the prevailing environmental conditions, may be suboptimal under future conditions. Fish species are often poikilothermic and, therefore, may be particularly vulnerable to temperature changes. This will make low sensitivity to temperature more important for fish than for livestock and other terrestrial species. Second, climate change may facilitate outbreaks of existing and new pathogens or parasites. To cope with the challenges above, 3 major adaptive strategies are identified. First, general 'robustness' will become a key trait in aquaculture, whereby fish will be less vulnerable to current and new diseases while at the same time thriving in a wider range of temperatures. Second, aquaculture activities, such as input power, transport, and feed production contribute to greenhouse gas emissions. Selection for feed efficiency as well as defining a breeding goal that minimizes greenhouse gas emissions will reduce impacts of aquaculture on climate change. Finally, the limited adoption of breeding programs in aquaculture is a major concern. This implies inefficient use of resources for feed, water, and land. Consequently, the carbon footprint per kg fish produced is greater than when fish from breeding programs would be more heavily used. Aquaculture should use genetically improved and robust organisms not suffering from inbreeding depression. This will require using fish from well-managed selective breeding programs with proper inbreeding control and breeding goals. Policymakers and breeding organizations should provide incentives to boost selective breeding programs in aquaculture for more robust fish tolerating climatic change.

Genetic conservation in applied tree breeding programs.

Treesearch

R. Johnson; B. St. Clair; S. Lipow

2001-01-01

This paper reviews how population size and structure impacts the maintenance of genetic variation in breeding and gene resource populations. We discuss appropriate population sizes for low frequency alleles and point out some examples of low frequency alleles in the literature. Development of appropriate breeding populations and gene resource populations are discussed...

The development of genomics applied to dairy breeding

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) has profoundly changed dairy cattle breeding in the last decade and can be defined as the use of genomic breeding values (GEBV) in selection programs. The GEBV is the sum of the effects of dense DNA markers across the whole genome, capturing all the quantitative trait loci (QT...

Using Economics and Genetics To Produce Leaner Pork.

ERIC Educational Resources Information Center

Welch, Mary A., Ed.

1994-01-01

The booklet describes the STAGES (Swine Testing and Genetic Evaluation System) program developed at Purdue University (Indiana), along with the USDA, National Pork Producers Council and swine breed associations. By selecting breeding stock from a coded catalogue developed by STAGES, producers are able to select the best breeding stock for more…

Breeding Perspectives and Programs at East Lansing

USDA-ARS?s Scientific Manuscript database

USDA-ARS sugar beet breeding activities for both Aphanomyces resistance and CMS/O-type conversion at East Lansing reach back to the 1940’s, with variety testing activities at Michigan State University reaching back to circa 1911. Many of those contributions are well known in the sugar beet breeding ...

Increasing the efficiency of traditional cacao breeding using whole genome sequencing information.

USDA-ARS?s Scientific Manuscript database

Unfortunately, 80% of the genotypes from the "hybrid seeds" are unproductive in farmers' fields. In 1999 the USDA and Mars Inc. initiated a Marker Assisted Selection (MAS) program for cacao that has reduces many of the problems in traditional breeding. One limitation of the MAS program is the distan...

Phenotypic evidence suggests a possible major-gene element to weevil resistance in Sitka spruce

Treesearch

John N. King; René I. Alfaro; Peter Ott; Lara vanAkker

2012-01-01

The weevil resistance breeding program against the white pine weevil, Pissodes strobi Peck (Coleoptera: Curculionidae), particularly for Sitka spruce (Picea sitchensis (Bong.) Carr), is arguably one of the most successful pest resistance breeding programs for plantation forest species, and it has done a lot to rehabilitate...

Applying SNP marker technology in the cacao breeding program at the Cocoa Research Institute of Ghana

USDA-ARS?s Scientific Manuscript database

In this investigation 45 parental cacao plants and five progeny derived from the parental stock studied were genotyped using six SNP markers to determine off-types or mislabeled clones and to authenticate crosses made in the Cocoa Research Institute of Ghana (CRIG) breeding program. Investigation wa...

Varieties from the USDA are the foundation of the Florida specialty citrus industry

USDA-ARS?s Scientific Manuscript database

The Florida citrus industry is poised to grow diverse new cultivars from the USDA breeding program, the University of Florida breeding program, and from importation of budwood from new selections from around the world. The top six cultivars of specialty citrus from the USDA (‘Murcott’, ‘Sunburst’, ‘...

The forest and the trees: Applications for molecular markers in the Pecan Breeding Program

USDA-ARS?s Scientific Manuscript database

Inventory specific verification of accession identity is crucial to the function of the National Collection of Genetic Resources (NCGR) for Pecans and Hickories, and is an increasingly important component of the USDA ARS Pecan Breeding Program. The foundation of the NCGR is the living trees maintai...

Developments in amphibian captive breeding and reintroduction programs.

PubMed

Harding, Gemma; Griffiths, Richard A; Pavajeau, Lissette

2016-04-01

Captive breeding and reintroduction remain high profile but controversial conservation interventions. It is important to understand how such programs develop and respond to strategic conservation initiatives. We analyzed the contribution to conservation made by amphibian captive breeding and reintroduction since the launch of the International Union for Conservation of Nature (IUCN) Amphibian Conservation Action Plan (ACAP) in 2007. We assembled data on amphibian captive breeding and reintroduction from a variety of sources including the Amphibian Ark database and the IUCN Red List. We also carried out systematic searches of Web of Science, JSTOR, and Google Scholar for relevant literature. Relative to data collected from 1966 to 2006, the number of species involved in captive breeding and reintroduction projects increased by 57% in the 7 years since release of the ACAP. However, there have been relatively few new reintroductions over this period; most programs have focused on securing captive-assurance populations (i.e., species taken into captivity as a precaution against extinctions in the wild) and conservation-related research. There has been a shift to a broader representation of frogs, salamanders, and caecilians within programs and an increasing emphasis on threatened species. There has been a relative increase of species in programs from Central and South America and the Caribbean, where amphibian biodiversity is high. About half of the programs involve zoos and aquaria with a similar proportion represented in specialist facilities run by governmental or nongovernmental agencies. Despite successful reintroduction often being regarded as the ultimate milestone for such programs, the irreversibility of many current threats to amphibians may make this an impractical goal. Instead, research on captive assurance populations may be needed to develop imaginative solutions to enable amphibians to survive alongside current, emerging, and future threats. © 2015 Society for Conservation Biology.

Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice

PubMed Central

Shrestha, Rosemary; Matteis, Luca; Skofic, Milko; Portugal, Arllet; McLaren, Graham; Hyman, Glenn; Arnaud, Elizabeth

2012-01-01

The Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) is developed for the Integrated Breeding Platform (IBP) (http://www.integratedbreeding.net/) by several centers of The Consultative Group on International Agricultural Research (CGIAR): bioversity, CIMMYT, CIP, ICRISAT, IITA, and IRRI. Integrated breeding necessitates that breeders access genotypic and phenotypic data related to a given trait. The CO provides validated trait names used by the crop communities of practice (CoP) for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries. The trait information is completed by the description of the measurement methods and scales, and images. The trait dictionaries used to produce the Integrated Breeding (IB) fieldbooks are synchronized with the CO terms for an automatic annotation of the phenotypic data measured in the field. The IB fieldbook provides breeders with direct access to the CO to get additional descriptive information on the traits. Ontologies and trait dictionaries are online for cassava, chickpea, common bean, groundnut, maize, Musa, potato, rice, sorghum, and wheat. Online curation and annotation tools facilitate (http://cropontology.org) direct maintenance of the trait information and production of trait dictionaries by the crop communities. An important feature is the cross referencing of CO terms with the Crop database trait ID and with their synonyms in Plant Ontology (PO) and Trait Ontology (TO). Web links between cross referenced terms in CO provide online access to data annotated with similar ontological terms, particularly the genetic data in Gramene (University of Cornell) or the evaluation and climatic data in the Global Repository of evaluation trials of the Climate Change, Agriculture and Food Security programme (CCAFS). Cross-referencing and annotation will be further applied in the IBP. PMID:22934074

The use of integer programming to select bulls across breeding companies with volume price discounts.

PubMed

McConnel, M B; Galligan, D T

2004-10-01

Optimization programs are currently used to aid in the selection of bulls to be used in herd breeding programs. While these programs offer a systematic approach to the problem of semen selection, they ignore the impact of volume discounts. Volume discounts are discounts that vary depending on the number of straws purchased. The dynamic nature of volume discounts means that, in order to be adequately accounted for, they must be considered in the optimization routine. Failing to do this creates a missed economic opportunity because the potential benefits of optimally selecting and combining breeding company discount opportunities are not captured. To address these issues, an integer program was created which used binary decision variables to incorporate the effects of quantity discounts into the optimization program. A consistent set of trait criteria was used to select a group of bulls from 3 sample breeding companies. Three different selection programs were used to select the bulls, 2 traditional methods and the integer method. After the discounts were applied using each method, the integer program resulted in the lowest cost portfolio of bulls. A sensitivity analysis showed that the integer program also resulted in a low cost portfolio when the genetic trait goals were changed to be more or less stringent. In the sample application, a net benefit of the new approach over the traditional approaches was a 12.3 to 20.0% savings in semen cost.

Review of functional markers for improving cooking, eating, and the nutritional qualities of rice

PubMed Central

Lau, Wendy C. P.; Rafii, Mohd Y.; Ismail, Mohd R.; Puteh, Adam; Latif, Mohammad A.; Ramli, Asfaliza

2015-01-01

After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers’ preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated. PMID:26528304

Genome characterization of Sugarcane Yellow Leaf Virus with special reference to RNAi based molecular breeding.

PubMed

Khalil, Farghama; Yueyu, Xu; Naiyan, Xiao; Di, Liu; Tayyab, Muhammad; Hengbo, Wang; Islam, Waqar; Rauf, Saeed; Pinghua, Chen

2018-05-04

Sugarcane is an essential crop for sugar and biofuel. Globally, its production is severely affected by sugarcane yellow leaf disease (SCYLD) caused by Sugarcane Yellow Leaf Virus (SCYLV). Many aphid vectors are involved in the spread of the disease which reduced the effectiveness of cultural and chemical management. Empirical methods of plant breeding such as introgression from wild and cultivated germplasm were not possible or at least challenging due to the absence of resistance in cultivated and wild germplasm of sugarcane. RNA interference (RNAi) transformation is an effective method to create virus-resistant varieties. Nevertheless, limited progress has been made due to lack of comprehensive research program on SCYLV based on RNAi technique. In order to show improvement and to propose future strategies for the feasibility of the RNAi technique to cope SCYLV, genome-wide consensus sequences of SCYLV were analyzed through GenBank. The coverage rates of every consensus sequence in SCYLV isolates were calculated to evaluate their practicability. Our analysis showed that single consensus sequence from SCYLV could not work well for RNAi based sugarcane breeding programs. This may be due to high mutation rate and continuous recombination within and between various viral strains. Alternative multi-target RNAi strategy is suggested to combat several strains of the viruses and to reduce the silencing escape. The multi-target small interfering RNA (siRNA) can be used together to construct RNAi plant expression plasmid, and to transform sugarcane tissues to develop new sugarcane varieties resistant to SCYLV. Copyright © 2018 Elsevier Ltd. All rights reserved.

Management practices associated with conception rate and service rate of lactating Holstein cows in large, commercial dairy herds.

PubMed

Schefers, J M; Weigel, K A; Rawson, C L; Zwald, N R; Cook, N B

2010-04-01

Data from lactating Holstein cows in herds that participate in a commercial progeny testing program were analyzed to explain management factors associated with herd-average conception and service rates on large commercial dairies. On-farm herd management software was used as the source of data related to production, reproduction, culling, and milk quality for 108 herds. Also, a survey regarding management, facilities, nutrition, and labor was completed on 86 farms. A total of 41 explanatory variables related to management factors and conditions that could affect conception and service rate were considered in this study. Models explaining conception and service rates were developed using a machine learning algorithm for constructing model trees. The most important explanatory variables associated with conception rate were the percentage of repeated inseminations between 4 and 17 d post-artificial insemination, stocking density in the breeding pen, length of the voluntary waiting period, days at pregnancy examination, and somatic cell score. The most important explanatory variables associated with service rate were the number of lactating cows per breeding technician, use of a resynchronization program, utilization of soakers in the holding area during the summer, and bunk space per cow in the breeding pen. The aforementioned models explained 35% and 40% of the observed variation in conception rate and service rate, respectively, and underline the association of herd-level management factors not strictly related to reproduction with herd reproductive performance. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Characterization of smallholder pig breeding practices within a rural commune of North Central Vietnam.

PubMed

Ieda, Nahoko; Van Bui, Quang; Nguyen, Nga Thi Duong; Lapar, Lucy; Marshall, Karen

2015-08-01

This case study focused on a pig production system in a rural area of North Central Vietnam, with a focus on describing household pig breeding practices and estimating herd demographic parameters, particularly on reproduction. One hundred five households undertaking small-scale piglet production were surveyed, with information gathered on 3268 individual pigs. Pig keeping contributed variably to the overall household livelihood portfolio, with female household members as the main decision makers, contributors to labor, and beneficiaries of income from the pig enterprise. All households kept between one and four young or adult sows, with 69% of these sows of a local breed type (predominantly Mong Cai), 28% a cross between a local sow and an exotic sow (predominantly Large White), and the remainder (3%) as exotic sows. Eighty-eight percent of the piglets produced were cross-bred, while 12% were local breed. No adult males were kept by the surveyed households, reflecting the common use of artificial insemination for mating purposes. The most common breeding system practiced-the keeping of Mong Cai females and production of cross-bred piglets-capitalizes on the small body size and high fecundity of the sows and the fast growth rate and leanness of the cross-bred piglets. The survey tool used, which was based on farmer recall of events over the preceding 12-month period, appeared to give reasonable results although some recall bias could be detected. This case study will serve as an entry point to planned broader scale characterization and development of pig breeding systems in North Central Vietnam.

TILLING for plant breeding.

PubMed

Sharp, Peter; Dong, Chongmei

2014-01-01

TILLING is widely used in plant functional genomics. Mutagenesis and SNP detection is combined to allow for the isolation of mutations in genes of interest. It can also be used as a plant breeding tool, whereby variation in known or candidate genes of interest to breeding programs is generated. Here we describe a simple low-cost TILLING procedure.

Breeding for improved potato nutrition: High amylose starch potatoes show promise as fiber source

USDA-ARS?s Scientific Manuscript database

Potato starch is composed of approximately 75% amylopectin and 25% amylose. We are interested in breeding for higher amylose content, which would increase the fiber content of potato and decrease glycemic index. In order to make progress in a breeding program, we have developed a high throughput ass...

A matter of taste: Improving flavor of fresh potatoes

USDA-ARS?s Scientific Manuscript database

Breeding for improved potato flavor has not been a high priority in US breeding programs. It is a difficult trait to breed for because it cannot be done in a high throughput manner and it requires an understanding of the complex biochemistry of flavor compounds and effects of cooking on those compou...

Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing.

PubMed

Li, Shan; Zheng, Yun-Chao; Cui, Hai-Rui; Fu, Hao-Wei; Shu, Qing-Yao; Huang, Jian-Zhong

Mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding program. Although γ ray irradiation has been widely used since the 1960s in the breeding of about 200 economically important plant species, molecular elucidation of its genetic effects has so far been achieved largely by analysis of target genes or genomic regions. In the present study, the whole genomes of six γ-irradiated M 2 rice plants were sequenced; a total of 144-188 million high-quality (Q>20) reads were generated for each M 2 plant, resulting in genome coverage of >45 times for each plant. Single base substitution (SBS) and short insertion/deletion (Indel) mutations were detected at the average frequency of 7.5×10 -6 -9.8×10 -6 in the six M 2 rice plants (SBS being about 4 times more frequent than Indels). Structural and copy number variations, though less frequent than SBS and Indel, were also identified and validated. The mutations were scattered in all genomic regions across 12 rice chromosomes without apparent hotspots. The present study is the first genome-wide single-nucleotide resolution study on the feature and frequency of γ irradiation-induced mutations in a seed propagated crop; the findings are of practical importance for mutation breeding of rice and other crop species.

9 CFR 145.93 - Terminology and classification; flocks and products.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Influenza Clean. This program is intended to be the basis from which the breeding-hatchery industry may conduct a program for the prevention and control of the H5/H7 subtypes of avian influenza. It is intended to determine the presence of the H5/H7 subtypes of avian influenza in meat-type waterfowl breeding...

9 CFR 145.93 - Terminology and classification; flocks and products.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Influenza Clean. This program is intended to be the basis from which the breeding-hatchery industry may conduct a program for the prevention and control of the H5/H7 subtypes of avian influenza. It is intended to determine the presence of the H5/H7 subtypes of avian influenza in meat-type waterfowl breeding...

9 CFR 145.93 - Terminology and classification; flocks and products.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Influenza Clean. This program is intended to be the basis from which the breeding-hatchery industry may conduct a program for the prevention and control of the H5/H7 subtypes of avian influenza. It is intended to determine the presence of the H5/H7 subtypes of avian influenza in meat-type waterfowl breeding...

Validation and Implementation of Marker-Assisted Selection (MAS) for PVY Resistance (Ryadg gene) in a Tetraploid Potato Breeding Program

USDA-ARS?s Scientific Manuscript database

The gene Ryadg from S. tuberosum ssp. andigena provides extreme resistance to PVY. This gene has been mapped to chromosome XI and linked PCR-based DNA markers have been identified. Advanced tetraploid russeted potato clones developed by the U.S. Pacific Northwest Potato Breeding Program with Ryadg P...

A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON)

PubMed Central

Flury, Christine; Matasci, Giona; Joerin, Florent; Widmer, Ivo; Joost, Stéphane

2017-01-01

Background In 2007, the Food and Agriculture Organization of the United Nations (FAO) initiated the Global plan of action for Farm Animal Genetic Resources (FAnGR). The main goal of this plan is to reduce further loss of genetic diversity in farm animals, so as to protect and promote the diversity of farm animal resources. An important step to reach this goal is to monitor and prioritize endangered breeds in the context of conservation programs. Methodology/Web portal implementation The GENMON WebGIS platform is able to monitor FAnGR and to evaluate the degree of endangerment of livestock breeds. The system takes into account pedigree and introgression information, the geographical concentration of animals, the cryo-conservation plan and the sustainability of breeding activities based on socio-economic data as well as present and future land use conditions. A multi-criteria decision tool supports the aggregation of the multi-thematic indices mentioned above using the MACBETH method, which is based on a weighted average using satisfaction thresholds. GENMON is a monitoring tool to reach subjective decisions made by a government agency. It relies on open source software and is available at http://lasigsrv2.epfl.ch/genmon-ch. Results/Significance GENMON allows users to upload pedigree-information (animal ID, parents, birthdate, sex, location and introgression) from a specific livestock breed and to define species and/or region-specific weighting parameters and thresholds. The program then completes a pedigree analysis and derives several indices that are used to calculate an integrated score of conservation prioritization for the breeds under investigation. The score can be visualized on a geographic map and allows a fast, intuitive and regional identification of breeds in danger. Appropriate conservation actions and breeding programs can thus be undertaken in order to promote the recovery of the genetic diversity in livestock breeds in need. The use of the platform is illustrated by means of an example based on three local livestock breeds from different species in Switzerland. PMID:28453561

A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON).

PubMed

Duruz, Solange; Flury, Christine; Matasci, Giona; Joerin, Florent; Widmer, Ivo; Joost, Stéphane

2017-01-01

In 2007, the Food and Agriculture Organization of the United Nations (FAO) initiated the Global plan of action for Farm Animal Genetic Resources (FAnGR). The main goal of this plan is to reduce further loss of genetic diversity in farm animals, so as to protect and promote the diversity of farm animal resources. An important step to reach this goal is to monitor and prioritize endangered breeds in the context of conservation programs. The GENMON WebGIS platform is able to monitor FAnGR and to evaluate the degree of endangerment of livestock breeds. The system takes into account pedigree and introgression information, the geographical concentration of animals, the cryo-conservation plan and the sustainability of breeding activities based on socio-economic data as well as present and future land use conditions. A multi-criteria decision tool supports the aggregation of the multi-thematic indices mentioned above using the MACBETH method, which is based on a weighted average using satisfaction thresholds. GENMON is a monitoring tool to reach subjective decisions made by a government agency. It relies on open source software and is available at http://lasigsrv2.epfl.ch/genmon-ch. GENMON allows users to upload pedigree-information (animal ID, parents, birthdate, sex, location and introgression) from a specific livestock breed and to define species and/or region-specific weighting parameters and thresholds. The program then completes a pedigree analysis and derives several indices that are used to calculate an integrated score of conservation prioritization for the breeds under investigation. The score can be visualized on a geographic map and allows a fast, intuitive and regional identification of breeds in danger. Appropriate conservation actions and breeding programs can thus be undertaken in order to promote the recovery of the genetic diversity in livestock breeds in need. The use of the platform is illustrated by means of an example based on three local livestock breeds from different species in Switzerland.

Acceleration of genetic gain in cattle by reduction of generation interval.

PubMed

Kasinathan, Poothappillai; Wei, Hong; Xiang, Tianhao; Molina, Jose A; Metzger, John; Broek, Diane; Kasinathan, Sivakanthan; Faber, David C; Allan, Mark F

2015-03-02

Genomic selection (GS) approaches, in combination with reproductive technologies, are revolutionizing the design and implementation of breeding programs in livestock species, particularly in cattle. GS leverages genomic readouts to provide estimates of breeding value early in the life of animals. However, the capacity of these approaches for improving genetic gain in breeding programs is limited by generation interval, the average age of an animal when replacement progeny are born. Here, we present a cost-effective approach that combines GS with reproductive technologies to reduce generation interval by rapidly producing high genetic merit calves.

Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations

PubMed Central

Collard, Bert C. Y.; Vera Cruz, Casiana M.; McNally, Kenneth L.; Virk, Parminder S.; Mackill, David J.

2008-01-01

Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information—coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools—provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to “bridge the application gap” between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs. PMID:18528527

Effects of parental number and duration of the breeding period on the effective population size and genetic diversity of a captive population of the endangered Tokyo bitterling Tanakia tanago (Teleostei: Cyprinidae).

PubMed

Kubota, Hitoshi; Watanabe, Katsutoshi

2012-01-01

The maintenance of genetic diversity is one of the chief concerns in the captive breeding of endangered species. Using microsatellite and mtDNA markers, we examined the effects of two key variables (parental number and duration of breeding period) on effective population size (N(e) ) and genetic diversity of offspring in an experimental breeding program for the endangered Tokyo bitterling, Tanakia tanago. Average heterozygosity and number of alleles of offspring estimated from microsatellite data increased with parental number in a breeding aquarium, and exhibited higher values for a long breeding period treatment (9 weeks) compared with a short breeding period (3 weeks). Haplotype diversity in mtDNA of offspring decreased with the reduction in parental number, and this tendency was greater for the short breeding period treatment. Genetic estimates of N(e) obtained with two single-sample estimation methods were consistently higher for the long breeding period treatment with the same number of parental fish. Average N(e) /N ratios were ranged from 0.5 to 1.4, and were high especially in the long breeding period with small and medium parental number treatments. Our results suggest that the spawning intervals of females and alternative mating behaviors of males influence the effective size and genetic diversity of offspring in bitterling. To maintain the genetic diversity of captive T. tanago, we recommend that captive breeding programs should be conducted for a sufficiently long period with an optimal level of parental density, as well as using an adequate number of parents. © 2011 Wiley Periodicals, Inc.

There is room for selection in a small local pig breed when using optimum contribution selection: a simulation study.

PubMed

Gourdine, J L; Sørensen, A C; Rydhmer, L

2012-01-01

Selection progress must be carefully balanced against the conservation of genetic variation in small populations of local breeds. Well-defined breeding programs with specified selection traits are rare in local pig breeds. Given the small population size, the focus is often on the management of genetic diversity. However, in local breeds, optimum contribution selection can be applied to control the rate of inbreeding and to avoid reduced performance in traits with high market value. The aim of this study was to assess the extent to which a breeding program aiming for improved product quality in a small local breed would be feasible. We used stochastic simulations to compare 25 scenarios. The scenarios differed in size of population, selection intensity of boars, type of selection (random selection, truncation selection based on BLUP breeding values, or optimum contribution selection based on BLUP breeding values), and heritability of the selection trait. It was assumed that the local breed is used in an extensive system for a high-meat-quality market. The simulations showed that in the smallest population (300 female reproducers), inbreeding increased by 0.8% when selection was performed at random. With optimum contribution selection, genetic progress can be achieved that is almost as great as that with truncation selection based on BLUP breeding values (0.2 to 0.5 vs. 0.3 to 0.5 genetic SD, P < 0.05), but at a considerably decreased rate of inbreeding (0.7 to 1.2 vs. 2.3 to 5.7%, P < 0.01). This confirmation of the potential utilization of OCS even in small populations is important in the context of sustainable management and the use of animal genetic resources.

Defining a breeding objective for Nile tilapia that takes into account the diversity of smallholder production systems.

PubMed

Omasaki, S K; van Arendonk, J A M; Kahi, A K; Komen, H

2016-10-01

In general, livestock and fish farming systems in developing countries tend to be highly diverse in terms of agro-ecological conditions and market orientation. There are no studies that have investigated if and how this diversity translates to varying preferences for breeding objective traits. This is particularly important for breeding programmes that are organized on a national level (e.g. government-supported nucleus breeding programmes). The aim of this study was to investigate whether Nile tilapia farmers with diverse production systems and economic constraints have different preferences for breeding objective traits. The second objective was to derive a consensus breeding goal, using weighted goal programming that could be used for a national breeding programme for Nile tilapia. A survey was conducted among 100 smallholder Nile tilapia farmers in Kenya to obtain preference values for traits of economic importance, by using multiple pairwise comparisons. Individual and group preference values were estimated using analytical hierarchy process. Low-income farmers preferred harvest weight, while medium- and high-income farmers preferred growth rate and survival. Grouping farmers according to market objective (fingerling production or fattening) showed that fingerling producers preferred growth rate and survival, while fattening farmers preferred harvest weight, height and thickness. Weighted goal programming was used to obtain consensus preference values, and these were used to derive desired gains for a breeding goal of a national breeding programme that takes into account the diversity of smallholder production systems. © 2016 Blackwell Verlag GmbH.

Managing cows: an ethnography of breeding practices and uses of reproductive technology in contemporary dairy farming in Lombardy (Italy).

PubMed

Grasseni, Cristina

2007-06-01

The aim of this article is to contribute detailed ethnographic material to broaden the scope of what we mean by reproductive technology. Technology can be defined not only by a series of laboratory techniques (such as artificial insemination and embryo transfer) that are drafted into the daily management of the animal body, but also by a range of on-farm management strategies and working routines, as well as the cultural dispositions, social networks and tacit knowledge of the actors involved. RT is communicated to lay operators and disseminated amongst semi-professional figures such as breed experts, herd inspectors and technical consultants. The practical contexts in which reproductive knowledge is popularized and applied provide ample scope for local negotiations, resistance and conflict. Professional knowledge about breed-improvement is personalised and appropriated by operators and plays a role in power relations and the exercise of personal charisma as well as being specific to context, in particular the nuances of pre-existing relationships of trust, friendship, kinship or hierarchy. No wonder then that many ambivalences and compromises coexist in the practice of applying 'reproductive knowledge' to breed selection.

Strategies for selecting and breeding EAB-resistant ash

Treesearch

Jennifer L. Koch; Kathleen Knight; Therese Poland; David W. Carey; Daniel A. Herms; Mary E. Mason

2011-01-01

Breeding for pest resistance in forest trees is a proven approach for managing both native and nonnative insects and diseases. A recent study by the Food and Agriculture Organization of the United Nations reports 255 forest tree breeding programs for insect or disease resistance in 33 diff erent countries (http://www.fao.org/forestry/26445/en/). Advantages to...

Toxoplasmosis in sand cats (Felis margarita) and other animals in the Breeding Centre for Endangered Arabian Wildlife in the United Arab Emirates

USDA-ARS?s Scientific Manuscript database

The Sand cat (Felis margarita) is a small-sized felid occurring in the United Arab Emirates (UAE). The Sand cat captive breeding program at the Breeding Centre for Endangered Arabian Wildlife (BCEAW), Sharjah, UAE, has experienced high newborn mortality rates, and congenital toxoplasmosis was recent...

Monitoring goals and programs of the U.S. Fish and Wildlife Service

Treesearch

John R. Sauer

1993-01-01

The United States Fish and Wildlife Service coordinates several surveys that collect information on the population status of migratory birds in North America. The North American Breeding Bird Survey is the primary source of population information on nongame birds during the breeding season, and waterfowl surveys are conducted during breeding and wintering seasons. The...

Maintenance of a high level of reproductive performance in the beef cow herd.

PubMed

Wiltbank, J N

1983-03-01

To insure a high consistent reproductive program in a cow herd, 90 to 95 per cent of the cows must calve early each year and wean a heavy calf. To accomplish this, the producer should follow these steps: 1. Feed heifers to reach a target weight consistent with their breed. 2. Breed heifers 45 days to a bull known to sire small calves (Longhorn or Jersey or a proven bull within a breed). Also consider cows with Brahman blood to decrease birth weight. 3. Use a 60-day breeding season in the cow herd. 4. Have cows in good to moderate body condition at calving time. 5. Have cows gaining weight three weeks before breeding and during the breeding season. 6. Remove calves for 48 hours at the start of the breeding season. 7. Breed to fertile bulls.

Animal breeding strategies can improve meat quality attributes within entire populations.

PubMed

Berry, D P; Conroy, S; Pabiou, T; Cromie, A R

2017-10-01

The contribution of animal breeding to changes in animal performance is well documented across a range of species. Once genetic variation in a trait exists, then breeding to improve the characteristics of that trait is possible, if so desired. Considerable genetic variation exists in a range of meat quality attributes across a range of species. The genetic variation that exists for meat quality is as large as observed for most performance traits; thus, within a well-structured breeding program, rapid genetic gain for meat quality could be possible. The rate of genetic gain can be augmented through the integration of DNA-based technologies into the breeding program; such DNA-based technologies should, however, be based on thousands of DNA markers dispersed across the entire genome. Genetic and genomic technologies can also have beneficial impact outside the farm gate as a tool to segregate carcasses or meat cuts based on expected meat quality features. Copyright © 2017 Elsevier Ltd. All rights reserved.

Accuracy of genomic selection in European maize elite breeding populations.

PubMed

Zhao, Yusheng; Gowda, Manje; Liu, Wenxin; Würschum, Tobias; Maurer, Hans P; Longin, Friedrich H; Ranc, Nicolas; Reif, Jochen C

2012-03-01

Genomic selection is a promising breeding strategy for rapid improvement of complex traits. The objective of our study was to investigate the prediction accuracy of genomic breeding values through cross validation. The study was based on experimental data of six segregating populations from a half-diallel mating design with 788 testcross progenies from an elite maize breeding program. The plants were intensively phenotyped in multi-location field trials and fingerprinted with 960 SNP markers. We used random regression best linear unbiased prediction in combination with fivefold cross validation. The prediction accuracy across populations was higher for grain moisture (0.90) than for grain yield (0.58). The accuracy of genomic selection realized for grain yield corresponds to the precision of phenotyping at unreplicated field trials in 3-4 locations. As for maize up to three generations are feasible per year, selection gain per unit time is high and, consequently, genomic selection holds great promise for maize breeding programs.

77 FR 25192 - Wild Bird Conservation Act; Receipt of Application for Approval of a Cooperative Breeding Program

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-27

... Conservation Act of 1992 (WBCA). DATES: Written data, comments, or requests for a copy of this application must... to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Under...-FF09A30000] Wild Bird Conservation Act; Receipt of Application for Approval of a Cooperative Breeding Program...

Production objectives and trait preferences of village poultry producers of Ethiopia: implications for designing breeding schemes utilizing indigenous chicken genetic resources

PubMed Central

van der Waaij, Liesbeth H.; Dessie, Tadelle; van Arendonk, Johan A. M.

2010-01-01

To generate information essential for the implementation of breeding schemes suitable for village poultry producers in Ethiopia, a survey was conducted aimed at defining the socioeconomic characteristics of the production environments in different geographic regions, understanding the important functions of chickens, identifying farmers’ choice of chicken breeds and the underlying factors that determine the choice of genetic stock used. The survey included both questionnaire survey and a participatory group discussion. A total of 225 households (45 households from each of five Woredas) were interviewed. The questionnaire was designed to collect data covering general information on village poultry production such as socio-management characteristics, production objectives, population structure, breed choice and trait preferences, market preferences of specific traits, and farmers’ selection practices. The participatory farmers’ discussions were designed to involve stakeholders in defining the breeding objective “traits” and deriving their relative importance in the production environment based on the different functions of chickens and “traits” identified in the interviews. The results showed that production of eggs for consumption is the principal function of chickens in most regions followed by the use as source of income and meat for home consumption. The production system in all geographic regions studied revealed similar features generally characterized by extensive scavenging management, absence of immunization programs, increased risk of exposure of birds to disease and predators, and reproduction entirely based on uncontrolled natural mating and hatching of eggs using broody hens. Farmers’ ratings of indigenous chickens with respect to modern breeds showed the highest significance of the adaptive traits in general, and the superior merits of indigenous chickens to high yielding exotic breeds in particular. Adaptation to the production environment was the most important attribute of chickens in all the study areas. The high significance attributed to reproduction traits indicates the need for maintaining broody behavior and high level of hatchability while breeding for improved productivity of indigenous chickens for village conditions. The market price of chickens is primarily dictated by weight, but farmers rated growth (males) and number of eggs followed by growth (females) as the production traits they would like the most to be improved. Therefore, the ultimate breeding goal should be to develop a dual-purpose breed based on indigenous chicken genetic resources with any of the comb types other than single for all the regions studied having the most preferred white body plumage for farmers in the Amhara region and red body plumage for those in Oromia, Benshangul-Gumuz, and Southern regions. PMID:20512411

Production objectives and trait preferences of village poultry producers of Ethiopia: implications for designing breeding schemes utilizing indigenous chicken genetic resources.

PubMed

Dana, Nigussie; van der Waaij, Liesbeth H; Dessie, Tadelle; van Arendonk, Johan A M

2010-10-01

To generate information essential for the implementation of breeding schemes suitable for village poultry producers in Ethiopia, a survey was conducted aimed at defining the socioeconomic characteristics of the production environments in different geographic regions, understanding the important functions of chickens, identifying farmers' choice of chicken breeds and the underlying factors that determine the choice of genetic stock used. The survey included both questionnaire survey and a participatory group discussion. A total of 225 households (45 households from each of five Woredas) were interviewed. The questionnaire was designed to collect data covering general information on village poultry production such as socio-management characteristics, production objectives, population structure, breed choice and trait preferences, market preferences of specific traits, and farmers' selection practices. The participatory farmers' discussions were designed to involve stakeholders in defining the breeding objective "traits" and deriving their relative importance in the production environment based on the different functions of chickens and "traits" identified in the interviews. The results showed that production of eggs for consumption is the principal function of chickens in most regions followed by the use as source of income and meat for home consumption. The production system in all geographic regions studied revealed similar features generally characterized by extensive scavenging management, absence of immunization programs, increased risk of exposure of birds to disease and predators, and reproduction entirely based on uncontrolled natural mating and hatching of eggs using broody hens. Farmers' ratings of indigenous chickens with respect to modern breeds showed the highest significance of the adaptive traits in general, and the superior merits of indigenous chickens to high yielding exotic breeds in particular. Adaptation to the production environment was the most important attribute of chickens in all the study areas. The high significance attributed to reproduction traits indicates the need for maintaining broody behavior and high level of hatchability while breeding for improved productivity of indigenous chickens for village conditions. The market price of chickens is primarily dictated by weight, but farmers rated growth (males) and number of eggs followed by growth (females) as the production traits they would like the most to be improved. Therefore, the ultimate breeding goal should be to develop a dual-purpose breed based on indigenous chicken genetic resources with any of the comb types other than single for all the regions studied having the most preferred white body plumage for farmers in the Amhara region and red body plumage for those in Oromia, Benshangul-Gumuz, and Southern regions.

Genetic diversity, population structure, and correlations between locally adapted zebu and taurine breeds in Brazil using SNP markers.

PubMed

Campos, Bárbara Machado; do Carmo, Adriana Santana; do Egito, Andrea Alves; da Mariante, Arthur Silva; do Albuquerque, Maria Socorro Muaés; de Gouveia, João José Simoni; Malhado, Carlos Henrique Mendes; Verardo, Lucas Lima; da Silva, Marcos Vinícius Gualberto Barbosa; Carneiro, Paulo Luiz Souza

2017-12-01

Genetic diversity is one of the most important issues in studies on conservation of cattle breeds and endangered species. The objective of this study was to estimate the levels of genetic differentiation between locally adapted taurine (Bos taurus taurus) and zebu (Bos taurus indicus) breeds in Brazil, which were genotyped for more than 777,000 SNPs. The fixation index (F ST ), principal component analysis (PCA), and Bayesian clustering were estimated. The F ST highlighted genetic differentiation between taurine and zebu breeds. The taurine lines, Caracu and Caracu Caldeano, had significant genetic differentiation (F ST close to 5%) despite their recent selection for different uses (meat and milk). This genetic variability can be used for conservation of locally adapted animals, as well as for breeding programs on zebu breeds. Introgression of zebu in locally adapted breeds was identified, especially in Curraleiro Pé-Duro breed. The Gyr breed, however, had low breed purity at genomic level due to its very heterogeneous mixing pattern.

Helping Couples Fulfill the "Highest of Life's Goals": Mate Selection, Marriage Counselling, and Genetic Counseling in United States.

PubMed

Stillwell, Devon

2016-02-01

This article traces the history of modern genetic counseling to mate selection and marriage counselling practices of the early-20th century. Mate selection revolved around a belief that human heredity could be improved and genetic diseases eradicated through better breeding. Marriage counselling, though interested in reproduction, was also concerned with the emotional and psychological well-being of couples. These two practices coalesced most obviously in the work of well-known geneticist Sheldon Reed. Even as marriage and genetic counselling diverged in the post-WWII period, vestiges of these practices remain in contemporary counseling experiences with family planning and genetic screening programs. Emphasizing points of continuity between "positive" eugenic ideologies and modern genetic practices elaborates the diverse origins of genetic counseling. It also exposes how genetic counselors have become involved in genetic enterprises beyond standard clinical settings, and prods at key issues in the interaction between genetic science and social values.

Using breed composition, breed differences, selection tools, and new technologies to optimize commercial cattle production and allocation of beef cattle in research programs

USDA-ARS?s Scientific Manuscript database

Indicators of breed composition such as hair color and ear length often result in increased or decreased prices of young calves marketed into feedlots. Similarly, feedlot research trials are often initiated with blended cattle from multiple sources with little more than coat color used as a blockin...

Research in forest genetics and tree breeding at the University of Wisconsin

Treesearch

D.T. Lester

1970-01-01

The genetics and breeding group in the Department of Forestry now has two faculty members and five graduate students. We are now a part of the Plant Breeding and Plant Genetics Group which includes six departments and twenty-six faculty members in an interdepartmental program of graduate teaching and research. Close cooperators are the Department of Plant Pathology at...

National Plant Genome Initiative

DTIC Science & Technology

2004-01-01

trials have also identified new objectives for vegetable breeding programs, expedited by knowledge and tools from crop genomics and farmer demand...The same tools and resources are being applied to develop improved crops and new breeding strategies, as well. With the sequencing of the rice genome...marker-assisted breeding strategies for wheat • Establishment of a comparative cereal genomics database, Gramene, which uses the complete rice

Genomic Selection For Bacterial Cold Water Disease Resistance In Rainbow Trout Reveals Large Within-Family Variation That Cannot Be Exploited In Traditional Family-based Selective Breeding

USDA-ARS?s Scientific Manuscript database

Selective breeding is an effective strategy to improve resistance to specific pathogens, and thus has the potential to mitigate antibiotic use in aquaculture. Large family sizes of aquaculture species permits family-based selective breeding programs, but the need for specific-pathogen-free nucleus p...

Improved charge breeding efficiency of light ions with an electron cyclotron resonance ion source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vondrasek, R.; Kutsaev, Sergey; Delahaye, P.

2012-11-15

The Californium Rare Isotope Breeder Upgrade is a new radioactive beam facility for the Argonne Tandem Linac Accelerator System (ATLAS). The facility utilizes a {sup 252}Cf fission source coupled with an electron cyclotron resonance ion source to provide radioactive beam species for the ATLAS experimental program. The californium fission fragment distribution provides nuclei in the mid-mass range which are difficult to extract from production targets using the isotope separation on line technique and are not well populated by low-energy fission of uranium. To date the charge breeding program has focused on optimizing these mid-mass beams, achieving high charge breeding efficienciesmore » of both gaseous and solid species including 14.7% for the radioactive species {sup 143}Ba{sup 27+}. In an effort to better understand the charge breeding mechanism, we have recently focused on the low-mass species sodium and potassium which up to present have been difficult to charge breed efficiently. Unprecedented charge breeding efficiencies of 10.1% for {sup 23}Na{sup 7+} and 17.9% for {sup 39}K{sup 10+} were obtained injecting stable Na{sup +} and K{sup +} beams from a surface ionization source.« less

Improved charge breeding efficiency of light ions with an electron cyclotron resonance ion source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vondrasek, R.; Delahaye, P.; Kutsaev, Sergey

2012-11-01

The Californium Rare Isotope Breeder Upgrade is a new radioactive beam facility for the Argonne Tandem Linac Accelerator System (ATLAS). The facility utilizes a 252Cf fission source coupled with an electron cyclotron resonance ion source to provide radioactive beam species for the ATLAS experimental program. The californium fission fragment distribution provides nuclei in the mid-mass range which are difficult to extract from production targets using the isotope separation on line technique and are not well populated by low-energy fission of uranium. To date the charge breeding program has focused on optimizing these mid-mass beams, achieving high charge breeding efficiencies ofmore » both gaseous and solid species including 14.7% for the radioactive species 143Ba27+. In an effort to better understand the charge breeding mechanism, we have recently focused on the low-mass species sodium and potassium which up to present have been difficult to charge breed efficiently. Unprecedented charge breeding efficiencies of 10.1% for 23Na7+ and 17.9% for 39K10+ were obtained injecting stable Na+ and K+ beams from a surface ionization source.« less

Prevalence and inheritance of and selection for elbow arthrosis in Bernese mountain dogs and Rottweilers in Sweden and benefit: cost analysis of a screening and control program.

PubMed

Swenson, L; Audell, L; Hedhammar, A

1997-01-15

To determine the prevalence and charges over time in the prevalence of elbow arthrosis in Bernese Mountain Dogs and Rottweilers, to ascertain whether prevalence or severity of elbow arthrosis was associated with sex of the dogs, age at the time of elbow joint examination, or ancestral background, to determine the effects of selective breeding, and to conduct an economic evaluation of the elbow arthrosis program operated by the Swedish Kennel Club. Analysis of radiographic evaluations of elbow joint conformity. 4,515 dogs from 2 breeds registered by the Swedish Kennel Club. All radiographs were scrutinized by a single radiologist (LA), and elbow joint conformation was classified as normal or arthrotic, with the degree of arthrosis classified as 1, 2, or 3. Decreasing prevalence of elbow arthrosis corresponding to selection of breeding stock and high heritabilities was found. Sex differences were documented in both breeds, but with contradictory directions. This was interpreted as breed differences in the distribution of genes related to elbow arthrosis. Economic analyses showed that costs of screening and registration of elbow joints was less than the value of dogs estimated to have been saved from moderate and severe elbow arthrosis in both breeds. Documented effects of age suggest that all dogs should be screened at the same age, rather than screening a few dogs at an older, more revealing age. In screening and control programs based on an open registry with access to family records, decreasing prevalence of elbow arthrosis can be expected, and related to selection of breeding stock.

Tracking the Genetic Stability of a Honey Bee (Hymenoptera: Apidae) Breeding Program With Genetic Markers.

PubMed

Bourgeois, Lelania; Beaman, Lorraine

2017-08-01

A genetic stock identification (GSI) assay was developed in 2008 to distinguish Russian honey bees from other honey bee stocks that are commercially produced in the United States. Probability of assignment (POA) values have been collected and maintained since the stock release in 2008 to the Russian Honey Bee Breeders Association. These data were used to assess stability of the breeding program and the diversity levels of the contemporary breeding stock through comparison of POA values and genetic diversity parameters from the initial release to current values. POA values fluctuated throughout 2010-2016, but have recovered to statistically similar levels in 2016 (POA(2010) = 0.82, POA(2016) = 0.74; P = 0.33). Genetic diversity parameters (i.e., allelic richness and gene diversity) in 2016 also remained at similar levels when compared to those in 2010. Estimates of genetic structure revealed stability (FST(2009/2016) = 0.0058) with a small increase in the estimate of the inbreeding coefficient (FIS(2010) = 0.078, FIS(2016) = 0.149). The relationship among breeding lines, based on genetic distance measurement, was similar in 2008 and 2016 populations, but with increased homogeneity among lines (i.e., decreased genetic distance). This was expected based on the closed breeding system used for Russian honey bees. The successful application of the GSI assay in a commercial breeding program demonstrates the utility and stability of such technology to contribute to and monitor the genetic integrity of a breeding stock of an insect species. Published by Oxford University Press on behalf of Entomological Society of America 2017. This work is written by US Government employees and is in the public domain in the US.

Environmental enrichment affects adrenocortical stress responses in the endangered black-footed ferret

USGS Publications Warehouse

Poessel, S.A.; Biggins, D.E.; Santymire, R.M.; Livieri, T.M.; Crooks, K.R.; Angeloni, L.

2011-01-01

Potential stressors of wildlife living in captivity, such as artificial living conditions and frequent human contact, may lead to a higher occurrence of disease and reduced reproductive function. One successful method used by wildlife managers to improve general well-being is the provision of environmental enrichment, which is the practice of providing animals under managed care with environmental stimuli. The black-footed ferret (Mustela nigripes) is a highly-endangered carnivore species that was rescued from extinction by removal of the last remaining individuals from the wild to begin an ex situ breeding program. Our goal was to examine the effect of environmental enrichment on adrenocortical activity in ferrets by monitoring fecal glucocorticoid metabolites (FGM). Results demonstrated that enrichment lowered FGM in juvenile male ferrets, while increasing it in adult females; enrichment had no effect on FGM in juvenile females and adult males. These results correspond with our findings that juvenile males interacted more with the enrichment items than did adult females. However, we did not detect an impact of FGM on the incidence of disease or on the ability of ferrets to become reproductive during the following breeding season. We conclude that an environmental enrichment program could benefit captive juvenile male ferrets by reducing adrenocortical activity. ?? 2011 Elsevier Inc.

Environmental enrichment affects adrenocortical stress responses in the endangered black-footed ferret.

PubMed

Poessel, Sharon A; Biggins, Dean E; Santymire, Rachel M; Livieri, Travis M; Crooks, Kevin R; Angeloni, Lisa

2011-07-01

Potential stressors of wildlife living in captivity, such as artificial living conditions and frequent human contact, may lead to a higher occurrence of disease and reduced reproductive function. One successful method used by wildlife managers to improve general well-being is the provision of environmental enrichment, which is the practice of providing animals under managed care with environmental stimuli. The black-footed ferret (Mustela nigripes) is a highly-endangered carnivore species that was rescued from extinction by removal of the last remaining individuals from the wild to begin an ex situ breeding program. Our goal was to examine the effect of environmental enrichment on adrenocortical activity in ferrets by monitoring fecal glucocorticoid metabolites (FGM). Results demonstrated that enrichment lowered FGM in juvenile male ferrets, while increasing it in adult females; enrichment had no effect on FGM in juvenile females and adult males. These results correspond with our findings that juvenile males interacted more with the enrichment items than did adult females. However, we did not detect an impact of FGM on the incidence of disease or on the ability of ferrets to become reproductive during the following breeding season. We conclude that an environmental enrichment program could benefit captive juvenile male ferrets by reducing adrenocortical activity. Copyright © 2011 Elsevier Inc. All rights reserved.

Evaluation of Canine Sperm and Management of Semen Disorders.

PubMed

Kolster, Kara A

2018-04-17

Semen evaluation of the male dog is a critical step in any canine infertility work-up. Assessment of total sperm count, sperm viability, and sperm morphology are the mainstay of breeding soundness evaluation. Adjunct tests, such as ultrasonography and serum hormone levels, can aid in diagnosis. Pharmacologic treatments, dietary supplements, and management practices may help improve breeding success in subfertile dogs. This article discusses a clinically practical approach to assessing sperm abnormalities and fertility in male dogs. Copyright © 2018 Elsevier Inc. All rights reserved.

Advances in Japanese pear breeding in Japan

PubMed Central

Saito, Toshihiro

2016-01-01

The Japanese pear (Pyrus pyrifolia Nakai) is one of the most widely grown fruit trees in Japan, and it has been used throughout Japan’s history. The commercial production of pears increased rapidly with the successive discoveries of the chance seedling cultivars ‘Chojuro’ and ‘Nijisseiki’ around 1890, and the development of new cultivars has continued since 1915. The late-maturing, leading cultivars ‘Niitaka’ and ‘Shinko’ were released during the initial breeding stage. Furthermore, systematic breeding by the Horticultural Research Station (currently, NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NIFTS)) began in 1935, which mainly aimed to improve fruit quality by focusing on flesh texture and black spot disease resistance. To date, 22 cultivars have been released, including ‘Kosui’, ‘Hosui’, and ‘Akizuki’, which are current leading cultivars from the breeding program. Four induced mutant cultivars induced by gamma irradiation, which exhibit some resistance to black spot disease, were released from the Institute of Radiation Breeding. Among these cultivars, ‘Gold Nijisseiki’ has become a leading cultivar. Moreover, ‘Nansui’ from the Nagano prefectural institute breeding program was released, and it has also become a leading cultivar. Current breeding objectives at NIFTS mainly combine superior fruit quality with traits related to labor and cost reduction, multiple disease resistance, or self-compatibility. Regarding future breeding, marker-assisted selection for each trait, QTL analyses, genome-wide association studies, and genomic selection analyses are currently in progress. PMID:27069390

Application of DNA fingerprinting to the recovery program of the endangered Puerto Rican parrot

USGS Publications Warehouse

Brock, M.K.; White, B.N.

1992-01-01

The Puerto Rican parrot was reduced to 13 animals in 1975 and as a conservation measure, a captive population was established from a few founders taken from the wild between 1973 and 1983. The number of successful breeding pairs in captivity has been !ow, and the captive breeding program has not been as productive as that of the closely related Hispaniolan parrot. Therefore, a genetic study was initiated to examine the relative levels of relatedness of the captive founders using levels of bandsharing in DNA fingerprints. Unrelated captive founder Puerto Rican parrots had the same average level of bandsharing (0.41) as second-degree relatives of the Hispaniolan parrot (0.38, P > 0,05), with an inbreeding coefficient of 0.04. High levels of bandsharing (>40%) between pairs of males and females correlated with reproductive failure, suggesting that inbreeding depression is partly responsible for the !ow number of' breeding pairs. Consequently, DNA profiling can be used to guide the captive breeding program for the Puerto Rican parrot, and other endangered species, by identifying pairs of males and females with low levels of bandsharing.

The Program for Regional and International Shorebird Monitoring (PRISM)

USGS Publications Warehouse

Bart, J.; Andres, B.; Brown, S.; Donaldson, G.; Harrington, B.; Johnston, V.; Jones, S.; Morrison, R.I.G.; Skagen, S.K.

2005-01-01

This report describes the "Program for Regional and International Shorebird Monitoring" (PRISM). PRISM is being implemented by a Canada-United States Shorebird Monitoring and Assessment Committee formed in 2001 by the Canadian Shorebird Working Group and the U.S. Shorebird Council. PRISM provides a single blueprint for implementing the shorebird conservation plans recently completed in Canada and the United States. The goals of PRISM are to (1) estimate the size of breeding population of 74 shorebird taxa in North America; (2) describe the distribution, abundance, and habitat relationships for each of these taxa; (3) monitor trends in shorebird population size; (4) monitor shorebird numbers at stopover locations, and; (5) assist local managers in meeting their shorebird conservation goals. PRISM has four main components: arctic and boreal breeding surveys, temperate breeding surveys, temperate non-breeding surveys, and neotropical surveys. Progress on, and action items for, each major component are described. The more important major tasks for immediate action are carrying out the northern surveys, conducting regional analyses to design the program of migration counts, and evaluating aerial photographic surveys for migration and winter counts.

Invited review: Current state of genetic improvement in dairy sheep.

PubMed

Carta, A; Casu, Sara; Salaris, S

2009-12-01

Dairy sheep have been farmed traditionally in the Mediterranean basin in southern Europe, central Europe, eastern Europe, and in Near East countries. Currently, dairy sheep farming systems vary from extensive to intensive according to the economic relevance of the production chain and the specific environment and breed. Modern breeding programs were conceived in the 1960s. The most efficient selection scheme for local dairy sheep breeds is based on pyramidal management of the population with the breeders of nucleus flocks at the top, where pedigree and official milk recording, artificial insemination, controlled natural mating, and breeding value estimation are carried out to generate genetic progress. The genetic progress is then transferred to the commercial flocks through artificial insemination or natural-mating rams. Increasing milk yield is still the most profitable breeding objective for several breeds. Almost all milk is used for cheese production and, consequently, milk content traits are very important. Moreover, other traits are gaining interest for selection: machine milking ability and udder morphology, resistance to diseases (mastitis, internal parasites, scrapie), and traits related to the nutritional value of milk (fatty acid composition). Current breeding programs based on the traditional quantitative approach have achieved appreciable genetic gains for milk yield. In many cases, further selection goals such as milk composition, udder morphology, somatic cell count, and scrapie resistance have been implemented. However, the possibility of including other traits of selective interest is limited by high recording costs. Also, the organizational effort needed to apply the traditional quantitative approach limits the diffusion of current selection programs outside the European Mediterranean area. In this context, the application of selection schemes assisted by molecular information, to improve either traditional dairy traits or traits costly to record, seems to be attractive in dairy sheep. At the moment, the most effective strategy seems to be the strengthening of research projects aimed at finding causal mutations along the genes affecting traits of economic importance. However, genome-wide selection seems to be unfeasible in most dairy sheep breeds.

Population structure and inbreeding from pedigree analysis of purebred dogs.

PubMed

Calboli, Federico C F; Sampson, Jeff; Fretwell, Neale; Balding, David J

2008-05-01

Dogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breed-specific selective breeding patterns. To address the lack of such studies we have exploited one of the world's most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, >90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index Psi for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare.

Limits to captive breeding of mammals in zoos.

PubMed

Alroy, John

2015-06-01

Captive breeding of mammals in zoos is the last hope for many of the best-known endangered species and has succeeded in saving some from certain extinction. However, the number of managed species selected is relatively small and focused on large-bodied, charismatic mammals that are not necessarily under strong threat and not always good candidates for reintroduction into the wild. Two interrelated and more fundamental questions go unanswered: have the major breeding programs succeeded at the basic level of maintaining and expanding populations, and is there room to expand them? I used published counts of births and deaths from 1970 to 2011 to quantify rates of growth of 118 captive-bred mammalian populations. These rates did not vary with body mass, contrary to strong predictions made in the ecological literature. Most of the larger managed mammalian populations expanded consistently and very few programs failed. However, growth rates have declined dramatically. The decline was predicted by changes in the ratio of the number of individuals within programs to the number of mammal populations held in major zoos. Rates decreased as the ratio of individuals in programs to populations increased. In other words, most of the programs that could exist already do exist. It therefore appears that debates over the general need for captive-breeding programs and the best selection of species are moot. Only a concerted effort could create room to manage a substantially larger number of endangered mammals. © 2015, Society for Conservation Biology.

Birds of Upland Oak Forests in the Arkansas Ozarks: Present Community Structure and Potential Impacts of Burning, Borers, and Forestry Practices

Treesearch

Kimberly Smith; Michael Mlodinow; Janet S. Self; Thomas M. Haggerty; Tamara R. Hocut

2004-01-01

Based on published works, our own research, and the U.S. Forest Service’s R8 Bird database, we characterize breeding bird communities in mesic and xeric upland hardwood forests of the Arkansas Ozarks. Although 59 species have been recorded as breeding, typical breeding assemblages in mesic forests are 20-25 species, with only 5 species commonly found in xeric forests....

Foreword: Contributions of Arctic PRISM to monitoring western hemispheric shorebirds

USGS Publications Warehouse

Skagen, Susan K.; Smith, Paul A.; Andres, Brad A.; Donaldson, Garry; Brown, Stephen; Bart, Jonathan R.; Johnston, Victoria H.

2012-01-01

Long-term monitoring of populations is of paramount importance to understanding responses of organisms to global environmental change and to evaluating whether conservation practices are yielding intended results through time (Wiens 2009). The population status of many shorebird species, the focus of this volume, remain poorly known. Long-distance migrant shorebirds have proven particularly difficult to monitor, in part because of their highly inaccessible regions. As migrant shorebirds travel the length of the hemisphere, the congregate and disperse in ways that vary among species, locations, and years, presenting serious challenges to designing and implementing monitoring programs. Rigorous field and quantitative methods that estimate population size and monitor trends are vitally needed to direct and evaluate effective conservation measures. Many management efforts depend on unbiased population size estimates; for examples, the shorebird conservation plans for both Canada and the United States seek to restore populations to levels calculated for the 1970s based on the best information available from existing surveys. Further, federal wildlife agencies within the United States and Canada have mandates to understand the state of their nations' resources under various conventions for the protection of migratory birds. Accurate estimates of population size are vital statistics for a variety of conservation activities, such as prioritizing species for conservation action and setting management targets. Areas of essential habitat, such as those designated under the Western Hemisphere Shorebird Reserve Network, the Important Bird Areas program of BirdLife Internationals and the National Audubon Society, or Canada's National Wildlife Areas program, are all evaluated on the basis of proportions of species' populations which they contain. The size, and trends in size, of a species' population are considered key information for assessing its vulnerability and subsequent listing under the U.S. Endangered Species Act and the Canadian Species at Risk Act. To meet the need for information on population size and trends, shorebird biologists from Canada and the United States proposed a shared blueprint for shorebird monitoring across the Western Hemisphere in the late 1990s; this effort was undertaken in concert with the development of the Canadian and the U.S. Shorebird Conservation Plans. Soon thereafter, partners in the monitoring effort adopted the name "Program for Regional and International Shorebird Monitoring" (PRISM). Among the primary objectives of PRISM were to estimate the population sizes and trends of breeding North American shorebirds and describe their distributions. PRISM members evaluated ongoing and potential monitoring approached to address 74 taxa (including subspecies) and proposed a combination of arctic and boreal breeding surveys, temperate breeding and non-breeding surveys, and neotropical surveys.

Intrabreed Stratification Related to Divergent Selection Regimes in Purebred Dogs May Affect the Interpretation of Genetic Association Studies

PubMed Central

Chang, Melanie L.; Yokoyama, Jennifer S.; Branson, Nick; Dyer, Donna J.; Hitte, Christophe; Overall, Karen L.

2009-01-01

Until recently, canine genetic research has not focused on population structure within breeds, which may confound the results of case–control studies by introducing spurious correlations between phenotype and genotype that reflect population history. Intrabreed structure may exist when geographical origin or divergent selection regimes influence the choices of potential mates for breeding dogs. We present evidence for intrabreed stratification from a genome-wide marker survey in a sample of unrelated dogs. We genotyped 76 Border Collies, 49 Australian Shepherds, 17 German Shepherd Dogs, and 17 Portuguese Water Dogs for our primary analyses using Affymetrix Canine v2.0 single-nucleotide polymorphism (SNP) arrays. Subsets of autosomal markers were examined using clustering algorithms to facilitate assignment of individuals to populations and estimation of the number of populations represented in the sample. SNPs passing stringent quality control filters were employed for explicitly phylogenetic analyses reconstructing relationships between individuals using maximum parsimony and Bayesian methods. We used simulation studies to explore the possible effects of intrabreed stratification on genome-wide association studies. These analyses demonstrate significant stratification in at least one of our primary breeds of interest, the Border Collie. Demographic and pedigree data suggest that this population substructure may result from geographic isolation or divergent selection regimes practiced by breeders with different breeding program goals. Simulation studies indicate that such stratification could result in false discovery rates significant enough to confound genome-wide association analyses. Intrabreed stratification should be accounted for when designing and interpreting the results of case–control association studies using purebred dogs.

Evaluating Methods of Updating Training Data in Long-Term Genomewide Selection

PubMed Central

Neyhart, Jeffrey L.; Tiede, Tyler; Lorenz, Aaron J.; Smith, Kevin P.

2017-01-01

Genomewide selection is hailed for its ability to facilitate greater genetic gains per unit time. Over breeding cycles, the requisite linkage disequilibrium (LD) between quantitative trait loci and markers is expected to change as a result of recombination, selection, and drift, leading to a decay in prediction accuracy. Previous research has identified the need to update the training population using data that may capture new LD generated over breeding cycles; however, optimal methods of updating have not been explored. In a barley (Hordeum vulgare L.) breeding simulation experiment, we examined prediction accuracy and response to selection when updating the training population each cycle with the best predicted lines, the worst predicted lines, both the best and worst predicted lines, random lines, criterion-selected lines, or no lines. In the short term, we found that updating with the best predicted lines or the best and worst predicted lines resulted in high prediction accuracy and genetic gain, but in the long term, all methods (besides not updating) performed similarly. We also examined the impact of including all data in the training population or only the most recent data. Though patterns among update methods were similar, using a smaller but more recent training population provided a slight advantage in prediction accuracy and genetic gain. In an actual breeding program, a breeder might desire to gather phenotypic data on lines predicted to be the best, perhaps to evaluate possible cultivars. Therefore, our results suggest that an optimal method of updating the training population is also very practical. PMID:28315831

Preliminary analysis on hybrid vigor in Indonesian indigenous and crossbred cattle population using data from published studies

NASA Astrophysics Data System (ADS)

Prastowo, S.; Widi, TSM; Widyas, N.

2017-04-01

Hybrid vigor or heterosis is the phenomenon where a crossbreed progeny has better performance compared to its parents. Heterosis can be quantified relative to the mid-parents value or relative to one of its parent’s population average by crossing two breeds. Crossbreeding is aimed to increase the production performance of local breeds. According to the Indonesian government policy, crossbreeding program is one of main strategies to achieve meat self-sufficiency. We explore the possibilities observing of heterosis exhibited by crossing Bali and Peranakan Onggole (PO) cattle as local breed with the exotic breed based on the published data. In this paper, growth and reproductive traits from Bali and PO from year 2000-2010 were used for analysis. Moreover, Limousine and Simmental exotic breed data were collected from official information of artificial insemination (AI) centre. Data in growth trait (chest girth, mature weight, weaning weight and yearling weight) in all breeds and their crosses were then analysed using standard heterosis estimation method. Result, shows that crossbred offspring perform better in the growth trait in relative to Bali and PO as local breed. Specifically in Bali crossed with PO, the offspring shown better estimated heterosis effect in yearling weight compared to both parents. Despite heterosis were observed in some traits, careful planning of crossbreeding program is a must in order to avoid the loss of genetic variance.

An attempt to eradicate Herpesvirus simiae from a rhesus monkey breeding colony.

PubMed

Sauber, J J; Fanton, J W; Harvey, R C; Golden, J G

1992-10-01

In the fall of 1987 an attempt to establish a Herpesvirus simiae (B-virus)-negative rhesus monkey (Macaca mulatta) breeding colony was initiated at the Armstrong Laboratory. A serologic testing program was used to identify all monkeys into groups that were either positive or negative to B-virus based on serologic tests. Segregation of the groups allowed the creation of breeding harems that were exclusively seropositive or -negative to B-virus. Animals that were serologically positive were kept in breeding to maintain infant production levels not unlike those previous to segregation. Decreasing numbers of animals converted to a positive status during the first three serum tests for B-virus in the program. During 1990, an increase in the number of monkeys converting to positive status and the discovery of an indeterminate status demonstrated that latency of B-virus in the rhesus may have the potential to defeat an eradication attempt not conscientiously pursued.

Integrating modelling and phenotyping approaches to identify and screen complex traits - Illustration for transpiration efficiency in cereals.

PubMed

Chenu, K; van Oosterom, E J; McLean, G; Deifel, K S; Fletcher, A; Geetika, G; Tirfessa, A; Mace, E S; Jordan, D R; Sulman, R; Hammer, G L

2018-02-21

Following advances in genetics, genomics, and phenotyping, trait selection in breeding is limited by our ability to understand interactions within the plants and with their environments, and to target traits of most relevance for the target population of environments. We propose an integrated approach that combines insights from crop modelling, physiology, genetics, and breeding to identify traits valuable for yield gain in the target population of environments, develop relevant high-throughput phenotyping platforms, and identify genetic controls and their values in production environments. This paper uses transpiration efficiency (biomass produced per unit of water used) as an example of a complex trait of interest to illustrate how the approach can guide modelling, phenotyping, and selection in a breeding program. We believe that this approach, by integrating insights from diverse disciplines, can increase the resource use efficiency of breeding programs for improving yield gains in target populations of environments.

Habitat availability is a more plausible explanation than insecticide acute toxicity for U.S. grassland bird species declines.

PubMed

Hill, Jason M; Egan, J Franklin; Stauffer, Glenn E; Diefenbach, Duane R

2014-01-01

Grassland bird species have experienced substantial declines in North America. These declines have been largely attributed to habitat loss and degradation, especially from agricultural practices and intensification (the habitat-availability hypothesis). A recent analysis of North American Breeding Bird Survey (BBS) "grassland breeding" bird trends reported the surprising conclusion that insecticide acute toxicity was a better correlate of grassland bird declines in North America from 1980-2003 (the insecticide-acute-toxicity hypothesis) than was habitat loss through agricultural intensification. In this paper we reached the opposite conclusion. We used an alternative statistical approach with additional habitat covariates to analyze the same grassland bird trends over the same time frame. Grassland bird trends were positively associated with increases in area of Conservation Reserve Program (CRP) lands and cropland used as pasture, whereas the effect of insecticide acute toxicity on bird trends was uncertain. Our models suggested that acute insecticide risk potentially has a detrimental effect on grassland bird trends, but models representing the habitat-availability hypothesis were 1.3-21.0 times better supported than models representing the insecticide-acute-toxicity hypothesis. Based on point estimates of effect sizes, CRP area and agricultural intensification had approximately 3.6 and 1.6 times more effect on grassland bird trends than lethal insecticide risk, respectively. Our findings suggest that preserving remaining grasslands is crucial to conserving grassland bird populations. The amount of grassland that has been lost in North America since 1980 is well documented, continuing, and staggering whereas insecticide use greatly declined prior to the 1990s. Grassland birds will likely benefit from the de-intensification of agricultural practices and the interspersion of pastures, Conservation Reserve Program lands, rangelands and other grassland habitats into existing agricultural landscapes.

Hybrid wheat: quantitative genetic parameters and consequences for the design of breeding programs.

PubMed

Longin, Carl Friedrich Horst; Gowda, Manje; Mühleisen, Jonathan; Ebmeyer, Erhard; Kazman, Ebrahim; Schachschneider, Ralf; Schacht, Johannes; Kirchhoff, Martin; Zhao, Yusheng; Reif, Jochen Christoph

2013-11-01

Commercial heterosis for grain yield is present in hybrid wheat but long-term competiveness of hybrid versus line breeding depends on the development of heterotic groups to improve hybrid prediction. Detailed knowledge of the amount of heterosis and quantitative genetic parameters are of paramount importance to assess the potential of hybrid breeding. Our objectives were to (1) examine the extent of midparent, better-parent and commercial heterosis in a vast population of 1,604 wheat (Triticum aestivum L.) hybrids and their parental elite inbred lines and (2) discuss the consequences of relevant quantitative parameters for the design of hybrid wheat breeding programs. Fifteen male lines were crossed in a factorial mating design with 120 female lines, resulting in 1,604 of the 1,800 potential single-cross hybrid combinations. The hybrids, their parents, and ten commercial wheat varieties were evaluated in multi-location field experiments for grain yield, plant height, heading time and susceptibility to frost, lodging, septoria tritici blotch, yellow rust, leaf rust, and powdery mildew at up to five locations. We observed that hybrids were superior to the mean of their parents for grain yield (10.7 %) and susceptibility to frost (-7.2 %), leaf rust (-8.4 %) and septoria tritici blotch (-9.3 %). Moreover, 69 hybrids significantly (P < 0.05) outyielded the best commercial inbred line variety underlining the potential of hybrid wheat breeding. The estimated quantitative genetic parameters suggest that the establishment of reciprocal recurrent selection programs is pivotal for a successful long-term hybrid wheat breeding.

Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress.

PubMed

Fernández, Jesús; Toro, Miguel Á; Sonesson, Anna K; Villanueva, Beatriz

2014-01-01

The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program.

Breeding nursery tissue collection for possible genomic analysis

USDA-ARS?s Scientific Manuscript database

Phenotyping is considered a major bottleneck in breeding programs. With new genomic technologies, high throughput genotype schemes are constantly being developed. However, every genomic technology requires phenotypic data to inform prediction models generated from the technology. Forage breeders con...

Rindsel: an R package for phenotypic and molecular selection indices used in plant breeding.

PubMed

Perez-Elizalde, Sergío; Cerón-Rojas, Jesús J; Crossa, José; Fleury, Delphine; Alvarado, Gregorio

2014-01-01

Selection indices are estimates of the net genetic merit of the individual candidates for selection and are calculated based on phenotyping and molecular marker information collected on plants under selection in a breeding program. They reflect the breeding value of the plants and help breeders to choose the best ones for next generation. Rindsel is an R package that calculates phenotypic and molecular selection indices.

Genetic counseling in the era of molecular diagnostics.

PubMed

Traas, Anne M; Casal, Margret; Haskins, Mark; Henthorn, Paula

2006-08-01

Veterinarians with an interest in theriogenology will often be asked by small animal clients for advice concerning hereditary diseases in their breeds. Many new DNA-based tests for analysis of genetic diseases and traits (e.g. coat color) are now available for use by both breeders and veterinarians. With appropriate interpretation, these tests can be invaluable tools in a breeding program. For example, they can be used to produce animals free of specific diseases, to quickly eliminate a disease from an entire breed, or to select for specific traits in breeding stock. Selection strategies that do not take into account maintaining genetic diversity of the breed may be detrimental and reduce the potential for future improvement.

Genomics to feed a switchgrass breeding program

USDA-ARS?s Scientific Manuscript database

Development of improved cultivars is one of three pillars, along with sustainable production and efficient conversion, required for dedicated cellulosic bioenergy crops to succeed. Breeding new cultivars is a long, slow process requiring patience, dedication, and motivation to realize gains and adva...

Pituophis ruthveni (Louisiana pinesnake) Reproduction/breeding phenology

Treesearch

Josh B. Pierce; Craig Rudolph; Christopher A. Melder; Beau B. Gregory

2016-01-01

Determing the reproductive phenology of snakes is important since it marks a time period where snakes are particularly vulnerable to predation. In addition, knowledge of reproductive phenology may help captive breeding programs specify appropriate times to pair snakes for reproduction.

Insight into the genetic composition of South African Sanga cattle using SNP data from cattle breeds worldwide.

PubMed

Makina, Sithembile O; Whitacre, Lindsey K; Decker, Jared E; Taylor, Jeremy F; MacNeil, Michael D; Scholtz, Michiel M; van Marle-Köster, Este; Muchadeyi, Farai C; Makgahlela, Mahlako L; Maiwashe, Azwihangwisi

2016-11-15

Understanding the history of cattle breeds is important because it provides the basis for developing appropriate selection and breed improvement programs. In this study, patterns of ancestry and admixture in Afrikaner, Nguni, Drakensberger and Bonsmara cattle of South Africa were investigated. We used 50 K single nucleotide polymorphism genotypes that were previously generated for the Afrikaner (n = 36), Nguni (n = 50), Drakensberger (n = 47) and Bonsmara (n = 44) breeds, and for 394 reference animals representing European taurine, African taurine, African zebu and Bos indicus. Our findings support previous conclusions that Sanga cattle breeds are composites between African taurine and Bos indicus. Among these breeds, the Afrikaner breed has significantly diverged from its ancestral forebears, probably due to genetic drift and selection to meet breeding objectives of the breed society that enable registration. The Nguni, Drakensberger and Bonsmara breeds are admixed, perhaps unintentionally in the case of Nguni and Drakensberger, but certainly by design in the case of Bonsmara, which was developed through crossbreeding between the Afrikaner, Hereford and Shorthorn breeds. We established patterns of admixture and ancestry for South African Sanga cattle breeds, which provide a basis for developing appropriate strategies for their genetic improvement.

Novel optimum contribution selection methods accounting for conflicting objectives in breeding programs for livestock breeds with historical migration.

PubMed

Wang, Yu; Bennewitz, Jörn; Wellmann, Robin

2017-05-12

Optimum contribution selection (OCS) is effective for increasing genetic gain, controlling the rate of inbreeding and enables maintenance of genetic diversity. However, this diversity may be caused by high migrant contributions (MC) in the population due to introgression of genetic material from other breeds, which can threaten the conservation of small local populations. Therefore, breeding objectives should not only focus on increasing genetic gains but also on maintaining genetic originality and diversity of native alleles. This study aimed at investigating whether OCS was improved by including MC and modified kinships that account for breed origin of alleles. Three objective functions were considered for minimizing kinship, minimizing MC and maximizing genetic gain in the offspring generation, and we investigated their effects on German Angler and Vorderwald cattle. In most scenarios, the results were similar for Angler and Vorderwald cattle. A significant positive correlation between MC and estimated breeding values of the selection candidates was observed for both breeds, thus traditional OCS would increase MC. Optimization was performed under the condition that the rate of inbreeding did not exceed 1% and at least 30% of the maximum progress was achieved for all other criteria. Although traditional OCS provided the highest breeding values under restriction of classical kinship, the magnitude of MC in the progeny generation was not controlled. When MC were constrained or minimized, the kinship at native alleles increased compared to the reference scenario. Thus, in addition to constraining MC, constraining kinship at native alleles is required to ensure that native genetic diversity is maintained. When kinship at native alleles was constrained, the classical kinship was automatically lowered in most cases and more sires were selected. However, the average breeding value in the next generation was also lower than that obtained with traditional OCS. For local breeds with historical introgressions, current breeding programs should focus on increasing genetic gain and controlling inbreeding, as well as maintaining the genetic originality of the breeds and the diversity of native alleles via the inclusion of MC and kinship at native alleles in the OCS process.

Breeding for resistance in Norway spruce to the root and butt rot fungi Heterobasidion spp

Treesearch

G. Swedjemark; A.K. Borg-Karlson; B. Karlsson

2012-01-01

Results from previous studies of resistance in Norway spruce (Picea abies (L.) Karst.) to the pathogens Heterobasidion spp. show significant genotypic variation in fungal growth and spore susceptibility among Norway spruce clones. The genetic variation and the heritability are large enough for practical breeding purposes and...

Weather, disease, and wheat breeding effects on Kansas wheat varietal yields, 1985 to 2011

USDA-ARS?s Scientific Manuscript database

Wheat (Triticum aestivum L.) yields in Kansas have increased due to wheat breeding and improved agronomic practices, but are subject to climate and disease challenges. The objective of this research is to quantify the impact of weather, disease, and genetic improvement on wheat yields of varieties g...

Tree-breeding technique: some effects of continuous bagging

Treesearch

Jonathan W. Wright

1951-01-01

In tree-breeding operations, it is standard practice to protect the tree flowers with vegetable parchment or sausage-casing bags during the pollination period so no unwanted pollen can get to them. Since the bags often damage the tree, they are usually removed as soon as the pollination period ends - within 2 or 3 weeks.

Atlantic salmon brood stock management and breeding handbook

USGS Publications Warehouse

Kincaid, Harold L.; Stanley, Jon G.

1989-01-01

Anadromus runs of Atlantic salmon have been restored to the Connecticut, Merrimack, Pawcatuck, Penobscot, and St. Croix rivers in New England by the stocking of more than 8 million smolts since 1948. Fish-breeding methods have been developed that minimize inbreeding and domestication and enhance natural selection. Methods are available to advance the maturation of brood stock, control the sex of production lots and store gametes. Current hatchery practices emphasize the use of sea-run brood stock trapped upon return to the rivers and a limited number of captive brood stock and rejuvenated kelts. Fish are allowed to mature naturally, after which they are spawned and incubated artificially. Generally, 1-year smolts are produced, and excess fish are stocked as fry in headwater streams. Smolts are stocked during periods of rising water in spring. Self-release pools are planned that enable smolts to choose the emigration time. Culturists keep good records that permit evaluation of the performance of strains and the effects of breeding practices. As Atlantic salmon populations expand, culturists must use sound breeding methods that enhance biotic potential while maintaining genetic diversity and protecting unique gene pools.

Diversity of macro- and micronutrients in the seeds of lentil landraces.

PubMed

Karaköy, Tolga; Erdem, Halil; Baloch, Faheem S; Toklu, Faruk; Eker, Selim; Kilian, Benjamin; Özkan, Hakan

2012-01-01

Increasing the amount of bioavailable mineral elements in plant foods would help to improve the nutritional status of populations in developing countries. Legume seeds have the potential to provide many essential nutrients. It is important to have information on genetic variations among different lentil populations so that plant breeding programs can use new varieties in cross-breeding programs. The main objective of this study was to characterize the micro- and macronutrient concentrations of lentil landraces seeds collected from South-Eastern Turkey. We found impressive variation in the micro- and macroelement concentrations in 39 lentil landraces and 7 cultivars. We investigated the relationships of traits by correlation analysis and principal component analysis (PCA). The concentrations of several minerals, particularly Zn, were positively correlated with other minerals, suggesting that similar pathways or transporters control the uptake and transport of these minerals. Some genotypes had high mineral and protein content and potential to improve the nutritional value of cultivated lentil. Cross-breeding of numerous lentil landraces from Turkey with currently cultivated varieties could improve the levels of micro- and macronutrients of lentil and may contribute to the worldwide lentil quality breeding program.

Cost and accuracy of advanced breeding trial designs in apple

PubMed Central

Harshman, Julia M; Evans, Kate M; Hardner, Craig M

2016-01-01

Trialing advanced candidates in tree fruit crops is expensive due to the long-term nature of the planting and labor-intensive evaluations required to make selection decisions. How closely the trait evaluations approximate the true trait value needs balancing with the cost of the program. Designs of field trials of advanced apple candidates in which reduced number of locations, the number of years and the number of harvests per year were modeled to investigate the effect on the cost and accuracy in an operational breeding program. The aim was to find designs that would allow evaluation of the most additional candidates while sacrificing the least accuracy. Critical percentage difference, response to selection, and correlated response were used to examine changes in accuracy of trait evaluations. For the quality traits evaluated, accuracy and response to selection were not substantially reduced for most trial designs. Risk management influences the decision to change trial design, and some designs had greater risk associated with them. Balancing cost and accuracy with risk yields valuable insight into advanced breeding trial design. The methods outlined in this analysis would be well suited to other horticultural crop breeding programs. PMID:27019717

Long-term spatial heterogeneity in mallard distribution in the Prairie pothole region

USGS Publications Warehouse

Janke, Adam K.; Anteau, Michael J.; Stafford, Joshua D.

2017-01-01

The Prairie Pothole Region (PPR) of north-central United States and south-central Canada supports greater than half of all breeding mallards (Anas platyrhynchos) annually counted in North America and is the focus of widespread conservation and research efforts. Allocation of conservation resources for this socioeconomically important population would benefit from an understanding of the nature of spatiotemporal variation in distribution of breeding mallards throughout the 850,000 km2 landscape. We used mallard counts from the Waterfowl Breeding Population and Habitat Survey to test for spatial heterogeneity and identify high- and low-abundance regions of breeding mallards over a 50-year time series. We found strong annual spatial heterogeneity in all years: 90% of mallards counted annually were on an average of only 15% of surveyed segments. Using a local indicator of spatial autocorrelation, we found a relatively static distribution of low-count clusters in northern Montana, USA, and southern Alberta, Canada, and a dynamic distribution of high-count clusters throughout the study period. Distribution of high-count clusters shifted southeast from northwestern portions of the PPR in Alberta and western Saskatchewan, Canada, to North and South Dakota, USA, during the latter half of the study period. This spatial redistribution of core mallard breeding populations was likely driven by interactions between environmental variation that created favorable hydrological conditions for wetlands in the eastern PPR and dynamic land-use patterns related to upland cropping practices and government land-retirement programs. Our results highlight an opportunity for prioritizing relatively small regions within the PPR for allocation of wetland and grassland conservation for mallard populations. However, the extensive spatial heterogeneity in core distributions over our study period suggests such spatial prioritization will have to overcome challenges presented by dynamic land-use and climate patterns in the region, and thus merits additional monitoring and empirical research to anticipate future population distribution. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Characterization of saccharum species germplasm for starch content

USDA-ARS?s Scientific Manuscript database

The renewed interest in wild Saccharum species germplasm across sugarcane breeding programs has been necessitated by the need to widen the genetic base of breeding populations. Modern sugarcane cultivars were derived from inter-specific hybridization between S. officinarum and S. spontaneum. Very fe...

50 CFR 13.11 - Application procedures.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Rescue Center Program 50 CFR 23 No fee CITES Registration of Commercial Breeding Operations for Appendix—I Wildlife 50 CFR 23 100 —Renewal of Registration of Commercial Breeding Operations for Appendix-I..., POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS...

Routine DNA testing

USDA-ARS?s Scientific Manuscript database

Routine DNA testing. It’s done once you’ve Marker-Assisted Breeding Pipelined promising Qantitative Trait Loci within your own breeding program and thereby established the performance-predictive power of each DNA test for your germplasm under your conditions. By then you are ready to screen your par...

Lettuce and spinach breeding

USDA-ARS?s Scientific Manuscript database

Lettuce and spinach production is beset by numerous biotic an abiotic challenges. This report to the California Leafy Greens Research Program annual meeting provides an update by the ‘Genetic Enhancement of Lettuce, Spinach, Melon, and Related Species’ project at Salinas on the genetics and breeding...

“Looking over the Backyard Fence”: Householders and Mosquito Control

PubMed Central

Mainali, Samir; Lamichhane, Ram Sharan; Clark, Kim; Beatty, Shelley; Fatouros, Maria; Neville, Peter; Oosthuizen, Jacques

2017-01-01

(1) Background: Vector-borne diseases are a significant public health problem in Western Australia. Mosquitoes are responsible for the transmission of a number of pathogens and may pose a serious nuisance problem. Prevention efforts in the State are multi-faceted and include physical, chemical, and cultural control methods for restricting mosquito breeding. This is less complex where breeding areas are located within public open spaces. In Australia’s developed urban areas, breeding sites are, however, frequently located within private residential landholdings, where the scope of public health officials to act is constrained by law and practicality. Consequently, mosquito prevention in these locations is predominantly the responsibility of the residents. This research addressed a gap, both in understanding the degree to which “backyard” mosquito breeding has the potential to contribute to local mosquito problems, and in assessing what residents “think and do” about mosquito control within their home environment. (2) Methods: The study was conducted in the Town of Bassendean, a metropolitan Local Government Area of Perth, Western Australia, in close proximity to two natural, productive mosquito breeding sites, namely Ashfield Flats and Bindaring Park. A total of 150 householders were randomly surveyed during the summer of 2015–2016, to gauge residents’ knowledge, attitudes, and practices (KAP (knowledge, attitudes, and practices) Survey) in regards to mosquitoes, their breeding and ecology, and avoidance or minimization strategies. The survey comprised nine questions covering residents’ knowledge (3 questions), attitudes (3 questions), and practices (3 questions), as well as additional questions regarding the basic demographics of the resident. Larvae were collected from backyard containers and reared to adults for species identification. A series of Encephalitis Vector Surveillance carbon dioxide (EVS CO2) traps were also deployed, to assess adult mosquito density and species composition. (3) Results: Aedes notoscriptus (Skuse), a known container-inhabiting species, accounted for just over 50% of all mosquitoes identified. Most residents were aware of mosquito-borne disease and its risk in their local area. While the majority (79%) of the sample correctly identified Ross River virus as the most common infection in WA, a significant gap in the general knowledge of residents in regards to mosquito biology and breeding habits, was noted. Furthermore, only 50% of residents reported using personal protective measures to reduce mosquito bites and only one in six residents undertook physical or chemical mosquito control around their home. Additionally, 60% of respondents believed that mosquito control was “a job for the council and the state government”, rather than for individual householders. (4) Conclusions: A significant gap in the knowledge of residents in the study area existed in regards to the general knowledge of mosquitoes and their breeding habits; types of treatments that could be employed within the home; and the residents’ responsibility for the management of mosquito breeding on their private property. A public education campaign has been deployed to educate the residents. PMID:28257079

Prediction of insemination outcomes in Holstein dairy cattle using alternative machine learning algorithms.

PubMed

Shahinfar, Saleh; Page, David; Guenther, Jerry; Cabrera, Victor; Fricke, Paul; Weigel, Kent

2014-02-01

When making the decision about whether or not to breed a given cow, knowledge about the expected outcome would have an economic impact on profitability of the breeding program and net income of the farm. The outcome of each breeding can be affected by many management and physiological features that vary between farms and interact with each other. Hence, the ability of machine learning algorithms to accommodate complex relationships in the data and missing values for explanatory variables makes these algorithms well suited for investigation of reproduction performance in dairy cattle. The objective of this study was to develop a user-friendly and intuitive on-farm tool to help farmers make reproduction management decisions. Several different machine learning algorithms were applied to predict the insemination outcomes of individual cows based on phenotypic and genotypic data. Data from 26 dairy farms in the Alta Genetics (Watertown, WI) Advantage Progeny Testing Program were used, representing a 10-yr period from 2000 to 2010. Health, reproduction, and production data were extracted from on-farm dairy management software, and estimated breeding values were downloaded from the US Department of Agriculture Agricultural Research Service Animal Improvement Programs Laboratory (Beltsville, MD) database. The edited data set consisted of 129,245 breeding records from primiparous Holstein cows and 195,128 breeding records from multiparous Holstein cows. Each data point in the final data set included 23 and 25 explanatory variables and 1 binary outcome for of 0.756 ± 0.005 and 0.736 ± 0.005 for primiparous and multiparous cows, respectively. The naïve Bayes algorithm, Bayesian network, and decision tree algorithms showed somewhat poorer classification performance. An information-based variable selection procedure identified herd average conception rate, incidence of ketosis, number of previous (failed) inseminations, days in milk at breeding, and mastitis as the most effective explanatory variables in predicting pregnancy outcome. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Rapid genetic diversification within dog breeds as evidenced by a case study on Schnauzers.

PubMed

Streitberger, K; Schweizer, M; Kropatsch, R; Dekomien, G; Distl, O; Fischer, M S; Epplen, J T; Hertwig, S T

2012-10-01

As a result of strong artificial selection, the domesticated dog has arguably become one of the most morphologically diverse vertebrate species, which is mirrored in the classification of around 400 different breeds. To test the influence of breeding history on the genetic structure and variability of today's dog breeds, we investigated 12 dog breeds using a set of 19 microsatellite markers from a total of 597 individuals with about 50 individuals analysed per breed. High genetic diversity was noted over all breeds, with the ancient Asian breeds (Akita, Chow Chow, Shar Pei) exhibiting the highest variability, as was indicated chiefly by an extraordinarily high number of rare and private alleles. Using a Bayesian clustering method, we detected significant genetic stratification within the closely related Schnauzer breeds. The individuals of these three recently differentiated breeds (Miniature, Standard and Giant Schnauzer) could not be assigned to a single cluster each. This hidden genetic structure was probably caused by assortative mating owing to breeders' preferences regarding coat colour types and the underlying practice of breeding in separate lineages. Such processes of strong artificial disruptive selection for different morphological traits in isolated and relatively small lineages can result in the rapid creation of new dog types and potentially new breeds and represent a unique opportunity to study the evolution of genetic and morphological differences in recently diverged populations. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

Genetic Parameters and the Impact of Off-Types for Theobroma cacao L. in a Breeding Program in Brazil

PubMed Central

DuVal, Ashley; Gezan, Salvador A.; Mustiga, Guiliana; Stack, Conrad; Marelli, Jean-Philippe; Chaparro, José; Livingstone, Donald; Royaert, Stefan; Motamayor, Juan C.

2017-01-01

Breeding programs of cacao (Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genetic architecture of cacao, in this study, 13 years of phenotypic data collected from four progeny trials in Bahia, Brazil were analyzed jointly in a multisite analysis. Three separate analyses (multisite, single site with and without off-types) were performed to estimate genetic parameters from statistical models fitted on nine important agronomic traits (yield, seed index, pod index, % healthy pods, % pods infected with witches broom, % of pods other loss, vegetative brooms, diameter, and tree height). Genetic parameters were estimated along with variance components and heritabilities from the multisite analysis, and a trial was fingerprinted with low-density SNP markers to determine the impact of off-types on estimations. Heritabilities ranged from 0.37 to 0.64 for yield and its components and from 0.03 to 0.16 for disease resistance traits. A weighted index was used to make selections for clonal evaluation, and breeding values estimated for the parental selection and estimation of genetic gain. The impact of off-types to breeding progress in cacao was assessed for the first time. Even when present at <5% of the total population, off-types altered selections by 48%, and impacted heritability estimations for all nine of the traits analyzed, including a 41% difference in estimated heritability for yield. These results show that in a mixed model analysis, even a low level of pedigree error can significantly alter estimations of genetic parameters and selections in a breeding program. PMID:29250097

Density gradient centrifugation of sperm from a subfertile stallion and effect of seminal plasma addition on fertility.

PubMed

Mari, Gaetano; Castagnetti, Carolina; Rizzato, Giovanni; Mislei, Beatrice; Iacono, Eleonora; Merlo, Barbara

2011-06-01

Stallions are not selected for fertility but for other criteria (pedigree, conformation, performances, progeny), therefore valuable but subfertile stallions with poor semen quality are frequently used in commercial breeding programs. The object of this study was to evaluate whether sperm selection through a silane-coated silica colloid gradient centrifugation, with or without the addition of seminal plasma of a high fertile stallion, could improve the pregnancy rates of an oligospermic valuable stallion in a commercial breeding program. In 2008 breeding season (experiment 1, n=104 mares), simple centrifugation and density gradient centrifugation of the sperm were compared. In 2009 and 2010 breeding seasons (experiment 2, n=125 mares), the effect of the addition of 5% seminal plasma to the extender after sperm selection was evaluated. In all mares deep horn uterine insemination was performed with 1 ml containing 50×10(6) morphologically normal progressive motile spermatozoa, 24-30 h after induction of ovulation with hCG. Pregnancy diagnosis by ultrasonography was performed 14 days following ovulation. Results showed a higher per cycle pregnancy rate (P>0.05) when sperm selection through a density gradient was used (62% vs. 42.3%, exp 1), while the addition of 5% seminal plasma did not influence the outcome (45.9% vs. 47.6%, exp 2) (P>0.05). An age-related decrease in the fertility of the stallion was observed when comparing the results from the different breeding seasons (P<0.05). In conclusion, sperm selection through a discontinuous density gradient enabled a normal per cycle pregnancy rate to be achieved from an oligospermic-subfertile stallion in a commercial breeding program, and no differences were observed regarding the addition of seminal plasma. Copyright © 2011 Elsevier B.V. All rights reserved.

Effects of management practices on grassland birds: Prairie Falcon

USGS Publications Warehouse

DeLong, John P.; Steenhof, Karen

2004-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 4,000 published and unpublished papers. A range map is provided to indicate the breeding, year-round, and nonbreeding ranges in the United States and southern Canada. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region.

Effects of management practices on grassland birds: Greater Prairie-Chicken

USGS Publications Warehouse

Svedarsky, W. Daniel; Toepfer, J.E.; Westemeier, R.L.; Robel, R.J.

2003-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the breeding distribution of Greater Prairie-Chicken in the United States and southern Canada. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species’ breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management is posted at the Web site mentioned below.

Mukhabarah as Sharia Financing Model in Beef Cattle Farm Entrepise

NASA Astrophysics Data System (ADS)

Asnawi, A.; Amrawaty, A. A.; Nirwana

2018-02-01

Financing constraints on beef cattle farm nowadays have received attention by the government through distributed various assistance programs and program loans through implementing banks. The existing financing schemes are all still conventional yet sharia-based. The purpose of this research is to formulate financing pattern for sharia beef cattle farm. A qualitative and descriptive approach is used to formulate the pattern by considering the profit-sharing practices of the beef cattle farmers. The results of this study have formulated a financing pattern that integrates government, implementing banks, beef cattle farmers group and cooperative as well as breeders as its members. This pattern of financing is very accommodating of local culture that develops in rural communities. It is expected to be an input, especially in formulating a business financing policy Sharia-based beef cattle breeding.

We Made Your Bed, Why Won’t You Lie in It? Food Availability and Disease May Affect Reproductive Output of Reintroduced Frogs

PubMed Central

Valdez, Jose; Stockwell, Michelle; Fardell, Loren; Clulow, Simon; Clulow, John; Mahony, Michael

2016-01-01

Mitigation to offset the impacts of land development is becoming increasingly common, with reintroductions and created habitat programs used as key actions. However, numerous reviews cite high rates of poor success from these programs, and a need for improved monitoring and scientific testing to evaluate outcomes and improve management actions. We conducted extensive monitoring of a released population of endangered green and golden bell frogs, Litoria aurea, within a created habitat, as well as complementary surveys of a surrounding wild population. We then compared differences between the created habitat and natural ponds where extant frogs either bred or didn’t breed in order to determine factors that contributed to the breeding failure within the created habitat. We evaluated differences of L. aurea abundance, abundance of other fauna, vegetation, water quality, habitat structure, invasive fish, and disease between the three pond types (created habitat, breeding ponds, non-breeding ponds). We discovered that vegetation and invertebrate diversity were low within the created habitat, potentially reducing energy and nutritional resources required for breeding. Also, a greater proportion of frogs in the created habitat were carrying the chytrid fungal pathogen, Batrachochytrium dendrobatidis, compared to the wild populations. In addition to causing the potentially fatal disease, chytridiomycosis, this pathogen has been shown to reduce reproductive functioning in male L. aurea, and subsequently may have reduced reproductive activities in the created habitat. Conspecific attraction, pond hydrology, and aquatic vegetation may also have had some influence on breeding behaviours, whilst the presence of the invasive mosquitofish, Gambusia holbrooki, and heterospecific tadpoles were unlikely to have deterred L. aurea from breeding within the created habitat. Through the use of scientific testing and monitoring, this study is able to make recommendations for future amphibian breed and release programs, and suggests planting a diversity of plant species to attract invertebrates, creating some permanent ponds, connecting habitat with existing populations, trialling artificial mating calls, and following recommendations to reduce the prevalence of disease within the population. PMID:27463095

Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers.

PubMed

Bigi, D; Marelli, S P; Randi, E; Polli, M

2015-12-01

Very little research into genetic diversity of Italian native dog breeds has been carried out so far. In this study we aimed to estimate and compare the genetic diversity of four native Italian shepherd dog breeds: the Maremma, Bergamasco, Lupino del Gigante and Oropa shepherds. Therefore, some cosmopolitan dog breeds, which have been widely raised in Italy for a long time past, have also been considered to check possible influence of these dog populations on the Italian autochthonous breeds considered here. A total of 212 individuals, belonging to 10 different dog breeds, were sampled and genotyped using 18 autosomal microsatellite loci. We analyzed the genetic diversity of these breeds, within breed diversity, breed relationship and population structure. The 10 breeds considered in this study were clearly genetically differentiated from each other, regardless of current population sizes and the onset of separate breeding history. The level of genetic diversity explained 20% of the total genetic variation. The level of H E found here is in agreement with that found by other studies. The native Italian breeds showed generally higher genetic diversity compared with the long established, well-defined cosmopolitan dog breeds. As the Border Collie seems closer to the Italian breeds than the other cosmopolitan shepherd dogs considered here, a possible utilization of this breed to improve working performance in Italian traditional working shepherd dogs cannot be ignored. The data and information found here can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability.

Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds.

PubMed

Yurchenko, Andrey; Yudin, Nikolay; Aitnazarov, Ruslan; Plyusnina, Alexandra; Brukhin, Vladimir; Soloshenko, Vladimir; Lhasaranov, Bulat; Popov, Ruslan; Paronyan, Ivan A; Plemyashov, Kirill V; Larkin, Denis M

2018-01-01

One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.

Parentage assignment with genomic markers: a major advance for understanding and exploiting genetic variation of quantitative traits in farmed aquatic animals

PubMed Central

Vandeputte, Marc; Haffray, Pierrick

2014-01-01

Since the middle of the 1990s, parentage assignment using microsatellite markers has been introduced as a tool in aquaculture breeding. It now allows close to 100% assignment success, and offered new ways to develop aquaculture breeding using mixed family designs in commercial conditions. Its main achievements are the knowledge and control of family representation and inbreeding, especially in mass spawning species, above all the capacity to estimate reliable genetic parameters in any species and rearing system with no prior investment in structures, and the development of new breeding programs in many species. Parentage assignment should not be seen as a way to replace physical tagging, but as a new way to conceive breeding programs, which have to be optimized with its specific constraints, one of the most important being to well define the number of individuals to genotype to limit costs, maximize genetic gain while minimizing inbreeding. The recent possible shift to (for the moment) more costly single nucleotide polymorphism markers should benefit from future developments in genomics and marker-assisted selection to combine parentage assignment and indirect prediction of breeding values. PMID:25566319

Cryopreservation of apple (Malus spp.): development, progress and future prospects

USDA-ARS?s Scientific Manuscript database

Apple (Malus sp.) is one of the most economically important temperate fruit crops. Wild Malus genetic resources and existing cultivars provide valuable genes for breeding new elite cultivars and rootstocks through traditional and biotechnological breeding programs. Over the last three decades, great...

Pedigree reconstruction with genome-wide markers in potato

USDA-ARS?s Scientific Manuscript database

Reliable pedigree information facilitates a scientific approach to breeding, but errors can be introduced in many stages of a breeding program. Our objective was to use single nucleotide polymorphisms (SNPs) to check the pedigree records of elite North American potato germplasm. A population of 635 ...

Postweaning nutritional programming of ovarian development in beef heifers

USDA-ARS?s Scientific Manuscript database

From weaning to breeding, nutritional management of replacement females is critical to their lifetime productivity. Traditionally, cereal grains have been used to develop replacement heifers to enter the breeding system at a younger age. Overfeeding heifers decreases the number of calves weaned, w...

Post-weaning nutritional programming of ovarian development in beef heifers

USDA-ARS?s Scientific Manuscript database

From weaning to breeding, the nutritional management of replacement females is critical to their lifetime productivity. Traditionally, cereal grains have been used to develop replacement heifers to enter the breeding system at a younger age. However, overfeeding heifers decreased number of calves ...

Plant breeding for harmony between agriculture and the environment

USDA-ARS?s Scientific Manuscript database

Crop improvements made since the 1950’s coupled with inexpensive agronomic inputs (fertilizers, herbicides, etc.) have resulted in agricultural production that has kept pace with population growth. Breeding programs primarily focus on improving a crop’s environmental adaptability and biotic stress t...

Genomic Tools in Cowpea Breeding Programs: Status and Perspectives

PubMed Central

Boukar, Ousmane; Fatokun, Christian A.; Huynh, Bao-Lam; Roberts, Philip A.; Close, Timothy J.

2016-01-01

Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved varieties available to farmers, thereby boosting cowpea production and productivity in SSA. PMID:27375632

Senior Laboratory Animal Technician | Center for Cancer Research

Cancer.gov

PROGRAM DESCRIPTION The Laboratory Animal Sciences Program (LASP) provides exceptional quality animal care and technical support services for animal research performed at the National Cancer Institute at the Frederick National Laboratory for Cancer Research. LASP executes this mission by providing a broad spectrum of state-of-the-art technologies and services that are focused on the design, generation, characterization and application of genetically engineered and biological animal models of human disease, which are aimed at the development of targeted diagnostics and therapies. LASP contributes to advancing human health, developing new treatments, and improving existing treatments for cancer and other diseases while ensuring safe and humane treatment of animals. KEY ROLES/RESPONSIBILITIES The Senior Laboratory Animal Technician will be responsible for: Daily tasks associated with the care, breeding and treatment of research animals for experimental purposes Management of rodent breeding colonies consisting of multiple, genetically complex strains and associated record keeping and database management Colony management procedures including: tail clipping, animal identification, weaning Data entry consistent with complex colony management Collection of routine diagnostic samples Coordinating shipment of live animals and specimens Performing rodent experimental procedures including basic necropsy and blood collection Observation and recording of physical signs of animal health Knowledge of safe working practices using chemical carcinogen and biological hazards Work schedule may include weekend and holiday hours This position is in support of the Center for Cancer Research (CCR).

Traditional livestock breeding practices of men and women Somali pastoralists: trait preferences and selection of breeding animals.

PubMed

Marshall, K; Mtimet, N; Wanyoike, F; Ndiwa, N; Ghebremariam, H; Mugunieri, L; Costagli, R

2016-12-01

Somalia, one of the world's poorest countries, has livestock as the mainstay of the economy, with an estimated 65% of the population engaged in the livestock sector. This paper presents a gendered study on the traditional livestock breeding practices of Somali pastoralists for camels, cattle, sheep and goats, with a focus on documenting livestock traits of importance, the criteria used to select male breeding animals and the criteria used to cull female breeding animals. Data for the study were obtained by performing participatory rural appraisals (PRAs) with separate male and female pastoral groups from 20 settlements of the Tog-Dheer region of Somaliland (in north-western Somalia). In total, more than 500 pastoralists were involved. In terms of livestock ownership, goats were the most common species kept (97% of all households), followed by sheep (64%), camels (37%) and cattle (9%), with considerable herd size variation across households. Traits of key importance to the pastoralists varied by species and gender of the PRA group, but included adaptedness to harsh environmental conditions, high market value/high meat production and high milk production. The pastoralists practised sensible criteria for the selection of male breeding animals for all species, capturing aspects of productivity (milk yield, reproduction), adaptedness (good hardiness) and marketability (body size and conformation). Similarly, they practised sensible criteria for culling of female breeding animals, with females removed from the herd primarily for poor performance, but also to meet the livelihood needs of the family. Differences in the selection and culling criteria were noted by species, as well as gender of the pastoralists. On the whole, there was strong alignment between the livestock selection criteria used by the Somali pastoralists, their reasons for keeping livestock and the market requirements. This is not surprising given the intimate and long-standing relationship between Somali pastoralists and their livestock. © 2016 The Authors. Journal of Animal Breeding and Genetics published by Blackwell Verlag GmbH.

Short-term breeding bird response to two harvest practices in a bottomland hardwood forest

Treesearch

Charles A. Harrison; John C. Kilgo

2004-01-01

Clearcutting is the preferred timber harvest method in bottomland hardwood forests because it is most likely to result in regeneration of preferred species. However, clearcutting generally has negative impacts on forest birds. Patch-retention harvesting may provide similar silvicultural benefits, but its effects on birds are unknown. We surveyed breeding birds in uncut...

Effects of long-term forest management on a regional avifauna

Treesearch

John C. Kilgo; Kathleen E. Franzreb; Sidney A. Gauthreaux; Karl V. Miller; Brian R. Chapman

2000-01-01

We compared breeding bird populations on and off of the Savannah River Site, SC, to determine whether management practices have affected abundance and composition of the resident avifauna. We assessed relative abundance by comparing Breeding Bird Survey (BBS) data from six routes off the Savannah River Site with three surrogate routes generated using point-count data...

Batrachochytrium dendrobatidis in amphibians confiscated from illegal wildlife trade and used in an ex situ breeding program in Brazil.

PubMed

De Paula, C D; Pacífico-Assis, E C; Catão-Dias, J L

2012-03-20

This paper describes an outbreak of chytridiomycosis affecting a group of Dendrobates tinctorius, a Neotropical anuran species, confiscated from the illegal wildlife trade and housed in a private zoo in Brazil as part of an ex situ breeding program. We examined histological sections of the skin of 30 D. tinctorius and 20 Adelphobates galactonotus individuals. Twenty D. tinctorius (66.7%) and none of the A. galactonotus were positive for Batrachochytrium dendrobatidis (Bd). Multiple development stages of Bd infection were observed. The reasons for the inter-specific difference in the rate of infection could not be determined, and further studies are advised. Because the examined population consisted of confiscated frogs, detailed epidemiological aspects could not be investigated, and the source of the fungus remains uncertain. The existence of ex situ amphibian populations is important for protecting species at higher risk in the wild, and ex situ amphibian conservation and breeding programs in Brazil may be established using confiscated frogs as founders. However, this paper alerts these programs to the urgency of strict quarantine procedures to prevent the introduction of potential pathogens, particularly Bd, into ex situ conservation programs.

Citrus breeding, genetics and genomics in Japan

PubMed Central

Omura, Mitsuo; Shimada, Takehiko

2016-01-01

Citrus is one of the most cultivated fruits in the world, and satsuma mandarin (Citrus unshiu Marc.) is a major cultivated citrus in Japan. Many excellent cultivars derived from satsuma mandarin have been released through the improvement of mandarins using a conventional breeding method. The citrus breeding program is a lengthy process owing to the long juvenility, and it is predicted that marker-assisted selection (MAS) will overcome the obstacle and improve the efficiency of conventional breeding methods. To promote citrus molecular breeding in Japan, a genetic mapping was initiated in 1987, and the experimental tools and resources necessary for citrus functional genomics have been developed in relation to the physiological analysis of satsuma mandarin. In this paper, we review the progress of citrus breeding and genome researches in Japan and report the studies on genetic mapping, expression sequence tag cataloguing, and molecular characterization of breeding characteristics, mainly in terms of the metabolism of bio-functional substances as well as factors relating to, for example, fruit quality, disease resistance, polyembryony, and flowering. PMID:27069387

Effectors as tools in disease resistance breeding against biotrophic, hemibiotrophic, and necrotrophic plant pathogens.

PubMed

Vleeshouwers, Vivianne G A A; Oliver, Richard P

2014-03-01

One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.

Differences in innate and adaptive immune response traits of Pahari (Indian non-descript indigenous breed) and Jersey crossbred cattle.

PubMed

Verma, Subhash; Thakur, Aneesh; Katoch, Shailja; Shekhar, Chander; Wani, Aasim Habib; Kumar, Sandeep; Dohroo, Shweta; Singh, Geetanjali; Sharma, Mandeep

2017-10-01

Cattle are an integral part of the largely agrarian economy of India. Indigenous breeds of cattle comprise about 80% of total cattle population of the country and contribute significantly to the overall milk production. There are 40 recognized indigenous breeds of cattle and a number of uncharacterized non-descript cattle. Pahari cattle of Himachal Pradesh in Northern India are one such non-descript indigenous breed. Here we describe a comprehensive evaluation of haematobiochemical parameters and innate and adaptive immune response traits of Pahari cattle and a comparison with Jersey crossbred cattle. The study shows demonstrable differences in the two breeds with respect to some innate and adaptive immunological traits. This is a first attempt to characterize immune response traits of Pahari cattle and the results of the study provide an understanding of breed differences in immune status of cattle which could be useful for their breeding and conservations programs. Copyright © 2017 Elsevier B.V. All rights reserved.

Breeding season survival and breeding incidence of female Mottled Ducks on the upper Texas gulf coast

USGS Publications Warehouse

Rigby, Elizabeth A.; Haukos, David A.

2012-01-01

Previous Mottled Duck (Anas fulvigula) studies suggested that high female breeding season survival may be caused by low nesting effort, but few breeding season estimates of survival associated with nesting effort exist on the western Gulf Coast. Here, breeding season survival (N = 40) and breeding incidence (N = 39) were estimated for female Mottled Ducks on the upper Texas coast, 2006–2008. Females were fitted with backpack radio transmitters and visually relocated every 3–4 days. Weekly survival was estimated using the Known Fate procedure of program MARK with breeding incidence estimated as the annual proportion of females observed nesting or with broods. The top-ranked survival model included a body mass covariate and held weekly female survival constant across weeks and years (SW = 0.986, SE = 0.006). When compared to survival across the entire year estimated from previous band recovery and age ratio analysis, survival rate during the breeding season did not differ. Breeding incidence was well below 100% in all years and highly variable among years (15%–63%). Breeding season survival and breeding incidence were similar to estimates obtained with implant transmitters from the mid-coast of Texas. The greatest breeding incidence for both studies occurred when drought indices indicated average environmental moisture during the breeding season. The observed combination of low breeding incidence and high breeding season survival support the hypothesis of a trade-off between the ecological cost of nesting effort and survival for Mottled Duck females. Habitat cues that trigger nesting are unknown and should be investigated.

Crossing eastern cottonwood in the greenhouse

Treesearch

R. E. Farmer; W. L. Nance

1968-01-01

Eastern cottonwood (Populus deltoides Bartr.) is the subject of breeding programs designed to develop planting stock with potential for rapid growth, desirable wood properties, and pest resistance (4). Techniques for making controlled crosses within the species are essential to breeding, and their development constitutes an early phase of genetics...

New Brahman breed improvement program at STARS

USDA-ARS?s Scientific Manuscript database

At the USDA, ARS, Subtropical Agricultural Research Station (STARS) in Brooksville, Florida we have initiated a new ambitious research project that many believe will have a positive influence on the Brahman breed. This research was developed from a meeting held at STARS that included past and prese...

Lessons from Cotton: Research Projects Following Development of a Community-based Genotyping Array

USDA-ARS?s Scientific Manuscript database

High-throughput, cost-effective genotyping arrays provide a standardized resource for plant breeding communities that can be used for a wide range of applications at a suitable pace for integrating pertinent information into breeding programs. Traditionally, crop research communities will target dev...

Can genomics boost productivity of orphan crops?

USDA-ARS?s Scientific Manuscript database

Advances in genomics over the past 20 years have enhanced the precision and efficiency of breeding programs in many temperate cereal crops. One of the first applications of genomics-assisted breeding has been the introgression of loci for resistance to biotic stresses or major quantitative trait loc...

Genomic selection for Bacterial Cold Water Disease resistance in rainbow trout

USDA-ARS?s Scientific Manuscript database

Selective breeding is an effective strategy to improve resistance to specific pathogens, and thus has the potential to mitigate antibiotic use in aquaculture. Large family sizes of aquaculture species permits family-based selective breeding programs, but the need for specific-pathogen-free nucleus p...

Inheritance of rainbow trout Oncorhynchus mykiss spleen size and correlation with bacterial cold water disease resistance

USDA-ARS?s Scientific Manuscript database

Infectious disease causes substantial loss in aquaculture and selective breeding for increased innate resistance offers an attractive strategy for controlling disease. In 2005, the NCCCWA implemented a selective breeding program to increase rainbow trout survival following challenge with Flavobacte...

Genetic parameters for milk production traits and breeding goals for Gir dairy cattle in Brazil.

PubMed

Prata, M A; Faro, L E; Moreira, H L; Verneque, R S; Vercesi Filho, A E; Peixoto, M G C D; Cardoso, V L

2015-10-19

To implement an animal breeding program, it is important to define the production circumstances of the animals of interest to determine which traits of economic interest will be selected for the breeding goal. The present study defined breeding goals and proposed selection indices for milk production and quality traits of Gir dairy cattle. First, a bioeconomic model was developed to calculate economic values. The genetic and phenotypic parameters were estimated based on records from 22,468 first-lactation Gir dairy cows and their crosses for which calving occurred between 1970 and 2011. Statistical analyses were carried out for the animal model, with multitrait analyses using the restricted maximum likelihood method. Two situations were created in the present study to define the breeding goals: 1) including only milk yield in the breeding goal (HGL1) and 2) including fat and protein in addition to the milk yield (HGL2). The heritability estimates for milk, protein, and fat production were 0.33 ± 0.02, 0.26 ± 0.02, and 0.24 ± 0.02, respectively. All phenotypic and genetic correlations were highly positive. The economic values for milk, fat, and protein were US$0.18, US$0.27, and US$7.04, respectively. The expected economic responses for HGL2 and for HGL1 were US$126.30 and US$79.82, respectively. These results indicate that milk component traits should be included in a selection index to rank animals evaluated in the National Gir Dairy Breeding Program developed in Brazil.

The reproductive endocrinology and behavior of Vancouver Island marmot (Marmota vancouverensis).

PubMed

Keeley, T; Goodrowe, K L; Graham, L; Howell, C; MacDonald, S E

2012-01-01

The Vancouver Island marmot (Marmota vancouverensis; VIM) is one of North America's most endangered species with fewer than 150 individuals remaining in the wild. A captive breeding program was established across four facilities in Canada as an insurance population and source of animals for reintroduction to the wild. The purpose of this study was to gather information about the basic reproductive biology and behavior of this species, which is essential to improve captive breeding programs. Regular fecal samples were obtained from adult female (n = 14) and male (n = 10) marmots, 2 years of age and older, over 1-3 breeding seasons (2-3 months duration posthibernation) for steroid hormone analysis. Enzyme immunoassays were validated for quantifying fecal testosterone metabolite concentrations for males, and fecal estrogen and progesterone metabolite concentrations for females. Results indicated that fecal progesterone metabolite concentrations can be used to monitor ovulation and pregnancy. Behavioral monitoring through infrared video surveillance was conducted in four breeding pairs over a 2-year period (n = 7 behavioral profiles). Breeding behaviors correlated strongly with changes in reproductive endocrine profiles. A high frequency of play behavior or "wrestling" was observed in conjunction with breeding activity before an elevation in progesterone metabolite concentrations. Impending parturition was associated with increased aggression and exclusion of the male from the maternal nestbox as well as an increase in nesting activity. Observational data combined with hormonal analysis suggest that female VIMs are induced ovulators and that multiple breeding attempts may be required for ovulation and conception. Gestation appears to be approximately 34 days from peak breeding activity (32 days from estimated ovulation). Fecal testosterone concentrations suggest that testicular activity is seasonal with the reproductive activity occurring immediately posthibernation. Monitoring breeding behavior is a useful means of indicating estrus, conception and pregnancy, which can also be supported by the hormonal analysis of daily fecal samples of individual animals. © 2011 Wiley Periodicals, Inc.

The indigenous Somba cattle of the hilly Atacora region in North-West Benin: threats and opportunities for its sustainable use.

PubMed

Dossa, Luc Hippolyte; Vanvanhossou, Fridaïus Ulrich Sèyi

2016-02-01

The objective of this study was to characterize the declining Somba cattle population in its production system context. Two-hundred-twenty-four (224) cattle farm-households were surveyed in the Boukombe district, the natural habitat of the breed in North-West Benin. Information on their socioeconomic characteristics and on their herd management practices were recorded using a semi-structured questionnaire. In addition, 15 body measurements were recorded from 102 adult cattle. Three types of breeders were distinguished: the owners-herders (54.0 %); the absentee owners (40.2 %) and the professional herders (5.8 %). The average cattle herd sizes were 4.7 ± 3.70 and 58.6 ± 22.83 heads for owner-managed and entrusted herds, respectively. Offtakes were more associated with sociocultural purposes (75.5 %) than market. While crop farming was the main occupation and income source of their owners, the Somba cattle were used for ploughing during the rainy season. In contrast to the widely accepted belief that this indigenous genetic resource is mainly threatened by crossbreeding and/or replacement, our findings suggest high mortalities due to diseases, feed and water shortages and poor reproduction management as the main causes of the decline of this cattle population. Somba cattle generally have short horns and a small body size. However, bulls have significantly (P ≤ 0.05) longer horns (21.2 ± 16.44 cm against 13.9 ± 7.21 cm), higher height at withers (99.7 ± 6.97 cm against 95.9 ± 5.76 cm) and body length (149.7 ± 12.87 cm against 146.8 ± 11.01 cm) than cows. All surveyed farmers expressed their willingness and readiness to participate in and contribute materially or financially to any program towards a sustainable use and preservation of this breed which they perceived as hardy and embedded in their culture. We therefore argue that strategies for its sustainable use and conservation should consist of simultaneously improving general herd management practices, organizing farmers and involving them in participatory breed improvement programs.

Dystocia in nine British breeds of cattle and its relationship to the dimensions of the dam and calf.

PubMed

Schwabe, A E; Hall, S J

The degree of assistance provided at 1353 calvings from 954 heifers and cows of nine breeds of British cattle (Ayrshire, British White, Dexter, Friesian/Holstein type, Gloucester, Kerry, Longhorn, Shetland and White Park) was recorded and analysed in terms of the dimensions of the dam and the calf. The sires had been chosen in accordance with normal farming practice. A heavy calf did not lead to dystocia. Assistance at calving was most frequently provided in the Ayrshire herd, which was used for veterinary teaching. There were very few difficult calvings in the seven rare breeds, but this was as likely to have been due to management policy as to the breed characteristics. A large tuber coxae measurement was associated with ease of calving, particularly in the Dexter. The breeds showed a wide range of pelvic dimensions and therefore provide a source of genetic variation.

Contributions of Arctic PRISM to monitoring western hemispheric shorebirds

USGS Publications Warehouse

Skagen, Susan K.; Smith, Paul A.; Andres, Brad A.; Donaldson, Garry; Brown, Stephen

2012-01-01

Long-term monitoring of populations is of paramount importance to understanding responses oforganisms to global environmental change and to evaluating whether conservation practices are yielding intended results through time (Wiens 2009). The population status of many shorebird species, the focus of this volume, remain poorly known. Long-distance migrant shorebirds have proven particularly difficult to monitor, in part because of their highly migratory nature and ranges that extend into highly inaccessible regions. As migrant shorebirds travel the length of the hemisphere, they congregate and disperse in ways that vary among species, locations, and years, presenting serious challenges to designing and implementing monitoring programs. Rigorous field and quantitative methods that estimate population size and monitor trends are vitally needed to direct and evaluate effective conservation measures. Many management efforts depend on unbiased population size estimates; for example, the shorebird conservation plans for both Canada and the United States seek to restore populations to levels calculated for the 1970s based on the best information available from existing surveys. Further, federal wildlife agencies within the United States and Canada have mandates to understand the state of their nations' resources under various conventions for the protection of migratory birds. Accurate estimates of population size are vital statistics for a variety of conservation activities, such as prioritizing species for conservation action and setting management targets. Areas of essential habitat, such as those designated under the Western Hemisphere Shorebird Reserve Network, the Important Bird Areas program of BirdLife International and the National Audubon Society, or Canada's National Wildlife Areas program, are all evaluated on the basis ofproportions of species' populations which they contain. The size, and trends in size, ofa species' population are considered key information for assessing its vulnerability and subsequent listing under the U.S. Endangered Species Act and the Canadian Species at Risk Act. To meet the need for information on population size and trends, shorebird biologists from Canada and the United States proposed a shared blueprint for shorebird monitoring across the Western Hemisphere in the late 1990s; this effort was undertaken in concert with the development of the Canadian and U.S. Shorebird Conservation Plans (Donaldson et al. 2000, Brown et aL 2001). Soon thereafter, partners in the monitoring effort adopted the name "Program for Regional and International Shorebird Monitoring" (PRISM). Among the primary objectives of PRISM were to estimate the population sizes and trends of breeding North American shorebirds and describe their distributions (Bart et al. 2002). PRISM members evaluated ongoing and potential monitoring approaches to address 74 taxa (including subspecies) and proposed a combination of arctic andboreal breeding surveys, temperate breeding and non-breeding surveys, and neotropical surveys.

Simulating a base population in honey bee for molecular genetic studies

PubMed Central

2012-01-01

Background Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding value estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has a distinct genetic and reproductive biology. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee. Results Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1) the position of markers on each chromosome, (2) allele frequency, (3) χ2 statistics for Hardy-Weinberg equilibrium, (4) a sorted list of markers with a minor allele frequency less than or equal to the input value, (5) average r2 values of linkage disequilibrium between all simulated marker loci pair for all generations and (6) average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. Conclusion We developed a software program that takes into account the genetic and reproductive biology specific to the honey bee and that can be used to constitute a genomic dataset compatible with the simulation studies necessary to optimize breeding programs. The source code together with an instruction file is freely accessible at http://msproteomics.org/Research/Misc/honeybeepopulationsimulator.html PMID:22520469

Simulating a base population in honey bee for molecular genetic studies.

PubMed

Gupta, Pooja; Conrad, Tim; Spötter, Andreas; Reinsch, Norbert; Bienefeld, Kaspar

2012-06-27

Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding value estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has a distinct genetic and reproductive biology. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee. Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1) the position of markers on each chromosome, (2) allele frequency, (3) χ(2) statistics for Hardy-Weinberg equilibrium, (4) a sorted list of markers with a minor allele frequency less than or equal to the input value, (5) average r(2) values of linkage disequilibrium between all simulated marker loci pair for all generations and (6) average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. We developed a software program that takes into account the genetic and reproductive biology specific to the honey bee and that can be used to constitute a genomic dataset compatible with the simulation studies necessary to optimize breeding programs. The source code together with an instruction file is freely accessible at http://msproteomics.org/Research/Misc/honeybeepopulationsimulator.html.

Review: Towards the agroecological management of ruminants, pigs and poultry through the development of sustainable breeding programmes. II. Breeding strategies.

PubMed

Phocas, F; Belloc, C; Bidanel, J; Delaby, L; Dourmad, J Y; Dumont, B; Ezanno, P; Fortun-Lamothe, L; Foucras, G; Frappat, B; González-García, E; Hazard, D; Larzul, C; Lubac, S; Mignon-Grasteau, S; Moreno, C R; Tixier-Boichard, M; Brochard, M

2016-11-01

Agroecology uses ecological processes and local resources rather than chemical inputs to develop productive and resilient livestock and crop production systems. In this context, breeding innovations are necessary to obtain animals that are both productive and adapted to a broad range of local contexts and diversity of systems. Breeding strategies to promote agroecological systems are similar for different animal species. However, current practices differ regarding the breeding of ruminants, pigs and poultry. Ruminant breeding is still an open system where farmers continue to choose their own breeds and strategies. Conversely, pig and poultry breeding is more or less the exclusive domain of international breeding companies which supply farmers with hybrid animals. Innovations in breeding strategies must therefore be adapted to the different species. In developed countries, reorienting current breeding programmes seems to be more effective than developing programmes dedicated to agroecological systems that will struggle to be really effective because of the small size of the populations currently concerned by such systems. Particular attention needs to be paid to determining the respective usefulness of cross-breeding v. straight breeding strategies of well-adapted local breeds. While cross-breeding may offer some immediate benefits in terms of improving certain traits that enable the animals to adapt well to local environmental conditions, it may be difficult to sustain these benefits in the longer term and could also induce an important loss of genetic diversity if the initial pure-bred populations are no longer produced. As well as supporting the value of within-breed diversity, we must preserve between-breed diversity in order to maintain numerous options for adaptation to a variety of production environments and contexts. This may involve specific public policies to maintain and characterize local breeds (in terms of both phenotypes and genotypes), which could be used more effectively if they benefited from the scientific and technical resources currently available for more common breeds. Last but not least, public policies need to enable improved information concerning the genetic resources and breeding tools available for the agroecological management of livestock production systems, and facilitate its assimilation by farmers and farm technicians.

Visualization of Genome Diversity in German Shepherd Dogs.

PubMed

Mortlock, Sally-Anne; Booth, Rachel; Mazrier, Hamutal; Khatkar, Mehar S; Williamson, Peter

2015-01-01

A loss of genetic diversity may lead to increased disease risks in subpopulations of dogs. The canine breed structure has contributed to relatively small effective population size in many breeds and can limit the options for selective breeding strategies to maintain diversity. With the completion of the canine genome sequencing project, and the subsequent reduction in the cost of genotyping on a genomic scale, evaluating diversity in dogs has become much more accurate and accessible. This provides a potential tool for advising dog breeders and developing breeding programs within a breed. A challenge in doing this is to present complex relationship data in a form that can be readily utilized. Here, we demonstrate the use of a pipeline, known as NetView, to visualize the network of relationships in a subpopulation of German Shepherd Dogs.

Top 5 exotic clones for potato breeding

USDA-ARS?s Scientific Manuscript database

Wild and cultivated relatives of potato feature prominently in breeding programs. In this short article, I describe five exotic clones that have promising traits for the future of the US potato industry. They include M6, an inbred line of S. chacoense that provides a source of genes for self-compati...

Population analysis of 60 worldwide cattle breeds using high-density (700k)SNP genotyping

USDA-ARS?s Scientific Manuscript database

Genetic differences associated with speciation, breed formation, or local adaptation can help inform efforts to preserve and to effectively utilize individuals in selection programs as well as assist in accurately identifying genomic region’s importance through genome-wide association studies. To th...

Cross-transferability of SSR markers in Osmanthus

USDA-ARS?s Scientific Manuscript database

Developing a molecular tool kit for hybrid breeding of Osmanthus species and related genera is an important step in creating a systematic breeding program for this species. To date, molecular resources have been aimed solely at O. fragrans with little work to develop markers for other species and cu...

Selection efficiency for raspberry postharvest shelf life affected by storage temperature and harvest season

USDA-ARS?s Scientific Manuscript database

Improved postharvest quality is an important goal for fresh-market raspberry breeding programs. To determine if warm or cold storage following harvest would better facilitate the breeding selection process for the assessment of postharvest decay and bleed, pesticide-free fruit from cultivars and bre...

Utilization of a major brown rust resistance gene in sugarcane breeding

USDA-ARS?s Scientific Manuscript database

Brown rust, caused by Puccinia melanocephala has had devastating effects on sugarcane (Saccharum spp.) breeding programs and on commercial production. The discovery of Bru1, a major gene conferring resistance to brown rust represented a substantial breakthrough and markers for the detection of Bru1 ...

Breeding FHB-resistant soft winter wheat: progress and prospects

USDA-ARS?s Scientific Manuscript database

Soft winter wheat (Triticum aestivum L.) breeding programs in the US have used two general approaches to developing FHB-resistant cultivars: 1) incorporation of Fhb1 plus other minor QTL from Asian wheat cultivars and their derivatives and 2) reliance on resistance native to the soft winter wheat ge...

Temperate non-breeding surveys - a key to shorebird conservation

Treesearch

Sue Thomas

2005-01-01

Completion of the United States and Canadian shorebird conservation plans recently identified and prioritized shorebird monitoring, management, and conservation needs in the Western Hemisphere. We present an emerging approach to monitor shorebird use of temperate non-breeding areas under the Program for Regional and International Shorebird Monitoring (PRISM). This...

50 CFR 15.23 - Permits for zoological breeding or display programs.

Code of Federal Regulations, 2012 CFR

2012-10-01

... education protocol that provides information on educational materials on the ecology and/or conservation... self-sustaining population of the exotic bird species in captivity; (iii) A statement on efforts to... the population from which the exotic bird was or would be removed; (4) Whether the breeding or display...

50 CFR 15.23 - Permits for zoological breeding or display programs.

Code of Federal Regulations, 2014 CFR

2014-10-01

... education protocol that provides information on educational materials on the ecology and/or conservation... self-sustaining population of the exotic bird species in captivity; (iii) A statement on efforts to... the population from which the exotic bird was or would be removed; (4) Whether the breeding or display...

50 CFR 15.23 - Permits for zoological breeding or display programs.

Code of Federal Regulations, 2013 CFR

2013-10-01

... education protocol that provides information on educational materials on the ecology and/or conservation... self-sustaining population of the exotic bird species in captivity; (iii) A statement on efforts to... the population from which the exotic bird was or would be removed; (4) Whether the breeding or display...

Feeding & Management of Dairy Calves & Heifers. Teacher's Guide.

ERIC Educational Resources Information Center

Bjoraker, Walt

This guide is designed to assist postsecondary and secondary teachers of agriculture in their use of the University of Wisconsin bulletin "Raising Dairy Replacements" in their dairy science instructional program. Eight lessons are provided in this unit: breeding decisions, management of cows from breeding to calving, care at calving time, the…

Breeding black walnuts in the age of genomics

Treesearch

Mark V. Coggeshall; Jeanne Romero-Severson

2013-01-01

Molecular markers have been used in several walnut species to help reconstruct breeding program pedigrees, to characterize genetic structure in natural Juglans populations, to determine the impact of different timber harvest scenarios on residual levels of genetic diversity, and to quantify the effects of interspecific hybridization on subsequent...

Assessing the breeding potential of extra-long staple germplasm in an upland cotton breeding program

USDA-ARS?s Scientific Manuscript database

Fiber quality improvement of upland cotton (Gossypium hirsutum L.) is essential to increase the value and competitiveness of cotton fiber. The closely related allotetraploid species G. barbadense has long been targeted as a source of beneficial fiber quality alleles. Although interspecific hybridiza...

GGE analysis of ratooning ability in Louisiana sugarcane breeding

USDA-ARS?s Scientific Manuscript database

Ratooning ability is an important sugarcane growth habit that affects profitability. Ratooning ability is the ability of sugarcane to regrow after harvesting and it is measured in this research as the percentage of second ratoon of a trait to plant cane. In sugarcane breeding programs, it is time co...

Development of the first consensus genetic map of intermediate wheatgrass (Thinopyrum intermedium) using genotyping-by-sequencing

USDA-ARS?s Scientific Manuscript database

Intermediate wheatgrass (Thinopyrum intermedium) has been identified as a candidate for domestication and improvement as a perennial grain, forage, and biofuel crop by several active breeding programs. To accelerate this process using genomics-assisted breeding, efficient genotyping methods and gen...

QTLs detected for individual sugars and soluble solids content in apple

USDA-ARS?s Scientific Manuscript database

Sweetness is one of the most important fruit quality traits in breeding programs, determining the overall quality and flavor-perception of apples. Selecting for this trait using conventional breeding methods is challenging due to the complexity of its genetic control. In order to improve the efficie...

What's the latest on USDA citrus scion breeding?

USDA-ARS?s Scientific Manuscript database

In its 120 year history, the USDA citrus scion breeding program has provided the mainstays of the Florida specialty citrus industry. In the last few years, the USDA has released US Early Pride mandarin, US Seedless Pineapple sweet orange and most recently, US Furr/US Furr-ST mandarin. Clearly huangl...

Towards the elucidation of the cytoplasmic diversity of North American Grape Breeding Programs

USDA-ARS?s Scientific Manuscript database

Plants have an intriguing tripartite genetic system: Nuclear genome × Mitochondria × Plastids, and their interactions may impact germplasm breeding. In grapevine, the study of cytoplasmic genomes has been limited, and their role with respect to grapevine germplasm diversity has not been elucidated y...

Genetic diversity and association mapping of mineral element concentrations in spinach leaves

USDA-ARS?s Scientific Manuscript database

Spinach is one of the healthiest vegetables in the human diet due to its high concentrations of nutrients and mineral elements. Breeding new spinach cultivars with high nutritional value is one of the main goals in spinach breeding programs worldwide, and identification of single nucleotide polymorp...

USE OF NEUTRON IRRADIATIONS IN THE BROOKHAVEN MUTATIONS PROGRAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miksche, J.P.; Shapiro, S.

1963-01-01

Many plant species were irradiated with x rays, thermal and fast neutrons, andd gamma radiation during the past 10 yr of the cooperative mutations program and adjunct mutation breeding program. Four major concepts and/ or approaches related to the use of mutagenic agents in plant breeding that have evolved are discussed. It was concluded that outcrossing between treated and nontreated populations must be reckoned with, and consequently the two populations should be separated before a true measure of mutation induction can be ascertained; chromosome rearrangement studies are useful, with particular emphasis on inducing disease resistance; work concerned with tissue reorgandizationmore » and rearrangement as related to chimera production and basic understanding of tissue ontogeny, particularly with fruit crops andd horticultural crops is promising; and the effectiveness of responses of plant tissues to neutrons and other mutagenic agents is extremely variable and more basic work is needed before the full potentialities of mutation breeding as a tool in crop improvement can be appreciated. (auth)« less

Effects of human disturbance on the breeding success of gulls

Treesearch

Henry C. Robert; C. John Ralph

1975-01-01

A number of factors have been suggested as affecting reproductive success in gulls. In this study we have attempted to isolate the effect of human disturbance on breeding success. We held other factors such as age of birds, terrain, and density of colony as constant as was practicable with a varied colony environment. There have been several previous discussions of the...

Merging pedigree databases to describe and compare mating practices and gene flow between pedigree dogs in France, Sweden and the UK.

PubMed

Wang, S; Leroy, G; Malm, S; Lewis, T; Strandberg, E; Fikse, W F

2017-04-01

Merging pedigree databases across countries may improve the ability of kennel organizations to monitor genetic variability and health-related issues of pedigree dogs. We used data provided by the Société Centrale Canine (France), Svenska Kennelklubben (Sweden) and the Kennel Club (UK) to study the feasibility of merging pedigree databases across countries and describe breeding practices and international gene flow within the following four breeds: Bullmastiff (BMA), English setter (ESE), Bernese mountain dog (BMD) and Labrador retriever (LBR). After merging the databases, genealogical parameters and founder contributions were calculated according to the birth period, breed and registration country of the dogs. Throughout the investigated period, mating between close relatives, measured as the proportion of inbred individuals (considering only two generations of pedigree), decreased or remained stable, with the exception of LBR in France. Gene flow between countries became more frequent, and the origins of populations within countries became more diverse over time. In conclusion, the potential to reduce inbreeding within purebred dog populations through exchanging breeding animals across countries was confirmed by an improved effective population size when merging populations from different countries. © 2016 Blackwell Verlag GmbH.

Molecular characterization of high performance inbred lines of Brazilian common beans.

PubMed

Cardoso, P C B; Veiga, M M; de Menezes, I P P; Valdisser, P A M R; Borba, T C O; Melo, L C; Del Peloso, M J; Brondani, C; Vianello, R P

2013-02-06

The identification of germplasm genetic variability in breeding programs of the common bean (Phaseolus vulgaris) is essential for determining the potential of each combination of parent plants to obtain superior genotypes. The present study aimed to estimated the extent of genetic diversity in 172 lineages and cultivars of the common bean by integrating five tests of value for cultivation and use (VCU) that were conducted over the last eight years by the breeding program of Embrapa Arroz e Feijão in Brazil. Nine multilocus genotyping systems composed of 36 fluorescent microsatellite markers distributed across 11 different chromosomes of the common bean were used, of which 24 were polymorphic in all trials. One hundred and eighty-seven alleles were identified, with an average of 7.79 alleles per locus and an average gene diversity of 0.65. The combined probability of identity for all loci was 1.32 x 10(-16). Lineages that are more genetically divergent between the selection cycles were identified, allowing the breeding program to develop a crossbreed between elite genotypes with a low degree of genetic relatedness. HE values ranged from 0.31 to 0.63, with a large reduction in the genetic base over successive selection cycles. The test showed a significant degree of differentiation (FST = 0.159). Private alleles (26%) were identified and can be directly incorporated into the gene pool of cultivated germplasm, thereby contributing effectively to the expansion of genetic diversity in this bean-breeding program.

High genetic diversity of Jatropha curcas assessed by ISSR.

PubMed

Díaz, B G; Argollo, D M; Franco, M C; Nucci, S M; Siqueira, W J; de Laat, D M; Colombo, C A

2017-05-31

Jatropha curcas L. is a highly promising oilseed for sustainable production of biofuels and bio-kerosene due to its high oil content and excellent quality. However, it is a perennial and incipiently domesticated species with none stable cultivar created until now despite genetic breeding programs in progress in several countries. Knowledge of the genetic structure and diversity of the species is a necessary step for breeding programs. The molecular marker can be used as a tool for speed up the process. This study was carried out to assess genetic diversity of a germplasm bank represented by J. curcas accessions from different provenance beside interspecific hybrid and backcrosses generated by IAC breeding programs using inter-simple sequence repeat markers. The molecular study revealed 271 bands of which 98.9% were polymorphic with an average of 22.7 polymorphic bands per primer. Genetic diversity of the germplasm evaluated was slightly higher than other germplasm around the world and ranged from 0.55 to 0.86 with an average of 0.59 (Jaccard index). Cluster analysis (UPGMA) revealed no clear grouping as to the geographical origin of accessions, consistent with genetic structure analysis using the Structure software. For diversity analysis between groups, accessions were divided into eight groups by origin. Nei's genetic distance between groups was 0.14. The results showed the importance of Mexican accessions, congeneric wild species, and interspecific hybrids for conservation and development of new genotypes in breeding programs.

The genome-wide structure of two economically important indigenous Sicilian cattle breeds.

PubMed

Mastrangelo, S; Saura, M; Tolone, M; Salces-Ortiz, J; Di Gerlando, R; Bertolini, F; Fontanesi, L; Sardina, M T; Serrano, M; Portolano, B

2014-11-01

Genomic technologies, such as high-throughput genotyping based on SNP arrays, provided background information concerning genome structure in domestic animals. The aim of this work was to investigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (Ne), and the patterns of linkage disequilibrium (LD) in 2 economically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. To understand the genetic relationship and to place both Sicilian breeds in a global context, genotypes from 134 other domesticated bovid breeds were used. Principal component analysis showed that the Sicilian cattle breeds were closer to individuals of Bos taurus taurus from Eurasia and formed nonoverlapping clusters with other breeds. Between the Sicilian cattle breeds, MOD was the most differentiated, whereas the animals belonging to the CIN breed showed a lower value of assignment, the presence of substructure, and genetic links with the MOD breed. The average molecular inbreeding and coancestry coefficients were moderately high, and the current estimates of Ne were low in both breeds. These values indicated a low genetic variability. Considering levels of LD between adjacent markers, the average r(2) in the MOD breed was comparable to those reported for others cattle breeds, whereas CIN showed a lower value. Therefore, these results support the need of more dense SNP arrays for a high-power association mapping and genomic selection efficiency, particularly for the CIN cattle breed. Controlling molecular inbreeding and coancestry would restrict inbreeding depression, the probability of losing beneficial rare alleles, and therefore the risk of extinction. The results generated from this study have important implications for the development of conservation and/or selection breeding programs in these 2 local cattle breeds.

Genome-wide analysis highlights genetic dilution in Algerian sheep.

PubMed

Gaouar, S B S; Lafri, M; Djaout, A; El-Bouyahiaoui, R; Bouri, A; Bouchatal, A; Maftah, A; Ciani, E; Da Silva, A B

2017-03-01

Algeria represents a reservoir of genetic diversity with local sheep breeds adapted to a large range of environments and showing specific features necessary to deal with harsh conditions. This remarkable diversity results from the traditional management of dryland by pastoralists over centuries. Most of these breeds are poorly productive, and the economic pressure leads farmers to realize anarchic cross-breeding (that is, not carried out in the framework of selection plans) with the hope to increase animal's conformation. In this study, eight of the nine local Algerian sheep breeds (D'men, Hamra, Ouled-Djellal, Rembi, Sidaoun, Tazegzawt, Berber and Barbarine) were investigated for the first time by genome-wide single-nucleotide polymorphism genotyping. At an international scale, Algerian sheep occupied an original position shaped by relations with African and European (particularly Italian) breeds. The strong genetic proximity with Caribbean and Brazilian breeds confirmed that the genetic make-up of these American breeds was largely influenced by the Atlantic slave trade. At a national scale, an alarming genetic dilution of the Berber (a primitive breed) and the Rembi was observed, as a consequence of uncontrolled mating practices with Ouled-Djellal. A similar, though less pronounced, phenomenon was also detected for the Barbarine, another ancestral breed. Genetic originality appeared to be better preserved in Tazegzawt, Hamra, D'men and Sidaoun. These breeds should be given high priority in the establishment of conservation plans to halt their progressive loss. For Berber and Barbarine that also occur in the bordering neighbor countries, urgent concerted transnational actions are needed.

Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse

PubMed Central

2013-01-01

Background Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Results Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species. Conclusions When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied. PMID:23281913

Non-invasive monitoring of reproductive and stress hormones in the endangered red panda (Ailurus fulgens fulgens).

PubMed

Beaulah Budithi, Neema Raja; Kumar, Vinod; Yalla, Suneel Kumar; Rai, Upashna; Umapathy, Govindhaswamy

2016-09-01

The red panda (Ailurus fulgens fulgens) is classified as endangered due to its declining population, habitat fragmentation and poaching. Efforts are being made to breed them in captivity as part of nationwide conservation breeding program. This study aimed to standardize Enzyme immunoassays (EIAs) to monitor reproductive (Progesterone metabolite, Testosterone) and stress hormone (Cortisol) in red panda. For this purpose, we collected 1471 faecal samples from four females and one male over a period of one year from Padmaja Naidu Himalayan Zoological Park, Darjeeling, India. HPLC confirmed the presence of immunoreactive 5α-pregnan-3α-ol-20-one, testosterone and cortisol metabolites in faecal samples. Using 5α-pregnan-3α-ol-20-one EIA, we were able to monitor reproduction and detect pregnancy in one of the females, which successfully conceived and delivered during the study period. We were also able to monitor testosterone and cortisol in faecal samples of the red panda. Faecal testosterone levels were found in higher concentration in breeding season than in non-breeding season. Faecal cortisol concentrations showed a negative relationship with ambient temperature and peaked during winter months in all animals. Standardization of EIAs and faecal hormone monitoring would facilitate red panda conservation breeding programs in India and elsewhere. Copyright © 2016 Elsevier B.V. All rights reserved.

Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia

PubMed Central

Iwata, Hiroyoshi; Hayashi, Takeshi; Terakami, Shingo; Takada, Norio; Sawamura, Yutaka; Yamamoto, Toshiya

2013-01-01

Although the potential of marker-assisted selection (MAS) in fruit tree breeding has been reported, bi-parental QTL mapping before MAS has hindered the introduction of MAS to fruit tree breeding programs. Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. Selection based on genomic predictions of breeding values (genomic selection: GS) is another alternative for MAS. This study examined the potential of GWAS and GS in pear breeding with 76 Japanese pear cultivars to detect significant associations of 162 markers with nine agronomic traits. We applied multilocus Bayesian models accounting for ordinal categorical phenotypes for GWAS and GS model training. Significant associations were detected at harvest time, black spot resistance and the number of spurs and two of the associations were closely linked to known loci. Genome-wide predictions for GS were accurate at the highest level (0.75) in harvest time, at medium levels (0.38–0.61) in resistance to black spot, firmness of flesh, fruit shape in longitudinal section, fruit size, acid content and number of spurs and at low levels (<0.2) in all soluble solid content and vigor of tree. Results suggest the potential of GWAS and GS for use in future breeding programs in Japanese pear. PMID:23641189

Domestication and Breeding of Tomatoes: What have We Gained and What Can We Gain in the Future?

PubMed Central

Bai, Yuling; Lindhout, Pim

2007-01-01

Background It has been shown that a large variation is present and exploitable from wild Solanum species but most of it is still untapped. Considering the thousands of Solanum accessions in different gene banks and probably even more that are still untouched in the Andes, it is a challenge to exploit the diversity of tomato. What have we gained from tomato domestication and breeding and what can we gain in the future? Scope This review summarizes progress on tomato domestication and breeding and current efforts in tomato genome research. Also, it points out potential challenges in exploiting tomato biodiversity and depicts future perspectives in tomato breeding with the emerging knowledge from tomato-omics. Conclusions From first domestication to modern breeding, the tomato has been continually subjected to human selection for a wide array of applications in both science and commerce. Current efforts in tomato breeding are focused on discovering and exploiting genes for the most important traits in tomato germplasm. In the future, breeders will design cultivars by a process named ‘breeding by design’ based on the combination of science and technologies from the genomic era as well as their practical skills. PMID:17717024

Population structure and genetic differentiation of livestock guard dog breeds from the Western Balkans.

PubMed

Ceh, E; Dovc, P

2014-08-01

Livestock guard dog (LGD) breeds from the Western Balkans are a good example of how complex genetic diversity pattern observed in dog breeds has been shaped by transition in dog breeding practices. Despite their common geographical origin and relatively recent formal recognition as separate breeds, the Karst Shepherd, Sarplaninac and Tornjak show distinct population dynamics, assessed by pedigree, microsatellite and mtDNA data. We genotyped 493 dogs belonging to five dog breeds using a set of 18 microsatellite markers and sequenced mtDNA from 94 dogs from these breeds. Different demographic histories of the Karst Shepherd and Tornjak breeds are reflected in the pedigree data with the former breed having more unbalanced contributions of major ancestors and a realized effective population size of less than 20 animals. The highest allelic richness was found in Sarplaninac (5.94), followed by Tornjak (5.72), whereas Karst Shepherd dogs exhibited the lowest allelic richness (3.33). Similarly, the highest mtDNA haplotype diversity was found in Sarplaninac, followed by Tornjak and Karst Shepherd, where only one haplotype was found. Based on FST differentiation values and high percentages of animals correctly assigned, all breeds can be considered genetically distinct. However, using microsatellite data, common ancestry between the Karst Shepherd and Sarplaninac could not be reconstructed, despite pedigree and mtDNA evidence of their historical admixture. Using neighbour-joining, STRUCTURE or DAPC methods, Sarplaninac and Caucasian Shepherd breeds could not be separated and additionally showed close proximity in the NeighborNet tree. STRUCTURE analysis of the Tornjak breed demonstrated substructuring, which needs further investigation. Altogether, results of this study show that the official separation of these dog breeds strongly affected the resolution of genetic differentiation and thus suggest that the relationships between breeds are not only determined by breed relatedness, but in small populations even more importantly by stochastic effects. © 2014 Blackwell Verlag GmbH.

Mammary gland and milk fatty acid composition of two dairy goat breeds under feed-restriction.

PubMed

Palma, Mariana; Alves, Susana P; Hernández-Castellano, Lorenzo E; Capote, Juan; Castro, Noemí; Argüello, Anastasio; Matzapetakis, Manolis; Bessa, Rui J B; de Almeida, André M

2017-08-01

Goat dairy products are an important source of animal protein in the tropics. During the dry season, pasture scarcity leads animals to lose up to 40% of their body weight, a condition known as Seasonal Weight Loss (SWL) that is one of the major constraints in ruminant production. Breeds with high tolerance to SWL are relevant to understand the physiological responses to pasture scarcity so they could be used in programs for animal breeding. In the Canary Islands there are two dairy goat breeds with different levels of tolerance to SWL: the Palmera, susceptible to SWL; and the Majorera, tolerant to SWL. Fat is one of the milk components most affected by environmental and physiological conditions. This study hypothesises that feed-restriction affects Majorera and Palmera breeds differently, leading to different fatty acid profiles in the mammary gland and milk. An interaction between breed and feed-restriction was observed in the mammary gland. Feed-restriction was associated with an increase in oleic acid and a decrease in palmitic acid percentage in the Palmera breed whereas no differences were observed in the Majorera breed. Palmitic and oleic acids together constituted around 60% of the total fatty acids identified, which suggests that Palmera breed is more susceptible to SWL. In milk, feed-restriction affected both breeds similarly. Regarding the interaction of the breed with the treatment, we also observed similar responses in both breeds, but this influence affects only around 2% of the total fatty acids. In general, Majorera breed is more tolerant to feed-restriction.

Impact of including growth, carcass and feed efficiency traits in the breeding goal for combined milk and beef production systems.

PubMed

Hietala, P; Juga, J

2017-04-01

Improving feed efficiency in dairy cattle could result in more profitable and environmentally sustainable dairy production through lowering feed costs and emissions from dairy farming. In addition, beef production based on dairy herds generates fewer greenhouse gas emissions per unit of meat output than beef production from suckler cow systems. Different scenarios were used to assess the profitability of adding traits, excluded from the current selection index for Finnish Ayrshire, to the breeding goal for combined dairy and beef production systems. The additional breeding goal traits were growth traits (average daily gain of animals in the fattening and rearing periods), carcass traits (fat covering, fleshiness and dressing percentage), mature live weight (LW) of cows and residual feed intake (RFI) traits. A breeding scheme was modeled for Finnish Ayrshire under the current market situation in Finland using the deterministic simulation software ZPLAN+. With the economic values derived for the current production system, the inclusion of growth and carcass traits, while preventing LW increase generated the highest improvement in the discounted profit of the breeding program (3.7%), followed by the scenario where all additional traits were included simultaneously (5.1%). The use of a selection index that included growth and carcass traits excluding LW, increased the profit (0.8%), but reduced the benefits resulted from breeding for beef traits together with LW. A moderate decrease in the profit of the breeding program was obtained when adding only LW to the breeding goal (-3.1%), whereas, adding only RFI traits to the breeding goal resulted in a minor increase in the profit (1.4%). Including beef traits with LW in the breeding goal showed to be the most potential option to improve the profitability of the combined dairy and beef production systems and would also enable a higher rate of self-sufficiency in beef. When considering feed efficiency related traits, the inclusion of LW traits in the breeding goal that includes growth and carcass traits could be more profitable than the inclusion of RFI, because the marginal costs of measuring LW can be expected to be lower than for RFI and it is readily available for selection. In addition, before RFI can be implemented as a breeding objective, the genetic correlations between RFI and other breeding goal traits estimated for the studied population as well as information on the most suitable indicator traits for RFI are needed to assess more carefully the consequences of selecting for RFI.

Establishment of American chestnuts (Castanea dentata) bred for blight (Cryphonectria parasitica ) resistance: influence of breeding and nursery grading

Treesearch

Stacy L. Clark; Scott E. Schlarbaum; Arnold M. Saxton; Frederick V. Hebard

2016-01-01

European and American chestnut species (Castanea) have been decimated by exotic species, most notably chestnut blight (Cryphonectria parasitica), since the early nineteenth century. Backcross breeding programs that transfer blight disease resistance from Chinese chestnut (C. mollissima) into American...

Sustaining the future of plant breeding: The critical role of the USDA-ARS National Plant Germplasm System

USDA-ARS?s Scientific Manuscript database

Plant breeders require genetic diversity in their breeding programs to develop cultivars that are productive, nutritious, tolerant of biotic and abiotic stresses, and make efficient use of water and fertilizer. The USDA-ARS National Plant Germplasm System (NPGS) is a major source for global plant ge...

Dissecting genotype × environment interactions and trait correlations present in the Pee Dee cotton germplasm collection following seventy years of plant breeding

USDA-ARS?s Scientific Manuscript database

Genotype × environment interactions and trait correlations significantly impact efforts to develop high yield, high quality, and environmentally stable Upland cotton (Gossypium hirsutum L.) cultivars. Knowledge of both can and should be used to design optimal breeding programs and effective selectio...

Tandem selection for fusiform rust sisease resistance to develop a clonal elite breeding population of loblolly pine

Treesearch

Steve McKeand; Saul Garcia; Josh Steiger; Jim Grissom; Ross Whetten; Fikret Isik

2012-01-01

The elite breeding populations of loblolly pine (Pinus taeda L.) in the North Carolina State University Cooperative Tree Improvement Program are intensively managed for short-term genetic gain. Fusiform rust disease, caused by the fungus Cronartium quercuum f. sp. fusiforme, is the most economically...

Proceedings of the symposium on isozymes of North American forest trees and forest insects; July 27, 1979; Berkeley, California

Treesearch

M. Thompson Conkle

1981-01-01

These 10 symposium papers discuss gene resource management, basic genetics, genetic variation between and within tree species, genetic variability and growth, comparisons of tree life history characteristics, genetic variation in forest insects, breeding systems, and applied uses of isozymes in breeding programs.

Development and integration of an SSR-based molecular identity database into sugarcane breeding program

USDA-ARS?s Scientific Manuscript database

Sugarcane breeding is very difficult and it takes 12 to 14 years to develop a new cultivar for commercial production. This is because sugarcane varieties are highly polyploid, inter-specific hybrids with 100 to 130 chromosomes that may vary across geographical areas. Other obstacles/constraints incl...

Index-in-retrospect and breeding objectives characterizing genetic improvement programs for South African Nguni cattle

USDA-ARS?s Scientific Manuscript database

The objective of the current study was to describe the historical selection applied to Nguni cattle in South Africa. Index-in-retrospect methods were applied to data originating from the National Beef Cattle Improvement Scheme. Data used were estimated breeding values (EBV) for animals born during t...

Biobanking genetic resources: Challenges and implementation at the USDA National Animal Germplasm Program

USDA-ARS?s Scientific Manuscript database

There is adequate infrastructure in the US to identify and acquire germplasm from the major beef and dairy cattle and swine breeds. However, when we venture outside these species the same tasks become more difficult because of a lack of breed associations, databases that include genotypic and pheno...

Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers

USDA-ARS?s Scientific Manuscript database

Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize lines developed and/or widely used by CIMMYT breeding programs both in Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population stru...

Rebuilding Hawaii’s Anthurium germplasm collection for cultivar and species preservation, breeding, and biotechnological research

USDA-ARS?s Scientific Manuscript database

Anthurium is the third most important floriculture crop in Hawaii, grown mainly as a cut flower. The University of Hawaii (UH) has a well-established anthurium breeding program since 1950, with a germplasm collection assembled from backyard growers, hobbyists, researchers and collection trips from c...

Honey bee stock genotypes do not affect the level of physiological responses to chalkbrood fungus, Ascosphaera apis.

USDA-ARS?s Scientific Manuscript database

Breeding honey bees (Apis mellifera) for physiological resistance to diseases is a highly desirable and environmentally safe approach to increasing colony survival. Selection of desirable traits is a critical element of any breeding program. In this study we investigate whether honey bee stocks dif...

Parameter-based stochastic simulation of selection and breeding for multiple traits

Treesearch

Jennifer Myszewski; Thomas Byram; Floyd Bridgwater

2006-01-01

To increase the adaptability and economic value of plantations, tree improvement professionals often manage multiple traits in their breeding programs. When these traits are unfavorably correlated, breeders must weigh the economic importance of each trait and select for a desirable aggregate phenotype. Stochastic simulation allows breeders to test the effects of...

What can be Learned from Silage Breeding Programs?

NASA Astrophysics Data System (ADS)

Lorenz, Aaron J.; Coors, James G.

Improving the quality of cellulosic ethanol feedstocks through breeding and genetic manipulation could significantly impact the economics of this industry. Attaining this will require comprehensive and rapid characterization of large numbers of samples. There are many similarities between improving corn silage quality for dairy production and improving feedstock quality for cellulosic ethanol. It was our objective to provide insight into what is needed for genetic improvement of cellulosic feedstocks by reviewing the development and operation of a corn silage breeding program. We discuss the evolving definition of silage quality and relate what we have learned about silage quality to what is needed for measuring and improving feedstock quality. In addition, repeatability estimates of corn stover traits are reported for a set of hybrids. Repeatability of theoretical ethanol potential measured by near-infrared spectroscopy is high, suggesting that this trait may be easily improved through breeding. Just as cell wall digestibility has been factored into the latest measurements of silage quality, conversion efficiency should be standardized and included in indices of feedstock quality to maximize overall, economical energy availability.

Genome engineering in ornamental plants: Current status and future prospects.

PubMed

Kishi-Kaboshi, Mitsuko; Aida, Ryutaro; Sasaki, Katsutomo

2018-03-13

Ornamental plants, like roses, carnations, and chrysanthemums, are economically important and are sold all over the world. In addition, numerous cut and garden flowers add colors to homes and gardens. Various strategies of plant breeding have been employed to improve traits of many ornamental plants. These approaches span from conventional techniques, such as crossbreeding and mutation breeding, to genetically modified plants. Recently, genome editing has become available as an efficient means for modifying traits in plant species. Genome editing technology is useful for genetic analysis and is poised to become a common breeding method for ornamental plants. In this review, we summarize the benefits and limitations of conventional breeding techniques and genome editing methods and discuss their future potential to accelerate the rate breeding programs in ornamental plants. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance

PubMed Central

Miah, Gous; Rafii, Mohd Y.; Ismail, Mohd R.; Puteh, Adam B.; Rahim, Harun A.; Islam, Kh. Nurul; Latif, Mohammad Abdul

2013-01-01

Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR), and they are typically composed of 1–6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS) can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS in rice breeding programs aimed at improving blast resistance in this species. We also discuss the various advantages, disadvantages and uses of microsatellite markers relative to other molecular marker types. PMID:24240810

Single-Step BLUP with Varying Genotyping Effort in Open-Pollinated Picea glauca.

PubMed

Ratcliffe, Blaise; El-Dien, Omnia Gamal; Cappa, Eduardo P; Porth, Ilga; Klápště, Jaroslav; Chen, Charles; El-Kassaby, Yousry A

2017-03-10

Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters, as well as rankings of selection candidates, using single-step genomic evaluation (HBLUP). In this study, two traits with diverse heritabilities [tree height (HT) and wood density (WD)] were assessed at various levels of family genotyping efforts (0, 25, 50, 75, and 100%) from a population of white spruce ( Picea glauca ) consisting of 1694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada. The results revealed that HBLUP bivariate analysis is effective in reducing the known bias in heritability estimates of open-pollinated populations, as it exposes hidden relatedness, potential pedigree errors, and inbreeding. The addition of genomic information in the analysis considerably improved the accuracy in breeding value estimates by accounting for both Mendelian sampling and historical coancestry that were not captured by the contemporary pedigree alone. Increasing family genotyping efforts were associated with continuous improvement in model fit, precision of genetic parameters, and breeding value accuracy. Yet, improvements were observed even at minimal genotyping effort, indicating that even modest genotyping effort is effective in improving genetic evaluation. The combined utilization of both pedigree and genomic information may be a cost-effective approach to increase the accuracy of breeding values in forest tree breeding programs where shallow pedigrees and large testing populations are the norm. Copyright © 2017 Ratcliffe et al.

Efficient Breeding by Genomic Mating.

PubMed

Akdemir, Deniz; Sánchez, Julio I

2016-01-01

Selection in breeding programs can be done by using phenotypes (phenotypic selection), pedigree relationship (breeding value selection) or molecular markers (marker assisted selection or genomic selection). All these methods are based on truncation selection, focusing on the best performance of parents before mating. In this article we proposed an approach to breeding, named genomic mating, which focuses on mating instead of truncation selection. Genomic mating uses information in a similar fashion to genomic selection but includes information on complementation of parents to be mated. Following the efficiency frontier surface, genomic mating uses concepts of estimated breeding values, risk (usefulness) and coefficient of ancestry to optimize mating between parents. We used a genetic algorithm to find solutions to this optimization problem and the results from our simulations comparing genomic selection, phenotypic selection and the mating approach indicate that current approach for breeding complex traits is more favorable than phenotypic and genomic selection. Genomic mating is similar to genomic selection in terms of estimating marker effects, but in genomic mating the genetic information and the estimated marker effects are used to decide which genotypes should be crossed to obtain the next breeding population.

Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement

PubMed Central

Spindel, J E; Begum, H; Akdemir, D; Collard, B; Redoña, E; Jannink, J-L; McCouch, S

2016-01-01

To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with demand. Genomic selection (GS) is a new technique that helps accelerate the rate of genetic gain in breeding by using whole-genome data to predict the breeding value of offspring. Here, we describe a new GS model that combines RR-BLUP with markers fit as fixed effects selected from the results of a genome-wide-association study (GWAS) on the RR-BLUP training data. We term this model GS + de novo GWAS. In a breeding population of tropical rice, GS + de novo GWAS outperformed six other models for a variety of traits and in multiple environments. On the basis of these results, we propose an extended, two-part breeding design that can be used to efficiently integrate novel variation into elite breeding populations, thus expanding genetic diversity and enhancing the potential for sustainable productivity gains. PMID:26860200

Effects of clearcutting, patch cutting, and low-density shelterwoods on breeding birds and tree regeneration in New Hampshire northern hardwoods

Treesearch

Mariko Yamasaki; Christine A. Costello; William B. Leak

2014-01-01

Clearcutting is an effective regeneration practice for northern hardwoods in New England. However, in esthetically sensitive areas forest managers sometimes use methods that soften the visual impact, such as smaller clearcuts (patch cuts) or low-density shelterwoods. It is unclear if these methods produce the same effects as clearcuts on tree regeneration and breeding...

Methods to address poultry robustness and welfare issues through breeding and associated ethical considerations

PubMed Central

Muir, William M.; Cheng, Heng-Wei; Croney, Candace

2014-01-01

As consumers and society in general become more aware of ethical and moral dilemmas associated with intensive rearing systems, pressure is put on the animal and poultry industries to adopt alternative forms of housing. This presents challenges especially regarding managing competitive social interactions between animals. However, selective breeding programs are rapidly advancing, enhanced by both genomics and new quantitative genetic theory that offer potential solutions by improving adaptation of the bird to existing and proposed production environments. The outcomes of adaptation could lead to improvement of animal welfare by increasing fitness of the animal for the given environments, which might lead to increased contentment and decreased distress of birds in those systems. Genomic selection, based on dense genetic markers, will allow for more rapid improvement of traits that are expensive or difficult to measure, or have a low heritability, such as pecking, cannibalism, robustness, mortality, leg score, bone strength, disease resistance, and thus has the potential to address many poultry welfare concerns. Recently selection programs to include social effects, known as associative or indirect genetic effects (IGEs), have received much attention. Group, kin, multi-level, and multi-trait selection including IGEs have all been shown to be highly effective in reducing mortality while increasing productivity of poultry layers and reduce or eliminate the need for beak trimming. Multi-level selection was shown to increases robustness as indicated by the greater ability of birds to cope with stressors. Kin selection has been shown to be easy to implement and improve both productivity and animal well-being. Management practices and rearing conditions employed for domestic animal production will continue to change based on ethical and scientific results. However, the animal breeding tools necessary to provide an animal that is best adapted to these changing conditions are readily available and should be used, which will ultimately lead to the best possible outcomes for all impacted. PMID:25505483

Linkage disequilibrium, persistence of phase, and effective population size in Spanish local beef cattle breeds assessed through a high-density single nucleotide polymorphism chip.

PubMed

Cañas-Álvarez, J J; Mouresan, E F; Varona, L; Díaz, C; Molina, A; Baro, J A; Altarriba, J; Carabaño, M J; Casellas, J; Piedrafita, J

2016-07-01

Linkage disequilibrium (LD) and persistence of phase are fundamental approaches for exploring the genetic basis of economically important traits in cattle, including the identification of QTL for genomic selection and the estimation of effective population size () to determine the size of the training populations. In this study, we have used the Illumina BovineHD chip in 168 trios of 7 Spanish beef cattle breeds to obtain an overview of the magnitude of LD and the persistence of LD phase through the physical distance between markers. Also, we estimated the time of divergence based on the persistence of the LD phase and calculated past from LD estimates using different alternatives to define the recombination rate. Estimates of average (as a measure of LD) for adjacent markers were close to 0.52 in the 7 breeds and decreased with the distance between markers, although in long distances, some LD still remained (0.07 and 0.05 for markers 200 kb and 1 Mb apart, respectively). A panel with a lower boundary of 38,000 SNP would be necessary to launch a successful within-breed genomic selection program. Persistence of phase, measured as the pairwise correlations between estimates of in 2 breeds at short distances (10 kb), was in the 0.89 to 0.94 range and decreased from 0.33 to 0.52 to a range of 0.01 to 0.08 when marker distance increased from 200 kb to 1 Mb, respectively. The magnitude of the persistence of phase between the Spanish beef breeds was similar to those found in dairy breeds. For across-breed genomic selection, the size of the SNP panels must be in the range of 50,000 to 83,000 SNP. Estimates of past showed values ranging from 26 to 31 for 1 generation ago in all breeds. The divergence among breeds occurred between 129 and 207 generations ago. The results of this study are relevant for the future implementation of within- and across-breed genomic selection programs in the Spanish beef cattle populations. Our results suggest that a reduced subset of the SNP panel would be enough to achieve an adequate precision of the genomic predictions.

Different Seed Selection and Conservation Practices for Fresh Market and Dried Chile Farmers in Aguascalientes, Mexico

PubMed Central

de Jesús Luna-Ruíz, José; Gepts, Paul

2010-01-01

Different Seed Selection and Conservation Practices for Fresh Market and Dried Chile Farmers in Aguascalientes, Mexico. The process of selecting and saving seed is the most basic and oldest of agricultural practices. In today’s modern and highly capital-intensive agriculture, seeds are often treated like another chemical input. This study sought to examine seed selection and saving practices among chile farmers in Aguascalientes, Mexico, where both industrial and traditional agriculture are practiced. We observed a clear division among farmers who plant chile peppers commercially. Sixty-eight chile pepper farmers were surveyed in order to document seed selection and saving practices. Fifteen respondents (22%) planted chile peppers destined for the fresh market and all utilized purchased commercial seed of F1 hybrid varieties. Fifty-three farmers (78%) planted chiles to be dried and either saved their own or purchased seeds that others had saved and selected. Farmers who saved their own seed sought to maintain an ideotype, rather than directionally select for certain traits, much like Cleveland et al. (2000) chronicled in central Mexican maize farmers. Farmers would benefit from a participatory plant-breeding program in order to maintain productive seed stock for the continued cultivation of dried chile pepper in the state. PMID:21212817

Different Seed Selection and Conservation Practices for Fresh Market and Dried Chile Farmers in Aguascalientes, Mexico.

PubMed

Kraft, Kraig H; de Jesús Luna-Ruíz, José; Gepts, Paul

2010-12-01

Different Seed Selection and Conservation Practices for Fresh Market and Dried Chile Farmers in Aguascalientes, Mexico. The process of selecting and saving seed is the most basic and oldest of agricultural practices. In today's modern and highly capital-intensive agriculture, seeds are often treated like another chemical input. This study sought to examine seed selection and saving practices among chile farmers in Aguascalientes, Mexico, where both industrial and traditional agriculture are practiced. We observed a clear division among farmers who plant chile peppers commercially. Sixty-eight chile pepper farmers were surveyed in order to document seed selection and saving practices. Fifteen respondents (22%) planted chile peppers destined for the fresh market and all utilized purchased commercial seed of F1 hybrid varieties. Fifty-three farmers (78%) planted chiles to be dried and either saved their own or purchased seeds that others had saved and selected. Farmers who saved their own seed sought to maintain an ideotype, rather than directionally select for certain traits, much like Cleveland et al. (2000) chronicled in central Mexican maize farmers. Farmers would benefit from a participatory plant-breeding program in order to maintain productive seed stock for the continued cultivation of dried chile pepper in the state.

Breeding of tomorrow's chickens to improve well-being.

PubMed

Cheng, H-W

2010-04-01

Chickens, as well as other animals, have the ability to change their behavior (behavioral plasticity) and physiology (physiological plasticity) based on the costs and benefits to fit their environment (adaptation). Through natural selection, the population preserves and accumulates traits that are beneficial and rejects those that are detrimental in their prevailing environments. The surviving populations are able to contribute more genes associated with beneficial traits for increased fitness to subsequent generations. Natural selection is slow but constant; working over multiple generations, the changes to the population often appear silent or undetectable at a given point in history. Chickens were domesticated from the wild red jungle fowl. The principle of domestication of chickens, as well as other farm animals, by humans is similar to that of natural selection: selecting the best animals with the highest survivability and reproducibility (artificial selection). Compared with natural selection, the process of artificial selection is motivated by human needs and acts more rapidly with more visible results over a short time period. This process has been further accelerated following the development of current breeding programs and the emergence of specialized breeding companies. A laying hen, for example, produces more than 300 hundred eggs a year, whereas a jungle fowl lays 4 to 6 eggs in a year. During the domestication process, chickens retained their capability to adapt to their housing environments, which is usually achieved by genetic changes occurring with each subsequent generation. Genes control the behavioral, physiological, immunological, and psychological responses of animals to stressors, including environmental stimulations. With advances in understanding of genetic mediation of animal physiology and behavior and the discovery of the genome sequences of many species, animal production breeding programs can be improved in both speed and efficiency. Modern chicken breeding programs have the potential to be operated successfully in the breeding of tomorrow's chickens with high production efficiency and optimal welfare, resulting from resistance to stress, disease, or both.

A Philosophical Twist to the Scholar-Practitioner Tradition

ERIC Educational Resources Information Center

Bailey, Scott; Gautam, Chetanath

2015-01-01

A new breed of leader is needed for American public schools, one who can both promote the public good and meet modern accountability demands. Often referred to as a scholar-practitioner, this type of leader blends theory with practice, philosophizing practice while practicing a philosophy. Such blending in a person is not simple, however, because…

Mating programs including genomic relationships

USDA-ARS?s Scientific Manuscript database

Computer mating programs have helped breeders minimize pedigree inbreeding and avoid recessive defects by mating animals with parents that have fewer common ancestors. With genomic selection, breed associations, AI organizations, and on-farm software providers could use new programs to minimize geno...

Strategies for Selecting Crosses Using Genomic Prediction in Two Wheat Breeding Programs.

PubMed

Lado, Bettina; Battenfield, Sarah; Guzmán, Carlos; Quincke, Martín; Singh, Ravi P; Dreisigacker, Susanne; Peña, R Javier; Fritz, Allan; Silva, Paula; Poland, Jesse; Gutiérrez, Lucía

2017-07-01

The single most important decision in plant breeding programs is the selection of appropriate crosses. The ideal cross would provide superior predicted progeny performance and enough diversity to maintain genetic gain. The aim of this study was to compare the best crosses predicted using combinations of mid-parent value and variance prediction accounting for linkage disequilibrium (V) or assuming linkage equilibrium (V). After predicting the mean and the variance of each cross, we selected crosses based on mid-parent value, the top 10% of the progeny, and weighted mean and variance within progenies for grain yield, grain protein content, mixing time, and loaf volume in two applied wheat ( L.) breeding programs: Instituto Nacional de Investigación Agropecuaria (INIA) Uruguay and CIMMYT Mexico. Although the variance of the progeny is important to increase the chances of finding superior individuals from transgressive segregation, we observed that the mid-parent values of the crosses drove the genetic gain but the variance of the progeny had a small impact on genetic gain for grain yield. However, the relative importance of the variance of the progeny was larger for quality traits. Overall, the genomic resources and the statistical models are now available to plant breeders to predict both the performance of breeding lines per se as well as the value of progeny from any potential crosses. Copyright © 2017 Crop Science Society of America.

Long-term on-farm participatory maize breeding by stratified mass selection retains molecular diversity while improving agronomic performance.

PubMed

Alves, Mara Lisa; Belo, Maria; Carbas, Bruna; Brites, Cláudia; Paulo, Manuel; Mendes-Moreira, Pedro; Brites, Carla; Bronze, Maria do Rosário; Šatović, Zlatko; Vaz Patto, Maria Carlota

2018-02-01

Modern maize breeding programs gave rise to genetically uniform varieties that can affect maize's capacity to cope with increasing climate unpredictability. Maize populations, genetically more heterogeneous, can evolve and better adapt to a broader range of edaphic-climatic conditions. These populations usually suffer from low yields; it is therefore desirable to improve their agronomic performance while maintaining their valuable diversity levels. With this objective, a long-term participatory breeding/on-farm conservation program was established in Portugal. In this program, maize populations were subject to stratified mass selection. This work aimed to estimate the effect of on-farm stratified mass selection on the agronomic performance, quality, and molecular diversity of two historical maize populations. Multilocation field trials, comparing the initial populations with the derived selection cycles, showed that this selection methodology led to agronomic improvement for one of the populations. The molecular diversity analysis, using microsatellites, revealed that overall genetic diversity in both populations was maintained throughout selection. The comparison of quality parameters between the initial populations and the derived selection cycles was made using kernel from a common-garden experiment. This analysis showed that the majority of the quality traits evaluated progressed erratically over time. In conclusion, this breeding approach, through simple and low-cost methodologies, proved to be an alternative strategy for genetic resources' on-farm conservation.

Oral fluid samples used for PRRSV acclimatization program and sow performance monitoring in endemic PRRS-positive farms.

PubMed

Woonwong, Yonlayong; Kedkovid, Roongtham; Arunorat, Jirapat; Sirisereewan, Chaitawat; Nedumpun, Teerawut; Poonsuk, Korakrit; Panyasing, Yaowalak; Poolperm, Pariwat; Boonsoongnern, Alongkot; Thanawongnuwech, Roongroje

2018-02-01

An effective gilt acclimatization program is one of the most important management strategies for controlling porcine reproductive and respiratory syndrome virus (PRRSV) infection. Recently, oral fluid samples have been used as alternative diagnostic samples for various swine diseases. This study utilized oral fluids for PRRSV monitoring during the gilt acclimatization period in PRRSV endemic farms. The study was performed in two selected commercial breeding herds (farm A and farm B). PRRSV RNA and PRRSV-specific antibodies were monitored using oral fluid and serum samples. Sow performance parameters related to PRRSV infection were recorded and assessed. After PRRSV exposure during acclimatization, viral RNA was demonstrated in oral fluids from 1 to 10 weeks post-exposure (WPE). PRRSV RNA was detected in serum at 1 and 4 WPE in farm A and at 1, 4, 8, and 12 WPE in farm B. Prolonged viremia of gilts from farm B was possibly due to re-infection (within the herd) and later, reproductive problems were found in the breeding herd. The correlation of PRRSV RNA concentration in oral fluids and serum was evident. The S/P ratio values of PRRSV antibodies in oral fluid samples were higher and had similar patterns of antibody responses to the serum samples. The results suggest that the use of oral fluid samples for PRRSV monitoring during gilt acclimatization in endemic farms is effective, convenient, practical, and economical and would be most beneficial when used with other parameters.

On the value of the phenotypes in the genomic era.

PubMed

Gonzalez-Recio, O; Coffey, M P; Pryce, J E

2014-12-01

Genetic improvement programs around the world rely on the collection of accurate phenotypic data. These phenotypes have an inherent value that can be estimated as the contribution of an additional record to genetic gain. Here, the contribution of phenotypes to genetic gain was calculated using traditional progeny testing (PT) and 2 genomic selection (GS) strategies that, for simplicity, included either males or females in the reference population. A procedure to estimate the theoretical economic contribution of a phenotype to a breeding program is described for both GS and PT breeding programs through the increment in genetic gain per unit of increase in estimated breeding value reliability obtained when an additional phenotypic record is added. The main factors affecting the value of a phenotype were the economic value of the trait, the number of phenotypic records already available for the trait, and its heritability. Furthermore, the value of a phenotype was affected by several other factors, including the cost of establishing the breeding program and the cost of phenotyping and genotyping. The cost of achieving a reliability of 0.60 was assessed for different reference populations for GS. Genomic reference populations of more sires with small progeny group sizes (e.g., 20 equivalent daughters) had a lower cost than those reference populations with either large progeny group sizes for fewer genotyped sires, or female reference populations, unless the heritability was large and the cost of phenotyping exceeded a few hundred dollars; then, female reference populations were preferable from an economic perspective. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Comparative genetic diversity in a sample of pony breeds from the U.K. and North America: a case study in the conservation of global genetic resources.

PubMed

Winton, Clare L; Plante, Yves; Hind, Pamela; McMahon, Robert; Hegarty, Matthew J; McEwan, Neil R; Davies-Morel, Mina C G; Morgan, Charly M; Powell, Wayne; Nash, Deborah M

2015-08-01

Most species exist as subdivided ex situ daughter population(s) derived from a single original group of individuals. Such subdivision occurs for many reasons both natural and manmade. Traditional British and Irish pony breeds were introduced to North America (U.S.A. and Canada) within the last 150 years, and subsequently equivalent breed societies were established. We have analyzed selected U.K. and North American equivalent pony populations as a case study for understanding the relationship between putative source and derived subpopulations. Diversity was measured using mitochondrial DNA and a panel of microsatellite markers. Genetic signatures differed between the North American subpopulations according to historical management processes. Founder effect and stochastic drift was apparent, particularly pronounced in some breeds, with evidence of admixture of imported mares of different North American breeds. This demonstrates the importance of analysis of subpopulations to facilitate understanding the genetic effects of past management practices and to lead to informed future conservation strategies.

The contribution of efficient production of monozygotic twins to beef cattle breeding

PubMed Central

HASHIYADA, Yutaka

2017-01-01

Production of sires with high breeding potential is indispensable for prompt and reliable breeding using their semen in the cattle industry. Currently, in Japan, we aim to further the production of Japanese black sires via a new breeding system that uses genetically homologous monozygotic twins so that better growth performance and carcass traits can be translated to the increased production of beef with higher economic value. Several studies have reported that monozygotic twins are produced by embryo bisection. On the other hand, with the evolution and stabilization of in vitro fertilization technology, it has become possible to produce multiple monozygotic twin calves from blastomeres separated from a cleavage-stage embryo. This review attempts to clarify breeding practices through revalidation of the factors that affect the production efficiency of monozygotic twin calves by embryo bisection. Furthermore, the establishment of a system for monozygotic twin embryo production via the simplified technique of blastomere separation is reviewed while showing data from our previously performed studies. PMID:29033399

Genotype by environment interaction and the use of unbalanced historical data for genomic selection in an international wheat breeding program

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) offers breeders the possibility of using historic data and unbalanced breeding trials to form training populations for predicting the performance of new lines. However, in using datasets that are unbalanced over time and space, there is increasing exposure to particular genoty...

A 100-year review: Methods and impact of genetic selection in dairy cattle—From daughter–dam comparisons to deep learning algorithms

USDA-ARS?s Scientific Manuscript database

In the early 1900s, breed society herdbooks had been established, and milk recording programs were in their infancy. Farmers were interested in improving the productivity of dairy cattle, but the foundations of population genetics, quantitative genetics, and animal breeding had not yet been laid. Li...

Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus 'Robusta 5' accessions

USDA-ARS?s Scientific Manuscript database

Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large effect QTL for fire blight resistance has been pre...

Breed effects and genetic parameter estimates for calving difficulty and birth weight in a multi-breed population

USDA-ARS?s Scientific Manuscript database

Birth weight (BWT) and calving difficulty (CD) were recorded on 4,579 first parity females from the Germplasm Evaluation (GPE) program at the U.S. Meat Animal Research Center (USMARC). Both traits were analyzed using a bivariate animal model with direct and maternal effects. Calving difficulty was...

Early generation selection at multiple locations may identify potato parents that produce more widely adapted progency

USDA-ARS?s Scientific Manuscript database

Potato production in the eastern U.S. occurs over a wide range of environments from Maine to Florida; many of these states do not have a breeding program. Initial selections are usually made at the breeding location for more than two years before undergoing evaluation elsewhere, at which point, few...

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

USDA-ARS?s Scientific Manuscript database

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’ × ...

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2014 CFR

2014-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits..., at the time of the application, the exotic bird is still in the wild, has already been removed from the wild, or was bred in captivity; (2) If the exotic bird is still in the wild or was taken from the...

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2013 CFR

2013-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits..., at the time of the application, the exotic bird is still in the wild, has already been removed from the wild, or was bred in captivity; (2) If the exotic bird is still in the wild or was taken from the...

Efficiency of including first-generation information in second-generation ranking and selection: results of computer simulation.

Treesearch

T.Z. Ye; K.J.S. Jayawickrama; G.R. Johnson

2006-01-01

Using computer simulation, we evaluated the impact of using first-generation information to increase selection efficiency in a second-generation breeding program. Selection efficiency was compared in terms of increase in rank correlation between estimated and true breeding values (i.e., ranking accuracy), reduction in coefficient of variation of correlation...

The first research plantings of third-generation, third-backcross American chestnut (Castanea dentata) in the southeastern United States

Treesearch

Stacy Clark; S.E. Schlarbaum; F,V Saxton

2014-01-01

Production of American chestnut (Castanea dentata) resistant to the chestnut blight fungus (Cryphonectria parasitica) is being conducted currently through traditional breeding and genetic transformation. Sufficient material for field testing is currently available from The American Chestnut Foundation’s backcross breeding program. We planted approximately 4500 chestnut...

Background on the development of a nonfunded cooperative agreement between USDA’s Agricultural Research Service (ARS) and the Council on Dairy Cattle Breeding (CDCB)

USDA-ARS?s Scientific Manuscript database

Dairy producers, dairy record providers, breed associations, artificial-insemination companies, and the Animal Improvement Programs Laboratory, which is part of USDA’s Agricultural Research Service (ARS) in Beltsville, Maryland, have collaborated for many decades to provide the dairy industry with i...

Seroprevalence of antibodies to Toxoplasma gondii in Gordon's wild cat (Felis silvestris gordoni) in the Middle East

USDA-ARS?s Scientific Manuscript database

The Sand cat (Felis margarita) is a small-sized felid occurring in the United Arab Emirates (UAE). The Sand cat captive breeding program at the Breeding Centre for Endangered Arabian Wildlife (BCEAW), Sharjah, UAE, has until recently been severely compromised by very high newborn mortality rates. Tw...

Breeding trees resistant to insects and diseases: putting theory into application

Treesearch

Richard A. Sniezko; Jennifer Koch

2017-01-01

Tree species world-wide are under increasing threat from diseases and insects, many of which are non-native. The integrity of our natural, urban and plantation forest ecosystems, and the services they provide are seriously imperiled. Breeding programs that harness the natural genetic resistance within tree species can provide a durable solution to these threats. In...

Family indices for seed-orchard selection

Treesearch

Gene Namkoong

1966-01-01

Many seed orchard programs include a stage at which clones or seedlings are culled on the basis of progeny tests. Though breeding systems which involve progeny testing differ in efficiency, they all provide information on an individual's breeding value through its own performance and that of parental or seedling relatives. A combined index on any one trait, using...

Breeding graft-compatible Douglas-fir rootstocks (Pseudotsuga menziesii (Mirb.) Franco).

Treesearch

D.L. Copes

1999-01-01

A study encompassing 24 years was conducted to determine if a breeding program could produce highly graft-compatible rootstocks. Twenty-seven trees of apparent high graft compatibility were selected and crossed to produce 226 control-pollinated families. Seedlings were grown, field planted, and grafted with test scions. Graft unions from field tests were evaluated...

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

USDA-ARS?s Scientific Manuscript database

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...

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness

PubMed Central

Bink, Marco CAM; van Heerwaarden, Joost; Chancerel, Emilie; Boury, Christophe; Lesur, Isabelle; Isik, Fikret; Bouffier, Laurent; Plomion, Christophe

2016-01-01

Background Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches. Results The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait. Conclusions This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program. PMID:27806077

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness.

PubMed

Bartholomé, Jérôme; Bink, Marco Cam; van Heerwaarden, Joost; Chancerel, Emilie; Boury, Christophe; Lesur, Isabelle; Isik, Fikret; Bouffier, Laurent; Plomion, Christophe

2016-01-01

Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches. The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait. This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program.

Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed.

PubMed

Schiavo, G; Galimberti, G; Calò, D G; Samorè, A B; Bertolini, F; Russo, V; Gallo, M; Buttazzoni, L; Fontanesi, L

2016-04-01

In this study, we investigated at the genome-wide level if 20 years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni  < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population. © 2015 Stichting International Foundation for Animal Genetics.

A Qualitative Evidence of the Breeding Sites of Anopheles arabiensis Patton (Diptera: Culicidae) in and Around Kassala Town, Eastern Sudan

PubMed Central

Hamza, Asma Mahmoud; El Rayah, El Amin

2016-01-01

Anopheles arabiensis Patton (Diptera: Culicidae) is considered the most efficient malaria vector in eastern Sudan. This study aims to characterize the breeding sites of An. arabiensis throughout the year in and around Kassala town, eastern Sudan. Diverse larval habitat types were visited and characterized based on the habitat type and chemical composition. Mosquito larvae were found in many diverse habitats. During the rainy season, rain pools and water bodies created by the seasonal Gash River serve as the main breeding sites. In the dry season, irrigation canals, seepage from water pipes, neglected wells, artificial containers, and man-made ditches serve as the main breeding sites. Breeding water showed a pH of 7.9 and a low concentration of the total dissolved salts. The results of this study may be considered in planning and implementing larval control programs in the area. PMID:27547039

Adaptive traits of indigenous cattle breeds: The Mediterranean Baladi as a case study.

PubMed

Shabtay, Ariel

2015-11-01

Generally taken, breeds of Bos taurus ancestry are considered more productive, in comparison with Bos indicus derived breeds that present enhanced hardiness and disease resistance, low nutritional requirements and higher capability of feed utilization. While breeds of B. taurus have been mostly selected for intensive production systems, indigenous cattle, developed mostly from indicine and African taurines, flourish in extensive habitats. Worldwide demographic and economic processes face animal production with new challenges - the increasing demand for animal food products. Intensification of animal husbandry is thus a desired goal in stricken parts of the world. An introduction of productive traits to indigenous breeds might serve to generate improved biological and economic efficiencies. For this to succeed, the genetic merit of traits like efficiency of feed utilization and product quality should be revealed, encouraging the conservation initiatives of indigenous cattle populations, many of which are already extinct and endangered. Moreover, to overcome potential genetic homogeneity, controlled breeding practices should be undertaken. The Baladi cattle are a native local breed found throughout the Mediterranean basin. Purebred Baladi animals are rapidly vanishing, as more European breeds are being introduced or used for backcrosses leading to improved production. The superiority of Baladi over large-framed cattle, in feedlot and on Mediterranean pasture, with respect to adaptability and efficiency, is highlighted in the current review. Copyright © 2015 Elsevier Ltd. All rights reserved.

Enhancing the diversity of breeding invertebrates within field margins of intensively managed grassland: Effects of alternative management practices.

PubMed

Fritch, Rochelle A; Sheridan, Helen; Finn, John A; McCormack, Stephen; Ó hUallacháin, Daire

2017-11-01

Severe declines in biodiversity have been well documented for many taxonomic groups due to intensification of agricultural practices. Establishment and appropriate management of arable field margins can improve the diversity and abundance of invertebrate groups; however, there is much less research on field margins within grassland systems. Three grassland field margin treatments (fencing off the existing vegetation "fenced"; fencing with rotavation and natural regeneration "rotavated" and; fencing with rotavation and seeding "seeded") were compared to a grazed control in the adjacent intensively managed pasture. Invertebrates were sampled using emergence traps to investigate species breeding and overwintering within the margins. Using a manipulation experiment, we tested whether the removal of grazing pressure and nutrient inputs would increase the abundance and richness of breeding invertebrates within grassland field margins. We also tested whether field margin establishment treatments, with their different vegetation communities, would change the abundance and richness of breeding invertebrates in the field margins. Exclusion of grazing and nutrient inputs led to increased abundance and richness in nearly all invertebrate groups that we sampled. However, there were more complex effects of field margin establishment treatment on the abundance and richness of invertebrate taxa. Each of the three establishment treatments supported a distinct invertebrate community. The removal of grazing from grassland field margins provided a greater range of overwintering/breeding habitat for invertebrates. We demonstrate the capacity of field margin establishment to increase the abundance and richness in nearly all invertebrate groups in study plots that were located on previously more depauperate areas of intensively managed grassland. These results from grassland field margins provide evidence to support practical actions that can inform Greening (Pillar 1) and agri-environment measures (Pillar 2) of the Common Agricultural Policy (CAP). Before implementing specific management regimes, the conservation aims of agri-environment measures should be clarified by defining the target species or taxonomic groups.

Community knowledge, awareness and preventive practices regarding dengue fever in Puducherry - South India.

PubMed

Jeelani, S; Sabesan, S; Subramanian, S

2015-06-01

To ascertain the knowledge, attitudes and practices of adult population in Puducherry, India, regarding Dengue Fever (DF). A cross-sectional survey was carried out to assess the Knowledge, Awareness and Preventive practices (KAP) among a selected community in Puducherry on DF, following a major dengue outbreak in 2012. Between October 2012 & February 2013, an epidemiological survey was conducted among 400 households (HHs) from the most affected areas during dengue outbreak, which came under eight health delivery jurisdictions i.e. Primary Health Centres (PHCs) in Puducherry. Knowledge of dengue and the use of preventive measures were assessed by means of a pre-tested structured questionnaire. Logistic regression analysis was done to examine the association between different levels of education and income status with the knowledge of DF. The DF knowledge map was created based on the results achieved through the questionnaire using Arc GIS 10.2 software. Although about 86% of the participants had heard of dengue, although there was no adequate knowledge on dengue vector breeding habitat as 68% of the respondents thought drains & garbage as breeding places of dengue vectors. Only 25% of participants were aware of clean water as a breeding habitat. Insufficient knowledge of disease symptoms was found, with fever (59%) being the most common symptom. There is a lack of in-depth knowledge on dengue epidemiology in the Puducherry community and observation revealed that more needs to be done by the Government as well as community members to prevent vector mosquito breeding. Copyright © 2015 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

A rapid method to increase the number of F₁ plants in pea (Pisum sativum) breeding programs.

PubMed

Espósito, M A; Almirón, P; Gatti, I; Cravero, V P; Anido, F S L; Cointry, E L

2012-08-16

In breeding programs, a large number of F₂ individuals are required to perform the selection process properly, but often few such plants are available. In order to obtain more F₂ seeds, it is necessary to multiply the F₁ plants. We developed a rapid, efficient and reproducible protocol for in vitro shoot regeneration and rooting of seeds using 6-benzylaminopurine. To optimize shoot regeneration, basic medium contained Murashige and Skoog (MS) salts with or without B5 Gamborg vitamins and different concentrations of 6-benzylaminopurine (25, 50 and 75 μM) using five genotypes. We found that modified MS (B5 vitamins + 25 μM 6-benzylaminopurine) is suitable for in vitro shoot regeneration of pea. Thirty-eight hybrid combinations were transferred onto selected medium to produce shoots that were used for root induction on MS medium supplemented with α-naphthalene-acetic acid. Elongated shoots were developed from all hybrid genotypes. This procedure can be used in pea breeding programs and will allow working with a large number of plants even when the F₁ plants produce few seeds.

The Spring of Systems Biology-Driven Breeding.

PubMed

Lavarenne, Jérémy; Guyomarc'h, Soazig; Sallaud, Christophe; Gantet, Pascal; Lucas, Mikaël

2018-05-12

Genetics and molecular biology have contributed to the development of rationalized plant breeding programs. Recent developments in both high-throughput experimental analyses of biological systems and in silico data processing offer the possibility to address the whole gene regulatory network (GRN) controlling a given trait. GRN models can be applied to identify topological features helping to shortlist potential candidate genes for breeding purposes. Time-series data sets can be used to support dynamic modelling of the network. This will enable a deeper comprehension of network behaviour and the identification of the few elements to be genetically rewired to push the system towards a modified phenotype of interest. This paves the way to design more efficient, systems biology-based breeding strategies. Copyright © 2018 Elsevier Ltd. All rights reserved.

Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication

PubMed Central

Speller, Camilla F.; Kemp, Brian M.; Wyatt, Scott D.; Monroe, Cara; Lipe, William D.; Arndt, Ursula M.; Yang, Dongya Y.

2010-01-01

Although the cultural and nutritive importance of the turkey (Meleagris gallopavo) to precontact Native Americans and contemporary people worldwide is clear, little is known about the domestication of this bird compared to other domesticates. Mitochondrial DNA analysis of 149 turkey bones and 29 coprolites from 38 archaeological sites (200 BC–AD 1800) reveals a unique domesticated breed in the precontact Southwestern United States. Phylogeographic analyses indicate that this domestic breed originated from outside the region, but rules out the South Mexican domestic turkey (Meleagris gallopavo gallopavo) as a progenitor. A strong genetic bottleneck within the Southwest turkeys also reflects intensive human selection and breeding. This study points to at least two occurrences of turkey domestication in precontact North America and illuminates the intensity and sophistication of New World animal breeding practices. PMID:20133614

Nest-site competition between invasive and native cavity nesting birds and its implication for conservation.

PubMed

Charter, Motti; Izhaki, Ido; Ben Mocha, Yitzchak; Kark, Salit

2016-10-01

Nesting cavities are often a limited resource that multiple species use. There is an ongoing discussion on whether invasive cavity nesting birds restrict the availability of this key limited resource. While the answer to this question has important conservation implications, little experimental work has been done to examine it. Here, we aimed to experimentally test whether alien cavity nesting birds affect the occupancy of cavities and the resulting breeding success of native cavity breeders in a large urban park located in Tel Aviv, Israel. Over three breeding seasons, we manipulated the entry size of nest boxes and compared the occupancy and breeding success of birds in nest boxes of two treatments. These included nest boxes with large-entrance and small-entrance holes. The large-entrance holes allowed access for both the native and invasive birds (the two main aliens in the park are the common mynas and rose-ringed parakeets). The smaller-entrance boxes, on the other hand, allowed only the smaller sized native cavity breeders (great tits and house sparrows) to enter the boxes but prevented the alien species from entering. We found that the large-entrance nest boxes were occupied by five different bird species, comprising three natives (great tit, house sparrow, Scops owl) and two invasive species (common myna, rose-ringed parakeet) while the small-entrance boxes were only occupied by the two native species. The alien common mynas and rose-ringed parakeets occupied 77.5% of the large-entrance nest boxes whereas native species, mainly great tits, occupied less than 9% of the large-entrance boxes and 36.5% of the small-entrance boxes. When examining the occupancy of those cavities that were not occupied by the aliens, natives occupied both the small and large-entrance nest boxes equally. Three quarters (78%) of the great tits breeding in the large-entrance boxes were usurped by common mynas during the breeding season and as a result breeding success was significantly lower for great tits breeding in the large-entrance boxes compared with the small-entrance boxes. The results of this study suggests that the invasive alien species can reduce the breeding potential of native cavity breeders both by exploiting the limited breeding resource (nest cavities) and by directly usurping cavities already occupied by the native species. Since the majority of large-entrance nest boxes were occupied by the larger alien birds, less native species bred in the limited number of unoccupied large-entrance nest boxes because of exploitation competition. We propose that for management purposes, nest-box programs that alter the entrance size of available natural cavities may be a practical approach, reducing the competition between native cavity breeders and alien invasive birds, and especially benefiting the smaller native cavity breeders. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of management practices on grassland birds: Lesser Prairie-Chicken

USGS Publications Warehouse

Jamison, Brent E.; Dechant, Jill A.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Euliss, Betty R.

2002-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 4,000 published and unpublished papers. A range map is provided to indicate the breeding distribution of Lesser Prairie-Chicken in the United States and southern Canada. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species’ breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management is posted at the Web site mentioned below.

Effects of management practices on grassland birds: Brewer's sparrow

USGS Publications Warehouse

Walker, Brett L.

2004-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species’ breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management is posted at the Web site mentioned below.

Effects of management practices on grassland birds: Merlin

USGS Publications Warehouse

Konrad, Paul M.

2004-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the breeding, year-round, and nonbreeding ranges in the United States and southern Canada. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species’ breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management is posted at the Web site mentioned below.

Effects of management practices on grassland birds: Golden eagle

USGS Publications Warehouse

DeLong, John P.

2004-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 4,000 published and unpublished papers. A range map is provided to the breeding, year-round, and nonbreeding ranges in the United States and southern Canada. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species’ breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management is posted at the Web site mentioned below.

Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel.

PubMed

Mancini, Giordano; Gargani, Maria; Chillemi, Giovanni; Nicolazzi, Ezequiel Luis; Marsan, Paolo Ajmone; Valentini, Alessio; Pariset, Lorraine

2014-02-01

In this study we used a medium density panel of SNP markers to perform population genetic analysis in five Italian cattle breeds. The BovineSNP50 BeadChip was used to genotype a total of 2,935 bulls of Piedmontese, Marchigiana, Italian Holstein, Italian Brown and Italian Pezzata Rossa breeds. To determine a genome-wide pattern of positive selection we mapped the F st values against genome location. The highest F st peaks were obtained on BTA6 and BTA13 where some candidate genes are located. We identified selection signatures peculiar of each breed which suggest selection for genes involved in milk or meat traits. The genetic structure was investigated by using a multidimensional scaling of the genetic distance matrix and a Bayesian approach implemented in the STRUCTURE software. The genotyping data showed a clear partitioning of the cattle genetic diversity into distinct breeds if a number of clusters equal to the number of populations were given. Assuming a lower number of clusters beef breeds group together. Both methods showed all five breeds separated in well defined clusters and the Bayesian approach assigned individuals to the breed of origin. The work is of interest not only because it enriches the knowledge on the process of evolution but also because the results generated could have implications for selective breeding programs.

Genetic characterization of Bombyx mori (Lepidoptera: Bombycidae) breeding and hybrid lines with different geographic origins.

PubMed

Furdui, Emilia M; Mărghitaş, Liviu A; Dezmirean, Daniel S; Paşca, Ioan; Pop, Iulia F; Erler, Silvio; Schlüns, Ellen A

2014-01-01

The domesticated silkworm Bombyx mori L. comprises a large number of geographical breeds and hybrid lines. Knowing the genetic structure of those may provide information to improve the conservation of commercial lines by estimating inbreeding over generations and the consequences of excessive use of those lineages. Here, we analyzed the genetic diversity of seven breeds and eight hybrid lines from Eastern Europe and Asia using highly polymorphic microsatellites markers to determine its genetical impact on their use in global breeding programs. No consistent pattern of deviation from Hardy-Weinberg equilibrium was found for most breed and hybrids; and the absence of a linkage disequilibrium also suggests that the strains are in equilibrium. A principal coordinate analysis revealed a clear separation of two silkworm breeds from the rest: one (IBV) originated from India and the other one (RG90) from Romania/Japan. The tendency of the other breeds from different geographic origins to cluster together in a general mix might be due to similar selection pressures (climate and anthropogenic factors) in different geographic locations. Phylogenetic analyses grouped the different silkworm breeds but not the hybrids according to their geographic origin and confirmed the pattern found in the principal coordinate analysis. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

Speed breeding is a powerful tool to accelerate crop research and breeding.

PubMed

Watson, Amy; Ghosh, Sreya; Williams, Matthew J; Cuddy, William S; Simmonds, James; Rey, María-Dolores; Asyraf Md Hatta, M; Hinchliffe, Alison; Steed, Andrew; Reynolds, Daniel; Adamski, Nikolai M; Breakspear, Andy; Korolev, Andrey; Rayner, Tracey; Dixon, Laura E; Riaz, Adnan; Martin, William; Ryan, Merrill; Edwards, David; Batley, Jacqueline; Raman, Harsh; Carter, Jeremy; Rogers, Christian; Domoney, Claire; Moore, Graham; Harwood, Wendy; Nicholson, Paul; Dieters, Mark J; DeLacy, Ian H; Zhou, Ji; Uauy, Cristobal; Boden, Scott A; Park, Robert F; Wulff, Brande B H; Hickey, Lee T

2018-01-01

The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand 1 . This slow improvement rate is attributed partly to the long generation times of crop plants. Here, we present a method called 'speed breeding', which greatly shortens generation time and accelerates breeding and research programmes. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum) and pea (Pisum sativum), and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. We demonstrate that speed breeding in fully enclosed, controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent (SSD) and potential for adaptation to larger-scale crop improvement programs. Cost saving through light-emitting diode (LED) supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing and genomic selection, accelerating the rate of crop improvement.

Genetic Characterization of Bombyx mori (Lepidoptera: Bombycidae) Breeding and Hybrid Lines With Different Geographic Origins

PubMed Central

Furdui, Emilia M.; Mărghitaş, Liviu A.; Dezmirean, Daniel S.; Paşca, Ioan; Pop, Iulia F.; Erler, Silvio; Schlüns, Ellen A.

2014-01-01

Abstract The domesticated silkworm Bombyx mori L. comprises a large number of geographical breeds and hybrid lines. Knowing the genetic structure of those may provide information to improve the conservation of commercial lines by estimating inbreeding over generations and the consequences of excessive use of those lineages. Here, we analyzed the genetic diversity of seven breeds and eight hybrid lines from Eastern Europe and Asia using highly polymorphic microsatellites markers to determine its genetical impact on their use in global breeding programs. No consistent pattern of deviation from Hardy–Weinberg equilibrium was found for most breed and hybrids; and the absence of a linkage disequilibrium also suggests that the strains are in equilibrium. A principal coordinate analysis revealed a clear separation of two silkworm breeds from the rest: one (IBV) originated from India and the other one (RG 90 ) from Romania/Japan. The tendency of the other breeds from different geographic origins to cluster together in a general mix might be due to similar selection pressures (climate and anthropogenic factors) in different geographic locations. Phylogenetic analyses grouped the different silkworm breeds but not the hybrids according to their geographic origin and confirmed the pattern found in the principal coordinate analysis. PMID:25502023

Optimum allocation of test resources and comparison of breeding strategies for hybrid wheat.

PubMed

Longin, C Friedrich H; Mi, Xuefei; Melchinger, Albrecht E; Reif, Jochen C; Würschum, Tobias

2014-10-01

The use of a breeding strategy combining the evaluation of line per se with testcross performance maximizes annual selection gain for hybrid wheat breeding. Recent experimental studies confirmed a high commercial potential for hybrid wheat requiring the design of optimum breeding strategies. Our objectives were to (1) determine the optimum allocation of the type and number of testers, the number of test locations and the number of doubled haploid lines for different breeding strategies, (2) identify the best breeding strategy and (3) elaborate key parameters for an efficient hybrid wheat breeding program. We performed model calculations using the selection gain for grain yield as target variable to optimize the number of lines, testers and test locations in four different breeding strategies. A breeding strategy (BS2) combining the evaluation of line per se performance and general combining ability (GCA) had a far larger annual selection gain across all considered scenarios than a breeding strategy (BS1) focusing only on GCA. In the combined strategy, the production of testcross seed conducted in parallel with the first yield trial for line per se performance (BS2rapid) resulted in a further increase of the annual selection gain. For the current situation in hybrid wheat, this relative superiority of the strategy BS2rapid amounted to 67 % in annual selection gain compared to BS1. Varying a large number of parameters, we identified the high costs for hybrid seed production and the low variance of GCA in hybrid wheat breeding as key parameters limiting selection gain in BS2rapid.

Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds.

PubMed

Sudrajad, P; Seo, D W; Choi, T J; Park, B H; Roh, S H; Jung, W Y; Lee, S S; Lee, J H; Kim, S; Lee, S H

2017-02-01

The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high-density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (N e ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and N e in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15-0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small N e values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and N e for each breed reflect the breeding strategy applied. The N e for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract. © 2016 Stichting International Foundation for Animal Genetics.

PrP genotype frequencies and risk evaluation for scrapie in dairy sheep breeds from southern Italy.

PubMed

Martemucci, Giovanni; Iamartino, Daniela; Blasi, Michele; D'Alessandro, Angela Gabriella

2015-12-01

Concerns regarding scrapie in sheep breeding have increased in the last few decades. The present study was carried out in dairy sheep breeds from southern Italy. In order to find breeding animals resistant to scrapie, the PrP genes of 1,205 animals from entire flocks of dairy native Apulian Leccese and Altamurana breeds, and Sicilian Comisana breed, were analysed for polymorphisms at codons 136, 154, and 171 related to scrapie resistance/susceptibility. The Altamurana breed was considered as two populations (Alt-Cav and Alt-Cra-Zoe), based on presumed cross-breeding. A total of five alleles and ten different genotypes were found. The ARQ allele was predominant for all breeds followed by ARR, the most resistant allele to scrapie, which was highly prevalent in Comisana (50%) and in native Alt-Cav (42.4%). The VRQ allele, associated with the highest susceptibility to scrapie, was detected at not negligeable levels in allocthonous Comisana (3.5%), at a low frequency (0.2%) in native Leccese and Alt-Cra-Zoe, while it was absent in Alt-Cav. The frequencies of PrP genotypes with a very low susceptibility risk to scrapie (R1) was higher in Comisana and Alt-Cav. The most susceptible genotype, ARQ/VRQ, was found only in Comisana. Within the Altamurana breed, there were notable differences between Alt-Cav and Alt-Cra-Zoe sheep. The Alt-Cav was characterised by the absence of VRQ and AHQ alleles and by the higher frequency of the ARR/ARR genotype (18.7%). Breeding programs, mainly in endangered breeds such as Altamurana, should be conducted gradually, combining resistance to scrapie, maintenance of genetic variability, and production. Copyright © 2015 Elsevier B.V. All rights reserved.

Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays.

PubMed

Michailidou, S; Tsangaris, G; Fthenakis, G C; Tzora, A; Skoufos, I; Karkabounas, S C; Banos, G; Argiriou, A; Arsenos, G

2018-06-01

In the present study, genome-wide genotyping was applied to characterize the genetic diversity and population structure of three autochthonous Greek breeds: Boutsko, Karagouniko and Chios. Dairy sheep are among the most significant livestock species in Greece numbering approximately 9 million animals which are characterized by large phenotypic variation and reared under various farming systems. A total of 96 animals were genotyped with the Illumina's OvineSNP50K microarray beadchip, to study the population structure of the breeds and develop a specialized panel of single-nucleotide polymorphisms (SNPs), which could distinguish one breed from the others. Quality control on the dataset resulted in 46,125 SNPs, which were used to evaluate the genetic structure of the breeds. Population structure was assessed through principal component analysis (PCA) and admixture analysis, whereas inbreeding was estimated based on runs of homozygosity (ROHs) coefficients, genomic relationship matrix inbreeding coefficients (F GRM ) and patterns of linkage disequilibrium (LD). Associations between SNPs and breeds were analyzed with different inheritance models, to identify SNPs that distinguish among the breeds. Results showed high levels of genetic heterogeneity in the three breeds. Genetic distances among breeds were modest, despite their different ancestries. Chios and Karagouniko breeds were more genetically related to each other compared to Boutsko. Analysis revealed 3802 candidate SNPs that can be used to identify two-breed crosses and purebred animals. The present study provides, for the first time, data on the genetic background of three Greek indigenous dairy sheep breeds as well as a specialized marker panel that can be applied for traceability purposes as well as targeted genetic improvement schemes and conservation programs.

Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds.

PubMed

Onzima, R B; Upadhyay, M R; Mukiibi, R; Kanis, E; Groenen, M A M; Crooijmans, R P M A

2018-02-01

Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H O ) and expected (H E ) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f 4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes. © 2018 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

Mating programs including genomic relationships and dominance effects

USDA-ARS?s Scientific Manuscript database

Computer mating programs have helped breeders minimize pedigree inbreeding and avoid recessive defects by mating animals with parents that have fewer common ancestors. With genomic selection, breed associations, AI organizations, and on-farm software providers could use new programs to minimize geno...

Major advances in globalization and consolidation of the artificial insemination industry.

PubMed

Funk, D A

2006-04-01

The artificial insemination (AI) industry in the United States has gone through many consolidations, mergers, and acquisitions over the past 25 yr. There are 5 major AI companies in the United States today: 3 large cooperatives, 1 private company, and 1 public company. The latter 2 have majority ownership outside of the United States. The AI industry in the United States progeny-tests more than 1,000 Holstein young sires per year. Because healthy, mature dairy bulls are capable of producing well over 100,000 straws of frozen semen per year, only a relatively small number of bulls are needed to breed the world's population of dairy cows. Most AI companies in the United States do not own many, if any, females and tend to utilize the same maternal families in their breeding programs. Little differences exist among the selection programs of the AI companies in the United States. The similarity of breeding programs and the extreme semen-production capabilities of bulls have contributed to difficulties the AI companies have had in developing genetically different product lines. Exports of North American Holstein genetics increased steadily from the 1970s into the 1990s because of the perceived superiority of North American Holsteins for dairy traits compared with European strains, especially for production. The breeding industry moved towards international genetic evaluations of bulls in the 1990s, with the International Bull Evaluation Service (Interbull) in Sweden coordinating the evaluations. The extensive exchange of elite genetics has led to a global dairy genetics industry with bulls that are closely related, and the average inbreeding level for the major dairy breeds continues to increase. Genetic markers have been used extensively and successfully by the industry for qualitative traits, especially for recessive genetic disorders, but markers have had limited impact for quantitative traits. Selection emphasis continues to migrate away from production traits and towards nonproduction traits, especially towards health and fitness traits. Specifically, fertility has arguably become the major breeding and management issue facing dairy farmers today. Some producers have implemented crossbreeding programs in an effort to capitalize on heterosis, and crossbreeding will almost certainly need to be a bigger part of the AI companies business in the years ahead.

Genome-wide association study for identifying loci that affect fillet yield, carcass, and body weight traits in rainbow trout (Oncorhynchus mykiss)

USDA-ARS?s Scientific Manuscript database

Fillet yield (FY, %) is an economically important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has not received much attention in breeding programs because it is difficult to measure on a large number of fish and it cannot be directly measured on breeding c...

Exploring pima and upland cross-combinations to identify fusarium oxysporum f. sp. vasinfectum race 4 resistant cottons by combining ability of superior cultivars

USDA-ARS?s Scientific Manuscript database

A cotton breeding program strives to identify the best performance cultivars or breeding lines which can be used as parents in crosses. Multi-cross combinations provide the means of performance of each parent and assess the combining ability or productivity of parents through the hybridization proce...

Regional breeding bird monitoring in Western Great Lakes National Forests

Treesearch

JoAnn Hanowski; Jim Lind; Nick Danz; Gerald Niemi; Tim Jones

2005-01-01

We established breeding bird monitoring programs in three National Forests in northern Minnesota (Superior and Chippewa in 1991) and northern Wisconsin (Chequamegon in 1992). A total of 134, 169, and 132 stands (1,272 survey points) have been surveyed annually in these forests through 2002. We examined trends in relative abundance for 53 species in the Chequamegon, 51...

Identification of genomic region controlling resistance to aflatoxin contamination in a peanut recombinant inbred line population (Tifrunner XGT-C20)

USDA-ARS?s Scientific Manuscript database

In peanut, limited genetic variation for disease resistance is available in breeding programs necessitating the identification of stable resistance sources for use in cultivar development. ‘Tifrunner’ is a runner cultivar while ‘GT-C20’ is a Spanish-type breeding line with resistance to aflatoxin co...

Impact of changes in weight, fat depth, and loin muscle depth on carcass yield and value and implications for selection and pricing of rams from terminal-sire sheep breeds

USDA-ARS?s Scientific Manuscript database

Breeding objectives and selection indexes are necessary to support comprehensive genetic improvement programs. This study used off-test body weights (OTBW) or chilled carcass weights (CCW), ultrasonic measurements of fat depth (USFD, mm), and predicted ultrasound loin muscle depths (USLMD, mm) from ...

Inter- and intraspecific grafting and breeding of five-needle pines

Treesearch

Clifford E. Ahlgren

1970-01-01

The forest tree improvement work at the Center was started in 1949 with the introduction of some of Dr. Riker's grafted eastern white pine selections. Subsequently a program of selecting, grafting, breeding and testing for resistance was begun. The work was initiated at Basswood Lake (15 miles NE of Ely, Minnesota) rather than elsewhere on a more accessible site...

A Strategy for the Third Breeding Cycle of Loblolly Pine in the Southeastern U.S.

Treesearch

S.E. McKeand; F.E. Bridgwater

1998-01-01

A strategy for the North Carolina State University - Industry Cooperative Tree Improvement Program's third-cycle breeding for loblolly pine (Pinus taeda L.) was developed to provide genetic gain in the short-term as well as to maintain genetic diversity so that long-term genetic gains will also be possible. Our strategy will be to manage a...

Integration of selective breeding and vaccination to improve disease resistance in aquaculture: Application to control bacterial cold water disease

USDA-ARS?s Scientific Manuscript database

Bacterial cold water disease (BCWD) is a frequent cause of elevated mortality in rainbow trout and the development of effective control strategies is a priority within the U.S. A goal of the NCCCWA breeding program is to produce germplasm with superior growth and survival following exposure to infe...

Captive-breeding of captive and wild-reared Gunnison sage-grouse.

PubMed

Apa, Anthony D; Wiechman, Lief A

2016-01-01

Gunnison sage-grouse (Centrocercus minimus) distribution in North America has decreased over historical accounts and has received federal protection under the Endangered Species Act. We investigated captive-breeding of a captive-flock of Gunnison sage-grouse created from individuals reared in captivity from wild-collected eggs we artificially incubated. We also introduced wild-reared individuals into captivity. Our captive-flock successfully bred and produced fertile eggs. We controlled the timing and duration of male-female breeding interactions and facilitated a semi-natural mating regime. Males established a strutting ground in captivity that females attended for mate selection. In 2010, we allowed females to establish eight nests, incubate, and hatch eggs. Females in captivity were more successful incubating nests than raising broods. Although there are many technical, financial, and logistic issues associated with captive-breeding, we recommend that federal biologists and managers work collaboratively with state wildlife agencies and consider developing a captive-flock as part of a comprehensive conservation strategy for a conservation-reliant species like the Gunnison sage-grouse. The progeny produced from a captive-rearing program could assist in the recovery if innovative approaches to translocation are part of a comprehensive proactive conservation program. © 2015 Wiley Periodicals, Inc.

Dynamics of habitat selection in birds: adaptive response to nest predation depends on multiple factors.

PubMed

Devries, J H; Clark, R G; Armstrong, L M

2018-05-01

According to theory, habitat selection by organisms should reflect underlying habitat-specific fitness consequences and, in birds, reproductive success has a strong impact on population growth in many species. Understanding processes affecting habitat selection also is critically important for guiding conservation initiatives. Northern pintails (Anas acuta) are migratory, temperate-nesting birds that breed in greatest concentrations in the prairies of North America and their population remains below conservation goals. Habitat loss and changing land use practices may have decoupled formerly reliable fitness cues with respect to nest habitat choices. We used data from 62 waterfowl nesting study sites across prairie Canada (1997-2009) to examine nest survival, a primary fitness metric, at multiple scales, in combination with estimates of habitat selection (i.e., nests versus random points), to test for evidence of adaptive habitat choices. We used the same habitat covariates in both analyses. Pintail nest survival varied with nest initiation date, nest habitat, pintail breeding pair density, landscape composition and annual moisture. Selection of nesting habitat reflected patterns in nest survival in some cases, indicating adaptive selection, but strength of habitat selection varied seasonally and depended on population density and landscape composition. Adaptive selection was most evident late in the breeding season, at low breeding densities and in cropland-dominated landscapes. Strikingly, at high breeding density, habitat choice appears to become maladaptive relative to nest predation. At larger spatial scales, the relative availability of habitats with low versus high nest survival, and changing land use practices, may limit the reproductive potential of pintails.

Contribution of research to management and recovery of the roseate tern: review of a twelve-year project

USGS Publications Warehouse

Nisbet, I.C.T.; Spendelow, J.A.

1999-01-01

The Northwest Atlantic population of the Roseate Tern (Sterna dougallii) is largely confined to a small breeding area along the northeast coast of the USA between 40? and 42?N. This population was listed as endangered in the USA in 1987 because it was dangerously concentrated into a few breeding sites (85% on two islands in the 1980s). The nesting population in the area from Long Island, New York to Cape Cod, Massachusetts has been studied intensively since 1987, in conjunction with a program of management of the breeding colonies. This paper summarizes the results of the research program and discusses the extent to which it has contributed to effective management. The regional population now numbers about 4,000 breeding pairs and has been increasing slowly since 1987, except between 1991 and 1992 when it declined by about 17%. This decline was probably caused by Hurricane `Bob' in August 1991. Roseate Terns have specialized foraging habits and are concentrated into a small number of foraging areas near the nesting colonies. The historically important breeding sites were taken over by large gulls between 1930 and 1972. Many of the terns moved to less suitable sites near the mainland, where they are subject to predation by mainland-based predators. Despite this, Roseate Terns breed with high success at many sites. The sex-ratio is skewed towards females; about 12% of nests are attended by female-female pairs. The annual adult survival rate (0.83) is unusually low for a seabird. Most mortality occurs away from the breeding grounds, but the winter quarters remained unknown until one roost site was found in Brazil in 1995-1997. A major management goal has been to restore former colony-sites by eliminating nesting gulls, but the success of some of these projects has been questionable because they may have attracted birds to sites with higher levels of predation. Although the research has yielded important information about the biology and demography of the species, it has taken longer than expected to obtain and analyze data from multiple sites on this long-lived species. Most work has been carried out at breeding sites: critical studies on feeding ecology and winter ecology have been hampered by insufficient funding and the paucity of self-motivated biologists. Hence, the program has not yet provided all the keys to restoring the population.

Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs

PubMed Central

Anderson, Heidi; Davison, Stephen; Hughes, Angela M.; Bouirmane, Julia; Lindqvist, Johan; Lytle, Katherine M.; Ganesan, Balasubramanian; Ottka, Claudia; Ruotanen, Päivi; Forman, Oliver P.; Fretwell, Neale; Cole, Cynthia A.; Lohi, Hannes

2018-01-01

Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding. Limited data on frequencies of genetic disease variants across breeds exists, and the disease heritage of mixed breed dogs remains poorly explored to date. Advances in genetic screening technologies now enable comprehensive investigations of the canine disease heritage, and generate health-related big data that can be turned into action. We pursued population screening of genetic variants implicated in Mendelian disorders in the largest canine study sample examined to date by examining over 83,000 mixed breed and 18,000 purebred dogs representing 330 breeds for 152 known variants using a custom-designed beadchip microarray. We further announce the creation of MyBreedData (www.mybreeddata.com), an online updated inherited disorder prevalence resource with its foundation in the generated data. We identified the most prevalent, and rare, disease susceptibility variants across the general dog population while providing the first extensive snapshot of the mixed breed disease heritage. Approximately two in five dogs carried at least one copy of a tested disease variant. Most disease variants are shared by both mixed breeds and purebreds, while breed- or line-specificity of others is strongly suggested. Mixed breed dogs were more likely to carry a common recessive disease, whereas purebreds were more likely to be genetically affected with one, providing DNA-based evidence for hybrid vigor. We discovered genetic presence of 22 disease variants in at least one additional breed in which they were previously undescribed. Some mutations likely manifest similarly independently of breed background; however, we emphasize the need for follow up investigations in each case and provide a suggested validation protocol for broader consideration. In conclusion, our study provides unique insight into genetic epidemiology of canine disease risk variants, and their relevance for veterinary medicine, breeding programs and animal welfare. PMID:29708978

Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs.

PubMed

Donner, Jonas; Anderson, Heidi; Davison, Stephen; Hughes, Angela M; Bouirmane, Julia; Lindqvist, Johan; Lytle, Katherine M; Ganesan, Balasubramanian; Ottka, Claudia; Ruotanen, Päivi; Kaukonen, Maria; Forman, Oliver P; Fretwell, Neale; Cole, Cynthia A; Lohi, Hannes

2018-04-01

Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding. Limited data on frequencies of genetic disease variants across breeds exists, and the disease heritage of mixed breed dogs remains poorly explored to date. Advances in genetic screening technologies now enable comprehensive investigations of the canine disease heritage, and generate health-related big data that can be turned into action. We pursued population screening of genetic variants implicated in Mendelian disorders in the largest canine study sample examined to date by examining over 83,000 mixed breed and 18,000 purebred dogs representing 330 breeds for 152 known variants using a custom-designed beadchip microarray. We further announce the creation of MyBreedData (www.mybreeddata.com), an online updated inherited disorder prevalence resource with its foundation in the generated data. We identified the most prevalent, and rare, disease susceptibility variants across the general dog population while providing the first extensive snapshot of the mixed breed disease heritage. Approximately two in five dogs carried at least one copy of a tested disease variant. Most disease variants are shared by both mixed breeds and purebreds, while breed- or line-specificity of others is strongly suggested. Mixed breed dogs were more likely to carry a common recessive disease, whereas purebreds were more likely to be genetically affected with one, providing DNA-based evidence for hybrid vigor. We discovered genetic presence of 22 disease variants in at least one additional breed in which they were previously undescribed. Some mutations likely manifest similarly independently of breed background; however, we emphasize the need for follow up investigations in each case and provide a suggested validation protocol for broader consideration. In conclusion, our study provides unique insight into genetic epidemiology of canine disease risk variants, and their relevance for veterinary medicine, breeding programs and animal welfare.

Bird community response to filter strips in Maryland

USGS Publications Warehouse

Blank, P.J.; Dively, G.P.; Gill, D.E.; Rewa, C.A.

2011-01-01

Filter strips are strips of herbaceous vegetation planted along agricultural field margins adjacent to streams or wetlands and are designed to intercept sediment, nutrients, and agrichemicals. Roughly 16,000 ha of filter strips have been established in Maryland through the United States Department of Agriculture's Conservation Reserve Enhancement Program. Filter strips often represent the only uncultivated herbaceous areas on farmland in Maryland and therefore may be important habitat for early-successional bird species. Most filter strips in Maryland are planted to either native warm-season grasses or cool-season grasses and range in width from 10.7 m to 91.4 m. From 2004 to 2007 we studied the breeding and wintering bird communities in filter strips adjacent to wooded edges and non-buffered field edges and the effect that grass type and width of filter strips had on bird community composition. We used 5 bird community metrics (total bird density, species richness, scrub-shrub bird density, grassland bird density, and total avian conservation value), species-specific densities, nest densities, and nest survival estimates to assess the habitat value of filter strips for birds. Breeding and wintering bird community metrics were greater in filter strips than in non-buffered field edges but did not differ between cool-season and warm-season grass filter strips. Most breeding bird community metrics were negatively related to the percent cover of orchardgrass (Dactylis glomerata) in ???1 yr. Breeding bird density was greater in narrow (60 m) filter strips. Our results suggest that narrow filter strips adjacent to wooded edges can provide habitat for many bird species but that wide filter strips provide better habitat for grassland birds, particularly obligate grassland species. If bird conservation is an objective, avoid planting orchardgrass in filter strips and reduce or eliminate orchardgrass from filter strips through management practices. Copyright ?? 2011 The Wildlife Society.

Molecular Breeding of Rice Restorer Lines and Hybrids for Brown Planthopper (BPH) Resistance Using the Bph14 and Bph15 Genes.

PubMed

Wang, Hongbo; Ye, Shengtuo; Mou, Tongmin

2016-12-01

The development of hybrid rice is a practical approach for increasing rice production. However, the brown planthopper (BPH), Nilaparvata lugens Stål, causes severe yield loss of rice (Oryza sativa L.) and can threaten food security. Therefore, breeding hybrid rice resistant to BPH is the most effective and economical strategy to maintain high and stable production. Fortunately, numerous BPH resistance genes have been identified, and abundant linkage markers are available for molecular marker-assisted selection (MAS) in breeding programs. Hence, we pyramided two BPH resistance genes, Bph14 and Bph15, into a susceptive CMS restorer line Huahui938 and its derived hybrids using MAS to improve the BPH resistance of hybrid rice. Three near-isogenic lines (NILs) with pyramided Bph14 and Bph15 were obtained by molecular marker-assisted backcross (MAB) and phenotypic selection. The genomic components of these NILs were detected using the whole-genome SNP (Single nucleotide polymorphism) array, RICE6K, suggesting that the recurrent parent genome (RPG) recovery of the NILs was 87.88, 87.70 and 86.62 %, respectively. BPH bioassays showed that the improved NILs and their derived hybrids carrying homozygous Bph14 and Bph15 were resistant to BPH. However, the hybrids with heterozygous Bph14 and Bph15 remained susceptible to BPH. The developed NILs showed no significant differences in major agronomic traits and rice qualities compared with the recurrent parent. Moreover, the improved hybrids derived from the NILs exhibited better agronomic performance and rice quality compared with the controls under natural field conditions. This study demonstrates that it is essential to stack Bph14 and Bph15 into both the maternal and paternal parents for developing BPH-resistant hybrid rice varieties. The SNP array with abundant DNA markers is an efficient tool for analyzing the RPG recovery of progenies and can be used to monitor the donor segments in NILs, thus being extremely important for rice molecular breeding.

A 100-Year Review: Methods and impact of genetic selection in dairy cattle-From daughter-dam comparisons to deep learning algorithms.

PubMed

Weigel, K A; VanRaden, P M; Norman, H D; Grosu, H

2017-12-01

In the early 1900s, breed society herdbooks had been established and milk-recording programs were in their infancy. Farmers wanted to improve the productivity of their cattle, but the foundations of population genetics, quantitative genetics, and animal breeding had not been laid. Early animal breeders struggled to identify genetically superior families using performance records that were influenced by local environmental conditions and herd-specific management practices. Daughter-dam comparisons were used for more than 30 yr and, although genetic progress was minimal, the attention given to performance recording, genetic theory, and statistical methods paid off in future years. Contemporary (herdmate) comparison methods allowed more accurate accounting for environmental factors and genetic progress began to accelerate when these methods were coupled with artificial insemination and progeny testing. Advances in computing facilitated the implementation of mixed linear models that used pedigree and performance data optimally and enabled accurate selection decisions. Sequencing of the bovine genome led to a revolution in dairy cattle breeding, and the pace of scientific discovery and genetic progress accelerated rapidly. Pedigree-based models have given way to whole-genome prediction, and Bayesian regression models and machine learning algorithms have joined mixed linear models in the toolbox of modern animal breeders. Future developments will likely include elucidation of the mechanisms of genetic inheritance and epigenetic modification in key biological pathways, and genomic data will be used with data from on-farm sensors to facilitate precision management on modern dairy farms. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Transcriptome and Complexity-Reduced, DNA-Based Identification of Intraspecies Single-Nucleotide Polymorphisms in the Polyploid Gossypium hirsutum L.

PubMed Central

Zhu, Qian-Hao; Spriggs, Andrew; Taylor, Jennifer M.; Llewellyn, Danny; Wilson, Iain

2014-01-01

Varietal single nucleotide polymorphisms (SNPs) are the differences within one of the two subgenomes between different tetraploid cotton varieties and have not been practically used in cotton genetics and breeding because they are difficult to identify due to low genetic diversity and very high sequence identity between homeologous genes in cotton. We have used transcriptome and restriction site−associated DNA sequencing to identify varietal SNPs among 18 G. hirsutum varieties based on the rationale that varietal SNPs can be more confidently called when flanked by subgenome-specific SNPs. Using transcriptome data, we successfully identified 37,413 varietal SNPs and, of these, 22,121 did not have an additional varietal SNP within their 20-bp flanking regions so can be used in most SNP genotyping assays. From restriction site−associated DNA sequencing data, we identified an additional 3090 varietal SNPs between two of the varieties. Of the 1583 successful SNP assays achieved using different genotyping platforms, 1363 were verified. Many of the SNPs behaved as dominant markers because of coamplification from homeologous loci, but the number of SNPs acting as codominant markers increased when one or more subgenome-specific SNP(s) were incorporated in their assay primers, giving them greater utility for breeding applications. A G. hirsutum genetic map with 1244 SNP markers was constructed covering 5557.42 centiMorgan and used to map qualitative and quantitative traits. This collection of G. hirsutum varietal SNPs complements existing intra-specific SNPs and provides the cotton community with a valuable marker resource applicable to genetic analyses and breeding programs. PMID:25106949

Behavioral profiles of dog breeds.

PubMed

Hart, B L; Miller, M F

1985-06-01

Breed behavior profiles were obtained by a method that was quantitative and free of personal biases. The profiles concerned 13 traits, eg, excitability, snapping at children, watchdog barking, and affection demand, which are of interest to people wanting dogs as pets. Authorities for the development of the profiles were 48 small animal veterinarians and 48 obedience judges, randomly selected from directories so as to represent equally men and women, and eastern, central, and western geographic regions of the United States. Each authority was asked to rank on each of the behavioral traits a list of 7 breeds chosen randomly from a list of 56 breeds. The data were analyzed in a custom-designed computer program that pooled the data and then ranked all 56 breeds on the basis of the 13 traits. The results indicated that some behavioral traits discriminate between breeds better than others. An examination of sample profiles indicated the feasibility of developing a statistically meaningful behavioral profile that integrates comparative rankings of several authorities balanced as to representation of geographic location, sex, and type of experience with dogs.

Productive performance of the dairy cattle Girolando breed mediated by the fat-related genes DGAT1 and LEP and their polymorphisms.

PubMed

Cardoso, S R; Queiroz, L B; Goulart, V Alonso; Mourão, G B; Benedetti, E; Goulart, L R

2011-12-01

Candidate genes have been associated with milk production in bovines, such as the diacylglycerol O-acyltransferase 1 (DGAT1) and leptin (LEP); however, they have not been simultaneously investigated nor have been evaluated in the Brazilian Girolando breed (Gir×Holstein, backcrossed to Holstein). Our aim was to determine the influence of fat-related genes, DGAT1 and LEP, and their polymorphisms on performance traits of milk production in the Girolando breed. Results indicated that the K allele of the DGAT1 gene showed a significant association with total and average daily milk production with additive effect. The LEP gene showed that the A allele and its homozygote are highly prevalent and almost fixed in this population and may have been favorably selected during backcrossing for the origin of this breed. The important impact of the K allele of the DGAT1 gene on milk production corroborates the initiative of performing marker-assisted selections with this gene in breeding programs of the Girolando breed. Copyright © 2011 Elsevier Ltd. All rights reserved.

Genetic analysis of prolactin gene in Pakistani cattle.

PubMed

Uddin, Raza Mohy; Babar, Masroor Ellahi; Nadeem, Asif; Hussain, Tanveer; Ahmad, Shakil; Munir, Sadia; Mehboob, Riffat; Ahmad, Fridoon Jawad

2013-10-01

Prolactin (PRL) is a polypeptide hormone, secreted mainly by the anterior pituitary gland. It is involved in many endocrine activities. The key functions of PRL are related to reproduction and lactation in mammals. To ascertain the presence of polymorphisms in the bovine PRL gene (bPRL), the bPRL gene was sequenced. Five mutations were identified in exonic region and eleven in associated intronic regions in 100 cattle from four Pakistani cattle breeds. Haplotype of predicted amino acid changes represent a common alteration at codon 222 from R-Arginine into K-Lysine in all four breeds. Significant statistical variations were observed in the distribution of single nucleotide polymorphism (SNP) in various cattle populations. However, on basis of present study, an association of these SNPs with milk performance traits in four Pakistani cow breeds cannot be truly replicated but at least can be effective DNA markers for some of the breeds studied. Linkage analysis between these SNPs on larger populations can be useful for the association with milk production traits. Furthermore, present study may be used for marker-assisted selection and management in cattle breeding program in local cattle breeds.

Lessons learned from the dog genome.

PubMed

Wayne, Robert K; Ostrander, Elaine A

2007-11-01

Extensive genetic resources and a high-quality genome sequence position the dog as an important model species for understanding genome evolution, population genetics and genes underlying complex phenotypic traits. Newly developed genomic resources have expanded our understanding of canine evolutionary history and dog origins. Domestication involved genetic contributions from multiple populations of gray wolves probably through backcrossing. More recently, the advent of controlled breeding practices has segregated genetic variability into distinct dog breeds that possess specific phenotypic traits. Consequently, genome-wide association and selective sweep scans now allow the discovery of genes underlying breed-specific characteristics. The dog is finally emerging as a novel resource for studying the genetic basis of complex traits, including behavior.

How well can captive breeding programs conserve biodiversity? A review of salmonids

PubMed Central

Fraser, Dylan J

2008-01-01

Captive breeding programs are increasingly being initiated to prevent the imminent extinction of endangered species and/or populations. But how well can they conserve genetic diversity and fitness, or re-establish self-sustaining populations in the wild? A review of these complex questions and related issues in salmonid fishes reveals several insights and uncertainties. Most programs can maintain genetic diversity within populations over several generations, but available research suggests the loss of fitness in captivity can be rapid, its magnitude probably increasing with the duration in captivity. Over the long-term, there is likely tremendous variation between (i) programs in their capacity to maintain genetic diversity and fitness, and (ii) species or even intraspecific life-history types in both the severity and manner of fitness-costs accrued. Encouragingly, many new theoretical and methodological approaches now exist for current and future programs to potentially reduce these effects. Nevertheless, an unavoidable trade-off exists between conserving genetic diversity and fitness in certain instances, such as when captive-bred individuals are temporarily released into the wild. Owing to several confounding factors, there is also currently little evidence that captive-bred lines of salmonids can or cannot be reintroduced as self-sustaining populations. Most notably, the root causes of salmonid declines have not been mitigated where captive breeding programs exist. Little research has also addressed under what conditions an increase in population abundance due to captive-rearing might offset fitness reductions induced in captivity. Finally, more empirical investigation is needed to evaluate the genetic/fitness benefits and risks associated with (i) maintaining captive broodstocks as either single or multiple populations within one or more facilities, (ii) utilizing cryopreservation or surrogate broodstock technologies, and (iii) adopting other alternatives to captive-rearing such as translocations to new habitats. Management recommendations surrounding these issues are proposed, with the aim of facilitating meta-analyses and more general principles or guidelines for captive-breeding. These include the need for the following: (i) captive monitoring to involve, a priori, greater application of hypothesis testing through the use of well-designed experiments and (ii) improved documentation of procedures adopted by specific programs for reducing the loss of genetic diversity and fitness. PMID:25567798

Production objectives, trait and breed preferences of farmers keeping N'Dama, Fulani Zebu and crossbred cattle and implications for breeding programs.

PubMed

Traoré, S A; Markemann, A; Reiber, C; Piepho, H P; Valle Zárate, A

2017-04-01

Many local livestock breeds in developing countries are being replaced by exotic breeds, leading to a loss of genetic resources. In southern Mali, for the past two decades, a trend towards increasing crossbreeding between the trypanotolerant N'Dama cattle and the trypano-susceptible Fulani Zebu cattle has been taking place. A survey with 160 farmers owning a cattle herd was carried out in southern Mali to investigate their production objectives, as well as trait and breed preferences and correlated socio-economic determinants in order to understand farmers' breeding decisions and to identify comparative advantages of three breed groups (N'Dama, Fulani Zebu and crossbreds) raised in the study area. Data were analyzed using an exploded logit model. The reasons for raising cattle, as well as trait and breed preferences reflected the multiple objectives of the farmers. Draught power and savings were the most important production objectives. Productive traits were ranked highest; farmers reported large body size as the most preferred trait, followed by fertility, draught ability and milk yield. Crossbreds were the favored breed group. Breed preferences were mainly explained by 'resistance to disease' for N'Dama cattle and 'high market price' for Fulani Zebu and crossbred cattle. Production objectives, trait and breed preferences were mainly influenced by farmer group (local farmers and settled transhumants). Local farmers put comparatively more emphasis on livestock functions linked to crop production such as draught power. They had a higher preference for traction ability as a selection trait and preferred N'Dama over Fulani Zebu cattle. Settled transhumants emphasized milk yield as a selection trait and preferred Fulani Zebu over N'Dama. The results indicate that the trend towards more crossbreeding will continue putting the N'Dama breed under high risk of genetic dilution in southern Mali. The N'Dama cattle remain a valuable breed due to their adaptive traits such as disease and drought tolerance and their good traction ability, fulfilling the diverse objectives of local farmers. Crossbreeding was found to be a promising breeding strategy, which might contribute to the maintenance of the local breed, provided that breeding schemes are thoroughly planned and organized.

Lesser scaup breeding probability and female survival on the yukon flats, Alaska

USGS Publications Warehouse

Martin, K.H.; Lindberg, M.S.; Schmutz, J.A.; Bertram, M.R.

2009-01-01

Information on the ecology of waterfowl breeding in the boreal forest is lacking, despite the boreal region's importance to continental waterfowl populations and to duck species that are currently declining, such as lesser scaup (Aythya affinis). We estimated breeding probability and breeding season survival of female lesser scaup on the Yukon Flats National Wildlife Refuge, Alaska, USA, in 2005 and 2006. We captured and marked 93 lesser scaup with radiotransmitters during prelaying and nesting periods. Although all marked lesser scaup females were paired throughout prelaying and incubation periods, we estimated breeding probability over both years as 0.12 (SE = 0.05, n = 67) using telemetry. Proportion of lesser scaup females undergoing rapid follicle growth at capture in 2006 was 0.46 (SE = 0.11, n = 37), based on concentration of yolk precursors in blood plasma. By combining methods based on telemetry, yolk precursors, and postovulatory follicles, we estimated maximum breeding probability as 0.68 (SE = 0.08, n = 37) in 2006. Notably, breeding probability was positively related to female body mass. Survival of female lesser scaup during the nesting and brood-rearing periods was 0.92 (SE = 0.05) in 2005 and 0.86 (SE = 0.08) in 2006. Our results suggest that breeding probability is lower than expected for lesser scaup. In addition, the implicit assumption of continental duck-monitoring programs that all paired females attempt to breed should be reevaluated. Recruitment estimates based on annual breeding-pair surveys may overestimate productivity of scaup pairs in the boreal forest. ?? The Wildlife Society.

Genomic-based-breeding tools for tropical maize improvement.

PubMed

Chakradhar, Thammineni; Hindu, Vemuri; Reddy, Palakolanu Sudhakar

2017-12-01

Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions. Heterosis breeding introduced in early 90 s improved maize yields significantly, but genetic gains is still a mirage, particularly for crop growing under marginal environments. Application of molecular markers has accelerated the pace of maize breeding to some extent. The availability of array of sequencing and genotyping technologies offers unrivalled service to improve precision in maize-breeding programs through modern approaches such as genomic selection, genome-wide association studies, bulk segregant analysis-based sequencing approaches, etc. Superior alleles underlying complex traits can easily be identified and introgressed efficiently using these sequence-based approaches. Integration of genomic tools and techniques with advanced genetic resources such as nested association mapping and backcross nested association mapping could certainly address the genetic issues in maize improvement programs in developing countries. Huge diversity in tropical maize and its inherent capacity for doubled haploid technology offers advantage to apply the next generation genomic tools for accelerating production in marginal environments of tropical and subtropical world. Precision in phenotyping is the key for success of any molecular-breeding approach. This article reviews genomic technologies and their application to improve agronomic traits in tropical maize breeding has been reviewed in detail.

Understanding crop genetic diversity under modern plant breeding.

PubMed

Fu, Yong-Bi

2015-11-01

Maximizing crop yield while at the same time minimizing crop failure for sustainable agriculture requires a better understanding of the impacts of plant breeding on crop genetic diversity. This review identifies knowledge gaps and shows the need for more research into genetic diversity changes under plant breeding. Modern plant breeding has made a profound impact on food production and will continue to play a vital role in world food security. For sustainable agriculture, a compromise should be sought between maximizing crop yield under changing climate and minimizing crop failure under unfavorable conditions. Such a compromise requires better understanding of the impacts of plant breeding on crop genetic diversity. Efforts have been made over the last three decades to assess crop genetic diversity using molecular marker technologies. However, these assessments have revealed some temporal diversity patterns that are largely inconsistent with our perception that modern plant breeding reduces crop genetic diversity. An attempt was made in this review to explain such discrepancies by examining empirical assessments of crop genetic diversity and theoretical investigations of genetic diversity changes over time under artificial selection. It was found that many crop genetic diversity assessments were not designed to assess diversity impacts from specific plant breeding programs, while others were experimentally inadequate and contained technical biases from the sampling of cultivars and genomes. Little attention has been paid to theoretical investigations on crop genetic diversity changes from plant breeding. A computer simulation of five simplified breeding schemes showed the substantial effects of plant breeding on the retention of heterozygosity over generations. It is clear that more efforts are needed to investigate crop genetic diversity in space and time under plant breeding to achieve sustainable crop production.

Familiarity with and uptake of alternative methods to control sheep gastro-intestinal parasites on farms in England.

PubMed

Moore, Hope; Pandolfi, Fanny; Kyriazakis, Ilias

2016-05-15

A questionnaire was distributed electronically amongst sheep farmers in England; it aimed to provide a quantification of current anthelmintic practices, farmer awareness of the issue of anthelmintic resistance (AR) and the uptake, awareness and opinions surrounding conventional and alternative methods of nematode control. The majority of farmers relied on several anthelmintics and used faecal egg counts to identify worm problems. Although farmers were aware of the issue of AR amongst helminth parasites in the UK, there was a disconnection between such awareness and on farm problems and practice of nematode control. Grazing management was used by 52% of responders, while breeding for resistance and bioactive forages by 22 and 18% respectively. Farms with more than 500 ewes, and farmers who felt nematodes were a problem, had a higher probability of using selective breeding. Farmers who considered their wormer effective, had a qualification in agriculture and whose staff did not include any family members, were more likely to use bioactive forages; the opposite was the case if farmers dosed their lambs frequently. Amongst the alternatives, highest preference was for selective breeding and vaccination, if the latter was to become commercially available, with more respondents having a preference for breeding than actually using it. Several barriers to the uptake of an alternative were identified, the most influential factor being the cost to set it up and the length of time for which it would remain effective. The disconnection between awareness of AR and practice of nematode control on farm reinforces the need for emphasising the links between the causes of AR and the consequences of strategies to address its challenge. Copyright © 2016 Elsevier B.V. All rights reserved.

Identification of breeding objectives for Begait goat in western Tigray, North Ethiopia.

PubMed

Abraham, Hagos; Gizaw, Solomon; Urge, Mengistu

2018-06-21

A sound breeding objective is the basis for genetic improvement in overall economic merit of farm animals. Begait goat is one of the identified breeds in Ethiopia, which is a multipurpose breed as it serves as source of cash income and source of food (meat and milk). Despite its importance, no formal breeding objectives exist for Begait goat. The objective of the present study was to identify breeding objectives for the breed through two approaches: using own-flock ranking experiment and developing deterministic bio-economic models as a preliminary step towards designing sustainable breeding programs for the breed. In the own-flock ranking experiment, a total of 45 households were visited at their homesteads and were asked to select, with reasons, the first best, second best, third best, and the most inferior does from their own flock. Age, previous reproduction, and production information of the identified animals were inquired; live body weight and some linear body measurements were taken. The bio-economic model included performance traits (weights, daily weight gain, kidding interval, litter size, milk yield, kid mortality, pregnancy, and replacement rates) and economic (revenue and costs) parameters. It was observed that there was close agreement between the farmers' ranking and bio-economic model results. In general, the results of the present study indicated that Begait goat owners could improve performance of their goats and profitability of their farms by selecting for 6-month weight, litter size, pre-weaning kid survival rate, and milk yield.

New World cattle show ancestry from multiple independent domestication events

PubMed Central

McTavish, Emily Jane; Decker, Jared E.; Schnabel, Robert D.; Taylor, Jeremy F.; Hillis, David M.

2013-01-01

Previous archeological and genetic research has shown that modern cattle breeds are descended from multiple independent domestication events of the wild aurochs (Bos primigenius) ∼10,000 y ago. Two primary areas of domestication in the Middle East/Europe and the Indian subcontinent resulted in taurine and indicine lines of cattle, respectively. American descendants of cattle brought by European explorers to the New World beginning in 1493 generally have been considered to belong to the taurine lineage. Our analyses of 47,506 single nucleotide polymorphisms show that these New World cattle breeds, as well as many related breeds of cattle in southern Europe, actually exhibit ancestry from both the taurine and indicine lineages. In this study, we show that, although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. New World cattle breeds, such as Texas Longhorns, provide an opportunity to study global population structure and domestication in cattle. Following their introduction into the Americas in the late 1400s, semiferal herds of cattle underwent between 80 and 200 generations of predominantly natural selection, as opposed to the human-mediated artificial selection of Old World breeding programs. Our analyses of global cattle breed population history show that the hybrid ancestry of New World breeds contributed genetic variation that likely facilitated the adaptation of these breeds to a novel environment. PMID:23530234

Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa)

PubMed Central

Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R.

2015-01-01

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models. PMID:25785447

Eucalyptus applied genomics: from gene sequences to breeding tools.

PubMed

Grattapaglia, Dario; Kirst, Matias

2008-01-01

Eucalyptus is the most widely planted hardwood crop in the tropical and subtropical world because of its superior growth, broad adaptability and multipurpose wood properties. Plantation forestry of Eucalyptus supplies high-quality woody biomass for several industrial applications while reducing the pressure on tropical forests and associated biodiversity. This review links current eucalypt breeding practices with existing and emerging genomic tools. A brief discussion provides a background to modern eucalypt breeding together with some current applications of molecular markers in support of operational breeding. Quantitative trait locus (QTL) mapping and genetical genomics are reviewed and an in-depth perspective is provided on the power of association genetics to dissect quantitative variation in this highly diverse organism. Finally, some challenges and opportunities to integrate genomic information into directional selective breeding are discussed in light of the upcoming draft of the Eucalyptus grandis genome. Given the extraordinary genetic variation that exists in the genus Eucalyptus, the ingenuity of most breeders, and the powerful genomic tools that have become available, the prospects of applied genomics in Eucalyptus forest production are encouraging.

Machine Learning Model Analysis of Breeding Habitats for the Black-necked Crane in Central Asian Uplands under Anthropogenic Pressures.

PubMed

Han, Xuesong; Guo, Yumin; Mi, Chunrong; Huettmann, Falk; Wen, Lijia

2017-07-21

The black-necked crane (Grus nigricollis) is the only alpine crane species and is endemic to the Tibetan Plateau. The breeding habitats of this species are poorly understood, which greatly hampers practical research and conservation work. Using machine learning methods and the best-available data from our 7,000-kilometer mega-transect survey and open access data, we built the first species distribution model (SDM) to analyze the black-necked crane's breeding habitats. Our model showed that current conservation gaps account for 26.7% of its predicted breeding habitats. Specifically, the northern parts of the Hengduan Mountains and the southeastern Tibet Valley, the northern side of the middle Kunlun Mountains, parts of the Pamir Plateau, the northern Pakistan Highlands and the western Hindu Kush should be considered as its main potential breeding areas. Additionally, our model suggested that the crane prefers to breed in alpine meadows at an elevation over 2,800 m, a maximum temperature of the warmest month below 20.5 °C, and a temperature seasonality above 7,800 units. The identified conservation gaps and potential breeding areas can aid in clearly prioritizing future conservation and research, but more attention and study should be directed to the unassessed Western Development of China to secure this endangered crane lineage and other wildlife on the Tibetan Plateau.

Epidemiology of ocular disorders presumed to be inherited in three small Italian dog breeds in Italy.

PubMed

Guandalini, Adolfo; Di Girolamo, Nicola; Corvi, Roberta; Santillo, Daniele; Andreani, Valentina; Pinzo, Barbara

2017-12-28

To describe the prevalence and the types of eye disorders that are known or presumed to be inherited (KP-HED) in three small Italian dog breeds. Three small Italian dog breeds: Maltese, Bolognese, and Italian Greyhound. All dogs of the breeds selected for this prospective observational study that underwent a complete ophthalmic examination between 1994 and 2015 were included. General and proportional KP-HED prevalence with 95% confidence intervals were reported. Three hundred and six of 462 dogs were affected by at least one KP-HED (66.2%; 95% CI: 61.8%-70.4%). In the entire population, the five most common KP-HED were cataract (n = 122; rate on the total number of KP-HED: 31.4%), entropion (n = 56; 14.4%), keratoconjunctivitis sicca (n = 33; 8.5%), retinal dysplasia (n = 24; 6.2%), and persistent pupillary membrane (iris to iris) (n = 21; 5.4%). The most common KP-HED in each breed were cataracts in the Maltese (35.1%) and in the Bolognese (24.2%), and presentation of vitreous in the anterior chamber in the Italian Greyhound (46.7%). Clinicians should be aware of KP-HED that commonly affect three small Italian dog breeds. Breed standards should be reconsidered, and breeding programs should be directed at limiting such disorders. © 2017 American College of Veterinary Ophthalmologists.

Phenotyping maize for adaptation to drought

PubMed Central

Araus, Jose L.; Serret, María D.; Edmeades, Gregory O.

2012-01-01

The need of a better adaptation of crops to drought is an issue of increasing urgency. However, enhancing the tolerance of maize has, therefore, proved to be somewhat elusive in terms of plant breeding. In that context, proper phenotyping remains as one of the main factors limiting breeding advance. Topics covered by this review include the conceptual framework for identifying secondary traits associated with yield response to drought and how to measure these secondary traits in practice. PMID:22934056

Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds.

PubMed

Mastrangelo, Salvatore; Di Gerlando, Rosalia; Tolone, Marco; Tortorici, Lina; Sardina, Maria Teresa; Portolano, Baldassare

2014-10-10

The recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. The aim of this work was to investigate the patterns of linkage disequilibrium (LD), the genetic diversity and population structure in Valle del Belice, Comisana, and Pinzirita dairy sheep breeds using the Illumina Ovine SNP50K Genotyping array. Average r (2) between adjacent SNPs across all chromosomes was 0.155 ± 0.204 for Valle del Belice, 0.156 ± 0.208 for Comisana, and 0.128 ± 0.188 for Pinzirita breeds, and some variations in LD value across chromosomes were observed, in particular for Valle del Belice and Comisana breeds. Average values of r (2) estimated for all pairwise combinations of SNPs pooled over all autosomes were 0.058 ± 0.023 for Valle del Belice, 0.056 ± 0.021 for Comisana, and 0.037 ± 0.017 for Pinzirita breeds. The LD declined as a function of distance and average r (2) was lower than the values observed in other sheep breeds. Consistency of results among the several used approaches (Principal component analysis, Bayesian clustering, F ST, Neighbor networks) showed that while Valle del Belice and Pinzirita breeds formed a unique cluster, Comisana breed showed the presence of substructure. In Valle del Belice breed, the high level of genetic differentiation within breed, the heterogeneous cluster in Admixture analysis, but at the same time the highest inbreeding coefficient, suggested that the breed had a wide genetic base with inbred individuals belonging to the same flock. The Sicilian breeds were characterized by low genetic differentiation and high level of admixture. Pinzirita breed displayed the highest genetic diversity (He, Ne) whereas the lowest value was found in Valle del Belice breed. This study has reported for the first time estimates of LD and genetic diversity from a genome-wide perspective in Sicilian dairy sheep breeds. Our results indicate that breeds formed non-overlapping clusters and are clearly separated populations and that Comisana sheep breed does not constitute a homogenous population. The information generated from this study has important implications for the design and applications of association studies as well as for development of conservation and/or selection breeding programs.

Marker-assisted selection in plant breeding for salinity tolerance.

PubMed

Ashraf, M; Akram, N A; Mehboob-Ur-Rahman; Foolad, M R

2012-01-01

Marker-assisted selection (MAS) is the process of using morphological, biochemical, or DNA markers as indirect selection criteria for selecting agriculturally important traits in crop breeding. This process is used to improve the effectiveness or efficiency of selection for the traits of interest in breeding programs. The significance of MAS as a tool for crop improvement has been extensively investigated in different crop -species and for different traits. The use of MAS for manipulating simple/qualitative traits is straightforward and has been well reported. However, MAS for the improvement of complex/polygenic traits, including plant tolerance/resistance to abiotic stresses, is more complicated, although its usefulness has been recognized. With the recent advances in marker technology, including high-throughput genotyping of plants, together with the development of nested association mapping populations, it is expected that the utility of MAS for breeding for stress tolerance traits will increase. In this chapter, we describe the basic procedure for using MAS in crop breeding for salt tolerance.

Prevalence of coccidiosis among village and exotic breed of chickens in Maiduguri, Nigeria

PubMed Central

Lawal, Jallailudeen Rabana; Jajere, Saleh Mohammed; Ibrahim, Umar Isa; Geidam, Yaqub Ahmed; Gulani, Isa Adamu; Musa, Gambo; Ibekwe, Benjamin U.

2016-01-01

Aim: Coccidiosis is an important enteric parasitic disease of poultry associated with significant economic losses to poultry farmers worldwide. This survey was conducted from June 2014 through July 2015 with the main goal of investigating the prevalence and associated risk factors of coccidiosis among village and exotic breeds of chickens in Maiduguri, Northeastern Nigeria. Materials and Methods: A total of 600 fecal samples from live and slaughtered birds comprising 284 young, 141, growers and 175 adult birds; 379 male and 221 female birds; 450 exotic and 150 local breeds of birds were randomly collected either as bird’s fresh droppings or cutting open an eviscerated intestine of slaughtered birds, while noting their age, sex, and breeds. Samples were analyzed using standard parasitological methods and techniques. Results: An overall prevalence rate of 31.8% (95% confidence interval: 28.07-35.52) was obtained. Higher prevalence rates were recorded in growing birds 58.9% (50.78-67.02), female birds 35.3% (29.00-41.60), exotic birds 42.4% (37.83-46.97), and broiler birds 68.7% (61.28-76.12). Similarly, higher infection rates were also observed among birds sampled from Mairi ward 66.7% (56.03-77.37), intensive management system 46.5% (41.61-51.39), and constructed local cages 54.0% (46.02-61.98). The difference in prevalence of coccidiosis among age groups, breeds, among exotic breeds, sampling sites, husbandry management systems, and litter management systems was statistically significant (<0.0001). However, no significant difference (p>0.05) of infection rates was observed in sex. Conclusion: Coccidiosis is endemic in both commercial and backyard poultry farms in Maiduguri due to poor management practices encouraging Eimeria oocysts build-up. It is therefore, recommended that poultry farmers should practice strict biosecurity measures on their farms, creating awareness on the prevalence of coccidiosis, routine vaccination against coccidiosis and educating poultry farmers on the need for maintaining good hygienic standards and good flock health management. PMID:27397991

Effects of management practices on grassland birds: Clay-colored Sparrow

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Nenneman, Melvin P.; Euliss, Betty R.

1998-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Western Meadowlark

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Zimmerman, Amy L.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Chestnut-collared Longspur

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Nenneman, Melvin P.; Euliss, Betty R.

1998-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Baird's Sparrow

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Nenneman, Melvin P.; Euliss, Betty R.

1998-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Nelson's Sharp-tailed Sparrow

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Rabie, Paul A.; Euliss, Betty R.

2002-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: McCown's Longspur

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Rabie, Paul A.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Burrowing Owl

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Rabie, Paul A.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Long-billed Curlew

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Rabie, Paul A.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Upland Sandpiper

USGS Publications Warehouse

Dechant, Jill A.; Dinkins, Meghan F.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Parkin, Barry D.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Lark Sparrow

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Parkin, Barry D.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Horned Lark

USGS Publications Warehouse

Dinkins, Meghan F.; Zimmerman, Amy L.; Dechant, Jill A.; Parkin, Barry D.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Euliss, Betty R.

2000-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Willet

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Parkin, Barry D.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Sedge Wren

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Parkin, Barry D.; Euliss, Betty R.

1998-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Field Sparrow

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Parkin, Barry D.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Bobolink

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Zimmerman, Amy L.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Lark Bunting

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Zimmerman, Amy L.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Vesper Sparrow

USGS Publications Warehouse

Dechant, Jill A.; Dinkins, Meghan F.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Euliss, Betty R.

2000-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Dickcissel

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Zimmerman, Amy L.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Ferruginous Hawk

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Zimmerman, Amy L.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: American Bittern

USGS Publications Warehouse

Dechant, Jill A.; Sondreal, Marriah L.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Zimmerman, Amy L.; Euliss, Betty R.

1999-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on grassland birds: Swainson's Hawk

USGS Publications Warehouse

Dechant, Jill A.; Dinkins, Meghan F.; Johnson, Douglas H.; Igl, Lawrence D.; Goldade, Christopher M.; Euliss, Betty R.

2000-01-01

Information on the habitat requirements and effects of habitat management on grassland birds were summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species' nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species' response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species' breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; for a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management, use the Grassland and Wetland Birds Bibliography on the home page of this resource.

Effects of management practices on wetland birds: Yellow Rail

USGS Publications Warehouse

Goldade, Christopher M.; Dechant, Jill A.; Johnson, Douglas H.; Zimmerman, Amy L.; Jamison, Brent E.; Church, James O.; Euliss, Betty R.

2002-01-01

Information on the habitat requirements and effects of habitat management on wetland birds were summarized from information in more than 500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although the BBS may not capture the presence of elusive waterbird species, the BBS is a standardized survey and the range maps, in many cases, represent the most consistent information available on species’ distributions. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The section on brood parasitism summarizes information on intra- and interspecific parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes recommendations for habitat management provided in the literature. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of wetland birds and their responses to habitat management is posted at the Web site mentioned below.

Effects of management practices on wetland birds: Virginia rail

USGS Publications Warehouse

Zimmerman, Amy L.; Dechant, Jill A.; Jamison, Brent E.; Johnson, Douglas H.; Goldade, Christopher M.; Church, James O.; Euliss, Betty R.

2002-01-01

Information on the habitat requirements and effects of habitat management on wetland birds were summarized from information in more than 500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although the BBS may not capture the presence of elusive waterbird species, the BBS is a standardized survey and the range maps, in many cases, represent the most consistent information available on species’ distributions. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The section on brood parasitism summarizes information on intra- and interspecific parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes recommendations for habitat management provided in the literature. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of wetland birds and their responses to habitat management is posted at the Web site mentioned below.

Effects of management practices on wetland birds: Black tern

USGS Publications Warehouse

Zimmerman, Amy L.; Dechant, Jill A.; Johnson, Douglas A.; Goldade, Christopher M.; Jamison, Brent E.; Euliss, Betty R.

2002-01-01

Information on the habitat requirements and effects of habitat management on wetland birds were summarized from information in more than 500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although the BBS may not capture the presence of elusive waterbird species, the BBS is a standardized survey and the range maps, in many cases, represent the most consistent information available on species’ distributions. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The section on brood parasitism summarizes information on intra- and interspecific parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes recommendations for habitat management provided in the literature. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of grassland birds and their responses to habitat management is posted at the Web site mentioned below.

Effects of management practices on wetland birds: American Avocet

USGS Publications Warehouse

Dechant, Jill A.; Zimmerman, Amy L.; Johnson, Douglas H.; Goldade, Christopher M.; Jamison, Brent E.; Euliss, Betty R.

2002-01-01

Information on the habitat requirements and effects of habitat management on wetland birds were summarized from information in more than 500 published and unpublished papers. A range map is provided to indicate the relative densities of the species in North America, based on Breeding Bird Survey (BBS) data. Although the BBS may not capture the presence of elusive waterbird species, the BBS is a standardized survey and the range maps, in many cases, represent the most consistent information available on species’ distributions. Although birds frequently are observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America, including areas that could not be mapped using BBS data. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species, especially those habitats that occur in the Great Plains. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The section on brood parasitism summarizes information on intra- and interspecific parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations in the Great Plains, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes recommendations for habitat management provided in the literature. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of wetland birds and their responses to habitat management is posted at the Web site mentioned below.

Effects of management practices on grassland birds: Greater Sage-Grouse

USGS Publications Warehouse

Rowland, Mary M.

2004-01-01

Information on the habitat requirements and effects of habitat management on Greater Sage-Grouse was summarized from information in more than 5,500 published and unpublished papers. A range map is provided to indicate the current range of Greater Sage-Grouse (adapted from Schroeder et al. 2004). Although birds may be observed outside the breeding range indicated, the maps are intended to show areas where managers might concentrate their attention. It may be ineffectual to manage habitat at a site for a species that rarely occurs in an area. The species account begins with a brief capsule statement, which provides the fundamental components or keys to management for the species. A section on breeding range outlines the current breeding distribution of the species in North America. The suitable habitat section describes the breeding habitat and occasionally microhabitat characteristics of the species. Details on habitat and microhabitat requirements often provide clues to how a species will respond to a particular management practice. A table near the end of the account complements the section on suitable habitat, and lists the specific habitat characteristics for the species by individual studies. A special section on prey habitat is included for those predatory species that have more specific prey requirements. The area requirements section provides details on territory and home range sizes, minimum area requirements, and the effects of patch size, edges, and other landscape and habitat features on abundance and productivity. It may be futile to manage a small block of suitable habitat for a species that has minimum area requirements that are larger than the area being managed. The Brown-headed Cowbird (Molothrus ater) is an obligate brood parasite of many grassland birds. The section on cowbird brood parasitism summarizes rates of cowbird parasitism, host responses to parasitism, and factors that influence parasitism, such as nest concealment and host density. The impact of management depends, in part, upon a species’ nesting phenology and biology. The section on breeding-season phenology and site fidelity includes details on spring arrival and fall departure for migratory populations, peak breeding periods, the tendency to renest after nest failure or success, and the propensity to return to a previous breeding site. The duration and timing of breeding varies among regions and years. Species’ response to management summarizes the current knowledge and major findings in the literature on the effects of different management practices on the species. The section on management recommendations complements the previous section and summarizes specific recommendations for habitat management provided in the literature. If management recommendations differ in different portions of the species’ breeding range, recommendations are given separately by region. The literature cited contains references to published and unpublished literature on the management effects and habitat requirements of the species. This section is not meant to be a complete bibliography; a searchable, annotated bibliography of published and unpublished papers dealing with habitat needs of shrub-steppe birds and their responses to habitat management is posted at the Web site mentioned below.

9 CFR 145.15 - Diagnostic surveillance program for low pathogenic avian influenza.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false Diagnostic surveillance program for low pathogenic avian influenza. 145.15 Section 145.15 Animals and Animal Products ANIMAL AND PLANT... PLAN FOR BREEDING POULTRY General Provisions § 145.15 Diagnostic surveillance program for low...

9 CFR 145.15 - Diagnostic surveillance program for low pathogenic avian influenza.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Diagnostic surveillance program for low pathogenic avian influenza. 145.15 Section 145.15 Animals and Animal Products ANIMAL AND PLANT... PLAN FOR BREEDING POULTRY General Provisions § 145.15 Diagnostic surveillance program for low...

An Ideal Remedial Reading Program.

ERIC Educational Resources Information Center

Boettcher, Judith A.

An ideal secondary level remedial reading program would be based on the philosophy that both freedom and structure are required, that learning demands involvement and feedback, and that success breeds success. Such programs should be structured (i.e., based on clearly defined content and a clearly designated mode of presentation). There are many…

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives.

PubMed

Crossa, José; Pérez-Rodríguez, Paulino; Cuevas, Jaime; Montesinos-López, Osval; Jarquín, Diego; de Los Campos, Gustavo; Burgueño, Juan; González-Camacho, Juan M; Pérez-Elizalde, Sergio; Beyene, Yoseph; Dreisigacker, Susanne; Singh, Ravi; Zhang, Xuecai; Gowda, Manje; Roorkiwal, Manish; Rutkoski, Jessica; Varshney, Rajeev K

2017-11-01

Genomic selection (GS) facilitates the rapid selection of superior genotypes and accelerates the breeding cycle. In this review, we discuss the history, principles, and basis of GS and genomic-enabled prediction (GP) as well as the genetics and statistical complexities of GP models, including genomic genotype×environment (G×E) interactions. We also examine the accuracy of GP models and methods for two cereal crops and two legume crops based on random cross-validation. GS applied to maize breeding has shown tangible genetic gains. Based on GP results, we speculate how GS in germplasm enhancement (i.e., prebreeding) programs could accelerate the flow of genes from gene bank accessions to elite lines. Recent advances in hyperspectral image technology could be combined with GS and pedigree-assisted breeding. Copyright © 2017 Elsevier Ltd. All rights reserved.

A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate.

PubMed

Takai, Toshiyuki; Adachi, Shunsuke; Taguchi-Shiobara, Fumio; Sanoh-Arai, Yumiko; Iwasawa, Norio; Yoshinaga, Satoshi; Hirose, Sakiko; Taniguchi, Yojiro; Yamanouchi, Utako; Wu, Jianzhong; Matsumoto, Takashi; Sugimoto, Kazuhiko; Kondo, Katsuhiko; Ikka, Takashi; Ando, Tsuyu; Kono, Izumi; Ito, Sachie; Shomura, Ayahiko; Ookawa, Taiichiro; Hirasawa, Tadashi; Yano, Masahiro; Kondo, Motohiko; Yamamoto, Toshio

2013-01-01

Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity.

A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate

PubMed Central

Takai, Toshiyuki; Adachi, Shunsuke; Taguchi-Shiobara, Fumio; Sanoh-Arai, Yumiko; Iwasawa, Norio; Yoshinaga, Satoshi; Hirose, Sakiko; Taniguchi, Yojiro; Yamanouchi, Utako; Wu, Jianzhong; Matsumoto, Takashi; Sugimoto, Kazuhiko; Kondo, Katsuhiko; Ikka, Takashi; Ando, Tsuyu; Kono, Izumi; Ito, Sachie; Shomura, Ayahiko; Ookawa, Taiichiro; Hirasawa, Tadashi; Yano, Masahiro; Kondo, Motohiko; Yamamoto, Toshio

2013-01-01

Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity. PMID:23985993

Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

PubMed Central

Wallner, Barbara; Vogl, Claus; Shukla, Priyank; Burgstaller, Joerg P.; Druml, Thomas; Brem, Gottfried

2013-01-01

The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3) are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion “Eclipse” or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices. PMID:23573227

Prevalence and risk factors for mast cell tumours in dogs in England.

PubMed

Shoop, Stephanie Jw; Marlow, Stephanie; Church, David B; English, Kate; McGreevy, Paul D; Stell, Anneliese J; Thomson, Peter C; O'Neill, Dan G; Brodbelt, David C

2015-01-01

Mast cell tumour (MCT) appears to be a frequent tumour type in dogs, though there is little published in relation to its frequency in dogs in the UK. The current study aimed to investigate prevalence and risk factors for MCTs in dogs attending English primary-care veterinary practices. Electronic patient records from practices participating in the VetCompass animal surveillance project between July 2007 and June 2013 were searched for MCT diagnosis. Various search terms and standard diagnostic terms (VeNom codes) identified records containing MCT diagnoses, which were evaluated against clinical criteria for inclusion to the study. MCT prevalence for the entire dataset and specific breed types were calculated. Descriptive statistics characterised MCT cases and multivariable logistic regression methods evaluated risk factors for association with MCT (P < 0.05). Within a population of 168,636 dogs, 453 had MCT, yielding a prevalence of 0.27% (95% confidence interval (CI) 0.24% - 0.29%). The highest breed type specific prevalences were for the Boxer at 1.95% (95% CI 1.40% - 2.51%), Golden Retriever at 1.39% (0.98% - 1.81%) and Weimaraner at 0.85% (95% CI 0.17% to 1.53%). Age, insurance status, neuter status, weight and breed type were associated with MCT diagnosis. Of dogs of specific breed type, the Boxer, Pug and Staffordshire Bull Terrier showed greater odds of MCT diagnosis compared with crossbred dogs. Conversely, the German Shepherd Dog, Border Collie, West Highland White Terrier, Springer Spaniel and Cocker Spaniel had reduced odds of MCT diagnosis compared with crossbred dogs. No association was found between MCT diagnosis and sex. This study highlights a clinically significant prevalence of MCT and identifies specific breed types with predisposition to MCT, potentially aiding veterinarian awareness and facilitating diagnosis.

9 CFR 3.2 - Indoor housing facilities.

Code of Federal Regulations, 2013 CFR

2013-01-01

... those breeds that cannot tolerate lower temperatures without stress or discomfort (such as short-haired... in maintaining good housekeeping practices, adequate cleaning, adequate inspection of animals, and...

9 CFR 3.2 - Indoor housing facilities.

Code of Federal Regulations, 2012 CFR

2012-01-01

... those breeds that cannot tolerate lower temperatures without stress or discomfort (such as short-haired... in maintaining good housekeeping practices, adequate cleaning, adequate inspection of animals, and...

9 CFR 3.2 - Indoor housing facilities.

Code of Federal Regulations, 2014 CFR

2014-01-01

... those breeds that cannot tolerate lower temperatures without stress or discomfort (such as short-haired... in maintaining good housekeeping practices, adequate cleaning, adequate inspection of animals, and...

Influence of cow breed type, age and previous lactation status on cow height, calf growth, and patterns of body weight, condition, and blood metabolites for cows grazing bahiagrass pastures

USDA-ARS?s Scientific Manuscript database

Economic analysis has revealed that in most parts of the country, the largest economic costs for cattle production are for winter feed. This study was initiated to evaluate the effect of two winter nutrition programs on three breeds of cows grazing bahiagrass pastures in central Florida. Data on 4...

Estimation of the number and demographics of companion dogs in the UK

PubMed Central

2011-01-01

Background Current estimates of the UK dog population vary, contain potential sources of bias and are based on expensive, large scale, public surveys. Here, we evaluate the potential of a variety of sources for estimation and monitoring of the companion dog population in the UK and associated demographic information. The sources considered were: a public survey; veterinary practices; pet insurance companies; micro-chip records; Kennel Club registrations; and the Pet Travel Scheme. The public survey and subpopulation estimates from veterinary practices, pet insurance companies and Kennel Club registrations, were combined to generate distinct estimates of the UK owned dog population using a Bayesian approach. Results We estimated there are 9.4 (95% CI: 8.1-11.5) million companion dogs in the UK according to the public survey alone, which is similar to other recent estimates. The population was judged to be over-estimated by combining the public and veterinary surveys (16.4, 95% CI: 12.5-21.5 million) and under-estimated by combining the public survey and insured dog numbers (4.8, 95% CI: 3.6-6.9 million). An estimate based on combining the public survey and Kennel Club registered dogs was 7.1 (95% CI: 4.5-12.9) million. Based on Bayesian estimations, 77 (95% CI: 62-92)% of the UK dog population were registered at a veterinary practice; 42 (95% CI: 29-55)% of dogs were insured; and 29 (95% CI: 17-43)% of dogs were Kennel Club registered. Breed demographics suggested the Labrador was consistently the most popular breed registered in micro-chip records, with the Kennel Club and with J. Sainsbury's PLC pet insurance. A comparison of the demographics between these sources suggested that popular working breeds were under-represented and certain toy, utility and miniature breeds were over- represented in the Kennel Club registrations. Density maps were produced from micro-chip records based on the geographical distribution of dogs. Conclusions A list containing the breed of each insured dog was provided by J. Sainsbury's PLC pet insurance without any accompanying information about the dog or owner. PMID:22112367

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds.

PubMed

Makina, Sithembile O; Taylor, Jeremy F; van Marle-Köster, Este; Muchadeyi, Farai C; Makgahlela, Mahlako L; MacNeil, Michael D; Maiwashe, Azwihangwisi

2015-01-01

Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r (2)≥ 0.20 would require about 30,000-50,000 SNPs. However, r (2)≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

PubMed Central

Makina, Sithembile O.; Taylor, Jeremy F.; van Marle-Köster, Este; Muchadeyi, Farai C.; Makgahlela, Mahlako L.; MacNeil, Michael D.; Maiwashe, Azwihangwisi

2015-01-01

Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2≥ 0.20 would require about 30,000–50,000 SNPs. However, r2≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa. PMID:26648975

Breeding-assisted genomics.

PubMed

Poland, Jesse

2015-04-01

The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition. Copyright © 2015 Elsevier Ltd. All rights reserved.

Exploitation of induced 2n-gametes for plant breeding.

PubMed

Younis, Adnan; Hwang, Yoon-Jung; Lim, Ki-Byung

2014-02-01

Unreduced gamete formation derived via abnormal meiotic cell division is an important approach to polyploidy breeding. This process is considered the main driving force in spontaneous polyploids formation in nature, but the potential application of these gametes to plant breeding has not been fully exploited. An effective mechanism for their artificial induction is needed to attain greater genetic variation and enable efficient use of unreduced gametes in breeding programs. Different approaches have been employed for 2n-pollen production including interspecific hybridization, manipulation of environmental factors and treatment with nitrous oxide, trifluralin, colchicine, oryzalin and other chemicals. These chemicals can act as a stimulus to produce viable 2n pollen; however, their exact mode of action, optimum concentration and developmental stages are still not known. Identification of efficient methods of inducing 2n-gamete formation will help increase pollen germination of sterile interspecific hybrids for inter-genomic recombination and introgression breeding to develop new polyploid cultivars and increase heterozygosity among plant populations. Additionally, the application of genomic tools and identification and isolation of genes and mechanisms involved in the induction of 2n-gamete will enable increased exploitation in different plant species, which will open new avenues for plant breeding.

Economic evaluation of alternative crossbreeding systems involving four breeds of swine. I. The simulation model.

PubMed

McLaren, D G; Buchanan, D S; Williams, J E

1987-10-01

A static, deterministic computer model, programmed in Microsoft Basic for IBM PC and Apple Macintosh computers, was developed to calculate production efficiency (cost per kg of product) for nine alternative types of crossbreeding system involving four breeds of swine. The model simulates efficiencies for four purebred and 60 alternative two-, three- and four-breed rotation, rotaterminal, backcross and static cross systems. Crossbreeding systems were defined as including all purebred, crossbred and commercial matings necessary to maintain a total of 10,000 farrowings. Driving variables for the model are mean conception rate at first service and for an 8-wk breeding season, litter size born, preweaning survival rate, postweaning average daily gain, feed-to-gain ratio and carcass backfat. Predictions are computed using breed direct genetic and maternal effects for the four breeds, plus individual, maternal and paternal specific heterosis values, input by the user. Inputs required to calculate the number of females farrowing in each sub-system include the proportion of males and females replaced each breeding cycle in purebred and crossbred populations, the proportion of male and female offspring in seedstock herds that become breeding animals, and the number of females per boar. Inputs required to calculate the efficiency of terminal production (cost-to-product ratio) for each sub-system include breeding herd feed intake, gilt development costs, feed costs and labor and overhead costs. Crossbreeding system efficiency is calculated as the weighted average of sub-system cost-to-product ratio values, weighting by the number of females farrowing in each sub-system.

Breeding of Acrocomia aculeata using genetic diversity parameters and correlations to select accessions based on vegetative, phenological, and reproductive characteristics.

PubMed

Coser, S M; Motoike, S Y; Corrêa, T R; Pires, T P; Resende, M D V

2016-10-17

Macaw palm (Acrocomia aculeata) is a promising species for use in biofuel production, and establishing breeding programs is important for the development of commercial plantations. The aim of the present study was to analyze genetic diversity, verify correlations between traits, estimate genetic parameters, and select different accessions of A. aculeata in the Macaw Palm Germplasm Bank located in Universidade Federal de Viçosa, to develop a breeding program for this species. Accessions were selected based on precocity (PREC), total spathe (TS), diameter at breast height (DBH), height of the first spathe (HFS), and canopy area (CA). The traits were evaluated in 52 accessions during the 2012/2013 season and analyzed by restricted estimation maximum likelihood/best linear unbiased predictor procedures. Genetic diversity resulted in the formation of four groups by Tocher's clustering method. The correlation analysis showed it was possible to have indirect and early selection for the traits PREC and DBH. Estimated genetic parameters strengthened the genetic variability verified by cluster analysis. Narrow-sense heritability was classified as moderate (PREC, TS, and CA) to high (HFS and DBH), resulting in strong genetic control of the traits and success in obtaining genetic gains by selection. Accuracy values were classified as moderate (PREC and CA) to high (TS, HFS, and DBH), reinforcing the success of the selection process. Selection of accessions for PREC, TS, and HFS by the rank-average method permits selection gains of over 100%, emphasizing the successful use of the accessions in breeding programs and obtaining superior genotypes for commercial plantations.

Estimation of the genetic diversity in tetraploid alfalfa populations based on RAPD markers for breeding purposes.

PubMed

Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

2011-01-01

Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon's information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

Temporal Dynamics and Spatial Patterns of Aedes aegypti Breeding Sites, in the Context of a Dengue Control Program in Tartagal (Salta Province, Argentina).

PubMed

Espinosa, Manuel; Weinberg, Diego; Rotela, Camilo H; Polop, Francisco; Abril, Marcelo; Scavuzzo, Carlos Marcelo

2016-05-01

Since 2009, Fundación Mundo Sano has implemented an Aedes aegypti Surveillance and Control Program in Tartagal city (Salta Province, Argentina). The purpose of this study was to analyze temporal dynamics of Ae. aegypti breeding sites spatial distribution, during five years of samplings, and the effect of control actions over vector population dynamics. Seasonal entomological (larval) samplings were conducted in 17,815 fixed sites in Tartagal urban area between 2009 and 2014. Based on information of breeding sites abundance, from satellite remote sensing data (RS), and by the use of Geographic Information Systems (GIS), spatial analysis (hotspots and cluster analysis) and predictive model (MaxEnt) were performed. Spatial analysis showed a distribution pattern with the highest breeding densities registered in city outskirts. The model indicated that 75% of Ae. aegypti distribution is explained by 3 variables: bare soil coverage percentage (44.9%), urbanization coverage percentage(13.5%) and water distribution (11.6%). This results have called attention to the way entomological field data and information from geospatial origin (RS/GIS) are used to infer scenarios which could then be applied in epidemiological surveillance programs and in the determination of dengue control strategies. Predictive maps development constructed with Ae. aegypti systematic spatiotemporal data, in Tartagal city, would allow public health workers to identify and target high-risk areas with appropriate and timely control measures. These tools could help decision-makers to improve health system responses and preventive measures related to vector control.

Temporal Dynamics and Spatial Patterns of Aedes aegypti Breeding Sites, in the Context of a Dengue Control Program in Tartagal (Salta Province, Argentina)

PubMed Central

Espinosa, Manuel; Weinberg, Diego; Rotela, Camilo H.; Polop, Francisco; Abril, Marcelo; Scavuzzo, Carlos Marcelo

2016-01-01

Background Since 2009, Fundación Mundo Sano has implemented an Aedes aegypti Surveillance and Control Program in Tartagal city (Salta Province, Argentina). The purpose of this study was to analyze temporal dynamics of Ae. aegypti breeding sites spatial distribution, during five years of samplings, and the effect of control actions over vector population dynamics. Methodology/Principal Findings Seasonal entomological (larval) samplings were conducted in 17,815 fixed sites in Tartagal urban area between 2009 and 2014. Based on information of breeding sites abundance, from satellite remote sensing data (RS), and by the use of Geographic Information Systems (GIS), spatial analysis (hotspots and cluster analysis) and predictive model (MaxEnt) were performed. Spatial analysis showed a distribution pattern with the highest breeding densities registered in city outskirts. The model indicated that 75% of Ae. aegypti distribution is explained by 3 variables: bare soil coverage percentage (44.9%), urbanization coverage percentage(13.5%) and water distribution (11.6%). Conclusions/Significance This results have called attention to the way entomological field data and information from geospatial origin (RS/GIS) are used to infer scenarios which could then be applied in epidemiological surveillance programs and in the determination of dengue control strategies. Predictive maps development constructed with Ae. aegypti systematic spatiotemporal data, in Tartagal city, would allow public health workers to identify and target high-risk areas with appropriate and timely control measures. These tools could help decision-makers to improve health system responses and preventive measures related to vector control. PMID:27223693

Genetic evaluation of the Association of Zoos and Aquariums Matschie's tree kangaroo (Dendrolagus matschiei) captive breeding program.

PubMed

McGreevy, Thomas J; Dabek, Lisa; Husband, Thomas P

2011-01-01

Matschie's tree kangaroo (Dendrolagus matschiei) is an endangered species that has been bred in captivity since the 1970s. In 1992, the Tree Kangaroo Species Survival Plan(®) (TKSSP) was established to coordinate the captive management of Association of Zoos and Aquariums (AZA) D. matschiei. The TKSSP makes annual breeding recommendations primarily based on the mean kinship (MK) strategy. Captive breeding programs often use the MK strategy to preserve genetic diversity in small populations-to avoid the negative consequences of inbreeding and retain their adaptive potential. The ability of a captive breeding program to retain the population's genetic diversity over time can be evaluated by comparing the genetic diversity of the captive population to wild populations. We analyzed DNA extracted from blood and fecal samples from AZA (n = 71), captive (n = 28), and wild (n = 22) D. matschiei using eight microsatellite markers and sequenced the partial mitochondrial DNA control region gene. AZA D. matschiei had a similar expected heterozygosity (H(e) = 0.595 ± 0.184) compared with wild D. matschiei (H(e) = 0.628 ± 0.143), but they had different allelic frequencies (F(ST) = 0.126; P < 0.001). AZA D. matschiei haplotype diversity was almost two times lower than wild D. matschiei Ĥ = 0.740 ± 0.063. These data will assist management of AZA D. matschiei and serve as a baseline for AZA and wild D. matschiei genetic diversity values that could be used to monitor future changes in their genetic diversity. © 2010 Wiley Periodicals, Inc.

Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice

PubMed Central

Hori, Kiyosumi; Kataoka, Tomomori; Miura, Kiyoyuki; Yamaguchi, Masayuki; Saka, Norikuni; Nakahara, Takahiro; Sunohara, Yoshihiro; Ebana, Kaworu; Yano, Masahiro

2012-01-01

To identify quantitative trait loci (QTLs) associated with the primary target traits for selection in practical rice breeding programs, backcross inbred lines (BILs) derived from crosses between temperate japonica rice cultivars Nipponbare and Koshihikari were evaluated for 50 agronomic traits at six experimental fields located throughout Japan. Thirty-three of the 50 traits were significantly correlated with heading date. Using a linkage map including 647 single-nucleotide polymorphisms (SNPs), a total of 122 QTLs for 38 traits were mapped on all rice chromosomes except chromosomes 5 and 9. Fifty-eight of the 122 QTLs were detected near the heading date QTLs Hd16 and Hd17 and the remaining 64 QTLs were found in other chromosome regions. QTL analysis of 51 BILs having homozygous for the Koshihikari chromosome segments around Hd16 and Hd17 allowed us to detect 40 QTLs associated with 27 traits; 23 of these QTLs had not been detected in the original analysis. Among the 97 QTLs for the 30 traits measured in multiple environments, the genotype-by-environment interaction was significant for 44 QTLs and not significant for 53 QTLs. These results led us to propose a new selection strategy to improve agronomic performance in temperate japonica rice cultivars. PMID:23226082

Short communication: bulk tank total bacterial count in dairy sheep: factors of variation and relationship with somatic cell count.

PubMed

Gonzalo, C; Carriedo, J A; Beneitez, E; Juárez, M T; De La Fuente, L F; San Primitivo, F

2006-02-01

A total of 9,353 records for bulk tank total bacterial count (TBC) were obtained over 1 yr from 315 dairy ewe flocks belonging to the Sheep Improvement Consortium (CPO) in Castilla-León (Spain). Analysis of variance showed significant effects of flock, breed, month within flock, dry therapy, milking type and installation, and logSCC on logTBC. Flock and month within flock were important variation factors as they accounted for 22.0 and 22.1% of the variance, respectively. Considerable repeatability values were obtained for both random factors. Hand milking and bucket-milking machines elicited highest logTBC (5.31), whereas parlor systems with looped milkline (5.01) elicited the lowest logTBC. The implementation of dry therapy practice (5.12) showed significantly lower logTBC than when not used (5.25). Variability in logTBC among breeds ranged from 5.24 (Awassi) to 5.07 (Churra). However, clinical outbreaks of contagious agalactia did not increase TBC significantly. A statistically significant relationship was found between logTBC and logSCC, the correlation coefficient between the variables being r = 0.23. Programs for improving milk hygiene should be implemented for both total bacterial count and somatic cell count variables at the same time.

Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

PubMed Central

2010-01-01

Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA) were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95). With breed information, 30 cows and three bulls were identified (q > 0.95) that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10) relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P < 0.001). The four Algarvia bulls had Y-haplotypes H6Y2 and H11Y2, common in Portuguese cattle. The mtDNA composition showed prevalence of T3 matrilines and presence of the African-derived T1a haplogroup. This analysis confirmed the genetic proximity of Algarvia and Garvonesa breeds (Fst = 0.028, P > 0.05). Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50) to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that can be considered remnants of the Algarvia breed. Results of genetic diversity and conservation analyses provide objective information to establish a management program to reconstitute the Algarvia breed. PMID:20540741

Integrating genomic selection into dairy cattle breeding programmes: a review.

PubMed

Bouquet, A; Juga, J

2013-05-01

Extensive genetic progress has been achieved in dairy cattle populations on many traits of economic importance because of efficient breeding programmes. Success of these programmes has relied on progeny testing of the best young males to accurately assess their genetic merit and hence their potential for breeding. Over the last few years, the integration of dense genomic information into statistical tools used to make selection decisions, commonly referred to as genomic selection, has enabled gains in predicting accuracy of breeding values for young animals without own performance. The possibility to select animals at an early stage allows defining new breeding strategies aimed at boosting genetic progress while reducing costs. The first objective of this article was to review methods used to model and optimize breeding schemes integrating genomic selection and to discuss their relative advantages and limitations. The second objective was to summarize the main results and perspectives on the use of genomic selection in practical breeding schemes, on the basis of the example of dairy cattle populations. Two main designs of breeding programmes integrating genomic selection were studied in dairy cattle. Genomic selection can be used either for pre-selecting males to be progeny tested or for selecting males to be used as active sires in the population. The first option produces moderate genetic gains without changing the structure of breeding programmes. The second option leads to large genetic gains, up to double those of conventional schemes because of a major reduction in the mean generation interval, but it requires greater changes in breeding programme structure. The literature suggests that genomic selection becomes more attractive when it is coupled with embryo transfer technologies to further increase selection intensity on the dam-to-sire pathway. The use of genomic information also offers new opportunities to improve preservation of genetic variation. However, recent simulation studies have shown that putting constraints on genomic inbreeding rates for defining optimal contributions of breeding animals could significantly reduce achievable genetic gain. Finally, the article summarizes the potential of genomic selection to include new traits in the breeding goal to meet societal demands regarding animal health and environmental efficiency in animal production.

Genomics of pear and other Rosaceae fruit trees

PubMed Central

Yamamoto, Toshiya; Terakami, Shingo

2016-01-01

The family Rosaceae includes many economically important fruit trees, such as pear, apple, peach, cherry, quince, apricot, plum, raspberry, and loquat. Over the past few years, whole-genome sequences have been released for Chinese pear, European pear, apple, peach, Japanese apricot, and strawberry. These sequences help us to conduct functional and comparative genomics studies and to develop new cultivars with desirable traits by marker-assisted selection in breeding programs. These genomics resources also allow identification of evolutionary relationships in Rosaceae, development of genome-wide SNP and SSR markers, and construction of reference genetic linkage maps, which are available through the Genome Database for the Rosaceae website. Here, we review the recent advances in genomics studies and their practical applications for Rosaceae fruit trees, particularly pear, apple, peach, and cherry. PMID:27069399

Genomics of pear and other Rosaceae fruit trees.

PubMed

Yamamoto, Toshiya; Terakami, Shingo

2016-01-01

The family Rosaceae includes many economically important fruit trees, such as pear, apple, peach, cherry, quince, apricot, plum, raspberry, and loquat. Over the past few years, whole-genome sequences have been released for Chinese pear, European pear, apple, peach, Japanese apricot, and strawberry. These sequences help us to conduct functional and comparative genomics studies and to develop new cultivars with desirable traits by marker-assisted selection in breeding programs. These genomics resources also allow identification of evolutionary relationships in Rosaceae, development of genome-wide SNP and SSR markers, and construction of reference genetic linkage maps, which are available through the Genome Database for the Rosaceae website. Here, we review the recent advances in genomics studies and their practical applications for Rosaceae fruit trees, particularly pear, apple, peach, and cherry.

Future animal improvement programs applied to global populations

USDA-ARS?s Scientific Manuscript database

Breeding programs evolved gradually from within-herd phenotypic selection to local and regional cooperatives to national evaluations and now international evaluations. In the future, breeders may adapt reproductive, computational, and genomic methods to global populations as easily as with national ...

Mating programs including genomic relationships and dominance effects

USDA-ARS?s Scientific Manuscript database

Breed associations, artificial-insemination organizations, and on-farm software providers need new computerized mating programs for genomic selection so that genomic inbreeding could be minimized by comparing genotypes of potential mates. Efficient methods for transferring elements of the genomic re...

Evaluation of the spatial and temporal distribution of and risk factors for Bluetongue serotype 1 epidemics in sheep Extremadura (Spain), 2007-2011.

PubMed

Pascual-Linaza, Ana V; Martínez-López, Beatriz; Pfeiffer, Dirk U; Moreno, José Carlos; Sanz, Cristina; Sánchez-Vizcaíno, José Manuel

2014-10-01

Extremadura has been one of the regions in Spain most severely affected by Bluetongue (BT) epidemics. The first incursion of BTV, which was successfully eradicated one year later, occurred in 2004, involving the BTV-serotype 4. However, a second incursion occurred in September 2007, this time involving serotype 1. Since then, the implementation of intensive vaccination programs have significantly reduced BTV-1 occurrence, but the disease has not been completely eradicated yet. This study aimed to provide, for the first time, a complete description of the spatial and temporal patterns of BTV-1 occurrence in sheep in Extremadura from 2007 to 2011 and to identify the risk factors that contributed to the seasonal occurrence of BTV-1 in this region. The results showed that risk factors contributing to BTV-1 occurrence in sheep changed between 2007 and 2011. Initially, when the population was still immunologically naïve, the main risk factors for BTV-1 occurrence were extensive management practices, large sheep farms and Culicoides abundance on farms. However, after the implementation of vaccination, other factors became more relevant for BTV-1 occurrence, mostly related to BTV reservoirs, such as the proximity of cattle farms or the introduction of cattle into farms. The Talaverana sheep breed also seemed to be associated with a significantly higher risk of BTV-1 occurrence, although it may be due to confounding factors, such as the geographical concentration of where this breed is kept and/or management practises used for this breed. The results of this study suggest that preventive and control strategies, including vaccination and active surveillance strategies, should be primarily focused on cattle farms kept in close vicinity to sheep flocks as well as in high-risk sheep farms (i.e. farms with a large farm size keeping both cattle and sheep and with a high number of animal introductions). Methods and results presented here may be used to guide decisions for the annual update of the control and eradication program in Spain. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Factors influencing breeding success, ovarian cyclicity, and cub survival in zoo-managed tigers (Panthera tigris).

PubMed

Saunders, Sarah P; Harris, Tara; Traylor-Holzer, Kathy; Beck, Karen Goodrowe

2014-01-10

Understanding factors that influence reproduction and offspring survival in zoo populations is critical for management of threatened and endangered species. Examination of long-term data (1989-2011) compiled from the Association of Zoos and Aquarium's zoo-managed tiger breeding program provides the basis for a more thorough understanding of reproduction and scientifically based decisions for effective population management in this endangered felid. Biological and management-related factors that could influence tiger breeding success and cub survival were evaluated using logistic mixed models. Breeding success improved with female age until approximately age five, then declined thereafter. Experienced female breeders had greater breeding success than inexperienced females. Litter size was most predictive of cub survival, with average-sized litters (3-4 cubs) experiencing the highest proportional survival. Management-related factors, such as whether the breeding institution had a recent tiger litter and whether both animals were already located at the same institution, also influenced breeding success and cub survival. These results highlight the importance of institutional husbandry experience and the need to retain knowledge through staff turnovers to achieve optimal reproductive success. Using fecal estrogen data, frequency of ovarian cyclicity and mean cycle length did not differ by female age or parity; thus, lack of cyclicity and/or increased cycle duration are not likely explanations for declining breeding success with age. These results provide valuable reproductive information that should improve scientific management of zoo-based tiger populations. Copyright © 2013 Elsevier B.V. All rights reserved.

9 CFR 3.5 - Mobile or traveling housing facilities.

Code of Federal Regulations, 2014 CFR

2014-01-01

... temperatures, for those breeds that cannot tolerate lower temperatures without stress or discomfort (such as... sufficient illumination to aid in maintaining good housekeeping practices, adequate cleaning, adequate...

9 CFR 3.5 - Mobile or traveling housing facilities.

Code of Federal Regulations, 2012 CFR

2012-01-01

... temperatures, for those breeds that cannot tolerate lower temperatures without stress or discomfort (such as... sufficient illumination to aid in maintaining good housekeeping practices, adequate cleaning, adequate...

9 CFR 3.5 - Mobile or traveling housing facilities.

Code of Federal Regulations, 2013 CFR

2013-01-01

... temperatures, for those breeds that cannot tolerate lower temperatures without stress or discomfort (such as... sufficient illumination to aid in maintaining good housekeeping practices, adequate cleaning, adequate...

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2010 CFR

2010-10-01

...-sustaining population in captivity of the exotic bird species; (iii) Details on the system of recordkeeping... the exotic bird species in the world; (v) Details on the funding of this program; and (vi) Plans for... program intended to enhance the survival of the population from which the exotic bird species was or would...

Initial insights on the performances and management of dairy cattle herds combining two breeds with contrasting features.

PubMed

Magne, M A; Thénard, V; Mihout, S

2016-05-01

Finding ways of increasing animal production with low external inputs and without compromising reproductive performances is a key issue of livestock systems sustainability. One way is to take advantage of the diversity and interactions among components within livestock systems. Among studies that investigate the influence of differences in animals' individual abilities in a herd, few focus on combinations of cow breeds with contrasting features in dairy cattle herds. This study aimed to analyse the performances and management of such multi-breed dairy cattle herds. These herds were composed of two types of dairy breeds: 'specialist' (Holstein) and 'generalist' (e.g. Montbeliarde, Simmental, etc.). Based on recorded milk data in southern French region, we performed (i) to compare the performances of dairy herds according to breed-type composition: multi-breed, single specialist breed or single generalist breed and (ii) to test the difference of milk performances of specialist and generalist breed cows (n = 10 682) per multi-breed dairy herd within a sample of 22 farms. The sampled farmers were also interviewed to characterise herd management through multivariate analysis. Multi-breed dairy herds had a better trade-off among milk yield, milk fat and protein contents, herd reproduction and concentrate-conversion efficiency than single-breed herds. Conversely, they did not offer advantages in terms of milk prices and udder health. Compared to specialist dairy herds, they produce less milk with the same concentrate-conversion efficiency but have better reproductive performances. Compared to generalist dairy herds, they produce more milk with better concentrate-conversion efficiency but have worse reproductive performances. Within herds, specialist and generalist breed cows significantly differed in milk performances, showing their complementarity. The former produced more milk for a longer lactation length while the latter produced milk with higher protein and fat contents and had a slightly longer lactation rank. Our results also focus on the farmers' management of multi-breed dairy herds underlying herd performances. Three strategies of management were identified and structured along two main axes. The first differentiates farmers according to their animal-selection practices in relation with their objectives of production: adapting animal to produce milk with low-feeding inputs v. focussing on milk yield trait to intensify milk production. The second refers to the purpose farmers give to multi-breed dairy herds: milk v. milk/meat production. These initial insights on the performances and management of multi-breed dairy herds contribute to better understanding the functioning of ruminant livestock systems based on individual variability.

Japanese plums (Prunus salicina Lindl.) and phytochemicals--breeding, horticultural practice, postharvest storage, processing and bioactivity.

PubMed

Fanning, Kent J; Topp, Bruce; Russell, Dougal; Stanley, Roger; Netzel, Michael

2014-08-01

Previous reviews of plum phytochemical content and health benefits have concentrated on the European plum, Prunus domestica L. However, the potential bioactivity of red- and dark red-fleshed Japanese plums, Prunus salicina Lindl., so-called blood plums, appears to warrant a significant increase in exposure, as indicated in a recent review of the whole Prunus genus. Furthermore, Japanese plums are the predominant plum produced on an international basis. In this review the nutrient and phytochemical content, breeding, horticultural practice, postharvest treatment and processing as well as bioactivity (emphasising in vivo studies) of Japanese plum are considered, with a focus on the anthocyanin content that distinguishes the blood plums. © 2014 State of Queensland Journal of the Science of Food and Agriculture © 2014 Society of Chemical Industry.

Mitochondrial sequencing reveals five separate origins of 'black' Apis mellifera (Hymenoptera: Apidae) in eastern Australian commercial colonies.

PubMed

Oxley, P R; Oldroyd, B P

2009-04-01

Establishment of a closed population honey bee, Apis mellifera L. (Hymenoptera: Apidae), breeding program based on 'black' strains has been proposed for eastern Australia. Long-term success of such a program requires a high level of genetic variance. To determine the likely extent of genetic variation available, 50 colonies from 11 different commercial apiaries were sequenced in the mitochondrial cytochrome oxidase I and II intergenic region. Five distinct and novel mitotypes were identified. No colonies were found with the A. mellifera mellifera mitotype, which is often associated with undesirable feral strains. One group of mitotypes was consistent with a caucasica origin, two with carnica, and two with ligustica. The results suggest that there is sufficient genetic diversity to support a breeding program provided all these five sources were pooled.

Optimization of reproductive management programs using lift chart analysis and cost-sensitive evaluation of classification errors.

PubMed

Shahinfar, Saleh; Guenther, Jerry N; Page, C David; Kalantari, Afshin S; Cabrera, Victor E; Fricke, Paul M; Weigel, Kent A

2015-06-01

The common practice on most commercial dairy farms is to inseminate all cows that are eligible for breeding, while ignoring (or absorbing) the costs associated with semen and labor directed toward low-fertility cows that are unlikely to conceive. Modern analytical methods, such as machine learning algorithms, can be applied to cow-specific explanatory variables for the purpose of computing probabilities of success or failure associated with upcoming insemination events. Lift chart analysis can identify subsets of high fertility cows that are likely to conceive and are therefore appropriate targets for insemination (e.g., with conventional artificial insemination semen or expensive sex-enhanced semen), as well as subsets of low-fertility cows that are unlikely to conceive and should therefore be passed over at that point in time. Although such a strategy might be economically viable, the management, environmental, and financial conditions on one farm might differ widely from conditions on the next, and hence the reproductive management recommendations derived from such a tool may be suboptimal for specific farms. When coupled with cost-sensitive evaluation of misclassified and correctly classified insemination events, the strategy can be a potentially powerful tool for optimizing the reproductive management of individual farms. In the present study, lift chart analysis and cost-sensitive evaluation were applied to a data set consisting of 54,806 insemination events of primiparous Holstein cows on 26 Wisconsin farms, as well as a data set with 17,197 insemination events of primiparous Holstein cows on 3 Wisconsin farms, where the latter had more detailed information regarding health events of individual cows. In the first data set, the gains in profit associated with limiting inseminations to subsets of 79 to 97% of the most fertile eligible cows ranged from $0.44 to $2.18 per eligible cow in a monthly breeding period, depending on days in milk at breeding and milk yield relative to contemporaries. In the second data set, the strategy of inseminating only a subset consisting of 59% of the most fertile cows conferred a gain in profit of $5.21 per eligible cow in a monthly breeding period. These results suggest that, when used with a powerful classification algorithm, lift chart analysis and cost-sensitive evaluation of correctly classified and misclassified insemination events can enhance the performance and profitability of reproductive management programs on commercial dairy farms. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genetic Modification of Short Rotation Poplar Biomass Feedstock for Efficient Conversion to Ethanol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dinus, R.J.

2000-08-30

The Bioenergy Feedstock Development Program, Environmental Sciences Division, Oak Ridge National Laboratory is developing poplars (Populus species and hybrids) as sources of renewable energy, i.e., ethanol. Notable increases in adaptability, volume productivity, and pest/stress resistance have been achieved via classical selection and breeding and intensified cultural practices. Significant advances have also been made in the efficiencies of harvesting and handling systems. Given these and anticipated accomplishments, program leaders are considering shifting some attention to genetically modifying feedstock physical and chemical properties, so as to improve the efficiency with which feedstocks can be converted to ethanol. This report provides an in-depthmore » review and synthesis of opportunities for and feasibilities of genetically modifying feedstock qualities via classical selection and breeding, marker-aided selection and breeding, and genetic transformation. Information was collected by analysis of the literature, with emphasis on that published since 1995, and interviews with prominent scientists, breeders, and growers. Poplar research is well advanced, and literature is abundant. The report therefore primarily reflects advances in poplars, but data from other species, particularly other shortrotation hardwoods, are incorporated to fill gaps. An executive summary and recommendations for research, development, and technology transfer are provided immediately after the table of contents. The first major section of the report describes processes most likely to be used for conversion of poplar biomass to ethanol, the various physical and chemical properties of poplar feedstocks, and how such properties are expected to affect process efficiency. The need is stressed for improved understanding of the impact of change on both overall process and individual process step efficiencies. The second part documents advances in trait measurement instrumentation and methodology. The importance of these and future developments is emphasized, since trait measurement constitutes the largest cost associated with adding additional traits to improvement efforts, regardless of genetic approach. In subsequent sections, recent and projected advances in classical selection and breeding, marker-aided selection, and genetic transformation are documented and used to evaluate the feasibility of individual approaches. Interviews with specialists engaged in research and development on each approach were given particular emphasis in gauging feasibilities and defining future needs and directions. Summaries of important findings and major conclusions are presented at the end of individual sections. Closing portions describe the targeted workshop, conducted in December 1999 and list interviewees and literature cited in the text. Information obtained at the workshop was used to improve accuracy, refine conclusions, and recommend priorities for future research, development, and technology transfer.« less

A multi-environmental study of recent breeding progress on nitrogen use efficiency in wheat (Triticum aestivum L.).

PubMed

Cormier, Fabien; Faure, Sébastien; Dubreuil, Pierre; Heumez, Emmanuel; Beauchêne, Katia; Lafarge, Stéphane; Praud, Sébastien; Le Gouis, Jacques

2013-12-01

By comparing 195 varieties in eight trials, this study assesses nitrogen use efficiency improvement in high and low nitrogen conditions in European winter wheat over the last 25 years. In a context where European agriculture practices have to deal with environmental concerns and nitrogen (N) fertiliser cost, nitrogen use efficiency (NUE) has to be improved. This study assessed genetic progress in winter wheat (Triticum aestivum L.) NUE. Two hundred and twenty-five European elite varieties were tested in four environments under two levels of N. Global genetic progress was assessed on additive genetic values and on genotype × N interaction, covering 25 years of European breeding. To avoid sampling bias, quality, precocity and plant height were added as covariates in the analyses when needed. Genotype × environment interactions were highly significant for all the traits studied to such an extent that no additive genetic effect was detected on N uptake. Genotype × N interactions were significant for yield, grain protein content (GPC), N concentration in straw, N utilisation, and NUE. Grain yield improvement (+0.45 % year(-1)) was independent of the N treatment. GPC was stable, thus grain nitrogen yield was improved (+0.39 % year(-1)). Genetic progress on N harvest index (+0.12 % year(-1)) and on N concentration in straw (-0.52 % year(-1)) possibly revealed improvement in N remobilisation. There has been an improvement of NUE additive genetic value (+0.33 % year(-1)) linked to better N utilisation (+0.20 % year(-1)). Improved yield stability was detected as a significant improvement of NUE in low compared to high N conditions. The application of these results to breeding programs is discussed.

Genetic variation and comparison of orchardgrass (Dactylis glomerata L.) cultivars and wild accessions as revealed by SSR markers.

PubMed

Xie, W G; Lu, X F; Zhang, X Q; Huang, L K; Cheng, L

2012-02-24

Orchardgrass is a highly variable, perennial forage grass that is cultivated throughout temperate and subtropical regions of the world. Despite its economic importance, the genetic relationship and distance among and within cultivars are largely unknown but would be of great interest for breeding programs. We investigated the molecular variation and structure of cultivar populations, compared the level of genetic diversity among cultivars (Baoxing, Anba, Bote, and Kaimo), subspecies (Dactylis glomerata ssp Woronowii) and advanced breeding line (YA02-116) to determine whether there is still sufficient genetic diversity within presently used cultivars for future breeding progress in China. Twenty individuals were analyzed from each of six accessions using SSR markers; 114 easily scored bands were generated from 15 SSR primer pairs, with an average of 7.6 alleles per locus. The polymorphic rate was 100% among the 120 individuals, reflecting a high degree of genetic diversity. Among the six accessions, the highest genetic diversity was observed in Kaimo (H = 0.2518; I = 0.3916; P = 87.3%) and 02-116 had a lower level of genetic diversity (H = 0.1806; I = 0.2788; P = 58.73%) compared with other cultivars tested. An of molecular variance revealed a much larger genetic variation within accessions (65%) than between them (35%). This observation suggests that these cultivars have potential for providing rich genetic resource for further breeding program. Furthermore, the study also indicated that Chinese orchardgrass breeding has involved strong selection for adaptation to forage production, which may result in restricted genetic base of orchardgrass cultivar.

The relative role of captive breeding and of zoo-bred animals in North American conservation translocations.

PubMed

Brichieri-Colombi, Typhenn A; Lloyd, Natasha A; Mcpherson, Jana M; Moehrenschlager, Axel

2018-06-19

With the loss of biodiversity accelerating, conservation translocations such as reintroductions are becoming an increasingly common conservation tool. Conservation translocations must source individuals for release from either wild or captive-bred populations. We asked what proportion of North American conservation translocations rely on captive breeding, and to what extent zoos and aquaria (hereafter zoos) fulfill captive breeding needs. Our comprehensive literature review indicates that North American conservation translocations published before 2014 involved captive breeding for 162 (58%) of the 279 animal species translocated. Fifty-four zoos contributed animals for release; the fourty species of animals bred for release by zoos represents only 14% of all animal species for which conservation translocations were published, and only 25% of all animal species that were bred for releases occurring in North America. Zoo contributions varied by taxon, ranging from zoo-bred animals released in 42% of amphibian conservation translocations to zero contributions for marine invertebrates. Proportional involvement of zoos in captive breeding programs for release has increased over time as has the proportion of translocation-focused scientific papers co-authored by zoo professionals. While zoos also contribute to conservation translocations through education, funding, and professional expertise, increasing the contribution of animals for release in responsible conservation translocation programs presents a future conservation need and opportunity. We especially encourage increased dialogue and planning between the zoo community, academic institutions, and governments to optimize the direct contribution zoos can make to wildlife conservation through conservation translocations. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Population and habitat viability assessment for the Wyoming toad (Bufo baxteri): Final workshop report

USGS Publications Warehouse

2001-01-01

The Wyoming toad was listed as an endangered species under the Endangered Species Act on January 17, 1984, with a recovery plan approved in 1991. Currently the total population of the Wyoming toad includes approximately 200 animals in the captive breeding program and as few as 62 toads surviving at reintroduction sites in the Laramie Basin based upon fall 2000 survey data (after releases of more than 10,000 toads and tadpoles since 1995). Necessary conservation measures include improving reproduction and survival in the captive breeding program, improving survival at reintroduction sites, developing techniques to control the effects of the amphibian chytrid fungus, and eliminating threats and further habitat degradation in the wild.