scholarly journals Origin Specific Genomic Selection: A Simple Process To Optimize the Favorable Contribution of Parents to Progeny

2020 ◽  
Vol 10 (7) ◽  
pp. 2445-2455 ◽  
Author(s):  
Chin Jian Yang ◽  
Rajiv Sharma ◽  
Gregor Gorjanc ◽  
Sarah Hearne ◽  
Wayne Powell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Computer Simulation ◽  
Genomic Selection ◽  
Target Selection ◽  
Wild Relatives ◽  
Arms Race ◽  
Crop Breeding ◽  
Simple Process ◽  
Nested Association Mapping ◽  
Exotic Alleles

Modern crop breeding is in constant demand for new genetic diversity as part of the arms race with genetic gain. The elite gene pool has limited genetic variation and breeders are trying to introduce novelty from unadapted germplasm, landraces and wild relatives. For polygenic traits, currently available approaches to introgression are not ideal, as there is a demonstrable bias against exotic alleles during selection. Here, we propose a partitioned form of genomic selection, called Origin Specific Genomic Selection (OSGS), where we identify and target selection on favorable exotic alleles. Briefly, within a population derived from a bi-parental cross, we isolate alleles originating from the elite and exotic parents, which then allows us to separate out the predicted marker effects based on the allele origins. We validated the usefulness of OSGS using two nested association mapping (NAM) datasets: barley NAM (elite-exotic) and maize NAM (elite-elite), as well as by computer simulation. Our results suggest that OSGS works well in its goal to increase the contribution of favorable exotic alleles in bi-parental crosses, and it is possible to extend the approach to broader multi-parental populations.

scholarly journals Origin Specific Genomic Selection: a simple process to optimize the favourable contribution of parents to progeny

2019 ◽  
Author(s):  
Chin Jian Yang ◽  
Rajiv Sharma ◽  
Gregor Gorjanc ◽  
Sarah Hearne ◽  
Wayne Powell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Computer Simulation ◽  
Genomic Selection ◽  
Target Selection ◽  
Wild Relatives ◽  
Arms Race ◽  
Crop Breeding ◽  
Simple Process ◽  
Nested Association Mapping ◽  
Exotic Alleles

AbstractModern crop breeding is in constant demand for new genetic diversity as part of the arms race with genetic gain. The elite gene pool has limited genetic variation and breeders are trying to introduce novelty from unadapted germplasm, landraces and wild relatives. For polygenic traits, currently available approaches to introgression are not ideal, as there is a demonstrable bias against exotic alleles during selection. Here, we propose a partitioned form of genomic selection, called Origin Specific Genomic Selection (OSGS), where we identify and target selection on favourable exotic alleles. Briefly, within a population derived from a bi-parental cross, we isolate alleles originating from the elite and exotic parents, which then allows us to separate out the predicted marker effects based on the allele origins. We validated the usefulness of OSGS using two nested association mapping (NAM) datasets: barley NAM (elite-exotic) and maize NAM (elite-elite), as well as by computer simulation. Our results suggest that OSGS works well in bi-parental crosses, and it is possible to extend the approach to broader multi-parental populations.

scholarly journals Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Emmanuel A. Lozada-Soto ◽  
Christian Maltecca ◽  
Duc Lu ◽  
Stephen Miller ◽  
John B. Cole ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Beef Cattle ◽  
Genomic Selection ◽  
Inbreeding Depression ◽  
Growth Traits ◽  
Effective Population ◽  
Angus Cattle ◽  
Genomic Inbreeding ◽  
Chromosome Segments ◽  
The Impact

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

scholarly journals Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Ghazal Ghobadi ◽  
Alireza Etminan ◽  
Ali Mehras Mehrabi ◽  
Lia Shooshtari
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Wild Relatives ◽  
Resolving Power ◽  
Start Codon ◽  
Aegilops Cylindrica ◽  
Aegilops Crassa

Abstract Background Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. Results Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. Conclusion The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

scholarly journals Why and How to Switch to Genomic Selection: Lessons From Plant and Animal Breeding Experience

2021 ◽  
Vol 12 ◽  
Author(s):  
◽  
Aline Fugeray-Scarbel ◽  
Catherine Bastien ◽  
Mathilde Dupont-Nivet ◽  
Stéphane Lemarié
Keyword(s):  
Genetic Diversity ◽  
Genomic Selection ◽  
Plant Species ◽  
Animal Species ◽  
Animal Breeding ◽  
Breeding Cycle ◽  
Breeding Programs ◽  
The Third ◽  
Wide Range ◽  
Selection For

The present study is a transversal analysis of the interest in genomic selection for plant and animal species. It focuses on the arguments that may convince breeders to switch to genomic selection. The arguments are classified into three different “bricks.” The first brick considers the addition of genotyping to improve the accuracy of the prediction of breeding values. The second consists of saving costs and/or shortening the breeding cycle by replacing all or a portion of the phenotyping effort with genotyping. The third concerns population management to improve the choice of parents to either optimize crossbreeding or maintain genetic diversity. We analyse the relevance of these different bricks for a wide range of animal and plant species and sought to explain the differences between species according to their biological specificities and the organization of breeding programs.

scholarly journals Influence of breeding strategy on genetic diversity of individuals

2021 ◽  
pp. 1168-1174
Author(s):  
A.A. Poroshina ◽  
◽  
D.Yu. Sherbakov ◽  
Keyword(s):  
Genetic Diversity ◽  
Computer Simulation ◽  
Molecular Evolution ◽  
Microsatellite Markers ◽  
Simulation Model ◽  
Sexual Reproduction ◽  
Asexual Reproduction ◽  
Reproductive Strategy ◽  
Breeding Strategy ◽  
Computer Simulation Model

Abstract. Using a computer simulation model, we tried to investigate how the transition from sexual reproduction to asexual reproduction will affect the population of diploid organisms with a neutral character of molecular evolution. At the same time, special attention was paid to the specificity of microsatellite markers. In this paper, we develop fast and inexpensive methods for assessing the changes in populations that occur with a change in reproductive strategy.

Techniques and key issues in collecting crop wild relatives

2021 ◽  
pp. 155-184
Author(s):  
Michael Way ◽  
Keyword(s):  
Genetic Diversity ◽  
Best Practice ◽  
Seed Quality ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Wild Plant ◽  
Genetic Sampling ◽  
Key Issues ◽  
Essential Resource ◽  
Seed Collections

The genetic diversity found in populations of crop wild relatives is an essential resource for future crop breeding, but populations are at risk of loss before germplasm has been fully conserved in genebanks. This chapter describes best practice for targeting and identifying species, and review knowledge about the variation in wild plant populations to guide the timing of collecting and approaches for genetic sampling. Indicators are presented for seed quality, ripeness and dispersal. Techniques for collection of seed, herbarium vouchers and associated data are reviewed with examples drawn from the Adapting Agriculture to Climate Change (Crop Wild Relative) project. Further research is needed to find optimal approaches for handling of seed to ensure high longevity of seed collections, and improved tools are needed to guide sampling of genetic diversity of crop wild relatives.

scholarly journals The Genetic Diversity of Cranberry Crop Wild Relatives, Vaccinium macrocarpon Aiton and V. oxycoccos L., in the US, with Special Emphasis on National Forests

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1446
Author(s):  
Lorraine Rodriguez-Bonilla ◽  
Karen A. Williams ◽  
Fabian Rodríguez Bonilla ◽  
Daniel Matusinec ◽  
Andrew Maule ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
The United States ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Vaccinium Macrocarpon ◽  
Ex Situ ◽  
National Forests ◽  
United States Department ◽  
The Us

Knowledge of the genetic diversity in populations of crop wild relatives (CWR) can inform effective strategies for their conservation and facilitate utilization to solve agricultural challenges. Two crop wild relatives of the cultivated cranberry are widely distributed in the US. We studied 21 populations of Vaccinium macrocarpon Aiton and 24 populations of Vaccinium oxycoccos L. across much of their native ranges in the US using 32 simple sequence repeat (SSR) markers. We observed high levels of heterozygosity for both species across populations with private alleles ranging from 0 to 26. For V. macrocarpon, we found a total of 613 alleles and high levels of heterozygosity (HO = 0.99, HT = 0.75). We also observed high numbers of alleles (881) and levels of heterozygosity (HO = 0.71, HT = 0.80) in V. oxycoccos (4x). Our genetic analyses confirmed the field identification of a native population of V. macrocarpon on the Okanogan-Wenatchee National Forest in the state of Washington, far outside the previously reported range for the species. Our results will help to inform efforts of the United States Department of Agriculture Agricultural Research Service (USDA-ARS) and the United States Forest Service (USFS) to conserve the most diverse and unique wild cranberry populations through ex situ preservation of germplasm and in situ conservation in designated sites on National Forests.

Sign in / Sign up

Export Citation Format

Share Document