Optimizing purebred selection for crossbred performance using QTL with different degrees of dominance

Dekkers, Jack; Chakraborty, Reena

doi:10.1051/gse:2004003

Cited by 9 publications

(7 citation statements)

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“…Heterosis that is caused by heterozygosity in single loci is responsible for survival rate by increasing reproductive fitness [22]. Hayes and Miller (2000) showed that dominance effect was needed in mate selection to exploit previously untapped genetic variation [23], while Dekkers and Chakraborty (2004) stressed maximization of crossbred performance by incorporating information from overdominant QTL [24]. Kim et al [8] found that many QTL for growth and carcass quality had a (over) dominant mode of gene action in a cross between Angus and Brahman cattle [8].…”

Section: Resultsmentioning

confidence: 99%

A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo

Gao

Kim

et al. 2016

Asian-Australas J Anim Sci

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ObjectiveA whole genome association study was conducted to identify single nucleotide polymorphisms (SNPs) with additive and dominant effects for growth and carcass traits in Korean native cattle, Hanwoo.MethodsThe data set comprised 61 sires and their 486 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers were genotyped with the 35,968 SNPs that were embedded in the Illumina bovine SNP 50K beadchip and six growth and carcass quality traits were measured for the steers. A series of lack-of-fit tests between the models was applied to classify gene expression pattern as additive or dominant.ResultsA total of 18 (0), 15 (3), 12 (8), 15 (18), 11 (7), and 21 (1) SNPs were detected at the 5% chromosome (genome) - wise level for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA) and marbling score, respectively. Among the significant 129 SNPs, 56 SNPs had additive effects, 20 SNPs dominance effects, and 53 SNPs both additive and dominance effects, suggesting that dominance inheritance mode be considered in genetic improvement for growth and carcass quality in Hanwoo. The significant SNPs were located at 33 quantitative trait locus (QTL) regions on 18 Bos Taurus chromosomes (i.e. BTA 3, 4, 5, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 20, 23, 26, 28, and 29) were detected. There is strong evidence that BTA14 is the key chromosome affecting CWT. Also, BTA20 is the key chromosome for almost all traits measured (WWT, YWT, LMA).ConclusionThe application of various additive and dominance SNP models enabled better characterization of SNP inheritance mode for growth and carcass quality traits in Hanwoo, and many of the detected SNPs or QTL had dominance effects, suggesting that dominance be considered for the whole-genome SNPs data and implementation of successive molecular breeding schemes in Hanwoo.

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Section: Resultsmentioning

confidence: 99%

A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo

Gao

Kim

et al. 2016

Asian-Australas J Anim Sci

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“…In fact, selection at the purebred level reduces the need for the crossbred testing that is required for CCPS, thereby saving important test resources and enabling the short generation intervals of purebred selection. However, Dekkers and Chakraborty [ 33 ] discussed the benefit of GS for improving CP and suggested that it may be limited if marker effects are estimated from purebred nucleus data since the resulting EBV are strictly relevant to the studied population and environment only and may not help much to improve selection for CP if substantial G × E and genotype-by-genetic (G × G) background interactions are present. In this study, we considered the G × G due to dominance and not that due to differences in the physical environment.…”

Section: Discussionmentioning

confidence: 99%

Maximizing crossbred performance through purebred genomic selection

Esfandyari

Sørensen

Bijma

2015

Genetics Selection Evolution

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BackgroundIn livestock production, many animals are crossbred, with two distinct advantages: heterosis and breed complementarity. Genomic selection (GS) can be used to select purebred parental lines for crossbred performance (CP). Dominance being the likely genetic basis of heterosis, explicitly including dominance in the GS model may be an advantage to select purebreds for CP. Estimated breeding values for CP can be calculated from additive and dominance effects of alleles that are estimated using pure line data. The objective of this simulation study was to investigate the benefits of applying GS to select purebred animals for CP, based on purebred phenotypic and genotypic information. A second objective was to compare the use of two separate pure line reference populations to that of a single reference population that combines both pure lines. These objectives were investigated under two conditions, i.e. either a low or a high correlation of linkage disequilibrium (LD) phase between the pure lines.ResultsThe results demonstrate that the gain in CP was higher when parental lines were selected for CP, rather than purebred performance, both with a low and a high correlation of LD phase. For a low correlation of LD phase between the pure lines, the use of two separate reference populations yielded a higher gain in CP than use of a single reference population that combines both pure lines. However, for a high correlation of LD phase, marker effects that were estimated using a single combined reference population increased the gain in CP.ConclusionsUnder the hypothesis that performance of crossbred animals differs from that of purebred animals due to dominance, a dominance model can be used for GS of purebred individuals for CP, without using crossbred data. Furthermore, if the correlation of LD phase between pure lines is high, accuracy of selection can be increased by combining the two pure lines into a single reference population to estimate marker effects.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0099-3) contains supplementary material, which is available to authorized users.

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“…The integration of QTL information into breeding decision might enable to predict non-additive effects. However, inclusion of data from crossbred animals is required to reach higher accuracy compared to phenotypic selection ( Dekkers and Chakraborty, 2004 ). Biologically meaningful markers, such as causative genes, candidate genes within gene-pathways or markers in strong linkage disequilibrium (LD) with the causative mutation might overcome the poor prediction of crossbred performance using information from purebreds only.…”

Section: Breeding Using Molecular Genetic Markersmentioning

confidence: 99%

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

Jonas

Koning

2015

Front. Genet.

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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.

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Optimizing purebred selection for crossbred performance using QTL with different degrees of dominance

Cited by 9 publications

References 8 publications

A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo

A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo

Maximizing crossbred performance through purebred genomic selection

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

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