Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations

Дементьева, Н. В.; Митрофанова, О.В.; Dysin, Artem P.; Kudinov, Andrei A.; Stanishevskaya, Olga I.; Larkina, Tatiana A.; Plemyashov, Kirill; Griffin, Darren K.; Romanov, Michael N; Смарагдов, М. Г.

doi:10.1016/j.animal.2021.100171

Cited by 16 publications

(12 citation statements)

References 46 publications

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“…A higher value of F ROH inbreeding coefficient, which was observed in RW chickens (0.195 vs. 0.172) ( Table 2 ), may reflect the origin of the studied RW population from a small number of founders [ 11 ]. A slight excess of heterozygotes observed in the RW population may be a consequence of a lower selection pressure and selection for a variety of breeding traits [ 15 , 18 ] as compared to WC [ 23 ]. Genetic drift can be considered another possible reason that led to a significant deviation in the number of heterozygotes among RW chickens as compared to that expected under Hardy–Weinberg equilibrium.…”

Section: Discussionmentioning

confidence: 99%

“…As a result of the long-term selection for critically low temperatures, the RS phenotypes were characterized by exceptional cold tolerance of neonatal chicks; their snowy-white down at day-old presumably caused by a recessive mutant gene, sw, for snow-white down [14,15]; and elevated resistance to a few neoplastic diseases, such as Marek's disease, leukemia, and carcinomas [11]. The current RG population was more recently derived from the RS as a result of a one-time telic crossing with White Leghorns in 2006 not selected further for cold tolerance and subjected to random mating in 2000-2013 [12,[16][17][18].…”

Section: Introductionmentioning

confidence: 99%

“…The latter, in turn, was distinguished by more numerous monomorphic markers and longer linkage disequilibrium (LD) regions as well a greater number of runs of homozygosity (ROHs), their greater mean length, and a higher ROH-based inbreeding coefficient. The RG population had the smallest LD values and the largest effective population size [ 12 , 17 , 18 ]. In an additional GWAS using the Illumina Chicken 60K SNP iSelect BeadChip, nine SNPs were reported in the RG population that demonstrated significant associations with egg production traits and coincided with ROHs [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

“…[ 23 , 24 , 25 , 26 ]. In Russia, a few WC crossbred strains are maintained in the RRIFAGB gene pool collection and have been explored in the genome-wide scanning studies using the Illumina BeadChip [ 17 , 18 ]. They demonstrated a reduced genetic diversity because of small population size, and lower ROH metrics due to crossbreeding effects [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

“…Several genome-wide studies have been undertaken to detect the genomic footprints of artificial selection in large numbers of chicken breeds (e.g., [ 37 , 38 , 39 , 40 , 41 ]). Despite the initial chicken genome research efforts undertaken so far at the RRIFAGB [ 17 , 18 ], a comparative in-depth search for selection sweeps in chicken breeds of Russian origin at the genome-wide level have not been carried out and would be much anticipated.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Abdelmanova

Dotsev

Romanov

et al. 2021

Biology

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Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Abdelmanova

Dotsev

Romanov

et al. 2021

Biology

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Application potential of chicken DNA chip in domestic pigeon species – Preliminary results

Balog

Mizeranschi²,

Wanjala

et al. 2023

Saudi Journal of Biological Sciences

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Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study

Pocrnić

Obšteter

Gaynor

et al. 2023

Preprint

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Nucleus-based breeding programs are characterized by intense selection that results in high genetic gain, which inevitably means reduction of genetic variation in the breeding population. Therefore, genetic variation in such breeding systems is typically managed systematically, for example, by avoiding mating the closest relatives to limit progeny inbreeding. However, intense selection requires maximum effort to make such breeding programs sustainable in the long-term. The objective of this study was to use simulation to evaluate the long-term impact of genomic selection on genetic mean and variance in an intense layer chicken breeding program. We developed a large-scale stochastic simulation of an intense layer chicken breeding program to compare conventional truncation selection to genomic truncation selection optimized with either minimization of progeny inbreeding or full-scale optimal contribution selection. We compared the programs in terms of genetic mean, genic variance, conversion efficiency, rate of inbreeding, effective population size, and accuracy of selection. Our results confirmed that genomic truncation selection has immediate benefits compared to conventional truncation selection in all specified metrics. A simple minimization of progeny inbreeding after genomic truncation selection did not provide any significant improvements. Optimal contribution selection was successful in having better conversion efficiency and effective population size compared to genomic truncation selection, but it must be fine-tuned for balance between loss of genetic variance and genetic gain. In our simulation, we measured this balance using trigonometric penalty degrees between truncation selection and a balanced solution and concluded that the best results were between 45 and 65. This balance is specific to the breeding program and depends on how much immediate genetic gain a breeding program may risk vs. save for the future. Furthermore, our results show that the persistence of accuracy is better with optimal contribution selection compared to truncation selection. In general, our results show that optimal contribution selection can ensure long-term success in intensive breeding programs using genomic selection.

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Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations

Cited by 16 publications

References 46 publications

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Application potential of chicken DNA chip in domestic pigeon species – Preliminary results

Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study

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