The study of selection signature and its applications on identification of candidate genes using whole genome sequencing data in chicken—a review

Bello, Semiu Folaniyi; Lawal, Raman Akinyanju; Adeola, Adeniyi C.; Nie, Qinghua

doi:10.1016/j.psj.2023.102657

Cited by 10 publications

(5 citation statements)

References 161 publications

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“…Compared to the results of previous studies on chicken [15,[17][18][19], the distribution and number of ROH in this population did not exhibit significant differences. ROH segments are commonly found on larger chromosomes, and most are classified as short in length (< 3 Mb).…”

Section: Discussioncontrasting

confidence: 95%

“…By utilizing ROH, scientists are able to better understand a population's evolutionary history, inbreeding levels, and changes in genomic homozygosity in specific environments [11][12][13]. In agricultural research, ROH analysis has become an important tool for identifying genes and selection signatures that are associated with economic traits in livestock [3,5,14,15]. Nevertheless, there are limitations in ROH research, mainly concerning the precise characterization of ROH in relation to the length and the number of loci [4,16].…”

Section: Introductionmentioning

confidence: 99%

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Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding

Li,

Lan,

Chen

et al. 2024

BMC Genomics

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Background The breeding of layers emphasizes the continual selection of egg-related traits, such as egg production, egg quality and eggshell, which enhance their productivity and meet the demand of market. As the breeding process continued, the genomic homozygosity of layers gradually increased, resulting in the emergence of runs of homozygosity (ROH). Therefore, ROH analysis can be used in conjunction with other methods to detect selection signatures and identify candidate genes associated with various important traits in layer breeding. Results In this study, we generated whole-genome sequencing data from 686 hens in a Rhode Island Red population that had undergone fifteen consecutive generations of intensive artificial selection. We performed a genome-wide ROH analysis and utilized multiple methods to detect signatures of selection. A total of 141,720 ROH segments were discovered in whole population, and most of them (97.35%) were less than 3 Mb in length. Twenty-three ROH islands were identified, and they overlapped with some regions bearing selection signatures, which were detected by the De-correlated composite of multiple signals methods (DCMS). Sixty genes were discovered and functional annotation analysis revealed the possible roles of them in growth, development, immunity and signaling in layers. Additionally, two-tailed analyses including DCMS and ROH for 44 phenotypes of layers were conducted to find out the genomic differences between subgroups of top and bottom 10% phenotype of individuals. Combining the results of GWAS, we observed that regions significantly associated with traits also exhibited selection signatures between the high and low subgroups. We identified a region significantly associated with egg weight near the 25 Mb region of GGA 1, which exhibited selection signatures and has higher genomic homozygosity in the low egg weight subpopulation. This suggests that the region may be play a role in the decline in egg weight. Conclusions In summary, through the combined analysis of ROH, selection signatures, and GWAS, we identified several genomic regions that associated with the production traits of layers, providing reference for the study of layer genome.

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Section: Discussioncontrasting

confidence: 95%

Section: Introductionmentioning

confidence: 99%

Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding

Li,

Lan,

Chen

et al. 2024

BMC Genomics

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“…Compared to commercial chickens, the meat and eggs of indigenous chickens are of better quality but are produced less efficiently [ 41 – 43 ]. The fundamental causes of this low efficiency are low selection intensity [ 6 ], limited studies involving genetic resource exploration, and failure to continuously develop characteristic traits. In fact, there is a lack of unified assessment standards for the evaluation of genetic resource conservation effects, and it is difficult to measure the purity of consanguinity, the level of population inbreeding and the genetic diversity of indigenous chickens.…”

Section: Discussionsupporting

confidence: 93%

“…These chickens harbor considerable phenotypic diversity and genetic variation, provide diversified animal products and play an important role in cultivating new breeds/lines in modern chicken breeding systems [ 3 ]. Indigenous chickens are often subjected to both domestication and selection; however, the selection effect is rather weak, and more genetic diversity is found in indigenous chickens than in commercial broilers [ 4 – 6 ]. Genetic and genomic studies on these chickens are relatively limited.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens

Tan,

Liu,

Dong

et al. 2024

BMC Genomics

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Background Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation of these modern breeds via admixture events. However, their confusing genetic backgrounds include a genomic footprint regulating complex traits, which is not conducive to modern animal breeding. Results To better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima’s D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively. Conclusion Based on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies.

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“…In this study, the neighbor-joining tree and PCA analysis showed that the three breeds were clustered by breed. Based on whole-genome sequencing data and combined with bioinformatics analysis, revealing the selection signals of important genetic traits remaining in the genome during animal domestication has become a mainstream approach [28][29][30]. Selection signals are the traces left on the genome of animals through long-term natural and artificial selection processes during domestication and typically manifest as linkage disequilibrium and reduced polymorphism at certain sites on both sides of the core variation [31].…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Sequencing for Identifying Candidate Genes Related to the Special Phenotypes of the Taihu Dianzi Pigeon

Zhang,

Mu,

Chang

et al. 2024

Animals

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The Taihu Dianzi pigeon is a breed native to China, and its special piebalding, crest, and polydactyly phenotypes are the result of artificial and natural selection. Here, we analyzed the genetic differences among three kinds of pigeons with different phenotypes at the genomic level. A selective sweep was conducted based on the fixation index (FST) and nucleotide diversity (π) ratio, and the results revealed that MC1R was related to the formation of the distinctive piebalding of the Taihu Dianzi pigeon. Combined with the results of genome-wide association studies, we identified candidate genes associated with the crest (SMYD and STOX2) and polydactyly (SLC52A3 and ANGPT4). The candidate genes identified in this study and their variants may be useful for understanding the genetic mechanism underlying the special phenotypes of the Taihu Dianzi pigeon. This study provides new insights into the genetic factors that may influence the formation of the special piebalding, crest, and polydactyly characteristics in pigeons.

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The study of selection signature and its applications on identification of candidate genes using whole genome sequencing data in chicken—a review

Cited by 10 publications

References 161 publications

Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding

Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding

Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens

Whole-Genome Sequencing for Identifying Candidate Genes Related to the Special Phenotypes of the Taihu Dianzi Pigeon

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