Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data

Chen, Yige; Wang, Xudong; Wang, Jinglin; Hou, Yinhui; Liu, Ying; Wang, Bo; Hu, Xiaojing; Zheng, Xianrui; Zhang, Xiaodong; Ding, Yueyun; Yin, Zhan

doi:10.3390/genes13122310

Cited by 2 publications

(1 citation statement)

References 45 publications

(44 reference statements)

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“…Ma et al identified signatures of artificial selection and loci related to intramuscular fat content and feed conversion ratio traits in Duroc Pigs [ 11 ]. In addition, a number of studies have been carried out to explore specific signatures of selection in Chinese indigenous pig breeds, including Anqing Six-End-White [ 12 , 13 ], Saba, Baoshan, Tunchang, Dingan [ 14 ], Meishan [ 15 ] and Lulai pigs [ 16 ]. Qiao et al analyzed genetic structures and mapped genomic regions affecting backfat thickness of Yunan black pigs [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs

Han

Tan

et al. 2023

Genes

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Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed, synthesized between HN pigs and American Duroc, and are subjected to selection for important traits, such as fast growth and excellent meat quality. However, the genomic differences, selection signatures and loci associated with important economic traits in YN black pigs and HN pigs are still not well understood. In this study, based on high-density SNP chip analysis of 159 samples covering commercial DLY (Duroc × Landrace × Large White) pigs, HN pigs and YN black pigs, we performed a comprehensive analysis of phylogenetic relationships and genetic diversity among the three breeds. Furthermore, we used composite likelihood ratio tests (CLR) and F-statistics (Fst) to identify specific signatures of selection associated with important economic traits and potential candidate genes. We found 147 selected regions (top 1%) harboring 90 genes based on genetic differentiation (Fst) in the YN-DLY group. In the HN-DLY group, 169 selected regions harbored 58 genes. In the YN-HN group, 179 selected regions harbored 77 genes. In addition, the QTLs database with the most overlapping regions was associated with triglyceride level, number of mummified pigs, hemoglobin and loin muscle depth for YN black pigs, litter size and intramuscular fat content for HN pigs, and humerus length, linolenic acid content and feed conversion ratio mainly in DLY pigs. Of note, overlapping 14 tissue-specific promoters’ annotation with the top Fst 1% selective regions systematically demonstrated the muscle-specific and hypothalamus-specific regulatory elements in YN black pigs. Taken together, these results contribute to an accurate knowledge of crossbreeding, thus benefitting the evaluation of production performance and improving the genome-assisted breeding of other important indigenous pig in the future.

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Section: Introductionmentioning

confidence: 99%

Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs

Han

Tan

et al. 2023

Genes

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Evaluating genomic inbreeding of two Chinese yak (Bos grunniens) populations

Chen,

Luo,

Jia

et al. 2024

BMC Genomics

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Background Yaks are a vital livestock in the Qinghai-Tibetan Plateau area for providing food products, maintaining sustainable ecosystems, and promoting cultural heritage. Because of uncontrolled mating, it is impossible to estimate inbreeding level of yak populations using the pedigree-based approaches. With the aims to accurately evaluate inbreeding level of two Chinese yak populations (Maiwa and Jiulong), we obtained genome-wide single nucleotide polymorphisms (SNPs) by DNA sequencing and calculated five SNP-by-SNP estimators ($$\:{F}_{HOM}$$, $$\:{F}_{L\&H}$$, $$\:{F}_{VR1}$$, $$\:{F}_{VR2}$$, and $$\:{F}_{YAN}$$), as well as two segment-based estimators of runs of homozygosity (ROH, $$\:{F}_{ROH}$$) and homozygous-by-descent (HBD, $$\:{F}_{HBD}$$). Functional implications were analyzed for the positional candidate genes located within the related genomic regions. Results A total of 151,675 and 190,955 high-quality SNPs were obtained from 71 Maiwa and 30 Jiulong yaks, respectively. Jiulong had greater genetic diversity than Maiwa in terms of allele frequency and nucleotide diversity. The two populations could be genetically distinguished by principal component analysis, with the mean differentiation index (Fst) of 0.0054. The greater genomic inbreeding levels of Maiwa yaks were consistently supported by all five SNP-by-SNP estimators. Based on simple proportion of homozygous SNPs ($$\:{F}_{HOM}$$), a lower inbreeding level was indicated by three successfully sequenced old leather samples that may represent historical Maiwa yaks about five generations ago. There were 3304 ROH detected among all samples, with mean and median length of 1.97 Mb and 1.0 Mb, respectively. A total of 94 HBD segments were found among all samples, whereas 92 of them belonged to the shortest class with the mean length of 10.9 Kb. Based on the estimates of $$\:{F}_{ROH}$$ and $$\:{F}_{HBD}$$, however, there was no difference in inbreeding level between Maiwa and Jiulong yaks. Within the genomic regions with the significant Fst or enriched by ROH, we found several candidate genes and pathways that have been reported to be related to diverse production traits in farm animals. Conclusions We successfully evaluated the genomic inbreeding level of two Chinese yak populations. Although different estimators resulted in inconsistent conclusions on their genomic inbreeding levels, our results may be helpful to implement the genetic conservation and utilization programs for the two yak populations.

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Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data

Cited by 2 publications

References 45 publications

Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs

Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs

Evaluating genomic inbreeding of two Chinese yak (Bos grunniens) populations

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