Genetic Diversity and Selective Signature in Dabieshan Cattle Revealed by Whole-Genome Resequencing

Guan, Xiwen; Zhao, Shuaiyang; Xiang, Weixuan; Jin, Hai; Chen, Ningbo; Lei, Chuzhao; Jia, Yutang; Liu, Xu

doi:10.3390/biology11091327

Cited by 9 publications

(9 citation statements)

References 66 publications

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“…Commercial breeds/populations with a long breeding history, such as East Asian taurine cattle, European taurine cattle and Eurasian taurine cattle, generally have lower nucleotide diversity. At the same time, the nucleotide diversities of North Chinese cattle breeds are all higher than that of these commercial cattle breeds/populations, which is consistent with previous research results (Guan et al., 2022; Li et al., 2023; Liu et al., 2022; Luo et al., 2022; Mei et al., 2018; Xia, Zhang, et al., 2021). In the North Chinese cattle, the nucleotide diversity of Qaidam cattle is higher than that of the other four breeds.…”

Section: Discussionsupporting

confidence: 91%

Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole‐genome re‐sequencing

Wei,

Li,

Yan

et al. 2024

Animal Genetics

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Qaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low‐oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole‐genome resequencing technology, along with 192 published sets of whole‐genome sequencing data of Indian indicine cattle, Chinese indicine cattle, North Chinese cattle breeds, East Asian taurine cattle, Eurasian taurine cattle and European taurine cattle as controls. It was found that Qaidam cattle have rich genetic diversity in Bos taurus, but the degree of inbreeding is also high, which needs further protection. The phylogenetic analysis, principal component analysis and ancestral component analysis showed that Qaidam cattle mainly originated from East Asian taurine cattle. Qaidam cattle had a closer genetic relationship with the North Chinese cattle breeds and the least differentiation from Mongolian cattle. Annotating the selection signals obtained by composite likelihood ratio, nucleotide diversity analysis, integrated haplotype score, genetic differentiation index, genetic diversity ratio and cross‐population extended haplotype homozygosity methods, several genes associated with immunity, reproduction, meat, milk, growth and adaptation showed strong selection signals. In general, this study provides genetic evidence for understanding the germplasm characteristics of Qaidam cattle. At the same time, it lays a foundation for the scientific and reasonable protection and utilization of genetic resources of Chinese local cattle breeds, which has great theoretical and practical significance.

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Section: Discussionsupporting

confidence: 91%

Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole‐genome re‐sequencing

Wei,

Li,

Yan

et al. 2024

Animal Genetics

Self Cite

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“…The genomic data could reflect a wide variety of historical developments, including species introductions and artificial selection [26]. The exploration of population genetic structure and genetic diversity can be regarded as essential for genetic evaluation, reflecting cross-breeding and the utilization of genetic resources [27]. In this study, the neighbor-joining tree and PCA analysis showed that the three breeds were clustered by breed.…”

Section: Discussionmentioning

confidence: 80%

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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“…GPX5 is speci cally expressed in mammalian epididymis and plays an important role in protecting sperm from lipid peroxidation damage, and also affects the fertility rate [50]. In cattle studies, GPX5 GPX6 has also been found to correlate with fertility [51,52].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association studies and mapping of ROH identifies candidate genes for growth traits in hybrid rabbits

Jia,

Xiao,

et al. 2024

Preprint

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Screening and identifying genes related to growth traits are critically important for the production of meat rabbits. Genome-wide association studies is an effective method for large-scale screening of genetic markers related to target traits. However, the performance of whole-genome association studies in meat rabbits candidate genes associated with the heterosis remains largely unknown. In this study, after quality control and filtering of genotype data, a total of 380 F2 hybrid rabbits (205 male rabbits, 175 female rabbits) with 78579 SNPs and 42018 ROH on the autosome were obtained. The phenotypic values and heterosis of 380 F2 hybrid rabbits at seven growth stages were compared and analyzed. The fitting of the Logistic growth curve model indicated that the rabbit at 49 days of age was a growth inflection point. At this time, the correlation between weight heterosis and ROH was − 0.1267 to 0.07436. Ultimately, we conducted a genome-wide association studies of genotypes and growth trait heterosis after quality control using a mixed linear model. A total of 10 significant SNP-sites were significantly associated with weight at 84 days of age, and 7 candidate genes associated with growth traits were identified in meat rabbits. Additionally, we also uncovering the functional roles and positions of 20 candidate genes associated with economic traits of meat rabbits in high-frequency ROH regions. This study identified potential genes related to meat rabbit growth, development and adaptability in high-frequency ROH regions. These research findings will provide a genomic reference and new insights for the selection and improvement of hybrid meat rabbits, as well as useful genetic markers for breeding important economic traits in domestic rabbits.

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Genetic Diversity and Selective Signature in Dabieshan Cattle Revealed by Whole-Genome Resequencing

Cited by 9 publications

References 66 publications

Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole‐genome re‐sequencing

Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole‐genome re‐sequencing

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

Genome-wide association studies and mapping of ROH identifies candidate genes for growth traits in hybrid rabbits

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