Whole-genome sequencing of endangered Zhoushan cattle suggests its origin and the association of MC1R with black coat colour

Jiang, Lihua; Kon, Tetsuo; Chen, Chunyan; Ichikawa, Ryota; Zheng, Qiyuan; Pei, Liyi; Takemura, Ikuyo; Nsobi, Lauden Hagai; Tabata, Hiromasa; Pan, Hao; Omori, Yoshihiro; Ogura, Atsushi

doi:10.1038/s41598-021-96896-2

Cited by 17 publications

(13 citation statements)

References 38 publications

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“…With the development of the next-generation sequencing technology and the enrichment of re-sequencing databases, genome-wide genetic analysis plays an increasingly significant role in the investigation and selection of germplasm resources of landraces ( Shen et al, 2020 ; Jiang et al, 2021 ; Xia et al, 2021 ; Zhang et al, 2021 ). A recent study on Dengchuan cattle showed that Dengchuan cattle are a taurine–indicine mixed breed ( Foissac et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Whole-Genome Sequencing of Endangered Dengchuan Cattle Reveals Its Genomic Diversity and Selection Signatures

Jin

Hanif

et al. 2022

Front. Genet.

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Dengchuan cattle are the only dairy yellow cattle and endangered cattle among Yunnan native cattle breeds. However, its genetic background remains unclear. Here, we performed whole-genome sequencing of ten Dengchuan cattle. Integrating our data with the publicly available data, Dengchuan cattle were observed to be highly interbred than other cattle in the dataset. Furthermore, the positive selective signals were mainly manifested in candidate genes and pathways related to milk production, disease resistance, growth and development, and heat tolerance. Notably, five genes (KRT39, PGR, KRT40, ESR2, and PRKACB) were significantly enriched in the estrogen signaling pathway. Moreover, the missense mutation in the PGR gene (c.190T > C, p.Ser64Pro) showed a homozygous mutation pattern with higher frequency (83.3%) in Dengchuan cattle. In addition, a large number of strong candidate regions matched genes and QTLs related to milk yield and composition. Our research provides a theoretical basis for analyzing the genetic mechanism underlying Dengchuan cattle with excellent lactation and adaptability, crude feed tolerance, good immune performance, and small body size and also laid a foundation for genetic breeding research of Dengchuan cattle in the future.

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Section: Introductionmentioning

confidence: 99%

Whole-Genome Sequencing of Endangered Dengchuan Cattle Reveals Its Genomic Diversity and Selection Signatures

Jin

Hanif

et al. 2022

Front. Genet.

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“…Studies have firmly established that the MC1R gene is a key player in UVR-induced tanning and DNA repair mechanisms [ 61 , 62 ]. It has been reported that the genetic variation of MC1R gene is associated with the pattern of hair coloration in domestic animals such as cattle, pigs, and chickens [ 63 , 64 , 65 ]. In particular, a recent study identified the MC1R gene in endangered Zhoushan cattle associated with their black coat color at the genomic level [ 63 ].…”

Section: Discussionmentioning

confidence: 99%

“…It has been reported that the genetic variation of MC1R gene is associated with the pattern of hair coloration in domestic animals such as cattle, pigs, and chickens [ 63 , 64 , 65 ]. In particular, a recent study identified the MC1R gene in endangered Zhoushan cattle associated with their black coat color at the genomic level [ 63 ]. Therefore, we speculate that the MC1R gene may be associated with melanin deposition in Bohai Black cattle, but its function needs further exploration.…”

Section: Discussionmentioning

confidence: 99%

Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data

Cheng

Liu

et al. 2022

Animals

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Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a comprehensive analysis of genomic variation in 10 Bohai Black cattle (five newly sequenced and five published) and the published whole-genome sequencing (WGS) data of 50 cattle representing five “core” cattle populations. The population structure analysis revealed that Bohai Black cattle harbored the ancestry with European taurine, Northeast Asian taurine, and Chinese indicine. The Bohai Black cattle demonstrated relatively high genomic diversity from the other cattle breeds, as indicated by the nucleotide diversity (pi), the expected heterozygosity (HE) and the observed heterozygosity (HO), the linkage disequilibrium (LD) decay, and runs of homozygosity (ROH). We identified 65 genes containing more than five non-synonymous SNPs (nsSNPs), and an enrichment analysis revealed the “ECM-receptor interaction” pathways associated with meat quality in Bohai Black cattle. Five methods (CLR, θπ, FST, θπ ratio, and XP-EHH) were used to find several pathways and genes carried selection signatures in Bohai Black cattle, including black coat color (MC1R), muscle development (ITGA9, ENAH, CAPG, ABI2, and ISLR), fat deposition (TBC1D1, CYB5R4, TUSC3, and EPS8), reproduction traits (SPIRE2, KHDRBS2, and FANCA), and immune system response (CD84, SLAMF1, SLAMF6, and CDK10). Taken together, our results provide a valuable resource for characterizing the uniqueness of Bohai Black cattle.

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“…Skin pigmentation is a complex trait. The genetic variants responsible for skin pigmentation have been broadly investigated in cattle (Dorshorst et al, 2015; Gutiérrez‐Gil et al, 2007; Jiang et al, 2021; Matsumoto et al, 2020; Schmutz & Dreger, 2013). Recently, the coat color in cattle has been manipulated using gene editing technique, though fundamentally epigenetics play a forefront role in regulating the color genes, particularly when the methylation event occurs at CpG islands (Laible et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Identification of differential methylome signatures of white pigmented skin patches in Nili Ravi buffalo of India

Gurao

Vasisth

Singh

et al. 2022

Environ and Mol Mutagen

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The DNA methylation events mark a major epigenetic change in the genome, reflecting non-genetic disease developments and varied phenotypes. The water buffalo is a dairy production animal with wide agro-climatic distribution in India. Breed-wise the coat color of water buffalo varies from ash-gray to jet black. A typical pigmentation pattern is found in one of the breeds of North India, Nili Ravi, with variedly distributed white patches. The DNA methylation pattern could potentially reveal the epigenetic factors responsible for the pigmentation patterns. To address this question, the DNA isolated from the skin tissues of Nili Ravi with varied white pigmentation and black Murrah buffaloes was subjected to reduced representation bisulfite sequencing. DNA methylation analysis revealed, 68.44%, 63.39%, and 47.94% of the promoter regions were hypermethylated in Nili Ravi over-white versus Murrah, Nili Ravi under-white versus Murrah, and Nili Ravi under-white versus Nili Ravi over-white, respectively. Major genes identified to be differentially methylated among over-white and under-white skin tissues in Nili Ravi included TBX2, SNAI2, HERC2, and CITED1. Overall the results have indicated differential methylation patterns to be potentially involved in hyper or hypopigmentation in Nili Ravi and Murrah buffaloes.

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Whole-genome sequencing of endangered Zhoushan cattle suggests its origin and the association of MC1R with black coat colour

Cited by 17 publications

References 38 publications

Whole-Genome Sequencing of Endangered Dengchuan Cattle Reveals Its Genomic Diversity and Selection Signatures

Whole-Genome Sequencing of Endangered Dengchuan Cattle Reveals Its Genomic Diversity and Selection Signatures

Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data

Identification of differential methylome signatures of white pigmented skin patches in Nili Ravi buffalo of India

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