Abstract
Whole-genome sequencing provides a powerful tool to obtain more genetic variability that could produce a range of benefits for cattle breeding industry. Nanyang (Bos indicus) and Qinchuan (Bos taurus) are two important Chinese indigenous cattle breeds with distinct phenotypes. To identify the genetic characteristics responsible for variation in phenotypes between the two breeds, in the present study, we for the first time sequenced the genomes of four Nanyang and four Qinchuan cattle with 10 to 12 fold on average of 97.86% and 98.98% coverage of genomes, respectively. Comparison with the Bos_taurus_UMD_3.1 reference assembly yielded 9,010,096 SNPs for Nanyang, and 6,965,062 for Qinchuan cattle, 51% and 29% of which were novel SNPs, respectively. A total of 154,934 and 115,032 small indels (1 to 3 bp) were found in the Nanyang and Qinchuan genomes, respectively. The SNP and indel distribution revealed that Nanyang showed a genetically high diversity as compared to Qinchuan cattle. Furthermore, a total of 2,907 putative cases of copy number variation (CNV) were identified by aligning Nanyang to Qinchuan genome, 783 of which (27%) encompassed the coding regions of 495 functional genes. The gene ontology (GO) analysis revealed that many CNV genes were enriched in the immune system and environment adaptability. Among several CNV genes related to lipid transport and fat metabolism, Lepin receptor gene (LEPR) overlapping with CNV_1815 showed remarkably higher copy number in Qinchuan than Nanyang (log2 (ratio) = -2.34988; P value = 1.53E-102). Further qPCR and association analysis investigated that the copy number of the LEPR gene presented positive correlations with transcriptional expression and phenotypic traits, suggesting the LEPR CNV may contribute to the higher fat deposition in muscles of Qinchuan cattle. Our findings provide evidence that the distinct phenotypes of Nanyang and Qinchuan breeds may be due to the different genetic variations including SNPs, indels and CNV.
Highlights
Integrating phenotypic variability with genomic variation is pivotal in both fundamental and applied biological sciences[1,2]
The primary goal of our present study was to provide a comprehensive list of sequence variation at the whole genome scale for two widespread Chinese cattle breeds (Nanyang and Qinchuan) and to identify potential loci that might be related to phenotypic differences between the two breeds
In previous studies, examining whole sequence variation is often relied on single nucleotide polymorphisms (SNPs) array[34], array comparative genomic hybridization [21,35] or exome sequencing [36]
Summary
Integrating phenotypic variability with genomic variation is pivotal in both fundamental and applied biological sciences[1,2]. Since the bovine genome was firstly sequenced from an inbred Hereford cow and her sire by capillary sequencing[10], the researches of resequencing and assembling genomes from different cattle breeds have quickly progressed. Kawahara-Miki et al.[12] resequenced the whole genome of a Japanese Kuchinoshima-Ushi cattle and revealed a total of 11,713 non-synonymous SNPs in protein-coding regions of 4,643 genes, and further phylogenetic analysis showed that the genetic background of Kuchinoshima-Ushi is quite distinct from the previously sequenced European domestic cattle breeds. Bickhart et al.[14] reported 1,265 CNV regions in six individuals from four American cattle breeds using high throughput sequencing. The genome resequencing of two North American breeds, Black Angus and Holstein, revealed 790 putative CNV regions, which could be considered to be promising genetic markers for the identification across the genomes[15]
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