基于全基因组重测序数据的新疆褐牛基因组结构变异检测及群体结构分析

doi:10.11843/j.issn.0366-6964.2024.08.016

Abstract

Abstract:

The aim of this study was to characterize the structural variations (SVs) in the genome of Xinjiang brown cattle, and on this basis, to explore the structural variations affected during the breeding process of Xinjiang brown cattle. Based on the whole genome resequencing data, the structural variation in the genomes of Xinjiang Brown cattle, their parents (Swiss brown cattle and Kazakh cattle) and Chinese Simmental cattle was examined using 3 software programs, Manta, Delly and Lumpy, and then analyzed the genomes of Xinjiang Brown cattle in comparison with the remaining 3 breeds using principal component analysis, construction of phylogenetic tree and fixation index (F_ST). The results showed that a total of 54 969 SVs were detected in the 4 cattle breeds, with the highest percentage of deletion-type variants (56.59%) and the lowest percentage of insertion-type variants (0.03%). Quantitatively, the distribution of these SVs on chromosomes showed a tendency of decreasing with larger chromosome numbers. Shared and breed-specific variants existed among different breeds, with the local breed Kazakh cattle possessing the highest number of specific SVs. The results of principal component analysis and phylogenetic tree revealed that Xinjiang brown cattle were closely related to Kazakh and Swiss brown cattle. A number of key genes related to milk production traits (PI4K2A, ELOVL3, ECHS1, SCD, TCF7L2, PNLIPRP2, BTRC, PLCE1), growth and development (BMP6, TLL2, MAPK9, ROR2), adaptability (PRKCB) and immunity (GSTO2, GSTO1) were mined out by selective signaling analysis, gene annotation and enrichment analysis. This study analyzed the characteristics of Xinjiang brown cattle in terms of structural variation and revealed some highly differentiated genes in the breeding process of Xinjiang brown cattle, which provided basic information for promoting the genetic improvement of Xinjiang brown cattle.

Key words: structural variation, whole genome resequencing, population structure analysis, Xinjiang brown cattle

CLC Number:

S823.2

Tao ZHANG, Jiaqi LI, Lei XU, Dan WANG, Menghua ZHANG, Tao ZHANG, Mengjie YAN, Weitao WANG, Shoumin FAN, Xixia HUANG. Detection and Population Structure Analysis of Genomic Structural Variation in Xinjiang Brown Cattle Based on Whole Genome Resequencing Data[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(8): 3427-3435.

Figures/Tables 5

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Detection and Population Structure Analysis of Genomic Structural Variation in Xinjiang Brown Cattle Based on Whole Genome Resequencing Data

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