保种场涪陵水牛及西南地区水牛品种间遗传结构与ROH分析

doi:10.11843/j.issn.0366-6964.2024.05.017

Abstract

Abstract: This study aimed to analyze the population genetic structure and runs of homozygosity (ROH) of Fuling buffalo and other swamp buffalo breeds in southwest China, and provide the theoretical basis for conservation and genetic improvement of Fuling buffalo. In this study, 26 Fuling buffaloes and one hybrid buffalo (FM_HY) were sequenced using whole-genome resequencing technology. The genome resequencing data of 68 swamp buffalo individuals in southwest China and 7 river buffalo individuals were downloaded from the NCBI database. All the genome data were used to obtain high-quality single nucleotide polymorphisms (SNPs) and to analyze the population genetic structure, ROH and inbreeding coefficient. The whole-genome resequencing results showed that the average sequencing depth of Fuling buffalo was 10×, and a total of 14 326 437 SNPs were identified after quality control. The population genetic structure analysis showed that there were significant differences between the Fuling buffalo and the neighboring areas swamp buffalo breeds including Yibin buffalo, Guizhou buffalo, Guizhou White buffalo and Yanjin buffalo. Dehong buffalo and Diandongnan buffalo were significantly different from the above 5 breeds. When the number of clusters was K=6, Fuling buffalo was divided into two groups, which had a unique population structure compared to the neighboring areas buffalo breeds. A total of 2 722 ROHs were detected in Fuling buffalo, Yibin buffalo and Guizhou buffalo. The 1 593 ROHs were identified in Fuling buffalo, and the 78.15% proportion of ROH was the short ROH with 1-2 Mb. Eight long ROH fragments>16 Mb were only detected in Fuling buffalo population, the longest being 24.56 Mb. Based on ROH, the average inbreeding coefficient of Fuling buffalo was 0.056 8, of which 7 individuals had higher inbreeding coefficient in 0.062 5-0.125 0. The average inbreeding coefficients of Guizhou buffalo and Yibin buffalo were 0.034 6 and 0.041 0, respectively. In conclusion, the population of Fuling buffalo in the conservation farm can be divided into two groups, which have a unique population structure compared to the other neighboring areas buffalo breeds, and 7 Fuling buffalo individuals in the conservation farm have inbreeding risk, so it is urgent to strengthen the protection and utilization of Fuling buffalo resources.

Key words: Fuling buffalo, population genetic structure, SNP, ROH, inbreeding coefficient

CLC Number:

S823.83

TU Yun, ZENG Yanan, ZHANG Zhenghao, HONG Rui, WANG Zhen, WU Ping, ZHOU Zeyang, YE Yiru, DU Yanan, ZUO Fuyuan, ZHANG Gongwei. Genetic Structure and Runs of Homozygosity Analysis of Fuling Buffalo and Southwest Buffalo Breeds[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 1989-1998.

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Genetic Structure and Runs of Homozygosity Analysis of Fuling Buffalo and Southwest Buffalo Breeds

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