利用全基因组选择信号方法鉴别影响猪肉滴水损失的候选基因

doi:10.11843/j.issn.0366-6964.2022.05.006

Abstract

Abstract: The purpose of this study was to identify candidate genes affecting drip loss of pork, and to lay a foundation for meat quality breeding of pigs. The experimental population in this study was 478 healthy Suhuai pigs with an average age of 237.95 days, including 290 castrated boars and 188 sows. The longissimus dorsi muscle samples of all individuals were collected, and then the drip loss (DL) phenotype data were measured by hanging bag method to calculate the estimated breeding value (EBV) of drip loss, and Suhuai pigs with top 10% (N=48) and bottom 10% (N=48) of EBV_DL were selected for genotyping using the GeneSeek GGP-Porcine 80 K SNP BeadChip (Illumnia). The fixation index (Fst) and integrated haplotype score (iHS) were used to detect the whole genome selection signals of Suhuai pigs. We selected SNP sites with iHS value in the top 5% and Fst ≥ 0.15 as the selected SNPs, then gene annotation was performed within the region of 50 kb upstream and downstream of the selected SNPs, and all genes were analyzed for KEGG and GO enrichment to identify candidate genes associated with drip loss of pork. After the quality control of chip typing data, 51 705 valid SNPs from 96 samples were used for subsequent analysis. A total of 175 SNPs were screened by Fst and iHS selective signal analysis, they were mainly located on chromosome 1, 6, 7 and 11, of which only 27 SNPs were located in the QTL regions that have been reported to affect the drip loss of pork. Gene annotations of the area around the selected SNPs showed that 175 significant SNPs were involved 73 genes. Among these genes, several genes have been reported to be related to muscle development and cell oxidative stress, including PACRG, EZR, MRTFA, LCP1 and VKORC1L1. The 5 genes were newly discovered functional candidate genes that were related to the drip loss of pork. Then, we genotyped 3 SNPs located on the intron of the functional candidate genes and on the QTL region, and analyzed the correlation between genotypes of the 3 SNPs and the drip loss in the whole Suhuai pig population. The results showed that rs340037952 located on the MRTFA gene was significantly associated with drip loss in Suhuai pig population (P<0.05), and rs320624660 located on the VKORC1L1 gene was extremely significantly associated with drip loss in Suhuai pig population (P<0.01). In this study, 175 selected SNPs were found through selection signal analysis, 5 candidate genes affecting drip loss were identified by gene function annotation, and 2 SNPs (rs340037952 and rs320624660) significantly associated with drip loss in Suhuai pigs population were identified on MRTFA and VKORC1L1 genes, which provided a preliminary basis for the breeding of drip loss in pigs.

Key words: pig, drip loss, selection signals, Fst, iHS, candidate genes

CLC Number:

S828.2

TAO Wei, HOU Liming, WANG Binbin, LIU Hang, LI Kaijun, YIN Yanzhen, GUO Hao, NIU Peipei, ZHANG Zongping, LI Qiang, HUANG Ruihua, LI Pinghua. Identification of Candidate Genes Affecting Drip Loss in Pork by Genome-wide Selection Signal Method[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(5): 1373-1383.

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Identification of Candidate Genes Affecting Drip Loss in Pork by Genome-wide Selection Signal Method

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