基于全基因组Fst和nSL分析鉴别苏淮猪中性洗涤纤维表观消化率相关候选基因位点

doi:10.11843/j.issn.0366-6964.2021.07.005

Abstract

Abstract: This study aimed to identify the selected gene regions related to the apparent NDF digestibility during the breeding process of Suhuai pigs (a national new breed containing 25% Huai pig lineage and 75% Large White pig lineage) and provide an important foundation for analyzing the genetic mechanism of crude fiber tolerance in Suhuai pigs. Firstly, the apparent digestibility of neutral detergent fiber (NDF) of 331 160-day-old Suhuai pigs were measured. The estimated breeding value (EBV) of apparent NDF digestibility in Suhuai pigs were calculated. Suhuai pigs with extremely high 10% (n=33) and extremely low 10% (n=33) of EBV_NDF were selected to perform 80K chip genotyping. The fixation index (Fst) and the number of segregating sites by length (nSL) methods were adopted to analyze the selection signals distribution in Suhuai pig populations, and to detect the candidate genes related to fiber digestion located in selected signal regions. Finally, the common SNPs of selected sites in the Fst and nSL analyses were selected to genotype in the whole group of Suhuai pigs, and then the association analysis between SNPs and apparent NDF digestibility was carried out to further determine the candidate SNPs related to the apparent NDF digestibility in Suhuai pigs. A total of 51 367 effective SNPs sites were used for the further analysis through the quality control of chip data of Suhuai pig populations with high and low apparent NDF digestibility. Furthermore, 146 selected signals regions and 361 selected genes were identified via Fst and nSL selection signals analysis. Among them, many genes had been reported to be related to intestinal health and intestinal development, including MTHFD1L, PHLPP1, TRPM6, MCC, NEDD9, UVRAG and KLF5. Only 8 common SNPs sites were identified in the two analyses. Association analysis results of SNPs with apparent NDF digestibility showed that rs81363074, rs327393763, and rs81404927 were significantly associated with apparent NDF digestibility (P<0.05), and the rs81347101 and rs318870857 were extremely significantly associated with the apparent NDF digestibility in Suhuai pig populations (P<0.01). Among them, the rs81363074 was located on the second intron of the MCC gene. One hundred and forty-six selected signals regions were identified based on the methods of Fst and nSL selection signals in Suhuai pigs with high and low apparent NDF digestibility. The selected candidate genes MTHFD1L, PHLPP1, TRPM6, MCC, NEDD9, UVRAG and KLF5 were identified to affect the apparent NDF digestibility in Suhuai pigs. Besides, 5 SNPs sites were significantly related to the apparent NDF digestibility. This results of this study provided an important foundation for analyzing the genetic mechanism of fiber tolerance trait in Suhuai pigs.

Key words: Suhuai pigs, apparent fiber digestibility, selection signals, Fst, nSL, genes related to fiber digestibility

CLC Number:

S828.2

LI Kaijun, HOU Liming, PU Guang, LIU Hang, LIU Gensheng, SHI Chuanzong, JIN Tong, ZHOU Juan, LI Pinghua, HUANG Ruihua. Identification of Candidate Gene Loci Related to Apparent NDF Digestibility of Suhuai Pigs Based on Genome-wide Fst and nSL Analyses[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(7): 1809-1819.

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Identification of Candidate Gene Loci Related to Apparent NDF Digestibility of Suhuai Pigs Based on Genome-wide Fst and nSL Analyses

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