猪RXRB基因SNPs检测及其与生长育肥和繁殖性状的关联分析

doi:10.11843/j.issn.0366-6964.2021.03.004

摘要/Abstract

摘要： 旨在研究猪RXRB基因多态性位点，并筛选与猪生长育肥和繁殖性状显著相关的SNPs，为种猪的遗传改良提供新的遗传标记位点。本研究通过采集962头健康大白猪（美系大白459头，法系大白503头）的血液DNA，利用直接测序法和PCR-RFLP技术分别检测两个品系大白猪RXRB基因SNP位点，并进行遗传多态性分析。利用SAS 8.0软件中的混合线性模型（Mixed）对RXRB基因SNP位点与表型性状值进行关联分析。利用Haploview 4.2软件对RXRB基因SNP位点进行连锁不平衡分析。结果显示，在两个品系大白猪群中共检测到10个SNPs，其中，美系大白有5个SNPs，法系大白有5个SNPs。经X²适合性检验，该10个SNPs在大白猪群体中均处于Hardy-Weinberg平衡状态（P>0.05）。关联分析结果表明，rs340542491、rs330162688和rs326226767与达100 kg体重日龄达到显著相关（P<0.05）；rs340542491、rs330162688、rs336609453和rs332169586与活体背膘厚达到显著相关（P<0.05）；rs340542491、rs325538588、rs691889709和rs323107853与初生重达到显著相关（P<0.05）；在体长中，仅rs324141460的GA基因型个体显著大于GG基因型（P<0.05）；rs325538588和rs80789331与眼肌面积达到显著相关（P<0.05）；在乳头数中，rs340542491和rs330162688与左乳头数达到极显著相关（P<0.01），rs324141460与左、右乳头数达到极显著相关（P<0.01），rs336609453和rs332169586与右乳头数达到显著相关（P<0.05）。连锁不平衡分析结果显示，在美系大白中，rs326226767-rs325538588处于强连锁不平衡状态（D’=0.96，r²=0.91>0.33），rs330162688-rs324141460处于完全连锁状态（D’=1），rs324141460-rs340542491处于完全连锁状态（D’=1），单倍型组合关联分析结果与单个SNP关联分析结果一致，单倍型组合与达100 kg体重日龄、活体背膘厚、初生重和乳头数等性状存在极显著（P<0.01）或显著（P<0.05）相关；在法系大白中，rs691889709-rs323107853处于完美连锁状态（D’=1，r²=1），单倍型组合关联分析结果显示，单倍型组合与体长和乳头数达到极显著（P<0.01）或显著（P<0.05）相关。以上结果提示，RXRB基因内的10个SNPs可以作为猪育种改良的分子标记，同时对深入研究该基因功能具有一定的参考意义。

关键词: RXRB, 关联分析, 连锁不平衡, 单倍型, 生长育肥, 繁殖性状, 猪

Abstract: The study aimed to identify the polymorphism of RXRB gene, screen SNPs significantly associated with growth, fattening and reproductive traits, and provide novel genetic markers for the genetic improvement of pigs. In this study, the blood genomic DNA of 962 healthy Large White pigs (459 American Large White pigs and 503 French Large White pigs) were sampled. The SNPs of RXRB gene were detected by direct sequencing, and PCR-RFLP methods and used to perform the genetic polymorphism analysis. The mixed linear model (Mixed) in SAS 8.0 software was used to analyze the association between the SNPs of RXRB gene and phenotypic traits. The Haploview 4.2 software was used to analyze the linkage disequilibrium of the SNPs. The results showed that a total of 10 SNPs were detected in the two strains of Large White pigs, of which there were 5 SNPs in the American Large White pigs and 5 SNPs in the French Large White pigs. According to the result of χ² test, the 10 SNPs were all under the Hardy-Weinberg equilibrium status (P>0.05). The results of association analysis showed that rs340542491, rs330162688 and rs326226767 were significantly associated with days at 100 kg body weight (P<0.05). The rs340542491, rs330162688, rs336609453 and rs332169586 were significantly associated with backfat thickness (P<0.05). The rs340542491, rs325538588, rs691889709 and rs323107853 were significantly associated with birth weight (P<0.05). For body length, only the individuals with genotype GA at rs324141460 were significantly larger than those with GG genotype (P<0.05). The rs325538588 and rs80789331 were significantly associated with the loin muscle area (P<0.05). The rs340542491 and rs330162688 were extremely significantly associated with number of left nipples (P<0.01). The rs324141460 was extremely significantly associated with number of left and right nipples (P<0.01). The rs336609453 and rs332169586 were significantly associated with the number of right nipples (P<0.05). The results of linkage disequilibrium analysis showed that rs326226767-rs325538588 was in a strong linkage disequilibrium status (D'=0.96, r²=0.91>0.33), rs330162688-rs324141460 was in a fully linkage status (D'=1), and rs324141460-rs340542491 was in a fully linked status (D'=1) in American Large White pigs. The results of association analysis of haplotype combinations were consistent with the results of the association analysis of single SNP; they were extremely significant (P<0.01) or significant (P<0.05) associated with days at 100 kg body weight, backfat thickness, birth weight and the number of nipples. In French Large White pigs, rs691889709-rs323107853 was in a fully linkage status (D'=1, r²=1). The associations between haplotype combinations and the body length, number of nipples reached extremely significant (P<0.01) or significant (P<0.05) levels. The results suggest that the 10 SNPs of RXRB gene can be used as molecular markers for pig breeding improvement, and provide the basis for the in-depth study of the function of RXRB.

Key words: RXRB, association analysis, linkage disequilibrium, haplotype, growth and fattening, reproduction traits, pig

中图分类号:

S828.2

彭雅鑫, 刘军, 赵诗瑜, 徐在言, 左波. 猪RXRB基因SNPs检测及其与生长育肥和繁殖性状的关联分析[J]. 畜牧兽医学报, 2021, 52(3): 596-609.

PENG Yaxin, LIU Jun, ZHAO Shiyu, XU Zaiyan, ZUO Bo. Detection of SNPs in Porcine RXRB Gene and Their Association Analysis with Growth, Fattening and Reproduction Traits[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(3): 596-609.

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