拷贝数变异全基因组关联鉴定猪骨率性状候选基因

doi:10.11843/j.issn.0366-6964.2019.11.004

摘要/Abstract

摘要： 旨在挖掘影响猪骨率性状的全基因组范围内的拷贝数变异（copy number variations，CNVs），并对其所覆盖的基因的作用模式及机理进行研究。本研究利用基于测序深度的CNVcaller软件对大白×民猪F2群体的拷贝数变异进行检测，利用TASSEL软件中的混合线性模型（mixed-linear model，MLM）对骨率性状进行基因组关联分析；查找数据库对CNVs所覆盖基因进行深入分析，利用RNA重测序对75日龄大白猪腿软骨中4个显著CNVs的表达进行检测。结果表明，在F2代群体中，共检测到3 027个CNVs，其中，共有1 251个为缺失，987个为多拷贝，789个为缺失和多拷贝均存在。与骨率在基因组水平相关的CNVs共有4个，均位于7号染色体。4个变异中，有两个未与任何基因重叠。显著性最高的CNV4与骨髓分化相关标记（MYADM）基因重合。对75日龄猪腿软骨基因的表达研究发现，在后腿软骨中仅CNV2的表达丰度较高，推测CNV2通过影响其内部基因的表达量影响骨率，CNV4可能在胚胎发育期起调控作用。综上所述，本研究成功鉴定出影响猪骨率性状的4个CNVs，其中，CNV2和CNV4为影响骨率性状的主效CNVs，推测CNV2通过影响其内部基因的表达量影响骨率，CNV4可能在胚胎发育期起调控作用并最终影响骨率。本试验为今后骨率性状的调控机理研究奠定了理论基础，为猪骨率性状的育种提供了参考。

Abstract: The aim of this study was to explore the genome-wide copy number variations (CNVs) affecting porcine bone rate traits, and to study the action mode and mechanism of the genes covered by these CNVs. CNVcaller software which based on the depth of sequencing were used to detect the copy number variations of the F2 population of the Large White×Min pig, and TASSEL mixed-linear model (MLM) were used to perform genome association analysis on the bone rate traits. The genes covered by CNVs were analyzed by seeking databases. The expression of the 4 significant CNVs in leg cartilage were detected by RNA resequencing in 75-day-old Large White pigs. A total of 3 027 CNVs were detected in F2 population, including 1 251 deletions, 987 multiple copies, and 789 deletions and multiple copies. There were 4 copy number variations associated with bone rate at genomic level, all on chromosome 7. Two of the four variants did not overlap with any gene. The most significant CNV (CNV4) could cover the myeloid associated differention marker(MYADM) gene. The study of gene expression in 75-days-old pigs showed that only CNV2 was highly expressed in hind leg cartilage. It was speculated that CNV2 could affect bone rate by affecting the expression of internal genes, and CNV4 might play a regulatory role in embryonic development. In summary, four CNVs affecting bone rate traits were successfully identified in pigs. It was speculated that CNV2 affected bone rate by affecting the expression of internal genes, and CNV4 might play the regulation role in embryonic development and finally affect bone rate. This study laid a theoretical foundation for researching the regulation mechanism of bone rate traits in the future and provided a reference for the breeding of bone rate traits in pig.

中图分类号:

S828.2

王立刚, 张跃博, 颜华, 张龙超, 侯欣华, 刘欣, 王立贤. 拷贝数变异全基因组关联鉴定猪骨率性状候选基因[J]. 畜牧兽医学报, 2019, 50(11): 2208-2214.

WANG Ligang, ZHANG Yuebo, YAN Hua, ZHANG Longchao, HOU Xinhua, LIU Xin, WANG Lixian. Identification of Candidate Genes for Porcine Bone Rate Traits by Genome-wide Association of Copy Number Variation[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(11): 2208-2214.

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