基因组分析对猪乳头数性状相关数量性状基因座鉴定

doi:10.3864/j.issn.0578-1752.211074

摘要/Abstract

摘要： 【目的】分析乳头数的变异，挖掘与乳头数相关的数量性状基因座（quantitative trait locus，QTL）和候选基因，为猪乳头数的选育研究提供重要分子标记。【方法】准确测定了709头苏淮猪（335头育肥猪和374头种猪）的左、右和总乳头数。对苏淮育肥猪进行80K芯片分型，并使用芯片数据计算左、右、总乳头数的遗传力和基因组估计育种值（genomic estimated breeding value, GEBV）。基于乳头数GEBV和表型排名，选择前10%的个体以及后10%的个体进行群体分化指数分析（fixation Index, F_ST）以检测高度分化的位点。接着，通过全基因组关联分析（genome wide association analysis, GWAS）鉴定与乳头数关联的位点，选择高度分化且与乳头数显著关联的位点作为候选位点，选择位于候选位点附近且功能注释后与乳头数相关的基因作为候选基因。最后，选择每个染色体上最显著的候选位点对709头苏淮猪进行乳头数关联分析，以验证上述位点的显著性。【结果】苏淮育肥猪左、右、总乳头数的变异系数分别为10.20%、9.26%、8.50%，遗传力分别为0.212、0.257、0.312。基于F_ST和GWAS分析，总共在7、13、16、18号染色体（Sus Scrofa Chromosome, SSC）上鉴定到20个乳头数的候选位点，这些候选位点可解释5.49%-8.03%的表型方差。其中，SSC7上与总乳头数关联的位点rs80894106与文献中报道的影响大白和杜洛克猪总乳头数的候选位点一致，但左乳头的候选位点rs81444134（26.51 Mb, SSC13）和rs81233299（8.13 Mb, SSC18）均为新发现的与乳头数相关的位点。有意思的是，左、右、总乳头的候选位点主要集中在SSC16上的6.36-10.66 Mb区间;连锁不平衡（linkage disequilibrium, LD）分析发现，区间内7.47-8.27 Mb的候选位点拟合成了一个795 Kb的单倍型块，且该单倍型块是新发现的影响乳头数的候选区域；单倍型块内的rs337606862（7.47 Mb）与右乳头和总乳头最显著关联，单倍型块内的3个位点均位于cadherin 18（CDH18）基因的内含子上，CDH18编码Ⅱ型钙黏附素，且钙黏附素与发育中组织细胞的识别、分选、增殖、凋亡以及乳腺癌的发生有关。因此，CDH18可能是新的影响猪乳头数的候选基因。再者，本研究对4个染色体上最显著的位点：rs81444134、rs80894106、rs337606862、rs81233299在709头苏淮猪中基因分型，经关联分析后发现，这些位点均与乳头数显著相关，可以作为潜在分子标记用于乳头数的选育。【结论】本研究通过基因组分析在苏淮猪群体中鉴定到20个与乳头数显著相关的位点。其中SSC13上的26.51 Mb和SSC18上的8.13 Mb是新的乳头数的候选QTLs，SSC16上的7.47-8.27 Mb也是新发现的乳头数的候选QTL，且区间内CDH18可能是新的影响猪乳头形成的候选基因。

关键词: F_ST, GWAS, 数量性状基因座（quantitative trait locus, QTL）, 苏淮猪, 乳头数, 候选基因

Abstract: 【Objective】The purposes of this study were to analyze the variation of teat number, to explore the quantitative trait locus (QTL) and candidate genes related to teat number, and to provide important molecular markers for the breeding of pig teat number.【Method】This study accurately measured left, right, total teat number of 709 Suhuai pigs (335 fattening pigs and 374 breeding pigs). Fattening pigs were selected for 80K chip genotyping and the heritability and genomic estimated breeding value (GEBV) of left, right and total teat number were calculated by chip data. Based on the rank of GEBV and phenotype of teat number, the top 10% individuals and the bottom 10% individuals were selected for Fixation Index (F_ST) analysis to detect highly differentiated loci. Then, the loci associated with teat number were identified by genome wide association analysis (GWAS) and loci which were highly differentiated and significantly associated with teat number were selected as candidate loci. Genes located near candidate loci and related to teat number after functional annotation were selected as candidate genes. Finally, the association analyses between the most significant candidate loci on each chromosome and teat number of 709 Suhuai pigs were performed to verify the significance of the above loci.【Result】The variation coefficients of left, right and total teat number of Suhuai fattening pigs were 10.20%, 9.26% and 8.50%, respectively, and the heritability were 0.212, 0.257 and 0.312, respectively. Based on F_ST and GWAS analyses, a total of 20 candidate loci on Sus scorfa chromosomes (SSC) 7, 13, 16 and 18 for teat number were identified and these candidate loci could explain 5.49%-8.03% of the phenotypic variance. Among them, locus rs80894106 on SSC7 associated with total teat number was consistent with the reported candidate locus of total teat number based on Large white and Duroc pig populations, but candidate loci rs81444134 (26.51 Mb, SSC13) and rs81233299 (8.13 Mb, SSC18) of left teat number were newly discovered loci related to teat number. Interestingly, candidate loci of left, right and total teat number were mainly concentrated in the 6.36-10.66 Mb interval on SSC16; Linkage disequilibrium (LD) analysis found that candidate loci in 7.47-8.27 Mb interval fit into a 795 Kb haplotype block, and this haplotype block was a newly discovered candidate area that affected teat number; rs337606862 (7.47 Mb) in the haplotype block was the most significantly SNP associated with the left and total teat number, and three loci in the haplotype block were all located on the intron of cadherin 18 (CDH18) gene; CDH18 gene encoded type II cadherin, and cadherin was related to the identification, sorting, proliferation, apoptosis of cells in developing tissue and the occurrence of breast cancer. Thus, CDH18 might be a new candidate gene that affected pig teat number. In addition, the most significant loci rs81444134, rs80894106, rs337606862 and rs81233299 on 4 chromosomes were genotyped in 709 Suhuai pigs in this study. After association analysis, these loci were significantly associated with teat number, and could be used as potential molecular markers for the selection of teat number.【Conclusion】In this study, 20 loci significantly related to teat number were identified in Suhuai pig population by genome analysis. Among them, 26.51 Mb on SSC13 and 8.13 Mb on SSC18 were new candidate QTLs for teat number. The 7.47-8.27 Mb on SSC16 was also a newly discovered candidate QTL for teat number, and CDH18 gene in this interval might be a new candidate gene that affected the formation of pig teat.

Key words: F_ST, , GWAS, , QTL, , Suhuai pig, , teat number, , candidate genes

尹彦镇, 侯黎明, 刘航, 陶伟, 石传宗, 刘锴月, 张萍, 牛培培, 李强, 李平华, 黄瑞华. 基因组分析对猪乳头数性状相关数量性状基因座鉴定[J]. 中国农业科学, 0, (): 1-.

YIN YanZhen, HOU LiMing, LIU Hang, TAO Wei, SHI ChuanZong, LIU KaiYue, ZHANG Ping, NIU PeiPei, LI Qiang, LI PingHua, HUANG RuiHua. Identifying New QTLs for Teat Number Traits of Pig by Genome Analysis[J]. Scientia Agricultura Sinica, 0, (): 1-.

[1]	江东, 王旭, 李仁静, 赵晓东, 戴祥生, 柳正葳. 基于GBS技术开展柚类资源群体遗传评价并发掘酸含量相关基因[J]. 中国农业科学, 2023, 56(8): 1547-1560.
[2]	董一帆, 任毅, 程宇坤, 王睿, 张志辉, 时晓磊, 耿洪伟. 冬小麦籽粒主要品质性状的全基因组关联分析[J]. 中国农业科学, 2023, 56(11): 2047-2063.
[3]	尹彦镇, 侯黎明, 刘航, 陶伟, 石传宗, 刘锴月, 张萍, 牛培培, 李强, 李平华, 黄瑞华. 基因组分析对猪乳头数相关数量性状基因座鉴定[J]. 中国农业科学, 2023, 56(10): 1994-2006.
[4]	张芳,任毅,曹俊梅,李法计,夏先春,耿洪伟. 基于SNP标记的小麦籽粒性状全基因组关联分析[J]. 中国农业科学, 2021, 54(10): 2053-2063.
[5]	刘晨曦,王彬彬,蒲广,张倩,曹旸,王欢,高琛,牛培培,李平华,黄瑞华. 苏淮猪抗腹泻MUC13基因rs319699771位点多态性及其与经济性状的关联[J]. 中国农业科学, 2019, 52(8): 1449-1457.
[6]	刘坤，张雪海，孙高阳，闫鹏帅，郭海平，陈思远，薛亚东，郭战勇，谢惠玲，汤继华，李卫华. 玉米株型相关性状的全基因组关联分析[J]. 中国农业科学, 2018, 51(5): 821-834.
[7]	董军，王京，梁微，马百全，董丽娟，马锋旺，符轩畅，李翠英. G.41×新疆野苹果树体生长性状的QTL精细定位及候选基因预测[J]. 中国农业科学, 2018, 51(11): 2155-2163.
[8]	时佳，翟胜男，刘金栋，魏景欣，白璐，高文伟，闻伟锷，何中虎，夏先春，耿洪伟. 普通小麦籽粒过氧化物酶活性全基因组关联分析[J]. 中国农业科学, 2017, 50(21): 4212-4227.
[9]	吴一尘，杜星，李平华，吴艳，王钧顺，刘红林，李齐发. 苏淮猪VRTN基因克隆、组织表达特征与多态性分析[J]. 中国农业科学, 2016, 49(18): 3639-3648.
[10]	王继英, 王海霞, 迟瑞宾, 郭建凤, 武英. 全基因组关联分析在畜禽中的研究进展[J]. 中国农业科学, 2013, 46(4): 819-829.
[11]	赵璞, 刘瑞响, 李成璞, 邢向茹, 曹晓良, 陶勇生, 张祖新. 基于掖478导入系的玉米产量性状QTL鉴定[J]. 中国农业科学, 2011, 44(17): 3508-3519.
[12]	张振华, 郭梁, 朱玉君, 樊叶杨, 庄杰云. 籼稻不同定位群体的抽穗期和株高QTL比较研究[J]. 中国农业科学, 2011, 44(15): 3069-3077.
[13]	杜景红,樊叶杨,吴季荣,庄杰云. 水稻第6染色体短臂产量性状QTL簇的分解[J]. 中国农业科学, 2008, 41(4): 939-945 .
[14]	李梦,林飞,黄菊,章元明. QTL精细定位影响因素的数学模型[J]. 中国农业科学, 2008, 41(2): 340-346 .
[15]	崔世友,陈华涛,喻德跃. 大豆叶片衰老QTL的初步定位[J]. 中国农业科学, 2007, 40(9): 2103-2108 .

基因组分析对猪乳头数性状相关数量性状基因座鉴定

Identifying New QTLs for Teat Number Traits of Pig by Genome Analysis

PDF

赞

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

Metrics

本文评价

推荐阅读 0