西门塔尔牛饱和脂肪酸含量的低密度芯片基因组预测

doi:doi: 10.11843/j.issn.0366-6964.2016.08.003

畜牧兽医学报 ›› 2016, Vol. 47 ›› Issue (8): 1539-1545.doi: doi: 10.11843/j.issn.0366-6964.2016.08.003

西门塔尔牛饱和脂肪酸含量的低密度芯片基因组预测

齐欣¹，张静静^1，2，樊惠中¹，李娟¹，胡鑫^1，3，刘飞^1，4，朱波¹，高雪¹，陈燕¹，张路培¹，高会江¹，李俊雅^1*

（1.中国农业科学院北京畜牧兽医研究所，北京 100193； 2.吉林农业大学动物科技学院，长春 130118；3.内蒙古民族大学动物科学技术学院，通辽 028000； 4.河北农业大学动物科技学院，保定 071000）

收稿日期:2015-03-06 出版日期:2016-08-23 发布日期:2016-09-08
通讯作者: 李俊雅，E-mail：JL1@iascaas.net.cn
作者简介:齐欣（1989-），女，天津人，硕士生，主要从事动物遗传育种与繁殖研究，E-mail：qixin8906@sina.com
基金资助:
农业部专项（CARS-38）；国家自然科学基金（31372294）；中国农业科学院科技创新工程经费(cxgc-ias-03)

Genomic Prediction for Saturated Fatty Acid Content in Simmental using Low Density Chip

QI Xin ¹，ZHANG Jing-jing ^1，2，FAN Hui-zhong¹，LI Juan¹，HU Xin^1，3，LIU Fei^1，4，ZHU Bo¹，GAO Xue ¹，CHEN Yan¹，ZHANG Lu-pei ¹，GAO Hui-jiang¹，LI Jun-ya^1*

(1.Institute of Animal Science，Chinese Academy of Agricultural Sciences，Beijing 100193，China；
2.College of Animal Science and Technology，Jilin Agricultural University，Changchun 130118，China；
3.College of Animal Science and Technology，Inner Mongolia University for Nationalities，Tongliao 028000，China；
4.College of Animal Science and Technology，Hebei Agricultural University，Baoding 071000，China)

Received:2015-03-06 Online:2016-08-23 Published:2016-09-08

摘要/Abstract

摘要：

旨在探索低密度芯片标记的筛选方法并评估不同低密度芯片的准确性。本研究采用BovineHD高密度芯片，检测西门塔尔牛基因组的SNP位点及其与饱和脂肪酸含量的关联性，根据P值或效应值筛选标记构成低密度芯片，使用IBS聚类分组和随机分组进行交叉验证，估计基因组育种值并评估其准确性。结果表明，在14号染色体的MYC基因附近有5个位点与饱和脂肪酸性状显著相关，可考虑作为西门塔尔牛脂肪酸含量的候选基因进行后续研究。根据P值筛选标记并使用IBS聚类分组进行交叉验证时，估计基因组育种值准确性最高，芯片密度达到7K时准确性趋于稳定。因此，本研究发现的标记位点可能对西门塔尔牛的脂肪酸含量存在一定影响，并且为低密度芯片标记位点的筛选提供参考资料。

关键词: 全基因组关联分析, 基因组选择, 低密度芯片, SNP, 西门塔尔牛

Abstract:

The objective of this study was to explore methods of selection markers and evaluate accuracies of low density (LD) chips.SNPs associated with saturated fatty acid（SFA） content were identified using BovineHD panel and genomic breeding value was evaluated using LD panels which were markers selected on the basis of P-value or effect value on Simmental bulls.Then we evaluated accuracy of genomic prediction via cross-validation (CV) methodologies based on identical by state (IBS) and random sample.A total of 5 SNPs were associated with SFA and adjacent to MYC gene on BTA14，which could be considered as candidate genes.Prediction was the most accurate when markers were selected on the basis of P-value and CV was IBS-based.The accuracy of genomic value in 7 000 SNPs panel was steady.In conclusion，this study identified several SNPs associated with SFA and provided reference for marker selection in LD panels for further study.

Key words: GWAS, genomic selection, low density chip, SNP, Simmental

中图分类号:

齐欣，张静静，樊惠中，李娟，胡鑫，刘飞，朱波，高雪，陈燕，张路培，高会江，李俊雅. 西门塔尔牛饱和脂肪酸含量的低密度芯片基因组预测[J]. 畜牧兽医学报, 2016, 47(8): 1539-1545.

QI Xin，ZHANG Jing-jing，FAN Hui-zhong，LI Juan，HU Xin，LIU Fei，ZHU Bo，GAO Xue，CHEN Yan，ZHANG Lu-pei，GAO Hui-jiang，LI Jun-ya. Genomic Prediction for Saturated Fatty Acid Content in Simmental using Low Density Chip[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2016, 47(8): 1539-1545.

参考文献

［1］MEUWISSEN T H，HAYES B J，GODDARD M E.Prediction of total genetic value using genome-wide dense marker maps［J］.Genetics， 2001，157(4)：1819-1829.
［2］KÖNIG S，SIMIANER H，WILLAM A.Economic evaluation of genomic breeding programs［J］.J Dairy Sci， 2009，92(1)：382-391.
［3］SCHAEFFER L R.Strategy for applying genome-wide selection in dairy cattle［J］.J Anim Breed Genet， 2006，123(4)：218-223.
［4］GODDARD M E，HAYES B J.Mapping genes for complex traits in domestic animals and their use in breeding programmes［J］.Nat Rev Genet， 2009，10(6)：381-391.
［5］HABIER D，FERNANDO R，KIZILKAYA K，et al.Extension of the bayesian alphabet for genomic selection［J］.BMC Bioinformatics， 2011，12：186.
［6］CLEVELAND M A，FORNI S，DEEB N，et al.Genomic breeding value prediction using three Bayesian methods and application to reduced density marker panels［J］.BMC Proc， 2010，4(Suppl 1)：S6.
［7］COSTER A，BASTIAANSEN J W，CALUS M P，et al.QTLMAS 2009：simulated dataset［J］.BMC Proc， 2010，4 (Suppl 1)：S3.
［8］WELLMANN R，PREUSS S，THOLEN E，et al.Genomic selection using low density marker panels with application to a sire line in pigs［J］.Genet Sel Evol， 2013，45：28.
［9］SUKHIJA P S，PALMQUIST D L.Rapid method for determination of total fatty acid content and composition of feedstuffs and feces［J］.J Agric Food Chem， 1988，36(6)：1202-1206.
［10］PURCELL S，NEALE B，TODD-BROWN K，et al.PLINK：a tool set for whole-genome association and population-based linkage analyses［J］.Am J Hum Genet， 2007，81(3)：559-575.
［11］ZHANG Q，BOICHARD D，HOESCHELE I，et al.Mapping quantitative trait loci for milk production and health of dairy cattle in a large outbred pedigree［J］.Genetics， 1998，149(4)：1959-1973.
［12］CASAS E，STONE R T，KEELE J W，et al.A comprehensive search for quantitative trait loci affecting growth and carcass composition of cattle segregating alternative forms of the myostatin gene［J］.J Anim Sci， 2001，79(4)：854-860.
［13］BOICHARD D，GROHS C，BOURGEOIS F，et al.Detection of genes influencing economic traits in three French dairy cattle breeds［J］.Genet Sel Evol， 2003，35(1)：77-101.
［14］BENNEWITZ J，REINSCH N，GROHS C，et al.Combined analysis of data from two granddaughter designs：A simple strategy for QTL confirmation and increasing experimental power in dairy cattle［J］.Genet Sel Evol， 2003，35(3)：319-338.
［15］CASAS E，SHACKELFORD S D，KEELE J W，et al.Detection of quantitative trait loci for growth and carcass composition in cattle［J］.J Anim Sci， 2003，81(12)：2976-2983.
［16］KAUPE B，BRANDT H，PRINZENBERG E M，et al.Joint analysis of the influence of CYP11B1 and DGAT1 genetic variation on milk production，somatic cell score，conformation，reproduction，and productive lifespan in German Holstein cattle［J］.J Anim Sci， 2007，85(1)：11-21.
［17］GUTIéRREZ-GIL B，WIENER P，NUTE G R，et al.Detection of quantitative trait loci for meat quality traits in cattle［J］.Anim Genet， 2008，39(1)：51-61.
［18］MCCLURE M C，MORSCI N S，SCHNABEL R D，et al.A genome scan for quantitative trait loci influencing carcass，post-natal growth and reproductive traits in commercial Angus cattle［J］.Anim Genet， 2010，41(6)：597-607.
［19］WANG C，HABIER D，PEIRIS B L，et al.Accuracy of genomic prediction using an evenly spaced，low-density single nucleotide polymorphism panel in broiler chickens［J］.Poult Sci， 2013，92(7)：1712-1723.
［20］ZHANG Z，DING X，LIU J，et al.Accuracy of genomic prediction using low-density marker panels［J］.J Dairy Sci， 2011，94(7)：3642-3650.
［21］THREADGILL D W，FRIES R，FABER L K，et al.The thyroglobulin gene is syntenic with the MYC and MOS protooncogenes and carbonic anhydrase II and maps to chromosome 14 in cattle［J］.Cytogenet Cell Genet， 1990，53(1)：32-36.
［22］GOODE E L，CHENEVIX-TRENCH G，SONG H，et al.A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24［J］.Nat Genet， 2010，42(10)：874-879.
［23］LANGE E M，JOHNSON A M，WANG Y，et al.Genome-wide association scan for variants associated with early-onset prostate cancer［J］.PLoS One， 2014，9(4)：e93436.
［24］YOKOTA S，SUGITA H，ARDIYANTI A，et al.Contributions of FASN and SCD gene polymorphisms on fatty acid composition in muscle from Japanese Black cattle［J］.Anim Genet， 2012，43(6)：790-792.
［25］SAATCHI M，GARRICK D J，TAIT R G JR，et al.Genome-wide association and prediction of direct genomic breeding values for composition of fatty acids in Angus beef cattlea［J］.BMC Genomics， 2013，14(1)：730.
［26］ZHANG S，KNIGHT T J，REECY J M，et al.DNA polymorphisms in bovine fatty acid synthase are associated with beef fatty acid composition［J］.Anim Genet， 2008，39(1)：62-70.
［27］ABE T，SABURI J，HASEBE H，et al.Novel mutations of the FASN gene and their effect on fatty acid composition in Japanese Black beef［J］.Biochem Genet， 2009，47(5-6)：397-411.
［28］LI C，ALDAI N，VINSKY M，et al.Association analyses of single nucleotide polymorphisms in bovine stearoyl-CoA desaturase and fatty acid synthase genes with fatty acid composition in commercial cross-bred beef steers［J］.Anim Genet， 2012，43(1)：93-97.
［29］JACOBS A A，DIJKSTRA J，HENDRIKS W H，et al.Comparison between stearoyl-CoA desaturase expression in milk somatic cells and in mammary tissue of lactating dairy cows［J］.J Anim Physiol Anim Nutr (Berl)， 2013，97(2)：353-362.
［30］ALIM M A，FAN Y P，WU X P，et al.Genetic effects of stearoyl-coenzyme A desaturase (SCD) polymorphism on milk production traits in the Chinese dairy population［J］.Mol Biol Rep， 2012，39(9)：8733-8740.
［31］BODDHIREDDY P，KELLY M J，NORTHCUTT S，et al.Genomic predictions in Angus cattle：comparisons of sample size，response variables，and clustering methods for cross-validation［J］.J Anim Sci， 2014，92(2)：485-497.
［32］BOLORMAA S，NETO L R，ZHANG Y D，et al.A genome-wide association study of meat and carcass traits in Australian cattle［J］.J Anim Sci， 2011，89(8)：2297-2309.

[1]	巩建飞, 岳静伟, 赵玲玲, 刘运鹏, 王立贤, 刘欣, 孙金海. 猪HMGA1基因的组织表达及其多态性与背膘厚的关联分析[J]. 畜牧兽医学报, 2019, 50(7): 1340-1346.
[2]	巩建飞, 岳静伟, 赵玲玲, 刘运鹏, 王立贤, 刘欣, 孙金海. 猪HMGA1基因的组织表达及其多态性与背膘厚的关联分析[J]. 畜牧兽医学报, 2019, 50(7): 1340-1346.
[3]	寸静宇, 刘秋月, 王翔宇, 狄冉, 胡文萍, 张效生, 张金龙, 赵永聚, 储明星. 小尾寒羊LHR基因组织表达、多态性及其与产羔性状的关联分析[J]. 畜牧兽医学报, 2019, 50(3): 495-506.
[4]	寸静宇, 刘秋月, 王翔宇, 狄冉, 胡文萍, 张效生, 张金龙, 赵永聚, 储明星. 小尾寒羊LHR基因组织表达、多态性及其与产羔性状的关联分析[J]. 畜牧兽医学报, 2019, 50(3): 495-506.
[5]	尹立林, 马云龙, 项韬, 朱猛进, 余梅, 李新云, 刘小磊, 赵书红. 全基因组选择模型研究进展及展望[J]. 畜牧兽医学报, 2019, 50(2): 233-242.
[6]	杜小龙, 王麒, 张乐超, 葛琳涵, 刘小辉, 王涵, 李兰会, 李祥龙. 山羊DCT基因启动子区甲基化水平、SNP与毛色特征关系研究[J]. 畜牧兽医学报, 2019, 50(2): 271-279.
[7]	侯浩宾, 李海静, 杨莉, 张新浩, 石田培, 王欣悦, 赵志达, 张莉. 德州驴NCAPG-DCAF16基因区域多态性与生长性状的关联分析[J]. 畜牧兽医学报, 2019, 50(2): 302-313.
[8]	彭潇, 尹立林, 梅全顺, 王海燕, 刘小磊, 朱猛进, 李新云, 付亮亮, 赵书红. 猪主要经济性状的基因组选择研究[J]. 畜牧兽医学报, 2019, 50(2): 439-445.
[9]	侯浩宾, 李海静, 杨莉, 张新浩, 石田培, 王欣悦, 赵志达, 张莉. 德州驴NCAPG-DCAF16基因区域多态性与生长性状的关联分析[J]. 畜牧兽医学报, 2019, 50(2): 302-313.
[10]	尹立林, 马云龙, 项韬, 朱猛进, 余梅, 李新云, 刘小磊, 赵书红. 全基因组选择模型研究进展及展望[J]. 畜牧兽医学报, 2019, 50(2): 233-242.
[11]	杜小龙, 王麒, 张乐超, 葛琳涵, 刘小辉, 王涵, 李兰会, 李祥龙. 山羊DCT基因启动子区甲基化水平、SNP与毛色特征关系研究[J]. 畜牧兽医学报, 2019, 50(2): 271-279.
[12]	彭潇, 尹立林, 梅全顺, 王海燕, 刘小磊, 朱猛进, 李新云, 付亮亮, 赵书红. 猪主要经济性状的基因组选择研究[J]. 畜牧兽医学报, 2019, 50(2): 439-445.
[13]	张跃博, 蒲蕾, 张金山, 颜华, 王立刚, 侯欣华, 刘欣, 高红梅, 王立贤, 张龙超. 杜洛克猪HLCS基因组织表达分析及其编码区多态性与剩余采食量的关联[J]. 畜牧兽医学报, 2018, 49(6): 1108-1115.
[14]	张跃博, 蒲蕾, 张金山, 颜华, 王立刚, 侯欣华, 刘欣, 高红梅, 王立贤, 张龙超. 杜洛克猪HLCS基因组织表达分析及其编码区多态性与剩余采食量的关联[J]. 畜牧兽医学报, 2018, 49(6): 1108-1115.
[15]	盛中华, 陈国宏, 潘玉春, 王起山, 张哲. 上海白猪(上系)基因组遗传变异检测与功能注释分析[J]. 畜牧兽医学报, 2018, 49(5): 887-896.

西门塔尔牛饱和脂肪酸含量的低密度芯片基因组预测

Genomic Prediction for Saturated Fatty Acid Content in Simmental using Low Density Chip

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

本文评价