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

Abstract

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.

CLC Number:

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.

0
/ / Recommend

Add to citation manager EndNote|Reference Manager|ProCite|BibTeX|RefWorks

URL: https://www.xmsyxb.com/EN/doi: 10.11843/j.issn.0366-6964.2016.08.003

https://www.xmsyxb.com/EN/Y2016/V47/I8/1539

References

［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.

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

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 0

Recommended Articles

Metrics

Comments