戴瑞奶绵羊产奶性状的全基因组关联分析

doi:10.11843/j.issn.0366-6964.2021.011.030

摘要/Abstract

摘要： 旨在通过对奶绵羊产奶性状的全基因组关联分析（GWAS），寻找和定位与奶绵羊产奶性状相关的遗传标记和功能基因。本研究以135只戴瑞奶绵羊为试验材料，基于全基因组重测序技术，通过SAMTOOLS进行单核苷酸多态性（SNP）检测，使用PLINK v1.90进行质控，利用GEMMA v 0.98.1的混合线性模型对质控结果进行奶绵羊产奶性状相关的全基因组关联分析。结果表明，有1个SNP与泌乳后90天日均产奶量在全基因组范围内显著相关，8个SNPs达到潜在显著关联，相关的候选基因包括TRNAQ-CUG-2、LOC114117240、ACADL、MYL1、CHD6、SLCO3A1；有2个SNPs与150天日均产奶量达潜在显著关联，相关的候选基因包括PRMT6、RNF180；有2个SNPs与泌乳周期达潜在显著关联，相关的候选基因包括PRMT6、TRNAW-CCA-68、TRNAS-GGA-61。进一步基因功能分析推测，ACADL、SLCO3A1可能是影响奶绵羊产奶性状的候选基因。本研究为奶绵羊产奶性状的分子机制解析提供了一定的基础，为我国奶绵羊新品种培育提供了一定的理论参考。

关键词: 全基因组关联分析, 戴瑞奶绵羊, 产奶性状, 重测序, 候选基因

Abstract: The study aimed to identify and map the genetic markers and functional genes which associated with milk production traits through genome-wide association analysis (GWAS) of milk production traits in Dairy Meade(DM) sheep. In this study, 135 DM sheep were collected and the whole genome resequencing technology was used. The single nucleotide polymorphisms (SNPs) were identified through SAMTOOLS software. The quality control (QC) was performed by Plink v1.90 software. The genome-wide association analysis of milk production traits in DM sheep was performed based on the QC results using the mixed linear model of GEMMA v 0.98.1. The results showed that there was one SNP which was significantly correlated and 8 SNPs were potentially significantly correlated with D90 average daily milk yield trait at genome-wide; The associated candidate genes included TRNAQ-CUG-2, LOC114117240, ACADL, MYL1, CHD6 and SLCO3A1. There were 2 SNPs which were potentially significantly correlated with D150 average daily milk yield trait; The associated candidate genes included PRMT6 and RNF180. There were 2 SNPs which were potentially significantly correlated with lactation period trait; The associated candidate genes included PRMT6, TRNAW-CCA-68 and TRNAS-GGA-61. Further gene functional analysis suggested that ACADL and SLCO3A1 were likely candidate genes which affect milk production traits of DM sheep. This study provides a certain basis for the exploration of milk production traits molecular mechanism in dairy sheep. The result could provide a certain theoretical reference for new dairy sheep breeding in China.

Key words: genome-wide association analysis, Dairy Meade(DM) sheep, milk production traits, resequencing, candidate gene

中图分类号:

S826.2

米布农, 张立果, 乌日汉, 郭玉林, 王春伟, 徐全忠, 冯爽, 李光鹏, 苏小虎, 张立. 戴瑞奶绵羊产奶性状的全基因组关联分析[J]. 畜牧兽医学报, 2021, 52(11): 3294-3303.

MI Bunong, ZHANG Liguo, BAI Urhan, GUO Yulin, WANG Chunwei, XU Quanzhong, FENG Shuang, LI Guangpeng, SU Xiaohu, ZHANG Li. Genome-wide Association Study of Milk Production Traits in Dairy Meade Sheep[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(11): 3294-3303.

参考文献 40

[1]	郑重, 张功, 任志强, 等. 我国奶绵羊产业现状与发展方向[J].中国乳业, 2019(8):27-31.ZHENG Z, ZHANG G, REN Z Q, et al. Current situation and development direction of dairy and sheep industry in China[J].China Dairy, 2019(8):27-31.(in Chinese)
[2]	KING M E, KING J E, POWELL C B.Sheep dairying in New Zealand-the Kingsmeade story[J].Proc N Z Soc Anim Prod, 2014, 74:58-61.
[3]	赵志达, 张莉.基因组选择在绵羊育种中的应用[J].遗传, 2019, 41(4):293-303.ZHAO Z D, ZHANG L.Applications of genome selection in sheep breeding[J].Hereditas, 2019, 41(4):293-303.(in Chinese)
[4]	张统雨, 朱才业, 杜立新, 等. 羊重要性状全基因组关联分析研究进展[J].遗传, 2017, 39(6):491-500.ZHANG T Y, ZHU C Y, DU L X, et al. Advances in genome-wide association studies for important traits in sheep and goats[J].Hereditas, 2017, 39(6):491-500.(in Chinese)
[5]	齐超, 谢岩, 吴晓平, 等. 基于全基因组信息鉴定中国荷斯坦牛产奶性状基因及功能注释[J].畜牧兽医学报, 2012, 43(6):872-877.QI C, XIE Y, WU X P, et al. Identification and annotation of genes affecting milk production traits in Chinese Holstein based on GWAS[J].Acta Veterinaria et Zootechnica Sinica, 2012, 43(6):872-877.(in Chinese)
[6]	LIU J J, LIANG A X, CAMPANILE G, et al. Genome-wide association studies to identify quantitative trait loci affecting milk production traits in water buffalo[J].J Dairy Sci, 2018, 101(1):433-444.
[7]	DENG T X, LIANG A X, LIANG S S, et al. Integrative analysis of transcriptome and GWAS data to identify the hub genes associated with milk yield trait in buffalo[J].Front Genet, 2019, 10:36.
[8]	SILVA A A, SILVA D A, SILVA F F, et al. GWAS and gene networks for milk-related traits from test-day multiple lactations in Portuguese Holstein cattle[J].J Appl Gene, 2020, 61(3):465-476.
[9]	ABDEL-SHAFY H, AWAD M A A, EL-REGALATY H, et al. Prospecting genomic regions associated with milk production traits in Egyptian buffalo[J].J Dairy Res, 2020, 87(4):389-396.
[10]	GARCÍA-GÁMEZ E, GUTIÉRREZ-GIL B, SAHANA G, et al. GWA analysis for milk production traits in dairy sheep and genetic support for a QTN influencing milk protein percentage in the LALBA gene[J].PLoS One, 2012, 7(10):e47782.
[11]	MOIOLI B, SCATÈ M C, STERI R, et al. Signatures of selection identify loci associated with milk yield in sheep[J].BMC Genet, 2013, 14(1):76.
[12]	LI H, WU X L, TAIT R G JR, et al. Genome-wide association study of milk production traits in a crossbred dairy sheep population using three statistical models[J].Anim Genet, 2020, 51(4):624-628.
[13]	SUTERA A M, RIGGIO V, MASTRANGELO S, et al. Genome-wide association studies for milk production traits in Valle del Belice sheep using repeated measures[J].Anim Genet, 2019, 50(3):311-314.
[14]	LI H, DURBIN R.Fast and accurate short read alignment with Burrows-Wheeler transform[J].Bioinformatics, 2009, 25(14):1754-1760.
[15]	MCKENNA A, HANNA M, BANKS E, et al. The Genome Analysis Toolkit:a MapReduce framework for analyzing next-generation DNA sequencing data[J].Genome Res, 2010, 20(9):1297-1303.
[16]	MAREES A T, DE KLUIVER H, STRINGER S, et al. A tutorial on conducting genome-wide association studies:quality control and statistical analysis[J].Int J Methods Psychiatr Res, 2018, 27(2):e1608.
[17]	郝兴杰, 胡林, 张淑君.全基因组关联分析方法的研究进展[J].畜牧兽医学报, 2016, 47(2):213-217.HAO X J, HU L, ZHANG S J.Progresses in research of genome-wide association study methods[J].Acta Veterinaria et Zootechnica Sinica, 2016, 47(2):213-217.(in Chinese)
[18]	ZHOU X, STEPHENS M.Genome-wide efficient mixed-model analysis for association studies[J].Nat Genet, 2012, 44(7):821-824.
[19]	YU J M, PRESSOIR G, BRIGGS W H, et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness[J]. Nat Genet, 2006, 38(2):203-208.
[20]	WANG K, LI M Y, HAKONARSON H.ANNOVAR:functional annotation of genetic variants from high-throughput sequencing data[J].Nucleic Acids Res, 2010, 38(16):e164.
[21]	YU G C, WANG L G, HAN Y Y, et al. ClusterProfiler:an R package for comparing biological themes among gene clusters[J].OMICS:J Integr Biol, 2012, 16(5):284-287.
[22]	GEBRESELASSIE G, BERIHULAY H, JIANG L, et al. Review on genomic regions and candidate genes associated with economically important production and reproduction traits in sheep (Ovies aries)[J].Animals, 2020, 10(1):33.
[23]	ZHAO X F, QIN W H, JIANG Y H, et al. ACADL plays a tumor-suppressor role by targeting Hippo/YAP signaling in hepatocellular carcinoma[J].npj Precis Oncol, 2020, 4:7.
[24]	ZHANG M H, SUNABA T, SUN Y T, et al. Acyl-CoA dehydrogenase long chain (ACADL) is a target protein of stylissatin A, an anti-inflammatory cyclic heptapeptide[J].J Antibiot, 2020, 73(8):589-592.
[25]	张少卿, 刘贤惠, 张成龙, 等. 整个泌乳周期牛乳脂肪酸变化与乳腺乳脂合成代谢的关联分析[J].中国奶牛, 2016(12):12-17.ZHANG S Q, LIU X H, ZHANG C L, et al. Correlation analysis between milk fatty acids change in a whole lactation period and breast milk fat synthesis metabolism[J].China Dairy Cattle, 2016(12):12-17.(in Chinese)
[26]	杨沛方, 陈伟, 覃海, 等. 猪MYL1和MYL2基因的mRNA在不同组织中的表达分析[J].基因组学与应用生物学, 2020, 39(7):2989-2994.YANG P F, CHEN W, QIN H, et al. Expression analysis of MYL1 and MYL2 genes in different tissues of large white pig[J].Genomics and Applied Biology, 2020, 39(7):2989-2994.(in Chinese)
[27]	LUTZ T, STÖGER R, NIETO A.CHD6 is a DNA-dependent ATPase and localizes at nuclear sites of mRNA synthesis[J].FEBS Lett, 2006, 580(25):5851-5857.
[28]	张雪莹.奶山羊过氧化物酶增殖物激活受体γ(PPARγ)基因启动子转录调控机理研究[D].杨凌:西北农林科技大学, 2018.ZHANG X Y.Transcriptional regulatory mechanisms of PPARγ gene promoter of dairy goat[D].Yangling:Northwest A&F University, 2018.(in Chinese)
[29]	BIONAZ M, LOOR J J.ACSL1, AGPAT6, FABP3, LPIN1, and SLC27A6 are the most abundant isoforms in bovine mammary tissue and their expression is affected by stage of lactation[J].J Nutr, 2008, 138(6):1019-1024.
[30]	IBEAGHA-AWEMU E M, PETERS S O, AKWANJI K A, et al. High density genome wide genotyping-by-sequencing and association identifies common and low frequency SNPs, and novel candidate genes influencing cow milk traits[J].Sci Rep, 2016, 6:31109.
[31]	LIU L Y, ZHOU J H, CHEN C J, et al. GWAS-based identification of new loci for milk yield, fat, and protein in Holstein cattle[J].Animals, 2020, 10(11):2048.
[32]	BEDFORD M T, CLARKE S G.Protein arginine methylation in mammals:who, what, and why[J].Mol Cell, 2009, 33(1):1-13.
[33]	BLACKWELL E, CEMAN S.Arginine methylation of RNA-binding proteins regulates cell function and differentiation[J].Mol Reprod Dev, 2012, 79(3):163-175.
[34]	CHEN C, NOTT T J, JIN J, et al. Deciphering arginine methylation:tudor tells the tale[J].Nat Rev Mol Cell Biol, 2011, 12(10):629-642.
[35]	LEE Y H, STALLCUP M R.Minireview:protein arginine methylation of nonhistone proteins in transcriptional regulation[J].Mol Endocrinol, 2009, 23(4):425-433.
[36]	MOWEN K A, SCHURTER B T, FATHMAN J W, et al. Arginine methylation of NIP45 modulates cytokine gene expression in effector T lymphocytes[J]. Mol Cell, 2004, 15(4):559-571.
[37]	CHAN L H, ZHOU L, NG K Y, et al. PRMT6 regulates RAS/RAF binding and MEK/ERK-mediated cancer stemness activities in hepatocellular carcinoma through CRAF methylation[J].Cell Rep, 2018, 25(3):690-701.e8.
[38]	罗举.蛋白质精氨酸甲基转移酶与相关疾病[J].国际病理科学与临床杂志, 2011, 31(5):404-409.LUO J.Protein arginine methyltransferase and the related diseases[J].International Journal of Pathology and Clinical Medicine, 2011, 35(5):404-409.(in Chinese)
[39]	WU Z Z, LIU H F, SUN W L, et al. RNF180 mediates STAT3 activity by regulating the expression of RhoC via the proteasomal pathway in gastric cancer cells[J].Cell Death Dis, 2020, 11(10):881.
[40]	LIU L, ZHANG Q.Identification and functional analysis of candidate gene VPS28 for milk fat in bovine mammary epithelial cells[J].Biochem Biophys Res Commun, 2019, 510(4):606-613.