利用简化基因组测序筛选安格斯牛生长相关的受选择基因

doi:10.11843/j.issn.0366-6964.2020.04.007

Abstract

Abstract: The aims of this study were to investigate the growth-related genes under selection in Angus cattle and provide a reference for identification of major genes for beef cattle growth. Blood samples of 72 Nanyang cows and 14 Black Angus cows were collected and used to isolate genomic DNA. The genome-wide SNP markers and genotypes of individuals were obtained by using SLAF-seq technology. Fst and π ratio values of each SNP were calculated for selecting the different genomic regions between the two breeds. Afterward, these identified regions were compared with the cattle growth QTLs in animal QTLdb. The overlapping regions were considered as candidate regions for further analysis. Genes within the overlapping regions were screened as candidate genes based on the gene annotation. Tissue expression status of candidate genes were checked in the "Expression Atlas" database. After filtering, 69 762 SNPs were remained for the further analysis. Using the 99% quantiles of Fst and π ratio values as thresholds, 33 genomic regions with high differences between the two breeds were screened. Among them, there were 16 genomic regions overlapped with the cattle growth QTLs. Within the 16 regions, 27 genes were located, among them, 4 genes (FXR1, ADAR, IGF1, MNF1) were related to bone/muscle development and growth regulation. FXR1 and MNF1 genes were highly expressed in the skeletal muscle. ADAR and IGF1 genes were highly expressed in the brain and liver, respectively. IGF1 gene can be considered as a major candidate gene for beef cattle growth, FXR1, ADAR and MNF1 genes are prioritized as potential candidate genes for further verification.

Key words: Nanyang cattle, growth trait, candidate gene, selective sweep, Fst

CLC Number:

S823.2

Lü Shijie, CHEN Fuying, JIN Lei, ZHANG Zijing, ZHU Xiaoting, SHI Qiaoting, XIN Xiaoling, CHU Qiuxia, BAI Zhonglin, WANG Eryao, XU Zhaoxue. Identification of Growth-Related Genes under Selection in Angus Cattle Using SLAF-seq[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(4): 713-721.

References 41

[1]	魏成斌,张彬,施巧婷,等.南阳牛种质资源个性描述[J].河南农业科学,2013,42(9):124-127.WEI C B,ZHANG B,SHI Q T,et al.Characteristics describing of Nanyang cattle genetic resource[J].Journal of Henan Agricultural Sciences,2013,42(9):124-127.(in Chinese)
[2]	滑留帅,陈付英,王璟,等.南阳牛基础母牛生长和繁殖规律研究[J].中国牛业科学,2017,43(4):7-11.HUA L S,CHEN F Y,WANG J,et al.Study on the growth and reproduction traits in Nanyang cows[J].China Cattle Science,2017,43(4):7-11.(in Chinese)
[3]	梅楚刚,王炜康,昝林森.安格斯牛生长发育规律、行为学特征及理化指标分析[J].家畜生态学报,2018,39(11):38-43.MEI C G,WANG W K,ZAN L S.The growth development patterns,behavior characteristics,and physiochemical indexes of Angus beef cattle[J].Journal of Domestic Animal Ecology,2018,39(11):38-43.(in Chinese)
[4]	STEPHAN W.Selective sweeps[J].Genetics,2019,211(1):5-13.
[5]	XU L Y,BICKHART D M,COLE J B,et al.Genomic signatures reveal new evidences for selection of important traits in domestic cattle[J].Mol Biol Evol,2015,32(3):711-725.
[6]	KEMPER K E,SAXTON S J,BOLORMAA S,et al.Selection for complex traits leaves little or no classic signatures of selection[J].BMC Genomics,2014,15:246.
[7]	ZHAO F P,MCPARLAND S,KEARNEY F,et al.Detection of selection signatures in dairy and beef cattle using high-density genomic information[J].Genet Sel Evol,2015,47:49.
[8]	张统雨,樊红樱,朱才业,等.利用可变窗口FST方法检测不同尾型呼伦贝尔羊尾部脂肪沉积相关基因[J].畜牧兽医学报, 2018,49(7):1354-1365.ZHANG T Y,FAN H Y,ZHU C Y,et al.Identification of candidate genes involved in fat deposition in Hulun Buir Sheep tails using FST within the variable window sizes[J].Acta Veterinaria et Zootechnica Sinica,2018,49(7):1354-1365.(in Chinese)
[9]	滑留帅,辛晓玲,王璟,等.利用混池重测序鉴定萨福克绵羊超数排卵关键调控基因[J].畜牧兽医学报, 2019,50(9):1813-1821.HUA L S,XIN X L,WANG J,et al.Identification of key regulatory genes for superovulation in Suffolk sheep by pool resequencing[J].Acta Veterinaria et Zootechnica Sinica,2019,50(9):1813-1821.(in Chinese)
[10]	刘嫣然,吴森,王晓宇,等.秦川肉牛FGF2基因多态性与其生长和肉质性状的关联分析[J].西北农林科技大学学报:自然科学版,2017,45(6):16-22,29.LIU Y R,WU S,WANG X Y,et al.Association of FGF2 gene polymorphism with growth and meat quality traits of Qinchuan beef cattle[J].Journal of Northwest A&F University:Natural Science Edition,2017,45(6):16-22,29.(in Chinese)
[11]	CHANG T,XIA J,XU L,et al.A genome-wide association study suggests several novel candidate genes for carcass traits in Chinese Simmental beef cattle[J].Anim Genet,2018,49(4):312-316.
[12]	HU Z L,PARK C A,REECY J M.Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB[J].Nucleic Acids Res,2019,47(D1):D701-D710.
[13]	徐怀超,昝林森,王洪宝,等.CRTC3基因多态性及基因型组合与秦川牛生长性状的关联分析[J].畜牧兽医学报, 2016,47(11):2184-2190.XU H C,ZAN L S,WANG H B,et al.Association of CRTC3 gene polymorphisms and genotype combination with growth traits of Qinchuan cattle[J].Acta Veterinaria et Zootechnica Sinica,2016,47(11):2184-2190.(in Chinese)
[14]	ZHUANG Z W,XU L Y,YANG J,et al.Weighted single-step genome-wide association study for growth traits in Chinese Simmental beef cattle[J].Genes,2020,11(2):189.
[15]	SMITH J L,WILSON M L,NILSON S M,et al.Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle[J].BMC Genomics,2019,20(1):926.
[16]	SUN X W,LIU D Y,ZHANG X F,et al.SLAF-seq:an efficient method of large-scale De novo SNP discovery and genotyping using high-throughput sequencing[J].PLoS One,2013,8(3):e58700.
[17]	WANG W H,WANG J Y,ZHANG T,et al.Genome-wide association study of growth traits in Jinghai Yellow chicken hens using SLAF-seq technology[J].Anim Genet,2019,50(2):175-176.
[18]	XIE D W,DAI Z G,YANG Z M,et al.Genome-wide association study identifying candidate genes influencing important agronomic traits of Flax (Linum usitatissimum L.) using SLAF-seq[J].Front Plant Sci,2018,8:2232.
[19]	陈付英,牛晖,施巧婷,等.郏县红牛生长发育性状全基因组关联分析[J].中国牛业科学,2018,44(5):24-28.CHEN F Y,NIU H,SHI Q T,et al.Genome-wide association analysis on growth traits of Jiaxian Red cattle[J].China Cattle Science,2018,44(5):24-28.(in Chinese)
[20]	吕世杰,陈付英,张子敬,等.南阳牛生长性状相关基因组区域全基因组关联分析[J].中国畜牧兽医,2020,47(1):74-82.LYU S J,CHEN F Y,ZHANG Z J,et al.Genomic regions associated with growth traits in Nanyang cattle using genome-wide association analysis[J].China Animal Husbandry & Veterinary Medicine,2020,47(1):74-82.(in Chinese)
[21]	KIM J,HANOTTE O,MWAI O A,et al.The genome landscape of indigenous African cattle[J].Genome Biol,2017,18(1):34.
[22]	ZHANG X G,ZHANG J H,HE X Y,et al.Genome-wide association study of major agronomic traits related to domestication in peanut[J].Front Plant Sci,2017,8:1611.
[23]	QIN M,LI C H,LI Z X,et al.Genetic diversities and differentially selected regions between Shandong indigenous pig breeds and western pig breeds[J].Front Genet,2020,10:1351.
[24]	R Core Team.R:a language and environment for statistical computing[R].Vienna,Austria:R Foundation for Statistical Computing,2018.
[25]	PFEIFER B,WITTELSBVRGER U,RAMOS-ONSINS S E,et al.PopGenome:an efficient Swiss army knife for population genomic analyses in R[J].Mol Biol Evol,2014,31(7):1929-1936.
[26]	DURINCK S,SPELLMAN P T,BIRNEY E,et al.Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt[J].Nat Protoc,2009,4(8):1184-1191.
[27]	HUANG D W,SHERMAN B T,LEMPICKI R A.Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources[J].Nat Protoc,2009,4(1):44-57.
[28]	HUANG D W,SHERMAN B T,LEMPICKI R A.Bioinformatics enrichment tools:paths toward the comprehensive functional analysis of large gene lists[J].Nucleic Acids Res,2009,37(1):1-13.
[29]	PAPATHEODOROU I,FONSECA N A,KEAYS M,et al.Expression Atlas:gene and protein expression across multiple studies and organisms[J].Nucleic Acids Res,2018,46(D1):D246-D251.
[30]	PETRYSZAK R,KEAYS M,TANG Y A,et al.Expression Atlas update-an integrated database of gene and protein expression in humans,animals and plants[J].Nucleic Acids Res,2016,44(D1):D746-D752.
[31]	MIENTJES E J,WILLEMSEN R,KIRKPATRICK L L,et al.Fxr1 knockout mice show a striated muscle phenotype:implications for Fxr1p function in vivo[J].Hum Mol Genet,2004,13(13):1291-1302.
[32]	PADJE S V,CHAUDHRY B,SEVERIJNEN L A,et al.Reduction in fragile X related 1 protein causes cardiomyopathy and muscular dystrophy in zebrafish[J].J Exp Biol,2009,212(16):2564-2570.
[33]	CAMBIER L,RASSAM P,CHABI B,et al.M19 modulates skeletal muscle differentiation and insulin secretion in pancreatic β-cells through modulation of respiratory Chain activity[J].PLoS One,2012,7(2):e31815.
[34]	LIU X,WANG L G,LIANG J,et al.Genome-Wide Association Study for certain carcass traits and organ weights in a Large White×Minzhu intercross porcine population[J].J Integr Agric,2014,13(12):2721-2730.
[35]	SAVVA Y A,RIEDER L E,REENAN R A.The ADAR protein family[J].Genome Biol,2012,13(12):252.
[36]	张跃博,欧阳峰正,王立刚,等.猪ADAR1基因cDNA全长克隆、序列信息及组织表达分析[J].畜牧兽医学报,2019,50(6):1135-1144.ZHANG Y B,OUYANG F Z,WANG L G,et al.The full-length cloning,sequence information and expression analysis of porcine ADAR1 gene[J].Acta Veterinaria et Zootechnica Sinica,2019,50(6):1135-1144.(in Chinese)
[37]	GUI L S,WANG Z Y,JIA J L,et al.IGF-1 gene polymorphisms influence bovine growth traits in Chinese Qinchuan Cattle[J].Kafkas Univ Vet Fak Derg,2018,24(3):387-392.
[38]	REYNA X F,MONTOYA H M,CASTRELLÓN V V,et al.Polymorphisms in the IGF1 gene and their effect on growth traits in Mexican beef cattle[J].Genet Mol Res,2010,9(2):875-883.
[39]	ROGBERG-MUÑOZ A,CANTET R J C,FER-NÁNDEZ M E,et al.Longitudinal analysis of the effects of IGF1-SnaBI genotypes on the growth curve of Angus bull calves[J].Livest Sci,2013,154(1-3):55-59.
[40]	牛召珊,董雅娟,宋少康,等.IGF-1基因在牛育种上的应用及展望[C]//中国畜牧兽医学会动物繁殖学分会第十五届学术研讨会论文集.天津:中国畜牧兽医学会,2010:299-306.NIU Z S,DONG Y J,SONG S K,et al.Application and prospect of IGF-1 gene in cattle breeding[C]//Proceedings of the 15th Session of Animal Reproduction Branch of Chinese Association of Animal Husbandry and Veterinary Medicine. Tianjin:Chinese Society of Animal Husbandry and Veterinary Medicine,2010:299-306.(in Chinese)
[41]	CHEN N B,CAI Y D,CHEN Q M,et al.Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia[J].Nat Commun,2018,9(1):2337.

Identification of Growth-Related Genes under Selection in Angus Cattle Using SLAF-seq

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References 41

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	KANG Jiawei, HUANG Xuankai, WANG Zhipeng, ZHANG Aizhen, MENG Fangrong, GAI Peng, BAO Junfu, SUN Kexin, SONG Shaokang, SUN Pan, CHEN Yichuan, ZHANG Lei, GAO Shengyue, CHANG Minghang. Estimation of Genetic Parameters for Growth, Reproduction, and Body Measurements Traits in Large White Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 1936-1944.
[2]	LEI Yanru, HU Xiaoyu, XU Chunhong, ZHANG Chenxi, DU Wenping, WANG Yangguang, LI Donghua, SUN Guirong, LI Wenting, KANG Xiangtao. Comparative Analysis of Growth, Carcass and Meat Quality Traits of Five Hybrid Combinations of Houdan Chicken [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1521-1535.
[3]	TANG Xinxin, ZHENG Jumei, LUO Na, YING Fan, ZHU Dan, LI Sen, LIU Dawei, AN Bingxing, WEN Jie, ZHAO Guiping, LI Hegang. Genetic Mechanism of Broiler Leg Disease Based on Genome-Wide Association Analysis [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 99-109.
[4]	WANG Zhenyu, ZHANG Saibo, LIU Wenhui, LIANG Dong, REN Xiaoli, YAN Lei, YAN Yuefei, GAO Tengyun, ZHANG Zhen, HUANG Hetian. Genomic Inbreeding Coefficient Analysis and Functional Gene Screening in Different Dairy Farms Based on SNP Chip Data [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2848-2857.
[5]	ZHANG Xiaoke, LIAO Weili, CHEN Xinyou, LI Tingting, YUAN Xiaolong, LI Jiaqi, HUANG Xiang, ZHANG Hao. Genome-wide Association Study for Identifying Candidate Genes of Growth Traits in Duroc Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1868-1876.
[6]	BI Yazhen, SHANG Mingyu, HU Wenping, ZHANG Li. Correlation and Regression Analysis among Growth Traits and Association Analysis of TRHDE Gene Polymorphism with Growth Traits in Sheep [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1415-1428.
[7]	LI Dengpan, MA Keyan, HAN Jintao, BAI Yaqin, LI Taotao, MA Youji. Detection and Analysis of Whole Genome Selection Signal of Yongdeng Qishan Sheep [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4577-4588.
[8]	ZHANG Changzheng, LI Desen, HUANG Min, FANG Xiaomin, ZHAO Weimin, REN Shouwen, DONG Huansheng, REN Jun, ZHOU Lisheng. An Imputed Whole-genome Sequence-based GWAS Approach Pinpoints Genetic Loci for Body Conformation at Birth and Teat Number Traits in Sushan Pig Population [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(1): 88-102.
[9]	MA Lixia, CAO Guowei, ZHU Hongfang, DENG Zhanzhao, CAI Zhengyun, ZHOU Chenghao, HAN Wei, GU Yaling, ZHANG Juan. Analysis of Genetic Variation in a Conserved Population of Jingyuan Chickens Based on RAD-seq [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(7): 2104-2117.
[10]	TAO Wei, HOU Liming, WANG Binbin, LIU Hang, LI Kaijun, YIN Yanzhen, GUO Hao, NIU Peipei, ZHANG Zongping, LI Qiang, HUANG Ruihua, LI Pinghua. Identification of Candidate Genes Affecting Drip Loss in Pork by Genome-wide Selection Signal Method [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(5): 1373-1383.
[11]	TANG Lin, WEI Dawei, WANG Shuzhe, LEI Zhaoxiong, GAO Xiaoqian, WANG Xingping, MA Yanfen, MA Yun. Transcriptional Regulation Analysis of Bovine ADIG Gene Promoter [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(3): 722-730.
[12]	LU Yujie, MO Jiayuan, QI Wenjing, ZHU Siran, YANG Lili, LIU Qiaoling, BU Yage, LAN Ganqiu, LIANG Jing. Population Genetic Structure and Selection Signatures Associated with Litter Size Trait in Several Chinese Indigenous Pig Breeds [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(2): 360-369.
[13]	LEI Zhihui, ZHANG Liping, ZHAO Hongchang, ZHU Shaohua, LU Zengkui, GUO Tingting, SUN Weibo, HE Xue, YUE Yaojing. Genome-wide Selection Signals Reveal Candidate Genes Associated with the Sheep of Hair Follicle Development and Depilation Traits [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(2): 381-390.
[14]	HE Jieyu, WANG Binhu, LIAO Zhu, XIE Hongtao, YI Guoqiang, LIU Yuwen, AO Hong, TANG Zhonglin. Estimation of Genetic Parameters of Main Growth Traits in Landrace and Large White Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(8): 2115-2123.
[15]	LI Kaijun, HOU Liming, PU Guang, LIU Hang, LIU Gensheng, SHI Chuanzong, JIN Tong, ZHOU Juan, LI Pinghua, HUANG Ruihua. Identification of Candidate Gene Loci Related to Apparent NDF Digestibility of Suhuai Pigs Based on Genome-wide Fst and nSL Analyses [J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(7): 1809-1819.