中国荷斯坦牛初产日龄遗传评估及全基因组关联分析

doi:10.11843/j.issn.0366-6964.2015.03.004

Abstract

Abstract:

Genome-wide association studies (GWAS) based on high throughput SNPs genotyping technology provided basis for exploring genes associated with fertility traits in Chinese Holsteins.Data of 19 111 heifers with calving records over a period of 10 years (2001-2011) were collected from Sanyuanlühe Dairy Cattle Breeding Center.Firstly，by AI-REML combined EM algorithm，DMU software (v 6.0) was used to estimate genetic parameters for age at first calving (AFC) based on animal model.Then GWAS was performed by the software PLINK (v 1.07) on the basis of the EBVs of calving traits of 2 172 Chinese Holstein heifers to identify genes affecting the fertility traits using the Illumina BovineSNPs50 BeadChip.The results showed that 1 700 SNPs was significantly associated with AFC at genome-wide level.Preliminarily，43 significant SNPs with P-valves smaller than 10^-15 were chosen to do the bioinformatics analyses.Among the 43 SNPs，12 were located on X chromosome，while some were within 1 Mb（20.42-21.52 Mb）on SSC7.In particular，the candidate genes of KLHL4，TRAM1，TRAM2，ZNF438 and MATK were related to some reproductive disturbances or diseases.The current study explored some novel SNPs as well as potential candidate genes associated with heifer calving traits，which can be used to unravel the genetic foundation of fertility traits in dairy cattle.

CLC Number:

S823.2

LIU Ao-xing， GUO Gang， WANG Ya-chun， GUO Xiang-yu， ZHANG Xu，LIU Lin，SHI Wan-hai， LI Xi-zhi，SU Guo-sheng，ZHANG Qin. Genetic Analysis and Genome Wide Association Studies for Age at first Calving in Chinese Holsteins[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2015, 46(3): 373-381.

0
/ / Recommend

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

URL: https://www.xmsyxb.com/EN/10.11843/j.issn.0366-6964.2015.03.004

https://www.xmsyxb.com/EN/Y2015/V46/I3/373

References

［1］OLSEN H G，HAYES B J，KENT M P，et al.A genome wide association study for QTL affecting direct and maternal effects of stillbirth and dystocia in cattle［J］.Anim Genet，2010，41(3)：273-280.
［2］BERRY D P，BASTIAANSEN J W M，VEERKAMP R F，et al.Genome-wide associations for fertility traits in Holstein-Friesian dairy cows using data from experimental research herds in four European countries［J］.Animal，2012，6(08)：1206-1215.
［3］KADRI N K，SAHANA G，CHARLIER C，et al.A 660-kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in nordic red cattle：Additional evidence for the common occurrence of balancing selection in livestock［J］.PLoS Genet，2014，10(1)：e1004049.
［4］WATHES D C，BRICKELL J S，BOURNE N E，et al.Factors influencing heifer survival and fertility on commercial dairy farms［J］.Animal，2008，2(8)：1135-1143.
［5］SEWALEM A，KISTEMAKER G J，MIGLIOR F.Relationship between female fertility and production traits in Canadian Holsteins［J］.J Dairy Sci，2010，93(9)：4427-4434.
［6］HUANG W，KIRKPATRICK B W，ROSA G J M，et al.A genome-wide association study using selective DNA pooling identifies candidate markers for fertility in Holstein cattle［J］.Anim Genet，2010，41(6)：570-578.
［7］WATHES D C，POLLOTT G E，JOHNSON K F，et al.Heifer fertility and carry over consequences for life time production in dairy and beef cattle［J］.Animal，2014，8(s1)：91-104.
［8］王晓，解小莉，王胜，等.中国荷斯坦牛乳房炎易感性及抗性的全基因组关联分析［J］.畜牧兽医学报，2013,44(12)：1907-1912.
WANG X，XIE X L，WANG S，et al.Genome-wide association study for mastitis susceptibility and resistance in Chinese Holsteins［J］.Acta Veterinaria et Zootechnica Sinica，2013,44(12)：1907-1912.（in Chinese）
［9］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.
［10］JIANG L，LIU J，SUN D，et al.Genome wide association studies for milk production traits in Chinese Holstein population［J］.PLoS ONE，2010，5(10)：e13661.
［11］SAHANA G，GULDBRANDTSEN B，BENDIXEN C，et al.Genome-wide association mapping for female fertility traits in Danish and Swedish Holstein cattle［J］.Anim Genet，2010，41(6)：579-588.
［12］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）
［13］PIRLO G，MIGLIOR F，SPERONI M.Effect of age at first calving on production traits and on difference between milk yield returns and rearing costs in Italian Holsteins［J］.J Dairy Sci，2000，83(3)：603-608.
［14］RUIZ-SÁNCHEZ R，BLAKE R W，CASTRO-GÁMEZ H M A，et al.Short communication：Changes in the association between milk yield and age at first calving in Holstein cows with herd environment level for milk yield［J］.J Dairy Sci，2007，90(10)：4830-4834.
［15］GHAVI HOSSEIN-ZADEH N.Estimation of genetic and phenotypic relationships between age at first calving and productive performance in Iranian Holsteins［J］.Tropical Anim Health Prod，2011，43(5)：967-973.
［16］郭翔羽，郭刚，李锡智，等.北京地区荷斯坦青年牛繁殖性状影响因素分析［J］.中国奶牛，2011，(24)：1-6.
GUO X Y，GUO G，LI X Z，et al.Analysis on the influence factors for reproductive traits of Holstein heifer in Beijing［J］.China Dairy Cattle，2011，(24)：1-6.（in Chinese）
［17］JAMROZIK J，FATEHI J，KISTEMAKER G J，et al.Estimates of genetic parameters for Canadian Holstein female reproduction traits［J］. J Dairy Sci，2005，88(6)：2199-2208.
［18］李钟淑，杨薇，吴昊，等.奶牛繁殖性状的育种值估计［J］.中国奶牛，2007，(9)：19-23.
LI Z S，YANG W，WU H，et al.Breeding value estimation of reproductive traits of dairy cattle［J］.J Dairy Sci，2007，(9)：19-23.（in Chinese）
［19］SAHANA G，GULDBRANDTSEN B，LUND M S.Genome-wide association study for calving traits in Danish and Swedish Holstein cattle［J］. J Dairy Sci，2011，94(1)：479-486.
［20］MINOZZI G，NICOLAZZI E L，STELLA A，et al.Genome wide analysis of fertility and production traits in Italian Holstein cattle［J］.PLoS ONE，2013，8(11)：e80219.
［21］PRYCE J E，BOLORMAA S，CHAMBERLAIN A J，et al.A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes［J］.J Dairy Sci，2010，93(7)：3331-3345.
［22］HÖGLUND J K，GULDBRANDTSEN B，SU G，et al.Genome scan detects quantitative trait loci affecting female fertility traits in Danish and Swedish Holstein cattle［J］.J Dairy Sci，2009，92(5)：2136-2143.
［23］FORTES M R S，DEATLEY K L，LEHNERT S A，et al.Genomic regions associated with fertility traits in male and female cattle：Advances from microsatellites to high-density chips and beyond［J］.Anim Reprod Sci，2013，141(1-2)：1-19.
［24］PEAGARICANO F，WEIGEL K A，KHATIB H.Genome-wide association study identifies candidate markers for bull fertility in Holstein dairy cattle［J］. Anim Genet，2012，43：65-71.
［25］LI C，SUN D，ZHANG S，et al.Genome wide association study identifies 20 novel promising genes associated with milk fatty acid traits in Chinese Holstein［J］.PLoS ONE，2014，9(5)：e96186.
［26］KOSOVA G，SCOTT N M，NIEDERBERGER C，et al.Genome-wide association study identifies candidate genes for male fertility traits in humans［J］.Am J Hum Genet，2012，90(6)：950-961.
［27］CHEROKI C，KREPISCHI-SANTOS A C，SZUHAI K，et al.Genomic imbalances associated with mullerian aplasia［J］.J Med Genet，2008，45(4)：228-232.
［28］ORESIC K，NG C L，TORTORELLA D.TRAM1 participates in human cytomegalovirus US2-and US11-mediated dislocation of an endoplasmic reticulum membrane glycoprotein［J］. J Biol Chem，2009，284(9)：5905-5914.
［29］NG C L，ORESIC K，TORTORELLA D.TRAM1 is involved in disposal of ER membrane degradation substrates［J］.Exp Cell Res，2010，316(13)：2113-2122.
［30］STEFANOVIC B，STEFANOVIC L，SCHNABL B，et al.TRAM2 protein interacts with endoplasmic reticulum Ca2+ pump Serca2b and is necessary for collagen type I synthesis［J］. Mol Cell Biol，2004，24(4)：1758-1768.
［31］ZHONG Z，WAN B，QIU Y，et al.Identification of a novel human zinc finger gene，ZNF438，with transcription inhibition activity［J］.J Biochem Mol Biol，2007，40(4)：517-524.
［32］ENAN M R，AHAMED A.DNA barcoding based on plastid matK and RNA polymerase for assessing the genetic identity of date (Phoenix dactylifera L.) cultivars［J］.Genet Mol Res，2014，13(2)：3527-3536.

[1]	MIAO Shu, AN Jishan, WANG Zuo, XIAO Dingfu, LAN Xinyi, LIU Lei, SHEN Weijun, WAN Fachun. Leucine Promotes the Proliferation of Bovine Myoblasts through PI3K-AKT Signaling Pathway [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 142-152.
[2]	NIU Yifan, YANG Baigao, ZHANG Peipei, ZHANG Hang, FENG Xiaoyi, CAO Jianhua, YU Zhou, HAO Haisheng, DU Weihua, ZOU Huiying, ZHU Huabin, MA Youji, ZHAO Xueming. Advances in Bovine Embryo Genome Selection [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4449-4457.
[3]	WANG Wenxiang, DU Lili, HU Junwei, ZHANG Yanxiang, MA Minghao, DUAN Rui, QIAN Cong, WANG Xinyue, LI Sanlu, ZHANG Changqing, ZHANG Lupei, GAO Xue, XU Lingyang, LI Junya, GAO Huijiang. Mining Candidate Genes Related to Meat Quality Traits of Longissimus Lumborum in Pingliang Red Steer Based on Transcriptome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4589-4604.
[4]	MA Haoran, ZHANG Lupei, JIN Shengyun, BAO Jinshan, LI Hongyan, GAO Huijiang, XU Lingyang, WANG Zezhao, LI Junya. Assessment of the Genomic Relationships for Chinese Indigenous Beef Cattle Using High-density SNP Chip [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4174-4185.
[5]	ZHANG Junxing, ZHANG Hailiang, HAN Liyun, MA Yanfen, WEN Wan, ZHOU Jiamin, TIAN Jia, LU Tingting, MA Yun, WANG Yachun. Analysis on the Influencing Factors of Wellness Traits in Holstein Lactating Cows in Ningxia [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2389-2401.
[6]	YANG Chuang, WU Longfei, LIU Guangbin, LI Yaokun, LIU Dewu, SUN Baoli. Expression Profile and Bioinformatics Analysis of lncRNA and Its Associated ceRNA Networks in Longissimus Dorsi from Lufeng Cattle and Leiqiong Cattle [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1951-1963.
[7]	GUO Mingpeng, MENG Yuan, WANG Honghao, WANG Yuan, CHE Leijie, SHEN Li, WANG Xi. Estimation of Genetic Parameters of Body Weight and Body Size Traits in Jinnan Cattle at Different Growth Stages [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1452-1464.
[8]	YU Shiqiang, LI Liuxue, ZHAO Xiaobo, ZHAO Huiying, TU Yan, ZHAO Yuchao, JIANG Linshu. Differences and Correlations of Lactation Performance in Chinese Holstein Dairy Cows at Different Lactation Stages and Somatic Levels [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1003-1014.
[9]	YANG Guang, XU Jing, LI Xin, HU Debao, GUO Yiwen, DING Xiangbin, GUO Hong, ZHANG Linlin. Effect of Interfering lncbMD on Proliferation and Differentiation of Bovine Skeletal Muscle Satellite Cells [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1015-1025.
[10]	MA Zhijie, WANG Shikang, ZHANG Weizhong, GUO Weixing, ZHAO Haiming, LEI Chuzhao. Y-chromosome Genomic Diversity and Paternal Origins of Qaidam Cattle and Mongolian Cattle [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1026-1033.
[11]	NIU Ruili, SONG Hanan, WU Yue, WANG Yunan, GAO Yefan, GUAN Weijun, ZONG Xianchun. Isolation, Culture and Biological Characteristics of Epidermal Stem Cells from Simmental Cattle [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(1): 168-177.
[12]	LI Hongwei, XU Lingyang, WANG Zezhao, CAI Wentao, ZHU Bo, CHEN Yan, GAO Xue, ZHANG Lupei, GAO Huijiang, LI Junya. Genome-wide Association Study of Slaughter Traits Based on Haplotype in Beef Cattle [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(12): 4232-4243.
[13]	CHANG Yao, SU Guosheng, LI Yanhua, LI Xiang, MA Zhu, WANG Yachun. Estimating Genetic Parameters for Body Weights using Pedigree and Genotype-pedigree based Approaches in Holstein Heifers [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(11): 3759-3768.
[14]	XU Jingyi, XU Haoqi, HU Lirong, ZHANG Fan, GAO Qing, LUO Hanpeng, ZHANG Hailiang, SHI Rui, LI Xiang, LIU Lin, GUO Gang, WANG Yachun. Association Analysis of MET Gene Single Nucleotide Polymorphism with Reproduction and Milk Production Traits in Chinese Holstein Cattle [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(11): 3769-3785.
[15]	WANG Chuanchuan, MU Tong, FENG Xiaofang, YU Baojun, ZHANG Juan, GU Yaling. Identification of Key Candidate Genes for Milk Fat Metabolism in Dairy Cows Based on Transcriptome Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(10): 3421-3433.

Genetic Analysis and Genome Wide Association Studies for Age at first Calving in Chinese Holsteins

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments