基于高通量测序技术的山羊遗传多样性及其生产性状研究进展

doi:10.16431/j.cnki.1671-7236.2017.10.019

Abstract

Abstract:

Recently, the widespread use of high-throughput sequencing technology and the development of bioinformatics have been greatly contributed to the development of farm animal genomics. Whole genome-wide analysis can facilitate the fine mapping of the molecular markers related to the production traits quickly and accurately, thus providing an important theoretical basis for genome selection breeding. Several thousand years of domestication and artificial selection produce many modern goat breeds with high production of milk, fiber, and meat, which become abundant production and living materials for human populations. Researchers have studied the genetic diversity and molecular mechanisms of production traits in goats using high-throughput sequencing technology, in order to identify candidate genes related to the excellent germplasm reliable markers for genetic improvement. In this review, we summarized the five-year research progress on the genetic diversity and production traits of goats including fiber, milk production and reproduction traits, mainly based on high-throughput sequencing technology. This paper provides a reference for the evaluation of the excellent goat genetic resources and the investigation of production trait related genes.

Key words: goat; production traits; genomics; transcriptome

CLC Number:

S813.3

SONG Shen, YANG Min, JIANG Lin, MA Yue-hui. Research Progress on Goat Genetic Diversity and Production Traits Based on High-throughput Sequencing Technology[J]. , 2017, 44(10): 2965-2972.

References

[1] International Chicken Genome Sequencing, Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution[J]. Nature, 2004, 432(7018):695-716.
[2] Bovine Genome Sequencing and Analysis Consortium, Elsik C G, Tellam R L, et al. The genome sequence of taurine cattle:A window to ruminant biology and evolution[J]. Science, 2009, 324(5926):522-528.
[3] Groenen M A, Archibald A L, Uenishi H, et al. Analyses of pig genomes provide insight into porcine demography and evolution[J]. Nature, 2012, 491(7424):393-398.
[4] Dong Y, Xie M, Jiang Y, et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)[J]. Nat Biotechnol, 2013, 31(2):135-141.
[5] Jiang Y, Xie M, Chen W, et al. The sheep genome illuminates biology of the rumen and lipid metabolism[J]. Science, 2014, 344(6188):1168-1173.
[6] Qiu Q, Zhang G, Ma T, et al. The yak genome and adaptation to life at high altitude[J]. Nat Genet, 2012, 44(8):946-949.
[7] Huang Y, Li Y, Burt D W, et al. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species[J]. Nat Genet, 2013, 45(7):776-783.
[8] Lu L, Chen Y, Wang Z, et al. The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver[J]. Genome Biol, 2015, 16:89.
[9] Tosser-Klopp G, Bardou P, Bouchez O, et al. Design and characterization of a 52K SNP chip for goats[J]. PLoS One, 2014, 9(1):e86227.
[10] Dong Y, Zhang X, Xie M, et al. Reference genome of wild goat (Capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication[J]. BMC Genomics, 2015, 16:431.
[11] Bickhart D M, Rosen B D, Koren S, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome[J]. Nat Genet, 2017, 49(4):643-650.
[12] Groeneveld L F, Lenstra J A, Eding H, et al. Genetic diversity in farm animals:A review[J]. Anim Genet, 2010, 41(Suppl 1):6-31.
[13] Lashmar S F, Visser C, Marle-Koster E. Validation of the 50K Illumina goat SNP chip in the South African Angora goat[J]. South African Journal Animal Science, 2015, 45(1):56-59.
[14] Mdladla K, Dzomba E F, Huson H J, et al. Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data[J]. Anim Genet, 2016, 47(4):471-482.
[15] Lashmar S F, Visser C,Marle-Koster E. SNP-based genetic diversity of South African commercial dairy and fiber goat breeds[J]. Small Ruminant Res, 2016, 136:65-71.
[16] Manunza A, Noce A, Serradilla J M, et al. A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds[J]. Genet Sel Evol, 2016, 48(1):52.
[17] Nicoloso L, Bomba L, Colli L, et al. Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip[J]. Genet Sel Evol, 2015, 47:62.
[18] Kim E S, Elbeltagy A R, Aboul-Naga A M, et al. Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment[J]. Heredity (Edinb), 2016, 116(3):255-264.
[19] Visser C, Lashmar S F, Van Marle-Koster E, et al. Genetic diversity and population structure in South African, French and Argentinian Angora goats from genome-wide SNP data[J]. PLoS One, 2016, 11(5):e0154353.
[20] Burren A, Neuditschko M, Signer-Hasler H, et al. Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds[J]. Anim Genet, 2016, 47(6):727-739.
[21] Kijas J W, Ortiz J S, McCulloch R, et al. Genetic diversity and investigation of polledness in divergent goat populations using 52088 SNPs[J]. Anim Genet, 2013, 44(3):325-335.
[22] Benjelloun B, Alberto F J, Streeter I, et al. Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data[J]. Front Genet, 2015, 6:107.
[23] Allain D, Roguet J M. Genetic and nongenetic factors influencing mohair production traits within the national selection scheme of Angora goats in France[J]. Livest Prod Sci, 2003, 82(2-3):129-137.
[24] Pereira F, Queiros S, Gusmao L, et al. Tracing the history of goat pastoralism:New clues from mitochondrial and Y chromosome DNA in North Africa[J]. Mol Biol Evol, 2009, 26(12):2765-2773.
[25] Liu H L, Wang T T, Wang J K, et al. Characterization of Liaoning cashmere goat transcriptome:Sequencing, de novo assembly, functional annotation and comparative analysis[J]. PLoS One, 2013, 8(10):e77062.
[26] Gao Y, Wang X, Yan H, et al. Comparative transcriptome analysis of fetal skin reveals key genes related to hair follicle morphogenesis in cashmere goats[J]. PLoS One, 2016, 11(3):e0151118.
[27] Welle M M,Wiener D J. The hair follicle:A comparative review of canine hair follicle anatomy and physiology[J]. Toxicol Pathol, 2016, 44(4):564-574.
[28] Zhu B, Xu T, Zhang Z P, et al. Transcriptome sequencing reveals differences between anagen and telogen secondary hair follicle-derived dermal papilla cells of the cashmere goat (Capra hircus)[J]. Physiol Genomics, 2014, 46(3):104-111.
[29] Fan Y X, Wu R B, Qiao X, et al. Hair follicle transcriptome profiles during the transition from anagen to catagen in Cashmere goat (Capra hircus)[J]. Genet Mol Res, 2015, 14(4):17904-17915.
[30] Geng R Q, Yuan C,Chen Y L. Exploring differentially expressed genes by RNA-Seq in cashmere goat (Capra hircus) skin during hair follicle development and cycling[J]. PLoS One, 2013, 8(4):462704.
[31] Yuan C, Wang X, Geng R, et al. Discovery of cashmere goat (Capra hircus) microRNAs in skin and hair follicles by Solexa sequencing[J]. Bmc Genomics, 2013, 14:511.
[32] Bai W L, Dang Y L, Yin R H, et al. Differential expression of microRNAs and their regulatory networks in skin tissue of Liaoning cashmere goat during hair follicle cycles[J]. Anim Biotechnol, 2016, 27(2):104-112.
[33] Liu Z, Xiao H, Li H, et al. Identification of conserved and novel microRNAs in cashmere goat skin by deep sequencing[J]. PLoS One, 2012, 7(12):e50001.
[34] Guo H, Cheng G, Li Y, et al. A screen for key genes and pathways involved in high-quality brush hair in the Yangtze River Delta White goat[J].PLoS One, 2017, 12(1):e0169820.
[35] Salama A A K, Badaoui B, Hamzaoui S, et al.RNA-sequencing analysis of milk somatic cells in heat-stressed dairy goats[A]. Adsa-Asas Joint Meeting[C]. 2015.
[36] Crisa A, Ferre F, Chillemi G, et al. RNA-sequencing for profiling goat milk transcriptome in colostrum and mature milk[J]. BMC Vet Res, 2016, 12(1):264.
[37] Ji Z, Wang G, Xie Z, et al. Identification and characterization of microRNA in the dairy goat (Capra hircus) mammary gland by Solexa deep-sequencing technology[J]. Mol Biol Rep, 2012, 39(10):9361-9371.
[38] Mobuchon L, Marthey S, Boussaha M, et al. Annotation of the goat genome using next generation sequencing of microRNA expressed by the lactating mammary gland:Comparison of three approaches[J]. Bmc Genomics, 2015, 16:285.
[39] Lin X Z, Luo J, Zhang L P, et al. miR-27a suppresses triglyceride accumulation and affects gene mRNA expression associated with fat metabolism in dairy goat mammary gland epithelial cells[J]. Gene, 2013, 521(1):15-23.
[40] Chen Z, Luo J, Sun S, et al. miR-148a and miR-17-5p synergistically regulate milk TAG synthesis via PPARGC1A and PPARA in goat mammary epithelial cells[J]. RNA Biol, 2017, 14(3):326-338.
[41] Wang H, Luo J, Chen Z, et al. microRNA-24 can control triacylglycerol synthesis in goat mammary epithelial cells by targeting the fatty acid synthase gene[J]. J Dairy Sci, 2015, 98(12):9001-9014.
[42] Shi H, Zhao W, Zhang C, et al. Transcriptome-wide analysis reveals the role of PPARgamma controlling the lipid metabolism in goat mammary epithelial cells[J]. Ppar Res, 2016, 2016:9195680.
[43] Miao X Y, Luo J, Sun S, et al. Genome-wide transcriptome analysis in the ovaries of two goats identifies differentially expreesed genes related to fecundity[J]. Gene, 2016, 582(1):69-76.
[44] Miao X Y, Luo Q, Zhao H, et al. Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu Black goats to explore the regulation of fecundity[J]. Sci Rep, 2016, 6:37983.
[45] Longpre K M, Kinstlinger N S, Mead E A, et al. Seasonal variation of urinary microRNA expression in male goats (Capra hircus) as assessed by next generation sequencing[J]. Gen Comp Endocrinol, 2014, 199(4):1-15.
[46] Gao X, Ye J, Yang C, et al. Screening and evaluating of long noncoding RNAs in the puberty of goats[J]. Bmc Genomics, 2017, 18(1):164.
[47] Wu J, Zhu H, Song W, et al. Identification of conservative microRNAs in Saanen dairy goat testis through deep sequencing[J]. Reprod Domest Anim, 2014, 49(1):32-40.
[48] Lai F N, Zhai H L, Cheng M, et al. Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus)[J]. Sci Rep, 2016, 6:38096.
[49] Ling Y H, Chen C H, Guo X F, et al. Identification and characterization of microRNAs in th eovaries of multiple and uniparous goat (Capra hircus) during folliclar phase[J]. Bmc Genomics, 2014, 15:339.
[50] Wang L J, Sun X W, Guo F Y, et al. Transcriptome analysis of the uniparous and multiparous goats ovaries[J]. Reprod Domest Anim, 2016, 51(6):877-885.
[51] Guan D, Luo N, Tan X, et al. Scanning of selection signature provides a glimpse into important economic traits in goats (Capra hircus)[J]. Sci Rep, 2016, 6:36372.
[52] Martin P M, Palhiere I, Ricard A, et al. Genome wide association study identifies new loci associated with undesired coat color phenotypes in Saanen goats[J]. PLoS One, 2016, 11(3):e0152426.
[53] Menzi F, Keller I, Reber I, et al. Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation[J]. Sci Rep, 2016, 6:28438.
[54] Becker D, Otto M, Ammann P, et al. The brown coat colour of Coppernecked goats is associated with a non-synonymous variant at the TYRP1 locus on chromosome 8[J]. Anim Genet, 2015, 46(1):50-54.
[55] Wang X, Liu J, Zhou G, et al. Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits[J]. Sci Rep, 2016, 6:38932.
[56] Ren H, Wang G, Jiang J, et al. Comparative transcriptome analysis by deep RNA sequencing at early stage of skin pigmentation in goats (Capra hircus)[Z]. BioRxiv, 2016.
[57] Ren H, Wang G, Chen L, et al. Genome-wide analysis of long non-coding RNAs at early stage of skin pigmentation in goats (Capra hircus)[J]. BMC Genomics, 2016, 17:67.

Research Progress on Goat Genetic Diversity and Production Traits Based on High-throughput Sequencing Technology

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	CHEN Kaiwen, ZHAO Yunjiao, WANG Lei, ZHANG Jianbo, MA Yuhong, WU Guofang. Transcriptome Analysis of Porcine Leydig Cells Under Different Oxygen Concentrations [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2185-2195.
[2]	SHI Jingu, HUANG Shanshan, HUANG Jiwei, CHEN Kunhai, HU Dasheng, ZHU Zhixiong, HAN Shuyu. Comparative Transcriptome Analysis of Streptococcus agalactiae from Tilapia Under High Temperature Stress [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2207-2216.
[3]	LYU Chunrong, LIANG Jiachong, SHAO Qingyong, WU Guoquan, ZHANG Yumei, QUAN Guobo. Effects of Sodium Pyruvate on the Quality of Frozen Goat Sperm [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2363-2369.
[4]	WANG Leping, PAN Yan, TAN Yizhou, LI Lei, HAN Kaiou, CAO Yajie, LI Jun, ZHOU Yuqing, LIAO Yuying, MA Dongxin, GONG Yu, PENG Hao, WANG Xiaoye. Isolation,Identification and Genome Analysis of Escherichia coli Phage vB_EcoP_GN07 [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1522-1531.
[5]	SONG Xingchao, MENG Jinzhu, ZHAO Yuanyuan, WU Zhenyang, AN Qingming. Cloning and Bioinformatics Analysis of MyoG Gene Promoter Region Sequence in Guizhou White Goat [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 893-903.
[6]	Sachula, WU Tiecheng, MA Yuejun, HE Yunmei, ZHU Lixian, HE Tuoya, WU Yuping, LIU Bin. Polymorphisms of Four Polyembryony Related Genes and Its Association Analysis with Litter Size in Cashmere Goats [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 1037-1047.
[7]	WEI Yirong, ZHENG Zihua, ZHANG Sanbao, SONG Ying, JIANG Haiyu, SUN Wenyue, CHENG Pengfei, LIU Yufan, ZOU Jianwei, HUANG Yanna, PAN Yan, JIANG Qinyang. Cloning,Bioinformatics Analysis and Tissue Expression of UCP1 Gene in Nubian Goats [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(2): 440-450.
[8]	QIN Zhiyun, JIANG Huaizhi. An Overview of Research on Skin Hair Follicle Development and Regulatory Mechanism in Sheep During the Fetal Period [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(2): 638-646.
[9]	DAN Yixin, XIANG Hua, ZHANG Huanrong, YANG Lu, REN Yupeng, XU Songwei, HE Honghong, ZHU Jiangjiang. Screening of Host Proteins Interacting with ORFV129 Protein and Cloning and Analysis of C1QBP Gene [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(1): 1-14.
[10]	PAN Siyao, ZHANG Dandan, LIU Quanhui, WANG Guodong, LYU Danwei, HUANG Ben. Effects of Inhibition of miR-142-3p on Lactation Function of Chemical Induced Mammary Epithelial Cells in Dairy Goats [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(1): 58-66.
[11]	LIU Zelin, YANG Juan, XU Mingzhu, ZHANG Nian, XIONG Qi, LIU Jingbo, TAO Hu. Association Analysis Between Polymorphisms of ZBP1 Gene and Lambing Performance in Goats [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(1): 161-173.
[12]	LONG Anju, YANG Suan, AI Jinxin, WENG Jimei, ZHANG Yiyu, CAI Huifen, LUO Weixing. Polymorphism of MC4R Gene and Its Association with Growth Traits in Qianbei Ma Goats [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(1): 198-209.
[13]	WANG Guang, ZOU Jiahao, ZHANG Yongtao, LI Dexian, LI Xueqing, YU Mengqi, CHEN Lu, YUAN Yuxin, LI Guang. Difference Analysis of Metabolites in Testis of Guanzhong Dairy Goats at Different Developmental Stages [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3453-3464.
[14]	FENG Xiaopin, LI Yinxia, ZHANG Chenjian, ZHANG Jun, MENG Chunhua, QIAN Yong, CAO Shaoxian. Coning and Polymorphism Identification of PLAG1 Gene and Its Association Analysis with Birth Weight and Body Size Traits in Boer Goats [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3465-3474.
[15]	TANG Jingyu, DU Hanyu, MENG Chunchun, LIU Guangqing. Cloning,Bioinformatics Analysis and Subcellular Localization of Interferon-stimulated Gene 15 in Goats [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2843-2854.