Biotechnology Bulletin ›› 2020, Vol. 36 ›› Issue (4): 175-184.doi: 10.13560/j.cnki.biotech.bull.1985.2019-0691
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LI Xiao-kai1, FAN Yi-xing1, QIAO Xian1, ZHANG Lei1, WANG Feng-hong1, WANG Zhi-ying1, WANG Rui-jun1,2,3, ZHANG Yan-jun1,2,3, LIU Zhi-hong1,2,3, WANG Zhi-xin1, HE Li-bing4, LI Jin-quan1,2,3, SU Rui1,2,3, ZHANG Jia-xin1
Received:
2019-08-02
Online:
2020-04-26
Published:
2020-04-30
LI Xiao-kai, FAN Yi-xing, QIAO Xian, ZHANG Lei, WANG Feng-hong, WANG Zhi-ying, WANG Rui-jun, ZHANG Yan-jun, LIU Zhi-hong, WANG Zhi-xin, HE Li-bing, LI Jin-quan, SU Rui, ZHANG Jia-xin. Research Progress of Goat Genome and Genetic Variation Map[J]. Biotechnology Bulletin, 2020, 36(4): 175-184.
[1] Zeder MA, Hesse B.The initial domestication of goats(Capra hircus)in the Zagros mountains 10, 000 years ago[J]. Science, 2000, 287(5461):2254-2257. [2] Daly KG, Maisano Delser P, Mullin VE, et al.Ancient goat genomes reveal mosaic domestication in the Fertile Crescent[J]. Science, 2018, 361(6397):85-88. [3] Devendra C.Dynamics of goat meat production in extensive systems in Asia:improvement of productivity and transformation of livelihoods[J]. Agrotechnology, 2015, 106(2):275-277. [4] Bertolini F, Servin B, Talenti A, et al.Signatures of selection and environmental adaptation across the goat genome post-domestication[J]. Genetics, Selection, Evolution, 2018, 50(1):421-444. [5] Boettcher PJ, Hoffmann I, Baumung R, et al.Genetic resources and genomics for adaptation of livestock to climate change[J]. Frontiers in Genetics, 2015, 5(461):107-109. [6] Bett RC, S Kosgey I, Bebe B, et al. Breeding goals for the Kenya dual purpose goat. I. model development and application to smallholder production systems[J]. Tropical Animal Health and Production, 2007, 39:477-492. [7] Zook JM, Chapman B, Wang J, et al.Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls[J]. Nature Biotechnology, 2014, 32(3):246-251. [8] Liao PY, H. Lee K. From SNPs to functional polymorphism:The insight into biotechnology applications[J]. Biochemical Engineering Journal, 2010, 49:149-158. [9] Kwok PY, Chen X.Detection of single nucleotide polymorphisms[J]. Current Issues in Molecular Biology, 2003, 5(2):43-60. [10] Davey JW, Hohenlohe PA, Etter PD, et al.Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J]. Nature Reviews. Genetics, 2011, 12(7):499-510. [11] Helyar SJ, Hemmer-Hansen J, Bekkevold D, et al.Application of SNPs for population genetics of nonmodel organisms:new opportunities and challenges[J]. Molecular Ecology Resources, 2011, 1:123-136. [12] Elsik CG, Tellam RL, Worley KC, et al.The genome sequence of taurine cattle:a window to ruminant biology and evolution[J]. Science, 2009, 324(5926):522-528. [13] Wade CM, Giulotto E, Sigurdsson S, et al.Genome sequence, comparative analysis, and population genetics of the domestic horse[J]. Science, 2009, 326(5954):865-867. [14] Groenen MA, Archibald AL, Uenishi H, et al.Analyses of pig genomes provide insight into porcine demography and evolution[J]. Nature, 2012, 491(7424):393-398. [15] 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]. Nature Biotechnology, 2013, 31(2):135-141. [16] 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. [17] Matukumalli LK, Lawley CT, Schnabel RD, et al.Development and characterization of a high density SNP genotyping assay for cattle[J]. PLoS One, 2009, 4(4):24-36. [18] Levy SE, Boone BE.Next-generation sequencing strategies[J]. Cold Spring Harbor Perspectives in Medicine, 2019, 9(7):a025791. [19] Zhang J, Chiodini R, Badr A, et al.The Impact of next-generation sequencing on genomics[J]. Journal of Genetics and Genomics, 2011, 38:95-109. [20] 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. [21] Qiao X, Su R, Wang Y, et al.Genome-wide target enrichment-aided chip design:a 66 K SNP chip for cashmere goat[J]. Scientific Reports, 2017, 7(1):8621-8633. [22] Bickhart DM, Rosen BD, Koren S, et al.Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome[J]. Nature Genetics, 2017, 49(4):643-650. [23] Vaiman D, Schibler L, Bourgeois F, et al.A linkage map of the male goats genome[J]. Genetics, 1996, 144:279-305. [24] Schibler L, Vaiman D, Oustry A, et al.Construction and extensive characterization of a goat bacterial artificial chromosome library with threefold genome coverage[J]. Mammalian Genome, 1998, 9(2):119-124. [25] Schibler L, Vaiman D, Oustry A, et al.Comparative gene mapping:a fine-scale survey of chromosome rearrangements between ruminants and humans[J]. Genome Research, 1998, 8(9):901-915. [26] Maddox JF.A presentation of the differences between the sheep and goat genetic maps[J]. Genetics, Selection, Evolution, 2005, 37(1):S1-S10. [27] Goss SJ, Harris H.New method for mapping genes in human chromosomes[J]. Nature, 1975, 255(5511):680-684. [28] Du XY, Womack EJ, Owens EK, et al.A whole-genome radiation hybrid panel for goat[J]. Small Ruminant Research, 2012, 105:114-116. [29] Du XY, Servin B, Womack JE, et al.An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae[J]. BMC Genomics, 2014, 15(625):625-640. [30] Schibler L, Di Meo GP, Cribiu EP, et al.Molecular cytogenetics and comparative mapping in goats(Capra hircus, 2n = 60)[J]. Cytogenetic and Genome Research, 2009, 126(1-2):77-85. [31] Le Provost F, Lepingle A, Martin P.A survey of the goat genome transcribed in the lactating mammary gland[J]. Mammalian Genome, 1996, 7(9):657-666. [32] Le Provost F, Schibler L, Oustry-Vaiman A, et al.Cytogenetic mapping of 25 goat mammary gland expressed sequence tags(ESTs)[J]. Genetics, Selection, Evolution, 2000, 32(3):311-320. [33] 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):1471-1486. [34] Liu Y, Wang LL, Li XY, et al.High-throughput sequencing of hair follicle development-related micrornas in cashmere goat at various fetal periods[J]. Saudi Journal of Biological Sciences, 2018, 25(7):1494-1508. [35] Liu ZH, Xiao HM, Li HP, et al.Identification of conserved and novel microRNAs in cashmere goat skin by deep sequencing[J]. PLoS One, 2012, 7(12):e50001. [36] Ling YH, Ren CH, Guo XF, et al.Identification and characterization of microRNAs in the ovaries of multiple and uniparous goats (Capra hircus)during follicular phase[J]. BMC Genomics, 2014, 15(339):1471-2164. [37] Ye J, Yao ZQ, Si WY, et al.Identification and characterization of microRNAs in the pituitary of pubescent goats[J]. Reproductive Biology and Endocrinology, 2018, 16(1):370-379. [38] Ma S, Wang Y, Zhou GX, et al.Synchronous profiling and analysis of mRNAs and ncRNAs in the dermal papilla cells from cashmere goats[J]. BMC Genomics, 2019, 20(1):5861-5875. [39] Guo JZ, Zhao W, Zhan SY, et al.Identification and expression profiling of miRNAome in goat longissimus dorsi muscle from prenatal stages to a neonatal stage[J]. PLoS One, 2016, 11(10):e0165764. [40] Zhan SY, Dong Y, Zhao W, et al.Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat[J]. BMC Genomics, 2016, 17(666):3009-3018. [41] Liu Y, Qi B, Xie J, et al.Filtered reproductive long non-coding RNAs by genome-wide analyses of goat ovary at different estrus periods[J]. BMC Genomics, 2018, 19(1):5268-5280. [42] Zhou GX, Kang DJ, Ma S, et al.Integrative analysis reveals ncRNA-mediated molecular regulatory network driving secondary hair follicle regression in cashmere goats[J]. BMC Genomics, 2018, 19(1):222-237. [43] Tosser-Klopp G, Bardou P, Cabau C, et al.Goat genome assembly, availability of an international 50K SNP chip and RH panel:an update of the international goat genome consortium projects[C]. San Diego, CA:Plant and Animal Genome, 2012. [44] Dong Y, Zhang XL, 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):431-441. [45] Low WY, Tearle R, Bickhart DM, et al.Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity[J]. Nature Communications, 2019, 10(1):260-270. [46] Simpson JT, Wong K, Jackman SD, et al.ABySS:a parallel assembler for short read sequence data[J]. Genome Research, 2009, 19(6):1117-1123. [47] Paszkiewicz K, Studholme DJ.De novo assembly of short sequence reads[J]. Briefings in Bioinformatics, 2010, 11(5):457-472. [48] Assefa S, Keane TM, Otto TD, et al.ABACAS:algorithm-based automatic contiguation of assembled sequences[J]. Bioinformatics, 2009, 25(15):1968-1969. [49] Seppey M, Manni M, Zdobnov EM.BUSCO:assessing genome assembly and annotation completeness[J]. Methods in Molecular Biology, 2019:9170-9173. [50] Siddiki AZ, Baten A, Billah M, et al.The genome of the Black Bengal goat(Capra hircus)[J]. BMC Research Notes, 2019, 12(1):362-364. [51] Faruque S, Chowdhury SA, Siddiquee NU, et al.Performance and genetic parameters of economically important traits of Black Bengal goat[J]. Journal of the Bangladesh Agricultural University, 2010, 8:67-78. [52] Pollex RL, Hegele RA.Copy number variation in the human genome and its implications for cardiovascular disease[J]. Circulation, 2007, 115(24):3130-3138. [53] Fontanesi L, Martelli PL, Beretti F, et al.An initial comparative map of copy number variations in the goat(Capra hircus)genome[J]. BMC Genomics, 2010, 11(639):1471-2164. [54] Liu M, Zhou Y, Rosen BD, et al.Diversity of copy number variation in the worldwide goat population[J]. Heredity, 2018, 6(10):150-161. [55] Benjelloun B, Alberto FJ, Streeter I, et al.Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats(Capra hircus)using WGS data[J]. Frontiers in Genetics, 2015, 6(107):107-121. [56] Zhang B, Chang L, Lan YX, et al.Genome-wide definition of selective sweeps reveals molecular evidence of trait-driven domestication among elite goat(Capra species)breeds for the production of dairy, cashmere, and meat[J]. Gigascience, 2018,7(12). doi:10.1093/gigascience/giy105. [57] Alberto FJ, Boyer F, Orozco-Terwengel P, et al.Convergent genomic signatures of domestication in sheep and goats[J]. Nature Communications, 2018, 9(1):813-822. [58] Li XK, Su R, Wan WT, et al.Identification of selection signals by large-scale whole-genome resequencing of cashmere goats[J]. Scientific Reports, 2017, 7(1):142-151. [59] Lee W, Ahn S, Taye M, et al.Detecting positive selection of Korean native goat populations using next-generation sequencing[J]. Molecules and Cells, 2016, 39(12):862-868. [60] Kim JY, Jeong S, Kim KH, et al.Discovery of genomic characteristics and selection signatures in Korean indigenous goats through comparison of 10 goat breeds[J]. Frontiers in Genetics, 2019, 10(699):699-716. [61] Cao YH, Xu H, Li R, et al.Genetic basis of phenotypic differences between Chinese Yunling black goats and Nubian goats revealed by allele-specific expression in their F1 hybrids[J]. Frontiers in Genetics, 2019, 10(145):145-156. [62] Lai FN, Zhai HL, Cheng M, et al.Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat(Capra hircus)[J]. Scientific Reports, 2016, 6. doi: 10.1038/srep38096. [63] Zhang SL, Cao XY, Li Y, et al.Detection of polled intersex syndrome(PIS)and its effect on phenotypic traits in goats[J]. Animal Biotechnology, 2019, 14:1-5. [64] Zhang RQ, Wang JJ, Zhang T, et al.Copy-number variation in goat genome sequence:A comparative analysis of the different litter size trait groups[J]. Gene, 2019, 696:40-46. [65] E GX, Zhao YJ, Huang YF. Selection signatures of litter size in Dazu black goats based on a whole genome sequencing mixed pools strategy[J]. Molecular Biology Reports, 2019, 7(10):4904-4911. [66] E GX, Jin ML, Zhao YJ, et al. Genome-wide analysis of Chongqing native intersexual goats using next-generation sequencing[J]. 3 Biotech, 2019, 9(3):99-112. [67] Wang XL, Liu J, Zhou GX, et al.Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits[J]. Scientific Reports, 2016, 6(38932):932-941. [68] Song S, Yao N, Yang M, et al.Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cash-mere goat(Capra hircus)[J]. BMC Genomics, 2016, 17(122):2449-2461. [69] Wang LL, Zhang YJ, Zhao M, et al.SNP discovery from transcrip-tome of cashmere goat skin[J]. Asian-Australasian Journal of Animal Sciences, 2015, 28(9):1235-1243. [70] Guan DL, Marmol-Sanchez E, Cardoso TF, et al.Genomic analysis of the origins of extant casein variation in goats[J]. Journal of Dairy Science, 2019, 102(6):5230-5241. [71] Hawe JS, Theis FJ, Heinig M.Inferring interaction networks from multi-omics data[J]. Frontiers in Genetics, 2019, 10(535):535-548. [72] Teng C, Du DZ, Xiao L, et al.Mapping and identifying a candidate gene(Bnmfs)for female-male sterility through whole-genome resequencing and RNA-Seq in rapeseed(Brassica napus L.)[J]. Frontiers in Plant Science, 2017, 8(2086):2086-2088. [73] Sun YV, Hu YJ.Integrative analysis of multi-omics data for discovery and functional studies of complex human diseases[J]. Advances in Genetics, 2016, 93:147-190. |
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