[1] | Quan C, Zhang XJ. Research strategies for the next step of genome-wide association study. Hereditas(Beijing), 2011, 33(2): 100-108. | [1] | 权晟, 张学军. 全基因组关联研究的深度分析策略. 遗传, 2011, 33(2): 100-108. | [2] | Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet, 2005, 6(2): 95-108. | [3] | Wang WY, Barratt BJ, Clayton DG, Todd JA. Genome- wide association studies: theoretical and practical concerns. Nat Rev Genet, 2005, 6(2): 109-118. | [4] | Wang JY, Wang HX, Chi RB, Guo JF, Wu Y. Progresses in research of genome-wide association studies in livestock and poultry. Scientia Agricultura Sinica, 2012, 46(4): 819-829. | [4] | 王继英, 王海霞, 迟瑞宾, 郭建凤, 武英. 全基因组关联分析在畜禽中的研究进展. 中国农业科学, 2012, 46(4): 819-829. | [5] | China national comission of animal genetics resources. Animal genetics resource in China——Sheep and Goats. Beijing: China Agricultural Press, 2011. | [5] | 国家畜禽遗传资源委员会组编. 中国畜禽遗传资源志—羊志. 北京: 中国农业出版社, 2011. | [6] | Dong Y, Xie M, Jiang Y, Xiao N, Du X, Zhang W, Tosser-Klopp G, Wang J, Yang S, Liang J, Chen W, Chen J, Zeng P, Hou Y, Bian C, Pan S, Li Y, Liu X, Wang W, Servin B, Sayre B, Zhu B, Sweeney D, Moore R, Nie W, Shen Y, Zhao R, Zhang G, Li J, Faraut T, Womack J, Zhang Y, Kijas J, Cockett N, Xu X, Zhao S, Wang J, Wang W. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol, 2013, 31(2): 135-141. | [7] | Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton J-A, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SMJ, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Fuentes-Utrilla P, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristiansen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, Oddy VH, Nicholas FW, McEwan JC, Kijas JW, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP. The sheep genome illuminates biology of the rumen and lipid metabolism. Science, 2014, 344(6188): 1168-1173. | [8] | Kijas JW, Townley D, Dalrymple BP, Heaton MP, Maddox JF, McGrath A, Wilson P, Ingersoll RG, McCulloch R, McWilliam S, Tang D, McEwan J, Cockett N, Oddy VH, Nicholas FW, Raadsma H for the International Sheep Genomics Consortium. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS One, 2009, 4(3): e4668. | [9] | Tosser-klopp G, Bardou P, Bouchez O, Cabau C, Crooijmans R, Dong Y, Donnadieutonon C, Eggen A, Heuven HC, Jamli S, Jiken A, Klopp C, Lawley C, McEwan J, Martin P, Moreno C, Mulsant P, Nabihoudine I, Pailhoux E, Palhière I, Rupp R, Sarry J, Sayre B, Tircazes A, Wang J, Wang W, Zhang W and the International Goat Genome Consortium. Design and characterization of a 52K SNP chip for goats. PLoS One, 2014, 9(1): e86227. | [10] | Zhu C, Fan H, Yuan Z, Hu S, Ma X, Xuan J, Wang H, Zhang L, Wei C, Zhang Q, Zhao F, Du L. Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays. Sci Rep, 2016, 6: 27822. | [11] | Becker D, Tetens J, Brunner A, Bürstel D, Ganter M, Kijas J for for International Sheep Genomics Consortium, Dr?gemüller C. Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene. PLoS One, 2010, 5(1): e8689. | [12] | Johnston SE, McEwan JC, Pickering NK, Kijas JW, Beraldi D, Pilkington JG, Pemberton JM, Slate J. Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population. Mol Ecol, 2011, 20(12): 2555-2566. | [13] | Kijas JW, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, San CM, Servin B, Mcculloch R, Whan V, Gietzen K, Paiva S, Barendse W, Raadsma H, McEwan B, other members of the International Sheep Genomics Consortium. Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol, 2012, 10(2): e1001258. | [14] | Kardos M, Luikart G, Bunch R, Dewey S, Edwards W, Mcwilliam S, Stephenson J, Allendorf FW, Hogg JT, Kijas J. Whole-genome resequencing uncovers molecular signatures of natural and sexual selection in wild bighorn sheep. Mol Ecol, 2015, 24(22): 5616-5632. | [15] | Wiedemar N, Dr?gemüller C. A 1.8-kb insertion in the 3'-UTR of RXFP2 is associated with polledness in sheep. Anim Genet, 2015, 46(4): 457-461. | [16] | Gesine L, Stefan K, Sophie R, Julia K, Boro M, Ingolf R, Ivica M. The 1.78-kb insertion in the 3′-untranslated region of RXFP2does not segregate with horn status in sheep breeds with variable horn status. Genet Sel Evol, 2016, 48: 78. | [17] | Zhao F, Wei C, Zhang L, Liu J, Wang G, Zeng T, Du L. A genome scan of recent positive selection signatures in three sheep populations. J Integr Agr, 2016, 15(1): 162-174. | [18] | Kijas JW. Haplotype-based analysis of selective sweeps in sheep. Genome, 2014, 57(8): 433-437. | [19] | Fariello MI, Servin B, Tosser-Klopp G, Rupp R, Moreno C, the International Sheep Genomics Consortium, San Cristobal M, Boitard S. Selection signatures in worldwide sheep populations. PLoS One, 2014, 9(8): e103813. | [20] | Kijas JW, Hadfield T, Sanchez MN, Cockett N. Genome-wide association reveals the locus responsible for four-horned ruminant. Anim Genet, 2016, 47(2): 258-262. | [21] | Greyvenstein OFC, Reich CM, Marle-Koster EV, Riley DG, Hayes BJ. Polyceraty (multi-horns) in Damara sheep maps to ovine chromosome 2. Anim Genet, 2016, 47(2): 263-266. | [22] | He X, Zhou Z, Pu Y, Chen X, Ma Y, Jiang L. Mapping the four-horned locus and testing the polled locus in three Chinese sheep breeds. Anim Genet, 2016, 47(5): 623-627. | [23] | Ren X, Yang GL, Peng WF, Zhao YX, Zhang M, Chen ZH, Wu FA, Kantanen J, Shen M, Li MH. A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries). Sci Rep, 2016, 6: 21111. | [24] | Wang Z, Zhang H, Yang H, Wang S, Rong E, Pei W, Li H, Wang N. Genome-wide association study for wool production traits in a Chinese Merino sheep population. PLoS One, 2014, 9(9): e107101. | [25] | Di J, Liu JF, Xu XM, Wang Q, Lazate A, Y LJ. Genome-wide association studies for wool and body mass traits in yearling fine wool sheep. Acta Agriculturae Boreali-Occidentalis Sinica, 2016, 25(4): 496-501. | [25] | 狄江, 刘剑锋, 徐新明, 王琼, 拉扎特, 于丽娟. 周岁细毛羊羊毛长度, 产毛量与体质量的全基因组关联分析. 西北农业学报, 2016, 25(4): 496-501. | [26] | Di J, Liu JF, Xu XM, Lazate A, Yu LJ. Genome-wide association studies on the wool staple crimp frequency in Chinese merino sheep (Xinjiang type). Xinjiang Agricultural Science, 2015(11): 2129-2135. | [26] | 狄江, 刘剑锋, 徐新明, 拉扎特, 于丽娟. 中国美利奴(新疆型)羊毛弯曲频率性状的全基因组关联分析. 新疆农业科学, 2015(11): 2129-2135. | [27] | Li MH, Tiirikka T, Kantanen J. A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries). Heredity, 2014, 112(2): 122-131. | [28] | Kijas J, Serrano M, McCulloch R, Li Y, Salces Ortiz J, Calvo J, Pérez-Guzmán M, the International Sheep Genomics Consortium. Genomewide association for a dominant pigmentation gene in sheep. J Anim Breed Genet, 2013, 130(6): 468-475. | [29] | Zhang L, Liu J, Zhao F, Ren H, Xu L, Jian L, Zhang S, Zhang X, Wei C, Lu G, Zheng Y, Du L. Genome-wide association studies for growth and meat production traits in sheep. PLos One, 2013, 8(6): e66569. | [30] | Zhang L, Ma X, Xuan J, Wang H, Yuan Z, Wu M, Liu R, Zhu C, Wei C, Zhao F, Du L. Identification of MEF2B and TRHDE gene polymorphisms related to growth traits in a New Ujumqin sheep population. PLoS One, 2016, 11(7): e0159504. | [31] | Ma X, Guan L, Xuan J, Wang H, Yuan Z, Wu M, Liu R, Zhu C, Wei C, Zhao F, Du L, Zhang L. Effect of polymorphisms in the CAMKMT gene on growth traits in Ujumqin sheep. Anim Genet, 2016, 47(5): 618-622. | [32] | Gholizadeh M, Rahimimianji G, Nejatijavaremi A. Genomewide association study of body weight traits in Baluchi sheep. J Genet, 2015, 94(1): 143-146. | [33] | Riggio V, Matika O, Pongwong R, Stear MJ, Bishop SC. Genome-wide association and regional heritability mapping to identify loci underlying variation in nematode resistance and body weight in Scottish Blackface lambs. Heredity, 2013, 110(5): 420. | [34] | Almamun HA, Kwan P, Clark SA, Ferdosi MH, Tellam R, Gondro C. Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight. Genet Sel Evol, 2014, 47(1): 66. | [35] | Matika O, Riggio V, Anselmemoizan M, Law AS, Pongwong R, Archibald AL, Bishop SC. Genome-wide association reveals QTL for growth, bone and in vivo carcass traits as assessed by computed tomography in Scottish Blackface lambs. Genet Sel Evol, 2015, 48(1): 11. | [36] | Demars J, Fabre S, Sarry J, Rossetti R, Gilbert H, Persani L, Tosserklopp G, Mulsant P, Nowak Z, Drobik W, Martyniuk, Bodin L. Genome-wide association studies identify two novel BMP15 mutations responsible for an atypical hyperprolificacy phenotype in sheep. PLoS Genet, 2013, 9(4): e1003482. | [37] | V?ge DI, Husdal M, Kent MP, Klemetsdal G, Boman IA. A missense mutation in growth differentiation factor 9 (GDF9) is strongly associated with litter size in sheep. BMC Genet, 2013, 14(1): 1. | [38] | Gholizadeh M, Rahimimianji G, Nejatijavaremi A, De Koning DJ, Jonas E. Genomewide association study to detect QTL for twinning rate in Baluchi sheep. J Genet, 2014, 93(2): 489-493. | [39] | Galloway SM, McNatty KP, Cambridge LM, Laitinen MP, Juengel JL, Jokiranta TS, McLaren RJ, Luiro K, Dodds KG, Montgomery GW, Beattie AE, Davis GH, Ritvos O. Mutations in an oocyte-derived growth factor gene (BMP15) cause increased ovulation rate and infertility in a dosage-sensitive manner. Nat genet, 2000, 25(3): 279-283. | [40] | Hanrahan JP, Gregan SM, Mulsant P, Mullen M, Davis GH, Powell R, Galloway SM. Mutations in the genes for oocyte-derived growth factors GDF9 and BMP15 are associated with both increased ovulation rate and sterility in Cambridge and Belclare sheep (Ovis aries). Biol Reprod, 2004, 70(4): 900-909. | [41] | Silva B, Castro E, Souza C, Paiva S, Sartori R, Franco M, Azevedo H, Silva T, Vieira A, Neves J, Melo EO. A new polymorphism in the growth and differentiation factor 9 (GDF9) gene is associated with increased ovulation rate and prolificacy in homozygous sheep. Anim Genet, 2011, 42(1): 89-92. | [42] | García-Gámez E, Gutiérrez-Gil B, Sahana G, Sánchez JP, Bayón Y, Arranz JJ. GWA analysis for milk production traits in dairy sheep and genetic support for a QTN influencing milk protein percentage in the LALBA gene. PLoS One, 2012, 7(10): e47782. | [43] | Garcia-Gámez E, Gutiérrez-Gil B, Suarez-Vega A, Fuente LFDL, Arranz JJ. Identification of quantitative trait loci underlying milk traits in Spanish dairy sheep using linkage plus combined linkage disequilibrium and linkage analysis approaches. J. Dairy Sci, 2013, 96(9): 6059-6069. | [44] | Zhao X, Onteru SK, Piripi S, Thompson KG, Blair HT, Garrick DJ, Rothschild MF. In a shake of a lamb's tail: using genomics to unravel a cause of chondrodysplasia in Texel sheep. Anim Genet, 2012, 43(Suppl. 1): 9-18. | [45] | Mousel MR, Reynolds JO, White SN. Genome-wide association identifies SLC2A9 and NLN gene regions as associated with entropion in domestic sheep. PLoS One, 2015, 10(6): e0128909. | [46] | Jawasreh K, Boettcher PJ, Stella A. Genome-wide association scan suggests basis for microtia in Awassi sheep. AnimGenet, 2016, 47(4): 504-506. | [47] | Riggio V, Pongwong R, Sallé G, Usai MG, Casu S, Moreno CR, Matika O, Bishop SC. A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations. J Anim Breed Genet, 2014, 131(6): 426-436. | [48] | Mucha S, Bunger L, Conington J. Genome-wide association study of footrot in Texel sheep. Genet Sel Evol, 2015, 47(1): 35. | [49] | Atlija M, Arranz J-J, Martinez-Valladares M, Gutiérrez- Gil B. Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array. Genet Sel Evol, 2016, 48(1): 4. | [50] | Gonzalez MV, Mousel MR, Herndon DR, Jiang Y, Dalrymple BP, Reynolds JO, Johnson WC, Herrmannhoesing LM, White SN. A divergent artiodactyl MYADM-like repeat is associated with erythrocyte traits and weight of lamb weaned in domestic sheep. PLoS One, 2013, 8(8): e74700. | [51] | Martin PM, Palhière I, Ricard A, Tosser-Klopp G, Rupp R. Genome wide association study identifies new loci associated with undesired coat color phenotypes in Saanen goats. PLoS One, 2016, 11(3): e0152426. | [52] | Lan R, Zhu L, Yao XR, Wang P, Shao QY, Hong QH. A genome-wide association analysis of goat litter size. Chinese Journal of Animal and Veterinary Sciences, 2015, 46(4): 549-554. | [52] | 兰蓉, 朱兰, 姚新荣, 王鹏, 邵庆勇, 洪琼花. 山羊产羔数全基因组关联分析. 畜牧兽医学报, 2015, 46(4): 549-554. | [53] | Martin P, Palhière I, Tosser-Klopp G, Rupp R. Heritability and genome-wide association mapping for supernumerary teats in French Alpine and Saanen dairy goats. J. Dairy Sci, 2016, 99(11): 8891-8900. | [54] | Minozzi G, Mattiello S, Grosso L, Crepaldi P, Chessa S, Pagnacco G. First insights in the genetics of caseous lymphadenitis in goats. Ital J Anim Sci, 2017, 16(1): 31-38. | [55] | Reber I, Keller I, Becker D, Flury C, Welle M, Dr?gemüller C. Wattles in goats are associated with the FMN1/GREM1 region on chromosome 10. Anim Genet, 2015, 46(3): 316-320. | [56] | Yang J, Zaitlen NA, Goddard ME, Visscher PM, Price AL. Advantages and pitfalls in the application of mixed-model association methods. Nat Genet, 2014, 46(2): 100-106. | [57] | Xu S. Mapping quantitative trait loci by controlling polygenic background effects. Genetics, 2013, 195(4): 1209-1222. | [58] | Price AL, Zaitlen NA, Reich D, Patterson N. New approaches to population stratification in genome-wide association studies. Nat Rev Genet, 2010, 11(7): 459-463. | [59] | Evangelou E, Ioannidis JP. Meta-analysis methods for genome-wide association studies and beyond. Nat Rev Genet, 2013, 14(6): 379-389. | [60] | Balding DJ. A tutorial on statistical methods for population association studies. Nat Rev Genet, 2006, 7(10): 781-791. | [61] | de Leeuw CA, Neale BM, Heskes T, Posthuma D. The statistical properties of gene-set analysis. Nat Rev Genet, 2016, 17(6): 353-364. | [62] | Wang K, Li M, Hakonarson H. Analysing biological pathways in genome-wide association studies. Nat Rev Genet, 2010, 11(12): 843-854. | [63] | Nielsen R. Molecular signatures of natural selection. Annu Rev Genet, 2005, 39: 197-218. | [64] | Civelek M, Lusis AJ. Systems genetics approaches to understand complex traits. Nat Rev Genet, 2014, 15(1): 34-48. | [65] | Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach. Nat Rev Genet, 2010, 11(7): 476-486. |
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