[1] 鲍晶晶,张 莉.畜禽基因组选择方法研究进展[J].中国畜牧兽医,2020,47(10):3297-3304. BAO J J,ZHANG L.Research progress on genomic selection methods in livestock and poultry[J].China Animal Husbandry & Veterinary Medicine,2020,47(10):3297-3304.(in Chinese) [2] MEUWISSEN T H,HAYES B J,GODDARD M E.Prediction of total genetic value using genome-wide dense marker maps[J].Genetics,2001,157(4):1819-1829. [3] GEORGES M,CHARLIER C,HAYES B.Harnessing genomic information for livestock improvement[J].Nature Reviews Genetics,2019,20(3):135-156. [4] XU Y,LIU X,FU J,et al.Enhancing genetic gain through genomic selection:From livestock to plants[J].Plant Communications,2020,1(1):100005. [5] WANG H,LI C,LI J,et al.Genomic selection for weaning weight in Alpine Merino sheep based on GWAS prior marker information [J].Animals,2024,14(13):1904. [6] XU H,WANG Z,WANG F,et al.Genome-wide association study and genomic selection of spike-related traits in bread wheat[J].Theoretical and Applied Genetics,2024,137(6):131. [7] ZONAED S A,MIAH G,ISLAM M S,et al.Goat genomic resources:The search for genes associated with its economic traits[J].International Journal of Genomics,2020,2020:5940205. [8] 陈滇黔,韩 勇,杨 洋,等.不同TMR对贵州黑山羊生长母羊育肥效果及血清指标的影响[J].中国畜牧杂志,2022,58(1):198-202. CHEN D Q,HAN Y,YANG Y,et al.Effects of different TMR on the fattening effect and serum indicators of Guizhou Black goat growing ewes [J].Chinese Journal of Animal Science,2022,58(1):198-202.(in Chinese) [9] ZHANG Y,WANG K,LIU J,et al.An 11-bp indel polymorphism within the CSN1S1 gene is associated with milk performance and body measurement traits in Chinese goats[J].Animals (Basel),2019,9(12):1114. [10] ZHOU A,DING Y,ZHANG X,et al.Whole-genome resequencing reveals new mutations in candidate genes for Beichuan-White goat prolificacya[J].Animal Biotechnology,2023,35(1):2258166. [11] DIETERS L S E,MEALE S J,QUIGLEY S P,et al.Meat quality characteristics of lot-fed Australian Rangeland goats are unaffected by live weight at slaughter[J].Meat Science,2021,175:108437. [12] KANG X,LI M,LIU M,et al.Copy number variation analysis reveals variants associated with milk production traits in dairy goats[J].Genomics,2020,112(6):4934-4937. [13] MANIMEKALAI R,SURESH G,GOVINDA K H,et al.Role of NGS and SNP genotyping methods in sugarcane improvement programs[J].Critical Reviews in Biotechnology,2020,40(6):865-880. [14] ARSLAN M.Whole-genome sequencing and genomic analysis of Norduz goat (Capra hircus)[J].Mammalian Genome,2023,34(3):437-448. [15] BELAY S,BELAY G,NIGUSSIE H,et al.Design and characterization of a 52K SNP chip for goats [J].PLoS One, 2014,9(1):e86227. [16] DI GERLANDO R,MASTRANGELO S,MOSCARELLI A,et al.Genomic structural diversity in local goats:Analysis of copy-number variations[J].Animals,2020,10(6):1040. [17] LUIGI-SIERRA M G,LANDI V,GUAN D,et al.A genome-wide association analysis for body,udder,and leg conformation traits recorded in Murciano-Granadina goats[J].Journal of Dairy Science,2020,103(12):11605-11617. [18] GUO Z,YANG Q,HUANG F,et al.Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip[J].Plant Communications,2021,2(6):100230. [19] CHANG L,ZHENG Y,LI S,et al.Identification of genomic characteristics and selective signals in Guizhou Black goat[J].BMC Genomics,2024,25(1):164. [20] THE ALL OF US RESEARCH PROGRAM GENOMICS INVESTIGATORS.Genomic data in the all of us research program[J]. Nature,2024,627(8003):340-346. [21] QU S,LU S,LIU Y,et al.Accurate genomic selection using low-density SNP panels preselected by maximum likelihood estimation[J].Aquaculture,2024,579:740154. [22] TAN X,LIU R,LI W,et al.Assessment the effect of genomic selection and detection of selective signature in broilers[J].Poultry Science,2022,101(6):101856. [23] BAINTER S A,MCCAULEY T G,FAHMY M M, et al.Comparing bayesian variable selection to lasso approaches for applications in psychology[J].Psychometrika,2023,88:1032-1055. [24] GUO H,YU Z,AN J,et al.A two-stage mutual information based Bayesian lasso algorithm for multi-locus genome-wide association studies[J].Entropy,2020,22(3):329. [25] SHUKU T,PHOON K,YOSHIDA I.Trend estimation and layer boundary detection in depth-dependent soil data using sparse Bayesian lasso[J].Computers and Geotechnics,2020,128:103845. [26] ROLLING W R,DORRANCE A E,MCHALE L K.Testing methods and statistical models of genomic prediction for quantitative disease resistance to Phytophthora sojae in soybean (Glycine max (L.) Merr) germplasm collections[J].Theoretical and Applied Genetics,2020,133(12):3441-3454. [27] HAMADANI A,GANAI N A,MUDASIR S,et al.Comparison of artificial intelligence algorithms and their ranking for the prediction of genetic merit in sheep[J].Scientific Reports,2022,12(1):18726. [28] HUNT C H,HAYES B J,VAN EEUWIJK F A,et al.Multi-environment analysis of sorghum breeding trials using additive and dominance genomic relationships[J].Theoretical and Applied Genetics,2020,133(3):1009-1018. [29] BAYER P E,PETEREIT J,DANILEVICZ M F,et al.The application of pangenomics and machine learning in genomic selection in plants[J].The Plant Genome,2021,14(3):e20112. [30] ALVES A A C,DA COSTA R M,BRESOLIN T,et al.Genome-wide prediction for complex traits under the presence of dominance effects in simulated populations using GBLUP and machine learning methods[J].Journal of Animal Science,2020,98(6):skaa179. [31] 李棉燕,王立贤,赵福平.机器学习在动物基因组选择中的研究进展[J].中国农业科学,2023,56(18):3682-3692. LI M Y,WANG L X,ZHAO F P.Research progress on machine learning for genomic selection in animals[J].Scientia Agricultura Sinica,2023,56(18):3682-3692.(in Chinese) [32] 丁纪强,李庆贺,张高猛,等.比较机器学习等算法对肉鸡产蛋性状育种值估计的准确性[J].畜牧兽医学报,2022,53(5):1364-1372. DING J Q,LI Q H,ZHANG G M,et al.Comparing the accuracy of estimated breeding value by several algorithms on laying traits in broilers[J].Acta Veterinaria et Zootechnica Sinica,2022,53(5):1364-1372.(in Chinese) [33] ESRAFILI TAZE KAND MOHAMMADDIYEH M,RAFAT S A,SHODJA J,et al.Selective genotyping to implement genomic selection in beef cattle breeding[J].Frontiers in Genetics,2023,14:1083106. [34] 李诚兰,郭婷婷,岳耀敬.基因组选择及其在羊育种中的应用研究进展[J].中国畜牧兽医,2023,50(2):616-625. LI C L,GUO T T,YUE Y J.Research advances on genomic selection and its application in sheep breeding[J].China Animal Husbandry & Veterinary Medicine,2023,50(2):616-625.(in Chinese) [35] YAN X,ZHANG T,LIU L,et al.Accuracy of genomic selection for important economic traits of cashmere and meat goats assessed by simulation study[J].Frontiers in Veterinary Science,2022,9:770539. [36] 王志英,洪 磊,李宏伟,等.基于GBLUP和Bayes方法实现山羊体重基因组选择[J].家畜生态学报,2019,40(7):22-26. WANG Z Y,HONG L,LI H W,et al.Genome selection of body weight in goats by GBLUP and Bayes methods[J].Journal of Domestic Animal Ecology,2019,40(7):22-26.(in Chinese) [37] 王凤红.山羊SNP芯片设计与内蒙古绒山羊重要经济性状全基因组关联分析及基因组选择研究[D].呼和浩特:内蒙古农业大学,2021. WANG F H.Goat SNP chip design and genome-wide association analysis and genome selection of important economic traits of Inner Mongolia cashmere goats [D].Hohhot:Inner Mongolia Agricultural University,2021.(in Chinese) [38] LI C,LI J,WANG H,et al.Genomic selection for live weight in the 14th month in Alpine Merino sheep combining GWAS information[J].Animals (Basel),2023,13(22):3516. [39] MIRKENA T,DUGUMA G,WILLAM A,et al.Community-based alternative breeding plans for indigenous sheep breeds in four agro-ecological zones of Ethiopia[J].Journal of Animal Breeding and Genetics,2012,129(3):244-253. [40] ZHU H,ZHANG Y,BAI Y,et al.Relationship between SNPs of POU1F1 gene and litter size and growth traits in Shaanbei White cashmere goats[J].Animals (Basel),2019,9(3):114. [41] ARAUJO A C,CARNEIRO P,OLIVEIRA H R,et al.SNP- and haplotype-based single-step genomic predictions for body weight,wool,and reproductive traits in North American Rambouillet sheep[J].Journal of Animal Breeding and Genetics,2023,140(2):216-234. [42] BRITO L F,CLARKE S M,MCEWAN J C,et al.Prediction of genomic breeding values for growth,carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip[J].BMC Genetics,2017,18(1):7. [43] SHUMBUSHO F,RAOUL J,ASTRUC J M,et al.Economic evaluation of genomic selection in small ruminants:A sheep meat breeding program[J].Animal,2016,10(6):1033-1041. [44] SANTOS B F,WERF J H,GIBSON J P,et al.Genetic and economic benefits of selection based on performance recording and genotyping in lower tiers of multi-tiered sheep breeding schemes[J].Genetics Selection Evolution,2017,49(1):10. [45] MARINA H,PELAYO R,GUTIERREZ-GIL B,et al.Low-density SNP panel for efficient imputation and genomic selection of milk production and technological traits in dairy sheep[J].Journal of Dairy Science,2022,105(10):8199-8217. [46] SCHOLTENS M,LOPEZ-VILLALOBOS N,LEHNERT K,et al.Advantage of including genomic information to predict breeding values for lactation yields of milk,fat,and protein or somatic cell score in a New Zealand dairy goat herd[J].Animals (Basel),2021,11(1):24. [47] NEGRO A,CESARANI A,CORTELLARI M,et al.A comparison of genetic and genomic breeding values in Saanen and Alpine goats[J].Animal,2024,18(4):101118. [48] OGET C,TEISSIER M,ASTRUC J,et al.Alternative methods improve the accuracy of genomic prediction using information from a causal point mutation in a dairy sheep model[Z].BMC Genomics,2019,20(1):719. [49] REXROAD C,VALLET J,MATUKUMALLI L K,et al.Genome to phenome:Improving animal health,production,and well-being—A new USDA blueprint for animal genome research 2018-2027[J].Frontiers in Genetics,2019,10:327. [50] ROCHA A O,CASTRO G C,DE CARVALHO F E,et al.PSVII-2 the impact of genomic information inclusion on breeding value prediction for a novel parasite resistance indicator trait in Brazilian Anglo-Nubian goats:A pilot study [J].Journal of Animal Science,2023,101(3):341-342. [51] VAHEDI S M,ARDETANI S S,BRITO L F,et al.Expanding the application of haplotype-based genomic predictions to the wild:A case of antibody response against Teladorsagia circumcincta in Soay sheep[J].BMC Genomics,2023,24:335. [52] DE LIMA L G,DE SOUZA N O B,RIOS R R,et al.Advances in molecular genetic techniques applied to selection for litter size in goats (Capra hircus):A review[J].Journal of Applied Animal Research,2020,48(1):38-44. [53] 张瑞锋,黄 珍,谢水华,等.猪全基因组选择技术发展现状和应用前景[J].中国畜牧杂志,2023,59(10):21-29. ZHANG R F,HUANG Z,XIE S H,et al.Development status and application prospects of pig whole genome selection technology [J].Chinese Journal of Animal Science,2023,59(10):21-29.(in Chinese) [54] 叶 雯,孙东晓,韩 博.全基因组重测序在畜禽研究领域的应用进展[J].中国畜牧兽医,2023,50(10):4125-4132. YE W,SUN D X,HAN B.Application progress on whole genome resequencing in farm animals[J].China Animal Husbandry & Veterinary Medicine,2023,50(10):4125-4132.(in Chinese) [55] FIEDER M,MITCHELL B L,GORDON S,et al.Ethnic identity and genome wide runs of homozygosity[J].Behavior Genetics,2021,51(4):405-413. [56] SONG H,DONG T,YAN X,et al.Genomic selection and its research progress in aquaculture breeding[J].Reviews in Aquaculture,2023,15(1):274-291. [57] ZHANG Y,RAN Y,NAGY I,et al.Targeted mutagenesis in ryegrass (Lolium spp.) using the CRISPR/Cas9 system[J].Plant Biotechnology Journal,2020,18(9):1854-1856. [58] SELLA G,BARTON N H.Thinking about the evolution of complex traits in the era of genome-wide association studies[J].Annual Review of Genomics and Human Genetics,2019,20:461-493. [59] SU J,JIANG J,ZHANG F,et al.Current achievements and future prospects in the genetic breeding of chrysanthemum:A review[J].Horticulture Research,2019,6:109. [60] ZHANG B,CHANG L,LAN X,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].Giga Science,2018,7(12):105. [61] XU N,SI W,LI M,et al.Genome-wide scan for selective footprints and genes related to cold tolerance in Chantecler chickens[J].Zoological Research,2021,42(6):710-720. [62] CAI Y,FU W,CAI D,et al.Ancient genomes reveal the evolutionary history and origin of cashmere-producing goats in China[J].Molecular Biology and Evolution,2020,37(7):2099-2109. [63] WANG T,YAN Z,ZHANG Y,et al.postGWAS:A web server for deciphering the causality post the genome-wide association studies[J].Computers in Biology and Medicine,2024,171:108108. [64] JIA B,LIANG J,LV C,et al.The characteristics of proteome and metabolome associated with contrasting sperm motility in goat seminal plasma[J].Scientific Reports,2021,11(1):15562. [65] 张顺进,寇浩玮,丁晓婷,等.全基因组选择技术在反刍动物遗传育种中的研究进展及其应用[J].农业生物技术学报,2021,29(3):571-578. ZHANG S J,KOU H W,DING X T,et al.The research progress and application of genomic-wide selection in ruminant genetics and breeding[J].Journal of Agricultural Biotechnology,2021,29(3):571-578.(in Chinese) |