ROH及其在绵羊遗传育种中的应用研究进展

doi:10.16431/j.cnki.1671-7236.2023.08.023

摘要/Abstract

摘要： 连续性纯合片段(runs of homozygosity,ROH)是基因组中的一段长纯合片段,不同长度的ROH和个体与共同祖先的亲缘背景相关联,亲缘关系越远ROH片段越短。在近交过程中,随着世代数的增加,子代个体从共同祖先遗传得到的ROH会被不断地打断重排。在整个遗传信息传递过程中,可以根据ROH的长短来判断个体间亲缘关系的亲近程度。ROH受种群近交、种群瓶颈、基因组特征、人工选择等多种因素的制约,这些制约因素会在其基因组上留下各种印记。ROH中有丰富的遗传信息,促使ROH成为研究绵羊基因组信息的新手段。近年来,随着高通量测序技术的发展,研究人员利用基因组ROH来评估近交程度和遗传多样性、推断种群结构和种群历史、筛选和鉴定重要经济性状功能基因,进行个体选择并追踪选择信号。因此,笔者就ROH产生原理、影响因素、检测方法及其在绵羊遗传育种中的应用等方面进行综述,以期能准确制定绵羊种质资源保护策略,为ROH在绵羊遗传育种中的应用提供理论依据。

关键词: 连续性纯合片段(ROH); 绵羊; 遗传育种

Abstract: Runs of homozygosity (ROH) is a long homozygosity segment in the genome.ROH of different lengths and individuals are associated with the genetic background of a common ancestor,and the farther of genetic relationship has the shorter ROH fragment.In the process of inbreeding,with the increase of the number of generations,the ROH inherited from the common ancestor of the offspring individuals will be constantly interrupted and rearranged.ROH is subject to a variety of factors such as population inbreeding,population bottleneck,genomic characteristics and artificial selection,etc.,which will leave various imprints on its genome.There is abundant genetic information in ROH fragments,which equip a new tool for studying sheep genome information.In recent years,with the development of high-throughput sequencing technology,researchers use genome ROH to assess inbreeding degrees and population diversity,infer population structure and history,screen and identify important economic trait genes,and carry out individual selection track selection signals.Therefore,the author summarized the generation principle,influencing factors,detection methods and the application of ROH in sheep genetic breeding,so as to accurately formulate the protection strategy of sheep germplasm resources and provide theoretical basis for the application of ROH in sheep genetic breeding.

Key words: runs of homozygosity (ROH); sheep; genetic breeding

中图分类号:

S813

孙丽侠, 卢曾奎, 袁超, 张丹, 刘建斌. ROH及其在绵羊遗传育种中的应用研究进展[J]. 中国畜牧兽医, 2023, 50(8): 3258-3266.

SUN Lixia, LU Zengkui, YUAN Chao, ZHANG Dan, LIU Jianbin. Research Progress of ROH and Its Application in Sheep Genetic Breeding[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(8): 3258-3266.

参考文献

[1] BROMAN K W,WEBER J L.Long homozygous chromosomal segments in reference families from the centre d'Étude du polymorphisme humain[J].The American Journal of Human Genetics,1999,65(6):1493-1500.
[2] GIBSON J,MORTON N E,COLLINS A.Extended tracts of homozygosity in outbred human populations[J].Human Molecular Genetics,2006,15(5):789-795.
[3] RUTH M,LOUISE L A,REHAB A R,et al.Runs of homozygosity in european populations[J].American Journal of Human Genetics,2008,83(5):359-372.
[4] KIRIN M,MCQUILLAN R,FRANKLIN C S,et al.Genomic runs of homozygosity record population history and consanguinity[J].PLoS One,2010,5(11):e13996.
[5] BOSSE M,MEGENS H,MADSEN O,et al.Regions of homozygosity in the porcine genome:Consequence of demography and the recombination landscape[J].PLoS Genetics,2017,8(11):e1003100.
[6] JULIA M,MATTHIAS K,RAUL T,et al.Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses[J].BMC Genomics,2015,16(1):764.
[7] BEYNON S E,SLAVOV G T,FARRE M,et al.Population structure and history of the Welsh sheep breeds determined by whole genome genotyping[J].BMC Genetics,2015,16(1):65
[8] WOODS C G,COX J,SPRINGELL K,et al.Quantification of homozygosity in consanguineous individuals with autosomal recessive disease[J].Amrican Journal of Human Genetics,2006,78(5):889-896.
[9] GHOREISHIFAR S M,MORADI-SHAHRBABAK H,PARNA N,et al.Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep[J].Archives Animal Breeding,2019,62(1):143-151.
[10] MEYERMANS R,GORSSEN W,WIJNROCX K,et al.Unraveling the genetic diversity of Belgian milk sheep using medium-density SNP genotypes[J].Animal Genetics,2020,51(2):258-265.
[11] STOFFEL M A,JOHNSTON S E,PILKINGTON J G,et al.Genetic architecture and lifetime dynamics of inbreeding depression in a wild mamma[J].Nature Communications,2021,12(1):2972.
[12] MEGDICHE S,MASTRANGELO S,BEN H M,et al.A combined multi-cohort approach reveals novel and known genome-wide selection signatures for wool traits in Merino and Merino-derived sheep breeds[J].Frontiers in Genetics,2019,10:1025.
[13] TAO L,HE X Y,WANG F Y,et al.Identification of genes associated with litter size combining genomic approaches in Luzhong mutton sheep[J].Animal Genetics,2021,52(4):545-549.
[14] SUMREDDEE P,HAY E H,TOGHIANI S,et al.Grid search approach to discriminate between old and recent inbreeding using phenotypic,pedigree and genomic information[J].BMC Genomics,2021,22(1):538.
[15] LYU X,YANG Q,ZHAO F,et al.Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed[J].Nucleic Acids Research,2021,49(16):9404-9423.
[16] ARBEITHUBER B,BETANCOURT A J,EBNER T,et al.Crossovers are associated with mutation and biased gene conversion at recombination hotspots[J].Proceedings of the National Acadeny Sciences of the United State of America,2015,112(7):2109-2114.
[17] GORSSEN W,MEYERMANS R,JANSSENS S,et al.A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species[J].Genetics Selection Evolution,2021,53(1):2.
[18] CHANG C C,CHOW C C,TELLIER L C,et al.Second-generation PLINK:Rising to the challenge of larger and richer datasets[J].Gigascience,2015,4:7.
[19] CURIK I,FERENČAKOVIĆ M,SÖLKNER J.Inbreeding and runs of homozygosity:A possible solution to an old problem[J].Livestock Science,2014,166:26-34.
[20] GUSEV A,LOWE J K,STOFFEL M,et al.Whole population,genome-wide mapping of hidden relatedness[J].Genome Research,2009,19(2):318-326.
[21] SUMREDDEE P,TOGHIANI S,HAY E H,et al.Runs of homozygosity and analysis of inbreeding depression[J].Journal of Animal Science,2020,98(12):skaa361.
[22] RINGBAUER H,NOVEMBRE J,STEINRUCKEN M.Parental relatedness through time revealed by runs of homozygosity in ancient DNA[J].Nature Communications,2021,12(1):5425.
[23] BROWNING B L,BROWNING S R.Improving the accuracy and efficiency of identity-by-descent detection in population data[J].Genetics,2013,194(2):459-471.
[24] SZPIECH Z A,BLANT A,PEMBERTON T J.GARLIC:Genomic autozygosity regions Likelihood-based inference and classification[J].Bioinformatics,2017,33(13):2059-2062.
[25] DRUET T,GAUTIER M.A model-based approach to characterize individual inbreeding at both global and local genomic scales[J].Molecular Ecology,2017,26(20):5820-5841.
[26] BISCARINI F,MASTRANGELO S,CATILLO G,et al.Insights into genetic diversity,runs of homozygosity and heterozygosity-rich regions in Maremmana semi-feral cattle using pedigree and genomic data[J].Animals (Basel),2020,10(12):2285.
[27] MACCIOTTA N,COLLI L,CESARANI A,et al.The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation,migration and crossbred events[J].Genetics Selection Evolution,2021,53(1):20.
[28] HOWRIGAN D P,SIMONSON M A,KELLER M C.Detecting autozygosity through runs of homozygosity:A comparison of three autozygosity detection algorithms[J].BMC Genomics,2011,12:460.
[29] TAO L,HE X,WANG X,et al.Litter size of sheep (Ovis aries):Inbreeding depression and homozygous regions[J].Genes (Basel),2021,12(1):109.
[30] WRIGHT S.Coefficients of inbreeding and relationship[J].The American Naturalist,1922,56(645):289-311.
[31] BANOS G,WIGGANS G R,POWELL R L.Impact of paternity errors in cow identification on genetic evaluations and international comparisons[J].Journal of Dairy Science,2001,84(11):2523-2529.
[32] BAAZAOUI I,BEDHIAF-ROMDHANI S,MASTRANGELO S,et al.Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area[J].Animal,2021,15(4):100193.
[33] DOEKES H P,VEERKAMP R F,BIJMA P,et al.Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle[J].Genetics Selection Evolution,2019,51(1):54.
[34] YANG J,LEE S H,GODDARD M E,et al.GCTA:A tool for genome-wide complex trait analysis[J].American Journal of Human Genetics,2011,88(1):76-82.
[35] VANRADEN P M.Efficient methods to compute genomic predictions[J].Journal of Dairy Science,2008,91(11):4414-4423.
[36] FERENCAKOVIC M,HAMZIC E,GREDLER B,et al.Runs of homozygosity reveal genome-wide autozygosity in the Austrian Fleckvieh cattle[J].Agriculturae Conspectus Scientificus (ACS),2011,76(4):325-328.
[37] WU X,ZHOU R,ZHANG W,et al.Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs[J].Animal Bioscience,2021,34(12):1895-1902.
[38] POLAK G,GURGUL A,JASIELCZUK I,et al.Suitability of pedigree information and genomic methods for analyzing inbreeding of Polish Cold-Blooded horses covered by conservation programs[J].Genes (Basel),2021,12(3):429.
[39] KIM E S,SONSTEGARD T S,VAN TASSELL C P,et al.The relationship between runs of homozygosity and inbreeding in Jersey cattle under selection[J].PLoS One,2015,10(7):e129967.
[40] HIDALGO J,CESARANI A,GARCIA A,et al.Genetic background and inbreeding depression in Romosinuano cattle breed in Mexico[J].Animals (Basel),2021,11(2):321.
[41] LUIGI-SIERRA M G,FERNANDEZ A,MARTINEZ A,et al.Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats[J].Journal of Animal Science Biotechnology,2022,13(1):35.
[42] ADAMS S M,DERKS M,MAKANJUOLA B O,et al.Investigating inbreeding in the turkey (Meleagris gallopavo) genome[J].Poultry Science,2021,100(11):101366.
[43] PERIPOLLI E,STAFUZZA N B,MUNARI D P,et al.Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle[J].BMC Genomics,2018,19(1):34.
[44] LIU J,SHI L,LI Y,et al.Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds[J].Journal of Animal Science Biotechnology,2021,12(1):95.
[45] SZMATOLA T,GURGUL A,JASIELCZUK I,et al.A Comprehensive analysis of runs of homozygosity of eleven cattle breeds representing different production types[J].Animals (Basel),2019,9(12):1024.
[46] DZOMBA E F,CHIMONYO M,PIERNEEF R,et al.Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data[J].BMC Genomics,2021,22(1):7.
[47] GRANERO A,ANAYA G,DEMYDA-PEYRAS S,et al.Genomic population structure of the main historical genetic lines of Spanish merino sheep[J].Animals (Basel),2022,12(10):1327.
[48] MOHAMADIPOOR S L,MOHAMMADABADI M,AMIRI G Z,et al.Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds[J].BMC Veterinery Research,2021,17(1):369.
[49] LEI Z,SUN W,GUO T,et al.Genome-wide selective signatures reveal candidate genes associated with hair follicle development and wool shedding in sheep[J].Genes (Basel),2021,12(12):1924.
[50] LUO R,ZHANG X,WANG L,et al.GLIS1,A potential candidate gene affect fat deposition in sheep tail[J].Molecular Biology Reports,2021,48(5):4925-4931.
[51] CESARANI A,GASPA G,CORREDDU F,et al.Genomic selection of milk fatty acid composition in Sarda dairy sheep:Effect of different phenotypes and relationship matrices on heritability and breeding value accuracy[J].Journal of Dairy Science,2019,102(4):3189-3203.
[52] TSARTSIANIDOU V,SANCHEZ-MOLANO E,KAPSONA V V,et al.A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep[J].Genetics Selection Evolution,2021,53(1):90.
[53] HE S,DI J,HAN B,et al.Genome-wide scan for runs of homozygosity identifies candidate genes related to economically important traits in Chinese Merino[J].Animals (Basel),2020,10(3):524.
[54] AHBARA A M,ROUATBI M,GHARBI M,et al.Genome-wide insights on gastrointestinal nematode resistance in autochthonous Tunisian sheep[J].Scientific Reports,2021,11(1):9250.
[55] AHBARA A M,KHBOU M K,RHOMDHANE R,et al.Genome variation in tick infestation and cryptic divergence in Tunisian indigenous sheep[J].BMC Genomics,2022,23(1):167.
[56] MASTRANGELO S,TOLONE M,SARDINA M T,et al.Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep[J].Genetics Selection Evolution,2017,49(1):84.
[57] MESZAROSOVA M,MESZAROS G,MORAVCIKOVA N,et al.Within-and between-breed selection signatures in the original and improved valachian sheep[J].Animals,2022,12(11):1346.
[58] ZAVAREZ L B,UTSUNOMIYA Y T,CARMO A S,et al.Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes[J].Frontiers In Genetics,2015,6:5.
[59] MARRAS G,GASPA G,SORBOLINI S,et al.Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy[J].Animal Genetics,2015,46(2):110-121.
[60] RODRIGUEZ-RAMILO S T,REVERTER A,LEGARRA A.Islands of runs of homozygosity indicate selection signatures in Ovis aries 6(OAR6) of French dairy sheep[J].JDS Communications,2021,2(3):132-136.
[61] CESARANI A,GASPA G,CORREDDU F,et al.Unravelling the effect of environment on the genome of Sarda breed ewes using runs of homozygosity[J]. Journal of Animal Breeding and Genetics,2022,139(3):292-306.
[62] SARAVANAN K A,PANIGRAHI M,KUMAR H,et al.Selection signatures in livestock genome:A review of concepts,approaches and applications[J].Livestock Science,2020,241:104257.
[63] DENISKOVA T,DOTSEV A,SELIONOVA M,et al.Biodiversity of Russian local sheep breeds based on pattern of runs of homozygosity[J].Diversity,2021,13(8):360.