China Animal Husbandry and Veterinary Medicine ›› 2023, Vol. 50 ›› Issue (8): 3258-3266.doi: 10.16431/j.cnki.1671-7236.2023.08.023
• Genetics and Breeding • Previous Articles
SUN Lixia1,2, LU Zengkui1,2, YUAN Chao1,2, ZHANG Dan1,2, LIU Jianbin1,2
Received:
2023-02-03
Published:
2023-07-27
CLC Number:
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.
[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. |
[1] | LI Xiaojie, HAN Jiangang, LIANG Benmeng, YE Shaohui, JIANG Lin, MA Yuehui. Research Advance on Available Genetic Markers for Important Economic Traits in Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(8): 3142-3156. |
[2] | BI Yazhen, SHANG Mingyu, XIONG Jinke, HU Wenping, HE Jianning, ZHANG Li. Polymorphism of SRP68 Gene and Its Association with Growth Traits in Hu Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(8): 3189-3198. |
[3] | ZHAO Mengyao, CHEN Xiaoliang, LI Xiunan, SU Lede, TIAN Ying, JIAN Ruizhen, YANG Yanyan, LI Haijun. Study on the Mechanism of the Double Lamb Trait Gene ADAMTS-1 in Mongolian Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(8): 3229-3238. |
[4] | WANG Chenguang, SUI Zhiyuan, ZHANG Yongjie, ZHANG Zhishuai, LI Xiaojun, XING Feng. Cloning and Bioinformatics Analysis of BMP7 Gene and Its Tissue Expression at Different Stages of Puberty in Dolang Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(7): 2629-2638. |
[5] | YAN Hang, HAO Wen, WANG Chengqian, WANG Huie. Differentially Expressed Genes and Bioinformatics Analysis of Superovulation Ovary in Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(7): 2740-2754. |
[6] | TAO Maohai, MENG Ke, RONG Xuan, QIANG Hao, NIE Wei, GUO Chenhao, FENG Dengzhen. Polymorphism of MSTN Gene and Its Association Analysis with Meat Quality Traits in Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(7): 2766-2776. |
[7] | WANG Saiqiao, ZHAO Lu, ZHAI Zhenhan, ZHANG Binglei, JIA Wanhang, WANG Yuqin. Tissue Expression and Bioinformatics Analysis of miR-449a/b Precursor Sequences in Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2175-2184. |
[8] | LIU Jinyu, ZHANG Yang, MA Xumei, ZHOU Qian, ZHOU Yang, ZHANG Chunxiang, SHI Lei, REN Youshe. Effects of Glutathione on Cryopreservation of Sheep Semen [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2388-2394. |
[9] | ZHANG Huaqiang, WANG Pinsheng, LI Xiao, WEI Panpeng, YAN Lingmin, JIANG Bingbing, WANG Zhaogui, WANG Xuefang, ZENG Huanqing, FAN Yi, GAO Zhenglong, WANG Xuebing. Effects of Fermented Hybrid Broussonetia papyrifera on Growth Performance, Meat Quality,Digestive Enzyme Activity and Intestinal Flora Structure of Hu Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1876-1887. |
[10] | ZHAO Qianming, QI Meng, XU Zeli, GONG Pihong, LU Chenyang, PEI Zhiyang, JIAN Fuchun, WANG Jiandong, JING Bo, NING Changsheng. Investigation of Intestinal Parasites Occurrence in Sheep and Environmental Contamination in Large-scale Housing Farms [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 2156-2165. |
[11] | CUI Shuang, Wurlig, Alder, XIAO Min, WANG Jianqiu, GONG Jian. Effects of Yeast Selenium Supplementation on Gastrointestinal Microflora in Sheep Under Grazing Conditions [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 952-965. |
[12] | ZHANG Yongjie, SUI Zhiyuan, ZHANG Zhishuai, WANG Chenguang, LI Xiaojun, XING Feng. Cloning and Bioinformatics Analysis of NPTX1 Gene and Its Tissues Expression at Puberty in Dolang Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 1048-1058. |
[13] | ZHANG Mingliang, ZHANG Hailong, MA Shipeng, WANG Cailian, LANG Xia. Effects of Zanthoxylum bungeanum Essential Oil on Production Performance and Gastrointestinal Tissue Structure of Small-tail Han Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(2): 556-563. |
[14] | LI Chenglan, GUO Tingting, YUE Yaojing. Research Advances on Genomic Selection and Its Application in Sheep Breeding [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(2): 616-625. |
[15] | 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. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||