Development and Application of 50K Liquid Phase Breeding Chip for Sheep(Ovis aries)
XU Ya-Nan1, CAO Li-Li2, SONG Li-Shuang1, LIU Xue-Fei1, LEI Jia-Ru1, JIANG Xi-Qing1, LI Guang-Peng1,*, YANG Lei1,*
1 State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China; 2 Department of Agriculture and Animal Husbandry of Inner Mongolia Autonomous Region, Hohhot 010070, China
Abstract：With the advancement of molecular breeding technologies, genomic selection based on SNP markers has become a key technical approach for improving the efficiency of genetic improvement. Sheep(Ovis aries) are livestock of significant economic value, and developing efficient breeding tools tailored to their populations is crucial to advancing the sheep industry. This study developed a 50K SNP liquid phase breeding chip for sheep breeding using genomic data and targeted capture sequencing technology. By integrating SNP data from 355 individuals in the iSheep database and resequencing data from 10 East Friesian sheep, 58 859 high-quality SNP loci were selected, including 31 729 core functional loci(53.91%). The average spacing between the selected SNPs is 43.9 kb, covering functional regions associated with important economic traits. Quality testing of the chip was conducted by randomly sampling 100 sheep, and the results demonstrated excellent performance in the sheep population: The map rate exceeded 99.7%, capture rate was higher than 76%, dup rate was below 12%, and the SNP call rate reached over 95.98%. Further genome-wide association analysis used this breeding chip to identify genetic loci influencing sheep growth traits(such as body weight, body length, abdominal girth, and chest girth). The results showed that the chip successfully identified multiple significant SNP loci associated with growth traits. This chip holds broad application prospects in sheep molecular breeding, particularly in breeding efforts related to important economic traits, as it can help improve breeding efficiency and advance sheep genetic improvement. This study provides a scientific basis for future molecular marker selection of sheep growth traits
徐亚男, 曹丽丽, 宋丽爽, 刘雪霏, 雷佳茹, 姜希卿, 李光鹏, 杨磊. 绵羊50K液相育种芯片的开发及应用[J]. 农业生物技术学报, 2026, 34(8): 1803-1815.
XU Ya-Nan, CAO Li-Li, SONG Li-Shuang, LIU Xue-Fei, LEI Jia-Ru, JIANG Xi-Qing, LI Guang-Peng, YANG Lei. Development and Application of 50K Liquid Phase Breeding Chip for Sheep(Ovis aries). 农业生物技术学报, 2026, 34(8): 1803-1815.
[1] 李利君, 汪代华, 赵云川, 等. 2025. 液相芯片技术及其在羊育种中的应用[J]. 中国畜禽种业, 21(12): 7-20. (Li L J, Wang D H, Zhao Y C, et al.2025. Liquid chip ttechnology and its application in caprid breeding[J]. The Chinese Livestock and Poultry Breeding, 21(12): 7-20.) [2] Ahbara A, Bahbahani H, Almathen F, et al.2018. Genome-wide variation, candidate regions and genes associated with fat deposition and tail morphology in ethiopian indigenous sheep[J]. Frontiers in Genetics, 9: 699. [3] Bakhtiarizadeh M R, Alamouti A A.2020. RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep[J]. Scientific Reports, 10(1): 13525. [4] Bolormaa S, Brown D J, Swan A A, et al.2017. Genomic prediction of reproduction traits for Merino sheep[J]. Animal Genetics, 48(3): 338-348. [5] Brito L F, Clarke S M, McEwan J C, et al.2017. 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, 18(1): 7. [6] Cao Y, Ai Y, Zhang X, et al.2023. Genome-wide epigenetic dynamics during postnatal skeletal muscle growth in Hu sheep[J]. Communications Biology, 6(1): 1077. [7] Cao Y H, Xu S S, Shen M, et al.2021. Historical introgression from wild relatives enhanced climatic adaptation and resistance to pneumonia in sheep[J]. Molecular Biology and Evolution, 38(3): 838-855. [8] Daetwyler H D, Swan A A, Werf J H, et al.2012. Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation[J]. Genetics, Selection, Evolution: GSE, 44(1): 33. [9] Dolebo A T, Khayatzadeh N, Melesse A, et al.2019. Genome-wide scans identify known and novel regions associated with prolificacy and reproduction traits in a sub-Saharan African indigenous sheep(Ovis aries)[J]. Mammalian Genome, 30(11-12): 339-352. [10] Druet T, Schrooten R, Roos R, et al.2010. Imputation of genotypes from different single nucleotide polymorphism panels in dairy cattle[J]. Journal of Dairy Science, 93(11): 5443-5454. [11] Duchemin S I, Colombani C, Legarra A, et al.2012. Genomic selection in the French Lacaune dairy sheep breed[J]. Journal of Dairy Science, 95(5): 2723-2733. [12] Gifford C A, Assiri A M, Satterfield M C, et al.2008. Receptor transporter protein 4(RTP4) in endometrium, ovary, and peripheral blood leukocytes of pregnant and cyclic ewes[J]. Biology of Reproduction, 79(3): 518-524. [13] Granleese T, Clark S A, Swan A A, et al.2015. Increased genetic gains in sheep, beef and dairy breeding programs from using female reproductive technologies combined with optimal contribution selection and genomic breeding values[J]. Genetics, Selection, Evolution: GSE, 47(1): 70. [14] Guillenea A, Su G, Lund M S, et al.2022. Genomic prediction in Nordic Red dairy cattle considering breed origin of alleles[J]. Journal of Dairy Science, 105(3): 2426-2438. [15] Guo T, Yuan, C, Liu, J, et al.2025. Design, validation, and application of a 1K liquid chip for genome-wide association analysis in Alpine Merino sheep[J]. Frontiers in veterinary science, 12: 1690580. [16] Guo Y, Bai F, Wang J, et al.2023. Design and characterization of a high-resolution multiple-SNP capture array by target sequencing for sheep[J]. Journal of Animal Science, 101: skac383. [17] Husien H M, Saleh A A, Hassanine N, et al.2024. The evolution and role of molecular tools in measuring diversity and genomic selection in livestock populations(traditional and up-to-date insights): A comprehensive exploration[J]. Veterinary Sciences, 11(12): 627. [18] Jibrila I, Ten N J, Vandenplas J, et al.2023. Impact of genomic preselection on subsequent ssGBLUP evaluation of preselected animals for scarcely recorded feed intake in pigs[J]. Journal of Animal Breeding and Genetics, 140(3): 253-263. [19] Johnsson M.2023. Genomics in animal breeding from the perspectives of matrices and molecules[J]. Hereditas, 160(1): 20. [20] Kardos M, Luikart G, Bunch R, et al.2015. Whole-genome resequencing uncovers molecular signatures of natural and sexual selection in wild bighorn sheep[J]. Molecular Ecology, 24(22): 5616-5632. [21] Lakhssassi K, Lahoz B, Sarto P, Iet al.2021. Genome-wide association study demonstrates the role played by the CD226 gene in Rasa Aragonesa sheep reproductive seasonality[J]. Animals(Basel), 11(4): 1171. [22] Li X, Lin B, Zhang X, et al.2022. Comparative transcriptomics in the hypothalamic-pituitary-gonad axis of mammals and poultry[J]. Genomics, 114(4): 110396. [23] Liu D, Li X, Wang L, et al.2024. Genome-wide association studies of body size traits in Tibetan sheep[J]. BMC Genomics, 25(1): 739. [24] Mamanova L, Coffey A J, Scott C E, et al.2010. Target-enrichment strategies for next-generation sequencing[J]. Nature Methods, 7(2): 111-118. [25] Manimekalai R, Suresh G, Kurup G H, et al.2020. Role of NGS and SNP genotyping methods in sugarcane improvement programs[J]. Critical Reviews in Biotechnology, 40(6): 865-880. [26] Megdiche S, Mastrangelo S, Ben Hamouda M, et al.2019. 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, 10: 1025. [27] Meuwissen T H, Hayes B J, Goddard M E.2001. Prediction of total genetic value using genome-wide dense marker maps[J]. Genetics, 157(4): 1819-1829. [28] Moghaddar N, Swan A A, van der Werf J H J.2017. Genomic prediction from observed and imputed high-density ovine genotypes[J]. Genetics, Selection, Evolution: GSE, 49(1): 40. [29] Ott A, Liu S, Schnable J C, et al.2017. tGBS®genotyping-by-sequencing enables reliable genotyping of heterozygous loci[J]. Nucleic Acids Research, 45(21): e178. [30] Pausch H, Jung S, Edel C, et al.2012. Genome-wide association study uncovers four QTL predisposing to supernumerary teats in cattle[J]. Animal Genetics , 43(6): 689-695. [31] Roffler G H, Amish S J, Smith S, et al.2016. SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate[J]. Molecular Ecology Resources, 16(5): 1147-1164. [32] Shumbusho F, Raoul J, Astruc J M, et al.2013. Potential benefits of genomic selection on genetic gain of small ruminant breeding programs[J]. Journal of Animal Science, 91(8): 3644-3657. [33] Talebi R, Szmatoa T, Mészáros G, et al.2020. Runs of homozygosity in modern chicken revealed by sequence data[J]. G3(Bethesda, Md.), 10(12): 4615-4623. [34] Thomson M J, Singh N, Dwiyanti M S, et al.2017. Large-scale deployment of a rice 6K SNP array for genetics and breeding applications[J]. Rice(New York, N.Y.), 10(1): 40. [35] Tian Y, Sun P, Liu W X, et al.2022. Single-cell RNA sequencing of the Mongolia sheep testis reveals a conserved and divergent transcriptome landscape of mammalian spermatogenesis[J]. The FASEB Journal, 36(6): e22348. [36] Wallace J G, Rodgers-Melnick E, Buckler E S.2018. On the road to breeding 4.0: Unraveling the good, the bad, and the boring of crop quantitative genomics[J]. Annual Review of Genetics, 52: 421-444. [37] Wang F, Liu J, Zeng Q, Zhuoga D.2022. Comparative analysis of long noncoding RNA and mRNA expression provides insights into adaptation to hypoxia in Tibetan sheep[J]. Scientific Reports, 12(1): 6597. [38] Wang W, Zhang X, Zhou X, et al.2019. Deep genome resequencing reveals artificial and natural selection for visual deterioration, plateau adaptability and high prolificacy in Chinese domestic sheep[J]. Frontiers in Genetics, 10: 300. [39] Wang Z H, Zhu Q H, Li X, et al.2021. iSheep: An integrated resource for sheep genome, variant and phenotype[J]. Frontiers in Genetics, 12: 714852. [40] Xue D, Ma Y, Li M, et al.2015. Mycoplasma ovipneumoniae induces inflammatory response in sheep airway epithelial cells via a MyD88-dependent TLR signaling pathway[J]. Veterinary Immunology and Immunopathology, 163(1-2): 57-66. [41] Yang J, Li W R, Lv F H, et al.2016. Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments[J]. Molecular Biology and Evolution, 33(10): 2576-2592. [42] Yang J, Zhang J, Du H, et al.2022. The vegetable SNP database: An integrated resource for plant breeders and scientists[J]. Genomics, 114(3): 110348. [43] Yilmaz O, Kizilaslan M, Arzik Y, et al.2022. Genome-wide association studies of preweaning growth and in vivo carcass composition traits in Esme sheep[J]. Journal of Animal Breeding and Genetics, 139(1): 26-39. [44] Zhang D Y, Zhang X X, Li F D, et al.2022. Whole-genome resequencing reveals molecular imprints of anthropogenic and natural selection in wild and domesticated sheep[J]. Zoological Research, 43(5): 695-705. [45] Zhang W, Luosang C C, Yuan C, et al.2024. Selection signatures of wool color in Gangba sheep revealed by genome-wide SNP discovery[J]. BMC Genomics, 25(1): 606.
