Genome-Wide Association Studies and Runs of Homozygosity Reveals Genetic Markers Associated with Reproductive Performance in Korean Duroc, Landrace, and Yorkshire Breeds

被引:1
|
作者
Mekonnen, Kefala Taye [1 ,2 ]
Lee, Dong-Hui [1 ]
Cho, Young-Gyu [1 ]
Son, Ah-Yeong [1 ]
Seo, Kang-Seok [1 ]
机构
[1] Sunchon Natl Univ, Dept Anim Sci & Technol, Sunchon 57922, South Korea
[2] Arsi Univ, Coll Agr & Environm Sci, Dept Anim Sci, Asella 193, Ethiopia
关键词
breed; candidate genes; genome; GWAS; Korea; NBA; run of homozygosity; TNB;
D O I
10.3390/genes15111422
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Background: Reproductive performance is critical in the pig industry, and improved sow performance could lead to increased economic benefits. GWAS and ROH analyses based on SNP array data were conducted to identify the breed-specific genetic architecture underlying the variation in NBA and TNB. Methods: A total of 7488 breeding pigs with phenotypic data from 1586 Duroc, 2256 Landrace, and 3646 Yorkshire breeds, along with 76,756 SNP markers from Korean grand-grand-parent (GGP) breeding farms, were used. Results: In the Duroc breeds, SNPs on SSC 9 and 17 were found to be associated with the SIDT2 and TGM2 genes, respectively. In the Landrace breed, PPP1R9A, LMTK2, and GTF2H3 on SSCs 9, 3, and 14, respectively, were associated with both TNB and NBA. With the Yorkshire breed genome, GRID1, DLGAP2, ZZEF1, PARG, RNF17, and NDUFAF5 in SSCs 14, 15, 12, 14, 11, and 17, respectively, were associated with NBA and TNB traits. These genes have distinct functions, ranging from synaptic transmission and cytoskeletal organization to DNA repair and cellular energy production. In the Duroc breed, six genes identified in the ROH islands were associated with various biological pathways, molecular functions, and cellular components. NT5DC1 was associated with metaphyseal chondrodysplasia, CRTAC1 with ion binding, CFAP43 with spermatogenic failure, CASC3 with intracellular mRNA localization, ERC2 with cellular component organization, and FOCAD with Focadhesin. In the Landrace and Yorkshire breeds, PDE6D was associated with GTPase inhibitor activity. Conclusions: Through GWAS and ROH analyses, we identified breed-specific SNP markers associated with NBA and TNB in three breed genotypes, providing insights for improving reproductive performance efficiency and contributing to future breeding strategies.
引用
收藏
页数:16
相关论文
共 50 条
  • [41] Genome-wide association study reveals serovar-associated genetic loci in Riemerella anatipestifer
    Zhishuang Yang
    Xueqin Yang
    Mingshu Wang
    Renyong Jia
    Shun Chen
    Mafeng Liu
    Xinxin Zhao
    Qiao Yang
    Ying Wu
    Shaqiu Zhang
    Juan Huang
    Xumin Ou
    Sai Mao
    Qun Gao
    Di Sun
    Bin Tian
    Dekang Zhu
    Anchun Cheng
    BMC Genomics, 25
  • [42] Genome-Wide Association Analysis Reveals Genetic Loci and Candidate Genes for Chest, Abdominal, and Waist Circumferences in Two Duroc Pig Populations
    Zhou, Shenping
    Ding, Rongrong
    Zhuang, Zhanwei
    Zeng, Haiyu
    Wen, Shuxian
    Ruan, Donglin
    Wu, Jie
    Qiu, Yibin
    Zheng, Enqin
    Cai, Gengyuan
    Yang, Jie
    Wu, Zhenfang
    Yang, Ming
    FRONTIERS IN VETERINARY SCIENCE, 2022, 8
  • [43] Genome-Wide Association Study for the Identification of Novel Genetic Variants Associated with the Risk of Neuroblastoma in Korean children
    Bae, Joon Seol
    Lee, Ji Won
    Yoo, Jung Eun
    Joung, Je-Gun
    Yoo, Keon Hee
    Koo, Hong Hoe
    Song, Yun-Mi
    Sung, Ki Woong
    CANCER RESEARCH AND TREATMENT, 2020, 52 (04): : 1251 - 1261
  • [44] Genome-wide association study identifies genomic regions associated with key reproductive traits in Korean Hanwoo cows
    Haque, Md Azizul
    Lee, Yun-Mi
    Ha, Jae-Jung
    Jin, Shil
    Park, Byoungho
    Kim, Nam-Young
    Won, Jeong-Il
    Kim, Jong-Joo
    BMC GENOMICS, 2024, 25 (01):
  • [45] Identification of genetic markers associated with milk production traits in Chinese Holstein cattle based on post genome-wide association studies
    Yang, Zhenwei
    Lian, Zhiquan
    Liu, Guangbin
    Deng, Ming
    Sun, Baoli
    Guo, Yongqing
    Liu, Dewu
    Li, Yaokun
    ANIMAL BIOTECHNOLOGY, 2021, 32 (01) : 67 - 76
  • [46] Genetic Analyses and Genome-Wide Association Studies on Pathogen Resistance of Bos taurus and Bos indicus Cattle Breeds in Cameroon
    Abanda, Babette
    Schmid, Markus
    Paguem, Archile
    Iffland, Hanna
    Preuss, Siegfried
    Renz, Alfons
    Eisenbarth, Albert
    GENES, 2021, 12 (07)
  • [47] Genome-Wide Association Studies, Runs of Homozygosity Analysis, and Copy Number Variation Detection to Identify Reproduction-Related Genes in Bama Xiang Pigs
    Mo, Jiayuan
    Lu, Yujie
    Zhu, Siran
    Feng, Lingli
    Qi, Wenjing
    Chen, Xingfa
    Xie, Bingkun
    Chen, Baojian
    Lan, Ganqiu
    Liang, Jing
    FRONTIERS IN VETERINARY SCIENCE, 2022, 9
  • [48] IDENTIFICATION OF GENETIC VARIATION SPECIFICALLY ASSOCIATED WITH PSORIATIC ARTHRITIS USING GENOME-WIDE ASSOCIATION STUDIES
    Canete, J. D.
    Aterido, A.
    Pinto, J. A.
    Gratacos, J.
    Queiro, R.
    Montilla, C.
    Torre-Alonso, J. C.
    Perez-Venegas, J.
    Fernandez-Nebro, A.
    Munoz-Fernandez, S.
    Gonzalez, C.
    Roig, D.
    Zarco, P.
    Erra, A.
    Rodriguez, J.
    Castaneda, S.
    Rubio, E.
    Salvador, G.
    Diaz-Torne, C.
    Blanco, R.
    Willisch-Dominguez, A.
    Mosquera, J. A.
    Vela, P.
    Tornero, J.
    Sanchez-Fernandez, S.
    Corominas, H.
    Ramirez, J.
    Pluma, A.
    Lopez-Corbeto, M.
    Lopez-Lasanta, M.
    Tortosa, R.
    Palau, N.
    Marsal, S.
    Julia, A.
    ANNALS OF THE RHEUMATIC DISEASES, 2017, 76 : 946 - 947
  • [49] Genome-wide association studies reveal genetic loci associated with plasma cholinesterase activity in ducks
    Xu, Y.
    Liu, H.
    Jiang, Y.
    Fan, W.
    Hu, J.
    Zhang, Y.
    Guo, Z.
    Xie, M.
    Huang, W.
    Liu, X.
    Zhou, Z.
    Hou, S.
    ANIMAL GENETICS, 2019, 50 (03) : 287 - 292
  • [50] Genome-wide association studies identify genetic variants associated with comorbidities of atopic dermatitis and psoriasis
    Saklatvala, J.
    Hartley, A.
    Ramessur, R.
    Budu-Aggrey, A.
    Brown, S. J.
    Smith, C.
    Min, J.
    Dand, N.
    Paternoster, L.
    JOURNAL OF INVESTIGATIVE DERMATOLOGY, 2022, 142 (12) : S231 - S231