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.
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页数:16
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