Comprehensive genome-wide analysis of genetic loci and candidate genes associated with litter traits in purebred Berkshire pigs of Korea.

IF 2.4 2区农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Animal Bioscience Pub Date : 2024-10-01 Epub Date: 2024-08-18 DOI:10.5713/ab.24.0046

Jun Park

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Abstract

Objective: The objective of this study was to identify genomic regions and candidate genes associated with the total number of piglets born (TNB), number of piglets born alive (NBA), and total number of stillbirths (TNS) in Berkshire pigs.

Methods: This study used a total of 11,228 records and 2,843 single-nucleotide polymorphism (SNP) data obtained from Illumina porcine 60 K and 80 K chips. The estimated genomic breeding values (GEBVs) and SNP effects were estimated using weighted single-step genomic BLUP (WssGBLUP).

Results: The heritabilities of the TNB, NBA, and TNS were determined using single-step genomic best linear unbiased prediction (ssGBLUP). The heritability estimates were 0.13, 0.12, and 0.015 for TNB, NBA, and TNS, respectively. When comparing the accuracy of breeding value estimates, the results using pedigree-based BLUP (PBLUP) were 0.58, 0.60, and 0.31 for TNB, NBA, and TNS, respectively. In contrast, the accuracy increased to 0.67, 0.66, and 0.42 for TNB, NBA, and TNS, respectively, when using WssGBLUP, specifically in the last three iterations. The results of weighted single-step genome-wide association studies (WssGWAS) showed that the highest variance explained for each trait was predominantly located in the Sus scrofa chromosome 5 (SSC5) region. Specifically, the variance exceeded 4% for TNB, 3% for NBA, and 6% for TNS. Within the SSC5 region (12.26 to 12.76 Mb), which exhibited the highest variance for TNB, 20 SNPs were identified, and five candidate genes were identified: TIMP3, SYN3, FBXO7, BPIFC, and RTCB.

Conclusion: The identified SNP markers for TNB, NBA, and TNS were expected to provide valuable information for genetic improvement as an understanding of their expression and genetic architecture in Berkshire pigs. With the accumulation of more phenotype and SNP data in the future, it is anticipated that more effective SNP markers will be identified.

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韩国纯种伯克希尔猪产仔性状相关遗传位点和候选基因的全基因组综合分析

研究目的本研究旨在确定与伯克希尔猪的出生仔猪总数（TNB）、活产仔猪总数（NBA）和死胎总数（TNS）相关的基因组区域和候选基因：本研究使用了从 Illumina 猪 60 K 和 80 K 芯片获得的 11,228 条记录和 2,843 个单核苷酸多态性 (SNP) 数据。使用加权单步基因组 BLUP（WssGBLUP）估算了估计的基因组育种值（GEBVs）和 SNP 效应：使用单步基因组最佳线性无偏预测（ssGBLUP）确定了 TNB、NBA 和 TNS 的遗传力。TNB、NBA和TNS的遗传力估计值分别为0.13、0.12和0.015。在比较育种值估计的准确性时，使用基于 pedigree 的 BLUP（PBLUP）得出的 TNB、NBA 和 TNS 的结果分别为 0.58、0.60 和 0.31。相比之下，在使用 WssGBLUP 时，特别是在最后三次迭代中，TNB、NBA 和 TNS 的准确率分别提高到 0.67、0.66 和 0.42。加权单步全基因组关联研究（WssGWAS）的结果表明，每个性状的最高方差解释主要位于苏氏猪第 5 号染色体（SSC5）区域。具体而言，TNB 的方差超过 4%，NBA 的方差超过 3%，TNS 的方差超过 6%。在 TNB 方差最大的 SSC5 区域（12.26 至 12.76 Mb）内，发现了 20 个 SNPs，并确定了 5 个候选基因：结论：：已鉴定的 TNB、NBA 和 TNS SNP 标记有望为遗传改良提供有价值的信息，因为人们可以了解它们在伯克希尔猪中的表达和遗传结构。随着今后表型和 SNP 数据的不断积累，预计将会发现更多有效的 SNP 标记。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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