■这项研究的目的是确定与出生仔猪总数(TNB)相关的基因组区域和候选基因,活着出生的仔猪数量(NBA),以及伯克希尔猪的死产总数(TNS)。
■:这项研究使用了从Illumina猪60K和80K芯片获得的总共11,228条记录和2,843条单核苷酸多态性(SNP)数据。使用加权单步基因组BLUP(WssGBLUP)估计估计的基因组育种值(GEBV)和SNP效应。
■:TNB的遗传力,NBA,和TNS使用单步基因组最佳线性无偏预测(ssGBLUP)确定。TNB的遗传力估计为0.13、0.12和0.015,NBA,和TNS,分别。当比较育种价值估计的准确性时,TNB使用基于谱系的BLUP(PBLUP)的结果分别为0.58、0.60和0.31,NBA,和TNS,分别。相比之下,TNB的精度提高到0.67、0.66和0.42,NBA,和TNS,分别,使用WssGBLUP时,特别是在最后三次迭代中。加权单步全基因组关联研究(WssGWAS)的结果表明,每个性状解释的最高方差主要位于Susscrofa5号染色体(SSC5)区域。具体来说,TNB的差异超过4%,3%的NBA,TNS占6%。在SSC5区域内(12.26至12.76Mb),表现出TNB的最高方差,确定了20个SNP,并确定了五个候选基因:TIMP3,SYN3,FBXO7,BPIFC,和RTCB。
■:已确定的TNB的SNP标记,NBA,和TNS有望为遗传改良提供有价值的信息,以了解它们在Berkshire猪中的表达和遗传结构。随着未来更多的表型和SNP数据的积累,预计将鉴定出更有效的SNP标记。
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.
CONCLUSIONS: 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.