Exploring dominance variance and loci contributing to dominance variation is important to understand the genetic architecture behind quantitative traits. The objectives of this study were i) to estimate dominance variances, ii) to detect quantitative trait loci (QTL) with dominant effects, and iii) to evaluate the power and the precision of identifying loci with dominance effect through post-hoc simulations, with applications for female fertility in Danish Holstein cattle. The female fertility records analyzed were number of inseminations (NINS), days from calving to first insemination (ICF), and days from the first to last insemination (IFL), covering both abilities to recycle and to get pregnant in the female reproductive cycle. There were 3,040 heifers and 4,483 cows with both female fertility records and Illumina BovineSNP50 BeadChip genotypes (35,391 single nucleotide polymorphisms (SNP) after quality control). Genomic best linear unbiased prediction (BLUP) models were used to estimate additive and dominance genetic variances. Linear mixed models were used for association analyses. A post-hoc simulation study was performed using genotyped heifers' data. In heifers, estimates of dominance genetic variances for female fertility traits were larger than additive genetic variances, but had large standard errors. The variance components for fertility traits in cows could not be estimated due to non-convergence of the statistical model. In total, five QTL located on chromosomes 9, 11 (2 QTL), 19, and 28 were identified and all of them showed both additive and dominance genetic effects. Among them, the SNP rs29018921 on chromosome 9 is close to a previously identified QTL in Nordic Holstein for interval between first and last insemination. This SNP is located in the 3' untranslated region of gene peptidylprolyl isomerase like 4 (PPIL4), which was shown to be associated with milk production traits in US Holstein cattle but not known for fertility-related functions. Simulations indicated that the current sample size had limited power to detect QTL with dominance effects for female fertility probably due to low QTL variance. More females need to be genotyped to achieve reliable mapping of QTL with dominance effects for female fertility.

译文

:探索优势变异和导致优势变异的基因座对于理解定量性状背后的遗传结构很重要。这项研究的目的是:i)估计优势变异,ii)检测具有显性效应的数量性状基因座(QTL),iii)评估通过事后模拟,丹麦荷斯坦牛的雌性育性应用。分析的女性生育率记录为受精次数(NINS),从产犊到第一次受精的天数(ICF)和从第一次受精到最后一次受精的天数(IFL),涵盖了女性生殖周期中的循环能力和受孕能力。有3,040头小母牛和4,483头母牛既有雌性育种记录,又有Illumina BovineSNP50 BeadChip基因型(质量控制后有35,391个单核苷酸多态性(SNP))。基因组最佳线性无偏预测(BLUP)模型用于估计加性和优势遗传方差。线性混合模型用于关联分析。使用基因型小母牛的数据进行了事后模拟研究。在小母牛中,女性育性性状的优势遗传方差估计值大于加性遗传方差,但标准误较大。由于统计模型的不收敛性,无法估计母牛生育力特征的方差成分。总共鉴定出了位于9号,11号(2个QTL),19号和28号染色体上的5个QTL,它们都显示了加性和优势遗传效应。其中,第9号染色体上的SNP rs29018921接近先前在Nordic Holstein中确定的QTL,在第一次和最后一次授精之间。该SNP位于像4(PPIL4)的肽基脯氨酰异构酶基因的3'非翻译区,已显示与美国荷斯坦牛的奶生产性状有关,但与生育力相关的功能未知。模拟表明,当前的样本量检测QTL的能力有限,可能对QTL的影响较小,这对女性的生育力具有主导作用。需要对更多的雌性进行基因分型以实现可靠的QTL定位,并具有显着的雌性育性效应。

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