Genome-wide selection signatures analysis of litter size in Dazu black goats using single-nucleotide polymorphism
Genome-wide selection signatures analysis of litter size in Dazu black goats using single-nucleotide polymorphism
复制标题
利用单核苷酸多态性对大足黑山羊产羔数进行全基因组选择特征分析
DOI：
10.1007/s13205-019-1869-3
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发表时间：
2019-09-01
期刊：
影响因子：
2.8
通讯作者：
Zeng, Yan
中科院分区：
文献类型：
--
作者：
E, Guang-Xin;Duan, Xing-Hai;Zeng, Yan
窝产仔数被认为是估测家畜生产力的最重要指标。中国地方山羊的产羔数高于其他国家的商品山羊品种，这可能有助于加速山羊育种的遗传改良。对31只第3胎产羔数标准差极差的大足黑山羊进行了全基因组选择性扫描分析，通过不同的分析方法确定了基因组的重要区域和候选基因。该分析共鉴定了33，917，703个变异，包括32，262，179个SNP和1，655，524个indel。此外，在个体水平上以95%的阈值，用pi、Tajima's D、pi A/pi B和F-ST获得了两个与产仔数相关的新候选基因（LRP 1 B和GLRB）。这两个基因被注释在五个GO术语（定位，结合，大分子复合物，膜部分，和膜）和两个途径（长期抑郁症和神经活性配体-受体相互作用途径）。连锁不平衡（LD）分析结果显示，在LRP 1B和GRID 2中，高产大足黑山羊与低产山羊表现出显着不同的LD模式。窝仔数变异性遗传力低，与家畜中发现的多种复杂因素有关。通过小样本量的全基因组选择性扫描分析获得清晰的解释和显著的信号是困难的。然而，我们调查了一些候选基因，特别是LRP 1B和GLRB，这可能为进一步研究提供有用的信息。
Litter size is considered to be the most important index for estimating domestic animal productivity. The number of indigenous goats in China with higher litter sizes than those of commercial breeds in other countries may be helpful for accelerating genetic improvements in goat breeding. We performed a genome-wide selective sweep analysis of 31 Dazu black goats with extreme standard deviation in litter size within the third fetus to identify significant genomic regions and candidate genes through different analyses. The analysis identified a total of 33,917,703 variants, including 32,262,179 SNPs and 1,655,524 indels. In addition, two novel candidate genes (LRP1B and GLRB), which are related to litter size, were obtained with pi, Tajima's D, pi A/pi B, and F-ST at the individual level with a 95% threshold for each parameter. These two genes were annotated in five GO terms (localization, binding, macromolecular complex, membrane part, and membrane) and two pathways (long-term depression and neuroactive ligand-receptor interaction pathway). Regarding the result of linkage disequilibrium (LD) analysis, in LRP1B and GRID2, the high-yield Dazu black goats exhibit significantly different LD patterns from low-yield goats. Litter size variability has low heritability and is related to multiple complex factors found in domestic animals. Obtaining a clear explanation and significant signal by genome-wide selective sweep analysis with a small sample size is difficult. However, we investigated some candidate genes, particularly LRP1B and GLRB, which may provide useful information for further research.