Zhang Jie, Zhao Kai, Hou Dan, Cai Junhuo, Zhang Qixiang, Cheng Tangren, Pan Huitang, Yang Weiru
Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 China.
Plant Mol Biol Report. 2017;35(1):37-46. doi: 10.1007/s11105-016-1000-4. Epub 2016 Aug 8.
Next-generation sequencing technologies provide opportunities to ascertain the genetic basis of phenotypic differences, even in the closely related cultivars via detection of large amount of DNA polymorphisms. In this study, we performed whole-genome re-sequencing of two mei cultivars with contrasting tree architecture. 75.87 million 100 bp pair-end reads were generated, with 92 % coverage of the genome. Re-sequencing data of two former upright mei cultivars were applied for detecting DNA polymorphisms, since we were more interested in variations conferring weeping trait. Applying stringent parameters, 157,317 mutual single nucleotide polymorphisms (SNPs) and 15,064 mutual insertions-deletions (InDels) were detected and found unevenly distributed within and among the mei chromosomes, which lead to the discovery of 220 high-density, 463 low-density SNP regions together with 80 high-density InDel regions. Additionally, 322 large-effect SNPs and 433 large-effect InDels were detected, and 10.09 % of the SNPs were observed in coding regions. 5.25 % SNPs in coding regions resulted in non-synonymous changes. Ninety SNPs were chosen randomly for validation using high-resolution melt analysis. 93.3 % of the candidate SNPs contained the predicted SNPs. Pfam analysis was further conducted to better understand SNP effects on gene functions. DNA polymorphisms of two known QTL loci conferring weeping trait and their functional effect were also analyzed thoroughly. This study highlights promising functional markers for molecular breeding and a whole-genome genetic basis of weeping trait in mei.
新一代测序技术为确定表型差异的遗传基础提供了机会，即使是在亲缘关系密切的品种中，也能通过检测大量的DNA多态性来实现。在本研究中，我们对两个树形结构截然不同的梅花品种进行了全基因组重测序。共产生了7587万个100bp的双端 reads，基因组覆盖率达92%。由于我们对赋予垂枝性状的变异更感兴趣，因此将两个之前直立型梅花品种的重测序数据用于检测DNA多态性。应用严格的参数，检测到157317个共同单核苷酸多态性（SNP）和15064个共同插入缺失（InDel），发现它们在梅花染色体内部和之间分布不均，这导致发现了220个高密度、463个低密度SNP区域以及80个高密度InDel区域。此外，还检测到322个大效应SNP和433个大效应InDel，并且在编码区观察到10.09%的SNP。编码区5.25%的SNP导致非同义变化。随机选择90个SNP使用高分辨率熔解分析进行验证。93.3%的候选SNP包含预测的SNP。进一步进行了Pfam分析以更好地了解SNP对基因功能的影响。还深入分析了两个已知赋予垂枝性状的QTL位点的DNA多态性及其功能效应。本研究突出了在梅花分子育种中具有前景的功能标记以及垂枝性状的全基因组遗传基础。
