Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

First author: Jinyu Wang; Affiliations: Iowa State University (爱荷华州立大学): Ames, USA

Corresponding author: Jianming Yu

Plant domestication provides a unique model to study genome evolution. Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domestication. Interestingly, domesticated accessions have significantly higher [A] and [T] values across genome-wide polymorphic sites than accessions sampled from the corresponding progenitor species. However, the relative contributions of different genomic regions to this genome divergence pattern and underlying mechanisms have not been well characterized. Here, we investigate the genome-wide base-composition patterns by analyzing millions of SNPs segregating among 100 accessions from a teosinte-maize comparison set and among 302 accessions from a wild-domesticated soybean comparison set. We show that non-genic part of the genome has a greater contribution than genic SNPs to the [AT]-increase observed between wild and domesticated accessions in maize and soybean. The separation between wild and domesticated accessions in [AT] values is significantly enlarged in non-genic and pericentromeric regions. Motif frequency and sequence context analyses show the motifs (PyCG) related to solar-UV signature are enriched in these regions, particularly when they are methylated. Additional analysis using population-private SNPs also implicates the role of these motifs in relatively recent mutations. With base-composition across polymorphic sites as a genome phenotype, genome scans identify a set of putative candidate genes involved in UV damage repair pathways. The [AT]-increase is more pronounced in genomic regions that are non-genic, pericentromeric, transposable elements; methylated; and with low recombination. Our findings establish important links among UV radiation, mutation, DNA repair, methylation, and genome evolution.

植物驯化为植物基因组演化提供了一个很好的研究模型。关于驯化相关的基因、遗传多样性、基因组结构以及表观基因组已经有了很多报道。然而有趣的是，作者发现驯化品种相比于对应的祖先未驯化物种在全基因组多态位点上的A和T碱基含量要更高。基因组上不同区域对于该分化模式的贡献以及背后潜在的分子机制还不清楚。本文，作者通过分析来自蜀黍-玉米比较组（100个品系）和来自野生-驯化大豆比较组（302个品系）的数百万个SNP研究了全基因组范围上的碱基组成模式。作者发现相比于基因区，非基因区SNP对于驯化品种较野生种AT含量高的贡献度更高。野生种与驯化种在非基因区和近着丝粒区的AT碱基含量差异更大。基序频率及序列组成分析显示与太阳UV辐射信号相关的PyCG基序显著在这些区域富集，尤其在这些基序被甲基化后。进一步利用群体特异性SNP分析同样显示了这些基序在相对于较近发生的突变中的作用。通过将多态性位点的碱基组成作为一个基因组表型，作者通过基因组扫描鉴定了一系列的参与UV损伤修复通路的候选基因。驯化品种基因组上AT碱基含量增加更加偏向于出现在非基因、近着丝粒、转座元件；甲基化并且重组率较低的区域。本文的研究在UV辐射、突变、DNA修复、甲基化和基因组演化之间建立了重要的联系。

通讯：Jianming Yu（https://www.agron.iastate.edu/people/jianming-yu）

个人简介：1994年，西北农林科技大学，农学学士；2000年，堪萨斯州立大学，植物遗传育种硕士；2003年，明尼苏达大学，植物遗传育种博士。

研究方向：植物遗传育种。

doi: https://doi.org/10.1186/s13059-019-1683-6

Journal: Genome Biology

Published date: April 25, 2019