Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

First author: Dongmei Yin; Affiliations: Henan Agricultural University (河南农业大学): Zhengzhou, China

Corresponding author: Z. Jeffrey Chen

Like many important crops, peanut is a polyploid that underwent polyploidization, evolution, and domestication. The wild allotetraploid peanut species Arachis monticola (A. monticola) is an important and unique link from the wild diploid species to cultivated tetraploid species in the Arachis lineage. However, little is known about A. monticola and its role in the evolution and domestication of this important crop. A fully annotated sequence of ≈2.6 Gb A. monticola genome and comparative genomics of the Arachis species is reported. Genomic reconstruction of 17 wild diploids from AA, BB, EE, KK, and CC groups and 30 tetraploids demonstrates a monophyletic origin of A and B subgenomes in allotetraploid peanuts. The wild and cultivated tetraploids undergo asymmetric subgenome evolution, including homoeologous exchanges, homoeolog expression bias, and structural variation (SV), leading to subgenome functional divergence during peanut domestication. Significantly, SV‐associated homoeologs tend to show expression bias and correlation with pod size increase from diploids to wild and cultivated tetraploids. Moreover, genomic analysis of disease resistance genes shows the unique alleles present in the wild peanut can be introduced into breeding programs to improve some resistance traits in the cultivated peanuts. These genomic resources are valuable for studying polyploid genome evolution, domestication, and improvement of peanut production and resistance.

与许多其它重要的作物一样，花生是一个经历过多倍化、演化和驯化的多倍体物种。野生的异源四倍体花生物种Arachis monticola是野生二倍体物种和栽培四倍体花生之间的关键联系。然而，目前我们对于Arachis monticola在花生的演化和驯化过程中的作用还不是很清楚。本文报道了2.6 Gb大小的Arachis monticola基因组组装，并且对花生物种的基因组进行了比较分析。对于来自AA、BB、EE、KK和CC群体的17个野生二倍体花生以及30个四倍体花生的基因组重建显示异源四倍体花生得A和B亚基因组是单系起源的。野生和栽培种花生都经历了不对称的亚基因组演化，包括同源交换、同源表达偏好以及结构变异，从而导致了花生驯化过程中亚基因组功能的差异化。结构变异相关的同源倾向于存在表达偏好，并且与豆荚大小由二倍体到野生和栽培种四倍体逐渐增加相关。此外，抗性基因的全基因组分析显示野生花生中特异存在的等位基因可以被引入育种项目中以提升栽培种花生的某些抗性性状。本文所报道的遗传资源对于研究多倍体演化、驯化以及花生产量和抗性的育种改良都具有重要的价值。

通讯：Z. Jeffrey Chen  (https://polyploidy.biosci.utexas.edu/polyploidy/principle-investigator)

个人简介：1984年，浙江农业大学，学士；1987年，南京农业大学，硕士；1993年，德克萨斯A&M大学，博士；1993-1995年，明尼苏达大学，博士后；1995-1999年，华盛顿大学，博士后 。

研究方向：植物多倍化和杂种优势的遗传和表观基础，及其对于作物驯化和改良的影响。

doi: https://doi.org/10.1002/advs.201901672

Journal: Advance Science

Published date: November 28, 2019