The Coix genome provides insights into Panicoideae evolution and papery hull domestication

First author: Chao Guo; Affiliations: Sichuan Agricultural University (四川农业大学): Chengdu, China

Corresponding author: Shufeng Zhou

Coix is a grass crop domesticated as early as Neolithic era. It is still widely cultivated for both highly nutritional food and medicinal use. However, the genetic study and breeding of this crop are hindered by lack of a sequenced genome. Here we report de novo sequencing and assembly of the 1,619 Mb genome of Coix, and annotation of 75.39% repeats and 39,629 protein-coding genes. Comparative genomics analysis showed that Coix is more closely related to sorghum rather than maize, but intriguingly only Coix and maize had a recent whole genome duplication event which was not detected in sorghum. We further constructed a genetic map and mapped several important traits especially the strength of hull. Selection of papery hull (thin, easy-dehulling) from the stony one (thick, hard-dehulling) in wild progenitors was a key step in Coix domestication. The papery hull makes seed easier to process and germinate. Anatomic and global transcriptome analysis revealed that the papery hull is resulted from inhibition of cell division and wall biogenesis. We also successfully demonstrated that seed hull pressure resistance is controlled by two major quantitative trait loci (QTLs), which are associated with hull thickness and color, respectively. The two QTLs were further fine mapped within intervals of 250 Kb and 146 Kb, respectively. These resources provide a platform for evolutionary studies and will facilitate molecular breeding of this important crop.

薏米是一个在新石器时代就已经被驯化的草类作物。现在，薏米仍作为营养食物和医药用途被广泛种植。然而，由于缺乏全基因组序列，对于薏米的遗传研究和育种阻滞不前。本文中，作者报道了薏米的全基因组草图，大小约为1.619Gb，其中75.39%为重复序列，共注释出39629个蛋白编码基因。比较基因组学分析显示薏米与高粱的亲缘关系要比与玉米的更近，但有趣的是，只有玉米和薏米基因组在近期发生了一次全基因组复制事件，而高粱基因组中并未检测到。作者进一步构建了一个薏米的遗传图谱，并且定位了一些重要的性状，比如薏米壳的强度。从具有厚而难去壳的坚壳（stony hull）的野生祖先种中选择薄而易去壳的软壳（papery hull）是薏米驯化过程中的一个关键步骤。具有软壳的种子更容易加工处理，同时也易于萌发。解剖学和转录组分析显示薏米软壳是由于细胞分裂和壁生物发生的抑制所导致的。作者还揭示了种子外壳压力抗性由两个主要的数量性状位点QTLs控制，分别与壳的厚度和颜色相关。作者进一步将这两个QTLs精细定位到了250Kb和140Kb的基因组区域。本文的研究将为薏米的演化研究提供一个平台，并有利于促进该重要作物的分子育种。

通讯：周树峰（https://maize.sicau.edu.cn/info/1014/1320.htm）

个人简介：1995-1997年，天津农学院，大专；2000-2003年，四川农业大学，硕士；2003-2006年，中科院植物研究所，博士。

研究方向：玉米、薏仁米等作物的遗传育种研究。

doi: https://doi.org/10.1016/j.molp.2019.11.008

Journal: Molecular Plant

Published date: November 24, 2019