The genome of kenaf (Hibiscus cannabinus L.) provides insights into bast fiber and leaf shape biogenesis

First author: Liwu Zhang; Affiliations: Fujian Agriculture and Forestry University (福建农林大学): Fuzhou, China

Corresponding author: Liwu Zhang

Kenaf is an ancient crop that is widely cultivated as a source of bast (phloem) fibers, the phytoremediation of heavy metal‐contaminated farmlands, and textile relevant compounds. Leaf shape played a unique role in kenaf improvement, due to the inheritance as a single locus and the association with fiber development in typical lobed‐leaf varieties. Here we report a high‐quality genome assembly and annotation for var. ‘Fuhong 952’ with 1,078 Mbp genome and 66,004 protein‐coding genes integrating single‐molecule real‐time sequencing, a high‐density genetic map, and high‐throughput chromosome conformation capture techniques. Gene mapping assists the identification of a homeobox transcription factor LATE MERISTEM IDENTITY 1 (HcLMI1) gene controlling lobed‐leaf. Virus‐induced gene silencing (VIGS) of HcLMI1 in a lobed‐leaf variety was critical to induce round‐like leaf formation. Candidate genes involved in cell wall formation were found in quantitative trait loci (QTL) for fiber yield and quality related traits. Comparative genomic and transcriptome analyses revealed key genes involved in bast fiber formation, among which there are twice as many cellulose synthase A (CesA) genes due to a recent whole‐genome duplication after divergence from Gossypium. Population genomic analysis showed two recent population bottlenecks in kenaf, suggesting domestication and improvement process have led to an increase in fiber biogenesis and yield. This chromosome‐scale genome provides an important framework and toolkit for sequence‐directed genetic improvement of fiber crops.

红麻是一种古老的作物，作为韧皮纤维来源、受重金属污染农田的修复植物以及纺织相关化合物来源而被广泛栽培种植，红麻的叶片形状在红麻的遗传改良过程中发挥着非常独特的作用，该性状由单基因位点控制，并且在典型的裂叶红麻品种中与纤维发育相关。本文中，作者基于单分子实时测序SMRT技术、一个高密度遗产图谱以及高通量染色体构象捕获技术Hi-C，报道了红麻品种Fuhong 952的高质量参考基因组，大小约为1078Mb，编码66004个蛋白编码基因。基因作图辅助定位了并鉴定了控制红麻裂叶的单基因为一个同源盒转录因子HcLMI1。在裂叶红麻品种中，通过病毒诱导HcLMI1基因沉默能够诱导形成类似圆形的叶片。在与纤维产量以及品质相关性状的数量性状位点中鉴定到了与细胞壁形成相关的候选基因。比较基因组学和转录组学分析揭示了作用于韧皮纤维形成的关键基因，其中，由于与棉属植物分化之后红麻基因组在最近发生过一次全基因组复制事件，因此纤维素合酶CesA基因的数量是棉属植物的两倍。群体基因组学分析显示红麻群体在最近发生过两次群体瓶颈事件，说明驯化和遗传改良导致了红麻纤维生物发生和产量的增加。本文所报道的红麻的染色体级别参考基因组为未来纤维作物的序列定向遗传改良提供了宝贵的遗传资源。

通讯：张立武（http://nxy.fafu.edu.cn/a2/54/c1167a41556/page.htm）

个人简介：2005-2010年，华中农业大学，博士；2010-2012年，华中农业大学，博士后。

研究方向：麻类作物基因组与遗传改良。

doi: https://doi.org/10.1111/pbi.13341

Journal: Plant Biotechnology Journal

First Published: January 23, 2020