Xia Zhiqiang, Du Zhenglin, Zhou Xincheng, Jiang Sirong, Zhu Tingting, Wang Le, Chen Fei, Carvalho Luiz, Zou Meiling, Becerra Lopez-Lavalle Luis Augusto, Zhang Xiaofei, Xu Liangye, Wang Zhenyu, Chen Meili, Guo Xin, Wang Shujuan, Li Mengtao, Li Yuanchao, Wang Haiyan, Liu Shisheng, Bao Yuting, Zhao Long, Zhang Chenji, Xiao Jianjia, Guo Fengguang, Shen Xu, Li Haozheng, Lu Cheng, Qiao Fei, Ceballos Hernan, Yan Huabing, Qin Xiaochun, Ma Ling, Zhang Huaifang, He Shuang, Zhao Wenming, Wan Yinglang, Chen Yinhua, Huang Dongyi, Li Kaimian, Liu Bin, Peng Ming, Zhang Weixiong, Møller Birger Lindberg, Chen Xin, Luo Ming-Cheng, Xiao Jingfa, Wang Wenquan
National Key Laboratory of Biotechnology and Breeding of Tropical Crops, Hainan University, Haikou 570228, China.
National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
Mol Plant. 2025 Jun 2;18(6):1047-1071. doi: 10.1016/j.molp.2025.05.014. Epub 2025 May 27.
Cassava is a highly resilient tropical crop that produces large, starchy storage roots and high biomass. However, how did cassava's remarkable environmental adaptability and key economic traits evolve from its wild species remain unclear. In this study, we obtained near complete telomere-to-telomere genome assemblies and their haplotype forms for the cultivar AM560, the wild ancestors FLA4047 and W14, constructed a graphic pan-genome of 30 representatives with a size of 1.15 Gb, and built a clarified evolutionary tree of 486 accessions. A comparison of structural variations and single-nucleotide variations between the ancestors and cultivated cassavas reveals predominant expansions and contractions of numbers of genes and gene families, which are mainly driven by transposons. Significant selective sweeping occurred in 122 footprints of genomes and affects 1,519 domesticated genes. We identify selective mutations in MeCSK and MeFNR2 that could promote photoreactions associated with MeNADP-ME in C photosynthesis in modern cassava. Coevolution of retard floral primordia and initiation of storage roots may arise from MeCOL5 variants with altered bindings to MeFT1, MeFT2, and MeTFL2. Mutations in MeMATE1 and MeGTR occur in sweet cassava, and MeAHL19 has evolved to regulate the biosynthesis, transport, and endogenous remobilization of cyanogenic glucosides in cassava. These extensive genomic and gene resources provided here, along with the findings on the evolutionary mechanisms responsible for beneficial traits in modern cultivars, lay a strong foundation for future breeding improvements of cassava.
木薯是一种适应能力极强的热带作物，能产出大型的淀粉质贮藏根和高生物量。然而，木薯卓越的环境适应性和关键经济性状是如何从其野生种演化而来的，仍不清楚。在本研究中，我们获得了栽培品种AM560及其野生祖先FLA4047和W14的近乎完整的端粒到端粒基因组组装及其单倍型形式，构建了一个由30个代表组成、大小为1.15 Gb的图形泛基因组，并构建了486份种质的清晰进化树。对祖先木薯和栽培木薯之间的结构变异和单核苷酸变异进行比较后发现，基因和基因家族数量主要发生了由转座子驱动的显著扩张和收缩。在122个基因组足迹中发生了显著的选择性清除，影响了1519个驯化基因。我们鉴定出MeCSK和MeFNR2中的选择性突变，这些突变可能促进现代木薯C4光合作用中与MeNADP-ME相关的光反应。延迟花原基和贮藏根起始的共同进化可能源于MeCOL5变体与MeFT1、MeFT2和MeTFL2结合的改变。MeMATE1和MeGTR的突变出现在甜木薯中，而MeAHL19已经进化到可调节木薯中氰苷的生物合成、运输和内源性再动员。这里提供的这些丰富的基因组和基因资源，以及关于现代品种有益性状进化机制的研究结果，为木薯未来的育种改良奠定了坚实基础。
