Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity

Wei Hu, Changmian Ji, Zhe Liang, Jianqiu Ye, Wenjun Ou, Zehong Ding, Gang Zhou, Weiwei Tie, Yan Yan, Jinghao Yang, Liming Ma, Xiaoying Yang, Yunxie Wei, Zhiqiang Jin, Jianghui Xie, Ming Peng, Wenquan Wang, Anping Guo, Biyu Xu, Jianchun GuoSongbi Chen, Mingcheng Wang, Yang Zhou, Xiaolong Li, Ruoxi Li, Xinhui Xiao, Zhongqing Wan, Feifei An, Jie Zhang, Qingyun Leng, Yin Li, Haitao Shi, Ray Ming, Kaimian Li

Research output: Contribution to journalArticlepeer-review


Background: Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome. Results: We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a genome-wide association study. Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits. We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes, which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes. Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava. Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content. Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility. We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis. The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB. Conclusions: This study provides insights into allelic variation in heterozygosity associated with key agronomic traits and cassava domestication. It also offers valuable resources for the improvement of cassava and other highly heterozygous crops.

Original languageEnglish (US)
Article number316
JournalGenome biology
Issue number1
StatePublished - Dec 2021


  • Agronomic traits
  • Cassava
  • Heterozygosity
  • Resequencing
  • Selection

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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