[Genomics] Cassava Pan-Genome Reveals Domestication and Adaptive Evolution

  • by Xiaofei Zhang

Understanding genetic diversity across cassava cultivars and wild relatives is essential for future crop improvement. Collaborating with researchers from Hainan University, the Chinese Academy of Tropical Agricultural Sciences, CIAT, UC Davis, EMBRAPA Brazil, and multiple genomic research institutes, we constructed a cassava pan-genome and haplotype map representing hundreds of accessions. The study identified over 1,500 candidate domestication genes and revealed genomic changes associated with photosynthesis, storage root formation, and cyanogenic compound metabolism. These genomic resources provide a powerful foundation for precision breeding and evolutionary research in cassava.

 

A scientific figure comprising a world map, phylogenetic tree, and heatmaps displaying data analyses.

Figure. Phylogenetic tree of 486 landraces and wild relatives and divergence time of species revealed by the pan genome of 30 representatives in cassava.

(A) Geographic distribution of cassava accessions.
(B) Phylogenetic tree of 486 accessions: all accessions were assigned to 5 clades. Group A: GLZ and its relatives, Group B: FLA, genotypes in the wild ancestor subspecies. Group C: landrace and hybrids probably rooted around Ecuador. Group D: with D1 and D2 subgroups covering landraces and cultivars distributed in Central Brazil, where cassava originated. Group E: E1–E3 are accessions mostly derived from Southern Brazil and include cold-tolerant accessions; E4–E7 are landraces and hybrids collected in East and West Africa.
(C) Population structure chart drawn by ADMIXTURE software.
(D) Phylogenetic analysis of subspecies based on 30 deep-sequenced and assembled genomes to construct a pan-genome: the domesticated cassava diverged from the closely related wild FLA subspecies approximately 5.6 MYA. Subsequently, the FLAs diverged from W14 around 6.9 MYA, and W14 further diverged from GLA after approximately 8.4 MYA.
(E) Principal-component analysis (PCA) of accessions showing clear differentiation among GLZs and their relatives, FLAs, and cultivated clones (MEs) (n = 482).
(F) The genetic differentiation (Fst) among GLAs, FLAs, and MEs.
(G) LD decays took place in GLAs, FLAs, ME C, ME D, and ME E groups.

Media Resources

Xia Z, Du Z, Zhou X, Jiang S, Zhu T, Wang L, Chen F, Carvalho L, Zou M, Becerra Lopez-Lavalle LA, Zhang X, Xu L, Wang Z, Chen M, Guo X, Wang S, Li M, Li Y, Wang H, Liu S, Bao Y, Zhao L, Zhang C, Xiao J, Guo F, Shen X, Li H, Lu C, Qiao F, Ceballos H, Yan H, Qin X, Ma L, Zhang H, He S, Zhao W, Wan Y, Chen Y, Huang D, Li K, Liu B, Peng M, Zhang W, Møller BL, Chen X, Luo MC, Xiao J, Wang W. Pan-genome and haplotype map of cassava cultivars and wild ancestors provide insights into its adaptive evolution and domestication. Mol Plant. 2025 Jun 2;18(6):1047-1071. doi: 10.1016/j.molp.2025.05.014. Epub 2025 May 27. PMID: 40437759.

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Science & Technology