The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum

IF 31.7 1区生物学 Q1 GENETICS & HEREDITY

Nature genetics Pub Date : 2025-01-03 DOI:10.1038/s41588-024-02033-w

Jisen Zhang, Yiying Qi, Xiuting Hua, Yongjun Wang, Baiyu Wang, Yongwen Qi, Yumin Huang, Zehuai Yu, Ruiting Gao, Yixing Zhang, Tianyou Wang, Yuhao Wang, Jing Mei, Qing Zhang, Gang Wang, Haoran Pan, Zhen Li, Shuangyu Li, Jia Liu, Nameng Qi, Xiaoxi Feng, Mingxing Wu, Shuqi Chen, Cuicui Du, Yihan Li, Yi Xu, Yaxue Fang, Panpan Ma, Qingyun Li, Yuanchang Sun, Xiaomin Feng, Wei Yao, Muqing Zhang, Baoshan Chen, Xinlong Liu, Ray Ming, Jianping Wang, Zuhu Deng, Haibao Tang

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Abstract

Modern sugarcane, a highly allo-autopolyploid organism, has a very complex genome. In the present study, the karyotype and genome architecture of modern sugarcane were investigated, resulting in a genome assembly of 97 chromosomes (8.84 Gb). The allopolyploid genome was divided into subgenomes from Saccharum officinarum (So_h) and S. spontaneum (Ss_h), with So_h dominance in the Saccharum hybrid (S. hybrid). Genome shock affected transcriptome dynamics during allopolyploidization. Analysis of an inbreeding population with 192 individuals revealed the underlying genetic basis of transgressive segregation. Population genomics of 310 Saccharum accessions clarified the breeding history of modern sugarcane. Using the haplotype-resolved S. hybrid genome as a reference, genome-wide association studies identified a potential candidate gene for sugar content from S. spontaneum. These findings illuminate the complex genome evolution of allopolyploids, offering opportunities for genomic enhancements and innovative breeding strategies for sugarcane.

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来源期刊

Nature genetics 生物-遗传学

CiteScore

43.00

自引率

2.60%

发文量

241

审稿时长

3 months

期刊介绍： Nature Genetics publishes the very highest quality research in genetics. It encompasses genetic and functional genomic studies on human and plant traits and on other model organisms. Current emphasis is on the genetic basis for common and complex diseases and on the functional mechanism, architecture and evolution of gene networks, studied by experimental perturbation. Integrative genetic topics comprise, but are not limited to: -Genes in the pathology of human disease -Molecular analysis of simple and complex genetic traits -Cancer genetics -Agricultural genomics -Developmental genetics -Regulatory variation in gene expression -Strategies and technologies for extracting function from genomic data -Pharmacological genomics -Genome evolution