Chloroplast genome diversity and phylogenetic insights of Saccharum spontaneum across Southeast Asia
文献类型： 外文期刊
作者： Li, Sicheng 1 ; Wang, Zhen 1 ; Xu, Chaohua 2 ; Zhang, Lijun 1 ; Zhang, Baoqing 3 ; Huang, Yuxin 3 ; Lu, Xin 2 ; Duan, Weixing 3 ; Yang, Xiping 1 ;
作者机构： 1.Guangxi Univ, State Key Lab Conservat & Utilizat Subtrop Agrobio, Guangxi Key Lab Sugarcane Biol, Nanning 530004, Peoples R China
2.Yunnan Acad Agr Sci, Sugarcane Res Inst, Natl Key Lab Biol Breeding Trop Crops, Kunming, Peoples R China
3.Guangxi Acad Agr Sci, Key Lab Sugarcane Biotechnol & Genet Improvement, Guangxi Key Lab Sugarcane Genet Improvement, Sugarcane Res Inst,Minist Agr & Rural Affairs, Nanning 530007, Guangxi, Peoples R China
关键词：
genetic diversity; pan-plastome; population structure;
期刊名称：PLANTS PEOPLE PLANET （ 影响因子：3.6； 五年影响因子：5.0 ）
ISSN：
年卷期： 2025 年
页码：
收录情况： SCI
摘要： Societal Impact StatementClimate change and threats to global food security have increased the urgency of conserving genetic resources in key crops like sugarcane. In this study, we analyzed the chloroplast genomes of wild sugarcane to assess their genetic diversity and population structure. We found a high level of diversity, regardless of geographic location, and patterns of diversity that differed from those in nuclear genome analyses of wild sugarcane. These findings enhance our understanding of wild sugarcane diversity and evolution, offering valuable resources for breeding and conservation strategies that promote climate resilience and sustainable agricultural development.Summary Although the chloroplast genome is generally conserved, it is highly valuable for studies in plant population genetics and evolution due to its maternal inheritance and homoplastic nature. In polyploid sugarcane (Saccharum spp.), chloroplast DNA simplifies sequence-based phylogenetic analysis. Given increasing climate challenges, C4 plants like sugarcane offer advantages under high-temperature and drought conditions. This study aimed to explore chloroplast genome variation and phylogeny in Saccharum spontaneum, a key wild progenitor of modern sugarcane. We analyzed 224 S. spontaneum accessions primarily from Southeast Asia, especially China. A comprehensive pan-plastome was constructed to assess genetic structure, haplotype diversity, and chloroplast genome characteristics. Phylogenetic relationships and population structure were also examined. The chloroplast genome displayed a conserved quadripartite structure ranging from 141,140 to 141,338 bp, with 130 genes. A total of 323 variations were identified, most in non-coding regions; however, notable coding region variations occurred in ndhF and psbD. Phylogenetic and structure analyses revealed five distinct genetic groups, with 126 haplotypes supporting the observed patterns of diversity. Our findings highlight substantial genetic differentiation within S. spontaneum and underscore the role of chloroplast variation in plant diversity. The study provides critical insights for conserving wild sugarcane germplasm and offers a basis for developing molecular markers to support breeding and biodiversity efforts under climate change pressures.
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