基于甘蔗及其近缘属参考基因组开发SSR标记及数据库

甘蔗(Saccharum spp.hybrid)是重要的糖料和能源作物.甘蔗基因组复杂,群体遗传学研究相对落后.目前,甘蔗参考基因组仍有待完善.利用甘蔗及其近缘属参考基因组开发甘蔗SSR标记及数据库有助于推动甘蔗群体遗传学的研究.本研究基于3个甘蔗种(割手密种、热带种和栽培种)和2个甘蔗近缘种(芒和高粱)的基因组进行SSR检测,统计各基因组SSR的数量和类型,挑选多态性好的SSR标记对104份甘蔗及近缘属种质材料进行遗传多样性分析.在5个物种的基因组中共鉴定到了1,860,645个SSR,以单核苷酸、二核苷酸和三核苷酸重复单元类型为主.基因组间SSR的共线性信息显示,甘蔗栽培种和其他物种间的亲...

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Published in作物学报 Vol. 51; no. 1; pp. 103 - 116
Main Authors 匡博文, 韦妳, 刘金典, 陈美燕, 毛兴洁, 段维兴, 杨细平
Format Journal Article
LanguageChinese
Published 广西大学亚热带农业生物资源保护与利用国家重点实验室,广西南宁 530004 12.01.2025
广西大学农学院植物科学国家级实验教学示范中心,广西南宁 530004%广西壮族自治区农业科学院甘蔗研究所,广西南宁 530004
Subjects
甘蔗
database
全基因重测序
数据库
SSR marker
whole genome re-sequencing
SSR标记
sugarcane
Online AccessGet full text
ISSN0496-3490
DOI10.3724/SP.J.1006.2025.44056

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Abstract 甘蔗(Saccharum spp.hybrid)是重要的糖料和能源作物.甘蔗基因组复杂,群体遗传学研究相对落后.目前,甘蔗参考基因组仍有待完善.利用甘蔗及其近缘属参考基因组开发甘蔗SSR标记及数据库有助于推动甘蔗群体遗传学的研究.本研究基于3个甘蔗种(割手密种、热带种和栽培种)和2个甘蔗近缘种(芒和高粱)的基因组进行SSR检测,统计各基因组SSR的数量和类型,挑选多态性好的SSR标记对104份甘蔗及近缘属种质材料进行遗传多样性分析.在5个物种的基因组中共鉴定到了1,860,645个SSR,以单核苷酸、二核苷酸和三核苷酸重复单元类型为主.基因组间SSR的共线性信息显示,甘蔗栽培种和其他物种间的亲缘关系由近到远为:R570、热带种、割手密种、芒、高粱;基于SSR及InDels标记的甘蔗种质资源的遗传多样性分析显示,斑茅92-105最先被单独划分,割手密种为一个类群,大茎野生种和热带种分为一个类群,栽培种为一个类群.最后,围绕5个基因组鉴定的SSR以及引物等相关信息,开发了一个基于Web界面的甘蔗SSR数据库.本研究为甘蔗研究和育种提供了重要的分子工具.
AbstractList 甘蔗(Saccharum spp.hybrid)是重要的糖料和能源作物.甘蔗基因组复杂,群体遗传学研究相对落后.目前,甘蔗参考基因组仍有待完善.利用甘蔗及其近缘属参考基因组开发甘蔗SSR标记及数据库有助于推动甘蔗群体遗传学的研究.本研究基于3个甘蔗种(割手密种、热带种和栽培种)和2个甘蔗近缘种(芒和高粱)的基因组进行SSR检测,统计各基因组SSR的数量和类型,挑选多态性好的SSR标记对104份甘蔗及近缘属种质材料进行遗传多样性分析.在5个物种的基因组中共鉴定到了1,860,645个SSR,以单核苷酸、二核苷酸和三核苷酸重复单元类型为主.基因组间SSR的共线性信息显示,甘蔗栽培种和其他物种间的亲缘关系由近到远为:R570、热带种、割手密种、芒、高粱;基于SSR及InDels标记的甘蔗种质资源的遗传多样性分析显示,斑茅92-105最先被单独划分,割手密种为一个类群,大茎野生种和热带种分为一个类群,栽培种为一个类群.最后,围绕5个基因组鉴定的SSR以及引物等相关信息,开发了一个基于Web界面的甘蔗SSR数据库.本研究为甘蔗研究和育种提供了重要的分子工具.
Abstract_FL Sugarcane (Saccharum spp.hybrid) is an important crop for both sugar production and bioenergy.However,due to the complexity of the sugarcane genome,research in its population genetics has lagged behind other crops.Currently,the reference genome for sugarcane still requires significant improvements.The development of SSR (Simple Sequence Repeat) markers and databases based on the genomes of sugarcane and its relatives will be instrumental in advancing population genetics research.In this study,we identified SSRs from the genomes of three sugarcane species (Saccharum spontaneum,Saccharum officinarum,and Saccharum spp.hybrid) and two related species (Miscanthus sinensis and Sorghum bicolor).We quantified and categorized the SSRs for each genome,selecting those with high polymorphism for the genetic diversity analysis of 104 sugarcane-related mate-rials.A total of 1,860,645 SSRs were identified across the five genomes,with mononucleotide,dinucleotide,and trinucleotide repeats being the most common.Synteny analysis of SSRs across the genomes revealed the evolutionary relationships among species,with the kinship order from closest to most distant being:R570,Saccharum officinarum,Saccharum spontaneum,Miscanthus sinensis,and Sorghum bicolor.Genetic diversity analysis using SSR and InDel markers showed that Banmao 92-105 was the first to diverge from other samples,with Saccharum spontaneum forming a distinct group,Saccharum robustum and Sac-charum officinarum clustering together,and Saccharum spp.hybrid forming its own separate group.Additionally,we developed a web-based database for sugarcane SSRs,which includes the identified SSRs from the five genomes,along with corresponding primers and other related information.This study provides a valuable molecular tool for sugarcane research and breeding efforts.
Author 段维兴
杨细平
毛兴洁
刘金典
陈美燕
匡博文
韦妳
AuthorAffiliation 广西大学亚热带农业生物资源保护与利用国家重点实验室,广西南宁 530004;广西大学农学院植物科学国家级实验教学示范中心,广西南宁 530004%广西壮族自治区农业科学院甘蔗研究所,广西南宁 530004
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Author_FL WEI Ni
LIU JinDian
MAO XingJie
YANG XiPing
KUANG BoWen
CHEN MeiYan
DUAN WeiXing
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Keywords 甘蔗
database
全基因重测序
数据库
SSR marker
whole genome re-sequencing
SSR标记
sugarcane
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广西大学农学院植物科学国家级实验教学示范中心,广西南宁 530004%广西壮族自治区农业科学院甘蔗研究所,广西南宁 530004
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