Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Qian Yan, Junting Feng, Jiezhen Chen, Yingjie Wen, Yonghua Jiang, Yingxiao Mai, Kan Huang, Hailun Liu, Hongsen Liu, Fachao Shi, Yanwei Hao, Changhe Cai, Canye Yu, Liangxi Ou, Rui Xia
{"title":"Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi","authors":"Qian Yan, Junting Feng, Jiezhen Chen, Yingjie Wen, Yonghua Jiang, Yingxiao Mai, Kan Huang, Hailun Liu, Hongsen Liu, Fachao Shi, Yanwei Hao, Changhe Cai, Canye Yu, Liangxi Ou, Rui Xia","doi":"10.1186/s13059-025-03693-5","DOIUrl":null,"url":null,"abstract":"Litchi, an economically important fruit crop in Southeast Asia, is renowned for its distinctive flavor and nutrient value, but its genetic diversity and genetic basis underlying fruit quality regulation remain largely unexplored. We re-sequence 276 litchi accessions collected globally and identify 54 million high-quality biallelic SNPs. We then analyze the population structure and reveal four main subgroups within the population. By phenotypic profiling of 21 fruit-quality-related traits, followed with genome-wide association study, we identify a plethora of candidate genes and genomic loci that are responsible for regulating seed and fruit quality traits. In particular, we characterize and experimentally validate an invertase gene, LcSAI, encoding an enzyme catalyzing the conversion of sucrose into reducing sugars, as a key regulator of sugar composition in litchi fruit, affecting the sweetness of litchi fruits. Our study demonstrates the genetic diversity and population structure of litchi. We delineate the genetic basis of fruit quality through comprehensive genomic analyses and phenotypic profiling. These findings provide valuable resources and knowledge for understanding the genetic basis of fruit quality in litchi, which contribute to the theoretical basis for further genetic improvement.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"98 1","pages":""},"PeriodicalIF":10.1000,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13059-025-03693-5","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Litchi, an economically important fruit crop in Southeast Asia, is renowned for its distinctive flavor and nutrient value, but its genetic diversity and genetic basis underlying fruit quality regulation remain largely unexplored. We re-sequence 276 litchi accessions collected globally and identify 54 million high-quality biallelic SNPs. We then analyze the population structure and reveal four main subgroups within the population. By phenotypic profiling of 21 fruit-quality-related traits, followed with genome-wide association study, we identify a plethora of candidate genes and genomic loci that are responsible for regulating seed and fruit quality traits. In particular, we characterize and experimentally validate an invertase gene, LcSAI, encoding an enzyme catalyzing the conversion of sucrose into reducing sugars, as a key regulator of sugar composition in litchi fruit, affecting the sweetness of litchi fruits. Our study demonstrates the genetic diversity and population structure of litchi. We delineate the genetic basis of fruit quality through comprehensive genomic analyses and phenotypic profiling. These findings provide valuable resources and knowledge for understanding the genetic basis of fruit quality in litchi, which contribute to the theoretical basis for further genetic improvement.
综合基因组和表型分析揭示了荔枝果实品质的遗传基础
荔枝是东南亚地区一种重要的经济水果作物,以其独特的风味和营养价值而闻名,但其遗传多样性和遗传基础在果实品质调控中的作用仍未得到充分研究。我们对全球收集的276份荔枝材料进行了重测序,鉴定出5400万个高质量的双等位基因snp。然后我们分析了人口结构,揭示了人口中的四个主要亚群。通过对21个果实品质相关性状的表型分析和全基因组关联研究,我们确定了大量负责调节种子和果实品质性状的候选基因和基因组位点。特别是,我们鉴定并实验验证了一个转化酶基因LcSAI,它编码一种催化蔗糖转化为还原糖的酶,是荔枝果实中糖成分的关键调节因子,影响荔枝果实的甜度。本研究揭示了荔枝的遗传多样性和群体结构。我们通过全面的基因组分析和表型分析来描述果实品质的遗传基础。这些发现为了解荔枝果实品质的遗传基础提供了宝贵的资源和知识,为进一步的遗传改良提供了理论依据。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信