Mapping of novel non-race 1 Verticillium wilt resistance QTLs in tomato using high-density linkage map construction

IF 3.9 2区农林科学 Q1 HORTICULTURE

Scientia Horticulturae Pub Date : 2025-05-01 DOI:10.1016/j.scienta.2025.114199

Sikandar Amanullah , Reza Shekasteband

{"title":"Mapping of novel non-race 1 Verticillium wilt resistance QTLs in tomato using high-density linkage map construction","authors":"Sikandar Amanullah , Reza Shekasteband","doi":"10.1016/j.scienta.2025.114199","DOIUrl":null,"url":null,"abstract":"<div><div>Verticillium wilt (VW), caused by the soil-borne fungal pathogen (<em>Verticillium dahliae</em>), poses a major threat to tomato production in temperate climates, including Western North Carolina and the nearby states. There is a dire need to develop disease-resistant lines by understanding the in-depth genetic basis of unexplored VW resistance in tomato germplasms. In this study, we developed segregating genetic mapping populations (F<sub>2</sub> and F<sub>3</sub>) derived from a cross between two tomato lines, with moderate resistance to non-race 1 isolates of <em>V. dahliae</em>. The statistical analysis of the disease incidence and severity across three different environments with a history of natural disease pressure showed a complex and polygenetic nature of the resistance in the germplasm affected by the environment. A high percentage of the progenies showed high VW resistance due to transgressive segregation in the mapping populations. Low-coverage whole-genome sequencing of 95 F<sub>2</sub> individuals was used to generate a high-density SNP database validated by the high-coverage whole-genome sequencing of the parental lines. The bioinformatics analysis revealed a total of 3269 high-quality SNP markers that were used for genetic linkage map construction spanning a total of 5516 cM in length and with an average spacing of 1.69 cM, and a moderate number of recombination events and high genomic collinearity. Multiple QTL mapping-based analyses identified 9 QTLs across five different chromosomes (2, 4, 5, 6, and 11), explaining a range of 4.40–13.36 % of the variation in VW disease severity. Three QTLs on chromosomes 4, 5, and 6 showed major effects; furthermore, two neighboring QTLs on chromosomes 4 and 5 derived from one of the parental lines are probably the same or loosely linked loci stable across the environments. The identified QTL-SNP markers also illustrated allele-specific contributions to the low disease severity index values across three different environments.</div></div>","PeriodicalId":21679,"journal":{"name":"Scientia Horticulturae","volume":"347 ","pages":"Article 114199"},"PeriodicalIF":3.9000,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Scientia Horticulturae","FirstCategoryId":"97","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0304423825002481","RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"HORTICULTURE","Score":null,"Total":0}

引用次数: 0

Abstract

Verticillium wilt (VW), caused by the soil-borne fungal pathogen (Verticillium dahliae), poses a major threat to tomato production in temperate climates, including Western North Carolina and the nearby states. There is a dire need to develop disease-resistant lines by understanding the in-depth genetic basis of unexplored VW resistance in tomato germplasms. In this study, we developed segregating genetic mapping populations (F₂ and F₃) derived from a cross between two tomato lines, with moderate resistance to non-race 1 isolates of V. dahliae. The statistical analysis of the disease incidence and severity across three different environments with a history of natural disease pressure showed a complex and polygenetic nature of the resistance in the germplasm affected by the environment. A high percentage of the progenies showed high VW resistance due to transgressive segregation in the mapping populations. Low-coverage whole-genome sequencing of 95 F₂ individuals was used to generate a high-density SNP database validated by the high-coverage whole-genome sequencing of the parental lines. The bioinformatics analysis revealed a total of 3269 high-quality SNP markers that were used for genetic linkage map construction spanning a total of 5516 cM in length and with an average spacing of 1.69 cM, and a moderate number of recombination events and high genomic collinearity. Multiple QTL mapping-based analyses identified 9 QTLs across five different chromosomes (2, 4, 5, 6, and 11), explaining a range of 4.40–13.36 % of the variation in VW disease severity. Three QTLs on chromosomes 4, 5, and 6 showed major effects; furthermore, two neighboring QTLs on chromosomes 4 and 5 derived from one of the parental lines are probably the same or loosely linked loci stable across the environments. The identified QTL-SNP markers also illustrated allele-specific contributions to the low disease severity index values across three different environments.

查看原文本刊更多论文

利用高密度连锁图谱构建番茄抗黄萎病新种质qtl

黄萎病（VW）由土壤传播的真菌病原体（黄萎病）引起，对温带气候的番茄生产构成重大威胁，包括北卡罗莱纳西部和附近各州。迫切需要通过深入了解番茄种质中未开发的大众抗性的遗传基础来开发抗病品系。在这项研究中，我们从两个番茄系的杂交中获得了分离的遗传定位群体（F2和F3），这些群体对大丽花病菌的非1种分离株具有中等抗性。对具有自然疾病压力史的三种不同环境下的发病率和严重程度的统计分析表明，受环境影响的种质资源的抗性具有复杂性和多遗传性。较高比例的子代由于测图群体的海侵隔离而表现出较高的VW抗性。利用95个F2个体的低覆盖全基因组测序建立高密度SNP数据库，并通过亲本系的高覆盖全基因组测序进行验证。生物信息学分析结果显示，共有3269个高质量SNP标记用于构建遗传连锁图谱，总长度为5516 cM，平均间距为1.69 cM，重组事件数量适中，基因组共线性高。基于多个QTL定位的分析确定了5条不同染色体（2、4、5、6和11）上的9个QTL，解释了4.40 - 13.36%的VW疾病严重程度变异范围。4、5、6号染色体上的3个qtl发挥了主要作用；此外，来自同一亲本系的4号和5号染色体上的两个相邻qtl可能是相同的或松散连接的位点，在不同的环境中稳定。所鉴定的QTL-SNP标记还说明了等位基因特异性对三种不同环境下的低疾病严重程度指数值的贡献。

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

Scientia Horticulturae 农林科学-园艺

CiteScore

8.60

自引率

4.70%

发文量

796

审稿时长

47 days

期刊介绍： Scientia Horticulturae is an international journal publishing research related to horticultural crops. Articles in the journal deal with open or protected production of vegetables, fruits, edible fungi and ornamentals under temperate, subtropical and tropical conditions. Papers in related areas (biochemistry, micropropagation, soil science, plant breeding, plant physiology, phytopathology, etc.) are considered, if they contain information of direct significance to horticulture. Papers on the technical aspects of horticulture (engineering, crop processing, storage, transport etc.) are accepted for publication only if they relate directly to the living product. In the case of plantation crops, those yielding a product that may be used fresh (e.g. tropical vegetables, citrus, bananas, and other fruits) will be considered, while those papers describing the processing of the product (e.g. rubber, tobacco, and quinine) will not. The scope of the journal includes all horticultural crops but does not include speciality crops such as, medicinal crops or forestry crops, such as bamboo. Basic molecular studies without any direct application in horticulture will not be considered for this journal.