Exploring ddRAD sequencing data of tomato genotypes evaluated for the heat stress tolerance

IF 1 Q3 MULTIDISCIPLINARY SCIENCES

Data in Brief Pub Date : 2024-10-01 DOI:10.1016/j.dib.2024.110982

Salvatore Graci, Amalia Barone

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引用次数: 0

Abstract

Climate change is a major concern for agricultural crops, and the selection of tolerant genotypes in response to abiotic stresses represents an important breeding strategy to reduce yield losses. In addition, the continuous development of new and more accurate high-throughput technologies for the analysis of DNA sequences is the key to improve biological understanding and application of biological knowledge. In the present work, 27 tomato genotypes already evaluated for their response under high temperature conditions were sequenced by using the ddRAD sequencing technology. The main goal was to provide genomic data useful for identifying candidate genes and variants to cope with current climate changes. Total genomic DNA was extracted from leaves and sequenced on the HiSeq2500 Illumina instrument. Raw reads of the dataset were processed using different bioinformatics tools to generate a Variant Calling Format (VCF) file. The availability of resources reporting polymorphisms among genomes of different genotypes provides a useful basis for studying tomato tolerance to current climate changes and can be used by researchers and breeders to investigate the molecular response mechanisms and develop new breeding programs, also aided by Marked Assisted Selection (MAS). The raw reads were deposited into SRA database (https://www.ncbi.nlm.nih.gov/sra/PRJNA1137563).

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探索番茄耐热胁迫基因型的 ddRAD 测序数据

气候变化是农作物面临的一个主要问题，选择耐受非生物胁迫的基因型是减少产量损失的重要育种策略。此外，不断开发新的、更准确的高通量 DNA 序列分析技术是提高生物认识和生物知识应用的关键。在本研究中，利用 ddRAD 测序技术对已评估过的 27 个番茄基因型在高温条件下的反应进行了测序。主要目的是提供基因组数据，以确定应对当前气候变化的候选基因和变体。从叶片中提取总基因组DNA，并在HiSeq2500 Illumina仪器上进行测序。使用不同的生物信息学工具处理数据集的原始读数，生成变异调用格式（VCF）文件。报告不同基因型基因组间多态性的资源为研究番茄对当前气候变化的耐受性提供了有用的基础，研究人员和育种人员可利用这些资源研究分子响应机制，并开发新的育种计划，标记辅助选择（MAS）也可起到辅助作用。原始读数已存入 SRA 数据库 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1137563)。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Data in Brief MULTIDISCIPLINARY SCIENCES-

CiteScore

3.10

自引率

0.00%

发文量

996

审稿时长

70 days

期刊介绍： Data in Brief provides a way for researchers to easily share and reuse each other''s datasets by publishing data articles that: -Thoroughly describe your data, facilitating reproducibility. -Make your data, which is often buried in supplementary material, easier to find. -Increase traffic towards associated research articles and data, leading to more citations. -Open up doors for new collaborations. Because you never know what data will be useful to someone else, Data in Brief welcomes submissions that describe data from all research areas.