Abstract

Tomato is an important vegetable crop for fresh and processed products. In the past decades, conventional breeding cum marker-assisted selection (MAS) has been deployed widely to develop modern tomato cultivars with desirable agronomic traits, market classes, and consumer preferences. The rapid developments in sequencing technologies with the reduced costs per sample, high-throughput single nucleotide polymorphism (SNP) genotyping platforms, and bioinformatics tools have revolutionized crop improvement programs, and deciphered the tomato genome sequence in 2012. Since then thousands of cultivated, its close relatives, and wild species have been genome resequenced to analyze structural variants population structure, genetic diversity, high-density map construction so on. Further, tomato pan-genomes have been constructed to search genomics regions associated with agronomic traits to expedite the breeding process. Importantly, genomics-assisted research has begun in tomatoes with the identification of genes, and SNP markers associated with phenotypic variation by applying genome resequencing, genome-wide association studies (GWAS) using SNP array, and genotyping-by-sequencing techniques. Further, the genomic selection (GS) method is expected to increase breeding efficiency and genetic gain rapidly. This review provides the latest information on progress in MAS to genome resequencing, pan-genomes, SNP genotyping, GWAS, and GS for genomics-assisted breeding in tomatoes.

摘要

番茄是一种重要的生鲜和加工产品蔬菜作物。在过去的几十年中，传统育种和标记辅助选择 (MAS) 已被广泛用于开发具有理想农艺性状、市场类别和消费者偏好的现代番茄品种。测序技术的快速发展以及降低每个样本的成本、高通量单核苷酸多态性 (SNP) 基因分型平台和生物信息学工具已经彻底改变了作物改良计划，并在 2012 年破译了番茄基因组序列。对近亲、野生物种进行基因组重测序，分析结构变异、种群结构、遗传多样性、高密度图谱构建等。更远，已构建番茄泛基因组以搜索与农艺性状相关的基因组学区域，以加快育种过程。重要的是，通过应用基因组重测序、使用 SNP 阵列的全基因组关联研究 (GWAS) 和测序技术进行基因分型，基因组学辅助研究已经开始在西红柿中识别基因和与表型变异相关的 SNP 标记。此外，基因组选择（GS）方法有望迅速提高育种效率和遗传增益。这篇综述提供了关于 MAS 在基因组重测序、泛基因组、SNP 基因分型、GWAS 和 GS 中用于番茄基因组学辅助育种的最新进展。通过应用基因组重测序、使用 SNP 阵列的全基因组关联研究 (GWAS) 和测序技术进行基因分型，与表型变异相关的 SNP 标记。此外，基因组选择（GS）方法有望迅速提高育种效率和遗传增益。这篇综述提供了关于 MAS 在基因组重测序、泛基因组、SNP 基因分型、GWAS 和 GS 中用于番茄基因组学辅助育种的最新进展。通过应用基因组重测序、使用 SNP 阵列的全基因组关联研究 (GWAS) 和测序技术进行基因分型，与表型变异相关的 SNP 标记。此外，基因组选择（GS）方法有望迅速提高育种效率和遗传增益。这篇综述提供了关于 MAS 在基因组重测序、泛基因组、SNP 基因分型、GWAS 和 GS 中用于番茄基因组学辅助育种的最新进展。