Weijie Xu, Chao Gong, Peiting Mai, Zhenxing Li, Baojuan Sun, Tao Li
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引用次数: 0
摘要
简介番茄（Solanum lycopersicum）是一种极具价值的水果作物。然而，由于缺乏科学、准确的品种鉴定方法和统一的国家标准，生产管理分散、不规范，导致品种混杂。这给种质资源的编目、保存以及番茄新品种的鉴定、推广和应用带来了相当大的困难：为了更好地了解代表性番茄品种的遗传多样性和种群结构，我们收集了过去 20 年中的 418 个番茄品种，并利用全基因组单核苷酸多态性（SNP）标记对其进行了分析。我们利用简化基因组测序技术初步评估了 418 份番茄种质资源的种群结构、遗传关系和遗传特征。共获得了 3,374,929 个筛选的 SNP 位点，分布在 12 条染色体上。根据这些 SNP 位点，418 份番茄样本被分为 6 个亚组：结果：利用主成分分析、种群结构分析和系统发育树分析确定了现有番茄种质资源的种群结构和遗传关系。严格的筛选标准从 50 个已验证的 SNP 位点中又鉴定出 15 个高质量的 DNA 指纹，从而有效地鉴定出 418 个番茄品种，并成功地将其转化为 KASP（竞争性等位基因特异性 PCR）标记：本研究是首次对大量番茄品种的多样性和种群结构进行全面评估的研究。总体而言，它标志着我们在了解番茄种群遗传组成方面取得了重大进展。研究结果拓宽了我们对番茄种质资源的多样性、系统发育和种群结构的认识。此外，这项研究还为今后分析番茄的遗传多样性、物种鉴定、产权纠纷和分子育种提供了科学依据和参考数据。
Genetic diversity and population structure analysis of 418 tomato cultivars based on single nucleotide polymorphism markers.
Introduction: Tomato (Solanum lycopersicum) is a highly valuable fruit crop. However, due to the lack of scientific and accurate variety identification methods and unified national standards, production management is scattered and non-standard, resulting in mixed varieties. This poses considerable difficulties for the cataloging and preservation of germplasm resources as well as the identification, promotion, and application of new tomato varieties.
Methods: To better understand the genetic diversity and population structure of representative tomato varieties, we collected 418 tomato varieties from the past 20 years and analyzed them using genome-wide single nucleotide polymorphism (SNP) markers. We initially assessed the population structure, genetic relationships, and genetic profiles of the 418 tomato germplasm resources utilizing simplified genome sequencing techniques. A total of 3,374,929 filtered SNPs were obtained and distributed across 12 chromosomes. Based on these SNP loci, the 418 tomatoes samples were divided into six subgroups.
Results: The population structure and genetic relationships among existing tomato germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Rigorous selection criteria identified 15 additional high-quality DNA fingerprints from 50 validated SNP loci, effectively enabling the identification of the 418 tomato varieties, which were successfully converted into KASP (Kompetitive Allele Specific PCR) markers.
Discussion: This study represents the first comprehensive investigation assessing the diversity and population structure of a large collection of tomato varieties. Overall, it marks a considerable advancement in understanding the genetic makeup of tomato populations. The results broadened our understanding of the diversity, phylogeny, and population structure of tomato germplasm resources. Furthermore, this study provides a scientific basis and reference data for future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding in tomatoes.
期刊介绍：
In an ever changing world, plant science is of the utmost importance for securing the future well-being of humankind. Plants provide oxygen, food, feed, fibers, and building materials. In addition, they are a diverse source of industrial and pharmaceutical chemicals. Plants are centrally important to the health of ecosystems, and their understanding is critical for learning how to manage and maintain a sustainable biosphere. Plant science is extremely interdisciplinary, reaching from agricultural science to paleobotany, and molecular physiology to ecology. It uses the latest developments in computer science, optics, molecular biology and genomics to address challenges in model systems, agricultural crops, and ecosystems. Plant science research inquires into the form, function, development, diversity, reproduction, evolution and uses of both higher and lower plants and their interactions with other organisms throughout the biosphere. Frontiers in Plant Science welcomes outstanding contributions in any field of plant science from basic to applied research, from organismal to molecular studies, from single plant analysis to studies of populations and whole ecosystems, and from molecular to biophysical to computational approaches.
Frontiers in Plant Science publishes articles on the most outstanding discoveries across a wide research spectrum of Plant Science. The mission of Frontiers in Plant Science is to bring all relevant Plant Science areas together on a single platform.
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