Department of Plant and Soil Science, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, Texas, United States of America.
PLoS One. 2020 Nov 23;15(11):e0242882. doi: 10.1371/journal.pone.0242882. eCollection 2020.
Solanum lycopersicoides is a wild nightshade relative of tomato with known resistance to a wide range of pests and pathogens, as well as tolerance to cold, drought and salt stress. To effectively utilize S. lycopersicoides as a genetic resource in breeding for tomato improvement, the underlying basis of observable traits in the species needs to be understood. Molecular markers are important tools that can unlock the genetic underpinnings of phenotypic variation in wild crop relatives. Unfortunately, DNA markers that are specific to S. lycopersicoides are limited in number, distribution and polymorphism rate. In this study, we developed a suite of S. lycopersicoides-specific SSR and indel markers by sequencing, building and analyzing a draft assembly of the wild nightshade genome. Mapping of a total of 1.45 Gb of S. lycopersicoides contigs against the tomato reference genome assembled a moderate number of contiguous reads into longer scaffolds. Interrogation of the obtained draft yielded SSR information for more than 55,000 loci in S. lycopersicoides for which more than 35,000 primers pairs were designed. Additionally, indel markers were developed based on sequence alignments between S. lycopersicoides and tomato. Synthesis and experimental validation of 345 primer sets resulted in the amplification of single and multilocus targets in S. lycopersicoides and polymorphic loci between S. lycopersicoides and tomato. Cross-species amplification of the 345 markers in tomato, eggplant, silverleaf nightshade and pepper resulted in varying degrees of transferability that ranged from 55 to 83%. The markers reported in this study significantly expands the genetic marker resource for S. lycopersicoides, as well as for related Solanum spp. for applications in genetics and breeding studies.
茄属植物野茄是番茄的野生近缘种，具有广泛的抗病虫害、抗寒、耐旱和耐盐能力。为了有效利用茄属植物野茄作为遗传资源，改良番茄品种，需要了解该物种中可观察性状的基础。分子标记是一种重要的工具，可以揭示野生作物近缘种表型变异的遗传基础。不幸的是，茄属植物野茄特有的 DNA 标记数量有限，分布和多态性率也较低。在本研究中，我们通过测序、构建和分析茄属植物野茄的基因组草图，开发了一套茄属植物野茄特异性 SSR 和插入缺失标记。将总共 1.45Gb 的茄属植物野茄 contigs 映射到组装好的番茄参考基因组上，将大量连续的reads 组装成长度更长的 scaffolds。对获得的草图进行分析，得到了茄属植物野茄 55000 多个位点的 SSR 信息，其中设计了 35000 多个引物对。此外，还基于茄属植物野茄和番茄之间的序列比对开发了插入缺失标记。合成并实验验证了 345 对引物，结果在茄属植物野茄中扩增出了单一位点和多位点的目标，以及茄属植物野茄和番茄之间的多态性位点。345 个标记在番茄、茄子、银叶茄和辣椒中的交叉物种扩增具有不同程度的可转移性，范围从 55%到 83%。本研究报道的标记显著扩展了茄属植物野茄以及相关茄属植物的遗传标记资源，可用于遗传学和育种研究。
