Calafiore Roberta, Ruggieri Valentino, Raiola Assunta, Rigano Maria M, Sacco Adriana, Hassan Mohamed I, Frusciante Luigi, Barone Amalia
Department of Agricultural Sciences, University of Naples Federico II Portici, Italy.
Department of Genetics, Faculty of Agriculture, Assiut University Assiut, Egypt.
Front Plant Sci. 2016 Apr 8;7:397. doi: 10.3389/fpls.2016.00397. eCollection 2016.
The tomato is a model species for fleshy fruit development and ripening, as well as for genomics studies of others Solanaceae. Many genetic and genomics resources, including databases for sequencing, transcriptomics and metabolomics data, have been developed and are today available. The purpose of the present work was to uncover new genes and/or alleles that determine ascorbic acid and carotenoids accumulation, by exploiting one Solanum pennellii introgression lines (IL7-3) harboring quantitative trait loci (QTL) that increase the content of these metabolites in the fruit. The higher ascorbic acid and carotenoids content in IL7-3 was confirmed at three fruit developmental stages. The tomato genome reference sequence and the recently released S. pennellii genome sequence were investigated to identify candidate genes (CGs) that might control ascorbic acid and carotenoids accumulation. First of all, a refinement of the wild region borders in the IL7-3 was achieved by analyzing CAPS markers designed in our laboratory. Afterward, six CGs associated to ascorbic acid and one with carotenoids metabolism were identified exploring the annotation and the Gene Ontology terms of genes included in the region. Variants between the sequence of the wild and the cultivated alleles of these genes were investigated for their functional relevance and their potential effects on the protein sequences were predicted. Transcriptional levels of CGs in the introgression region were extracted from RNA-Seq data available for the entire S. pennellii introgression lines collection and verified by Real-Time qPCR. Finally, seven IL7-3 sub-lines were genotyped using 28 species-specific markers and then were evaluated for metabolites content. These analyses evidenced a significant decrease in transcript abundance for one 9-cis-epoxycarotenoid dioxygenase and one L-ascorbate oxidase homolog, whose role in the accumulation of carotenoids and ascorbic acid is discussed. Comprehensively, the reported results demonstrated that combining genetic and genomic resources in tomato, including bioinformatics tools, was a successful strategy to dissect one QTL for the increase of ascorbic acid and carotenoids in tomato fruit.
番茄是肉质果实发育与成熟以及其他茄科植物基因组学研究的模式物种。目前已开发出许多遗传和基因组学资源，包括用于测序、转录组学和代谢组学数据的数据库，如今均可获取。本研究的目的是通过利用一个携带数量性状基因座（QTL）的野生潘那利番茄渐渗系（IL7 - 3）来发现决定抗坏血酸和类胡萝卜素积累的新基因和/或等位基因，该QTL可增加果实中这些代谢物的含量。在三个果实发育阶段均证实了IL7 - 3中抗坏血酸和类胡萝卜素含量较高。研究了番茄基因组参考序列和最近发布的潘那利番茄基因组序列，以鉴定可能控制抗坏血酸和类胡萝卜素积累的候选基因（CGs）。首先，通过分析我们实验室设计的CAPS标记，对IL7 - 3中野生区域边界进行了优化。之后，通过探索该区域内基因的注释和基因本体论术语，鉴定出六个与抗坏血酸相关的CGs和一个与类胡萝卜素代谢相关的CGs。研究了这些基因野生型和栽培型等位基因序列之间的变异的功能相关性，并预测了它们对蛋白质序列的潜在影响。从整个潘那利番茄渐渗系群体可用的RNA - Seq数据中提取渐渗区域内CGs的转录水平，并通过实时定量PCR进行验证。最后，使用28个物种特异性标记对七个IL7 - 3亚系进行基因分型，然后评估其代谢物含量。这些分析表明，一种9 - 顺式环氧类胡萝卜素双加氧酶和一种L - 抗坏血酸氧化酶同源物的转录丰度显著降低，并讨论了它们在类胡萝卜素和抗坏血酸积累中的作用。综合来看，所报道结果表明，结合番茄中的遗传和基因组学资源，包括生物信息学工具，是剖析一个增加番茄果实中抗坏血酸和类胡萝卜素含量的QTL的成功策略。
