A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity
A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity
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DOI：
10.1111/tpj.15770
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发表时间：
2022-05-18
期刊：
影响因子：
7.2
通讯作者：
Usadel, Bjoern
中科院分区：
文献类型：
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作者：
Powell, Adrian F.;Feder, Ari;Usadel, Bjoern
番茄的野生近缘种是番茄育种自然变异的宝贵来源，因为许多野生近缘种可以与栽培品种（茄属番茄）杂交。包括类番茄茄在内的几种植物已与番茄茄杂交，形成有序渐渗系（ILs），促进了所需性状的选育。尽管这些野生近缘种及其相关的ILs很有用，但很少有完整的基因组序列来帮助遗传和基因组研究。在这里，我们报道了番茄红素葡萄球菌LA2951染色体尺度的基因组组装，其中包含37938个预测的蛋白质编码基因。利用这一基因组组合，我们精确地划定了一组番茄葡萄球菌cv中番茄红素类葡萄球菌的渗入边界。VF36 x LA2951 ILs。我们通过鉴定酚类物质和类胡萝卜素的几个数量性状位点，包括潜在的候选基因，以及研究聚类Pto基因家族的基因组组织和免疫相关功能，证明了LA2951基因组的有用性。此外，R2R3MYB基因的合成分析揭示了茄子花青素产生的基因座的身份。基因组序列和IL图谱为研究果实营养品质性状、抗病性和环境胁迫能力提供了宝贵的资源。我们提出了一种新的野生物种番茄红素的基因组资源，我们用它来阐明负责花青素生产的茄子位点。我们还提供了IL边界映射，这有助于鉴定新的类胡萝卜素数量性状位点，其中一个位点可能是由未表征的番茄红素β -环化酶驱动的，我们证明了其功能。
Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome-scale genome assembly for S. lycopersicoides LA2951, which contains 37 938 predicted protein-coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36 x LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity-associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides, which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene beta-cyclase whose function we demonstrate.