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首页> 外文期刊>BMC Genomics >Tomato breeding in the genomics era: insights from a SNP array
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Tomato breeding in the genomics era: insights from a SNP array

机译：基因组学时代的番茄育种：SNP阵列的见解

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Background The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and high throughput genotyping. A set of 6000 SNPs was identified and 5528 of them were used to evaluate tomato germplasm at the level of species, varieties and segregating populations. Results From the 5528 SNPs, 1980 originated from 454-sequencing, 3495 from Illumina Solexa sequencing and 53 were additional known markers. Genotyping different tomato samples allowed the evaluation of the level of heterozygosity and introgressions among commercial varieties. Cherry tomatoes were especially different from round/beefs in chromosomes 4, 5 and 12. We were able to identify a set of 750 unique markers distinguishing S. lycopersicum ‘Moneymaker’ from all its distantly related wild relatives. Clustering and neighbour joining analysis among varieties and species showed expected grouping patterns, with S. pimpinellifolium as the most closely related to commercial tomatoesearlier results. Conclusions Our results show that a SNP search in only a few breeding lines already provides generally applicable markers in tomato and its wild relatives. It also shows that the Illumina bead array generated data are highly reproducible. Our SNPs can roughly be divided in two categories: SNPs of which both forms are present in the wild relatives and in domesticated tomatoes (originating from common ancestors) and SNPs unique for the domesticated tomato (originating from after the domestication event). The SNPs can be used for genotyping, identification of varieties, comparison of genetic and physical linkage maps and to confirm (phylogenetic) relations. In the SNPs used for the array there is hardly any overlap with the SolCAP array and it is strongly recommended to combine both SNP sets and to select a core collection of robust SNPs completely covering the entire tomato genome.
机译：背景技术番茄遗传和连锁研究的主要瓶颈是缺乏足够的分子标记。随着下一代测序和高通量基因分型技术的应用，这已经发生了根本性的变化。鉴定出一组6000个SNP，其中5528个被用于评估番茄种质的物种，品种和隔离种群水平。结果从5528个SNP中，1980年来自454测序，3495个来自Illumina Solexa测序，另外53个是已知标记。对不同番茄样品进行基因分型可以评估商品品种之间的杂合度和基因渗入水平。樱桃番茄与第4、5和12号染色体的圆形/牛肉特别不同。我们能够鉴定出750个独特的标记，将番茄裂殖酵母“ Moneymaker”与所有远缘野生亲戚区分开来。聚类和物种间的聚类和邻居加入分析显示了预期的分组模式，其中平菇S.pimpinellifolium与商业番茄关系最密切。结论我们的结果表明，仅在几个育种系中进行SNP搜索就已经提供了番茄及其野生近缘种中普遍适用的标记。它还表明，Illumina磁珠阵列生成的数据具有很高的重现性。我们的SNP大致可分为两类：野生亲戚和驯化番茄中均存在这两种形式的SNP（起源于共同祖先）和驯化番茄所特有的SNP（起源于驯化事件后）。 SNP可用于基因分型，品种鉴定，遗传和物理连锁图的比较以及确认（系统发育）关系。在用于阵列的SNP中，几乎没有与SolCAP阵列重叠的部分，强烈建议将两个SNP集组合在一起，并选择完全覆盖整个番茄基因组的健壮SNP的核心集合。

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