A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.).
A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.).
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DOI：
10.1111/pbi.12371
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发表时间：
2016-01
影响因子：
13.8
通讯作者：
O'Sullivan DM
中科院分区：
文献类型：
--
作者：
Webb A;Cottage A;Wood T;Khamassi K;Hobbs D;Gostkiewicz K;White M;Khazaei H;Ali M;Street D;Duc G;Stoddard FL;Maalouf F;Ogbonnaya FC;Link W;Thomas J;O'Sullivan DM
蚕豆 (Vicia faba L.) 是一种全球重要的固氮豆科植物，广泛种植在各种环境中。在这项工作中，我们从两个对比自交系的比对转录组中挖掘并验证了一组 845 个 SNP。通过 BLAST 分析将每个蚕豆 SNP 分配给单个苜蓿直系同源物。然后将这组同线锚定多态性作为单独的 KASP 检测进行验证，根据其信息量和在一组 37 个自交系上的性能进行分类，以及用于对六个作图群体进行基因分型的最佳性能 757 个标记。所得的六个连锁图被合并成一个共有图，其中 687 个 SNP 被放置在六个连锁组上，每个连锁组被认为对应于六个蚕豆染色体之一。这个基于序列的共识图用于探索与最密切相关的作物物种（扁豆）和最密切相关的全测序基因组（苜蓿）的同线性。在蚕豆和苜蓿之间发现了大片不间断的共线性，使得预测绘制的遗传区间中的基因内容和顺序相对简单。为了证明这一点，我们将花色基因映射到 Vf 2 号染色体的 2 cM 间隔，该间隔与 Mt3 高度共线。共线苜蓿染色体片段中的 78 个基因模型中明显的候选基因是先前表征的控制苜蓿花青素产生的 MtWD40-1 基因，Vf 直向同源物的重新测序显示该基因的整个 5' 端被推定为致病性缺失。
Faba bean (Vicia faba L.) is a globally important nitrogen‐fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence‐based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2‐cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40‐1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 5′ end of the gene.