Webb Anne, Cottage Amanda, Wood Thomas, Khamassi Khalil, Hobbs Douglas, Gostkiewicz Krystyna, White Mark, Khazaei Hamid, Ali Mohamed, Street Daniel, Duc Gérard, Stoddard Fred L, Maalouf Fouad, Ogbonnaya Francis C, Link Wolfgang, Thomas Jane, O'Sullivan Donal M
National Institute of Agricultural Botany, Cambridge, UK.
PGRO, Thornaugh, Peterborough, UK.
Plant Biotechnol J. 2016 Jan;14(1):177-85. doi: 10.1111/pbi.12371. Epub 2015 Apr 10.
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.
蚕豆（Vicia faba L.）是一种在全球具有重要意义的固氮豆科植物，广泛种植于各种不同的环境中。在这项研究中，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个单核苷酸多态性（SNP）。通过BLAST分析，每个蚕豆SNP都被定位到一个单一的苜蓿直系同源基因上。然后，将这组基于共线性定位的多态性作为单独的竞争性等位基因特异性PCR（KASP）分析进行验证，根据它们在37个自交系群体中的信息性和性能进行分类，并使用表现最佳的757个标记对六个作图群体进行基因分型。将得到的六个连锁图谱合并成一个单一的共识图谱，其中687个SNP位于六个连锁群上，每个连锁群推测对应于蚕豆的六条染色体之一。这个基于序列的共识图谱被用于探索与最密切相关的作物物种小扁豆以及最密切相关且已完成全基因组测序的苜蓿之间的共线性。在蚕豆和苜蓿之间发现了大片不间断的共线性区域，这使得预测定位遗传区间内的基因内容和顺序相对较为直接。作为一个例证，我们将一个花色基因定位到蚕豆2号染色体的一个2厘摩（cM）区间，该区间与苜蓿3号染色体（Mt3）高度共线性。在共线性苜蓿染色体片段的78个基因模型中，明显的候选基因是先前已鉴定的控制苜蓿花青素产生的MtWD40 - 1基因，对蚕豆直系同源基因的重测序显示该基因整个5'端存在一个推定的致病变异缺失。
