Flanking SNP markers for vicine–convicine concentration in faba bean (Vicia faba L.)

Khazaei, Hamid; O’Sullivan, Donal M.; Jones, Huw; Pitts, Nicholas; Sillanpää, Mikko J.; Pärssinen, Pertti; Manninen, Outi; Stoddard, Frederick L.

doi:10.1007/s11032-015-0214-8

Cited by 39 publications

(67 citation statements)

References 21 publications

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“…Figure 1 shows a typical alignment of contigs from several distinct Vf genotypes to a gene predicted by synteny to lie within the published VC interval (Khazaei et al, 2015). Over the 1534 bp contig, which covers the full coding region predicted in Medicago together with some 5′ and 3′-UTR sequence, there are 16 varietal Vf SNPs.…”

Section: Genomicsmentioning

confidence: 70%

Advances in Faba Bean Genetics and Genomics

O’Sullivan

Angra

2016

Front. Genet.

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Vicia faba L, is a globally important grain legume whose main centers of diversity are the Fertile Crescent and Mediterranean basin. Because of its small number (six) of exceptionally large and easily observed chromosomes it became a model species for plant cytogenetics the 70s and 80s. It is somewhat ironic therefore, that the emergence of more genomically tractable model plant species such as Arabidopsis and Medicago coincided with a marked decline in genome research on the formerly favored plant cytogenetic model. Thus, as ever higher density molecular marker coverage and dense genetic and even complete genome sequence maps of key crop and model species emerged through the 1990s and early 2000s, genetic and genome knowledge of Vicia faba lagged far behind other grain legumes such as soybean, common bean and pea. However, cheap sequencing technologies have stimulated the production of deep transcriptome coverage from several tissue types and numerous distinct cultivars in recent years. This has permitted the reconstruction of the faba bean meta-transcriptome and has fueled development of extensive sets of Simple Sequence Repeat and Single Nucleotide Polymorphism (SNP) markers. Genetics of faba bean stretches back to the 1930s, but it was not until 1993 that DNA markers were used to construct genetic maps. A series of Random Amplified Polymorphic DNA-based genetic studies mainly targeted at quantitative loci underlying resistance to a series of biotic and abiotic stresses were conducted during the 1990's and early 2000s. More recently, SNP-based genetic maps have permitted chromosome intervals of interest to be aligned to collinear segments of sequenced legume genomes such as the model legume Medicago truncatula, which in turn opens up the possibility for hypotheses on gene content, order and function to be translated from model to crop. Some examples of where knowledge of gene content and function have already been productively exploited are discussed. The bottleneck in associating genes and their functions has therefore moved from locating gene candidates to validating their function and the last part of this review covers mutagenesis and genetic transformation, two complementary routes to validating gene function and unlocking novel trait variation for the improvement of this important grain legume.

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Section: Genomicsmentioning

confidence: 70%

Advances in Faba Bean Genetics and Genomics

O’Sullivan

Angra

2016

Front. Genet.

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“…Many mapping populations are available in the community and we hope that the lower cost barriers will make it possible for more groups to be involved in trait mapping than are currently. For example, SNP markers from this study found to be polymorphic in population 5 (Table ) have been used to map QTL for stomatal traits (Khazaei et al ., ), low vicine–convicine (Khamassi et al ., ; Khazaei et al ., ) and a novel anthocyanin pigmentation locus, ssp1 (Khazaei et al ., ). Similarly, SNP markers from this study used to generate the linkage map for population 4 (Table ) have been found linked to a novel dwarfing locus, Dwf1 (K. Khamassi, K. Gostkiewicz, and D.M.…”

Section: Discussionmentioning

confidence: 99%

A SNP‐based consensus genetic map for synteny‐based trait targeting in faba bean (Vicia faba L.)

Webb

Cottage

Wood

et al. 2015

Plant Biotechnology Journal

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105

184

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SummaryFaba 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.

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“…The same population segregated for vicine-convicine content (Khazaei et al 2015), stipule spot pigmentation (Khazaei et al 2014a), green seed-coat color, and two loci affecting seed size (Khazaei et al 2014b). In most of these cases, synteny with the Medicago truncatula genome has allowed us to nominate candidates for the genes affecting these traits.…”

Section: Understanding and Using The Variationmentioning

confidence: 99%

“…The region in M. truncatula enclosing the syntenic region to the QTL for vicineconvicine concentration includes no genes identifiably associated with pyrimidine metabolism (Khazaei et al 2015), but has seven transcription factors, one of which could be the candidate for downregulation in the vc-mutation. Candidates for neofunctionalization of pyrimidine metabolism lie elsewhere in the genome.…”

Section: Understanding and Using The Variationmentioning

confidence: 99%