Dataset Information

Enhancing faba bean (Vicia faba L.) genome resources.

ABSTRACT: Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13 Gb) genome. In order to address this challenge, RNA-sequencing analysis was performed on faba bean (cv. Wizard) leaves. Read alignment to the faba bean reference transcriptome identified 16 300 high quality unigenes. In addition, Illumina paired-end sequencing was used to establish a baseline for genomic information assembly. Genomic reads were assembled de novo into contigs with a size range of 50-5000 bp. Over 85% of sequences did not align to known genes, of which ~10% could be aligned to known repetitive genetic elements. Over 26 000 of the reference transcriptome unigenes could be aligned to DNA-sequencing (DNA-seq) reads with high confidence. Moreover, this comparison identified 56 668 potential splice points in all identified unigenes. Sequence length data were extended at 461 putative loci through alignment of DNA-seq contigs to full-length, publicly available linkage marker sequences. Reads also yielded coverages of 3466× and 650× for the chloroplast and mitochondrial genomes, respectively. Inter- and intraspecies organelle genome comparisons established core legume organelle gene sets, and revealed polymorphic regions of faba bean organelle genomes.

SUBMITTER: Cooper JW

PROVIDER: S-EPMC5429004 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Enhancing faba bean (Vicia faba L.) genome resources.

Cooper James W JW Wilson Michael H MH Derks Martijn F L MFL Smit Sandra S Kunert Karl J KJ Cullis Christopher C Foyer Christine H CH

Journal of experimental botany 20170401 8

Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13 Gb) genome. In order to address this challenge, RNA-sequencing analysis was performed on faba bean (cv. Wizard) leaves. Read alignment to the faba bean reference transcriptome identified 16 300 high quality unigenes. In addition, Illumina paired-end sequencing was used to establish a b ...[more]

PMID: 28419381

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Project description:BACKGROUND: The development of genetic markers is complex and costly in species with little pre-existing genomic information. Faba bean possesses one of the largest and least studied genomes among cultivated crop plants and no gene-based genetic maps exist. Gene-based orthologous markers allow chromosomal regions and levels of synteny to be characterised between species, reveal phylogenetic relationships and chromosomal evolution, and enable targeted identification of markers for crop breeding. In this study orthologous codominant cross-species markers have been deployed to produce the first exclusively gene-based genetic linkage map of faba bean (Vicia faba), using an F6 population developed from a cross between the lines Vf6 (equina type) and Vf27 (paucijuga type). RESULTS: Of 796 intron-targeted amplified polymorphic (ITAP) markers screened, 151 markers could be used to construct a comparative genetic map. Linkage analysis revealed seven major and five small linkage groups (LGs), one pair and 12 unlinked markers. Each LG was comprised of three to 30 markers and varied in length from 23.6 cM to 324.8 cM. The map spanned a total length of 1685.8 cM. A simple and direct macrosyntenic relationship between faba bean and Medicago truncatula was evident, while faba bean and lentil shared a common rearrangement relative to M. truncatula. One hundred and four of the 127 mapped markers in the 12 LGs, which were previously assigned to M. truncatula genetic and physical maps, were found in regions syntenic between the faba bean and M. truncatula genomes. However chromosomal rearrangements were observed that could explain the difference in chromosome numbers between these three legume species. These rearrangements suggested high conservation of M. truncatula chromosomes 1, 5 and 8; moderate conservation of chromosomes 2, 3, 4 and 7 and no conservation with M. truncatula chromosome 6. Multiple PCR amplicons and comparative mapping were suggestive of small-scale duplication events in faba bean. This study also provides a preliminary indication for finer scale macrosynteny between M. truncatula, lentil and faba bean. Markers originally designed from genes on the same M. truncatula BACs were found to be grouped together in corresponding syntenic areas in lentil and faba bean. CONCLUSION: Despite the large size of the faba bean genome, comparative mapping did not reveal evidence for polyploidisation, segmental duplication, or significant rearrangements compared to M. truncatula, although a bias in the use of single locus markers may have limited the detection of duplications. Non-coding repetitive DNA or transposable element content provides a possible explanation for the difference in genome sizes. Similar patterns of rearrangements in faba bean and lentil compared to M. truncatula support phylogenetic studies dividing these species into the tribes Viceae and Trifoliae. However, substantial macrosynteny was apparent between faba bean and M. truncatula, with the exception of chromosome 6 where no orthologous markers were found, confirming previous investigations suggesting chromosome 6 is atypical. The composite map, anchored with orthologous markers mapped in M. truncatula, provides a central reference map for future use of genomic and genetic information in faba bean genetic analysis and breeding.

Project description:BackgroundFaba bean is an important starch-based protein crop produced worldwide. Soil acidity and aluminium toxicity are major abiotic stresses affecting its production, so in regions where soil acidity is a problem, there is a gap between the potential and actual productivity of the crop. Hence, we set out to evaluate acidity and aluminium tolerance in a range of faba bean germplasm using solution culture and pot experiments.MethodsA set of 30 accessions was collected from regions where acidity and aluminium are or are not problems. The accessions were grown in solution culture and a subset of 10 was grown first in peat and later in perlite potting media. In solution culture, morphological parameters including taproot length, root regrowth and root tolerance index were measured, and in the pot experiments the key measurements were taproot length, plant biomass, chlorophyll concentration and stomatal conductance.ResultResponses to acidity and aluminium were apparently independent. Accessions Dosha and NC 58 were tolerant to both stress. Kassa and GLA 1103 were tolerant to acidity showing less than 3% reduction in taproot length. Aurora and Messay were tolerant to aluminium. Babylon was sensitive to both, with up to 40% reduction in taproot length from acidity and no detectable recovery from Al3+ challenge.DiscussionThe apparent independence of the responses to acidity and aluminium is in agreement with the previous research findings, suggesting that crop accessions separately adapt to H+ and Al3+ toxicity as a result of the difference in the nature of soil parent materials where the accession originated. Differences in rankings between experiments were minor and attributable to heterogeneity of seed materials and the specific responses of accessions to the rooting media. Use of perlite as a potting medium offers an ideal combination of throughput, inertness of support medium, access to leaves for detection of their stress responses, and harvest of clean roots for evaluation of their growth.

Dataset Information

Enhancing faba bean (Vicia faba L.) genome resources.

Publications

Enhancing faba bean (Vicia faba L.) genome resources.

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