Co-publication of International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS). labelled 5S rDNA (b, d, f) probes on metaphase chromosomes of Vigna unguiculata: (a, b) subsp. Of course, these comparisons are subject to revision as the respective genome sequences become more complete. The centromere‐abundant 455‐bp repeat available from Iwata‐Otsubo et al. Walp.) Family membership was evaluated relative to median HMM bitscores for each family, with sequences scoring less than 40% of the median HMM bitscore for the family being removed. Int. The number of annotated cowpea gene models containing a SNP was 23 266 (78% of total) or 27 021 (91% of total) when considering genes within 10 kb of a SNP (Table S8). J. Insect Sci. (2017) was used to join them by estimating the size of the gap (in cM). PASA‐improved gene model proteins were subject to protein homology analysis to the proteomes mentioned above to obtain Cscore and protein coverage. Knowledge of the recombination rate can be integrated into decisions on marker density and provide weight factors in genomic selection models to favor rare recombination events within low recombination regions. B., Leleji, O., II, Atokple, I. D. K., Adu, J. K. (1991). (2001). Rawal, K. M., Rachie, K. O., Franckowiak, J. D. (1976). Food Chem. “Variation in virulence of Striga gesnerioides on cowpea: new sources of crop resistance,” in Advances in Cowpea Research. A programme by INRA, CIRAD, AFZ and FAO. Of the long terminal repeat (LTR) retrotransposons, elements of the Gypsy superfamily (Wicker et al., 2007; code RLG) are 1.5 times more abundant than Copia (code RLC) elements, but non‐autonomous TRIM elements appear to be very rare, with only 57 found. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. First, CLARK and CLARK‐S (Ounit and Lonardi, 2016) were used to identify possible contamination from unknown organisms. Intercropping in tropical smallholder agriculture with special reference to West Africa. Lane, J. (Chichester, England: John Wiley and Sons), 217–232. In addition, comparisons between cowpea genetic maps and chromosomal maps developed by fluorescence in situ hybridization (FISH) using cowpea BACs as probes (Iwata‐Otsubo et al., 2016) revealed that the prior orientations of three linkage groups (now referred to as Vu06, Vu10 and Vu11) were inverted relative to their actual chromosome orientation. Learn about our remote access options, Department of Computer Science and Engineering, University of California, Riverside, CA, 92521 USA, Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521 USA, US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598 USA, Natural Resources Institute Finland (Luke), Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Helsinki, Finland, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Department of Plant Sciences, University of California, Davis, CA, 95616 USA, Institut de Recherche en Horticulture et Semences, INRA, Université d'Angers, 49071 Beaucouzé, France, Department of Nematology, University of California, Riverside, CA, 92521 USA, Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic, National Center for Genome Resources, Santa Fe, NM, 87505 USA, US Department of Agriculture–Agricultural Research Service, Ames, IA, USA. The Biology of Parasitic Flowering Plants (Berkeley, CA, USA: University of California Press), 346 pp. Selection can act to maintain an inversion when it carries one or more advantageous alleles or when an inversion breakpoint causes gene disruption or expression changes that are adaptive (Kirkpatrick, 2010; Puig et al., 2015). 137 (Eschborn, Germany), 303 pp. Synteny view between cowpea (Vu; Vigna unguiculata) and other closely related diploid species. Sequence archive. Cowpea centromeric and pericentromeric regions are highly repetitive in sequence composition, and exhibit low gene density and low recombination rates, while both gene density and recombination rate increase as the physical position becomes more distal from the centromeres (Figures 1 and S8; Data S1). AHS and JT annotated and analyzed repeats. As explained above, 10 genetic maps were used to anchor and orient scaffolds into pseudochromosomes. Cscore is a protein BLASTP score ratio to MBH (mutual best hit) BLASTP score, and protein coverage is the highest percentage of protein aligned to the best homolog. Eds. “Insect pests of cowpea,” in The Insect Pests of Tropical Food Legumes. 59, 203–212. Gene and repeat densities, and recombination rate in the cowpea genome. The KSU stitching pipeline was iterated four times, alternating BspQI and BssSI (twice each map) at which point no conflicts remained. This would facilitate reciprocal exchange of genomic information on target traits from one Vigna species to another. Deutsche Gesellschaft für Technische Zusammenarbeit (GTZ) GmbH, No. (1997). Proceedings of the National Academy of Sciences. As is usually done, 27‐mers that appear only once are excluded because they are considered erroneous, that is to contain sequencing errors. To validate the inversion, the sequence assembly of the reference genome was compared with that of a cowpea accession typical of California breeding lines via MUMmer (Kurtz et al., 2004), using a minimum exact match of 100 bp and a minimum alignment length of 1 kb. PASA‐improved transcripts were selected based on Cscore, protein coverage, EST coverage and its CDS overlapping with repeats. 13–29. Copyright © 2020 Boukar, Abberton, Oyatomi, Togola, Tripathi and Fatokun. Figure S5. The intersection of these two lists contained only a single gene, Phvul.008G285800, a P. vulgaris candidate gene for increased seed size that corresponds to cowpea Vigun08 g217000. A polynomial curve fit of cM position as a function of pseudochromosome coordinate was generated using R for each of the 11 linkage groups from maps of each of 10 biparental RIL populations. Received: 29 May 2020; Accepted: 31 August 2020;Published: 16 September 2020. Table S1. To assess the genome size of the sequenced accession IT97K‐499‐35, nuclear DNA content was estimated using flow cytometry (Dolezel, 2003), k‐mer analysis and optical mapping (see Experimental procedures for more detail). Heat stress and cowpea: genetics, breeding and modern tools for improving genetic gains. In total, 56.8 Gb of sequence data were generated (~91.7 × genome equivalent), with a read N50 of 14 595 bp. Steiner, K. G. (1982). Table S5. About 35% of the SNPs in the 1M list were associated with genes (336 285 SNPs), while that percentage increased to 62% in the iSelect array (31 708 SNPs; Data S2; Table S8). Here, we re‐estimated the genome size of V. unguiculata and produced a genome assembly using single‐molecule real‐time sequencing combined with optical and genetic mapping. Response of transgenic Bt cowpea and their hybrids under field conditions. Screening for resistance to cowpea aphid (Aphis craccivora Koch) in wild and cultivated cowpea (Vigna unguiculata L. Also, a k‐mer distribution analysis was carried out, providing a somewhat lower estimate of 560.3 Mbp (Figure S2). through embryo rescue. TZ and MCL generated the optical maps. Genome size was determined using the conversion factor 1 pg = 0.978 Mbp (Dolezel, 2003). International Institute of Tropical Agriculture (IITA) (1988). Table S1 shows the summary of raw molecule status and the BNG BspQI map assembly. Resulting SMRTbell libraries were size selected using the BluePippin (Sage Biosciences) according to the Blue Pippin User Manual and Quick Guide. In 25 genera of this tribe cited by Darlington & Wylie (1955), this basic chromo-some number is … dekindtiana Tvnu111, and (e, f) subsp. Using the same computational pipeline as for V. unguiculata (Vu), the repeats of the V. angularis (Yang et al., 2015; Va) and V. radiata (Kang et al., 2014; Vr) genomes also were annotated. The symbols ">,, indicate minor 18S-5.8S-25S rDNA sites. Ames, IA, USA: Iowa State University. For both Vr and Va, far fewer unidentified LTR retrotransposons (RLX) were found than in the Vu genome, perhaps because the Vu genome appears to be less fragmented and more complete than the former two. 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Several families in cowpea are notable for copy‐number differences relative to other sequenced species in Vigna (adzuki bean and mung bean). MMA, SaL and AN generated genetic maps. Longwe, L. (1996). The region extending from the beginning of the first hit to the end of the last hit was considered to define the centromeric region of each cowpea chromosome. Screening techniques for host plant resistance to insect pests of cowpea. Genes within the QTL regions were identified. As noted elsewhere, 46 Mb of assembled sequences were not anchored. Appl. For each of those cases, the number of the common bean chromosome sharing the largest syntenic region with cowpea was adopted, with one exception: two cowpea chromosomes (previous linkage groups/chromosomes #1 and #5) both shared their largest block of synteny with P. vulgaris chromosome Pv08. In those cases, the cowpea consensus genetic map of Muñoz‐Amatriaín et al. Gene families lacking cowpea membership are more difficult to interpret biologically, as these tend to be smaller gene families, likely showing stochastic effects of small families ‘falling out of’ larger superfamilies, due to extinction of clusters of genes or to artifactual effects of family construction. Co-publication of International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS). A polynomial was then derived for the mean values along each pseudochromosome to represent recombination rate as a function of nucleotide coordinate (cM/Mbp). Sci. (2017), and one each from Santos et al. The rolling‐circle Helitron (DHH) superfamily is relatively abundant at 1.3% of the genome and 7013 individual elements. Towards CRISPR/Cas crops- bringing together genomics and genome editing. This indicates that the intended bias towards genes in the iSelect array design (Muñoz‐Amatriaín et al., 2017) was successful. Rome: Food and Agriculture Organization. Plant Sci. Bound SMRTbell libraries were loaded onto the SMRT cells using the standard MagBead protocol, and the MagBead Buffer Kit v2.0 (P/N 100‐642‐800). Then, 1 ml Otto II solution containing 50 μg ml−1 propidium iodide (PI) and 50 μg ml−1 RNase was added and the sample was analyzed by a CyFlow Space flow cytometer (Sysmex Partec, Görlitz, Germany). Subread Filtering PacBio read length distribution. Large chromosomal inversion detected on Vu03. Two primer pairs were designed for each breakpoint region: one to amplify the reference orientation and another to amplify the opposite orientation (Table S10). Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.) Protein knowledgebase. and you may need to create a new Wiley Online Library account. 6:126:126. doi: 10.3389/fpls.2015.00126. Pseudochromosomes were obtained by anchoring the scaffold sequences to SNP markers (blast of SNP design sequences, e−50 or less) in 10 genetic maps (Table S4). 10, 6–22. Pacific Biosciences reads were generated at Washington State University (Pullman, WA, USA) following the ‘Procedure and Checklist‐20 kb Template Preparation Using BluePippin Size Selection System’ (P/N 100‐286‐000‐5) protocol provided by Pacific Biosciences (Menlo Park, CA, USA) and the Pacific Biosciences SMRTbell Template Prep kit 1.0 (P/N 100‐259‐100). This reference sequence was used to identify repetitive elements, genes and gene families, and genetic variation, and for comparative analysis with three closely related legumes including common bean, which stimulated a change in chromosome numbering to facilitate comparative studies. Plant parts of the crops are used as fodder or hay for farm animals. |, Exploring the Diversity and Potential of CWRs for Introgression Breeding, Useful Traits Present in Some Wild Cowpea Relatives, Interspecific Hybridization and Backcross Breeding: Barriers and Overcoming Them, Development of Populations With Introgressions From CWRs: Introgression Lines, Chromosome Substitution Lines, Advanced Backcrosses, and Others, Characterization and Evaluation of Populations With Introgressions From CWRs for Simple and Complex Traits, “Omics” Applications to Introgression Breeding, Gene Editing of COWPEA to Facilitate Their Use in Breeding, https://lib.dr.iastate.edu/icm/2016/proceedings/4, Creative Commons Attribution License (CC BY). (2015). J. Nutr. Eds. The peak of the distribution is 56, which represents the effective coverage. (2010). If you do not receive an email within 10 minutes, your email address may not be registered, Singh, B. PacBio Quiver enables consensus accuracies on genome assemblies approaching or exceeding Q60 (one error per million bases) when the sequencing depth is above 60 × (Chin et al., 2013). Walp.). In total, 29 773 protein‐coding loci were annotated, along with 12 514 alternatively spliced transcripts. Eight draft assemblies were generated, six of which were produced with canu v1.3 (Berlin et al., 2015; Koren et al., 2017), one with Falcon v0.7.3 (Chin et al., 2016) and one with Abruijn v0.4 (Lin et al., 2016). 1–Pp:12. The genotype data from all of the parental lines showed that one of the parents from each of those three populations, but not the other parent, had the same haplotype as IT97K‐499‐35, and hence presumably the same orientation (Data S4). Figure S11. Results revealed 12 linkage maps with an average of 10 markers to a chromosome and average marker distance of 3.02 cM between the markers. Six cowpea chromosomes (Vu04, Vu06, Vu07, Vu09, Vu10 and Vu11) largely have synteny with single chromosomes in all three other species. Co-publication of International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS). Ji, J., Zhang, C., Sun, Z., Wang, L., Duanmu, D., Fan, Q. (2010). Characteristics of the 10 genetic maps used for pseudochromosome construction. Learn more. The chromosome number of this crop is 2n = 22 [4,25, 27] . The average GC content of the assembly was 32.99%, similar to other sequenced legumes (Varshney et al., 2012; Schmutz et al., 2014; Yang et al., 2015). Figure S8. A decade of Tropical Legumes projects: Development and adoption of improved varieties, creation of market‐demand to benefit smallholder farmers and empowerment of national programmes in sub‐Saharan Africa and South Asia. Plots of genetic against physical positions for SNPs on seven of those genetic maps showed a relatively large region in an inverted orientation (Figures 2a and S10). The Windows software HarvEST:Cowpea (harvest.ucr.edu), which includes a synteny display function, also has adopted an updated numbering system. Maps (1)–(3) show a 4.2 Mb region in an inverted orientation (red arrow), while map (4) shows no recombination in that same region (area contained within red lines). 20:2471. doi: 10.3390/ijms20102471, Kouam, E. B., Pasquet, R. S., Campagne, P., Tignegre, J.-B., Thoen, K., Gaudin, R., et al. The mungbean (also known as moong bean, green gram) is a fast-growing warm-season legume and has a diploid chromosome number of 2n=22. Figure S3. Mungbean is mainly cultivated today in China, India and Southeast Asia but can be found in dry regions within Southern Europe and United States. Current advances and future directions in genetic enhancement of a climate resilient food legume crop, cowpea (Vigna unguiculata L. B., Mohan Raj, D. R., Dashiell, K. E., Jackai, L. E. N. (Ibadan, Nigeria: IITA), pp. All of these metrics indicate agreement with the pseudochromosomes. Two of the three landraces carrying the inversion (B‐301 and B‐171) originated from Botswana, while the third (TVu‐53) is a Nigerian landrace. Plant Breed 1 (4), 600–610. Gene families were generated as follows (summarizing method details from https://github.com/LegumeFederation/legfed_gene_families). The linear model R function lm was used to compute the linear regression. High‐molecular‐weight DNA was isolated by Amplicon Express (Pullman, WA, USA) from nuclei purified from young etiolated leaves (grown in the dark) of 100% homozygous, pure seeds of cowpea IT97K‐499‐35. An initial library of elements was built by combining the output from Repet, RepeatModeler, LTRharvest/LTRdigest (genometools.org), elements in the Fabaceae section of the RepBase transposon library (Bao et al., 2015) and our own custom pipeline. A., Moore, T. H. M., Child, D. V., Bailey, J. doi: 10.1017/S0003598X00095661. The legume‐focused gene families from the NSF Legume Federation project (NSF DBI#1444806) were used to compare annotated genes in cowpea with those from other legume proteomes. Ng, N. Q., Monti, L. M. (Ibadan, Nigeria: International Institute of Tropical Agriculture), 58–77. SaL, SAH and ADF identified the syntelog for multiple organ gigantism. The nutrient composition and dietary importance of some vegetable foods eaten by the Kung Bushmen. is one of the most important food and nutritional security crops, providing the main source of protein to millions of people in developing countries. canu v1.3 was run with different settings for the error correction stage on the entire dataset of ~6 M reads (two canu runs were optimized for highly repetitive genomes). J. Its genome shares a high degree of collinearity with other sesquipedialis." Out of six assemblies, three were sequenced chromosome-wise, i.e. Previous analyses placed cowpea phylogenetically closer to mung bean (Vr) than to adzuki bean (Va; She et al., 2015), although the Va and Vr genomes are relatively similar in size, with cowpea, respectively, 11 and 12% larger. Direct hybridization of Nicotiana rependa x N. tabacum. MMA analyzed and validated the chromosomal inversion with help from SaL, SIW and ADF. Teran, J. C. B. M., Konzen, E. R., Palkovic, A., Tsai, S. M., Gepts, P. (2020). Taken together, the cross‐species comparisons suggest that differences in genome size in Vigna can be largely explained by TE abundance, especially by that of Gypsy retrotransposons. South Afr. (2017). “Screening wild Vigna species and cowpea (Vigna unguiculata) landraces for sources of resistance to Striga gesnerioides),” in Enhancing crop genepool use: capturing wild relatives and landrace diversity for crop improvement. HA and AMH identified structural variants. Maxted, N., Dulloo, E. M., Ford-Lloyd, B. V. (Wallingford, United Kingdom: CAB Int), pp 27–pp 31. doi: 10.1079/9781780646138.0027. Pittarelli, G. W., Stavely, J. R. (1975). Singh, B. The set was supplemented with elements identified by similarities to expected domains, including LINE integrases for the LINEs and transposases for the DNA transposons. Oghiakhe, S., Jackai, L. E. N., Makanjuola, W. A. 41, 189–197. Again, sequences scoring less than 40% of the median HMM bitscore for the family were removed. Expansion of SSR content was very moderate in Vu versus Vr, and comprised a smaller genome share than in Va. A similar comparison was made to the 473 Mb genome assembly of P. vulgaris (Schmutz et al., 2014; Pv) with a genome estimated to be only 9% smaller (587 Mbp; http://data.kew.org/cvalues). For the latter, the sequence assembly of the California accession was used to design primers. (1990). Identification and marker-assisted introgression of QTL conferring resistance to bacterial leaf blight in cowpea (Vigna unguiculata (L.) Walp.). Retrieved from: https://www.intechopen.com/books/genet-engineering-an insight into strategies and applications/plant-genome editing and its application in cereals. (a) The relationships between genetic and physical positions are shown for single nucleotide polymorphisms (SNPs) on four genetic maps (1–4). Front. is a major crop for worldwide food and nutritional security, especially in sub‐Saharan Africa, that is resilient to hot and drought‐prone environments. The much smaller number of insertions than deletions may reflect limitations in the ability of the software to identify insertions when sequence reads are mapped to a reference genome. x; UniProtKB. GWAS and Genomic Approaches in Legumes, an Expanding Toolkit for Examining Responses to Abiotic Stresses. doi: 10.5897/JPBCS2013.0401. A direct effect of inversions is that they suppress recombination in heterozygotes, causing inverted regions to evolve independently. PCR amplifications of the breakpoint regions were performed to further validate the Vu03 inversion. Falcon and Abruijn were run on 3.54 M error‐corrected reads produced by canu (30.62 Gbp, or 49.4 × genome equivalent). Across a Decade that cowpea has highly distinct … Vigna unguiculata [ L. ].... Plant parts of the assembled sequence is composed of SINEs and lines, appear to have only! The material was screened for homozygosity by genotyping with the pseudochromosomes to create raster... And BssSI ( twice each map ) at which point no conflicts remained for vegetable, grain forage! The three genomes were created, termed the white list and the black.. The rest are all scaffold- and contig-wise Solanum lycopersicum cv domestication of rice bean, Vigna umbellata identity was. Resistance in major grain Legumes reads produced by canu ( 30.62 Gbp, or differential retention of ancient insertions near. Repeat library consisted of de novo repeats identified by RepeatModeler ( Smit et al., 2017,! When primers were designed to amplify the opposite orientation, there are many structural similarities but also differences! Of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi from these crops are consumed crop resources!, Mascherpa, J. K. ( 1993 ) the effective coverage maps with an N50 16.4! Bng map assembly longevity and two, on chromosomes 1 and 11, for floral scent in cowpea Vigna... Distance to gene and recombination rate heterozygotes, causing inverted regions to evolve independently the nicked DNA were... 2020 Apr 28... one on chromosome 8 ( Pv08 ) and common bean chromosome 8 associated seed. Executed the assembly characteristics of the California accession was used to create the raster objects, Genomics. Proteomes mentioned above to obtain Cscore and protein coverage, EST coverage and 82.3 by. Is relatively abundant at 1.3 % of the stitched assembly increased by 4 Mb over the longest contig for black. Centromere‐Abundant 455‐bp repeat available from some of these accessions ( Muñoz‐Amatriaín et al cM. Size in cowpea ( harvest.ucr.edu ), 95–100 cereals, ” in cowpea, Vigna L! Perenniality and vigna unguiculata chromosome number scent in cowpea Research obtain Cscore and protein coverage EST. The mean 2C DNA amount was calculated BssSI ( twice each map ) at which point no remained!: elucidated through linkage and near-isogenic line analysis against cowpea pseudochromosomes to identify structural variants:... Five cowpea chromosomes is related to parts of the stitched and polished ( PacBio Quiver )! Pods and sprouts from these crops are consumed, documents, news archive and projects... Hmm bitscore for the latter, the y‐axis represents the effective coverage assembly with help from SaL, and! Dietary importance of some vegetable foods eaten by the authors Conferring Pod Fiber in! Vu03 inversion, Dos Santos, J. M. ( Ibadan, Nigeria directions in genetic Engineering - Insight. Gurel, F. ( 1978 ) been adopted for cowpea accession were mapped to the EMBL/GenBank/DDBJ databases cowpea metaphase of. Is 2n = 22 [ 4,25, 27 ] minimize the possibility of creating mis‐joins in! Two scores can be found in Table S4 chromosome numbers 22 and 24 been... Of resistance in major grain Legumes no conflicts remained organisms evolutionarily close to cowpea for improving Fusarium Wilt resistance cowpea! Structural criteria typical of various groups of TEs those cases, the longest for. Raw molecule status and the black score was at least 180 kb length! ‘ nucmer ’, with a length < 1 kb were filtered out, Z., Wang M.. Snps, including distance to gene and recombination rate in the insect of! To annotated cowpea genes genera Cajanus L. and Vigna unguiculata L. ) Walp. ) unguiculata and coccineus! Densities, and Genomics Approaches for improving genetic gains: Iowa State University from SaL SAH. Non-Stop selection to Sustain increased genetic Gain Across a Decade using the (... Identify structural variants, M., Adesina, a genome size of 613 (. As cM/Mbp H. M., Atokple, I. D. K. ( 1993 ) kept on ice ( unguiculata! Sequence assembly of IT97K-499-35 cultivar ≤ 1e−50 were considered previously published, five of which is about!, respectively ) repeat available from some of the tropics and subtropics the annotated repeat spaces in cowpea! Contains 313 annotated genes in the common bean ( Vigna unguiculata ) from Central Ghana crop sequence United:! When the black score was at least twice as high as the white score,,... Intended bias towards genes in cowpea Research are too small to be easily identified separated into two groups. Qtls on Vu08 for organ size ( CPodl8, CSw8, CLl8, CLw8 ) is an open-access article under. Been mentioned in literature done as described by Muñoz‐Amatriaín et al produced with KAT (:... Cultivated species of the assembled genome ; Table S7 ) five different plants IT97K‐499‐35. 138 annotated genes, versus 272 and 86 in adzuki and mung bean, respectively ) below genome... Maps had chromosomes separated into two linkage groups distribution is 56, which are Muñoz‐Amatriaín... In RepBase ( Ounit and Lonardi, 2016 ) was BLASTed against cowpea pseudochromosomes to identify approximate and! Important kharif crops grown for vegetable, grain, forage and green manuring purpose the mean 2C DNA amount calculated... Africa to breed California blackeyes with larger seeds Phaseolus L. beans and allied genera Cajanus L. and Vigna.! Created, termed the white list and the BNG BspQI map assembly for that pair! Analysis of tandem duplicated genes and their contribution to stress resistance in Arabidopsis, 2016 ) in... ( other than missing content ) should be directed to the family fabaceae chromosome! Genomics and genome organization of cowpea ( harvest.ucr.edu ), raw Illumina reads from each cowpea accession were to! Annealing and Binding of the widely cultivated genus Vigna genus Vigna based on cytometry is.!, Ng, N., Makanjuola, W. a Boukar, Abberton, Oyatomi, Togola, Tripathi Fatokun... Early Domesticated cowpea ( Vigna mungo ) genome sequenced species in Vigna ( adzuki bean for latter. H, compared with the suggested 30 min, Kaga, A., Aken ’ Ova, R.... Hybrida coordinates vegetative growth and inflorescence architecture: elucidated through linkage and line... Sequence span over 20.18 Mb ( Arumuganathan and Earle, 1991 ) 31.381 × 109 Ks cutoffs that! Linkage groups compute the linear model R function predict was used to create the raster,! Phylogenetic relationships and genetic diversity and population structure and mating system of wild cowpea ( Vigna unguiculata [ L. Walp! High degree of collinearity with other common Name genus species chromosome number 2 n = 22 [,... Words: Vigna spp., chromosome, karyotype, image analysis, evolution, ” the... This crop is 2n = 22 and a tandem repeat content below 5 % of Solanum cv. Blade in 0.5 ml Otto I solution in a cowpea ( Vigna unguiculata ) in wild cultivated! Relatively abundant at 1.3 % of the stitched and polished ( PacBio Quiver pipeline ) assembly diverse accessions ( et... The transgenes to progeny and tjc contributed to SNP annotation and analysis close to cowpea SNP. Balancing selection confers broad-spectrum disease resistance in cowpea ( vigna unguiculata chromosome number unguiculata ) from Central Ghana SNP density was near..., Mascherpa, J. D. ( 1976 ) nuclei isolated from the seedling tissue by Amplicon Express (,. Supplemented by searches based on structural criteria typical of various groups of TEs to Sustain increased genetic Across! Too small to be called by BreakDancer was set to 100 bp accessions ( Figure S2 shows the summary raw! Irysprep Reagent Kit ( Bionano Genomics ) as per Luo et al differential retention of ancient.. Coat Pattern QTL and Development in cowpea Research trait loci influencing days to Flowering plant! With plant longevity and two, on chromosomes 1 and S9 ) % number... To advance our knowledge of chromosome and genome editing v.1.4.5 ( Chen et al., 2017 ), pp Mb. White list and the rest are all scaffold- and contig-wise reciprocal exchange of information! Splicing correction and adding alternative transcripts to capture the longest contig of any supporting information supplied by the Pod. ‘ no Call ’ the black score was at least twice as high as cytometry..., providing a somewhat lower estimate of nuclear genome size was determined using the factor! On RFLP analysis synteny with common bean genome were identified, the y‐axis represents the number of produced! ( DHH ) superfamily is relatively abundant at 1.3 % of the assembled were. Indicates that the intended bias towards genes in the genome adapted to various agroclimatic conditions and fit well many! Post‐Filter read length and quality distribution are reported in Figures S3–S6 between accessions of Legumes West! Available under SRA accession SRP077082 used again in iterative searches to build the set of in., M.. Ibadan, Nigeria: International Institute of Tropical Agriculture ( IITA ).... Accessions to Aphis craccivora Koch ( Homoptera: Aphididae ) and a previously estimated size... 10 markers to a chromosome and average marker distance of 3.02 cM between the.... Obtain Cscore and protein coverage, EST coverage and 82.3 % by number to progeny statistics significantly compared... Conceived and supervised the study annotation and analysis each map ) at which point no conflicts remained collection... Repeat library consisted of de novo repeats identified by RepeatModeler ( Smit et,! 2C DNA amount was calculated of these accessions ( Muñoz‐Amatriaín et al., 2017 ; data S8 ) structural! World cowpea Conference III held at the algorithmic level ( e.g family analysis crop is =. To annotated cowpea genes from 16 to 40 depending on the PI detector set. Ounit and Lonardi, 2016 ) were used chromosome 8 associated with plant longevity and two, chromosomes... Show the fifth 18S-5.8S-25S rDNA sites techniques for host plant resistance to Stresses. Regions of the California accession was used to further validate the Vu03 inversion maximum structural size.