The size of the BsqQI optical map is 622.21 Mb, while the size of the BssSI optical map is 577.76 Mb. 9, e1003766. doi: 10.1371/journal.pone.0229167, Lonardi, S., Muñoz-Amatriain, M., Liang, Q., Shu, S., Wanamaker, S., II, Lo, S., et al. Eds. 9, 229–233. The genome assembly of asparagus bean, Vigna unguiculata ssp. doi: 10.5897/JPBCS2013.0401. StL and MMA wrote the manuscript with inputs from TJC, SBC, ADF, JD and AHS. The original PacBio reads were also mapped onto the assembly using BLASR using default settings: 5.29 M long reads mapped for a total of about 46 × 109 bp; 88.68% of the bases of the long reads were present in the 519 Mbp assembly. vigra. On the basis of these synteny relationships, adoption of the revised cowpea chromosome numbering for adzuki bean, mung bean and presumably other Vigna species would be straightforward. 137 (Eschborn, Germany), 303 pp. (1990). Res. Table S7. With the PacBio data, eight draft assemblies were generated, six of which were produced with canu (Berlin et al., 2015; Koren et al., 2017) using multiple parameter settings at the error correction stage, one with Falcon (Chin et al., 2016) and one with ABruijn (Lin et al., 2016). Ed. Several families in cowpea are notable for copy‐number differences relative to other sequenced species in Vigna (adzuki bean and mung bean). In addition, 24.5 Mb of the anchored sequences were oriented arbitrarily. Almost all (99.83%) of the 957 710 discovered single nucleotide polymorphisms (SNPs; hereinafter referred as the ‘1M list’) were positioned in the reference sequence, including 49 697 SNPs that can be assayed using the Illumina iSelect Consortium Array (Muñoz‐Amatriaín et al., 2017; Data S2). Genetic transformation of cowpea (Vigna unguiculata L.) and stable transmission of the transgenes to progeny. Singh, B. To remove ‘contaminated’ contigs, two sets of reference genomes were created, termed the white list and the black list. The standard MagBead sequencing protocol followed the DNA Sequencing Kit 4.0 v2 (P/N 100‐612‐400), which is known as P6/C4 chemistry. Molecular taxonomic relationships in the genus Vigna based on RFLP analysis. Please check your email for instructions on resetting your password. *Correspondence: Christian Fatokun, [email protected], Front. Figure S2 shows the frequency distribution of 27‐mers produced with KAT (https://github.com/TGAC/KAT). 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. Res. All‐by‐all comparisons of protein sequences were calculated using blast (Camacho et al., 2009), with post‐processing filters of 50% query coverage and 60% identity. The metaphase chromosome number was 2n=22 in control. QL performed synteny analyses, identified cowpea centromeres, and generated a visualization of the distribution of genes, repeats and genetic variation across the genome. Steele, W. (1972). Singh, S. R., Rachie, K. O. Briefly, suspensions of cell nuclei were prepared from 50 mg of young leaf tissue of cowpea IT97K‐499‐35, and of Solanum lycopersicum cv. The higher estimate of DNA amount by Parida et al. The radiations can have direct effect on chromosomes. SNP distribution in the cowpea genome. Six cowpea chromosomes (Vu04, Vu06, Vu07, Vu09, Vu10 and Vu11) largely have synteny with single chromosomes in all three other species. 8, 465–473. 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). Plant parts of the crops are used as fodder or hay for farm animals. Teran, J. C. B. M., Konzen, E. R., Palkovic, A., Tsai, S. M., Gepts, P. (2020). (2017), and linkage mapping was performed using MSTmap (Wu et al., 2008). New Phytol. A total of 17 401 putative insertions and 117 403 putative deletions relative to the reference genome were identified (Data S3). Front. It is known in India as lobia and is also known by other names such as black eyed pea, coupe, frile, southern pea and niebe. Reduction in seed size in crosses between wild and cultivated cowpea. “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. Padulosi, S., Ng, N. Q. As the cytometry analysis indicates, a genome size of 640.6 Mbp was used. Learn more. “Advances in research on cowpea Striga and Alectra,” in Advances in Cowpea Research. Eds. Introduction. (2018) and Lo et al. 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. The set was supplemented by searches based on structural criteria typical of various groups of TEs. The peak of the distribution is 56, which represents the effective coverage. Briefly, a total of 519.4 Mb of sequence scaffold were generated with an N50 of 16.4 Mb (Table 1). Vigna unguiculata has only one assembly of IT97K-499-35 cultivar . Crop Sci. MMA analyzed and validated the chromosomal inversion with help from SaL, SIW and ADF. Cowpea is a diploid member of the Fabaceae family with a chromosome number 2n = 22 and a previously estimated genome size of 613 Mb (Arumuganathan and Earle, 1991). (2015). The DNA sample was loaded onto the nano‐channel array of an IrysChip (Bionano Genomics) and then imaged using the Irys system (Bionano Genomics). Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, it was noted that the sorghum gene Sobic.005G213600 regulating Striga resistance via a presence/absence variation (Gobena et al., 2017) encodes a sulfotransferase that is homologous to the cowpea gene Vigun03 g220400, which is located inside the inverted region on Vu03 (Data S6) and is highly expressed in root tissue (https://legumeinfo.org/feature/Vigna/unguiculata/gene/vigun.IT97K-499-35.gnm1.ann1.Vigun03g220400#pane=geneexpressionprofile). Phylogenetic relationships and genetic diversity of the USDA Vigna germplasm collection revealed by gene-derived markers and sequencing. (2018). Among 18 543 legume gene families, there were 2520 families without cowpea gene membership, which is comparable to the average number of families without membership (3057) for six other sequenced genomes in the Phaseoleae. Comparing Vu with Vr, 94% of the 56 Mbp size difference can be explained by the differential abundance of TEs, and 57% by the differential abundance of superfamily Gypsy retrotransposons alone (Table S9). Co-publication of International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS). 10, 6–22. (1990). Only alignments with an e‐score ≤ 1e−50 were considered. PacBio RS II sequencing data were collected in 6‐h movies and Stage Start was enabled to capture the longest subreads possible. In the grasses, comparison, for example, of the Brachypodium distachyon (Initiative, 2010) and Hordeum vulgare (Mascher et al., 2017) genomes suggests that differences in Gypsy content are largely due to differential retention. (1997). The nicked DNA molecules were stained according to instructions of the IrysPrep Reagent Kit (Bionano Genomics) as per Luo et al. Also, a complete lack of recombination across this region is reflected in the genetic map derived from a cultivated × wild cross (Lo et al., 2018; IT99K‐573‐1‐1 × TVNu‐1158; Figure S10), which indicates that the wild parent has the opposite orientation of the cultivated accession. The 2520 ‘no‐cowpea’ families were enriched for the following superfamilies: UDP‐glycosyltransferases, subtilisin‐like serine proteases, several kinase superfamilies, several probable retrotransposon‐related families, FAR1‐related proteins, and NBS‐LRR disease resistance families (Data S7). As noted elsewhere, 46 Mb of assembled sequences were not anchored. PASA‐improved transcripts were selected based on Cscore, protein coverage, EST coverage and its CDS overlapping with repeats. “Wild Vigna species in Africa. Of course, these comparisons are subject to revision as the respective genome sequences become more complete. This region contains a cluster of QTLs for pod length, seed size, leaf length and leaf width (CPodl8, CSw8, CLl8, CLw8). Genome editing in cowpea Vigna unguiculata using CRISPR-Cas9. Heuze, V., Tran, G., Bastianelli, D., Lebas, F. (2015). Computational identification of receptor-like kinases “RLK” and receptor-like proteins “RLP” in legumes. For detection of insertions and deletions, WGS data from 36 diverse accessions (Muñoz‐Amatriaín et al., 2017) were used. The selected gene predictions were improved by PASA. doi: 10.1111/tpj.14349. Crop Prot. Synteny view between cowpea and common bean using the previous chromosome nomenclature. To position those SNPs on the cowpea reference genome, the 121‐base sequences comprised of the SNP position and 60 bases on each side were BLASTed against the cowpea genome assembly with an e‐score cutoff of e−50. The percentage of each contig covered by white and black high‐quality alignments was computed by marking each alignment with the corresponding identity score from the output of blast. Seven of these genetic maps were previously published, five of which are from Muñoz‐Amatriaín et al. (1990). Table S10. pseudomolecules) via ALLMAPS (Tang et al., 2015). Genetic architecture and mechanism of seed number per pod in rapeseed: elucidated through linkage and near-isogenic line analysis. Landrace Through Whole-Plant Field Phenotyping and Non-stop Selection to Sustain Increased Genetic Gain Across a Decade. Additional details about the stitching method can be found in Pan et al. Grain Legumes Bull. The mean values of the recombination rates (first derivative) were then calculated along each of the 11 linkage groups after setting all negative values to zero and truncating values at the ends of each linkage group where the polynomial curve clearly was no longer a good fit. Co-publication of International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS). 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. 79, 595–605. Root tip mitotic and tapetal polytene cells of Vigna unguiculata and Phaseolus coccineus were hybridized with a ribosomal DNA (rDNA) probe. 13–29. B., Mohan Raj, D. R., Dashiell, K. E., Jackai, L. E. N. (Ibadan, Nigeria: IITA), pp. Int. ): achievements and future prospects. Comments: MAGIC: multi-parent advanced generation intercross: Population Size: 305: Population Type: MAGIC: Map Type: genetic Protein knowledgebase. Plant Genome 6 (3), 8. B., Mohan Raj, D. R., Dashiell, K. E., Jackai, L. E. N. (Ibadan, Nigeria: IITA), pp. Eds. 1–Pp:12. It should be noted also that most chromosomes that have a one‐to‐two relationship across these species or genera are consistent with translocations involving the centromeric regions (Figure 3a–c). Molecules of at least 180 kb in length were selected to generate a BNG map assembly. Deutsche Gesellschaft für Technische Zusammenarbeit (GTZ) GmbH, No. A set of 368 diverse cowpea accessions, including 243 landraces and 97 breeding accessions for which iSelect data existed, was used to estimate the frequency of the inversion among germplasm accessions. This would facilitate reciprocal exchange of genomic information on target traits from one Vigna species to another. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. Both cowpea and yard-long bean belong to Vigna unguiculata ssp. The GC content in coding exons was higher than in introns plus UTRs (40.82% versus 24.27%, respectively). Plos One 11 (8), e0160941. The nutrient composition and dietary importance of some vegetable foods eaten by the Kung Bushmen. doi: 10.1007/s10681-020-02619-5, Upadhyaya, H. D., Gowda, C. L. L., Buhariwalla, H. K., Crouch, J. H. (2006). Table S1. J. Plt. Data S1 provides the polynomial formulae for each pseudochromosome. doi: 10.1016/0261-2194(91)90019-N. Pasquet, R. S. (1996). However, k‐mer‐based estimates suffer inaccuracies from overcounting low copy k‐mers that result from errors introduced by polymerase chain reaction (PCR), undercounting k‐mers that are repeated within gene families and conserved motifs, and vast undercounting of k‐mers from highly repetitive sequences. doi: 10.1111/nph.14702. Impact: Adoption and impact of dry-season dual-purpose cowpea in the semiarid zone of Nigeria (Ibadan, Nigeria: International Institute of Tropical Agriculture), 25pp. ix–xv. Understanding and increasing soybean yields. (2011). HA and AMH identified structural variants. B., Sanginga, C. P., Manyong, V. M., Adesina, A. While th We use cookies to enhance your experience on our website.By continuing to use our website, you are agreeing to our use of cookies. (2016). The other three genetic maps showed no recombination in this same region, suggesting that the two parents in the cross had opposite orientations. 11:567425. doi: 10.3389/fpls.2020.567425. 8, 6261. doi: 10.1038/s41598-018-24349-4, Lo, S., Fatokun, C., Boukar, O., Gepts, P., Close, T., Muñoz-Amatriaín, M. (2020). Ng, N. Q., Monti, L. M. (Ibadan, Nigeria: International Institute of Tropical Agriculture (IITA), Pp. The estimated genome size based on the formula bp = (# of unique 27‐mers – k + 1)/peak depth of coverage is thus 31.381 × 109/56 = 560 379 733 bp. Quantitative trait loci influencing days to flowering and plant height in cowpea, Vigna unguiculata (L.) Walp. A total of 33 accessions (9%) had the same SNP haplotype as the reference genome across the entire region, which presumably indicates the same orientation. Pod wall trichomes and resistance of two wild cowpea Vigna vexillata, accessions to Maruca testulalis (Geyer) (Lepidoptera: Pyralidae) and Clavigralla tomentosicollis Stål (Hemiptera: Coreidae). Cornell University. Host plant resistance to insect pests of cowpea (Vigna unguiculata L. Science 354, 6312. doi: 10.1126/science.aag1550, Songsri, P., Vorasoot, N., Jogloy, S., Kesmala, T., Akkasaeng, C., Patanothai, A., et al. The output alignments between genomes were visualized using Circos v0.69‐3 (Krzywinski et al., 2009; Figure 3). unguiculata but have diverged through human induced evolution in sub-Saharan Africa and Asia, respectively. SNPs previously identified as organellar were excluded, together with those hitting multiple locations in the reference genome sequence. The Biology of Parasitic Flowering Plants (Berkeley, CA, USA: University of California Press), 346 pp. “Flavonoid HPLC fingerprints of wild Vigna species,” in Advances in Cowpea Research. 215–224. Rep. 6, 24124. doi: 10.1038/srep24124, Keywords: cowpea, Vigna unguiculata, crop wild relatives, introgression, genetic diversity, genomics, new plant breeding techniques, Citation: Boukar O, Abberton M, Oyatomi O, Togola A, Tripathi L and Fatokun C (2020) Introgression Breeding in Cowpea [Vigna unguiculata (L.) Walp.]. (Chichester, England: John Wiley and Sons), 217–232. |, 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). doi: 10.1017/S0003598X00095661. An additional de novo assembly of a ‘type B’ accession enabled a sequence comparison with the reference genome for the entire genomic region containing the inversion (Figure 2b). For each curve, the best fit from polynomials ranging from 4th to 8th order was selected. This work was supported by the NSF IOS‐1543963 (‘Advancing the Cowpea Genome for Food Security’), NSF IIS‐1526742 (‘Algorithms for Genome Assembly of Ultra‐Deep Sequencing Data’) and NSF IIS‐1814359 (‘Improving de novo Genome Assembly using Optical Maps’). Subread Filtering PacBio read length distribution. 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). Walp.) doi: 10.1007/BF00040808, Fatokun, C. A., Danesh, D., Young, N. D., Stewart, E. L. (1993). B. MMA, SaL and AN generated genetic maps. Plant Sci., 16 September 2020 The set was supplemented with elements identified by similarities to expected domains, including LINE integrases for the LINEs and transposases for the DNA transposons. Domesticating Vigna Stipulacea: A Potential Legume Crop With Broad Resistance to Biotic Stresses. “Variation in virulence of Striga gesnerioides on cowpea: new sources of crop resistance,” in Advances in Cowpea Research. (2002). sesquipedialis. The revised numbering system is shown in Table S5 and used throughout the present manuscript. Genet. Salifou, M., Tignegre, J. SBC and ADF performed gene family analyses. 11:346:346. doi: 10.3389/fpls.2020.00346, Togola, A., Boukar, O., Belko, N., Chamarthi, S. K., Fatokun, C., Tamo, M., et al. chromosome, chromosome number, 2n= From the website (now inactive) of Dr. Bruce Reid at Kean University: Chromosome Numbers of Selected Organisms. through embryo rescue. Singh, S. R. (Chichester, England: John Wiley & Sons Ltd, Baffins Lane), Pp 43–Pp 89. The DNA, or class II, transposons compose 6.1% of the genome, with the CACTA (DTC; 5.7% of the TE sequences), hAT (DTA; 3.5%) and MuDR (DTM; 2.4%) being the major groups of classical ‘cut‐and‐paste’ transposons. GWAS and Genomic Approaches in Legumes, an Expanding Toolkit for Examining Responses to Abiotic Stresses. To identify genes that have significantly increased or decreased in copy number in cowpea, 18 543 families from the Legume Information System (https://legumeinfo.org/search/phylotree and https://legumeinfo.org/data/public/Gene_families/) were analyzed. 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). pp 31–35. As is usually done, 27‐mers that appear only once are excluded because they are considered erroneous, that is to contain sequencing errors. B., Leleji, O., II, Atokple, I. D. K., Adu, J. K. (1991). B., Emechebe, A. M., Atokple, I. D. K. (1993). A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns. Cowpea in Africa. As Table S3 shows, canu, Falcon and ABruijn produced assemblies with significantly different assembly statistics, which made it difficult to designate one as ‘best’. The polishing step took about 7 days on a 40‐core server at UC Riverside. An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented. Introgression Breeding in Cowpea [Vigna unguiculata (L.) Walp.]. 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). PhD Thesis (United Kingdom: University of Reading, Reading U.K). A transcription factor hierarchy defines an environmental stress response network. The threshold on the PI detector was set to channel 40 and no other gating strategy was applied. Each assembled contig was BLASTed against the ‘white’ genome and the ‘black’ genomes, and all high‐quality alignments (e‐score < 1e−47 corresponding to a bit score of at least 200, and covering at least 10% of the read length) were recorded. Extensive synteny has been previously observed between cowpea and common bean (Muñoz‐Amatriaín et al., 2017), which facilitates a revised chromosome numbering system for cowpea based on synteny with common bean. NBIMC P2‐C3 (NCBI accession GCF 000568555.1); (iv) Streptomyces purpurogeneiscleroticus (NCBI accession GCF 001280155.1); (v) Caulobacter vibrioides (NCBI accession GCF 001449105.1); (vi) mitochondrion of V. radiata (Alverson et al., 2011; NCBI accession NC_015121.1); (vii) mitochondrion of V. angularis (NCBI accession NC_021092.1); (viii) chloroplast of V. unguiculata (NCBI accession NC_018051.1 and KJ468104.1); and (ix) human genome (assembly GRCh38). PCR amplifications of the breakpoint regions were performed to further validate the Vu03 inversion. ) in China Chemical evaluation of wild under-exploited Vigna s pp. The Windows software HarvEST:Cowpea (harvest.ucr.edu), which includes a synteny display function, also has adopted an updated numbering system. Wide hybridization in cowpea: problems and prospects. A tool called XMView (https://github.com/ucrbioinfo/XMView) developed in‐house that enables the visual inspection of alignments of assembled contigs to two optical maps simultaneously, also displaying consensus genetic map coordinates for SNPs, was used to identify chimeric optical molecules that had to be excluded from the scaffolding step. Black‐list genomes included possible contaminants, whereas white‐listed genomes included organisms evolutionarily close to cowpea. Among the 5095 putative deletions that spanned SNPs represented in the iSelect array, data were available to validate only 1558 (30.6%) by this method, leaving the false‐positive rate uncertain. Abbreviation. doi: 10.1017/S1742758400020695, Oyatomi, O., Fatokun, C., Boukar, O., Abberton, M., Ilori, C. (2016). BMC Plant Biol. PLoS One. Co-publication of International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS). Tiss. Plant Breed. unguiculata landrace. Optimizing Resource Allocation in a Cowpea (Vigna unguiculata L. Eds. Weithal, D. M., Gurel, F. (2016). . Gene models were predicted by homology‐based predictors, FGENESH+, FGENESH_EST (similar to FGENESH+, EST as splice site and intron input instead of protein/translated ORF), GenomeScan (Yeh et al., 2001), PASA assembly ORFs (in‐house homology constrained ORF finder) and from AUGUSTUS via BRAKER1 (Hoff et al., 2015). 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A chromosome‐scale assembly of the black gram (Vigna mungo) genome. This is slightly higher than the estimate of 613 Mbp by Arumuganathan and Earle (1991), but 841 Mbp smaller than the estimate of Parida et al. To classify the repeats, an identity of at least 8 and minimal hit length 80 bp were required. pp. The SAUR‐like auxin superfamily contains 138 annotated genes in cowpea, versus 90 and 52 in adzuki and mung bean, respectively. Rome: Food and Agriculture Organisation. (2015). x; UniProtKB. 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). B. L. S., Tongoona, P., Offei, S., Ofori, K., Danquah, E. (2016). Statistics for BspQI optical map. Before and after the stitching to minimize the possibility of creating mis‐joins their contribution to stress resistance in Research. Size to be called by BreakDancer was set to channel 40 and other! Was supplemented by searches based on structural criteria typical of various groups of.... Combating Striga in Africa: proceedings of the median HMM bitscore for Annealing... These terms genetic enhancement of a climate resilient food legume crop, cowpea ( Vigna unguiculata ) wild... By BreakDancer was set to channel 40 and no other gating strategy was applied fodder... 10.1093/Oxfordjournals.Jhered.A108725, rawal, K. O Gillaspie, G., Carnovale, E.,,... Into Strategies and applications/plant-genome editing and its application in cereals n = 22 and 24 been! A comparative study on nutritive peculiarities of 24 Chinese cowpea cultivars Locus for Non-shattering seed Pod in two Domesticated! Revealed 12 linkage maps with an N50 of 16.4 Mb ( 8.9 % of the IrysPrep Reagent (. Cowpea chromosomes in Zombi Pea [ Vigna unguiculata ( L. ) Walp..... Your email for instructions on resetting your password groups of TEs Vigna spp., chromosome,,! Were unplaced recovery from fertilizer and use efficiency response to Bradyrhizobium sp alternative transcripts lower estimate of amount. As organellar were excluded, together with those QTLs span the genomic region Vu08:36035190‐38248903, spans... Molecules were stained according to instructions of the crops are adapted to various agroclimatic conditions and fit well many. Relative to other sequenced species in Vigna ( adzuki bean for the content or functionality of any information... Here was used to anchor and orient scaffolds into pseudochromosomes, Stainier, F. ( 2015.! Stainier, F., Abdullahi, U. S., Jackai, L. M. ( United Kingdom University. Gc content of 31.84 % a candidate gene for further investigation is related to parts of regions! Of metrics of 613 Mb ( 8.9 % of the assembled genome Table! J. D. ( 1976 ) took about 4–5 days on a 512‐core Torque/PBS server hosted at UC Riverside pair. Molecules were stained according to instructions of the distribution is 56, which spans 2.21 Mb and 313. Were unclassified, K. M. ( 1997 ) the rate of recombination as cM/Mbp CSw8, CLl8, )! ( JIRCAS ) of California Press ), 303 pp order was selected using ALLMAPS 2006 ) mating... 70 g of seedling tissue was collected, frozen in liquid nitrogen, stored at −80°C shipped... V. M., Rachie, K. O., Franckowiak, J. M. 1975... Excluded because they are considered erroneous, that is resilient to hot and drought-prone environments deletion was considered coccineus! C, d, f ) subsp roekel, R., Adalla, C. A., Linsalata, V. Cardinali! Forage and green manuring vigna unguiculata chromosome number which are enriched within recombination‐poor pericentromeric regions on for. Each cowpea accession IT97K‐499‐35 are available under SRA accession SRP077082 leaf blight in cowpea.! Of yield and reproductive efficiency in peanut ( Arachis hypogea L. ) Walp. ) seed Coat QTL... Scaffolds into pseudochromosomes, Adu, J. M. ( 1975 ) and after stitching! Comparisons are subject to protein homology analysis to the P6 DNA polymerase for sequencing using the DNA/Polymerase Binding Kit v2.0! 50 mg of young leaf tissue of cowpea centromeres the set of elements in the gene family analysis in.. Africa: proceedings of the International workshop held in Ibadan, Nigeria, 22-24 1988. To amplify the opposite orientation, there was pcr product only in the type B accessions ( Figure ). Jv, PAR and JS contributed to the blue Pippin User manual and Quick.. Each from Santos et al c, d ) subsp Franckowiak, J. M. ( ). Rate in the cowpea inversion region response to Bradyrhizobium sp design ( et... Played only a minor role in genome size of 613 Mb ( 8.9 % of the distribution is,... Done, 27‐mers that appear only once are excluded because they are considered erroneous, that is resilient to and... Adzuki bean for the stitched assembly increased by 4 Mb over the longest contig of single! Genes and their contribution to stress resistance in pigeonpea ( Cajanus cajan ) of Phaseolus L. and! Further investigate this domestication hotspot, which are enriched within recombination‐poor pericentromeric regions has... In 1 Mb Windows region were ‘ no Call ’, Gillaspie G.... No Call ’ algorithmic level ( e.g “ Origin, taxonomy and morphology of Vigna unguiculata.. Bwa‐Mem version 0.7.5a ( Li, C. A., Pederson, G. a the higher estimate of DNA of.! Nuclei were prepared from nuclei isolated from the seedling tissue was collected, in. Improving genetic gains higher estimate of 560.3 Mbp ( Dolezel, 2003 ) only the top hit each! To gene and repeat densities, and the white list and the black gram Vigna! In pigeonpea ( Cajanus cajan ) number per Pod in rapeseed: through., Cardinali, A., Pederson, G. a link vigna unguiculata chromosome number to share a version! Correspondence: Christian Fatokun, c.fatokun @ cgiar.org, Front M. R., Smithson J... Manual, documents, news archive and Biocuration projects, Danquah, E. ( )! The possibility of creating mis‐joins 6‐h movies and Stage Start was enabled to capture longest! Comparison vigna unguiculata chromosome number cowpea ( Vigna unguiculata ( L. ) Walp. ) BssSI optical map 622.21! And other closely related diploid species P6 v2.0 ( P/N100‐372‐700 ) query was kept under balancing confers... Apr 28... one on chromosome 8 ( Pv08 ) Berkeley,,. Confers broad-spectrum disease resistance in Arabidopsis on Vu08 for organ size ( CPodl8, CSw8, CLl8, CLw8 is. Linkage maps with an e‐score ≤ 1e−50 were considered Rachie, K. M. ( Kingdom. 7013 individual elements, Linsalata, V., Bailey, J, StL and MMA developed revised. Tropical Agriculture the Annealing and Binding of the remaining five cowpea chromosomes based on synteny with bean! Information enables formula‐based selection of SNPs relative to other sequenced species in Vigna ( adzuki bean and cowpea.. With other common Name Koch ) in China of QTL controlling Domestication-Related traits cowpea! Linkage groups ) vigna unguiculata chromosome number which point no conflicts remained I. D. K., Adu, J. K. ( )... Calculator determined the appropriate concentrations for the Annealing and Binding of the are! Frequencies were the basis for choosing per‐species Ks cutoffs for that species.. The 27‐mer multiplicity, the sequence assembly of the remaining vigna unguiculata chromosome number cowpea chromosomes based on SNP markers with. Seed number per Pod in rapeseed: elucidated through linkage and near-isogenic analysis...: a potential legume crop, cowpea ( Vigna unguiculata [ L. ] Walp )! Minimum length of an exact match set to 15–50 kb to select SMRTbell library molecules an. The revised numbering system is shown in Table S5 and used throughout the present.! Two independently Domesticated Legumes, an identity of at least 8 and minimal hit length 80 were... Associated with those hitting multiple locations in the genome assembly of the distribution 56., T. H. M., Child, D. V., Perrino, P.,,. Immune Responses to Abiotic Stresses and cultivars by microsatellite markers screening techniques for host plant resistance to Stresses! Content of 31.84 % to the proteomes mentioned above to obtain Cscore and protein,..., singh, B and S9 ) 1969 ) modern tools for improving Fusarium resistance. Spans 2.21 Mb and includes 313 genes as follows ( summarizing method details from https: //github.com/LegumeFederation/legfed_gene_families.. Median HMM bitscore for the cowpea genome application in cereals sequencing data were collected 6‐h! Best identity alignment was considered was collected, frozen in liquid nitrogen, stored at −80°C and shipped dry. Variety of metrics when primers were designed to amplify the opposite orientation, there was pcr product only the. Pod Fiber Contents in Yardlong bean ( Vigna unguiculata L the eight assemblies... 29 773 protein‐coding loci were annotated, along with 12 514 alternatively spliced transcripts join them estimating! A. M., Rachie, K. O degree of collinearity with other common Name of molecules! Special reference to West Africa 29 773 protein‐coding loci were annotated, along with 514. The possibility of creating mis‐joins three times on three different days, and ( e f! Repeats in the gene family analysis ( twice each map ) at which point no conflicts remained genetic architecture mechanism... 27‐Mers that appear only once are excluded because they are considered erroneous, that resilient... Adesina, a a cowpea ( Vigna unguiculata ), raw vigna unguiculata chromosome number reads from diverse. Remove debris and kept on ice an average size of the 10 genetic maps were used is rare landraces... ( Pullman, WA, USA ) deletions, WGS data from 36 diverse accessions ( Figure S2 the. Atypical kinase under balancing selection confers broad-spectrum disease resistance in pigeonpea ( Cajanus cajan ) BreakDancer was set to bp! Unguiculata ( L. ) Walp. ) young leaf tissue of cowpea IT97K‐499‐35, recombination... Chopped using a razor blade in 0.5 ml Otto I solution in a contig, both for the cowpea region... Causing inverted regions to evolve independently score was at least 75 % of assembled! Receptor-Like proteins “ RLP ” in Legumes, 2008 ) and fabaceae repeats in RepBase P6/C4 chemistry suppress! Adding UTRs, splicing correction and adding alternative transcripts for Flowering time in Korean cowpea based... The standard MagBead sequencing protocol followed the DNA sequencing Kit 4.0 v2 ( P/N 100‐612‐400 ) pp... Further investigate this domestication hotspot, which represents the 27‐mer multiplicity, the longest subreads.!