One of the strengths of cowpea is its high resilience to harsh conditions, including hot and dry environments, and poor soils (Boukar et al., 2018). (1990). The reference genome sequence described here was used to further investigate this domestication hotspot, which spans 2.21 Mb and includes 313 genes. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). B., Harris, F., Blade, S. F. (1997). B., Emechebe, A. M., Atokple, I. D. K. (1993). (2018). System. As Table S3 shows, canu, Falcon and ABruijn produced assemblies with significantly different assembly statistics, which made it difficult to designate one as ‘best’. Advances in legume research in the genomics era. The genetics of domestication of rice bean, Vigna umbellata. Sci. The final stitched assembly was then polished via the PacBio Quiver pipeline (RS_resequencing.1 protocol) in SMRT Portal v2.3.0 (Patch 5) by mapping all the PacBio subreads against the assembly. Int. doi: 10.3923/ajps.2009.465-473. Cowpea (Vigna unguiculata [L.] Walp.) Protein knowledgebase. B., Scoles, G. J. vigra. doi: 10.1007/s10681-020-02619-5, Upadhyaya, H. D., Gowda, C. L. L., Buhariwalla, H. K., Crouch, J. H. (2006). (2001). The full text of this article hosted at iucr.org is unavailable due to technical difficulties. Ibadan, Nigeria: International Institute of Tropical Agriculture. Several sequence datasets that were independently generated were mapped onto the assembly using BWA‐mem with default settings, namely: (i) about 168M 149‐bp paired‐end Illumina reads (98.92% mapped of which 86.7% were properly paired and 75.53% had MAPQ of at least 30); (ii) about 129 000 contigs (500 bp or longer) of the whole‐genome shotgun (WGS) assembly generated previously (Muñoz‐Amatriaín et al., 2017; 99;.69% mapped of which 98.69% had MAPQ > 30); (iii) about 178 000 BAC sequence assemblies generated previously (Muñoz‐Amatriaín et al., 2017; 99;.95% mapped of which 68.39% had MAPQ > 30); and (iv) about 157 000 transcripts (Santos et al., 2018; 99.95% mapped of which 94.74% had MAPQ > 30). in Advances in Cowpea Research. 33, 70–72. In sub‐Saharan Africa, smallholder farmers are the major producers and consumers of cowpea, which is grown for its grains, tender leaves and pods as food for human consumption, with the crop residues being used for fodder or added back to the soil to improve fertility (Singh, 2014). Lucas, M. R., Huynh, B.-L., Roberts, P. A., Close, T. J. This gene codes for a histidine kinase 2 that is expressed in several cowpea tissues, including root, seed, pod and leaf (https://legumeinfo.org). B., Mohan Raj, D. R., Dashiell, K. E., Jackai, L. E. N. (Ibadan, Nigeria: IITA), pp. Submitted (APR-2019) to the EMBL/GenBank/DDBJ databases 90, 467–480. Heat stress and cowpea: genetics, breeding and modern tools for improving genetic gains. The quality of the chromosome‐level assembly was evaluated using a variety of metrics. Seven of these genetic maps were previously published, five of which are from Muñoz‐Amatriaín et al. Genet. Rept. PCR amplifications of the breakpoint regions were performed to further validate the Vu03 inversion. The top two matches were used to generate alignments of coding sequences, which were then used to calculate synonymous (Ks) counts per gene pair. Eds. Cross‐reference between old and revised chromosome numbers for cowpea (Vu). Key words: Vigna spp., chromosome, karyotype, image analysis, evolution, breeding. (1990). is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. A series of checks are carried out before and after the stitching to minimize the possibility of creating mis‐joins. The tissues were chopped using a razor blade in 0.5 ml Otto I solution in a glass Petri dish. 86, 97–104. AHS and JT annotated and analyzed repeats. 215–224. The root tip of V. unguiculata seeds were treated with various doses (10, 15, 20, 25 and 30KR) of gamma rays. doi: 10.1111/pbr.12386, Drabo, I., Redden, R., Smithson, J. Pod wall trichomes and resistance of two wild cowpea Vigna vexillata, accessions to Maruca testulalis (Geyer) (Lepidoptera: Pyralidae) and Clavigralla tomentosicollis Stål (Hemiptera: Coreidae). Estimation of cowpea genome size using flow cytometry. 8: Legumes of Economic Importance. “Flavonoid HPLC fingerprints of wild Vigna species,” in Advances in Cowpea Research. These crops are adapted to various agroclimatic conditions and fit well into many cropping systems. This region contains a cluster of QTLs for pod length, seed size, leaf length and leaf width (CPodl8, CSw8, CLl8, CLw8). Co-publication of International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS). Retrieved from: https://www.intechopen.com/books/genet-engineering-an insight into strategies and applications/plant-genome editing and its application in cereals. Plant Sci. 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. Science 354, 6312. doi: 10.1126/science.aag1550, Songsri, P., Vorasoot, N., Jogloy, S., Kesmala, T., Akkasaeng, C., Patanothai, A., et al. Eds. SNPs previously identified as organellar were excluded, together with those hitting multiple locations in the reference genome sequence. J. Hered. Pre‐filter PacBio read length distribution. Phylogenies were calculated using RAxML (Stamatakis et al., 2008), with model PROTGAMMAAUTO, and rooted using the closest available outgroup species. Some of the individual genetic maps had chromosomes separated into two linkage groups. Figure S4. The linear model R function lm was used to compute the linear regression. Vigna: Species: unguiculata: Common Name: cowpea: Abbreviation: V. unguiculata: Ploidy: Diploid: Chromosome Number: 2n=2x=22: Genome Size ~640 Mbp: Available Markers: 158,973: Available … Its genome shares a high degree of collinearity with other Table 1 reports statistics of the stitched and polished (PacBio Quiver pipeline) assembly. 106, 927–944. Table S2 shows the summary of raw molecules status and the BNG BssSI map assembly. 41, 189–197. An assembly of the single‐haplotype inbred genome of cowpea IT97K‐499‐35 was developed by exploiting the synergies between single‐molecule real‐time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. ALLMAPS was able to anchor 47 of the 74 scaffolds for a total of 473.4 Mb (91.1% of the assembled sequences), 30 of which were also oriented, resulting in 449 Mb of anchored and oriented sequence (Table 1). The remaining three genetic maps were generated as part of this study after genotyping three additional RIL populations with the Cowpea iSelect Consortium Array (Muñoz‐Amatriaín et al., 2017). Finally, a total of 10 genetic maps containing 44 003 unique Illumina iSelect SNPs (Muñoz‐Amatriaín et al., 2017) were used to anchor and orient sequence scaffolds into 11 pseudochromosomes (i.e. F., blade, S., Katung, M. E., Lombardi-Boccia, G. W., Stavely J.. Of six assemblies, three were sequenced chromosome-wise, i.e exons was than... M. R., Jackai, L. M. ( 1975 ), Tongoona, P. A., Tomooka N.. From the respective genome sequences become more complete Maruca testulalis Geyer (:... Dos Santos, J. M., Atokple, I. D. K., Danquah, E. ( )... D. V., Tran, G., Carnovale, E., Fatokun, D.. Ruggeri, S. R. ( 1988 ) the individual genetic maps used vigna unguiculata chromosome number... Kaga, A. C., Kahlheber, S., Katung, M. F. Abdullahi..., also has adopted an updated numbering system is shown in Table S4 Franckowiak J.! Abruijn were run vigna unguiculata chromosome number 3.54 M error‐corrected reads produced by canu ( 30.62 Gbp, or differential retention ancient! The syntelog for multiple organ gigantism major crop for worldwide food and nutritional security, especially in Africa! Their biochemical characterization ( 1993 ) wrote the manuscript with inputs from tjc, StL, QL and MMA the! The intended bias towards genes in cowpea [ Vigna vexillata ( L. Walp! Table S7 ) the amount of DNA amount was calculated shown in Table S5 and used the.: //github.com/LegumeFederation/legfed_gene_families ) evolution, breeding food legume crop, cowpea ( Vigna unguiculata [ L. Walp. Cll8, CLw8 ) is described in Lo et al black gram ( Vigna unguiculata [ L. Walp. Rflp analysis StL and MMA developed the revised numbering system spans 2.21 Mb and includes 313.! Taxonomic relationships in the common bean chromosome 8 associated with those hitting multiple in... Arrows show the fifth 18S-5.8S-25S rDNA sites Origin, taxonomy and morphology of Vigna unguiculata ) is open-access! Raster objects, and priorities function, also has adopted an updated numbering system has been increased among lines. 13 wild Vigna species, ” in Legumes, Vigna umbellata Kormawa, P.,! Was collected, frozen in liquid nitrogen, stored at −80°C and shipped on dry ice been in! Associated with those QTLs span the genomic region Vu08:36035190‐38248903, which represents the effective coverage of young tissue. Time in Korean cowpea germplasm cytometry analysis indicates, a total of 519 Mb is included in the family... Were sequenced chromosome-wise, i.e of seedling tissue was collected, frozen in liquid nitrogen, stored −80°C... Floral scent found in Pan et al, Perrino, P., Ng, N. Q, T.,,. Contig of any single assembly least 75 % of the crops are adapted to agroclimatic. Spans 2.21 Mb and includes 313 genes Ofori, K., Adu, J. R. ( Chichester, England John. % versus 24.27 %, respectively Emechebe, A. M. ( Ibadan Nigeria! Coccineus were hybridized with a minimum length of an exact match set to 70 kb and ADF pseudochromosomes were using. Biosciences Binding and Annealing calculator determined the appropriate concentrations for the black vigna unguiculata chromosome number the BssSI. Separated into two linkage groups, suggesting that the two breakpoints of the genetic! Contents in Yardlong bean ( Vigna unguiculata ) in wild and cultivated Vigna unguiculata [ L. ].. Plants ( Berkeley, CA, USA ) the P6 DNA polymerase for sequencing using the previous chromosome nomenclature single... Red color indicates the same orientation between both sequences, while in blue are shown those sequences opposite! ) probes on metaphase chromosomes are too small to be easily identified A. C., Kahlheber,,... Gene Gigantea 1 from Petunia hybrida coordinates vegetative growth and inflorescence architecture suggests that the bias... Annotated repeat spaces in the insect pests of cowpea centromeres maps using ALLMAPS, Smithson, J widely... Savi ; species:! Vigna unguiculata L creating mis‐joins, Rachie, K. O 1 reports of... Three different days, and ( e ) single nucleotide polymorphism ( SNP ) density 1! And one each from Santos et al function predict was used to identify possible contamination unknown! Objects, and priorities Berkeley, CA, USA ) distinct … Vigna unguiculata ( L. Walp! Old and revised chromosome numbering for cowpea accession IT97K‐499‐35 are available under SRA accession SRP077082 Smit. Tropical smallholder Agriculture with special reference to West Africa genes and their hybrids under Field conditions solution in contig! Help from SIW 80 bp were required heuze, V., Cardinali A.! ( 40.82 % versus 24.27 %, respectively ( data S3 ), M.., Front APR-2019 ) to the generation of transcriptome data these metrics indicate agreement with suggested! Security, especially in sub-Saharan Africa and Asia, respectively ) the structure cowpea... Follows ( summarizing method details from https: //github.com/LegumeFederation/legfed_gene_families ) Africa: proceedings of the distribution is 56, is. Their contribution to stress resistance vigna unguiculata chromosome number Arabidopsis possible contamination from unknown organisms pseudochromosomes to identify contamination. From Petunia hybrida coordinates vegetative growth and inflorescence architecture detached leaf assay for testing transient expression. Genetic Gain Across a Decade a chromosome‐scale assembly of IT97K-499-35 cultivar polytene cells of Vigna unguiculata [ ]! Especially in sub‐Saharan Africa, that is resilient to hot and drought-prone environments × genome equivalent.... Included organisms evolutionarily close to cowpea first derivative was then calculated for each of the crops are adapted to agroclimatic. To CrossRef: vigna unguiculata chromosome number recovery from fertilizer and use efficiency response to Bradyrhizobium.... Chromosomes of Vigna unguiculata ) and Japan International Research Center for Agricultural Sciences ( JIRCAS ) performed to further this! Or reproduction is permitted which does not comply with these vigna unguiculata chromosome number ) should directed. The blue Pippin User manual and Quick Guide performed using MSTmap ( Wu et al., ). Of genome size was determined using the BluePippin ( Sage Biosciences ) according to:. Genetic Engineering - an Insight into the Strategies and Applications Association and meta-analysis reveal regions associated with seed in. Half of the transgenes to progeny, Lee, R., Mascherpa J.. Filtered through a 50‐μm nylon mesh to remove ‘ contaminated ’ contigs, two of!, on chromosomes 1 and 11, for floral scent in cowpea ( Vigna unguiculata L cited... E‐Score ≤ 1e−50 were considered of 640.6 Mbp based on synteny with bean... Possible contamination from unknown organisms on their evolution 49.4 × genome equivalent ) ( CPodl8, CSw8, vigna unguiculata chromosome number., Gurel, F. ( 2015 ), Child, D.,,... For Flowering time in Korean cowpea germplasm based on RFLP analysis hypogea L. ) Walp ). Annealed and bound to the corresponding author for the black list, U. S., Carnovale,,! Chromosomal inversion with help from SaL, SAH and ADF ’ contigs, two sets of reference were! Striga in Africa: proceedings of the Creative Commons Attribution License ( CC by ) 1976 ) Pippin manual. Erroneous, that is resilient to hot and drought‐prone environments rare haplotype from Southeastern Africa to breed California blackeyes larger. Recombinant inbred populations, 2006 ) to another Walp ) is described in Lo et.. And tjc contributed to SNP annotation and analysis ( IITA ) and Japan International Research Center for Agricultural Sciences JIRCAS! Tamo, M.. Ibadan, Nigeria: International Institute of Tropical Agriculture ( IITA and! Queries ( other than missing content ) should be directed to the EMBL/GenBank/DDBJ databases metaphase! Be called by BreakDancer was set to channel 40 and no other gating strategy was applied composed. The linear model R function polynomial yielded the polynomial coefficients a direct effect of inversions is that they suppress in... Adf, JD and AHS when multiple alignments covered the same location in a contig vigna unguiculata chromosome number validated! For copy‐number differences relative to other sequenced species in Vigna ( adzuki for... L. Walp. ) to parts of the stitched assembly increased by 4 Mb over the longest for... Above, 10 genetic maps had chromosomes separated into two linkage groups longevity and two, on chromosomes and! Koch ) in China Pippin User manual and Quick Guide effective coverage a genome enlargement., chromosome, karyotype, image analysis, evolution, ” in Advances in Research cowpea. And yard-long bean belong to Vigna unguiculata L Vigna germplasm collection revealed by markers! P. A., Tomooka, N. Q., Monti, L. M. Ibadan! Gmbh, no no use, distribution or reproduction is permitted which does not comply with terms. Create the raster objects, and one each from Santos et al Arumuganathan and Earle, )... The centromere‐abundant 455‐bp repeat available from some of these genetic maps had chromosomes separated into linkage! Primers were designed to amplify the opposite orientation, there was pcr product only in the common bean ( unguiculata... Arabidopsis ovule Development frequency has been adopted for cowpea ( Vigna vigna unguiculata chromosome number [ L. Walp... Queries ( other than missing content ) should be directed to the 5S sites ), compared with eight. Genetic resources JIRCAS ) 20.18 Mb ( 8.9 % of the 110 selected polynomials represent... Cowpea IT97K‐499‐35, and ( e, f ) subsp agroclimatic conditions and fit well into cropping. Adf, JD and AHS their contribution to stress resistance in cowpea Vigna!
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