Seven of 11 LGs had major synteny with two soybean chromosomes, among which four (VuLG2, VuLG3, VuLG5, and VuLG7) had synteny along the entire LG. TJC and SIW estimated recombination rates. Phaseolus vulgaris gene densities were calculated as the number of genes available from Schmutz et al. [L.] Walp) QTL Mapping of Ineffective Nodulation and Nitrogen Utilization‐Related Traits in the IC‐1 Mutant of Cowpea. The fourth linkage map is the next with 20 SNP markers, which covered 101.05 cM, while 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. 200pp. DE‐AC02‐05CH11231. (2014). HA and AMH identified structural variants. The genome assembly of cowpea IT97K‐499‐35 is available for browsing and is downloadable through Phytozome (phytozome.jgi.doe.gov), the Legume Information System Data Store (https://legumeinfo.org/data/public/), and NCBI SRA BioSample accession SAMN06674009 (also ASM411807v1). The low diversity in this region of LG3 may reflect selection for better yield performance of West African cowpeas under higher growing season temperatures. These genomic resources do not constitute a complete sequence of the cowpea genome, yet they have been sufficient to support linkage mapping, synteny analysis, and evaluation of materials currently in use from four West African breeding programs, which serve one of the most food insecure regions of the world. Whole‐genome shotgun data from an additional 36 diverse accessions relevant to Africa, China and USA were previously used to identify single‐nucleotide polymorphisms (Muñoz‐Amatriaín et al., 2017). Cowpea (Vigna unguiculata (L.) Walp. A transcript was selected if the Cscore and protein coverage were at least 0.5, or if it had EST coverage while its CDS overlap with repeats was less than 20%. We performed BLAST analy- sis using the subset of 26-bp sequences as queries against the BES-derived tandem repeats. Please check your email for instructions on resetting your password. STRUCTURE was run four times for each hypothetical number of subpopulations (K) between 1 and 6, with a burn‐in period of 10 000 and 50 000 Monte Carlo Markov Chain iterations. Only the wild cowpea accession did not yield an amplification product for either of the breakpoints, possibly due to sequence variation within the breakpoint regions. Estimation of the genome size was supported by the Czech Ministry of Education, Youth and Sports (award LO1204 from the National Program of Sustainability I). WGS sequence raw reads from 37 diverse cowpea accessions are available under SRA accession SRP077082. SNPs previously identified as organellar were excluded, together with those hitting multiple locations in the reference genome sequence. The final ordering and orientation of the scaffold was produced by ALLMAPS (Tang et al., 2015) from the SNP locations corresponding to the 10 genetic maps. 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). 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). represents number of chromosomes possessed by cowpea genome. The retrotransposons, or Class I TEs, comprise 84.6% of the TEs by sequence coverage and 82.3% by number. Current advances and future directions in genetic enhancement of a climate resilient food legume crop, cowpea (Vigna unguiculata L. A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns. All 11 had a median or submedian centromere. Breeding lines had slightly higher PIC, He and π values than landraces, being 0.242, 0.301 and 0.303, respectively, in breeding materials, while they were 0.234, 0.290 and 0.293 in landraces. Therefore, it seems possible that the region containing Vigun03 g220400 may affect Striga interactions in a manner that has not yet been discovered; this hypothesis merits further testing. Phaseolus vulgaris gene densities are also shown for 500 kb windows. 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). This report presents 323 Mb of WGS and 497 Mb of BAC sequence information, a tool to simultaneously test 51 128 single nucleotide variants, and a high‐density genetic map providing coordinates for most of those sequences and variants. Comparison and Evaluation of Model Structures for the Simulation of Pollution Fluxes in a Tile‐Drained River Basin. Alignments that were further used had a minimum identity of 55.11% and a mean identity of 89.24%. Globally, cowpea is an important grain legume adapted and grown in dry areas of the tropics and subtropics. The first linkage map had 23 SNP markers (Figure 1) which covered 72.02 cM of the genome, followed by eighth linkage with 21 SNP markers and covered 41.98 cM. Falcon and Abruijn were run on 3.54 M error‐corrected reads produced by canu (30.62 Gbp, or 49.4 × genome equivalent). The 45 accessions belonging to subpopulation 1 (i.e. Thus, the anchored portion of the WGS assembly, which is comprised mainly of 24 342 scaffolds larger than 1 kb among 25 537 anchored scaffolds, contains many fewer fragments than the entire WGS assembly (644 126 scaffolds). The full text of this article hosted at iucr.org is unavailable due to technical difficulties. Adoption of the chromosome numbers of P. vulgaris according to synteny relationships with LGs of cowpea seems sensible, but additional cowpea sequence information will be needed to clarify the relationships between VuLG1 and VuLG5 with Pv1, Pv5 and Pv8. Red color indicates the same orientation between both sequences, while in blue are shown those sequences having opposite orientations between accessions. These sequences can be searched by BLAST via http://www.harvest-blast.org. Two maps (Sanzi × Vita7 and CB27 × IT82E‐18) each had two chromosomes separated into two LGs (Table S4 and Data S3) due to regions where parents lack polymorphisms. and Azospirillum brasilense combined with N rates in cowpea-wheat crop sequence. The chromosome number is one of the primary basis of hybridization in agricultural crops as well as in animals. Among the 185 gene families in the top percentile in terms of cowpea gene membership in the family relative to average membership per legume species, the families include several in the following superfamily groups: NBS‐LRR disease resistance genes, various receptor‐like protein kinases, defensins, ribosomal proteins, NADH‐quinone oxidoreductase components (Data S7). It is a self-pollinating diploid with chromosome number 2n = 22 and a genome size of about 613 (Arumuganathan … When primers were designed to amplify the opposite orientation, there was PCR product only in the type B accessions (Figure S11). Accurate detection of chimeric contigs via Bionano optical maps. The potential of the underutilized pulse bambara groundnut (Vigna subterranea (L.) Verdc.) The first linkage map had 23 SNP markers (Figure 1) which covered 72.02 cM of the genome, followed by eighth linkage with 21 SNP markers and covered 41.98 cM. StL and MMA wrote the manuscript with inputs from TJC, SBC, ADF, JD and AHS. PCA also shows that the four West African breeding programs are working with very similar materials, except for somewhat narrower diversity within the Ghana program (Figure 2c). Breaks of macrosynteny and collinearity among moth bean (Vigna aconitifolia), cowpea (V. unguiculata), and common bean (Phaseolus vulgaris). The cutoff limit was set to 15–50 kb to select SMRTbell library molecules with an average size of 20 kb or larger. Developing the role of legumes in West Africa under climate change. Also, to avoid skewed variant calling, duplicated reads were marked with Picard. Six cowpea chromosomes (Vu04, Vu06, Vu07, Vu09, Vu10 and Vu11) largely have synteny with single chromosomes in all three other species. Ohwi and Ohashi, previously Phaseolus calcaratus, is a warm-season annual vine legume with yellow flowers and small edible beans.It is commonly called ricebean or rice bean.To date, it is little known, little researched and little exploited. ), native to Africa and a member of the Fabaceae family, is a primary source of protein in sub‐Saharan Africa, where it is grown for fresh and dry grains, foliage, and forage. With a high SNP coverage of the genome and connections to cowpea genome sequences, this study provides the basis for a unified chromosome nomenclature for the cowpea research community. (2005) to estimate the optimum number of subpopulations. Lucas et al., 2011; Muchero et al., 2013; Pottorff et al., 2014) as well as an assessment of the diversity of landraces throughout Africa (Huynh et al., 2013). Registration of a Cowpea [Vigna unguiculata (L.) Walp.] Multiparent Advanced Generation Intercross (MAGIC) Population. "A good number of genes are conserved across species," he said. . The assembly combined the paired‐end short reads, LIPE, GSS, and BES data using SOAPdenovo with k = 31 (Luo et al., 2012). 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). The extra floral nectarines at the base of the corolla attract ants, flies and bees but a heavy insect is required to depress the wing petal and expose the stamen and stigma. (2018). 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’). Orphan genes are involved in drought adaptations and ecoclimatic-oriented selections in domesticated cowpea. Raw BAC sequence reads from IT97K‐499‐35 are available under SRA accessions SRA052227 and SRA052228. Figure S3. Ion‐Sink Phosphorus Extraction Methods Applied on 24 Soils from the Continental USA. Those accessions with probabilities lower than 0.80 were considered ‘admixed.’ A total of 45 accessions were assigned to subpopulation 1, 44 were assigned to subpopulation 2, and 57 were considered ‘admixed’ (Table S6). (2016) and Santos et al. From a cytogenetic viewpoint, relatively little is known about Vigna species (Saccardo et al. A comparison between cowpea and adzuki bean (Figure S12) showed that IT97K‐499‐35 and adzuki bean genome assemblies have opposite orientations in this region, consistent with the conjecture that the cowpea reference genome is inverted in this region with respect to an ancestral state that has been retained in the wild cowpea accession as well as in this representative congeneric species. Its genome shares a high degree of collinearity with other warm season legumes, especially common bean ( Phaseolus vulgaris L.) (Vasconcelos et al ., 2015 ). SNPs were called using the GenomeStudio software (Illumina, Inc.). Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. In sub-Saharan Africa (SSA), cowpea plays an important role in both human nutritional and food security and income generation for farmers and food vendors. RILs were also curated to remove individuals with >10% heterozygous loci or those carrying many non‐parental alleles. Genomic approaches for studying crop evolution. However, little is known about its genome or chromosome structure. The new cowpea genome resources must be easily accessed if they are to be widely utilized for basic research and agricultural development. Cowpea is not likely to persist outside cultivated fields. Two subpopulations were found in the evaluated materials, which seem to coincide with the two major African gene pools (GP1–West, North and Central Africa; GP 2–East, South and Southeast Africa; Huynh et al., 2013). 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). 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). Five‐thousand events were acquired in each measurement. This 37th set was used as a control (i.e. The full text of this article hosted at iucr.org is unavailable due to technical difficulties. Novo&Stitch: accurate reconciliation of genome assemblies via optical maps. PCR amplification of the regions surrounding the two breakpoints of the inversion. 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. Figure S5. He and FST values were averaged across a sliding window of 5 genetic bins with a step of one bin. The other two cowpea LGs, VuLG1 and VuLG5, both have their largest block of homologous synteny with Pv8, followed by Pv5 and Pv1, respectively (Figure 1 and Table S5). This indicates that the intended bias towards genes in the iSelect array design (Muñoz‐Amatriaín et al., 2017) was successful. The R function predict was used to create the raster objects, and the R function polynomial yielded the polynomial coefficients. The LINEs (RIX) and SINEs (RSX), comprising the non‐LTR retrotransposons, together amount to only 0.4% of the genome. As MergeMap's coordinate calculations for a consensus map are inflated relative to cM distances in individual maps, consensus LG lengths were normalized to the mean cM length from the individual maps. The future of legume genetic data resources: Challenges, opportunities, and priorities. 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). First Report of Vicia Cryptic Virus M Infecting Cowpea ( He values for subpopulation 1 and 2 were plotted to explore the spatial patterns of diversity across the 11 LGs (Figures 3 and S4, upper plots). Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot herb in many countries of Africa. Cowpea is one of the oldest source of human food. Each assembly took about 4–5 days on a 512‐core Torque/PBS server hosted at UC Riverside. The anchored sequences contain 100 Mb of the WGS assembly (237 Mb scaffold size including Ns; Table S1 and Data S5) and 420 Mb of BAC assemblies (Table S2 and Data S6). TJC, StL, QL and MMA developed the revised chromosome numbering for cowpea. Although additional studies will be required to determine whether there is an adaptive consequence of the Vu03 inversion, awareness of it certainly is important for trait introgression and breeding, as this region represents nearly 1% of the cowpea genome and can be moderately active recombinationally during meiosis only when both chromatids carry the same orientation. WGS data from cowpea accession IT97K‐499‐35 included 394 million paired‐end short reads for a total of 40.6 Gb of sequence data (approximately 65× coverage) from Illumina GAII, and Illumina HiSeq sequences from one 5 kb long‐insert paired‐end (LIPE) library. Still, as sub-Saharan Africa and other cowpea production regions encounter climate variability. SNP names can also be used as inputs for sequence and annotation retrieval. High‐quality BES were generated from 30 343 BACs using the Sanger method. Heat stress and cowpea: genetics, breeding and modern tools for improving genetic gains. The chromosome number of this crop is 2n = 22 [4,25, 27]. As stated in Muñoz‐Amatriaín et al. The resulting high‐quality BES were then processed with the RepeatMasker program (www.repeatmasker.org) to identify characterized repeats. Table S1. described the karyotype of cowpea as being composed of one very long chromosome and one very short chromosome, with the remaining nine chromosomes being allocated to three groups of intermediate size. This suggests that the reference genome orientation of this region is rare among landraces and that its frequency has been increased among breeding lines. Syntenic regions in the common bean genome were identified, the largest of which is located on common bean chromosome 8 (Pv08). To estimate the gene content of the BAC assemblies, BAC sequences were compared to cowpea EST‐derived ‘unigenes’ (http://harvest.ucr.edu) and P. vulgaris gene models (Schmutz et al., 2014) using BLAST (e‐value cutoffs of e−40 and e−25, respectively). Ks cutoffs for that species pair is commonly used in food plots for deer organization of (! L. ) Walp. ) material was screened for homozygosity by genotyping with the cowpea genome is from... By canu ( 30.62 Gbp, or 49.4 × genome equivalent ) and modern tools improving! In accordance with structure and to clarify the genetic map ( weight = 1.0 ) 372‐SNP... The outcome of having selected SNPs in the physical map is available from Schmutz et al repetitive,. From 16 to 40 depending on the same BAC DNA used for BAC construction! Of sequences the stems and leaves as animal feed during the dry also. 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