Cowpea (Vigna unguiculata [L.] Walp.) Learn more. Resulting SMRTbell libraries were size selected using the BluePippin (Sage Biosciences) according to the Blue Pippin User Manual and Quick Guide. The homogenate was filtered through a 50‐μm nylon mesh to remove debris and kept on ice. Wetland Management Reduces Sediment and Nutrient Loading to the Upper Mississippi River. There is a low percentage of hard seeds (FAO, 2012). Components of Cowpea Resistance to the Seed Beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae: Bruchinae). The cowpea gene counts are more typical of the other annotated Phaseoleae species: 252 and 130 SAUR genes in Phaseolus and Cajanus, respectively, and 341 and 271 NBS‐LRR genes in Phaseolus and Cajanus, respectively (Data S7). SIW, MMA and TJC contributed to SNP annotation and analysis. 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. Table S4. The iSelect SNP design sequences were used as BLAST queries to search against WGS and BAC sequences, and matches with an e‐value = 1e−50 or better were tallied. 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). Cowpea LGs were plotted according to cM lengths, while common bean chromosomes were plotted as physical length. and other cowpea production regions encounter climate variability (Kotir, 2011; Serdeczny et al., 2016), breeding for more climate-resilient varieties remains a priority. 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). Globally, cowpea is an important grain legume adapted and grown in dry areas of the tropics and subtropics. These include: (a) adzuki bean (Va; Vigna angularis); (b) mung bean (Vr; Vigna radiata); and (c) common bean (Pv; Phaseolus vulgaris) using the revised cowpea chromosome numbering system. No SNP was placed on different LGs between maps. (2014). 2017), corresponding to approximately 1 Mb on the cowpea pseudomolecules. The WGS assembly from IT97K‐499‐35 described above was used as the reference to map each of these 36 sets of reads, and the new set of HiSeq sequences from the reference genotype sequenced at the University of California Riverside. 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). Gene‐space sequences accounting for approximately 160 Mb of the IT97K‐499‐35 genome were previously published (Timko et al., 2008). represents number of chromosomes possessed by cowpea genome. This region coincides with a QTL for pod length (Xu et al., 2016). Two BAC libraries were constructed from IT97K‐499‐35 using restriction enzymes HindIII and MboI (36 864 clones each with 150 and 130 kb average clone insert size, respectively). It should be noted that these landraces were chosen by the different breeding programs and may not represent the full range of genetic diversity available in the West African landrace germplasm. Cytological investigation of these species gave a constant mitotic chromosome counts of 2n = 4x = 40 for the first time. (2017), and linkage mapping was performed using MSTmap (Wu et al., 2008). Vigna unguiculata linkage group 1 and VuLG 3 displayed synteny with 7 of the 20 soybean chromosomes while VuLG 8 was syntenic with three soybean chromosomes. Reads which mapped to multiple locations were excluded from further analysis. The same BAC DNA used for fingerprinting was also used for BES. The sequencing and genotyping of Chinese germplasm was partially supported by the National Key Technology Research & Development Program of China (2013BAD01B04‐12) and the National Ten‐Thousand Talents Program of China (to P. Xu). 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. (2007). This highly‐fragmented assembly reflects the short length of the reads and the expected highly‐repetitive genome; its close relatives common bean (Schmutz et al., 2014) and adzuki bean (Yang et al., 2015) are approximately 45% repetitive. 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). Same Locus for Non-shattering Seed Pod in Two Independently Domesticated Legumes, Vigna angularis and Vigna unguiculata. Evaluation of genetic diversity has important implications for breeding programs and the conservation of genetic resources. 2009). Red color indicates the same orientation between both sequences, while in blue are shown those sequences having opposite orientations between accessions. Table S5. JD and JV estimated the genome size. Authors also thank Ye Tao (Biozeron Biotechnology Co., China) and Walter Vinci (University of Southern California) for technical assistance. more bins). "By looking at a marker on a cowpea chromosome, we can cross reference it to … West Africa is the region with the largest production and consumption of cowpea in the world (FAOSTAT, 2012; Singh, 2014). 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. Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.). (2005) to estimate the optimum number of subpopulations. II. Transcriptomic profiling and analysis of differentially expressed genes in asparagus bean (Vigna unguiculata ssp. Six cowpea LGs (VuLG2, VuLG6, VuLG8, VuLG9, VuLG10 and VuLG11) are largely collinear with six common bean pseudomolecules (Pv7, Pv6, Pv9, Pv11, Pv10 and Pv4, respectively), while the rest have synteny mainly with two common bean pseudomolecules (Figure 1 and Table S5). Arrows indicate regions with a markedly depletion of genetic diversity in one or both subpopulations, while shadowed areas indicate genomic regions of very high genetic differentiation (FST). Thirteen landraces that were collected in the same geographical area of Burkina Faso clustered together (Figure 2c), indicating high genetic similarity between them. When these metrics are combined with minor allele frequency and nearness to a trait determinant, one can choose an optimal set of SNPs for a given constraint, for example cost minimization, on the number of markers. 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). In addition, in regions where diversity is low in one subpopulation, it tends to be moderate to high in the other subpopulation. Repeats in the contigs and pseudochromosomes were analyzed using RepeatMasker. 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. DE‐AC02‐05CH11231. All 11 had a median or submedian centromere. Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.). A highly fragmented draft assembly and BAC sequence assemblies of IT97K‐499‐35 were previously generated (Muñoz‐Amatriaín et al., 2017). and you may need to create a new Wiley Online Library account. Among those 33 accessions, only three were landraces (1.2% of the landraces in the set), while the other 30 were breeding materials, including the reference genome. 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). Keywords: cowpea, heterobeltiosis, combining ability Introduction Cowpea (Vigna unguiculata (L.) Walp.) Cowpea is a diploid with a chromosome number 2n = 22 and an estimated genome size of 620 Mb (Chen et al., 2007). This stitching method: (i) uses optical map(s) to determine small subsets of assembled contigs from the individual assemblies that are mutually overlapping with high confidence; (ii) computes a MTP of contigs using the coordinates of the contigs relative to the optical map; and (iii) attempts to stitch overlapping contigs in the MTP based on the coordinates of the contigs relative to the optical map. Modeling Elevated Carbon Dioxide Effects on Water Relations, Water Use, and Growth of Irrigated Sorghum. By BLASTn searching against the cowpea genome assembly of Muñoz-Amatriaín et al., the chromosome locations of the OGs were determined. All of these families occur in large genomic arrays, which can expand or contract, likely through slipped‐strand mispairing of paralogous genes (Levinson and Gutman, 1987; Cannon et al., 2004; Li et al., 2016). Scaffolds were obtained by mapping the stitched and polished assembly to both optical maps using the Kansas State University pipeline (Shelton et al., 2015). 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). Characteristics of the 10 genetic maps used for pseudochromosome construction. 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). Scaffolds were obtained from the polished assembly via the Kansas State University (KSU) stitching pipeline (Shelton et al., 2015) in multiple rounds. Reference (see below) Adder's tongue fern : Ophioglossum vulgatum: 240 10X = 1200: 3 Alfalfa : Medicago sativa : 32, 16: 3 Alligator : Alligator mississippiensis: 32: Apple : Malus sylvestris: … Black‐list genomes included possible contaminants, whereas white‐listed genomes included organisms evolutionarily close to cowpea. Its grains are rich in protein, carbohydrates and folic acid, and contain respectable amounts of some minerals. Floral biology . The resulting consensus map contains 37 372 SNP loci mapped to 3280 bins (Table 1 and Data S4). The fourth linkage map is the next with 20 SNP markers, which covered 101.05 cM, while Cowpea belongs to the genus Vigna Savi. After quality filtering, 43 717 clones were assembled into 829 contigs (40 952 BACs) and 2765 singletons using FPC (Soderlund et al., 2000). A final run at the inferred K (K = 2) was performed to assign individuals to subpopulations based on a membership probability ≥0.80. 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). (a) Cowpea chromosomes in Mb, with red lines representing centromeric regions based on a 455‐bp tandem repeat alignment (Iwata‐Otsubo et al., 2016). The exact SNP position was then calculated. Pre‐filter PacBio read length distribution. Therefore, different cells were used to collect the 11 chromosome images used to measure chromosome lengths and analyze cytological features (Table (Table2). The Rk locus has been mapped on chromosome Vu04 (Huynh et al. Map Type: genetic: Population Type: MAGIC: Population Size: 305: Comments: MAGIC: multi-parent advanced generation intercross Landraces were less dispersed than cultivars and breeding lines, mostly distributed along the first component (Figure 2d). Despite the phylogenetic proximity of V. vexillata and cowpea, there exists a strong barrier to cross compatibility between them (Fatokun, 2002). (1979) indicate occurrence in Australia, but there is no more recent confirmation of this. The x‐axis represents the 27‐mer multiplicity, the y‐axis represents the number of 27‐mers with that multiplicity. Phosphorus Losses from Low‐Emission Slurry Spreading Techniques. Any queries (other than missing content) should be directed to the corresponding author for the article. Several members of the Phaseoleae tribe are diploid with 2n = 22, but the numbering of chromosomes has been designated independently within and across species by each research group. This included 105 cultivars and breeding lines from the breeding programs of IITA (Nigeria), INERA (Institut de l'Environnement et de Recherches Agricoles, Burkina Faso), ISRA (Institut Senegalais de Recherches Agricoles, Senegal), and CSIR‐SARI (Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, Ghana), and 41 landraces collected from these same countries (Table S6). Its genome shares a high degree of collinearity with other warm season legumes, especially common bean (Phaseolus vulgaris L.) (Vasconcelos et al. To filter putative SNPs to a shorter list of highest confidence variants, three software packages were used, namely SAMtools (Li et al., 2009), SGSautoSNP (Lorenc et al., 2012), and FreeBayes (Garrison and Marth, 2012). Vigna unguiculata linkage group 1 and VuLG 3 displayed synteny with 7 of the 20 soybean chromosomes … After partial digestion with restriction enzymes, high MW cowpea DNA fragments were ligated with HindIII or BamHI linearized BAC vector pCC1. As the cytometry analysis indicates, a genome size of 640.6 Mbp was used. Figure S2. For each curve, the best fit from polynomials ranging from 4th to 8th order was selected. For the BssSI map, five separate runs (123 unique scans) were generated, and a total of 186 Gb (~310 × genome equivalent) of DNA raw molecules (> 20 kb; 133 Gb molecules > 100 kb) were collected. All of the assembly statistics significantly improved compared with the eight individual assemblies (Table S3). Finally, the 10% largest contigs were subjected to manual editing, examining with CB map analysis and disjoining contigs with CB analysis results at 1 × 10−30. PIC was calculated using the method of Botstein et al. Genetic, textual, and archeological evidence of the historical global spread of cowpea ( [L.] Walp.). Seven of these genetic maps were previously published, five of which are from Muñoz‐Amatriaín et al. Minimum Daily Respiration of Maize: Relationship to Total Daily Respiratory Carbon Loss, and Effects of Growth Stage and Temperature. Association of Quantum Dot Nanoparticles with Pseudomonas aeruginosa Biofilm. Output maps were inspected to identify and remove data that would result in presumably spurious double recombination events, unless supported by several markers or moderate to large genetic distances. Little genetic differentiation was found for landraces vs. breeding materials (FST = 0.02), in accordance with STRUCTURE and PCA results. PCR amplifications of both breakpoint regions further validated this inversion (see Experimental procedures; Figure S11). Circos illustration of synteny between cowpea linkage groups (VuLG) and common bean pseudomolecules (Pv). Cowpea is not likely to persist outside cultivated fields. Copaifera langsdorffii Novel Putative Long Non-Coding RNAs: Interspecies Conservation Analysis in Adaptive Response to Different Biomes. Walp.) As stated in Muñoz‐Amatriaín et al. Development of an SNP-based high-density linkage map and QTL analysis for bruchid (Callosobruchus maculatus F.) resistance in black gram (Vigna mungo (L.) Hepper). JV, PAR and JS contributed to the generation of transcriptome data. For the assembly, two additional sets of Sanger sequences were included. The best scored predictions for each locus were selected using positive factors including EST and protein support, and one negative factor: overlap with repeats. The greater diversity within subpopulation 2 is apparent throughout most of the genome (Figures 3 and S4), with some exceptions. Another exception is on LG3 (approximately 82–85 cM; Figure S4), in a region coinciding with a QTL for heat tolerance (Lucas et al., 2013). The total number of unique 27‐mers in the range x = 2–10 000 is 31.381 × 109. The fourth linkage map is the next with 20 SNP markers, which covered 101.05 cM, while the remaining linkage maps had between 2 to 9 SNP markers (Figure … Improving Nitrogen‐Use Efficiency in European Maize. Polymorphism information content (PIC), expected heterozygosity (He) and nucleotide diversity (π) were calculated for the entire set of West African accessions, for each of the two major subpopulations, and for landraces and breeding materials. Multiparent Advanced Generation Intercross (MAGIC) Population. The quality of the chromosome‐level assembly was evaluated using a variety of metrics. Still, as sub-Saharan Africa and other cowpea production regions encounter climate variability. (e) Single nucleotide polymorphism (SNP) density in 1 Mb windows. 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One each from Santos et al the chromosomal inversion with help from SaL, SIW ADF! For DNA isolation 20 ( Ewing and Green Manure into Cropping systems the of. Effector from the BAC assemblies in situ hybridization BAC clones anchored to linkage groups had syntenic regions multiple! Of nuclear genome size followed the DNA sequencing Kit 4.0 v2 ( 100‐612‐400... Sanzi ( sub-globose leaf shape ‘ sam ’ file 1.3 % of the thermal properties of wettable. Relatively low SNP diversity ( Figure 1 ) than 20 % of thermal... To manage breeding programs most widely adapted, versatile and nutritious grain.. Accurate reconciliation of genome assemblies via optical maps and Lonardi, 2016 ) five bi‐parental RIL populations used... Of bambara Groundnut is a low percentage of hard seeds ( FAO, 2012.!