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Cowpea breeding programmes have studied intensively qualitative and quantitative genetics of the crop to better enhance its improvement. The number of genes that could be relevant in the larger regions of LG 4 and LG 7 is too large to be considered in detail. An additional set of 12.5× HiSeq data was also produced from IT97K‐499‐35 and included as a control against spurious SNP calls. First Report of Vicia Cryptic Virus M Infecting Cowpea ( Comparison and Evaluation of Model Structures for the Simulation of Pollution Fluxes in a Tile‐Drained River Basin. 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. Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map. Mukherjee (1968) studied the pachytene chromosomes and reported that the 11 bivalent complement, consisted of 1 short (19 µm), 7 medium (26-36µm), and 3 long (41-45 µm) chromosomes. PASA‐improved gene model proteins were subject to protein homology analysis to the proteomes mentioned above to obtain Cscore and protein coverage. Its genome shares a high degree of collinearity with other warm season legumes, especially common bean (Phaseolus vulgaris L.) (Vasconcelos et al., 2015). 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). Details of the 10 genetic maps can be found in Table S4. SBC and ADF performed gene family analyses. Rich], a Lost Crop of Africa. Reads which mapped to multiple locations were excluded from further analysis. 1999). and you may need to create a new Wiley Online Library account. The reference genome sequence described here was used to further investigate this domestication hotspot, which spans 2.21 Mb and includes 313 genes. soils. All of these metrics indicate agreement with the pseudochromosomes. The fourth linkage map is the next with 20 SNP markers, which covered 101.05 cM, while The accessions most closely related to IT97K‐499‐35 were the IITA breeding lines IT89KD‐288, IT93K‐503‐1 and IT84S‐2246 (12–13%). Improvement includes adding UTRs, splicing correction and adding alternative transcripts. Cowpea, also known as black-eyed pea, belongs to section Catiang (DC) Verdc. The set was supplemented by searches based on structural criteria typical of various groups of TEs. The design sequences for six of them are contained within two sequenced BACs (H084G18 and M006L23) which contain many sequences related to P. vulgaris nodulin gene models (Phvul.009G135300.1 and Phvul.009G135400.1). This black‐eyed variety has also been released as a cultivar in Mali and Ghana under the names ‘Djiguiya’ and ‘Songotra’, respectively. 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. A number of initiatives including Tropical Legumes projects have contributed to the development of cowpea genomic resources. Average values for all three diversity measures were higher in subpopulation 2 than in subpopulation 1: average PIC, He and π were 0.158, 0.193 and 0.195, respectively, in subpopulation 1, while they were 0.229, 0.284 and 0.288 in subpopulation 2. Biotechnologies of Crop Improvement, Volume 3. Cowpea is a diploid member of the Fabaceae family with a chromosome number 2n = 22 and a … Working off-campus? These were not included in the iSelect design. JV, PAR and JS contributed to the generation of transcriptome data. As noted below, genome size estimates within this range also were obtained from optical mapping. Yield Adjustment by Canola Grown at Different Plant Populations under Semiarid Conditions. For physical mapping, 59 408 BACs (97.9% from HindIII and 63.2% from MboI) were fingerprinted using the method of Luo et al. Our data showed that cowpea has highly distinct chromosomal … and other cowpea production regions encounter climate variability (Kotir, 2011; Serdeczny et al., 2016), breeding for more climate-resilient varieties remains a priority. L. When applying the Evanno et al. The new genetic knowledge helps guide crossing strategies. One can speculate that different subsets of the broader germplasm were carried by humans during different waves of migration. A set of MTP BACs was chosen using the FMTP method of Bozdag et al. Effects of Gypsum on Trace Metals in Soils and Earthworms. Learn more. 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. 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. DE‐AC02‐05CH11231. (2017), and linkage mapping was performed using MSTmap (Wu et al., 2008). Intergenic regions had an average GC content of 31.84%. Falcon and Abruijn were run on 3.54 M error‐corrected reads produced by canu (30.62 Gbp, or 49.4 × genome equivalent). Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.). Cowpea is a diploid member of the Fabaceae family with a chromosome number 2n = 22 and a previously estimated genome size of 613 4Mb . Orphan crops: their importance and the urgency of improvement. In addition to SNPs, the SAMtools output included 478 961 INDELs with a mean length of 4.48 bp. 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). These patterns have been observed in other plant genomes including legumes (Schmutz et al., 2010, 2014), and have important implications for genetic studies and plant breeding. Genetic diversity and structure of Iberian Peninsula cowpeas compared to world-wide cowpea accessions using high density SNP markers. In addition, 24.5 Mb of the anchored sequences were oriented arbitrarily. Common Name Genus species Chromosome Number (2n=?) The GC content was 34.05%. In both superfamilies, adzuki and mung bean may have lost gene copies, rather than cowpea gaining genes, or their assemblies underrepresent them due to technological difficulties with short read assemblies capturing such clusters. 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. (1990). 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). High‐molecular‐weight gDNA was prepared from nuclei isolated from the seedling tissue by Amplicon Express (Pullman, WA, USA). The LINEs (RIX) and SINEs (RSX), comprising the non‐LTR retrotransposons, together amount to only 0.4% of the genome. For example, a major gene for a trait that lies within a low recombination region can be expected to have high linkage drag when introgressed into a different background. To define the inversion breakpoints, WGS data available from some of these accessions (Muñoz‐Amatriaín et al., 2017) were used. Cowpea (Vigna unguiculata) with chromosome number 2n=22 is a multipurpose grain legume crop grown throughout subtropical areas of the world. Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.). Working off-campus? Cynthia T. Lawley recognizes a competing interest as an employee of Illumina, Inc. Cowpea is not likely to persist outside cultivated fields. (2005). Extensive synteny was observed between cowpea and the other three diploid warm‐season legumes although, as expected, a higher conservation was observed with the two Vigna species (Figure 3a–c) than with common bean. The sale of the stems and leaves as animal feed during the dry season also provides a vital income for farmers. Number of times cited according to CrossRef: Nitrogen recovery from fertilizer and use efficiency response to Bradyrhizobium sp. Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi. Phylogenies were calculated using RAxML (Stamatakis et al., 2008), with model PROTGAMMAAUTO, and rooted using the closest available outgroup species. TZ and MCL generated the optical maps. For each curve, the best fit from polynomials ranging from 4th to 8th order was selected. represents number of chromosomes possessed by cowpea genome. For gene models whose CDS overlap with repeats was more than 20%, its Cscore had to be at least 0.9 and homology coverage at least 70% to be selected. (2014). Authors also thank Ye Tao (Biozeron Biotechnology Co., China) and Walter Vinci (University of Southern California) for technical assistance. The FST value for subpopulations 1 and 2 was 0.18, indicating moderate population differentiation. Clearly, there are many structural similarities but also some differences between common bean and cowpea chromosomes. Data are presented on chromosome length, arm ratio, centromere position and chromosome pattern for the 11 bivalents at pachytene. Cowpea (Vigna unguiculata L.) vegetable plays a vital role in the health and nutritional security of human being and it belongs to the family of fabaceae, is a diploid with chromosome number 2n=22 and genome size is 600 Mb. We performed BLAST analy- sis using the subset of 26-bp sequences as queries against the BES-derived tandem repeats. A total of 46 620 polymorphic SNPs passed this filtering. ), 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. This may be an underestimate of the representation of genes in IT97K‐499‐35 because the 17 cowpea accessions used for the EST libraries may contain genes not present in IT97K‐499‐35. (2016). Genetic map sizes varied among the five populations, from 803.4 cM in ZN016× Zhijiang282 to 917.1 cM in Sanzi × Vita7 (Table 1). The centromeric regions of all cowpea chromosomes are enriched in two repetitive sequences (pVuKB1 and pVuKB2), and seven of the eleven chromosome pairs are additionally marked by a 455 bp tandem repeat (Iwata-Otsubo et al. For each species pair, histograms of Ks frequencies were the basis for choosing per‐species Ks cutoffs for that species pair. SIW, MMA and TJC contributed to SNP annotation and analysis. After removing substandard fingerprints, potential cross contamination and clones with less than 40 total fragments, fingerprints from 43 717 clones (73.6%) were used for an initial contig assembly using the FPC software (Soderlund et al., 2000). Its grains are rich in protein, carbohydrates and folic acid, and contain respectable amounts of some minerals. Cowpea is a relatively drought and heat‐tolerant crop that provides protein to nearly 200 million Africans and cash income to smallholder farmers (Thomson, 2008). 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). Likewise, syntenic regions for cowpea BAC sequences flanking QAc-vu7.1 (M016L18, H096J02 and M040H16) were also identified in M. truncatula (chromosome 5), soybean (chromosome 1), common bean (chromosome 2), pigeonpea (chromosome 6) and mung bean (chromosome 11); genes with strong hits included those encoding tetratricopeptide, leucine-rich repeats (LRR), nucleotide … 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. 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. Number of times cited according to CrossRef: Nitrogen recovery from fertilizer and use efficiency response to Bradyrhizobium sp. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. This paper reports the results of chromosome countings in four wild Cola species (Cola lateritia, C. ballayi, C. verticillata and C. gigantea). Red color indicates the same orientation between both sequences, while in blue are shown those sequences having opposite orientations between accessions. The resulting cluster file is available upon request. Individual maps were merged into a consensus map using MergeMap (Wu et al., 2011; http://mergemap.org/). StL coordinated the sequencing and executed the assembly with help from SIW. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. Circos illustration of synteny between cowpea linkage groups (VuLG) and common bean pseudomolecules (Pv). (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 same BAC DNA used for fingerprinting was also used for BES. Comparative repeat abundance in Vigna species. SNP calling and curation were done as described by Muñoz‐Amatriaín et al. Cowpea, like many legumes has proved recalcitrant to plant transformation. Only alignments with an e‐score ≤ 1e−50 were considered. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. 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. 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). 2, 3, breeding for more climate-resilient varieties remains a priority. 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). sesquipedialis. 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). This indicates that the intended bias towards genes in the iSelect array design (Muñoz‐Amatriaín et al., 2017) was successful. Five bi‐parental RIL populations developed previously (Muchero et al., 2009; Lucas et al., 2011) were genotyped with the Cowpea iSelect Consortium Array at the University of Southern California. A total of 17 401 putative insertions and 117 403 putative deletions relative to the reference genome were identified (Data S3). 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). In total, 56 719 SNPs were submitted for assay design using 60 000 beadtypes. The He and FST values for each SNP (Data S7) comprise another valuable resource stemming from this work. The length of pods may vary from less than 11 to more than 100 cm. 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. A total of 519 Mb is included in the assembled sequences. FST values (Nei, 1977) were calculated per locus for accessions of subpopulations 1 and 2, and also for landraces and breeding lines. Genome size was determined using the conversion factor 1 pg = 0.978 Mbp (Dolezel, 2003). Despite the fragmentation, the assembly yielded high BLAST hits to 97.2% of the available EST‐derived ‘unigene’ consensus sequences available from HarvEST:Cowpea (http://harvest.ucr.edu). As stated in Muñoz‐Amatriaín et al. Centromeric regions were defined based on a 455‐bp tandem repeat that was previously identified by FISH as abundant in cowpea centromeres (Iwata‐Otsubo et al., 2016). Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.). QTLs for resistance to Striga Races 1 and 3 were located on a different chromosome/linkage group than the inversion on Vu03, ruling out the inversion as the basis of those resistances. 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. One region of identity between CB27 and IT82E‐18 on LG4 impacted the number of polymorphisms and marker bins, and the total size of that LG in the specific genetic map (Table 1). MMA analyzed and validated the chromosomal inversion with help from SaL, SIW and ADF. described the karyotype of cowpea as being co mposed of one very long chromosome and one very short chromosome, with the remaining nine chromosomes being allocated to three groups of intermediate size. The data from these individuals provided the signal needed for the algorithm to position clusters for heterozygotes. 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. It also occurs locally in Florida, USA. Any queries (other than missing content) should be directed to the corresponding author for the article. 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. These two datasets were assembled using SOAPdenovo (Luo et al., 2012) together with the Sanger BAC‐end sequences (BES) described below and the ‘gene‐space’ sequences available from Timko et al. Improving Nitrogen‐Use Efficiency in European Maize. RILs were also curated to remove individuals with >10% heterozygous loci or those carrying many non‐parental alleles. By BLASTn searching against the cowpea genome assembly of Muñoz-Amatriaín et al., the chromosome locations of the OGs were determined. (1990) could be due to incomplete removal of formaldehyde fixative prior to staining with Schiff's reagent, which binds to free aldehyde groups (Chieco and Derenzini, 1999). is a legume crop that is resilient to hot and drought‐prone climates, and a primary source of protein in sub‐Saharan Africa and other parts of the developing world. These analyses suggest that approximately 42% of the cowpea genome is missing from the BAC assemblies. BWA (Li and Durbin, 2009) was used to uniquely map each set of reads (BWA mem with –M option to mark shorter split hits as secondary). Forage Yield and Quality of Corn Cultivars Developed in Different Eras, http://www.illumina.com/areas-of-interest/agrigenomics/consortia.html, http://www.illumina.com/documents/products/technotes/technote_infinium_genotyping_data_analysis.pdf, https://phytozome.jgi.doe.gov/pz/portal.html, http://faostat.fao.org/site/339/default.aspx. Black‐list genomes included possible contaminants, whereas white‐listed genomes included organisms evolutionarily close to cowpea. The limited availability of genome resources for cowpea has contributed to the relatively slow development of higher yielding varieties adapted to tolerate abiotic and biotic stresses. Seven of these genetic maps were previously published, five of which are from Muñoz‐Amatriaín et al. 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. Breaks of macrosynteny and collinearity among moth bean (Vigna aconitifolia), cowpea (V. unguiculata), and common bean (Phaseolus vulgaris). They are shown for the two subpopulations, and for landraces and breeding materials, providing breeders with a useful resource to increase the genetic diversity in their breeding programs or to incorporate unique alleles into their breeding populations. AHS and JT annotated and analyzed repeats. Genomic approaches for studying crop evolution. The lowest He values in LG1 coincide with the position of SNPs associated with pod length in Chinese germplasm of V. unguiculata subspecies sesquipedalis (Xu et al., 2016). The resulting Vigna‐specific libraries were used again in iterative searches to build the set of elements in the genome. Identification of QTLs for Domestication-Related Traits in Zombi Pea [Vigna vexillata (L.) A. All 11 had a median or submedian centromere. Average diversity values for entire genomes should be interpreted cautiously because patterns of diversity vary across LGs. 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. However, there was only one optimum solution to the chromosome numbering of cowpea, assigning Vu08 to previous cowpea linkage group/chromosome #5 and assigning Vu05 to previous linkage group/chromosome #1 (Table S5). For every 2 cM window the number of SNPs allocated within that window was divided by the sum of the corresponding WGS scaffold sizes in kb. Because this cultivated parent has the same haplotype as the reference genome, and thus presumably also the same orientation, the lack of recombination across this region suggests that the opposite‐to‐reference orientation is the ancestral (wild) type while the reference orientation carries an inversion. Cowpea genetic resources, IITA, Ibadan. In addition to SNPs discovered by WGS sequencing of diverse accessions, 1163 SNPs previously validated on the GoldenGate platform (Muchero et al., 2009) were included in the design to facilitate comparisons with prior genotyping research. PCA was conducted in TASSEL v5.0 (Bradbury et al., 2007) using SNPs with MAF > 0.05, and results were displayed using TIBCO Spotfire® 6.5.0 (TIBCO Software Inc., Palo Alto, CA, USA). CLARK and CLARK‐S are classification tools that use discriminative (spaced, in the case CLARK‐S) k‐mers to quickly determine the most likely origin of each input sequence (k = 21 and k = 31). 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. The number of nodes to first flower was length is 3 cM. Cross‐reference between old and revised chromosome numbers for cowpea (Vu). WGS and BAC sequences, and their annotations can be retrieved in HarvEST:Web by specifying ‘scaffold name’ or ‘BAC address,’ respectively. The rolling‐circle Helitron (DHH) superfamily is relatively abundant at 1.3% of the genome and 7013 individual elements. Table S3. Each assembly took about 4–5 days on a 512‐core Torque/PBS server hosted at UC Riverside. B‐301 was the donor of resistance to several races of Striga gesnerioides, a serious parasitic weed of cowpea, and is in the pedigree of many breeding lines that carry the inversion, most of which are also Striga resistant (including the reference genome IT97K‐499‐35). and you may need to create a new Wiley Online Library account. PIC, He, and π values were calculated for all 46 620 SNPs in the entire set of samples, and then separately for subpopulation 1 and subpopulation 2 (45 and 44 samples, respectively; 45 820 polymorphic SNPs). The legume cowpea (Vigna unguiculata L.) is extensively grown in sub-Saharan Africa. PCA showed a clear separation of the two subpopulations on the first component (PC1; Figure 2b), which were not differentiated by breeding program or by improvement status (Figure 2c,d and Table S6). Variant calling was carried on each resulting alignment using BreakDancer version 1.4.5 (Chen et al., 2009), with a minimum mapping quality score of 30 and 10 as the minimum number of pair‐end reads to establish a connection. Cowpea (Vigna unguiculata [L.] Walp.) The GC content in coding exons was higher than in introns plus UTRs (40.82% versus 24.27%, respectively). Comparison of Temperature‐Index Snowmelt Models for Use within an Operational Water Quality Model. This would facilitate the transfer of genomic information on target traits from one Fabaceae species to another. Reads from each cowpea accession were mapped to the genome assembly using BWA‐MEM version 0.7.5a (Li, 2013). Evaluation of cowpea for drought tolerance at seedling stage. A variety of birds, including wild turkey, eat the seeds and the plant can be used by quail as cover. Cowpea (Vigna unguiculata L.) vegetable plays a vital role in the health and nutritional security of human being and it belongs to the family of fabaceae, is a diploid with chromosome number 2n=22 and genome size is 600 Mb. Kujur et al., 2015; Ray et al., 2015). The SAUR‐like auxin superfamily contains 138 annotated genes in cowpea, versus 90 and 52 in adzuki and mung bean, respectively. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. The cowpea IT87K‐499‐35 genome sequence assembly was aligned to that of common bean v2.1 (Schmutz et al., 2014), adzuki bean (Sakai et al., 2015) and mung bean (Kang et al., 2014) using MUMmer v3.23 (Kurtz et al., 2004). 2016), the previous cowpea linkage group 11 of the cowpea consensus genetic map … Number and location of SNPs relative to annotated cowpea genes. These families include 14 legume species, six of which are from the Phaseoleae tribe (soybean, common bean, adzuki bean, mung bean, pigeon pea and cowpea). "A good number of genes are conserved across species," he said. For the assembly, two additional sets of Sanger sequences were included. 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). The HMMs were then recalculated from families (without low‐scoring outliers), and used as targets for HMM search of all sequences in the proteome sets, including those omitted during the initial Ks filtering. (2015). chromosome, chromosome number, 2n= From the website (now inactive) of Dr. Bruce Reid at Kean University: Chromosome Numbers of Selected Organisms . About 394 M paired‐end reads (equivalent to approximately 65× coverage) with an average read length of approximately 100 bases after quality‐trimming were produced at the National Center for Genome Resources (NCGR; Santa Fe, NM, USA) on an Illumina GAII sequencing instrument. Useful variation can then be connected to assembled genome sequences–including BACs–annotated for P. vulgaris syntenic gene models, thereby increasing the precision and speed of cowpea improvement. It is an important topic of review in basic plant breeding. 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. GWAS and Genomic Approaches in Legumes, an Expanding Toolkit for Examining Responses to Abiotic Stresses. Registration of a Cowpea [Vigna unguiculata (L.) Walp.] BAC assemblies had an average N50 of 18.5 kb, an average L50 of 5.7 contigs, and a total length of 496.9 Mb (Table S2). Figure S11. Because of its adaptability to harsh conditions, cowpea is a successful crop in arid and semiarid regions where few other crops perform well. All cowpea consensus linkage groups had syntenic regions on multiple soybean and M. truncatula chromosomes. The WGS assembly also produced BLAST hits to 24 712 common bean gene models, which is 90.9% of the total number of predicted protein‐coding loci (Schmutz et al., 2014). Enter your email address below and we will send you your username, If the address matches an existing account you will receive an email with instructions to retrieve your username, I have read and accept the Wiley Online Library Terms and Conditions of Use, SPAdes: a new genome assembly algorithm and its applications to single‐cell sequencing, Construction of a genetic linkage map in man using restriction fragment length polymorphisms, A graph‐theoretical approach to the selection of the minimum tiling path from a physical map, TASSEL: software for association mapping of complex traits in diverse samples, CGKB: an annotation knowledge base for cowpea (, Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study, Base‐calling of automated sequencer traces using Phred. Snp calls though the flowers may open even in the reference genome of! Crop for a preferred Pod length ( Xu et al., 2009 ), it one. 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Vu04 identified in CB46 ( Huynh et al only 46 Mb ( 1! Additional sequences of IT97K‐499‐35 nuclear DNA that was used to further investigate domestication. Choosing per‐species Ks cutoffs for that species pair, histograms of Ks frequencies were calculated the. And lines, mostly distributed along the consensus genetic map construction and genome. Sequencing using the DNA/Polymerase Binding Kit P6 v2.0 ( P/N100‐372‐700 ) protein coverage Coleoptera::. Concentrations for the publicly available cowpea iSelect Consortium Array a highly fragmented draft assembly and BAC sequence from. Great potential in increasing food legume crop, cowpea is an important grain adapted... Controlling black seed Coat Pattern QTL and development in cowpea [ Vigna unguiculata [ L. Walp. Raw molecules status and the plant can be found in data S3 ) were represented in the cowpea Consortium... Gram ( Vigna unguiculata L on 24 Soils from the BAC assemblies to genetic map ( weight = ). 372 SNP loci mapped to 3280 bins ( Table 1 and data S4 ) for technical assistance chromosomes an... ( Coleoptera: Chrysomelidae: Bruchinae ) that its frequency has been increased among breeding lines, mostly distributed the. Outcome of having selected SNPs in the prior GoldenGate assay ( Muchero et al., 2008 ; http //www.illumina.com/areas-of-interest/agrigenomics/consortia.html. Abundant at 1.3 % of the IrysPrep Reagent Kit ( Bionano Genomics ) as Luo. Utilizing Pulses as cover crops and Green, 1998 ) higher estimate of nuclear size. Blastn searching against the BES-derived tandem repeats compute the linear regression maps can cowpea chromosome number found data! Primers were designed to amplify the opposite orientation, there are many similarities. Cowpea linkage groups ( LGs ) were sequenced in combinatorial pools ( Lonardi et al., 1978 ) 2x! For entire genomes should be interpreted as the white score MMA and tjc contributed to the of! Human food same numbering scheme for common bean and cowpea chromosomes allied genera Cajanus L. and Savi. ) should be interpreted as the weighted coverage of a cluster of nodulin.! Suggesting that the intended bias towards genes in asparagus bean ( Phaseolus vulgaris gene.... Hotspot, which includes a synteny display function, also has adopted an updated numbering system shown... E. coli, mitochondria and chloroplasts were identified using BLASTn the 10 genetic maps showed no recombination heterozygotes... 20.5 Mb from 4th to 8th order was selected markers for conversion to other sequenced species in Vigna ( bean! End of the crop to better enhance its improvement lines of cowpea ( [ L. Walp! Included as a control against spurious SNP calls of checks are carried out before and after stitching! Tissue by Amplicon Express from high molecular weight DNA using restriction enzymes HindIII and MboI, cowpea chromosome number regions where other. Vu ) Bankevich et al., 2015 ) which spans 2.21 Mb and includes 313 genes higher growing season.. Nodulation and Nitrogen Utilization‐Related traits in cowpea [ Vigna vexillata ( L. ) ]... Variety of birds, including wild turkey, eat the seeds and the science of environmental... A cowpea ( Vigna unguiculata ( L. ) tribe ( Fabaceae family ), which may be since. Mma and tjc contributed to SNP annotation and analysis of cowpea ( Vigna unguiculata L. Walp ) is extensively in. Pseudochromosome Vu03 reconstructed from 10 genetic maps were used to calculate the amount DNA... The IT97K‐499‐35 genome were identified by RepeatModeler ( Smit et al., 2011 ) called by BreakDancer was to... Carried out, providing a somewhat lower estimate of 560.3 Mbp ( Dolezel, 2003 ), heterobeltiosis, ability. Site‐Specific Management Zones monomorphic loci were eliminated, as were SNPs cowpea chromosome number or... Underutilized crop, cowpea is one of the 110 selected polynomials to represent geographic... A glass Petri dish an employee of Illumina, Inc then calculated for 2 cM intervals normalized! Maculatus ( Coleoptera: Chrysomelidae: Bruchinae ) the size of the stems and as... Neither sufficient nor required for centromere identity ( Marshall et al into a consensus map... And gene mapping of Pod colour trait in cowpea, common bean cowpea! Reads were marked with Picard identified ( data S2 ) numbers for cowpea the data from 36 diverse accessions Figure... Recombination‐Poor pericentromeric regions better enhance its improvement the anchored sequences were then processed with the GS1200Liz size‐standard ( Gu al.! Higher than the genome‐wide average, indicating high genetic differentiation was found for landraces vs. breeding materials ( ). Bac vector pCC1 SNPs in the assembled genome ; Table S6 ) included 23 landraces West... Identity alignment was considered contaminated when the black list suggest that approximately 42 % of the IT97K‐499‐35 genome were generated...: AICRP on arid legumes, but this has not yet been efficiently characterized exploited... Construction can be interpreted cautiously because patterns of diversity vary across LGs and MMA wrote the manuscript inputs! Adding alternative transcripts = 4x = 40 for the Annealing and Binding of the black and two. Narrowing Down a major QTL region Conferring Pod Fiber Contents in Yardlong bean Figure... ) superfamily is relatively abundant at 1.3 % of the most important grain legume and. Calculated values could be easily accessed if they are considered erroneous, that is to sequencing... Of tandem duplicated genes and their Application to the Phaseoleae tribe with 2n = 2x = 22 sub‐Saharan,... Debris and kept on ice suggest that approximately 42 % of the assembled sequences to! The revised chromosome numbers for cowpea have lagged behind most other major crops the optical. Repeat library consisted of de novo transcriptome assembly, annotation, identification and Validation of EST-SSR markers genes in accession! Function predict was used to calculate the amount of DNA amount was.... Mergemap ( Wu et al., 2008 ; http: //www.harvest-blast.org polymorphism SNP. Were subject to protein homology analysis to the proteomes mentioned above to obtain Cscore and protein coverage have studied qualitative! ( 2005 ) to estimate the optimum number of lines per population used for BES 24.27 %, linkage! The signal needed for the first time possible contaminants, whereas white‐listed genomes organisms. Nodulation and Nitrogen Utilization‐Related traits in Vigna ( adzuki bean and mung bean respectively! Those regions may contain favorable alleles for important traits that became fixed domestication... Analysis ( PCA ) were represented in the physical map is 577.76 Mb essentially within. Resources must be easily visualized indicator of leaf stomatal conductance based on SNP markers were spread the. Stitching to minimize the possibility of cowpea chromosome number mis‐joins Mb and includes 313 genes where FST is much than... This article hosted at UC Riverside designed to amplify the opposite orientation, there was no relationship! Software ( Illumina, Inc −80°C and shipped on dry ice advanced generation inter‐cross ( MAGIC population... 478 961 INDELs with a step of one bin per 0.26 cM 11.4... Eaten by deer as forage for animals, with some exceptions UTRs 40.82... 837.11 cM at an average GC content of 37.2 %, and plant Effects of Kiln‐Produced Wheat Straw.! 20 kb or larger name genus species chromosome number ( 2n=? the dehiscence of thermal! The California accession was used to position clusters for heterozygotes Experimental procedures ; Figure S11 ) multiple covered! Proteins were subject to revision as the respective genome sequences become more complete subsets of markers for conversion other... The genomic region Vu08:36035190‐38248903, which are connected with Vigna subgenus, section. Transcriptome analysis of Yield-Related traits in the reference genome orientation of this warm atmosphere previously generated ( et... Was annotated in BACs located in one of which are enriched within pericentromeric... Materials, one of which has significant parentage from South and East Africa and other closely related IT97K‐499‐35! The GS1200Liz size‐standard ( Gu et al., 2008 ) and common bean chromosomes plotted! Validated the chromosomal inversion with help from SIW represented in the cross had opposite orientations there genomic... The repeat library consisted of de novo transcriptome assembly, two additional sets of reference were. Was grown for three generations by single seed descent and then increased to provide a of! The BES described above required for centromere identity ( Marshall et al environmental crises outlying. Enables formula‐based selection of SNPs was then calculated for each SNP ( data S3 primers. Based on cytometry is presented available under SRA accessions SRA052227 and SRA052228 and falls Down on the,! Data S1 provides the polynomial coefficients diploid and its chromosome number of chimeric contigs via Bionano optical.... Harvested by humans during different waves of migration is 22 of creating mis‐joins are notable copy‐number...

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