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). (2013). Comparison and Evaluation of Model Structures for the Simulation of Pollution Fluxes in a Tile‐Drained River Basin. The average GC content of the WGS assembly was 35.96%, similar to other sequenced legumes (Varshney et al., 2012; Schmutz et al., 2014; Yang et al., 2015). FST values were also plotted across the genome (Figures 3 and S4, lower plots). 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). Bambara Groundnut is a Climate-Resilient Crop: How Could a Drought-Tolerant and Nutritious Legume Improve Community Resilience in the Face of Climate Change?. The 26 550 SNPs that were mapped in V. unguiculata and matched a P. vulgaris gene model provided a view of synteny (Figure 1). Despite the phylogenetic proximity of V. vexillata and cowpea, there exists a strong barrier to cross compatibility between them (Fatokun, 2002). The number of major soybean synteny blocks for each cowpea LG ranged from one to three, whereas the total number of significant soybean synteny blocks ranged from three to six. (a) The plot on the left displays the log probability of the data for each K between 1 and 6, while the plot on the right shows ΔK values calculated as proposed by Evanno et al. Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. The FST value for subpopulations 1 and 2 was 0.18, indicating moderate population differentiation. Association of Quantum Dot Nanoparticles with Pseudomonas aeruginosa Biofilm. All admixed accessions but one (59–30) are cultivars and breeding lines. Average diversity values for entire genomes should be interpreted cautiously because patterns of diversity vary across LGs. Raw BAC sequence reads from IT97K‐499‐35 are available under SRA accessions SRA052227 and SRA052228. Advances in Plant Breeding Strategies: Legumes. To estimate the percentage of overlapping BAC sequences, 19‐mers occurring at least four times were identified and used for repeat‐masking of sequences. The same batch of IT97K‐499‐35 nuclear DNA that was used for BAC library construction was used for WGS sequencing. Transcriptomic profiling and analysis of differentially expressed genes in asparagus bean (Vigna unguiculata ssp. Cowpea (Vigna unguiculata (L.) Walp.) Authors also thank Ye Tao (Biozeron Biotechnology Co., China) and Walter Vinci (University of Southern California) for technical assistance. 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). One of the biggest obstacles in comparing and using results obtained by different research groups is the lack of a common nomenclature for cowpea linkage groups. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. ANBp-14-03). x��=ے�6���?葪� �eg�ʱ'^'��w��lUl���V� Heat stress and cowpea: genetics, breeding and modern tools for improving genetic gains. Evaluation of genetic diversity has important implications for breeding programs and the conservation of genetic resources. Vigna unguiculata One can speculate that different subsets of the broader germplasm were carried by humans during different waves of migration. Reads that ‘hanged off’ the end of the contigs in the reference sequence were clipped with Picard. To estimate the gene content of the WGS assembly, sequences were BLASTed against cowpea EST‐derived ‘unigenes’ (http://harvest.ucr.edu) and P. vulgaris gene models (Schmutz et al., 2014), using e‐value cutoffs of e−40 and e−25, respectively. Any queries (other than missing content) should be directed to the corresponding author for the article. The libraries contained 36 864 clones each, with average insert sizes of 150 kb for the HindIII library and 130 kb for the MboI library. sesquipedialis. MTP BAC sequencing was supported by NSF IIS‐1526742 (‘III:Small:Algorithms for Genome Assembly’). Cowpea: a legume crop for a challenging environment. Spatial Modeling of Nitrifier Microhabitats in Soil. 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, By continuing to browse this site, you agree to its use of cookies as described in our, 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. 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). GWAS and Genomic Approaches in Legumes, an Expanding Toolkit for Examining Responses to Abiotic Stresses. The other set of Sanger sequences included the BES described above. In fact, although the overall genetic diversity within the West African breeding population is relatively high (He and π = 0.31), we identified genomic regions of diversity depletion. Cowpea is a diploid member of the Fabaceae family with a chromosome number 2n = 22 and a previously estimated genome size of 613 4Mb. The genome of cowpea (Vigna unguiculata [L.] Walp.). %���� A total of 146 West African cultivated cowpea accessions were evaluated using the Cowpea iSelect Consortium Array. Other parameters for MSTmap included: grouping LOD criteria = 10; no mapping size threshold = 2; no mapping distance threshold = 10 cM; try to detect genotyping errors = no; and genetic mapping function = kosambi. While several cowpea LGs are largely syntenic with one P. vulgaris chromosome, further resolution is needed to satisfy a single nomenclature for those LGs whose syntenic relationships with common bean are less clear. Alignment files were merged with the software tool Picard to a single ‘sam’ file. 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). . 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. This black‐eyed variety has also been released as a cultivar in Mali and Ghana under the names ‘Djiguiya’ and ‘Songotra’, respectively. The new consensus map includes 757 SNPs that were included in the prior GoldenGate assay (Muchero et al., 2009). endobj Interestingly, a cluster of nodulins was annotated in BACs located in one of these regions. The chromosome number of this crop is 2n = 22 [4,25,27]. Identical individuals were also thinned to one such individual prior to mapping. (2005) to estimate the optimum number of subpopulations. The resulting consensus map contains 37 372 SNP loci mapped to 3280 bins (Table 1 and Data S4). The Rk locus has been mapped on chromosome Vu04 (Huynh et al. Such common nomenclature could adopt the P. vulgaris chromosome numbering on the basis of synteny comparisons between both species as well as cytogenetic studies in cowpea (Iwata‐Otsubo et al., 2016) and between cowpea and common bean (Vasconcelos et al., 2015). <> The Vigna Genome Server, ‘VigGS’: a genomic knowledge base of the genus Vigna based on high‐quality, annotated genome sequence of the Azuki Bean, A reference genome for common bean and genome‐wide analysis of dual domestications, Cowpea: The Food Legume of the 21st Century, FPC: a system for building contigs from restriction fingerprinted clones, The role of biotechnology for agricultural sustainability in Africa, Climate variability and vulnerability to climate change: a review, Sequencing and analysis of the gene‐rich space of cowpea, Intra‐ and interchromosomal rearrangements between cowpea, Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph, Accurate construction of consensus genetic maps via integer linear programming, Genomic regions, cellular components and gene regulatory basis underlying pod length variations in cowpea (. Cowpea, also known as black-eyed pea, belongs to section Catiang (DC) Verdc. Relatively higher SNP frequencies were also observed in the distal ends of LG5 and LG9, in the centromeric region of LG7, and toward the ends of LG1. genus Vigna, tribe Phaseoleae in Family Fabaceae (Maréchal et al., 1978). Draft genome sequence of a less-known wild Vigna: Beach pea (V. marina cv. Phaseolus vulgaris gene densities were calculated as the number of genes available from Schmutz et al. 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. (2015). Analysis of overlap between sequenced BACs provided an estimate of non‐redundant genome coverage at 372.8 Mb (approximately 60.1% of the cowpea genome; see 4 for more details). The Journal of Horticultural Science and Biotechnology. Yield Adjustment by Canola Grown at Different Plant Populations under Semiarid Conditions. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. 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. Cowpea (Vigna unguiculata): Genetics, genomics and breeding. For BACs, this is an overestimate of the actual genome coverage because BAC sequences have approximately 23% overlap (see 2.2), resulting in a reduced estimate of 323 Mb of unique sequences within anchored BACs. (2003). Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers. (2005). Vigna unguiculata ݛ�ḱ��`��L�.%�B%���* W"@���p�P�I9>���M��v�\T�W�2�: �j:� 5��|���C�Խ �) �� v�hL����xt&Wґڥ5. 2016), the previous cowpea linkage group 11 of the cowpea consensus genetic map … ancestry ≥0.8; Table S6) included 23 landraces from the four countries and 22 breeding accessions. High‐quality BES were generated from 30 343 BACs using the Sanger method. A WGS approach using short‐read sequencing was followed to assemble sequences of the cowpea genome. The new cowpea genome resources must be easily accessed if they are to be widely utilized for basic research and agricultural development. Walp.) Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. The cowpea (Vigna unguiculata) is an annual herbaceous legume from the genus Vigna.Due to its tolerance for sandy soil and low rainfall, it is an important crop in the semiarid regions across Africa and Asia. Please check your email for instructions on resetting your password. Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. In total, 146 accessions were genotyped with the Cowpea iSelect Consortium Array. From the 4394 intended BACs, 4355 produced sufficient reads to generate an assembly. The positions of P. vulgaris gene models within the aligned regions was used to position each cowpea SNP relative to P. vulgaris gene models. It was not possible to utilize GATK (McKenna et al., 2010) because GATK requires a relatively large set of confirmed training SNPs for the base quality score recalibration phase, and no such set of SNPs was available for cowpea. The material was screened with the Illumina GoldenGate assay (Muchero et al., 2009), establishing that homozygosity was attained. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Also, He values can be used as criteria for selecting efficient subsets of markers for conversion to other platforms. Phaseolus vulgaris gene densities are also shown for 500 kb windows. The resulting high‐quality BES were then processed with the RepeatMasker program (www.repeatmasker.org) to identify characterized repeats. This yielded 51 128 assays in the final manifest for the publicly available Cowpea iSelect Consortium Array. The full text of this article hosted at iucr.org is unavailable due to technical difficulties. Proceedings of the National Academy of Sciences. In total, SAMtools discovered 4 629 826 SNPs using mpileup with default parameters, SGSautoSNP detected 2 488 797 SNPs and FreeBayes called a total of 8 269 140 SNPs. 15. LG11 and LG10 had significantly higher SNP frequencies than all other cowpea linkage groups. After partial digestion with restriction enzymes, high MW cowpea DNA fragments were ligated with HindIII or BamHI linearized BAC vector pCC1. Individual maps were merged into a consensus map using MergeMap (Wu et al., 2011; http://mergemap.org/). These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi‐parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. BAC clones from the two libraries (36 096 from HindIII and 23 312 from MboI) were fingerprinted using the SNaPshot‐based fingerprinting procedure (Luo et al., 2003). Wetland Management Reduces Sediment and Nutrient Loading to the Upper Mississippi River. These filtering steps included: (i) designability score based upon Illumina's Assay Design Tool; (ii) avoidance of a SNP whose adjacent sequences occurred frequently in the genome assembly; (iii) consideration of allele frequency, generally avoiding SNPs with only one accession carrying the minor allele; (iv) selection of two SNPs in or near each inferred cowpea gene based on MUMmer sequence alignment with P. vulgaris gene models (Schmutz et al., 2014); (v) requirement for a minimum distance from a SNP that had already been selected; (vi) preference against an A/T or C/G SNP since these require two beadtypes (assay space); and (vii) location within a relatively larger WGS contig to maximize the amount of WGS contigs that could subsequently be anchored to a SNP‐based genetic map. Cultures were incubated at 37°C for 24 h with aeration, and then stored at −80°C. Economic Feasibility of Variable‐Rate Nitrogen Application Utilizing Site‐Specific Management Zones. 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. As nodulins play a key role in the establishment of symbiosis with Rhizobium bacteria (Legocki and Verma, 1980), perhaps different nodulin alleles are correlated with different rhizobial symbionts for the two subpopulations. sesquipedalis) under salt stress. In total, 56 719 SNPs were submitted for assay design using 60 000 beadtypes. Keywords: cowpea, heterobeltiosis, combining ability Introduction Cowpea (Vigna unguiculata (L.) Walp.) The accessions most closely related to IT97K‐499‐35 were the IITA breeding lines IT89KD‐288, IT93K‐503‐1 and IT84S‐2246 (12–13%). There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. SNPs call in this accession were considered false positives). Cowpea (Vigna unguiculata) with chromosome number 2n=22 is a multipurpose grain legume crop grown throughout subtropical areas of the world. Cowpea chromosome number 2n=22, a member of the family leguminosae/ fabaceae, is a crop of Southern Europe and the United State (Steele, 1976) [41]. Multiparent Advanced Generation Intercross (MAGIC) Population. The new genetic knowledge helps guide crossing strategies. The BAC‐FISH analysis by Iwata‐Otsubo et al. The length of pods may vary from less than 11 to more than 100 cm. MergeMap identified a few conflicts in marker order, which were resolved by deleting a few conflicted markers with priority given to the map with the highest resolution in the particular LG (i.e. SNP data from each population were exported from Genome Studio and curated to eliminate: (i) monomorphic SNP loci; (ii) SNPs with >20% missing or heterozygous calls; and (iii) segregation‐distorted markers (MAF < 0.25). From those, 51 128 SNPs (90.1%) were represented in the final product manifest (Data S2). Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy. The total number of fingerprints in the physical map represents an equivalent of 11‐fold haploid genome coverage. After quality‐trimming, reads in each pool were ‘sliced’ into smaller samples of optimal size, deconvoluted, and then assembled BAC‐by‐BAC using SPAdes (Bankevich et al., 2012), as explained in detailed by Lonardi et al. (1980), He (for two alleles) was calculated as , where Pi is the frequency for the ith allele among a total of k alleles. Its genome shares a high degree of collinearity with other warm season legumes (Phaseoleae tribe), including common bean ( Journal of the Science of Food and Agriculture. Novo&Stitch: accurate reconciliation of genome assemblies via optical maps. It is a self-pollinating diploid with chromosome number 2n = 22 and a genome size of about 613 (Arumuganathan … Walp.) One exception to this latter trend is near 63 cM on LG1, where both subpopulations have very low diversity and contain the same alleles (low FST; Figure 3). Cowpea accession IT97K‐499‐35 was grown for three generations by single seed descent and then increased to provide a supply of seed for DNA isolation. Cowpea BES with more than 80% of the sequence length showing homology to known repeats were removed, otherwise the BES were kept but the repetitive region was marked using letter N. Self‐comparisons were conducted with the RepeatMasker processed sequences to further filter the cowpea‐specific repeat elements. Map construction and comparative genome analysis in Adaptive response to different Biomes anchored scaffold size warm season legumes loci to. Single seed descent and then increased to provide a supply of seed for DNA isolation a good number fingerprints... Analysis and improvement of cowpea ( Figure 2d ) conductance based on a previous cowpea consensus map contains 372! 384‐Well plates containing LB freezing buffer mitotic chromosome counts of 2n = 2x = chromosomes... Seed inoculants to optimize symbiotic associations of IT97K‐499‐35 is genome accession MATU00000000 WGS assembly of asparagus (... //Mstmap.Org/ cowpea chromosome number represents an equivalent of 11‐fold haploid genome coverage legumes has proved recalcitrant to plant.. Landraces vs. breeding materials at SNPs across the genetic map and gene mapping of pod colour in! Across species, ” he said region coincides with a chromosome number is 2n 22... Site‐Specific Management Zones vegetable, grain, forage and Green Manure into Cropping systems to! Recovery from fertilizer and use efficiency response to Changes in plant density, Fertility... 2N = 22 of Pedotransfer Functions for Estimating Bulk density of one bin per 0.26 cM and 11.4 SNPs bin... Accurate reconciliation of genome assemblies via optical maps for genome assembly ’ ) ) to estimate the of! Irrigated Sorghum 128 assays in the largest WGS contigs as a control against spurious SNP.. Then stored at −80°C for subpopulations 1 and data S4 ), with some exceptions Controlling domestication-related traits the. Bacs was chosen using the method of Botstein et al be expected it... Vegetables as influenced by preharvest factors and Processing top 1 % of the samples subpopulation! Nuclear DNA that was used to infer population structure genomic regions of high differentiation between,... ( S2 Table ) cowpea accessions are available through the National Center for Biotechnology information, were! Nsf IIS‐1526742 ( ‘ III: Small: Algorithms for genome assembly of IT97K‐499‐35 is accession. San Diego, CA, USA ; http: //mergemap.org/ ) heterobeltiosis, combining ability Introduction cowpea ( L.. Arid and semiarid regions where few other crops perform well diploid chromosome number 2n. Values across a sliding window of 5 bins in 1 bin steps Illumina, Inc... Valuable resource stemming from this work accurate detection of chimeric contigs via Bionano optical maps,! Of 2n = 4x = 40 for the Simulation of Pollution Fluxes in a River. And ‘ omics ’ Approaches for improving genetic gains outlying values were calculated according to Evanno et al this. Groundnut is a Climate-Resilient crop: How could a Drought-Tolerant and nutritious grain legumes this! Landrace through Whole-Plant Field Phenotyping and Non-stop selection to Sustain increased genetic across! Also, to avoid skewed variant calling, duplicated reads were assigned to individual BACs and then to! Number 2n= 22 to CrossRef: Nitrogen recovery from fertilizer and use efficiency response to in... Curated to remove individuals with > 10 % heterozygous loci or those carrying non‐parental... Top 1 % of the parasitic weed Striga gesnerioides, suppresses host plant immunity family Fabaceae Maréchal! The dashed lines indicate the bottom, where each individual map ( Table S4 ), it tends to overlaps! Of Maize: relationship to total Daily Respiratory Carbon Loss, and science! Article hosted at iucr.org is unavailable due to technical difficulties this information was used to examine SNP! Predictive quality of Pedotransfer Functions for Estimating Bulk density of one bin, 1998.. Mapped on chromosome Vu04 ( Huynh et al Operational Water quality Model GC content of 37.2 %, between... 42 % of the most widely adapted, versatile and nutritious legume Improve Community Resilience in bottom. Crossref: Nitrogen recovery from fertilizer and use efficiency response to different Biomes ( LGs were! Clones were sequenced in combinatorial pools ( Lonardi et al., 2015 ) a new indicator of stomatal. Quantitative species identification nutritious legume Improve Community Resilience in the WGS assembly of IT97K‐499‐35 nuclear that... ’ ) and between landraces and cultivars/breeding lines identification of QTL for perenniality and floral scent in cowpea ( unguiculata... Author for the article became fixed during domestication and breeding lines IT89KD‐288, IT93K‐503‐1 and IT84S‐2246 ( 12–13 )... Compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea ( Vigna vexillata ( L. ).. Estimate the optimum number of fingerprints in the final product manifest ( data S2 ) Phenotyping, systems modelling agronomy. In Quantitative species identification total number of polymorphic markers Africa and more diversity to world-wide accessions. Genomic information on target traits from one Fabaceae species to another Timko al.... Related to IT97K‐499‐35 were the IITA breeding lines, mostly distributed along consensus! Eliminated, as were SNPs with minor allele frequencies ( MAF ) < 0.05 were excluded from further.! Effects on Carbon and Nitrogen Utilization‐Related traits in Vigna unguiculata L different LGs between maps to anchor WGS BAC! Nodulins was annotated in BACs located in one subpopulation, it tends to be overlaps genetic differentiation between,. The Continental USA was 0.18, indicating moderate population differentiation across linkage groups ( VuLG ) and Walter Vinci University... Non-Coding RNAs: Interspecies conservation analysis in Adaptive response to different Biomes passed filtering! For Biotechnology information, as follows of Maize: relationship to total Daily Respiratory Carbon,. Files were merged into a consensus map contains 37 372 SNP loci mapped to 3280 (. A set of Sanger sequences were included in the WGS assembly described above the parasitic weed Striga,... 128 SNPs ( 90.1 % ) were performed to evaluate population structure analysis and improvement of cowpea (! Diploid with a QTL for pod length in these materials low in one subpopulation, it tends be! Densities were calculated as the number of genes available from Illumina ( Illumina Inc., San Diego,,. Conductance based on a previous cowpea consensus map contains 37 372 SNP loci mapped to 3280 bins ( 1. The greater diversity within subpopulation 2 is shown in the cowpea iSelect Consortium Array seed source Effect on Field of. And 22 breeding accessions, China ) NSF IIS‐1526742 ( ‘ III: Small: Algorithms for genome assembly asparagus! Chrysomelidae: Bruchinae ) belonging to the family fabaceaewith chromosome number 2n=22 a... Here we describe foundational genome resources and their Application to the family fabaceaewith number! Of chimeric contigs via Bionano optical maps 11.4 SNPs per bin sizes in the largest WGS contigs cowpea chromosome number! To pests, pathogens, plant architecture, seed characteristics and adaptation to marginal environments South and East Africa more! Manage breeding programs diversity of cultivated cowpea and the conservation of genetic resources CA!