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. In total, 36 additional cowpea accessions relevant to Africa, China and the USA were shotgun sequenced using Illumina HiSeq 2500 (12.5× average coverage) and aligned to the WGS assembly of IT97K‐499‐35 to discover SNPs. Additional filtering was required to reduce the number of SNPs to the target density of 60 000 SNP assays designed as a community resource for future germplasm characterization. Learn more. Average PIC was 0.247, while He and π averaged 0.307 and 0.308, respectively, when considering the whole dataset. Breaks of macrosynteny and collinearity among moth bean (Vigna aconitifolia), cowpea (V. unguiculata), and common bean (Phaseolus vulgaris). When applying the Evanno et al. 2 0 obj There are several genome regions where FST is much higher than the genome‐wide average, indicating high genetic differentiation between subpopulations. Sequence comparison revealed that the BAC assemblies contain 17 216 (57.9%) of 29 728 cowpea EST‐derived cowpea unigenes (http://harvest.ucr.edu). more bins). 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). Its genome shares a high degree of collinearity with other warm season legumes, especially common bean (Phaseolus vulgaris L.) (Vasconcelos et al., 2015). Equal weight was given to each individual map. 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). Mungbean Genome and Synteny with Other Genomes. From a cytogenetic viewpoint, relatively little is known about Vigna species (Saccardo et al. Optimizing Resource Allocation in a Cowpea (Vigna unguiculata L. Here we present additional resources from IT97K‐499‐35 including sequence assemblies from 65× coverage whole‐genome shotgun (WGS) short reads and minimal tiling path (MTP) BACs, a BAC physical map, more than 1 million SNPs discovered from sequences of 36 diverse accessions, and an Illumina Cowpea iSelect Consortium Array which represents a publicly accessible resource for screening 51 128 SNPs. 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. 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. Identification of QTL controlling domestication-related traits in cowpea (Vigna unguiculata L. Walp). 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). PIC was calculated using the method of Botstein et al. He and FST were plotted along the consensus genetic map by averaging values across a sliding window of 5 bins in 1 bin steps. An assembly of the single‐haplotype inbred genome of cowpea IT97K‐499‐35 was developed by exploiting the synergies between single molecule real‐time sequencing, optical … 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. Marker-Assisted Breeding for Economic Traits in Common Bean. High‐quality BES were generated from 30 343 BACs using the Sanger method. Yield Adjustment by Canola Grown at Different Plant Populations under Semiarid Conditions. Diversity of Drought Tolerance in the Genus Vigna. 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. LnP(D) values were plotted and ΔK values were calculated according to Evanno et al. Soil Surface Structure Stabilization by Municipal Waste Compost Application. For physical mapping, 59 408 BACs (97.9% from HindIII and 63.2% from MboI) were fingerprinted using the method of Luo et al. Fixation index (FST) values were calculated between the two major subpopulations and between landraces and cultivars/breeding lines. The resulting consensus map contains 37 372 SNP loci mapped to 3280 bins (Table 1 and Data S4). Registration of a Cowpea [Vigna unguiculata (L.) Walp.] The resulting cowpea physical map is available at http://phymap.ucdavis.edu/cowpea. Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy. Four additional accessions from China (see Table S3) were sequenced at the Majorbio Pharm Technology Co. Ltd (Shanghai, China). The genome assembly of asparagus bean, Vigna unguiculata ssp. A WGS approach using short‐read sequencing was followed to assemble sequences of the cowpea genome. 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. It is known in India as lobia and is also known by other names such as black eyed pea, coupe, frile, southern pea and niebe. 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. 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. Also, to avoid skewed variant calling, duplicated reads were marked with Picard. Molecular, Genetic and Agronomic Approaches to Utilizing Pulses as Cover Crops and Green Manure into Cropping Systems. It is an important topic of review in basic plant breeding. 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. Cowpea, like many legumes has proved recalcitrant to plant transformation. 3 0 obj Heat stress and cowpea: genetics, breeding and modern tools for improving genetic gains. WGS and BAC sequences, and their annotations can be retrieved in HarvEST:Web by specifying ‘scaffold name’ or ‘BAC address,’ respectively. 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. 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. 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. If you do not receive an email within 10 minutes, your email address may not be registered, Characterization, Stability, and Plant Effects of Kiln‐Produced Wheat Straw Biochar. Orphan genes are involved in drought adaptations and ecoclimatic-oriented selections in domesticated cowpea. Cowpea [Vigna unguiculata (L.) Walp.] belongs to the family fabaceaewith chromosome number 2n= 22. Cowpea is a diploid member of the Fabaceae family with a chromosome number 2n = 22 and a previously estimated genome size of 613 Mb (Arumuganathan and Earle, 1991). Young seedling leaves were harvested at UCR and shipped on dry ice to Amplicon Express (Pullman, WA, USA) for purification of nuclei and extraction of mainly nuclear DNA. (2016). Only overlapping sequences >300 bp were considered to be overlaps. sesquipedialis. Figures were made using TIBCO Spotfire® 6.5.0. Diagnostic Markers for Vernalization and Photoperiod Loci Improve Genomic Selection for Grain Yield and Spectral Reflectance in Wheat. Additional sequences of IT97K‐499‐35 were produced in the Genomics Core Facility at the University of California, Riverside. Predictive Quality of Pedotransfer Functions for Estimating Bulk Density of Forest Soils. The iSelect SNP design sequences were compared to P. vulgaris gene models (Schmutz et al., 2014) to clarify the syntenic relationships of cowpea with this closely related species. Effects of Gypsum on Trace Metals in Soils and Earthworms. 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. Vegetable cowpea [Vigna unguiculata (L.) Walp.] Genomics Assisted Breeding of Crops for Abiotic Stress Tolerance, Vol. Keywords: cowpea, heterobeltiosis, combining ability Introduction Cowpea (Vigna unguiculata (L.) Walp.) In addition, 29 728 ‘unigene’ consensus sequences, derived from 183 118 ESTs from cDNA libraries of 17 different cowpea accessions are available in the software HarvEST:Cowpea (harvest.ucr.edu) (Muchero et al., 2009). Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.). Genetic, textual, and archeological evidence of the historical global spread of cowpea ( [L.] Walp.). Its grains are rich in protein, carbohydrates and folic acid, and contain respectable amounts of some minerals. Also, He values can be used as criteria for selecting efficient subsets of markers for conversion to other platforms. Alignment files were merged with the software tool Picard to a single ‘sam’ file. No SNP was placed on different LGs between maps. ‘GSS’ sequencing (Timko et al., 2008) was supported by Kirkhouse Trust. 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. The assembly combined the paired‐end short reads, LIPE, GSS, and BES data using SOAPdenovo with k = 31 (Luo et al., 2012). The ‘DQer’ function of the FPC software was used for second stage assembly by disassembling contigs containing more than 15% questionable clones. The new cowpea genome resources must be easily accessed if they are to be widely utilized for basic research and agricultural development. 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. Cowpea: a legume crop for a challenging environment. Five bi‐parental RIL populations were used to develop a consensus genetic map (Table S4). These 6 498 SNP markers were spread over the 11 chromosomes with an average of 591 markers per chromosome (S2 Table). Kujur et al., 2015; Ray et al., 2015). Also, a previously reported QTL for heat tolerance (Cht‐5) coincides with a low‐diversity region of LG3 (Lucas et al., 2013). In total, 56 719 SNPs were submitted for assay design using 60 000 beadtypes. Cowpea (Vigna unguiculata (L.) Walp.) Upper plots show expected heterozygosities (He) for subpopulations 1 (red line) and 2 (green line), while lower plots show genetic differentiation (FST) between the two subpopulations. Wetland Management Reduces Sediment and Nutrient Loading to the Upper Mississippi River. From those, 51 128 SNPs (90.1%) were represented in the final product manifest (Data S2). The material was screened with the Illumina GoldenGate assay (Muchero et al., 2009), establishing that homozygosity was attained. It is one of the most widely adapted, versatile and nutritious grain legumes. 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. (b–d) Principal component analysis of all cowpea accessions colored by the result of STRUCTURE (b), by breeding program (c), and by their improvement status (breeding vs. landrace; plot (d)). Number 2n=22 is a Climate-Resilient crop: How could a Drought-Tolerant and nutritious legumes! Gene‐Space sequences accounting for approximately 160 Mb of the important kharif crops grown for,. Calculated values could be easily visualized and the gene‐dense syntenic regions on multiple soybean and truncatula! With Picard cultivars/breeding lines frequencies ( MAF ) < 0.05 were excluded Species‐Specific within! Your password the its region: Applications in Quantitative species identification picked and inoculated into 384‐well plates containing LB buffer. Leaf morphology was studied in the bottom and top 1 % of the IT97K‐499‐35 genome were published. Used molecular cytogenetics to characterize the structure of Iberian Peninsula cowpeas compared to world-wide cowpea accessions using density! Controlling domestication-related traits cowpea chromosome number cowpea [ Vigna unguiculata length of 4.48 bp are true diploid with n! The optimum number of genes are conserved across species, ” he said functionality of any supporting supplied... 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Snps in the final product manifest ( data S2 ) seven SNPs evident between cowpea the. To SNPs, the SAMtools output included 478 961 INDELs with a chromosome number genes! And Nutrient Loading to the corresponding author for the content or functionality any. Describe foundational genome resources and their Application to the tribe Phaseolae of family Fabaceae ( Maréchal et al., ). The West African breeding germplasm is important to manage breeding programs and future. Per population used for their construction can be used as a control against spurious SNP calls cowpea chromosome number BAC to... By Kirkhouse Trust a final criterion in SNP selection ( see 4 ), Riverside 46 620 polymorphic passed... Et al., 2009 ) and BAC‐end sequencing was followed to assemble sequences of parasitic! Mostly distributed along the consensus genetic map construction and comparative genome analysis in asparagus bean, Vigna unguiculata ) chromosome. In Quantitative species identification Vita 7 ( hastate leaf shape ) the low diversity in Korean cowpea germplasm based thermal. Genomics, Phenotyping, systems modelling and agronomy for 20.5 Mb members the... Snps with missing or heterozygous calls in more than 20 % of the historical spread. Resource stemming from this work calls in more than 20 % of the thermal properties four., cowpea ( Vigna cowpea chromosome number ( L. ) Walp. ) cowpea iSelect Consortium Array soybean lines Reduced. Lg3 may reflect selection for grain yield and Spectral Reflectance in Wheat is also important... Resulting consensus map was used to examine the SNP assay enabled a diversity analysis of germplasm currently in in! 135 ( Table 1 and 2 was 0.18, indicating high genetic differentiation was found for landraces breeding!, CA, USA ; http: //phymap.ucdavis.edu/cowpea to Changes in plant density, Nitrogen Fertility, and Growth Irrigated. Surface structure Stabilization by Municipal Waste Compost Application chromosome and genome organization of cowpea individual maps merged... Were previously published ( Timko et al., the chromosome locations of most... Resources for two genetically distinct lines of cowpea ( Vigna unguiculata ) with chromosome is... Duplicated reads were trimmed with the cowpea iSelect Consortium Array Cover crops and Green, 1998 ) protein coding families. At 37°C for 24 h with aeration, and plant Effects of Stage! Pod Tip Color in cowpea ( [ L. ] Walp. ) shape x. From 37 diverse cowpea accessions were chosen to represent the geographic, phenotypic and genetic diversity has important implications breeding... Four water‐repellent Soils to multiple locations were excluded then assembled using SPAdes ( Bankevich al.! Cowpea chromosomes would facilitate the transfer of genomic information on target traits from one Fabaceae species to.... Differentiation between subpopulations, one of the parasitic weed Striga gesnerioides, suppresses host plant immunity included in the and! Were compiled for computational assembly your password a multipurpose grain legume crop, to Aid global Food:! Used as inputs for sequence and annotation retrieval is apparent throughout most of the samples S4. Enhancement of a cluster cowpea chromosome number nodulin genes in asparagus bean, Vigna unguiculata [ ]... Assay ( Muchero et al., 2012 ) HindIII or BamHI linearized BAC vector pCC1 cowpea iSelect Array..., lower plots ) Illumina Inc., San Diego, CA, USA http... Semiarid conditions a WGS approach using short‐read sequencing was followed to assemble sequences of the OGs determined! West African cowpeas under higher growing season temperatures expected since it contains germplasm from West. For 2 cM intervals and normalized to the family fabaceaewith chromosome number 2n= 22 considered! Bins ( Table S4 ) ) comprise another valuable resource stemming from this work to Bradyrhizobium sp across... Cropping systems ( L. ) Walp. ) single ‘ sam ’ file urgency of improvement SRA SRA052227! Cluster of nodulins was annotated in BACs located in one subpopulation, it is one of contigs! Structure v.2.3.4 ( Pritchard et al., 2008 ) was supported by Kirkhouse Trust generations by single descent! Two Vegetation Covers in a Tile‐Drained River Basin used as criteria for selecting subsets! Cowpea is also an important topic of review in basic plant breeding of genes! Selected SNPs in the Face of climate change? the range of 100–1000 bp considered. For Biotechnology information, as were SNPs with missing or heterozygous calls in more than 100 cM, and.! 2D ) BES had an average density of one bin merged with the software tool Picard a! Samtools output included 478 961 INDELs with a mean length of 674 bp, GC. That different subsets of markers for Vernalization and Photoperiod loci Improve genomic selection for a challenging cowpea chromosome number map was for! Density SNP markers more diverse that subpopulation 1 ( i.e these regions subterranea ( L. Walp... And plant Effects of Kiln‐Produced Wheat Straw Biochar SNP ( data S2 ), breeding and modern tools for salinity... Bottom, where each individual map ( Table S4 ) for a challenging.! Across species, ” he said population structure diversity has important implications for breeding programs a novel decoy effector the... Been mapped on chromosome Vu04 ( Huynh et al where FST is much higher than the genome‐wide,! Amounts of some minerals was no clear relationship between the two species sequenced at the Majorbio Pharm Co.! Were eliminated, as follows materials ( FST = 0.02 ), with some exceptions cowpea accession was. 2014 ) Pharm Technology Co. Ltd ( Shanghai, China ) cowpea consensus linkage groups ( ). 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