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). Each of the eight assemblies contributed a fraction of its contigs to the final assembly: 13% of the ‘minimal tiling path’ (MTP) contigs were from the FALCON assembly, 8% from the ABruijn assembly and the rest (79%) from the six canu assemblies, each ranging from 4 to 20%. The new consensus map includes 757 SNPs that were included in the prior GoldenGate assay (Muchero et al., 2009). 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). A highly fragmented draft assembly and BAC sequence assemblies of IT97K‐499‐35 were previously generated (Muñoz‐Amatriaín et al., 2017). Table S1. . The P. vulgaris genome sequence was the earliest among these species (Schmutz et al., 2014), thus establishing a precedent and rational basis for a more uniform chromosome numbering system. A variety of birds, including wild turkey, eat the seeds and the plant can be used by quail as cover. The repeat library consisted of de novo repeats identified by RepeatModeler (Smit et al., 2008) and Fabaceae repeats in RepBase. Association of Quantum Dot Nanoparticles with Pseudomonas aeruginosa Biofilm. 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. Also, a k‐mer distribution analysis was carried out, providing a somewhat lower estimate of 560.3 Mbp (Figure S2). Learn more. 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). Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot herb in many countries of Africa. Circos illustration of synteny between cowpea linkage groups (VuLG) and common bean pseudomolecules (Pv). The new genetic knowledge helps guide crossing strategies. Primer sequences used to validate the Vu03 inversion. Cowpea is a diploid member of the Fabaceae family with a chromosome number 2n = 22 and a previously estimated genome size of 613 4Mb . Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.). 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. Cowpea is eaten by deer as forage, and is commonly used in food plots for deer. Gene‐space sequences accounting for approximately 160 Mb of the IT97K‐499‐35 genome were previously published (Timko et al., 2008). and Azospirillum brasilense combined with N rates in cowpea-wheat crop sequence. Genomics-Assisted Breeding for Drought Tolerance in Cowpea. Quantitative trait loci influencing days to flowering and plant height in cowpea, Vigna unguiculata (L.) Walp. QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance. A WGS approach using short‐read sequencing was followed to assemble sequences of the cowpea genome. This black‐eyed variety has also been released as a cultivar in Mali and Ghana under the names ‘Djiguiya’ and ‘Songotra’, respectively. Scaffolds were obtained from the polished assembly via the Kansas State University (KSU) stitching pipeline (Shelton et al., 2015) in multiple rounds. (1979) indicate occurrence in Australia, but there is no more recent confirmation of this. OMGS: Optical Map-Based Genome Scaffolding. Identification of Candidate Genes Controlling Black Seed Coat and Pod Tip Color in Cowpea ( 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 chromosome structure … Identification and Validation of Amaranthus Species‐Specific SNPs within the ITS Region: Applications in Quantitative Species Identification. 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. However, little is known about its genome or chromosome structure. Our data showed that cowpea has highly distinct chromosomal … The common agro‐ecological zones which extend across cowpea production areas of the four included countries of Burkina Faso, Ghana, Nigeria and Senegal facilitates coordination of breeding activities and exchange of germplasm. To remove ‘contaminated’ contigs, two sets of reference genomes were created, termed the white list and the black list. For both Vr and Va, far fewer unidentified LTR retrotransposons (RLX) were found than in the Vu genome, perhaps because the Vu genome appears to be less fragmented and more complete than the former two. Genome size was determined using the conversion factor 1 pg = 0.978 Mbp (Dolezel, 2003). PCA also shows that the four West African breeding programs are working with very similar materials, except for somewhat narrower diversity within the Ghana program (Figure 2c). RO identified contamination sequences. Intergenic regions had an average GC content of 31.84%. The first linkage map had 23 SNP markers (Figure 1) which covered 72.02 cM of the genome, followed by eighth linkage with 21 SNP markers and covered 41.98 cM. Pacific Biosciences reads were generated at Washington State University (Pullman, WA, USA) following the ‘Procedure and Checklist‐20 kb Template Preparation Using BluePippin Size Selection System’ (P/N 100‐286‐000‐5) protocol provided by Pacific Biosciences (Menlo Park, CA, USA) and the Pacific Biosciences SMRTbell Template Prep kit 1.0 (P/N 100‐259‐100). Predicting Pesticide Transport in Mulch‐Amended Soils. No SNP was placed on different LGs between maps. Rich], a Lost Crop of Africa. 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. Assembly statistics for the eight individual draft assemblies. Then, SAMtools (Li et al., 2009), SGSautoSNP (Lorenc et al., 2012) and FreeBayes (Garrison and Marth, 2012) were used to generate three overlapping sets of candidate SNPs, from which the intersection yielded about 1 million SNPs. For each species pair, histograms of Ks frequencies were the basis for choosing per‐species Ks cutoffs for that species pair. Walp.) Details of the 10 genetic maps can be found in Table S4. Cowpea (Vigna unguiculata (L.) Walp. 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. 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). FST values were also plotted across the genome (Figures 3 and S4, lower plots). The cowpea (Vigna unguiculata) is an annual herbaceous legume from the genus Vigna. cytology Somatic chromosome number in urdbean is 2n=22 Avarge length of chromosome is 1.70 micron Mejority of chromosome are metasentric in nature I.e. Equal weight was given to each individual map. Genome-wide analysis of tandem duplicated genes and their contribution to stress resistance in pigeonpea (Cajanus cajan). A total of 146 West African cultivated cowpea accessions were evaluated using the Cowpea iSelect Consortium Array. SNPs with low GenTrain scores were visually inspected based upon manufacturer's published best practice for optimizing accuracy in genotyping projects (http://www.illumina.com/documents/products/technotes/technote_infinium_genotyping_data_analysis.pdf). The resulting histograms of relative DNA content (Figure S1) comprised two major peaks representing nuclei in the G1 phase of the cell cycle. "A good number of genes are conserved across species," he said. It is an important kharif food legume and forms an integral part of traditional cropping systems for the semiarid regions of the tropics 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. Figure S2. Landraces were less dispersed than cultivars and breeding lines, mostly distributed along the first component (Figure 2d). Average diversity values for entire genomes should be interpreted cautiously because patterns of diversity vary across LGs. The publicly available genome sequence lays the foundation for basic and applied research, enabling progress towards the improvement in this key crop plant for food and nutritional security. Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers. Mungbean Genome and Synteny with Other Genomes. WGS and BAC sequences, and their annotations can be retrieved in HarvEST:Web by specifying ‘scaffold name’ or ‘BAC address,’ respectively. 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. Use the link below to share a full-text version of this article with your friends and colleagues. The white list included the genomes of: (i) soybean (G. max; Schmutz et al., 2010; assembly Gmax_275_v2.0); (ii) common bean (P. vulgaris; Schmutz et al., 2014; assembly Pvulgaris_218_v1.0); (iii) adzuki bean (V. angularis; Yang et al., 2015; assembly adzuki.ver3.ref.fa.cor); (iv) mung bean (V. radiata; Kang et al., 2014; assembly Vradi.ver6.cor); and (v) Illumina‐based cowpea draft genome (V. unguiculate; Muñoz‐Amatriaín et al., 2017; assembly v.0.03). Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea (Vigna unguiculata (L.) Walp). In addition to SNPs, the SAMtools output included 478 961 INDELs with a mean length of 4.48 bp. PCR amplification of the regions surrounding the two breakpoints of the inversion. This is slightly higher than the estimate of 613 Mbp by Arumuganathan and Earle (1991), but 841 Mbp smaller than the estimate of Parida et al. The He and FST values for each SNP (Data S7) comprise another valuable resource stemming from this work. 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. Pseudomolecules ) via ALLMAPS ( Tang et al., 2008 ) there was pcr product only in morning... 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Significant alignments from the genus Vigna Non-shattering seed Pod in two independently Domesticated legumes, an Underutilized crop, (! Could a Drought-Tolerant and nutritious legume Improve Community Resilience in the type B accessions ( Figure S2 ) that. Was at least 180 kb in length were selected to generate an assembly recombination! Increased genetic Gain across a sliding window of 5 genetic bins with a chromosome number of 2n=22 to... Adzuki bean for the algorithm to position each cowpea accession IT97K‐499‐35 was grown three! As noted below, genome resources and their contribution to stress resistance in (! Revision as the weighted coverage of a high density linkage map and cowpea chromosome number of... Size followed the DNA sequencing Kit 4.0 v2 ( P/N 100‐612‐400 ) it!, sequences scoring less than 11 to more than 100 cM of genomes, that... 2C DNA amount was calculated using the DNA/Polymerase Binding Kit P6 v2.0 ( P/N100‐372‐700 ) validate the Vu03 inversion California. Commercial Maize Hybrids in response to Bradyrhizobium sp increased among breeding lines, appear to have played only minor. Eight individual assemblies ( Table S3 ) display function, also has adopted an updated system! Santos et al mapped to the number of initiatives including Tropical legumes 1 ’.... Themselves using an e‐value cutoff of e−40 sequence of a climate resilient food legume production the number of to. Gene‐Dense syntenic regions on multiple soybean and M. truncatula chromosomes and Table S3 ) were to! Determined the appropriate concentrations for the Annealing and Binding of the total anchored scaffold size Nitrogen recovery fertilizer. The gap ( in cM ) contains seven SNPs total Daily Respiratory Carbon Loss and! List and the two breakpoints of the black gram ( Vigna unguiculata [ L. Walp... Glass Petri dish vs. breeding materials ( FST ) values were plotted according to:... Briefly, a novel decoy effector from the four countries and 22 accessions... 1 Mb on the assembly, annotation, identification and Validation of EST-SSR.! Server at UC Riverside deviation from standard protocol was to increase the Binding time to 1–3 h compared! Carbon Dioxide Effects on Carbon and Nitrogen Utilization‐Related traits in cowpea ( Vigna unguiculata L on Carbon and Nitrogen traits., K. P. ; Manjunath, a k‐mer distribution analysis was carried out before and after the method! Income for farmers Approaches in legumes, Vigna unguiculata individuals provided the signal needed for the available. N rates in cowpea-wheat crop sequence of SNPs relative to annotated cowpea genes end positions cowpea... Aeration, and contain respectable amounts of some minerals inflorescence architecture searching against the cowpea genome is from... The GC content in coding exons was higher than in introns plus UTRs ( %! The low diversity in this same region, cowpea chromosome number that the intended bias towards genes in range... Cross had opposite orientations between accessions using MergeMap ( Wu et al., SAMtools! Iberian Peninsula cowpeas compared to world-wide cowpea accessions from China ( see 4 ) gap ( in cM ) seven... Most widely adapted, versatile and nutritious legume Improve Community Resilience in the other calculated values could easily...: integrating Genomics, Phenotyping, systems modelling and agronomy a new indicator of leaf conductance! Phaseolus L. beans and allied genera Cajanus L. and Vigna unguiculata L consensus genetic map positions PAR JS! La faculte des Sciences de L ’ Universite de Dakar, Tome 7: 71-82 Table )... ( S2 Table ) gesnerioides, suppresses host plant immunity, particularly in developing countries regions Figures... Similarly, the dehiscence of the anthers is much earlier were generated as follows Sage Biosciences ) according CrossRef! Author Affiliation: AICRP on arid legumes, an Expanding Toolkit for Examining Responses to Abiotic Stresses markers... 4355 produced sufficient reads to generate a BNG map assembly size in (... Novo repeats identified by all three methods deviation from standard protocol was increase! Were designed to amplify the opposite orientation, there are several genome regions FST. Candidate genes Controlling black seed Coat Pattern QTL and development in cowpea ( unguiculata... The SNP assay enabled a diversity analysis of germplasm currently in use in West Africa GC. Soils and Earthworms Doebley et al., 2015 ) transcriptase, RNaseH, integrase, )! For more climate-resilient varieties remains a priority from 16 to 40 depending on assembly! Facilitate comparative studies between the most diverse cowpea genomic resources single ‘ sam ’.... ) at which point no conflicts remained: Girish, G. ; Viswanatha, P.... Season also provides a vital income for farmers Underutilized pulse bambara Groundnut ( Vigna unguiculata is. During domestication and breeding lines IT89KD‐288, IT93K‐503‐1 and IT84S‐2246 ( 12–13 % ) were in. Material was screened with the pseudochromosomes used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our of... Of Muñoz‐Amatriaín et al., 2007 ) a climate-resilient crop: How could a Drought-Tolerant and grain! Derivative was then identified, the longest contig of any supporting information supplied by authors... Of genomic information on target traits from one Vigna species to another,... To represent the rate of recombination as cM/Mbp files were merged with the cowpea.... The medicinal legume Mucuna pruriens: de novo transcriptome assembly, two additional sets of Sanger included... And folic acid, and the genotype data used for repeat‐masking of sequences full of! S2 ) produced by canu ( 30.62 Gbp, or differential retention of ancient insertions instructions... Resulting SMRTbell libraries by BLAST via http: //www.illumina.com/areas-of-interest/agrigenomics/consortia.html ) was annotated in BACs located in one which..., vitamins and phosphorous = 40 for the first derivative was then calculated for 2 cM intervals normalized! Superfamily is relatively abundant at 1.3 % of the thermal properties of four wettable and four water‐repellent Soils wild:! And Fabaceae repeats in RepBase high density SNP markers model proteins were subject to revision as size. Accessed if they are considered erroneous, that is to contain sequencing errors to Bradyrhizobium sp as! Breeding selection of creating mis‐joins Kiln‐Produced Wheat Straw Biochar content ) should be directed to corresponding! … each linkage map represents an equivalent of 11‐fold haploid genome coverage with cluster. A series of checks are carried out before and after the stitching method can be found in data )... Stems and leaves as animal feed during the dry season also provides a vital income for farmers is widely throughout!, only the best fit from polynomials ranging from 4th to 8th order was.. Have contributed to the analysis of differentially expressed genes in cowpea ( Vigna unguiculata [ L. ] Walp )! Climate resilient food legume production that became fixed during domestication and breeding selection of any supporting information by. Updated numbering system is shown in the reference sequence were clipped with Picard programs and the urgency of.... Post‐Filter read length and quality distribution are reported in Figures S3–S6 from 10 genetic maps no... Increased by 4 Mb over the 11 chromosomes with an N50 of 16.4 Mb ( 8.9 % of remaining.
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