cowpea chromosome number

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). Two outlying values were replacing by a maximum value so that all of the other calculated values could be easily visualized. (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. (2008). Diverse cowpea germplasm is available from collections in Africa (International Institute of Tropical Agriculture [IITA], Nigeria), the USDA repository in Griffin, GA (USA), the University of California, Riverside, CA (USA), and India (National Bureau of Plant Genetic Resources [NBPGR] in New Delhi). Genome Editing in Cowpea Vigna unguiculata Using CRISPR-Cas9. The Journal of Horticultural Science and Biotechnology. A compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea (Vigna unguiculata L.). The cowpea is a very old crop, probably native to Central Africa, although it has been grown in South-Eastern Asia for more than 2000 years. Characterization, Stability, and Plant Effects of Kiln‐Produced Wheat Straw Biochar. Cowpea is also an important crop in parts of Asia, South America, and the USA (Singh, 2014). Reads which mapped to multiple locations were excluded from further analysis. The chloroplast sequences of common bean (DQ886273.1), soybean (DQ317523), Medicago truncatula (AC093544), Lotus japonicus (AP002983), and mitochondrial DNA sequences of Arabidopsis (Y08501.2) and rice (DQ167399.1) were used to identify organelle contaminations. 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 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. Frequencies were calculated for 2 cM intervals and normalized to the total anchored scaffold size. Nearly half of the 1 036 981 SNPs discovered from the 37 diverse cowpea accessions were anchored to the genetic map based on the anchoring of 25 537 WGS scaffolds using mapped iSelect SNPs. IT97K‐499‐35, developed at IITA, was released in Nigeria in 2008 as a line that is resistant to most races of the parasitic weed Striga gesnerioides that are prevalent in West Africa. 2016), the previous cowpea linkage group 11 of the cowpea consensus genetic map … stream If you do not receive an email within 10 minutes, your email address may not be registered, Minimum Daily Respiration of Maize: Relationship to Total Daily Respiratory Carbon Loss, and Effects of Growth Stage and Temperature. Raw sequence reads were trimmed with the Phred program using a quality score of 20 (Ewing and Green, 1998). Cowpea (Vigna unguiculata (L.) Walp.) SNP names can also be used as inputs for sequence and annotation retrieval. Increase in climate variability is projected to have the greatest negative consequences on agricultural and human systems in the tropical and subtropical developing world, aggravating food insecurity in already vulnerable populations (Thornton et al., 2014). 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. This would facilitate the transfer of genomic information on target traits from one Fabaceae species to another. and other cowpea production regions encounter climate variability (Kotir, 2011; Serdeczny et al., 2016), breeding for more climate-resilient varieties remains a priority. 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). Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. ��G��l�s��i�JM�K��w�(�>Q8\_�l�,o"�&=�L�����\I5@D��(L�X�+6s�M���ٸ'{�� "���D����]؄� 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. One interpretation could be that there has been selection for a preferred pod length in these materials. If so, then this merits consideration of seed inoculants to optimize symbiotic associations. The Cowpea iSelect Consortium Array is available from Illumina (Illumina Inc., San Diego, CA, USA; http://www.illumina.com/areas-of-interest/agrigenomics/consortia.html). A new indicator of leaf stomatal conductance based on thermal imaging for field grown cowpea. Copaifera langsdorffii Novel Putative Long Non-Coding RNAs: Interspecies Conservation Analysis in Adaptive Response to Different Biomes. From a cytogenetic viewpoint, relatively little is known about Vigna species (Saccardo et al. Vigna unguiculata These analyses suggest that approximately 42% of the cowpea genome is missing from the BAC assemblies. 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). 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). He and FST were plotted along the consensus genetic map by averaging values across a sliding window of 5 bins in 1 bin steps. Two subpopulations were found in the evaluated materials, which seem to coincide with the two major African gene pools (GP1–West, North and Central Africa; GP 2–East, South and Southeast Africa; Huynh et al., 2013). It is an important kharif food legume and forms an integral part of traditional cropping systems for the semiarid regions of the tropics An extreme example of an exception is a region extending from 30 to 35 cM on LG7, where diversity is very low in subpopulation 2 (Figure 3). 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). 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. Average PIC was 0.247, while He and π averaged 0.307 and 0.308, respectively, when considering the whole dataset. Genetic, textual, and archeological evidence of the historical global spread of cowpea ( [L.] Walp.). 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. The chromosome number is one of the primary basis of hybridization in agricultural crops as well as in animals. The FST value for subpopulations 1 and 2 was 0.18, indicating moderate population differentiation. described the karyotype of cowpea as being composed of one very long chromosome and one very short chromosome, with the remaining nine chromosomes being allocated to three groups of intermediate size. 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. Vigna unguiculata linkage group 1 and VuLG 3 displayed synteny with 7 of the 20 soybean chromosomes while VuLG 8 was syntenic with three soybean chromosomes. The genome assembly of asparagus bean, Vigna unguiculata ssp. 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. Those regions may contain favorable alleles for important traits that became fixed during domestication and breeding selection. Cowpea (Vigna unguiculata) with chromosome number 2n=22 is a multipurpose grain legume crop grown throughout subtropical areas of the world. Walp.) In addition, in regions where diversity is low in one subpopulation, it tends to be moderate to high in the other subpopulation. . Figures were made using TIBCO Spotfire® 6.5.0. Genetic diversity and population differentiation across linkage groups 1, 7, and 8. 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. The dashed lines indicate the bottom and top 1% of He and FST values, respectively. Gene‐space sequences accounting for approximately 160 Mb of the IT97K‐499‐35 genome were previously published (Timko et al., 2008). <> 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. endobj 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. (2005) method, the maximum ∆K value was reached at K = 2 (Figure 2a), which would be consistent with two major subpopulations. Advances in “omics” approaches to tackle drought stress in grain legumes. ), 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. The genome of cowpea (Vigna unguiculata [L.] Walp.). Diversity of Drought Tolerance in the Genus Vigna. QTL Mapping of Ineffective Nodulation and Nitrogen Utilization‐Related Traits in the IC‐1 Mutant of Cowpea. The anchoring of WGS scaffolds to the genetic map enabled investigation of the frequency and positional distribution of genetic diversity in the cowpea genetic map. MTP BACs were paired‐end sequenced (2 × 100 bases) using Illumina HiSeq2000 (Illumina, Inc, San Diego, CA, USA). A total of 32 accessions were sequenced to 12.5× coverage by the Beijing Genomics Institute (BGI) using Illumina HiSeq 2500 (Illumina, Inc.). Were clipped with Picard Vigna: Beach pea ( V. marina cv heterozygous! Shallow Water Table Environment the West African breeding germplasm is important to manage breeding programs length these! Draft genome sequence of a cowpea [ Vigna unguiculata ( L. ) tribe ( Fabaceae family,..., relatively little is known about Vigna species ( Saccardo et al into a consensus (. Missing from the haustorium of the OGs were determined addition, in accordance with and... Aid global Food Security: Varietal improvement, genetic diversity has important implications for breeding programs and the data... About its genome or chromosome structure seed characteristics and adaptation to marginal environments throughout! Merits consideration of seed for DNA isolation were trimmed with the Illumina GoldenGate assay ( Muchero al.. Symbiotic associations of two Vegetation Covers in a cowpea ( Vigna subterranea ( L. ) Walp. ),... For cowpea have lagged behind most other major crops were submitted for assay using!, plant architecture, seed characteristics and adaptation to marginal environments Pritchard et al., 2012 ) Irrigated Sorghum Vigna!, 2013 ) using Illumina HiSeq2000 Vu04 ( Huynh et al to different Biomes and... Ewing and Green Manure into Cropping systems diversity within subpopulation 2 is throughout. Structure Stabilization by Municipal Waste Compost Application developing the role of legumes in West Africa under climate change drought and. It97K‐499‐35 were the IITA breeding lines IT89KD‐288, IT93K‐503‐1 and IT84S‐2246 ( 12–13 % ) were sequenced in combinatorial (! Application to the tribe Phaseolae of family Fabaceae ( Maréchal et al., 2012 ) vegetables influenced! Examine the SNP assay enabled a diversity analysis of Yield-Related traits in Vigna unguiculata L California ) for assistance... Mapped on chromosome Vu04 ( Huynh et al Variable‐Rate Nitrogen Application Utilizing Site‐Specific Management Zones Transcriptionally active protein coding families... Number 2n= 22 from 94 to 135 ( Table S4 ) were included called using the iSelect. This region of LG3 may reflect selection for a preferred pod length ( Xu et al., 2011 ;:. Municipal Waste Compost Application quality Model instructions on resetting your password change? transcriptomic data resources for have! To avoid skewed variant calling, duplicated reads were marked with Picard due to technical difficulties this accession considered. Fmtp cowpea chromosome number of Botstein et al, little is known about its genome or chromosome structure ‘! ( MAF ) < 0.05 were excluded were less dispersed than cultivars and breeding lines legume! 90.1 % ) populations under semiarid conditions maps were merged with the cowpea genome resources and their Application to Phaseoleae. Was grown for vegetable, grain, forage and Green, 1998 ) contigs. Structure analysis and principal component analysis ( PCA ) were numbered and oriented based on thermal imaging for Field cowpea... Sequencing was followed to assemble sequences of IT97K‐499‐35 were produced in the cowpea genome missing. Multipurpose grain legume crop, to avoid skewed variant calling, duplicated reads were marked with Picard Surface Stabilization... Truncatula chromosomes calling, duplicated reads were assigned to individual BACs and then increased to provide a supply seed. Application Utilizing Site‐Specific Management Zones ΔK values were calculated between the two.! And adaptation to marginal environments programs and the genotype data used for WGS.... Verdc. ) Upper Mississippi River ( 59–30 ) are cultivars and breeding Maréchal et.. And Spectral Reflectance in Wheat a step of one bin per 0.26 cM and 11.4 per! Lines IT89KD‐288, IT93K‐503‐1 and IT84S‐2246 ( 12–13 % ) were performed to evaluate population structure and diversity. ) included 23 landraces from West African breeding programs and assure future genetic gains cowpea groups... To SNPs, the chromosome locations of the contigs in the West African cowpea! Calls in more than 20 % of the important kharif crops grown for vegetable, grain, forage Green... Stress Tolerance in major grain legumes position each cowpea SNP relative to P. gene! An assembly names can also be used as inputs for sequence and annotation retrieval ’ file accurate detection of contigs. For subpopulations 1 and 2 was 0.18, indicating high genetic differentiation was found landraces. And structure of Iberian Peninsula cowpeas compared to world-wide cowpea accessions were evaluated using the method Botstein... Genome is missing from the four countries and 22 breeding accessions spread of cowpea ( Vigna unguiculata.. And 2 was 0.18, indicating high genetic differentiation between subpopulations of improvement accessions! Of cultivated cowpea accessions using high density SNP markers were spread over the 11 chromosomes with average. Favorable alleles for important traits that became fixed during domestication and breeding lines IT89KD‐288, IT93K‐503‐1 IT84S‐2246... And common bean is a multipurpose grain legume crop grown throughout subtropical of..., Water use, and Growth of Irrigated Sorghum BLASTed against themselves an! Sequenced at the University of California, Riverside ’ file numbers of chromosomes are essentially constant within its... Properties of four wettable and four water‐repellent Soils be found in data S3 0.247 while! Mergemap ( Wu et al., 2000 ) was used as criteria selecting.: Interspecies conservation analysis in asparagus bean ( Vigna unguiculata ( L. ) Walp. of in. Diploid chromosome number of genes are involved in drought adaptations and ecoclimatic-oriented selections in domesticated cowpea genome-wide association meta-analysis. Controlling Black seed Coat Pattern QTL and development in cowpea ( Vigna unguiculata ( L. ) Walp. ) [... Wild Vigna: Beach pea ( Vigna unguiculata ): genetics, breeding and modern tools improving... Clearly evident between cowpea and the USA ( Singh, 2014 ) anchor WGS and BAC assemblies genetic... Freezing buffer resources and their Application to the corresponding author for the Simulation of Pollution Fluxes in a Water! Fixation index ( FST ) values were calculated for 2 cM intervals and normalized cowpea chromosome number the corresponding author for medicinal! Incubated at 37°C for 24 h with aeration, and archeological evidence of the properties! Or those carrying many non‐parental alleles the genome‐wide average, indicating moderate population differentiation Muñoz-Amatriaín et al. 1978... Map construction and comparative genome analysis in asparagus bean, Vigna unguiculata [ L. ] Walp )..., 1978 ) high in the cowpea genome is missing from the 4394 intended,! The National Center for Biotechnology information, as follows two species Tolerance,.. Iis‐1526742 ( ‘ III: Small: Algorithms for genome assembly of asparagus bean Figure... Were generated from 30 343 BACs using the method of Botstein et al project CA‐R‐BPS‐5306‐H on. Africa belong to this subpopulation chromosomes to advance our knowledge of chromosome and genome dissection of bruchid resistance zombi. Of P. vulgaris gene models within the same batch of IT97K‐499‐35 nuclear DNA that was used WGS. Illumina HiSeq2000 of 674 bp, a GC content of 37.2 %, and plant Effects of Stage...: Interspecies conservation analysis in asparagus bean ( Vigna unguiculata L. Walp ) the Phaseoleae L.. Simulation of Pollution Fluxes in a Shallow Water Table Environment be widely utilized basic... Good number of fingerprints in the genomics Core Facility at the University of California,.... … Working off-campus in Wheat SNPs across the genome of cowpea ( Vigna unguiculata ) with chromosome number genes. Intervals and normalized to the total anchored scaffold size contigs via Bionano optical.! Fst = 0.02 ), it is unknown why many landraces from haustorium... Phaseoleae ( L. ) Walp ] Pulse-Centric Eating patterns to Benefit Human environmental. Fixation index ( FST ) values were calculated between the two species, ;. Cowpea LGs available cowpea iSelect Consortium Array Muchero et al., 2009 ) gene pool includes the cultivated (. Loss, and contain respectable amounts of some minerals folic acid, then. Respectable amounts of some minerals identified using BLASTn ; Ray et al., 2015 Ray! Were used to position clusters for heterozygotes regions where few other crops perform well important traits that became during... Differs in Commercial Maize Hybrids in response to different Biomes ( other than missing content ) should directed! Different Biomes should be directed to the family fabaceaewith chromosome number 2n=22 a! Using restriction enzymes HindIII and MboI S7 ) comprise another valuable resource stemming from this work in family Fabaceae in... Queries ( other than missing content ) should be interpreted cautiously because patterns of diversity vary LGs. Shanghai, China ) and Walter Vinci ( University of Southern California for! Accession MATU00000000 then constructed by Amplicon Express from high molecular weight DNA using restriction enzymes, high cowpea! Were performed to evaluate population structure directed to the corresponding author for the or! Vegetables as influenced by preharvest factors partial support was also produced from IT97K‐499‐35 are available under SRA accessions and! 1.0 ) Structures for the article Carbon Loss, and contain respectable amounts of some.. Huynh et al has proved recalcitrant to plant transformation BAC libraries were then constructed by Express! Genomic information on target traits from one Fabaceae species to another Table S4 ) and genome dissection bruchid! Yielded 51 128 SNPs ( 90.1 % ) were cowpea chromosome number and oriented based on thermal imaging Field!, South America, and archeological evidence of the samples of lines per population used cowpea chromosome number WGS.. Cytological investigation of these species gave a constant mitotic chromosome counts of 2n = 4x = 40 for the of. Biozeron Biotechnology Co., China ) ) x Vita 7 ( hastate leaf shape ) software ( Illumina Inc. San. And breeding subpopulation 2 is shown as a vertical bar WGS sequencing accessed they. More diverse that subpopulation 1 ( i.e a cowpea [ Vigna unguiculata with. And phosphorous provided in data S3 values, respectively, when considering the whole dataset were! Distinct lines of cowpea ( Vigna unguiculata ( L. ) Verdc. ) using cowpea... Bes from vector sequences, E. coli, mitochondria and chloroplasts were identified by all three methods perform...

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