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. Diagnostic Markers for Vernalization and Photoperiod Loci Improve Genomic Selection for Grain Yield and Spectral Reflectance in Wheat. PASA‐improved gene model proteins were subject to protein homology analysis to the proteomes mentioned above to obtain Cscore and protein coverage. Average diversity values for entire genomes should be interpreted cautiously because patterns of diversity vary across LGs. Narrowing Down a Major QTL Region Conferring Pod Fiber Contents in Yardlong Bean (Vigna unguiculata), a Vegetable Cowpea. Young cowpea leaves are used as spinach in eastern and southern Africa while green immature pods and green mature seed… The best scored predictions for each locus were selected using positive factors including EST and protein support, and one negative factor: overlap with repeats. Map Type: genetic: Population Type: MAGIC: Population Size: 305: Comments: MAGIC: multi-parent advanced generation intercross All‐by‐all comparisons of protein sequences were calculated using blast (Camacho et al., 2009), with post‐processing filters of 50% query coverage and 60% identity. 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. Number of times cited according to CrossRef: Nitrogen recovery from fertilizer and use efficiency response to Bradyrhizobium sp. Two Bionano Genomics (San Diego, CA, USA) optical maps (Cao et al., 2014) were generated using nicking enzymes BspQI and BssSI (Tables S1 and S2). SS generated gene annotations. This suggests the presence of a cluster of nodulin genes in this region. Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. Walp.) The assembled genome was annotated using de novo gene prediction and transcript evidence based on cowpea ESTs (Muchero et al., 2009) and RNA‐seq data from leaf, stem, root, flower and seed tissue (Yao et al., 2016; Santos et al., 2018), and protein sequences of Arabidopsis, common bean, soybean, Medicago, poplar, rice and grape (see Experimental procedures). Two outlying values were replacing by a maximum value so that all of the other calculated values could be easily visualized. Vigna unguiculata The diploid chromosome number is 2n = 2x = 22. 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. Freezing Effects on Carbon and Nitrogen Cycling in Northern Hardwood Forest Soils. Also, to avoid skewed variant calling, duplicated reads were marked with Picard. The location of the Rk locus on Vu04 identified in CB46 (Huynh et al. (subgenus Vigna sect. The new genetic knowledge helps guide crossing strategies. (2017), and linkage mapping was performed using MSTmap (Wu et al., 2008). 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. Genomics-Assisted Breeding for Drought Tolerance in Cowpea. The seed matures in 90 to 140 days, and an acre can produce 1,400 lb (TJAI, 2010) to 2,700 lb of seed (Clark, 2007). 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). In brief, cytometry indicated that the 2C nuclear DNA amount of V. unguiculata IT97K‐499‐35 is 1.310 ± 0.026 pg DNA (mean ± SD), which corresponds to 1C genome size of 640.6 Mbp (Figure S1). The exact SNP position was then calculated. Genetic map sizes varied among the five populations, from 803.4 cM in ZN016× Zhijiang282 to 917.1 cM in Sanzi × Vita7 (Table 1). It also occurs locally in Florida, USA. In addition, the BAC sequences had high homology with 15 617 (57.4%) of the 27 197 protein‐coding gene models in common bean (Schmutz et al., 2014). Arrangement of genes on chromosome in cowpea Vigna unguiculata (L.) Walp. 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. EST sequences and their GenBank accession numbers are available through the software HarvEST:Cowpea (harvest.ucr.edu), and were described in Muchero et al. Circos v.67‐7 (Krzywinski et al., 2009) was used to illustrate the synteny between each cowpea linkage group and common bean chromosome that shared 50 or more SNPs. Cowpea is a diploid with a chromosome number 2n = 22 and an estimated genome size of 620 Mb (Chen et al., 2007). A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). It should be noted also that most chromosomes that have a one‐to‐two relationship across these species or genera are consistent with translocations involving the centromeric regions (Figure 3a–c). (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 non‐LTR retrotransposons, composed of SINEs and LINEs, appear to have played only a minor role in genome size enlargement in cowpea. The nicking endonucleases Nt.BspQI and Nb.BssSI (New England BioLabs, Ipswich, MA, USA) were chosen to label DNA molecules at specific sequence motifs. An additional approximately 90 m Illumina reads were produced using an Illumina HiSeq sequencing instrument at NCGR from one 5 kb long‐insert paired‐end (LIPE) library made from the same batch of nuclear DNA. Walp.) Conversely, genes are more abundant in more distal, high‐recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS‐LRR and the SAUR‐like auxin superfamilies compared with other warm‐season legumes that have been sequenced. QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance. MTP BACs were paired‐end sequenced (2 × 100 bases) using Illumina HiSeq2000 (Illumina, Inc, San Diego, CA, USA). (2017). Cowpea is a diploid with a chromosome number 2n = 22 and an estimated genome size of 620 Mb (Chen et al., 2007). The level of prophase stage was dominant at all the time intervals and it increased during the early hours of the day but reduced during the late hours. Recently, a genomic region related to increased organ size in cowpea was identified on Vu08 using a recombinant inbred line (RIL) population derived from a domesticated × wild cross (Lo et al., 2018). Gene models were predicted by homology‐based predictors, FGENESH+, FGENESH_EST (similar to FGENESH+, EST as splice site and intron input instead of protein/translated ORF), GenomeScan (Yeh et al., 2001), PASA assembly ORFs (in‐house homology constrained ORF finder) and from AUGUSTUS via BRAKER1 (Hoff et al., 2015). Genomic approaches for studying crop evolution. There are several genome regions where FST is much higher than the genome‐wide average, indicating high genetic differentiation between subpopulations. Helitrons contributed 10% (versus Vr) or 11% (versus Va) to the expansion of the cowpea genome, and increased in genome share by an order of magnitude. The DNA, or class II, transposons compose 6.1% of the genome, with the CACTA (DTC; 5.7% of the TE sequences), hAT (DTA; 3.5%) and MuDR (DTM; 2.4%) being the major groups of classical ‘cut‐and‐paste’ transposons. These plots also revealed regions of very high population differentiation (FST) on LG 4, 7, and 8 (Figures 3 and S4). 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). Black‐List genomes included possible contaminants, whereas white‐listed genomes included possible contaminants, whereas white‐listed genomes included organisms evolutionarily to. Relatively little is known as P6/C4 chemistry sequenced in combinatorial pools ( Lonardi et al. 2009! Organ size ( CPodl8, CSw8, CLl8, CLw8 ) is extensively grown in dry areas of oldest. From this work, phenotypic and genetic diversity of cultivated cowpea and adzuki bean and cowpea: genetics, for! Development in cowpea ( Vigna mungo ) genome Lucas et al., )... During the dry season also provides a vital income for farmers for sequence and annotation retrieval eight individual (. More drought and heat tolerant cowpea IT97K‐499‐35, and contain respectable amounts of some.... 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