A Novel Root-Knot Nematode Resistance QTL on Chromosome Vu01 in Cowpea.

The root-knot nematode (RKN) species Meloidogyne incognita and M. javanica cause substantial root system damage and suppress yield of susceptible cowpea cultivars. The narrow-based genetic resistance conferred by the Rk gene, present in some commercial cultivars, is not effective against Rk-virulent populations found in several cowpea production areas. The dynamics of virulence within RKN populations require a broadening of the genetic base of resistance in elite cowpea cultivars. As part of this goal, F1 and F2 populations from the cross CB46-Null (susceptible) x FN-2-9-04 (resistant) were phenotyped for M. javanica induced root-galling (RG) and egg-mass production (EM) in controlled growth chamber and greenhouse infection assays. In addition, F[Formula: see text] families of the same cross were phenotyped for RG on field sites infested with Rk-avirulent M. incognita and M. javanica The response of F1 to RG and EM indicated that resistance to RKN in FN-2-9-04 is partially dominant, as supported by the degree of dominance in the F2 and F[Formula: see text] populations. Two QTL associated with both RG and EM resistance were detected on chromosomes Vu01 and Vu04. The QTL on Vu01 was most effective against aggressive M. javanica, whereas both QTL were effective against avirulent M. incognita Allelism tests with CB46 x FN-2-9-04 progeny indicated that these parents share the same RKN resistance locus on Vu04, but the strong, broad-based resistance in FN-2-9-04 is conferred by the additive effect of the novel resistance QTL on Vu01. This novel resistance in FN-2-9-04 is an important resource for broadening RKN resistance in elite cowpea cultivars

Identification of QTL controlling domestication-related traits in cowpea (Vigna unguiculata L. Walp)

[EN] Cowpea (Vigna unguiculata L. Walp) is a warm-season legume with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea domestication involved considerable phenotypic changes from the wild progenitor, including reduction of pod shattering, increased organ size, and changes in flowering time. Little is known about the genetic basis underlying these changes. In this study, 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, days to flowering, 100-seed weight, pod length, leaf length, leaf width and seed number per pod). A high-density genetic map containing 17,739 single nucleotide polymorphisms was constructed and used to identify 16 quantitative trait loci (QTL) for these nine traits. Based on annotations of the cowpea reference genome, genes within these regions are reported. Four regions with clusters of QTL were identified, including one on chromosome 8 related to increased organ size. This study provides new knowledge of the genomic regions controlling domestication-related traits in cowpea as well as candidate genes underlying those QTL. This information can help to exploit wild relatives in cowpea breeding programsSIThis work was supported by grants from the Generation Challenge Program (TL1), the Feed the Future Innovation Lab for Climate Resilient Cowpea (Cooperative Agreement AID-OAA-A-13-00070), and the NSF BREAD project “Advancing the Cowpea Genome for Food Security’’ (Award #1543963)’’. Partial support was also provided by the Hatch Project CA-R-BPS-5306-H. Sassoum Lo was supported by funds from the West Africa Agricultural Productivity Program. We thank the International Institute of Tropical Agriculture for the RIL population. We also thank Abdou Souleymane (INRA, Niger) for helping to identify the wild parent, Stefano Lonardi and Steve Wanamaker (University of California Riverside, USA) for the cowpea genome sequence and annotations, and Dr. Paul Gepts (University of California Davis, USA) for his valuable input

The UCR Minicore: a resource for cowpea research and breeding

Special Issue on Legume Genomics[EN] Incorporation of new sources of genetic diversity into plant breeding programs is crucial for continuing to improve yield and quality, as well as tolerance to abiotic and biotic stresses. A minicore (the “University of California, Riverside (UCR) Minicore”) composed of 368 worldwide accessions of cultivated cowpea has been assembled, having been derived from the UCR cowpea collection. High-density genotyping with 51,128 SNPs followed by principal component and genetic assignment analyses identified six subpopulations in the UCR Minicore, mainly differentiated by cultivar group and geographic origin. All six subpopulations were present to some extent in West African material, suggesting that West Africa is a center of diversity for cultivated cowpea. Additionally, population structure analyses supported two routes of introduction of cowpea into the U.S.: (1) from Spain to the southwest U.S. through Northern Mexico and (2) from Africa to the southeast U.S. via the Caribbean. Genome-wide association studies (GWAS) narrowed several traits to regions containing strong candidate genes. For example, orthologs of the Arabidopsis FLOWERING LOCUS T lie within a major QTL for flowering time. In summary, this diverse, yet compact cowpea collection constitutes a suitable resource to identify loci controlling complex traits, consequently providing markers to assist with breeding to improve this crop of high relevance to global food and nutritional securitySIThis research was funded by the Feed the Future Innovation Lab for Climate Resilient Cowpea (USAID Cooperative Agreement AID-OAA-A-13-00070), the National Science Foundation BREAD project “Advancing the Cowpea Genome for Food Security” (NSF IOS-1543963), Hatch Project CA-R-BPS-5306-H. Also, M.C., I.C., and V.C. were supported by National Funds from FCT-Portuguese Foundation for Science and Technology under the project grant number UIDB/04033/202

A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns

[ENG] Herbivory is fundamental to the regulation of both global food webs and the extent of agricultural crop losses. Induced plant responses to herbivores promote resistance and often involve the perception of specific herbivore-associated molecular patterns (HAMPs); however, precisely defined receptors and elicitors associated with herbivore recognition remain elusive. Here, we show that a receptor confers signaling and defense outputs in response to a defined HAMP common in caterpillar oral secretions (OS). Staple food crops, including cowpea (Vigna unguiculata) and common bean (Phaseolus vulgaris), specifically respond to OS via recognition of proteolytic fragments of chloroplastic ATP synthase, termed inceptins. Using forward-genetic mapping of inceptin-induced plant responses, we identified a corresponding leucine-rich repeat receptor, termed INR, specific to select legume species and sufficient to confer inceptin-induced responses and enhanced defense against armyworms (Spodoptera exigua) in tobacco. Our results support the role of plant immune receptors in the perception of chewing herbivores and defenseSIGenotyping of cowpea accessions was supported by the Feed the Future Innovation Laboratory for Climate Resilient Cowpea (US Agency for International Development Cooperative Agreement AID-OAA-A-13-00070). OS analyses were supported by European Research Council Advanced Grant 788949. Research in the C.Z. laboratory was supported by The Gatsby Charitable Foundation and the Biotechnology and Biological Research Council (BB/P012574/1

The genome of cowpea (Vigna unguiculata [L.] Walp.)

[EN] Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. 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 and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. 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. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presentedS

Mapping Domestication-Related Traits and QTL Pyramiding in Cowpea [Vigna unguiculata (L.) Walp]

Cowpea (Vigna unguiculata [L.] Walp) is one of the most important food and nutritional security crops. It is one of the main sources of dietary protein and folic acid for millions of people in sub-Saharan Africa and other parts of the developing world. Cowpea is a diploid (2n = 22) with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea was domesticated in Africa, from where it spread into all continents and now is commonly grown in many parts of Asia, Europe, United States and Central and South America. Domestication of cowpea has, in general, resulted in a determinate growth habit, increased pod and seed size, early flowering, and reduction of pod shattering. However, the genetic control of these traits is largely unknown. This lack of domestication-related knowledge in cowpea has limited the utilization of broad germplasm for crop improvement. This dissertation investigates the genetic basis of domestication traits using recently developed genetic and genomic resources available for cowpea and studies the effect of two seed size loci in a different genetic background. In the first chapter, regions of the cowpea genome that played an important role in cowpea domestication were identified. A total of 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, days to flowering, 100-seed weight, pod length, leaf length, leaf width and seed number per pod). A high-density genetic map containing 17,739 single nucleotide polymorphisms was constructed and used to identify 16 quantitative trait loci (QTLs) for these nine traits. Four regions were identified showing QTL clustering for these traits, including one region on Vu08 where four QTLs related to increased organ size (seed weight, pod length, leaf length and leaf width) were mapped. Using sequence homology comparison with common bean, a candidate gene (Vigun08g217000) for increased organ size was identified. This gene codes for a histidine kinase 2 and the Arabidopsis ortholog AHK2 (AT5G35750.1) has been shown to regulate, among other things, plant organ size. The second chapter investigates the genetic basis of seed size, which is a main domestication target and one of the key yield determinants. A “mini-core” panel of 368 genetically diverse cowpea accessions, mainly landraces, was used to evaluate four seed size-related traits (seed weight, length, width, and density). A genome-wide association study (GWAS) and meta-analysis identified 17 loci associated with seed size. One locus was common to weight, width and length, suggesting pleiotropy. By integrating synteny based-analysis with common bean, six candidate genes (Vigun05g036000, Vigun05g039600, Vigun05g204200, Vigun08g217000, Vigun11g187000, and Vigun11g191300) which are implicated in multiple functional categories related to seed size were identified. In the third chapter, two seed size QTLs were targeted for introgression in the background of a popular cultivar from Senegal “Pakau”. Four combinations of the positive (large seed size) alleles of the two QTL were observed in the backcross progenies and were analyzed to test the effect on seed phenotype of these QTL in the Pakau genetic background: no positive QTL alleles, positive allele of Css-1 only, positive allele of Css-4 only, and positive alleles of both QTL.The results of this dissertation provide a basis for further fine mapping of genes controlling domestication traits and a foundation for the utilization and exploitation of diverse landraces and wild relatives in cowpea breeding programs

Pod shattering in grain legumes: emerging genetic and environment-related patterns.

A reduction in pod shattering is one of the main components of grain legume domestication. Despite this, many domesticated legumes suffer serious yield losses due to shattering, particularly under arid conditions. Mutations related to pod shattering modify the twisting force of pod walls or the structural strength of the dehiscence zone in pod sutures. At a molecular level, a growing body of evidence indicates that these changes are controlled by a relatively small number of key genes that have been selected in parallel across grain legume species, supporting partial molecular convergence. Legume homologs of Arabidopsis thaliana silique shattering genes play only minor roles in legume pod shattering. Most domesticated grain legume species contain multiple shattering-resistance genes, with mutants of each gene typically showing only partial shattering resistance. Hence, crosses between varieties with different genes lead to transgressive segregation of shattering alleles, producing plants with either enhanced shattering resistance or atavistic susceptibility to the trait. The frequency of these resistance pod-shattering alleles is often positively correlated with environmental aridity. The continued development of pod-shattering-related functional information will be vital for breeding crops that are suited to the increasingly arid conditions expected in the coming decades