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

Genome Resources for Climate‐Resilient Cowpea, an Essential Crop for Food Security

Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought‐prone climates, and a primary source of protein in sub‐Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K‐499‐35 include a whole‐genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. 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. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited‐input small‐holder farming and climate stress

Synthèse de nouveaux additifs phosphones incorporés dans des revêtements organiques pour la protection des surfaces métalliques

L objectif de cette thèse est la synthèse de nouveaux additifs phosphonés pour améliorer l adhésion des revêtements organiques sur les substrats métalliques. La masse molaire moyenne de ces additifs est de l ordre de 2000g/mol, et leurs températures de transition vitreuse sont proches de l ambiante. Nos recherches se sont orientées vers des terpolyméres et des cotéloméres méthacryliques phosphonés. En effet la télomérisation du méthacrylate de méthyle (MMA), du méthacrylate de butyle (MABu) et méthacrylate d isocyanatoéthyle (IEM) par le benzènethiol a permis d obtenir des terpolyméres méthacryliques. Ensuite, sur ces terpolyméres nous avons greffé des alcools phosphonés sur les fonctions isocyanates apportées par l IEM. D autre part nous avons synthétisé un nouveau méthacrylate phosphoné (MP) qui a été terpolymérisé avec le MMA/MABu par le benzènethiol. La synthèse de cotéloméres MMA et MABu par télomérisation avec des mercaptans fonctionnalisés par des groupements phosphonés a été étudiée. Après clivage les mono et diacides phosphoniques issus du clivage des esters des terpolymères et cotéloméres, ont donné lieu à des formulations de revêtements organiques déposés sur des substrats métalliques. Des cinétiques de migration suivies par analyses EDX, et des tests d adhésion et de corrosion au brouillard salin ont été réalisés. Il faut laisser reposer ces formulations sur les surfaces métalliques pour avoir une migration effective des atomes de phosphore vers l interface revêtement-métal. Les revêtements contenant des acides phosphoniques (IV , n) et (IV , n) tiennent jusqu à 1150 heuresThe purpose of this thesis is the synthesis of new phosphonated additives to improve the adhesion of organic coatings onto metallic substrates. The average molecular weight of these additives is about 2000g/mol and their glass transition temperatures are close to ambient. The research was oriented towards methacrylic phosphonated terpolymers and cotelomers. Indeed, the telomerization of methyl methacrylate (MMA), butyl methacrylate ( BuMA) and isocyanato ethyl methacrylate (IEM) with benzenethiol allowed to obtain methacrylic terpolymers. Then, phosphonated alcohols were grafted on these terpolymers, onto the isocyanate functions brought by IEM. Moreover, a new phosphonated methacrylate (PM) was synthethized and it was terpolymerized with MMA/BuMA, by benzenethiol. The synthesis of MMA and BuMA cotelomers by telomerization with mercaptans functionalized by phosphonated groups was studied. After cleavage the mono and di phosphonic acids issued from the cleavage of the esters on telomers and cotelomers were used in formulations of organic coatings deposited on metallic substrates. Kinetics of migration, followed by EDX analyses and tests of adhesion and corrosion to salt spray fog were realized. These formulations must be left and rest on the metallic surface to get an effective migration of the phosphorus towards the coating-metal interface. Coatings containing phosphonics acid (IV , n) and (IV , n) resist up to 1150 hoursMONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Isocyanatoethyl Methacrylate Telomerization and Cotelomerization

This article describes the use of isocyanatoethyl methacrylate (IEM) as a monomer in telomerization and cotelomerization reactions. First, the selectivity of benzenethiol addition to the unsaturation of IEM is proven. Even with an equimolar amount of reactants, benzenethiol reacts almost selectively with the ethylenic double bonds. The radical telomerization of IEM and its cotelomerization with MMA, in the presence of benzenethiol, has been achieved and shows that control of molecular weight is possible. Finally, the addition of a phosphonated alcohol to these telomers, followed by ester cleavage reactions, leads selectively to families of mono or diphosphonate products. The study of the thermal properties of the cotelomers shows that the degradation starts at 180 8C on the isocyanate group of IEM, and then on the ester group of MMA, and the decomposition is complete at 450 8C. The introduction of the phosphonated ester group decreases the glass transition temperature of the cotelomers, but after hydrolysis these values increase. O. A. Lam, Y. Hervaud, B. Boutevin Laboratoire de Chimie Macromole´culaire UMR-CNRS-5076, Ecole Nationale Supe´rieure de Chimie de Montpellier, 8 rue de l'Ecole Normale 34296 Montpellier cedex 5, France E-mail: [email protected] 356 Macromol. Chem. Phys. 2007, 208, 356–363 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim DOI: 10.1002/macp.20060035

Genomic tools in cowpea breeding programs: status and perspectives

Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved varieties available to farmers, thereby boosting cowpea production and productivity in SSA

Genomic Tools in Cowpea Breeding Programs: Status and Perspectives.

Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved varieties available to farmers, thereby boosting cowpea production and productivity in SSA

SNP genotypes of the international institute of tropical agriculture Cowpea Core

Cowpea (Vigna unguiculata [L.], Walp.) is a member of the family Fabaceae, subfamily Faboideae (a.k.a. Papillionoideae) and tribe Phaseoleae, along with other "warm season" legumes such as soybean, common bean, mung bean, adzuki bean, Bambara groundnut and others. The International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria maintains the world's largest collection of cowpea germplasm with a collection size of 16,460 accessions as of September 2023. Information on these accessions is available online (https://my.iita.org/accession2/collection.jspx?id=1), including passport data, characterization descriptors and images. A subset known as the "IITA Cowpea Core" is comprised of nearly 2,100 accessions (Mahalakshmi et al. 2007; doi: 10.1017/S1479262107837166). Here we present single nucleotide polymorphism (SNP) data for most of the accessions in the IITA Cowpea Core, along with a few simple observations resulting from analyses of the SNP data. The SNP data were generated using the Illumina iSelect Cowpea Consortium Array, described in Muñoz-Amatriaín et al. 2017 (doi: 10.1111/tpj.13404). A characteristic of this platform is that missing data (a.k.a. "nocall") is nearly always either attributable to a SNP assay that failed technically and is excluded from all samples ("zeroed") or a result of either the absence of a DNA segment in the genome or a sequence difference near the SNP position that precludes a successful assay. As a consequence, the frequency of "nocall" provides a broad indicator of whether or not a given accession is in the same species as cowpea. A few accessions in the IITA Cowpea Core are outliers, as follows. Three accessions (TVu-14726, TVu-16409, TVu-8383) had more than 31,000 nocalls (after excluding 1,863 zeroed SNPs) and fairly low (181 or 246) or moderate (1,337) heterozygous calls, indicating that these are not in the same species as cowpea. The passport data from IITA notes TVu-8383 as "wild" and TVu-14726 as "landrace". There is no additional passport information on TVu-16409, but based on its SNP characteristics TVu-16409 clearly also is not in the same species as cowpea. Three other accessions (TVu-5540, TVu-6968, TVu-14935) have from 8,985 to 10,025 nocalls (after excluding 1,863 zeroed SNPs), which indicates that these accessions are more closely related to cowpea, but also are from a different species. Among these three accessions, TVu-14935 also had 18,134 heterozygous SNPs, which indicates that the plant representing this accession was not highly inbred. Residual heterozygosity is a common characteristic among single plant representatives of germplasm accessions, which begin as one or more seeds collected from their original open-pollenating location and then proceed through a variable number of selfed generations to become more inbred in germplasm collections. Five accessions that are stated in the passport data to be from three V. unguiculata subspecies other than subspecies unguiculata had the same range of nocalls (708 to 943) as accessions reported to be subspecies unguiculata, consistent with the expectation that the cultivated subspecies all are closely related to each other. Two of these (TVu-3661 and TVu-3662) are stated in the passport data to be subspecies dekindtiana, which is generally considered to be the reservoir of variation for subspecies unguiculata, and one (TVu-3657) is stated to be subspecies cylindrica. The other two (TVu-3652, TVu-3656) of these five accessions are stated to be subspecies sesquipedalis, which has been well documented to be readily crossable with subspecies unguiculata. It should be noted also that there are several other accessions from Asia that are not specifically marked as sesquipedalis. Analysis of the overall population structure of the IITA Cowpea Core places these Asian accessions within the same sub-population as the accessions stated to be sub-species sesquipedalis. Based on principle component analysis, five sub-populations are evident among the IITA Cowpea Core, one from West Africa represented by Sanzi, another from West Africa represented by Suvita-2, one from Asia represented by TZ30 and ZN016, one from Northeast Africa, Europe and California represented by CB5-2, and one from South and East Africa represented by UCR779. It is anticipated that the IITA Cowpea Core SNP dataset can provide a useful resource for a number of genome-wide association studies (GWAS) and decisions related to germplasm management.Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: IOS-1543963Funding provided by: United States Agency for International DevelopmentCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000200Award Number: AID-OAA-A-13-00070Funding provided by: United States Agency for International DevelopmentCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000200Award Number: EDH-A-00-07-00005-00Funding provided by: Bill and Melinda Gates FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000865Award Number: OPP1114827Funding provided by: Crop TrustCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100018774Award Number:Young, tender leaf tissue was excised from one plant of each accession of the IITA Cowpea Core collection, then dried prior to DNA extraction. A total of 1,789 plants that provided leaf tissue were grown at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria and 15 at the IITA in Kano, Nigeria. Leaves from 1,655 of these plants were dried inside sealable plastic bags containing packets of silica gel, then shipped at ambient temperature from IITA (Ibadan and Kano) to the University of California in Riverside (UCR), California, USA. An additional 232 tissue samples from IITA Cowpea Core accessions that were included in the "UCR Minicore" (Muñoz-Amatriaín et al. 2021; doi: 10.1002/leg3.95) were prepared the same way (young leaves, dried with silica gel packets) from individual plants grown in greenhouses at UCR. DNA was extracted at UCR from each of these 1,887 dried leaf samples using either Qiagen (https://www.qiagen.com/us) DNeasy Plant or Machery-Nagel (https://www.mn-net.com/us/) NucleoMag kits. DNA was prepared at IITA from desiccated leaf tissue of an additional 149 accessions using a CETAB method, then these DNA solutions were sent to UCR at ambient temperature. All of these 2,036 DNA samples (10 µL each) were arranged in 96-well plates at UCR at concentrations ranging from 50 to 450 ng/µL, then transported to the University of Southern California Molecular Genomics Core facility (https://uscnorriscancer.usc.edu/molecular-genomics-core/) for single nucleotide polymorphism (SNP) genotyping using the Illumina (https://www.illumina.com/) iSelect Cowpea Consortium Array, which was described in Muñoz-Amatriaín et al. 2017. The tissue production, DNA extraction and genotyping occurred incrementally over a period of 6.5 years from May 2014 through November 2020. Raw SNP data and sample sheets were transferred to UCR by FTP, then imported into the Illumina GenomeStudio software using a cluster file developed in 2014 to 2015 at UCR for broad cowpea germplasm, then exported as "Forward Strand" in a tab-delimited text file. SNP data from seven diverse cowpea accessions (CB5-2, IT97K-499-35, Sanzi, Suvita-2, TZ30, UCR779, ZN016) that have been assembled as described in Liang et al. 2023 (doi: 10.1002/tpg2.20319) also were included, taking the total number of accessions in this dataset to 2,043. There was no apparent difference in the quality or completeness of the SNP data, regardless of the DNA extraction method or DNA concentration in this range. The orientation of the cowpea iSelect "Forward Strand" is arbitrary relative to the "Watson" strand of the assembled genome sequence of accession IT97K-499-35 (Lonardi et al. 2019; doi: 10.1111/tpj.14349). So, in addition to providing the SNP data as iSelect "Forward Strand", which has been used for numerous publications, here we provide the SNP data in a spreadsheet containing two sheets, with the first sheet being the SNPs according to the "Watson" strand, and the second sheet being the SNPs as iSelect "Forward Strand". Additional information in the spreadsheet includes chromosome (or contig if unmapped), nucleotide position in IT97K-499-35, and other information indicating confidence to use or exclude the data for a given SNP, as described in Liang et al. 2023 Table S03. Usage notes: The two-sheet SNP dataset is provided as a .xlsx file, which is a zipped, XML-based file format that can be opened with Microsoft Excel (Office 2007 or later), LibreOffice Calc, Google Sheets, Apache OpenOffice and others

Quantitative trait loci and genomic prediction for grain sugar and mineral concentrations of cowpea [Vigna unguiculata (L.) Walp.].

Development of high yielding cowpea varieties coupled with good taste and rich in essential minerals can promote consumption and thus nutrition and profitability. The sweet taste of cowpea grain is determined by its sugar content, which comprises mainly sucrose and galacto-oligosaccharides (GOS) including raffinose and stachyose. However, GOS are indigestible and their fermentation in the colon can produce excess intestinal gas, causing undesirable bloating and flatulence. In this study, we aimed to examine variation in grain sugar and mineral concentrations, then map quantitative trait loci (QTLs) and estimate genomic-prediction (GP) accuracies for possible application in breeding. Grain samples were collected from a multi-parent advanced generation intercross (MAGIC) population grown in California during 2016-2017. Grain sugars were assayed using high-performance liquid chromatography. Grain minerals were determined by inductively coupled plasma-optical emission spectrometry and combustion. Considerable variation was observed for sucrose (0.6-6.9%) and stachyose (2.3-8.4%). Major QTLs for sucrose (QSuc.vu-1.1), stachyose (QSta.vu-7.1), copper (QCu.vu-1.1) and manganese (QMn.vu-5.1) were identified. Allelic effects of major sugar QTLs were validated using the MAGIC grain samples grown in West Africa in 2017. GP accuracies for minerals were moderate (0.4-0.58). These findings help guide future breeding efforts to develop mineral-rich cowpea varieties with desirable sugar content