Genome-wide Association Studies of Photosynthetic and Agronomic Traits in Cowpea Collection.

Exploring genomic regions linked with drought tolerance and photosynthesis in cowpea could accelerate breeding of climate-resilient cowpea varieties A Genome-wide association study (GWAS) was conducted to identify marker-trait associations for agronomic and photosynthetic traits measured under well-watered and water-stressed conditions. One hundred and twelve cowpea accessions from IITA were phenotyped for agronomic and photosynthetic traits across three locations in two years: Ibadan, Ikenne (2020 and 2021) and Kano (2021 and 2022). The accessions were genotyped using 19,000 DArT-Seq SNP markers from which 9,210 markers were utilized for GWAS analysis using BLINK and mixed linear model (MLM) in GAPIT. Results revealed significant accession × environment interactions for measured traits while ΦPSII, ΦNO and ΦNPQ had significant and consistent correlations with grain yield across conditions. GWAS identified five SNP markers having consistent associations with grain yield under well-watered and water-stressed conditions and three markers associated with ΦNPQ and ΦNO. Gene annotations revealed Vigun04g169000 and Vigun08g168900 genes linked with grain yield and highly expressed under water-stressed conditions have functional roles in regulating plant development and adaptive response to environmental stress. Vigun07g133400, Vigun07g132700 and Vigun07g258000 genes linked with ΦNPQ and ΦNO are involved in activities controlling photoprotection and stress-induced damage in plants. This study identified natural genetic variation in cowpea and correlations between photosynthetic traits and grain yield under real-field drought conditions. The identified SNP markers upon validation would be valuable in marker-assisted selection and useful for cowpea breeders to harness the role of photosynthesis in genetic enhancement of cowpea tolerance to drought.

Phytoecdysteroids from Dioscorea dumetorum (Kunth) Pax. and their antioxidant and antidiabetic activities.

Diabetes is a significant global health challenge, affecting circa 540 million adults worldwide. Dioscorea dumetorum, a Nigerian folkloric antidiabetic plant is severely understudied in terms of its bioactive phytochemical constituents. Antidiabetic guided isolation of the tubers and peels of D. dumetorum afforded three phytoecdysteroids bearing a cis-fused A/B ring junction including two new ones: 24-hydroxymuristerone A (1) and 24-hydroxykaladasterone (2), alongside the known muristerone A (3). Additionally, 2,2',7,7'-tetramethoxy-[1,1'-biphenanthrene]-4,4',6,6'-tetraol (4), batatasin I (5), and dihydroresveratrol (6) were isolated. Structural elucidation relied on spectroscopic, spectrometric methods, and comparison with existing literature. The ethyl acetate extracts of both the tubers and peels of D. dumetorum exhibited the highest phenolic content, correlating with potent antioxidant activity. Compounds 4 (IC50 = 0.10 mg/mL) and 6 (IC50 = 0.22 mg/mL) demonstrated superior inhibitory effects against α-glucosidase compared to acarbose (IC50 = 0.63 mg/mL). In contrast, compounds 3, 4, and 5 showed reduced α-amylase inhibition, with IC50 values of 2.58, 3.78, and 1.12 mg/mL, respectively, compared to acarbose (IC50 = 0.42 mg/mL). These observed bioactivities validate the traditional use of D. dumetorum and contribute valuable phytochemical data to the scientific literature of the species.

The pattern of genetic variability in a core collection of 2,021 cowpea accessions.

Cowpea is a highly drought-adapted leguminous crop with great promise for improving agricultural sustainability and food security. Here, we report analyses derived from array-based genotyping of 2,021 accessions constituting a core subset of the world's largest cowpea collection, held at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. We used this dataset to examine genetic variation and population structure in worldwide cowpea. We confirm that the primary pattern of population structure is two geographically defined subpopulations originating in West and East Africa, respectively, and that population structure is associated with shifts in phenotypic distribution. Furthermore, we establish the cowpea core collection as a resource for genome-wide association studies by mapping the genetic basis of several phenotypes, with a focus on seed coat pigmentation patterning and color. We anticipate that the genotyped IITA Cowpea Core Collection will serve as a powerful tool for mapping complex traits, facilitating the acceleration of breeding programs to enhance the resilience of this crop in the face of rapid global climate change.

Genome-Wide association analysis of phenotypic traits in Bambara groundnut under drought-stressed and non-stressed conditions based on DArTseq SNP.

Introduction: Bambara groundnut (BG) (Vigna subterranea [L.] Verdc) is an indigenous, resilient, but underutilized leguminous crop that occurs mostly as genetically heterogeneous landraces with limited information on the drought tolerant attributes. This study elucidates the associations between sequencing-based diversity array technology (DArTseq) and phenotypic character as well as differing indices related to drought tolerance in one hundred accessions of Bambara groundnut. Methods: The field experiments were conducted at IITA research stations in Kano and Ibadan between 2016 and 2018 planting seasons. The experiments were arranged in randomised complete block design with three replications, under the different water regimes. The phenotypic traits evaluated was further to construct the dendrogram. Genome-wide association mapping was conducted based on 5927 DArTs loci with < 20% missing data. Results and Discussions: The genome wide association study predicted drought tolerance in Bambara accessions for geometric mean productivity (GMP) and stress tolerance index (STI). TVSu-423 had the highest GMP and STI values (28.50, 2.40), while TVSu-2017 had the lowest at GMP (1.74) and STI (0.01) respectively. The relative water content (%) was significantly higher for accessions; TVSu-266 (60.35, 61.49), TVSu-2 (58.29, 53.94), and TVSu-411 (55.17, 58.92) in 2016/2017 and 2017/2018, respectively. The phenotypic characters studied delineated the accessions into two major clusters and five distinct sub-clusters, indicating variations across all the geographical locations. The 5,927 DArTseq genomic markers in association with STI further grouped the 100 accessions into two main clusters. TVSu-1897 from Botswana (Southern Africa) was in the first cluster, while the remaining 99 accessions from Western, Central, and Eastern Africa made up the second cluster. The eight significant Quantitative Trait Loci (QTLs) (24346377|F|0-22:A>G-22:A>G, 24384105|F|0-56:A>G33 :A> G, 24385643|F|0-53:G>C-53:G>C, 24385696|F|0-43:A>G-43:A>G, 4177257|F|0-44:A>T-44:A>T, 4182070|F|0-66:G>A-66:G>A, 4183483|F|0-24:G>A-24:G>A, 4183904|F|0-11:C>T-11:C>T) identified with Bonferroni threshold was in association with STI, indicative of variations under the drought-stressed condition. The observation of consistent SNPs in the 2016 and 2017 planting seasons, as well as in combination with the 2016 and 2017 planting seasons, led to the designation of these QTLs as significant. The drought selected accessions could form basis for hybridization breeding. The identified quantitative trait loci could be useful in marker-assisted selection in drought molecular breeding programs.

Genome-Wide Association Study Revealed SNP Alleles Associated with Seed Size Traits in African Yam Bean (Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms).

Seed size is an important yield and quality-determining trait in higher plants and is also crucial to their evolutionary fitness. In African yam bean (AYB), seed size varies widely among different accessions. However, the genetic basis of such variation has not been adequately documented. A genome-wide marker-trait association study was conducted to identify genomic regions associated with four seed size traits (seed length, seed width, seed thickness, and 100-seed weight) in a panel of 195 AYB accessions. A total of 5416 SNP markers were generated from the diversity array technology sequence (DArTseq) genotype-by-sequencing (GBS)- approach, in which 2491 SNPs were retained after SNP quality control and used for marker-trait association analysis. Significant phenotypic variation was observed for the traits. Broad-sense heritability ranged from 50.0% (seed width) to 66.4% (seed length). The relationships among the traits were positive and significant. Genome-wide association study (GWAS) using the general linear model (GLM) and the mixed linear model (MLM) approaches identified 12 SNP markers significantly associated with seed size traits across the six test environments. The 12 makers explained 6.5-10.8% of the phenotypic variation. Two markers (29420334|F|0-52:C>G-52:C>G and 29420736|F|0-57:G>T-57:G>T) with pleiotropic effects associated with seed width and seed thickness were found. A candidate gene search identified five significant markers (100026424|F|0-37:C>T-37:C>T, 100041049|F|0-42:G>C-42:G>C, 100034480|F|0-31:C>A-31:C>A, 29420365|F|0-55:C>G-55:C>G, and 29420736|F|0-57:G>T-57:G>T) located close to 43 putative genes whose encoding protein products are known to regulate seed size traits. This study revealed significant makers not previously reported for seed size in AYB and could provide useful information for genomic-assisted breeding in AYB.

Genome wide association analysis of a stemborer egg induced "call-for-help" defence trait in maize.

Tritrophic interactions allow plants to recruit natural enemies for protection against herbivory. Here we investigated genetic variability in induced responses to stemborer egg-laying in maize Zea mays (L.) (Poaceae). We conducted a genome wide association study (GWAS) of 146 maize genotypes comprising of landraces, inbred lines and commercial hybrids. Plants were phenotyped in bioassays measuring parasitic wasp Cotesia sesamiae (Cameron) (Hymenoptera: Braconidae) attraction to volatiles collected from plants exposed to stemborer Chilo partellus (Swinhoe) (Lepidoptera: Crambidae) eggs. Genotyping-by-sequencing was used to generate maize germplasm SNP data for GWAS. The egg-induced parasitoid attraction trait was more common in landraces than in improved inbred lines and hybrids. GWAS identified 101 marker-trait associations (MTAs), some of which were adjacent to genes involved in the JA-defence pathway (opr7, aos1, 2, 3), terpene biosynthesis (fps3, tps2, 3, 4, 5, 7, 9, 10), benzoxazinone synthesis (bx7, 9) and known resistance genes (e.g. maize insect resistance 1, mir1). Intriguingly, there was also association with a transmembrane protein kinase that may function as a receptor for the egg elicitor and other genes implicated in early plant defence signalling. We report maize genomic regions associated with indirect defence and provide a valuable resource for future studies of tritrophic interactions in maize. The markers identified may facilitate selection of indirect defence by maize breeders.

Developing the role of legumes in West Africa under climate change.

West Africa is faced with significant challenges from climate change, including parts of the region becoming hotter with more variable rainfall. The Sahelian region in particular is already subject to severe droughts. To address this better adapted crop varieties (such as for cowpea) are clearly a central element, a complementary one is a greater use of resilient alternative crops especially underutilized legumes particularly Bambara groundnut, African yam bean, winged bean and Kersting's groundnut. Genetic diversity of these crops conserved in genebanks and farmer's field provides an opportunity to exploit climate resilient traits using cutting-edge genomic tools and to use genomics-assisted breeding to accelerate genetic gains in combination of rapid cycle breeding strategy to develop climate-resilient cultivars for sub-Saharan Africa.

Effect-directed profiling and identification of bioactive metabolites from field, in vitro-grown and acclimatized Musa spp. accessions using high-performance thin-layer chromatography-mass spectrometry.

Bananas and plantains (Musa spp.) are used as nutritious foods, and at the same time, are a source of phytoconstituents for the pharmaceutical industry. As biological activities of especially the pulp and peel of Musa spp. have been documented, this study investigated the variation in the secondary metabolite profiles of the leaves from field, in vitro-grown and acclimatized accessions. The genetic fidelity of the diverse accessions was assessed using diversity array technology sequencing. It showed that the in vitro-grown accessions were true-to-type with the field samples. The antioxidant and anticholinesterase activities of the samples from different culture systems (field and in vitro) were evaluated by UV-spectrophotometry and compared to high-performance thin-layer chromatography-effect-directed analysis (HPTLC-EDA). The latter was applied for the first time for effect-directed profiling of the polar and medium polar sample components via different biochemical and biological assays. Compound zones showed acetyl-/butylrylcholinesterase inhibition (zones 1-4), α-/ß-glucosidase inhibition (zones 1 and 2) as well as antioxidative (zones 1-3) and antimicrobial (zone 4) activities. Structures were preliminary assigned by HPTLC-HRMS. The HPTLC was effective for bioactivity-guided characterization of the bioactive constituents in Musa spp. accessions. Accumulation of useful metabolites, especially compounds with antioxidant and anticholinesterase properties, was higher in samples from in vitro system. This validated the use of plant tissue culturing as an alternative method for large scale production of plant material and supply of bioactive constituents.

Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas.

The north-western Indian Himalayas possesses vast diversity in common bean germplasm due to several years of natural adaptation and farmer's selection. Systematic efforts have been made for the first time for the characterization and use of this huge diversity for the identification of genes/quantitative trait loci (QTLs) for yield and yield-contributing traits in common bean in India. A core set of 96 diverse common bean genotypes was characterized using 91 genome-wide genomic and genic simple sequence repeat (SSR) markers. The study of genetic diversity led to the identification of 691 alleles ranging from 2 to 21 with an average of 7.59 alleles/locus. The gene diversity (expected heterozygosity, He) varied from 0.31 to 0.93 with an average of 0.73. As expected, the genic SSR markers detected less allelic diversity than the random genomic SSR markers. The traditional clustering and Bayesian clustering (structural analysis) analyses led to a clear cut separation of a core set of 96 genotypes into two distinct groups based on their gene pools (Mesoamerican and Andean genotypes). Genome-wide association mapping for pods/plant, seeds/pod, seed weight, and yield/plant led to the identification of 39 significant marker-trait associations (MTAs) including 15 major, 15 stable, and 13 both major and stable MTAs. Out of 39 MTAs detected, 29 were new MTAs reported for the first time, whereas the remaining 10 MTAs were already identified in earlier studies and therefore declared as validation of earlier results. A set of seven markers was such, which were found to be associated with multiple (two to four) different traits. The important MTAs will be used for common bean molecular breeding programs worldwide for enhancing common bean yield.

QTL mapping for some grain traits in bread wheat (Triticum aestivum L.).

Grain traits are important agronomic attributes with the market value as well as milling yield of bread wheat. In the present study, quantitative trait loci (QTL) regulating grain traits in wheat were identified. Data for grain area size (GAS), grain width (GWid), factor form density (FFD), grain length-width ratio (GLWR), thousand grain weight (TGW), grain perimeter length (GPL) and grain length (GL) were recorded on a recombinant inbred line derived from the cross of NW1014 × HUW468 at Meerut and Varanasi locations. A linkage map of 55 simple sequence repeat markers for 8 wheat chromosomes was used for QTL analysis by Composite interval mapping. Eighteen QTLs distributed on 8 chromosomes were identified for seven grain traits. Of these, five QTLs for GLWR were found on chromosomes 1A, 6A, 2B, and 7B, three QTLs for GPL were located on chromosomes 4A, 5A and 7B and three QTLs for GAS were mapped on 5D and 7D. Two QTLs were identified on chromosomes 4A and 5A for GL and two QTLs for GWid were identified on chromosomes 7D and 6A. Similarly, two QTLs for FFD were found on chromosomes 1A and 5D. A solitary QTL for TGW was identified on chromosome 2B. For several traits, QTLs were also co-localized on chromosomes 2B, 4A, 5A, 6A, 5D, 7B and 7D. The QTLs detected in the present study may be validated for specific crosses and then used for marker-assisted selection to improve grain quality in bread wheat.

Gene/QTL discovery for Anthracnose in common bean (Phaseolus vulgaris L.) from North-western Himalayas.

Common bean (Phaseolus vulgaris L.) is one of the most important grain legume crops in the world. The beans grown in north-western Himalayas possess huge diversity for seed color, shape and size but are mostly susceptible to Anthracnose disease caused by seed born fungus Colletotrichum lindemuthianum. Dozens of QTLs/genes have been already identified for this disease in common bean world-wide. However, this is the first report of gene/QTL discovery for Anthracnose using bean germplasm from north-western Himalayas of state Jammu & Kashmir, India. A core set of 96 bean lines comprising 54 indigenous local landraces from 11 hot-spots and 42 exotic lines from 10 different countries were phenotyped at two locations (SKUAST-Jammu and Bhaderwah, Jammu) for Anthracnose resistance. The core set was also genotyped with genome-wide (91) random and trait linked SSR markers. The study of marker-trait associations (MTAs) led to the identification of 10 QTLs/genes for Anthracnose resistance. Among the 10 QTLs/genes identified, two MTAs are stable (BM45 & BM211), two MTAs (PVctt1 & BM211) are major explaining more than 20% phenotypic variation for Anthracnose and one MTA (BM211) is both stable and major. Six (06) genomic regions are reported for the first time, while as four (04) genomic regions validated the already known QTL/gene regions/clusters for Anthracnose. The major, stable and validated markers reported during the present study associated with Anthracnose resistance will prove useful in common bean molecular breeding programs aimed at enhancing Anthracnose resistance of local bean landraces grown in north-western Himalayas of state Jammu and Kashmir.

Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers.

A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2-5). The average polymorphic information content (PIC) was 0.69 (range, 0.29-0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44-0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin.

QTL mapping of terminal heat tolerance in hexaploid wheat (T. aestivum L.).

High temperature (>30 °C) at the time of grain filling is one of the major causes of yield reduction in wheat in many parts of the world, especially in tropical countries. To identify quantitative trait loci (QTL) for heat tolerance under terminal heat stress, a set of 148 recombinant inbred lines was developed by crossing a heat-tolerant hexaploid wheat (Triticum aestivum L.) cultivar (NW1014) and a heat-susceptible (HUW468) cultivar. The F(5), F(6), and F(7) generations were evaluated in two different sowing dates under field conditions for 2 years. Using the trait values from controlled and stressed trials, four different traits (1) heat susceptibility index (HSI) of thousand grain weight (HSITGW); (2) HSI of grain fill duration (HSIGFD); (3) HSI of grain yield (HSIYLD); and (4) canopy temperature depression (CTD) were used to determine heat tolerance. Days to maturity was also investigated. A linkage map comprising 160 simple sequence repeat markers was prepared covering the whole genome of wheat. Using composite interval mapping, significant genomic regions on 2B, 7B and 7D were found to be associated with heat tolerance. Of these, two (2B and 7B) were co-localized QTL and explained more than 15 % phenotypic variation for HSITGW, HSIGFD and CTD. In pooled analysis over three trials, QTL explained phenotypic variation ranging from 9.78 to 20.34 %. No QTL × trial interaction was detected for the identified QTL. The three major QTL obtained can be used in marker-assisted selection for heat stress in wheat.