Falalou Hamidou

Genomewide Association Studies for 50 Agronomic Traits in Peanut Using the ‘Reference Set’ Comprising 300 Genotypes from 48 Countries of the Semi-Arid Tropics of the World

Peanut is an important and nutritious agricultural commodity and a livelihood of many small-holder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with on-going genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, high-resolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the ‘reference set’ of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three sub-groups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r2) predicted LD decay of 15–20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (pvalue >2.1×10–6) with wide phenotypic variance (PV) range (5.81–90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components.

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

Water use, transpiration efficiency and yield in cowpea (Vigna unguiculata) and peanut (Arachis hypogaea) across water regimes

Abstract. Genotypic variation in crop response to drought depends on agronomic, environmental and genetic factors, and only limited work has compared responses of crop species to water limitation. Twenty genotypes of peanut (Arachis hypogaea L.) and of cowpea (Vigna unguiculata (L.) Walp) were tested in lysimeters under well-watered (WW) and water-stress (WS) conditions during two seasons, a post-rainy season with high evapotranspiration and a rainy season with low evapotranspiration (ET), in order to assess: (i) variability in the agronomic response to stress within and between species across the seasons; (ii) the water requirement of the two crops in each season; and (iii) the stress effect on harvest index (HI), transpiration efficiency (TE), pod yield and haulm yield. Cowpea required less water than peanut during the two seasons, and water use in cowpea varied less across seasons than in peanut. Peanut yield was more sensitive to water stress than cowpea yield, although its water use under WS was higher than in cowpea. Also, under WS conditions, TE, HI and pod yield were more stable across season in cowpea than in peanut. In the post-rainy season, the decrease in pod yield and HI under WS was higher in peanut (95% and 80%, respectively) than in cowpea (70% and 35%). In addition, TE was less affected by WS in cowpea (5%) than in peanut (24%). HI explained a large part of yield variation in both crops, especially under WS. Under WW, water use explained a large portion of the residual yield variations unexplained by HI, although TE also explained a substantial part of the variation in cowpea. Under WS, the main determinant of residual yield variations in both crops was TE. Generally, genetic variation for water use, TE and HI was found in both species across water regimes and seasons. A notable exception was the absence of variation in peanut water use and TE in the rainy season. Our results showed that cowpea, with lower water requirement and efficient water use under a high-ET season, was more resilient to water-limited and high-ET conditions than peanut.

Determination of coefficient defining leaf area development in different genotypes, plant types and planting densities in peanut (Arachis hypogeae L.)

Highlights • A vigorous canopy development can shade weed competitors and enhance light interception.• We assess whether the coefficients that characterize the canopy development in a peanut crop model vary with genotype, density, and botanical type.• There was variation among genotype for the leaf canopy development parameters.• Botanical type and density did not alter the canopy development parameters.• The model predicted the leaf canopy development well.