BackgroundPearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal.ResultsWe identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (π), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage.ConclusionsWe identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2255-0) contains supplementary material, which is available to authorized users.

a b s t r a c tPearl millet (Pennisetum glaucum (L.) R. Br.) is an important hybrid crop in India. However, to date limited pearl millet hybrid development has been undertaken in West Africa (WA), which is the center of pearl millet origin and diversity and where this crop is most important outside India. Using a diverse set of WA pearl millet germplasm, objectives of this study were to determine the superiority of population hybrids over open-pollinated varieties for agro-morphological and agronomic traits in WA pearl millet germplasm; and (ii) to derive strategies for pearl millet hybrid breeding in WA, based on quantitativegenetic parameters, combining ability and heterotic patterns among geographically close versus distant pearl millet populations. A 10 × 10 factorial mating design was performed with four parental OPVs from each of five WA countries. The 100 population hybrids and their parents were tested for 14 traits at six locations in one year, thereby using contrasting locations to indirectly sample the rainfall variability inherent to WA pearl millet production environments. Grain yield showed an average panmictic midparent heterosis (PMpH) of 16.7%, ranging from −26 to 73%. The mean grain yield of hybrids based on inter-country crosses did not differ significantly from intra-country crosses. Geographic distance between parents was positively correlated with hybrid grain yield (r = 0.31), but not with PMpH . Some crosses between accessions from Niger/Nigeria and Senegal were outstanding. Predictability of population hybrid performance for grain yield was moderate based on midparent values (r = 0.43) and slightly better based on general combining ability (GCA) (r = 0.56). Overall, pearl millet hybrid breeding in WA seems very promising, but there do not seem to be clear "natural" heterotic groups among WA pearl millet landraces. Such heterotic groups as the basis of sustainable hybrid breeding need rather to be created systematically, by building on existing combining ability patterns and aiming to maximize combining ability between the groups.

Pearl millet [Pennisetum glaucum (L.) R. Br.] was domesticated in Sahelian West Africa. This highly outcrossing crop is one of the most important staple cereals in the semiarid tropics, adapted to very harsh rain‐fed conditions. Agro‐morphological characterization of local germplasm is very important to better understand existing diversity, ease targeted genetic broadening of breeding populations, and potentially link this knowledge to genotypic information. The objectives of our study were to (i) characterize West and Central African (WCA) pearl millet accessions based on their agro‐morphological traits; (ii) evaluate the possibility to group accessions based on their agro‐morphological characteristics; (iii) determine geographic patterns of phenotypic differentiation; and (iv) derive conclusions for pearl millet improvement in WCA. A total of 360 early‐to‐medium maturity accessions were phenotyped for 12 agro‐morphological traits at six environments in WCA. Wide ranges of all observed traits indicated a high diversity of the tested accessions. Principal component analysis revealed very large diversity within individual countries, especially within Mali and Burkina Faso. Some limited grouping of accessions from Niger, Senegal, Cameroon, Morocco, and Mauritania was observed for individual principal component axes. Geographical differentiation and country differences were detected for several traits. The results and data presented in our study reflect WCA pearl millets’ tremendous diversity and adaptability to a wide range of environments and give a sound basis for breeders to select and utilize this germplasm to serve the manifold needs of WCA pearl millet farmers.

The effects of harvest maturity of mangos (Mangifera indica L.) on storage tinder various low-temperature regimes and the influence of storage on quality development during subsequent ripening at higher temperatures were investigated. The capacity for storage of mango fruit depended on harvest maturity, storage temperature, and the time of harvest within the season. Development of peel and pulp color, soluble solids concentration, pH, and softening in `Amelie', `Tommy Atkins', and `Keitt' mangos occurred progressively during storage for up to 21 days at 12C. Based on the level of ripening change that occurred during 12C storage, immature fruit showed superior storage capacity than fruit harvested at more-advanced stages of physiological maturity. On transfer to ripening temperatures (25C); however, immature fruit failed to develop full ripeness characteristics. Mature and half-mature fruit underwent limited ripening during storage at 12C, the extent of which increased with progressive harvests during the season. Ripening changes during storage for 21 days were less at 8 and 10C than at 12C. Chilling injury, as indicated by inhibition of ripening, was found at all harvest stored at 8C, and in early season harvests stored at 10C. Fruit from mid- and late-season harvests stored better at 10 than at 12C, with no apparent signs of chilling injury. Flavor of mangos ripened after low-temperature storage was less acceptable than of those ripened immediately after harvest. Suggestions are made for maximizing storage potential by controlling harvest maturity and storage temperature for progressive harvests throughout the season.

Diets of West African (WA) smallholder farmers are built on pearl millet [Pennisetum glaucum (L.) R. Br.]. Sustainable pearl millet hybrid breeding is challenging in WA, mostly due to an extensive genetic diversity combined with a high degree of admixture. In the absence of natural heterotic groups, understanding combining ability patterns can enable systematic development of heterotic groups and make sustainable hybrid breeding feasible. The objectives of this study were to evaluate heterosis and combining ability patterns and their relationship with genetic distance among WA pearl millets based on population hybrids, and to derive conclusions for future breeding programs. Therefore, 17 open‐pollinated varieties (OPVs) were crossed in a diallel mating design and tested together with their offspring in nine environments over 2 yr in Niger and Senegal. Genetic distances between the OPVs were evaluated with twenty microsatellite markers. Average panmictic better‐parent heterosis (PBPH) was 18% (1–47%) for panicle yield. A principal coordinate analysis based on genotyping results separated parental OPVs clearly by geographic origin. Although there was no relationship between genetic distance among OPVs and PBPH, we confirmed good combining ability among selected OPVs from Niger vs. Senegal. The identified cultivars (Nigerien CIVT, H80‐10Gr, and Taram and Senegalese Thialack 2 and Souna 3) with high combining ability are recommended for founding divergent heterotic pools targeting long‐panicle pearl millet hybrids. Our study shows the benefits of population hybrids and represents an important step to identify combining ability patterns and initial heterotic groups for WA pearl millet hybrid breeding.

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food and a drought-tolerant cereal well adapted to Sub-Saharan Africa agro-ecosystems. An important diversity of pearl millet landraces has been widely conserved by farmers and therefore could help copping with climate changes and contribute to future food security. Hence, characterizing its genetic diversity and population structure can contribute to better assist breeding programs for a sustainable agricultural productivity enhancement. Toward this goal, a comprehensive panel of 404 accessions were used that correspond to 12 improved varieties, 306 early flowering and 86 late-flowering cultivated landraces from Senegal. Twelve highly polymorphic SSR markers were used to study diversity and population structure. Two genes, PgMADS11 and PgPHYC, were genotyped to assess their association to flowering phenotypic difference in landraces. Results indicate a large diversity and untapped potential of Senegalese pearl millet germplasm as well as a genetic differentiation between early- and late-flowering landraces. Further, a fine-scale genetic difference of PgPHYC and PgMADS11 (SNP and indel, respectively) and co-variation of their alleles with flowering time were found among landraces. These findings highlight new genetic insights of pearl millet useful to define heterotic populations for breeding, genomic association panel, or crosses for trait-specific mapping.

Pearl millet [Pennisetum glaucum (L.) R. Br] production on the acid sandy Sahelian soils in West Africa (WA) is severely limited by low plant-available phosphorus (P) in addition to erratic rainfall. We sought to examine the genetic variability for P uptake and P utilization efficiency in 180 WA pearl millet inbred lines or subsets thereof under low (LP) and high P (HP) conditions in one field and two pot experiments, determine the relationships among the measured traits and grain yield under field conditions at three other independent WA sites, and identify potential secondary selection traits for improving grain yield under LP. We observed genetic variation for P uptake and utilization in both seedling and mature plants. P utilization efficiency increased under LP conditions. Total P uptake was more important for grain production than P utilization under LP field conditions (r = 0.57*** vs r = 0.30***). The estimated response to indirect selection was positive for most of the measured morphological and P-efficiency parameters. We conclude that both seedling and mature plant traits are potentially useful as secondary traits in selection of pearl millet for low-P adaptation. These results should be validated using heterozygous pearl millet genetic materials. Ultimately, pearl millet breeding activities for low P tolerance in WA should be integrated with other system-oriented research such as nutrient cycling, intercropping or rotations with legumes, better crop-tree-livestock integration, and modest applications of locally available rock phosphate.

Pearl millet [Pennisetum glaucum (L.) R. Br] is a food security crop for millions living in drylands of Africa and Asia. Its production on acid sandy soils of the Sahel is limited by erratic rainfall and poor soil fertility, especially low P soils. We sought to elucidate the genetic variation in West and Central African landrace‐derived inbred lines for grain yield under low P conditions, to determine their performance as inbred lines per se and in hybrid combinations, and to determine quantitative‐genetic parameters to derive an appropriate breeding strategy to enhance grain yield under low P conditions. We evaluated a total of 155 landrace‐derived inbred lines as well as their testcrosses in four locations during two years under two treatments, high P (HP; with P fertilization) and low P (LP; without P fertilization). Results revealed significant effects for genotypes, P‐level, genotype × P‐level, as well as genotype × environment interactions. Grain yield reductions under LP treatment ranged from 7.9 to 35.5%, and 11.2 to 60.9% for inbred lines and testcrosses respectively, with positive midparent heterosis averaging 43.5% under LP. We conclude that direct selection of testcrosses under LP is more effective and that indirect selection for testross performance from inbred line performance is not desirable.