GWAS unveils features between early- and late-flowering pearl millets.

BACKGROUND: Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distinguished in Senegal: early-flowering Souna and late-flowering Sanio. Phenotypic variabilities related to flowering time play an important role in the adaptation of pearl millet to climate variability. A better understanding of the genetic makeup of these variabilities would make it possible to breed pearl millet to suit regions with different climates. The aim of this study was to characterize the genetic basis of these phenotypic differences. RESULTS: We defined a core collection that captures most of the diversity of cultivated pearl millets in Senegal and includes 60 early-flowering Souna and 31 late-flowering Sanio morphotypes. Sixteen agro-morphological traits were evaluated in the panel in the 2016 and 2017 rainy seasons. Phenological and phenotypic traits related with yield, flowering time, and biomass helped differentiate early- and late-flowering morphotypes. Further, using genotyping-by-sequencing (GBS), 21,663 single nucleotide polymorphisms (SNPs) markers with more than 5% of minor allele frequencies were discovered. Sparse non-negative matrix factorization (sNMF) analysis confirmed the genetic structure in two gene pools associated with differences in flowering time. Two chromosomal regions on linkage groups (LG 3) (~ 89.7 Mb) and (LG 6) (~ 68.1 Mb) differentiated two clusters among the early-flowering Souna. A genome-wide association study (GWAS) was used to link phenotypic variation to the SNPs, and 18 genes were linked to flowering time, plant height, tillering, and biomass (P-value < 2.3E-06). CONCLUSIONS: The diversity of early- and late-flowering pearl millet morphotypes in Senegal was captured using a heuristic approach. Key phenological and phenotypic traits, SNPs, and candidate genes underlying flowering time, tillering, biomass yield and plant height of pearl millet were identified. Chromosome rearrangements in LG3 and LG6 were inferred as a source of variation in early-flowering morphotypes. Using candidate genes underlying these features between pearl millet morphotypes will be of paramount importance in breeding for resilience to climatic variability.

Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces.

BACKGROUND: Pearl 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. RESULTS: We 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. CONCLUSIONS: We 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.

Ethnobotanical study of cowpea (Vigna unguiculata (L.) Walp.) in Senegal.

Cowpea (Vigna unguiculata) plays a key role in family farming systems in Senegal. It makes an essential contribution to economic, nutritional and food security. Although it is crucial, little is known about how farmers classify the diversity of local varieties or about the social practices associated with them. The aim of this study is to characterize the farming practices associated with growing cowpea in Senegal. Surveys were conducted involving 335 rural farmers living in 37 villages, spread across seven regions that produce cowpea. An average of ten farmers were randomly selected in each village. The results reveal that cowpea is a key feature of cropping systems in the studied area. Our findings highlight the high diversity of local cowpea varieties with 59 local names inventoried. In 75% of cases, the name refers to the seed's morphology or color. Cowpea production is more diverse in Diourbel and Louga and less diverse in the south. More than half the farmers (57%) acquired their cowpea seeds (early, semi-early and late maturity varieties) outside their village, either from markets, seed suppliers or NGOs. This new understanding of farmers' expertize in the management of cowpea and its local variability will help to valorize local diversity in breeding programs.

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.