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The taxonomic identification of species through analysis of the variation of orthologous DNA sequences, complement the information obtained with morphological characters. Cytogenetic studies indicate that polyploid taxa occur in the subfamily Opuntioideae, Opuntia ficus-indica, contributing to morphological variability in the individuals of a population, and influencing the correct identification of species. However, the lengths of the sequences in Opuntioideae are affected by the extraction of pure DNA. Different extraction methods were evaluated and modified, and a procedure was established to obtain good quality DNA, free of inhibitors for gene amplification by polymerase chain reaction. The ratio A260/A280 and A260/A230 ranged from 1.6 to 2.1, revealing absence of contamination with the modified protocol for DNA extraction from cotton leaves. This method is inexpensive compared to those of commercial manufacturers and, therefore, can be applied in studies with limited resources.

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.

Additional file 1: Table S1. List of accessions from the Senegalese pearl millet core collection. Table S2. Representativeness statistics of early-flowering Souna morphotype and late-flowering Sanio morphotypes within the core collection. %MD = Percentage of mean difference, %VD = Percentage of variance difference, %CR = Coincidence rate, and %VR = Variable rate. Table S3. Means, P-values and correlation with axis from the discriminant analysis (DA) of early- and late- flowering millets. Table S4. Significantly associated SNPs from GWAS, mapped in the pearl millet genome and associated with phenotypic traits. Figure S1. Genetic structure of Senegalese pearl millet landraces core collection at chromosome level (a-g) from chromosome 1 to chromosome 7, respectively. Figure S2. Discriminant analysis of (a) early-flowering (Axis1 = 98.49, Axis2 = 1.51) and (b) late-flowering morphotypes (Axis1 = 95.59, Axis2 = 4.41), from phenotypic traits of landraces from the core collection. Boxplots of (c) grain yield, (d) panicle yield, (e) spike thickness, (f) nodal tillering and (g) flag leaf length according to different subsets of early-flowering morphotype. Boxplots of (h) panicle yield, (i) grain yield and (j) nodal tillering according to different subsets of late-flowering morphotype.

International audience; 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.