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

Abstract Background Pearl millet, a dietary food for around 100 million people in Africa and in India, has a large diversity due to an extensive genetic diversity combined with a high degree of admixture with wild relatives. In Senegal, two major morphotypes are distinguished: early-flowering and late-flowering millets. The phenotypic variabilities according to the flowering time plays an important role in pearl millet adaptation to climate variability. A better understanding of the genetic makeup of these variabilities would allow breeding of pearl millet fitting different climatic areas. In this study, we aimed to characterize the genetic basis of these phenotypic differences. Results We defined a core collection capturing most of the diversity of cultivated pearl millet of Senegal, which includes 60 early-flowering Souna and 31 late-flowering Sanio. This panel was evaluated during the 2016 and 2017 rainy seasons at Nioro for 16 agro-morphological traits. Phenological and phenotypes traits linked with yield, flowering time, and biomass helped differentiated early- and late-flowering millets. Further, using genotyping-by-sequencing (GBS), 21,663 single nucleotide polymorphisms (SNPs) with minor allele frequencies of more than 5% were identified. Sparse Non-Negative Matrix Factorization (sNMF) analysis confirms the genetic structure in 2 gene pools associated with flowering time differences. Moreover, 2 chromosomal regions on linkage groups 3 (~ 89.7 Mb) and 6 (~ 68.1 Mb) differentiated the early-flowering into 2 clusters. Genome-wide analysis study (GWAS) was used to associate phenotypic variation to the SNPs and 18 genes were linked to flowering time, plant height, nodal tiller number, and biomass (P-value ˂ 2.3E-06). Conclusions The diversity of early- and late-flowering pearl millet landraces of Senegal was captured using a heuristic approach. Key phenology and phenotypic traits, SNPs, ad candidate genes underlying flowering time, tillering, biomass and plant height of pearl millet were identified. Chromosome rearrangements in LG 3 and 6 were implicated as a source of variation in early-flowering morphotypes. Using candidate genes underlying these features between pearl millet morphotypes would have paramount importance in breeding strategies under climate change scenarios.