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

Abstract

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) (~89.7Mb) and (LG 6) (~68.1Mb) 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.

Genomic footprints of selection in early-and late-flowering pearl millet landraces

“…Short cycle landraces had longer and heavier panicles compared to long cycle landraces, which had longer stems and shorter panicles. This finding was consistent with those of previous studies (Marchais, 1982;Dancette, 1983;Zongo et al, 1988;Akanvou et al, 2012;Diack et al, 2020) and was in accordance with the farmer's uses.…”

“…GWAS analysis was thus able to highlight other phenotypic traits and notably to detect a number of polymorphisms and genes associated with yield (Supplementary Tables 5, 6). Noteworthy, our combination of approaches appears to have been effective and relevant since we were able to detect genes that had been identified in previous studies with different samples and spatial scales [five genes identified by Diack et al (2020) and Rhoné et al (2020)], suggesting false discoveries were reduced and that our results could be mainstreamed to other pearl millet landraces.…”

“…Landrace variability has already been exploited by farmers to shorten flowering cycles, as a response to the 1970s and 1980s drought episodes, while conserving their varieties (Vigouroux et al, 2011;Dussert et al, 2015). Substantial effort has been made in the past decades to investigate genes associated with flowering cycle in pearl millet (Saïdou et al, 2009;Vigouroux et al, 2011;Lakis et al, 2012;Kumar et al, 2017;Diack et al, 2020). To date, only the role of PgPHYC gene has been really validated and some other QTLs were identified (Saïdou et al, 2009;Kumar et al, 2017).…”

“…We previously used the core collection from Senegal to identify genes involved in the agromorphological differentiation of the two flowering groups (Diack et al, 2020). This study identified a number of genetic markers associated with biomass, but did not identify genes clearly involved in flowering.…”

Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations

“…Although parts of the biosynthesis pathways regulating floral development have been verified to be relatively conserved across model plants (Litt and Kramer, 2010;Ruiz-Sola and Rodriguez-Concepcion, 2012;Saito et al, 2013), several studies on non-model plant species are needed to verify and investigate the multitude of functional alleles related to flowering time, floral shapes, pigmentation and petal numbers based on GWAS. For example, an SNP in the PPR gene was linked to flowering time leading to early-and late-flowering pearl millets (Diack et al, 2020). In another example, both known and novel genes associated with petal size were identified in rapeseed (Qian et al, 2021).…”