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) (~ 89.7 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.

Pearl Millet: A Climate-Resilient Nutricereal for Mitigating Hidden Hunger and Provide Nutritional Security

“…High allelic variation and polymorphism were recorded between pairs of parental lines of pearl millet after screening with SNP markers, and they were also mapped on all the seven linkage groups reflecting the distribution of the markers in the genome (Sehgal et al, 2012). Similarly, a panel 21,663 SNP markers were also discovered, depicting > 5% of minor allele frequencies by Diack et al (2020). Different types of molecular markers and genomic approaches ultimately provide a systematic knowledge on plant biology enabling MAB, which can accelerate the process of the development of new and resistant hybrids/varieties.…”

Genetic insights in pearl millet breeding in the genomic era: challenges and prospects

“…Allelic diversity of PgPHYC and PgMADS11 genes were assessed in landraces of pearl millet and the results revealed that the early flowering landraces carried allele for early flowering at PgPHYC locus and PgMADS11 locus showed significant differences in genotype frequencies (Diack et al 2017 ). In another study, Diack et al ( 2020 ) identified one SNP that is located on PgPPR gene encodes a pentatricopeptide repeat protein belonging to ATP DNA-binding cassette family involved in plant resistance and defense. Additionally, they identified one SNP on PgAAO1 gene that encodes an indole-3-acetaldehyde oxidase.…”

“…Association mapping in pearl millet revealed that there was a significant marker traits association for various agronomic traits such as stover dry matter yield, fresh stover yield, panicle harvest index, spike length, and so on (Varshney et al 2017 ). For tillering, one SNP on PgHK4 gene was identified which encodes a histidine kinase but no SNPs were identified for biomass (Diack et al 2020 ).…”

Genomic footprints of selection in early-and late-flowering 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.…”