Multi-locus genome-wide association analysis of grain yield, plant height, panicle length, and flowering time in the Senegalese pearl millet [Pennisetum glaucum (L.) R. Br.] germplasm

Abstract

Pearl millet [ Pennisetum glaucum (L.) R. Br.] is a staple cereal underpinning food and nutritional security across the semi-arid Sahel, yet locally calibrated genomic resources for its improvement in West Africa remain scarce. Improving its key agronomic traits is therefore a breeding priority, despite the crop’s inherent hardiness. This study characterized the genetic architecture of four agronomically decisive traits: grain yield, plant height, panicle length, and flowering time, in a Senegalese panel combining internationally derived PMiGAP inbred lines with locally adapted breeding material. Genotypes were evaluated across multiple Senegalese locations between July and October 2024 and genotyped on the DArTseq platform, yielding 14,718 high-quality SNPs. Analysis of variance revealed highly significant genotypic effects, with broad-sense heritability ranging from 0.75 to 0.91. Plant height, panicle length, and grain yield were positively correlated, whereas flowering time was negatively correlated with yield, consistent with an early-flowering drought-escape strategy. The association panel showed weak population structure (k = 2), and linkage disequilibrium decayed rapidly, falling below r 2 = 0.1 at approximately 8 kb. Genome-wide associations were tested in a subset of 137 stable genotypes using a multi-locus mixed-model approach with correction for population structure and kinship. Eleven marker–trait associations were detected across six of the seven pearl millet chromosomes (LOD 6.83–10.78), explaining 5.92% to 48.67% of phenotypic variance, with plant height the most extensively resolved trait. Candidate-gene annotation linked several markers to genes plausibly involved in cell expansion, inflorescence development, and hormone-mediated growth, including an expansin, an AP2/ERF transcription factor, and an auxin-conjugating glucosyltransferase. Flowering time associated with a single chromosome-2 locus implicated in auxin homeostasis, on the same chromosome as PHYTOCHROME C (PHYC), a principal flowering-time determinant in the crop. Together, these associations provide candidate targets for marker-assisted and genomic selection and offer a foundation for genomics-assisted pearl millet improvement in Senegal and the broader West African Sahel.