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
5 affiliations
- 1Makerere University Regional Centre for Crop Improvement (MaRCCI), College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
- 2Department of Crop Science and Horticulture, College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
- 3Centre National de Recherches Agronomiques de Bambey, Institut Sénégalais de Recherches Agricoles, Bambey, Senegal
- 4Department of Soil Science and Land Use Management, College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
- 5Centre d’Étude Régional pour l’Amélioration de l’Adaptation à la Sécheresse, Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
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 r2 = 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.
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BibTeX
@article{ba2026multilocus,
title = {{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}},
author = {Aliou Ba and Oumar Diack and Thomas L. Odong and Safiétou Tooli Fall and Richard Edema and Arfang Badji and Adama Faye and Tonny Obua and Mildred Ochwo-Ssemakula and Paul Gibson and Mamadou Mar and Jessica B. Bacourine and Yagouba Diao and Mahoussi K. Arnaud Djanta and Ndjido A. Kane and Phinehas Tukamuhabwa},
journal = {PLOS One},
year = {2026},
month = oct,
doi = {10.1371/journal.pone.0358045},
url = {https://doi.org/10.1371/journal.pone.0358045},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - 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
AU - Aliou Ba
AU - Oumar Diack
AU - Thomas L. Odong
AU - Safiétou Tooli Fall
AU - Richard Edema
AU - Arfang Badji
AU - Adama Faye
AU - Tonny Obua
AU - Mildred Ochwo-Ssemakula
AU - Paul Gibson
AU - Mamadou Mar
AU - Jessica B. Bacourine
AU - Yagouba Diao
AU - Mahoussi K. Arnaud Djanta
AU - Ndjido A. Kane
AU - Phinehas Tukamuhabwa
PY - 2026
DA - 2026/10/06
JO - PLOS One
DO - 10.1371/journal.pone.0358045
UR - https://doi.org/10.1371/journal.pone.0358045
AB - 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 r2 = 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.
SN - 1932-6203
ER -