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. Pheno...
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doaj-2dff20cf9bdc48abb3037aa115dadfa12020-11-25T04:07:18ZengBMCBMC Genomics1471-21642020-11-0121111110.1186/s12864-020-07198-2GWAS unveils features between early- and late-flowering pearl milletsOumar Diack0Ghislain Kanfany1Mame Codou Gueye2Ousmane Sy3Amadou Fofana4Hamidou Tall5Desalegn D. Serba6Leila Zekraoui7Cécile Berthouly-Salazar8Yves Vigouroux9Diaga Diouf10Ndjido Ardo Kane11Centre d’Étude Régional pour l’Amélioration de l’Adaptation à la Sécheresse, Institut Sénégalais de Recherches AgricolesCentre National de Recherches Agronomiques de Bambey, Institut Sénégalais de Recherches AgricolesCentre d’Étude Régional pour l’Amélioration de l’Adaptation à la Sécheresse, Institut Sénégalais de Recherches AgricolesCentre National de Recherches Agronomiques de Bambey, Institut Sénégalais de Recherches AgricolesCentre National de Recherches Agronomiques de Bambey, Institut Sénégalais de Recherches AgricolesCentre de Recherches Zootechniques de Kolda, Institut Sénégalais de Recherches AgricolesAgricultural Research Center-Hays, Kansas State UniversityLaboratoire mixte international Adaptation des Plantes et microorganismes associés aux Stress EnvironnementauxLaboratoire mixte international Adaptation des Plantes et microorganismes associés aux Stress EnvironnementauxUnité Mixte de Recherche DIADE, Institut de Recherche pour le DéveloppementLaboratoire Campus de Biotechnologies Végétales, Faculté des Sciences et Techniques, Université Cheikh Anta Diop de DakarCentre d’Étude Régional pour l’Amélioration de l’Adaptation à la Sécheresse, Institut Sénégalais de Recherches AgricolesAbstract 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.http://link.springer.com/article/10.1186/s12864-020-07198-2SenegalPearl milletMorphotypesFloweringDiversityGWAS |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Oumar Diack Ghislain Kanfany Mame Codou Gueye Ousmane Sy Amadou Fofana Hamidou Tall Desalegn D. Serba Leila Zekraoui Cécile Berthouly-Salazar Yves Vigouroux Diaga Diouf Ndjido Ardo Kane |
spellingShingle |
Oumar Diack Ghislain Kanfany Mame Codou Gueye Ousmane Sy Amadou Fofana Hamidou Tall Desalegn D. Serba Leila Zekraoui Cécile Berthouly-Salazar Yves Vigouroux Diaga Diouf Ndjido Ardo Kane GWAS unveils features between early- and late-flowering pearl millets BMC Genomics Senegal Pearl millet Morphotypes Flowering Diversity GWAS |
author_facet |
Oumar Diack Ghislain Kanfany Mame Codou Gueye Ousmane Sy Amadou Fofana Hamidou Tall Desalegn D. Serba Leila Zekraoui Cécile Berthouly-Salazar Yves Vigouroux Diaga Diouf Ndjido Ardo Kane |
author_sort |
Oumar Diack |
title |
GWAS unveils features between early- and late-flowering pearl millets |
title_short |
GWAS unveils features between early- and late-flowering pearl millets |
title_full |
GWAS unveils features between early- and late-flowering pearl millets |
title_fullStr |
GWAS unveils features between early- and late-flowering pearl millets |
title_full_unstemmed |
GWAS unveils features between early- and late-flowering pearl millets |
title_sort |
gwas unveils features between early- and late-flowering pearl millets |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2020-11-01 |
description |
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. |
topic |
Senegal Pearl millet Morphotypes Flowering Diversity GWAS |
url |
http://link.springer.com/article/10.1186/s12864-020-07198-2 |
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