1. Population genomics of sorghum (Sorghum bicolor) across diverse agroclimatic zones of Niger
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Maina, Fanna, Bouchet, Sophie, Marla, Sandeep R., Hu, Zhenbin, Wang, Jianan, Mamadou, Aissata, Abdou, Magagi, Saidou, Abdoul-Aziz, and Morris, Geoffrey P.
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Sorghum -- Genetic aspects ,Biological sciences - Abstract
Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed 516 Nigerien accessions for which local variety name, botanical race, and geographic origin were known. We discovered 144 299 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). We performed discriminant analysis of principal components (DAPC), which identified six genetic groups, and performed a genome scan for loci with high discriminant loadings. The highest discriminant coefficients were on chromosome 9, near the putative ortholog of maize flowering time adaptation gene Vgt1. Next, we characterized differentiation among local varieties and used a genome scan of pairwise [F.sub.ST] values to identify SNPs associated with specific local varieties. Comparison of varieties named for light- versus dark-grain identified differentiation near Tannin1, the major gene responsible for grain tannins. These findings could facilitate genomics-assisted breeding of locally adapted and farmer-preferred sorghum varieties for Niger. Key words: sorghum, agroclimatic zones, genomics, local adaptation, genomics-enabled breeding, sub Saharan Africa. L'amelioration de cultures dans les pays en developpement est importante afin d'assurer securite alimentaire. En Afrique de l'Ouest, particulierement au Niger, le sorgho (Sorghum bicolor) est cultive dans differentes zones agroclimatiques. Cependant les bases genetiques de leur adaptation locale sont peu decrites. Cette etude a pour objectifs de caracteriser la structure genetique du sorgho au Niger et d'identifier les regions genomiques associees a l'adaptation locale aux zones agroclimatiques et aux preferences des agriculteurs. L'analyse par le genotypage par sequencage (GBS) de 516 accessions du Niger, dont le nom local, la race botanique et l'origine sont connus, nous a permis d'identifier 144 299 polymorphismes nucleotidiques (SNPs). La methode d'analyse discriminante des composantes principales a identifie six clusters genetiques. Le balayage genomique des coefficients de discrimination a montre des locus aux coefficients eleves au niveau du chromosome 9, colocalises avec le gene Vgt1 responsable de la variation de la date de floraison. Aussi, nous avons caracterise la differentiation des varietes locales. Le balayage genomique de [F.sub.ST] entre les varietes locales Mota (grains blancs) et Jenjari (grains sombres) a identifie des locus pres du Tannin1, le gene responsable des tanins. Ces resultats permettront de faciliter la selection assistee par la genomique de varietes de sorgho localement adaptees et preferees en Niger. Mots-cles: sorgho, zones agroclimatiques, genomique, adaptation locale, selection genomique, Afrique subsaharienne., Introduction Sorghum (Sorghum bicolor L. Moench) is a major staple crop that is adapted to multiple agroclimatic zones of the world (Smith and Frederiksen 2000). In smallholder production systems of [...]
- Published
- 2018
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