Association mapping and genomic selection for sorghum adaptation to tropical soils of Brazil in a sorghum multiparental random mating population

Bernardino Karine C., de Menezes Cícero B., de Sousa Sylvia M., Guimaraes Claudia Teixeira, Carneiro Pedro C.S., Schaffert Robert E., Kochian Leon V., Hufnagel Maciel Bárbara, Pastina Maria Marta, Magalhaes Jurandir V.. 2021. Association mapping and genomic selection for sorghum adaptation to tropical soils of Brazil in a sorghum multiparental random mating population. Theoretical and Applied Genetics, 134 (1) : 295-312.

Quartile : Outlier, Sujet : HORTICULTURE / Quartile : Q1, Sujet : AGRONOMY / Quartile : Q1, Sujet : GENETICS & HEREDITY / Quartile : Q1, Sujet : PLANT SCIENCES

Résumé : Tropical soils where low phosphorus (P) and aluminum (Al) toxicity limit sorghum [Sorghum bicolor (L.) Moench] production are widespread in the developing world. We report on BRP13R, a multiparental random mating population (MP-RMP), which is commonly used in sorghum recurrent selection targeting tropical soil adaptation. Recombination dissipated much of BRP13R's likely original population structure and average linkage disequilibrium (LD) persisted up to 2.5 Mb, establishing BRP13R as a middle ground between biparental populations and sorghum association panels. Genome-wide association mapping (GWAS) identified conserved QTL from previous studies, such as for root morphology and grain yield under low-P, and indicated the importance of dominance in the genetic architecture of grain yield. By overlapping consensus QTL regions, we mapped two candidate P efficiency genes to a ~ 5 Mb region on chromosomes 6 (ALMT) and 9 (PHO2). Remarkably, we find that only 200 progeny genotyped with ~ 45,000 markers in BRP13R can lead to GWAS-based positional cloning of naturally rare, subpopulation-specific alleles, such as for SbMATE-conditioned Al tolerance. Genomic selection was found to be useful in such MP-RMP, particularly if markers in LD with major genes are fitted as fixed effects into GBLUP models accommodating dominance. Shifts in allele frequencies in progeny contrasting for grain yield indicated that intermediate to minor-effect genes on P efficiency, such as SbPSTOL1 genes, can be employed in pre-breeding via allele mining in the base population. Therefore, MP-RMPs such as BRP13R emerge as multipurpose resources for efficient gene discovery and deployment for breeding sorghum cultivars adapted to tropical soils.

Mots-clés Agrovoc : Sorghum bicolor, amélioration des plantes, sélection, génome, sélection récurrente, carte génétique, adaptation physiologique, génotype, locus, génomique, sol tropical, zone tropicale, diversité génétique (comme ressource), Sorghum

Mots-clés géographiques Agrovoc : Brésil

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Agences de financement hors UE : Consortium of International Agricultural Research Centers, Empresa Brasileira de Pesquisa Agropecuária, Fundação de Amparo à Pesquisa do Estado de Minas Gerais, Conselho Nacional de Desenvolvimento Científico e Tecnológico

Auteurs et affiliations

• Bernardino Karine C., UFV (BRA)
• de Menezes Cícero B., EMBRAPA (BRA)
• de Sousa Sylvia M., EMBRAPA (BRA)
• Guimaraes Claudia Teixeira, EMBRAPA (BRA)
• Carneiro Pedro C.S., UFV (BRA)
• Schaffert Robert E., EMBRAPA (BRA)
• Kochian Leon V., University of Saskatchewan (CAN)
• Hufnagel Maciel Bárbara, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-3515-2122
• Pastina Maria Marta, EMBRAPA (BRA) - auteur correspondant
• Magalhaes Jurandir V., EMBRAPA (BRA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/609587/)

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