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Genome-wide association study for grain mineral content in a Brazilian common bean diversity panel

Key message

QTNs significantly associated to nine mineral content in grains of common bean were identified. The accumulation of favorable alleles was associated with a gradually increasing nutrient content in the grain.

Abstract

Biofortification is one of the strategies developed to address malnutrition in developing countries, the aim of which is to improve the nutritional content of crops. The common bean (Phaseolus vulgaris L.), a staple food in several African and Latin American countries, has excellent nutritional attributes and is considered a strong candidate for biofortification. The objective of this study was to identify genomic regions associated with nutritional content in common bean grains using 178 Mesoamerican accessions belonging to a Brazilian Diversity Panel (BDP) and 25,011 good-quality single nucleotide polymorphisms. The BDP was phenotyped in three environments for nine nutrients (phosphorus, potassium, calcium, magnesium, copper, manganese, sulfur, zinc, and iron) using four genome-wide association multi-locus methods. To obtain more accurate results, only quantitative trait nucleotides (QTNs) that showed repeatability (i.e., those detected at least twice using different methods or environments) were considered. Forty-eight QTNs detected for the nine minerals showed repeatability and were considered reliable. Pleiotropic QTNs and overlapping genomic regions surrounding the QTNs were identified, demonstrating the possible association between the deposition mechanisms of different nutrients in grains. The accumulation of favorable alleles in the same accession was associated with a gradually increasing nutrient content in the grain. The BDP proved to be a valuable source for association studies. The investigation of different methods and environments showed the reliability of markers associated with minerals. The loci identified in this study will potentially contribute to the improvement of Mesoamerican common beans, particularly carioca and black beans, the main groups consumed in Brazil.

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Data availability

The data that support the findings of this study are available as supplementary material.

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Acknowledgements

The authors would like to thank the Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná) and the University of California, Davis (through the Gepts’ Lab) for supporting this research and the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior–Brasil (CAPES) for the scholarship to JD in Brazil and abroad (Finance Code 001).

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J.D., V.M.C., and L.S.A.G. conceived and designed the study; J.D. collected plant material, extracted DNA, and performed the genotyping; J.D., J.S.N., A.F.N., L.A.B.R., and D.M.Z. performed the phenotyping; J.D. and L.S.A.G. performed bioinformatics and statistical analyses; J.D. drafted the manuscript; J.D., V.M.C., J.S.N., D.M.Z., P.M.R, P.G., and L.S.A.G. edited and revised the final manuscript. All authors read and approved the final manuscript.

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Correspondence to Leandro Simões Azeredo Gonçalves.

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Delfini, J., Moda-Cirino, V., dos Santos Neto, J. et al. Genome-wide association study for grain mineral content in a Brazilian common bean diversity panel. Theor Appl Genet 134, 2795–2811 (2021). https://doi.org/10.1007/s00122-021-03859-2

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