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

Jessica Delfini,Paul Gepts,Vânia Moda-Cirino,Luriam Aparecida Brandão Ribeiro,Alison Fernando Nogueira,Douglas Mariani Zeffa,Paulo Maurício Ruas,Leandro Simões Azeredo Gonçalves,José Dos Santos Neto

doi:10.1007/s00122-021-03859-2

Abstract

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. 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.

Highlights

Of the leguminous plants consumed by humans, the common bean (Phaseolus vulgaris L.) has the highest worldwide demand and is widely cultivated, accounting for approximately 41.712 million hectares annually (RAWAL and NAVARRO 2019)
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 discovery of genes or genomic regions associated with the nutritional contents of common bean grains may accelerate the development of new biofortified cultivars

Summary

Introduction

Of the leguminous plants consumed by humans, the common bean (Phaseolus vulgaris L.) has the highest worldwide demand and is widely cultivated, accounting for approximately 41.712 million hectares annually (RAWAL and NAVARRO 2019). It is considered a staple food for the populations of numerous countries, in Latin America and Eastern and Southern Africa (Broughton et al 2003). The process of improving nutrient contents in crops is referred to as biofortification, which is known as a sustainable and economic strategy to address malnutrition in developing countries, considering its focus on improving the staple foods consumed on a daily basis (Dwivedi et al 2012). Genetic biofortification is considered the most effective option in terms of costs and efficiency, given that as inbred lines with higher nutrient contents are developed, they can be used on a large scale without requiring further investment (Cu et al 2020)

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