Identification of candidate genes for basal root whorl number and basal root number in common bean Phaseolus vulgaris L.

Abstract

Phaseolusvulgaris L. ha sido usada como un modelo para entender la arquitectura radical. El número de verticilos basales de raíz y número de raíces basales son rasgos importantes de la arquitectura radical, ya que su variación puede generar cambios en el ángulo de crecimiento de la raíz que influencian la exploración del suelo y por lo tanto la toma de agua y nutrientes. En este estudio 46 marcadores moleculares tipo SSR y SNP fueron mapeados en las 114 líneas adicionales de la población of DOR364 x G19833 con el fin de obtener una población analizada de mayor tamaño y validar los QTLs para los rasgos estudiados, identificados en estudios previos en las 87 líneas originales de la población. Adicionalmente se realizó una búsqueda de genes candidatos responsables de estos rasgos basándose en los marcadores asociados a los QTLs consistentes entre ambos estudios. Por último nuevos marcadores moleculares fueron diseñados para validar estos QTLs en diferentes poblaciones de fríjol común. aqui termina el resumen en español.

//Abstract: Phaseolus vulgarisL. has been used as a model for root architecture understanding. Basal Root Whorl Number (BRWN) and Basal Root Number (BRN) are important traits in root architecture, because their variation can generate changes in root growth angle that influence the soil exploration and therefore the uptake of water and nutrients. In this study 46 molecular markers including SSR and SNP were mapped in 114 extra lines of DOR364 x G19833 population in order to obtain a bigger analyzed population and to validate the QTLs for BRWN and BRN identified in previous studies in the first 87 lines of this population. In addition, a searching of candidate genes responsible of these traits was realized based in the markers sequences associated to consistent QTLs between both studies. Finally new molecular markers were designed to validate these QTLs in different common bean populations. Phenotypic evaluation of the 114 extra lines showed that 43.86% have two whorls, followed by three and four (30.70% and 9.65% respectively). In addition, most genotypes present eight basal roots (29.82%), followed by nine (19.30%) and ten (13.16%), while a few genotypes present high number of basal roots. Six QTLs were identified in 114 extra lines of the population in the chromosomes2, 3, 6, 7 and 8. In the chromosomes 10 and 11 previously found QTL could not be confirmed in the additional lines. Two regions appeared as largely consistent between different seasons on chromosomes 2 and 7 because QTLs were detected for three years. This indicates that these are constitutive QTLs that are expressed consistently in different environments. The markers associated with these QTLs were selected to investigate genes in chromosomes 2, 3, 6 and 7, and were aligned with common bean genome to determine the candidate genes. Ten genes were identified, two of which codified to an unknown protein and the others are expressed in roots or are involved in root tissue formation and in metabolic routes occurring in this organ. Eleven allele specific markers were designed in the flanking regions of QTLs detected in chromosomes two, seven and eleven, and they were evaluated in the parents of four Mesoamerican x DG populations to determine their polymorphism, their segregation and to confirm the QTL position and phenotypic contribution of both traits. Once the QTL validation experiment has been completed, the new breeding lines should be retained for subsequent research or ideally be given to the breeding program as new germplasm.