QTL mapping and identification of genes associated with the resistance to Acanthoscelides obtectus in cultivated common bean using a high-density genetic linkage map

Abstract

Background Common bean (Phaseolus vulgaris L.) is an important agricultural product with large nutritional value, and the insect pest Acanthoscelides obtectus (Say) seriously affects its product quality and commodity quality during storage. Few researches on genes of bruchid resistance have investigated in common bean cultivars. Results In this study, a bruchid-resistant cultivar black kidney bean and a highly susceptible accession Longyundou3 from different gene banks were crossed to construct a recombinant inbred line population. The genetic analysis indicated a quantitative inheritance of the bruchid resistance trait controlled by polygenes. A high-density genetic map of a total map distance of 1283.68 cM with an average interval of 0.61 cM between each marker was constructed using an F6 population of 157 recombinant inbred lines. The map has 3106 bin markers, containing 2,234,769 SNPs. Using the high-density genetic map, a new quantitative trait locus for the resistance to Acanthoscelides obtectus was identified on chromosome 6. New molecular markers based on the candidate region were developed, and this locus was further delimited to an interval of 122.3 kb between SSR markers I6–4 and I6–16 using an F2 population. This region comprised five genes. Phvul.006G003700, which encodes a bifunctional inhibitor, may be a potential candidate gene for bruchid resistance. Sequencing analysis of candidate gene identified a 5 bp insertion-deletion in promoter of gene Phvul.006G003700 between two parents. Expression analysis of candidate gene revealed that the expression level of Phvul.006G003700 in bruchid-resistant parent was markedly higher than that in bruchid-susceptible parent both in dry seeds and leaves. Conclusions A high-density genetic linkage map was constructed utilizing whole-genome resequencing and one new QTL for bruchid resistance was identified on chromosome 6 in common bean cultivar. Phvul.006G003700 (encoding a bifunctional inhibitor) may be a potential candidate gene. These results may form the basis for further research to reveal the bruchid resistance molecular mechanism of common bean.

Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance

“…Orthologs of the APA locus are present in tepary bean and transgenic azuki beans with tepary α ‐amylase inhibitor genes providing functional inhibition of insect α ‐amylases (Mirkov et al., 1994; Yamada et al., 2001). High resolution mapping of resistance to A. obtectus in a common bean recombinant inbred line population identified Phvul.006G003700 in the P. vulgaris v1.0 genome (Phvul.007G119178 in v2.1 P. vulgaris genome) as the causal gene which encodes an AAI‐LTSS (alpha‐amylase inhibitor [AAI], lipid transfer [LT] and seed storage [SS]) protein superfamily protein and speculated to function by inhibiting α ‐amylase (Li et al., 2022).…”

SeQual-Stream: approaching stream processing to quality control of NGS datasets

“…For example, SparkGATK [ 36 ], a framework for DNA analysis, has been used to detect allele-specific expression genes in plants [ 37 ]. SparkBWA [ 38 ], a DNA sequence alignment tool, has been used in [ 39 ] as part of the analysis pipeline to construct a high-density genetic linkage map for the common bean and identify a gene resistant to the bruchid, as well as to analyze the growth plasticity of bacteria in [ 40 ].…”

Introgression and Stability of Common Bean Weevil (Acanthoscelides obtectus [Say]) Resistance in Diverse Market Classes From the Andean Gene Pool of Common Bean

“…Li et al. (2022) also mapped one QTL for bruchid resistance on Pv06 using a bruchid‐resistant black bean. However, this QTL was in a different physical position to that of Kamfwa et al.…”

“…Kamfwa et al (2018) mapped the APA locus on Pv04 and reported additional resistance QTL on Pv06 using an Andean population of recombinant inbred lines derived from a cross of AO-3A and Solwezi. Li et al (2022) also mapped one QTL for bruchid resistance on Pv06 using a bruchid-resistant black bean. However, this QTL was in a different physical position to that of Kamfwa et al (2018).…”