Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.)

Bosen Jia; Robert L Conner; Waldo C Penner; Chunfang Zheng; Sylvie Cloutier; Anfu Hou; Xuhua Xia; Frank M You

doi:10.3390/ijms23147639

Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.)

Int J Mol Sci. 2022 Jul 11;23(14):7639. doi: 10.3390/ijms23147639.

Authors

Bosen Jia^{1

2}, Robert L Conner³, Waldo C Penner³, Chunfang Zheng¹, Sylvie Cloutier¹, Anfu Hou³, Xuhua Xia², Frank M You¹

Affiliations

¹ Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
² Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada.
³ Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.

Abstract

Common bean (Phaseolus vulgaris L.) is a food crop that is an important source of dietary proteins and carbohydrates. Marsh spot is a physiological disorder that diminishes seed quality in beans. Prior research suggested that this disease is likely caused by manganese (Mn) deficiency during seed development and that marsh spot resistance is controlled by at least four genes. In this study, genetic mapping was performed to identify quantitative trait loci (QTL) and the potential candidate genes associated with marsh spot resistance. All 138 recombinant inbred lines (RILs) from a bi-parental population were evaluated for marsh spot resistance during five years from 2015 to 2019 in sandy and heavy clay soils in Morden, Manitoba, Canada. The RILs were sequenced using a genotyping by sequencing approach. A total of 52,676 single nucleotide polymorphisms (SNPs) were identified and filtered to generate a high-quality set of 2066 SNPs for QTL mapping. A genetic map based on 1273 SNP markers distributed on 11 chromosomes and covering 1599 cm was constructed. A total of 12 stable and 4 environment-specific QTL were identified using additive effect models, and an additional two epistatic QTL interacting with two of the 16 QTL were identified using an epistasis model. Genome-wide scans of the candidate genes identified 13 metal transport-related candidate genes co-locating within six QTL regions. In particular, two QTL (QTL.3.1 and QTL.3.2) with the highest R² values (21.8% and 24.5%, respectively) harbored several metal transport genes Phvul.003G086300, Phvul.003G092500, Phvul.003G104900, Phvul.003G099700, and Phvul.003G108900 in a large genomic region of 16.8-27.5 Mb on chromosome 3. These results advance the current understanding of the genetic mechanisms of marsh spot resistance in cranberry common bean and provide new genomic resources for use in genomics-assisted breeding and for candidate gene isolation and functional characterization.

Keywords: Phaseolus vulgaris; QTL mapping; cranberry common bean; genome-wide association study (GWAS); genotyping by sequencing (GBS); marsh spot disease; single nucleotide polymorphisms (SNPs).

MeSH terms

Disease Resistance / genetics
Genetic Linkage
Phaseolus* / genetics
Phenotype
Plant Breeding
Polymorphism, Single Nucleotide
Quantitative Trait Loci / genetics
Vaccinium macrocarpon*
Wetlands

Grants and funding

The research was supported by the Manitoba Pulse and Soybean Growers, Agriculture and Agri-Food Canada, the Canadian Agricultural Partnership Pulse Science Cluster (CAP Pulse Cluster, ASC06 Activity 2), and Discovery Grant from Natural Science and Engineering Research Council of Canada (grant number: RGPIN/2018-03878).