Association mapping of agronomic and quality traits in USDA pea single-plant collection

• Published in: Molecular breeding 2015-02, Vol.35 (2), p.1-13, Article 75
• Main Authors: Cheng, Peng, Holdsworth, William, Ma, Yu, Coyne, Clarice J., Mazourek, Michael, Grusak, Michael A., Fuchs, Sam, McGee, Rebecca J.
• Format: Article
• Language: English
• Subjects: Agronomic crops; Agronomy; Association analysis; Biomedical and Life Sciences; Biotechnology; Carbohydrates; Collection; Color; Cultivars; Disease resistance; Flow resistance; Gene mapping; Genetic analysis; Genetic structure; Genotypes; Intermediates; Ionization; Ions; Life Sciences; Linkage disequilibrium; Low molecular weights; Mapping; Markers; Mass spectrometry; Mass spectroscopy; Molecular biology; Molecular weight; Nutrient concentrations; Organic chemistry; Pisum sativum; Plant biology; Plant Genetics and Genomics; Plant Pathology; Plant Physiology; Plant Sciences; Plants; Population structure; Seeds; Single-nucleotide polymorphism; Structural analysis
• ISSN: 1380-3743; 1572-9788
• DOI: 10.1007/s11032-015-0277-6

Association mapping is an efficient approach for the identification of the molecular basis of agronomic traits in crop plants. For this purpose in pea ( Pisum sativum L.), we genotyped and phenotyped individual lines of the single-plant-derived core collection of the USDA pea collection including accessions from 330 landraces and cultivars of Pisum sativum subsp. sativum var. sativum , 28 P . sativum subsp. elatius var. elatius , 16 P . sativum subsp. sativum var. arvense , four P . sativum subsp. elatius var. pumilio , three P . abyssinicum , two P . fulvum , and one P . sativum subsp. transcaucasicum. These 384 accessions were collected or donated from a total of 64 countries. The accessions were genotyped with 256 informative SNPs using a primer extension chemistry and matrix-assisted laser desorption/ionization (MALDI–TOF) mass spectrometry assay. Genetic structure analysis showed that the collection was structured into two main groups, corresponding roughly to the cultivated types/landraces and the more primitive form species and subspecies, with some intermediates. Linkage disequilibrium of pairwise loci and population structure of the collection were analyzed, and an association analysis between SNP genotypes and 25 valuable traits such as disease resistance, seed type/color, flower color, seed low molecular weight carbohydrate concentration, and seed mineral nutrient concentration was performed using a mixed linear model. A total of 71 marker–trait associations were detected as significant with 1–34 markers per trait based on the false discovery rate (FDR