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 < 0.05). This study demonstrates the potential of using association mapping to identify markers for pea breeding.
- Supplementary material: Phenotypic data for each trait of PSP collectionxlsx
Direct download, xlsx, 83 Kb.
- Supplementary material: Primers used in Sequenom MassArray for SNPsxlsx
Direct download, xlsx, 46 Kb.
- Supplementary material: Plot of mean likelihood L(K) and variance per K value from STRUCTUREData
Plot of mean likelihood L(K) and variance per K value from STRUCTURE (upper...
- Supplementary material: Linkage disequilibrium (LD) plot of 203 SNPs with the genetic distance (cM) information. Data
Lower left are linkage disequilibrium P values and upper right are r^2...
- Supplementary material: Intra-chromosomal LD (r^2) decay of marker pairs over all chromosomes as a function of genetic distance (cM)Data
The horizontal line indicates the 95th percentile distribution of unlinked r...
- Supplementary material: The linkage disequilibrium (LD) overview for the PSP collection calculated using 203 SNPsData
Direct download, docx, 21 Kb.
|Release Date|| |
|Contact Name|| |
McGee, Rebecca J.
|Public Access Level|| |
|Program Code|| |
005:040 - Department of Agriculture - National Research
|Bureau Code|| |
005:18 - Agricultural Research Service