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

posted on 2024-02-13, 13:27 authored by Peng Cheng, William L. Holdsworth, Yu Ma, Clarice J. Coyne, Michael Mazourek, Michael A. Grusak, Sam Fuchs, Rebecca J. McGee

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.

Resources in this dataset:




Data contact name

McGee, Rebecca J.

Data contact email


Molecular Breeding


  • Not specified

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

chromosome mapping; agronomic traits; crops; peas; Pisum sativum; genotyping; USDA; landraces; cultivars; single nucleotide polymorphism; chemistry; desorption; ionization; matrix-assisted laser desorption-ionization mass spectrometry; mass spectrometry; linkage disequilibrium; loci; population structure; genotype; disease resistance; color; flowers; molecular weight; carbohydrates; nutrient content; linear models; breeding; marker-assisted selection

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 301

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Cheng, Peng; Holdsworth, William L.; Ma, Yu; Coyne, Clarice J.; Mazourek, Michael; Grusak, Michael A.; Fuchs, Sam; McGee, Rebecca J. (2019). Data from: Association mapping of agronomic and quality traits in USDA pea single-plant collection. Molecular Breeding.

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