|Coyne, Clarice - Clare|
Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/12/2014
Publication Date: 2/8/2015
Citation: Cheng, P., Holdsworth, W., Ma, Y., Coyne, C.J., Mazourek, M., Grusak, M.A., Fuchs, S., Mcgee, R.J. 2015. Phylogenetic analysis and association mapping for agronomic and quality traits in the USDA pea single-plant collection. Molecular Breeding. 35:75. doi: 10.1007/s11032-015-0277-6. Interpretive Summary: domesticated legume crops. Dry pea ranks second to common bean as the most widely grown grain legume in the world, with a global production of 9.83 M tons in 2012 . Pea is a highly nutritious source of food and fodder, as it has high levels of protein, slowly digestible starch, soluble sugar, fiber, minerals and vitamins. Additionally, pea contributes to the quality of natural resources; pea requires minimal inputs and serves as a rotation crop in predominantly cereal-based cropping systems. Crops that follow pea benefit from nitrogen fixed by Rhizobium spp. bacteria that form symbiotic relationships with pea. Germplasm collections are important sources of genes for improving disease resistance and for maintaining valuable traits for breeding programs. Worldwide, there are approximately 16 national genebanks that contain important genetic diversity collections of Pisum. The USDA collection contains over 6000 accessions, including the pea core collection which is comprised of 384 accessions collected or donated from 64 countries. The core collection was constructed to maximize diversity of origin and flower color, using a proportional logarithmic model to determine the appropriate number of accessions per country. The USDA pea core collection has been evaluated extensively for a variety of agronomic and morphological traits, disease and pest resistances, stem and root traits and protein and micronutrient content. This information can be found through the USDA Agricultural Research Service’s Germplasm Resources Information Network (GRIN) National Plant Germplasm System database (www.ars-grin.gov/npgs/). Morphological descriptors are widely used in characterizing germplasm collections, but these can be unreliable due to environmental influence and genetic heterogeneity naturally associated with landraces; in contrast, molecular markers accurately represent the underlying genetic variation and become an important tool in maintaining germplasm collections, understanding relationships between taxa, and in elucidating genetic diversity. In the history of pea genetic studies, many types of molecular markers have been used with various levels of success. Recently, the growing availability of Single Nucleotide Polymorphism (SNP) markers and high-throughput parallel genotyping has facilitated genome-wide association studies (GWAS) as well as genomic selection. Association mapping based on linkage disequilibrium (LD) provides a powerful tool for studying complex quantitative traits in plants, using both genome-wide and candidate-gene approaches. Marker-trait associations (MTAs) have been widely identified in many plant germplasm collections such as maize, tomato, sorghum, soybean, rice and pea. In this study we describe the phylogenetic relationships of 384 accessions of the USDA PSP population as well as describe associations between important agronomic and quality traits and previously published gene-anchored SNP markers.
Technical Abstract: 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 single-plant (PSP) collection including accessions from 327 landraces and cultivars of Pisum sativum, 26 P. sativum subsp. elatius, 16 P. sativum var. arvense, 4 P. sativum var. pumilio, 3 P. sativum subsp. asiaticum, 3 P. abyssinicum, 2 P. fulvum, 2 Pisum spp., and 1 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 population was structured into two main groups, corresponding roughly to the cultivated types/landraces and the wild subspecies, with some intermediates. Linkage disequilibrium (LD) of pairwise loci and population structure were analyzed, and an association analysis between SNP genotypes and 37 valuable traits such as disease resistance, seed type/color, flower color, carbohydrate content, and mineral nutrient concentration were performed using a mixed linear model. A total of 43 marker trait associations (MTAs) were detected that were significant with 1-8 markers per trait. Some of these gene-anchored SNP markers revealed candidate genes and confirmed quantitative trait loci that have been identified previously. This study demonstrates the potential of using association mapping to identify markers for pea breeding.