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

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 collection including accessions from 330 landraces and cultivars of Pisum 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 1-34Electronic supplementary material The online version of this article (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.

Genetic diversity, population structure and association analysis in linseed (Linum usitatissimum L.)

“…In case of linseed different types of DNA based markers includingAFLP,RAPD,retrotransposon,ISSR,SSRs,SNPetc. havebeenusedforevaluatingthegenetic diversityandlinkage mapping (Cloutier et al 2010;Oh et al 2000;Spielmeyer et al 1998).OverothertypesofDNAmarkers,SSRsarewidelyused forgeneticdiversityandstructureanalysisinseveralcropplants (Cheng et al 2015;Yan et al 2009;Cane et al 2014;Cui et al 2013). In the present investigation, we applied 50 widely distributed SSRs to evaluate the genetic diversity and identify diverseaccessions/groupofaccessionsamongalargesetof168 accessionsoflinseed.Atotalof337allelesweredetectedfrom50 SSRswithanaverageof6.74allelesperSSRs.Thisaverageallele numberwasfoundtobehigherthanthatreportedearlier (RooseAmsalegetal.2006;Dengetal.2011;Palietal.2014;Soto-Cerda etal.2012Cloutieretal.2012b).Thehigherallelenumber mightbeduetothelargeanddiversesetofaccessionsandwidely distributed SSRs used in the present study.…”

“…Association mapping is widely being utilized for detecting marker-trait association based on the genetic resources routinely used for genetic improvement programs (Font I Forcada et al 2015;Cheng et al 2015;Yan et al 2009;Cai et al 2013). As compared to biparental QTL mapping, association mapping increases the range of natural variation that can be exploited in a single experiment and potential genomic regions could be identified (Jin et al 2010).…”

Genetic Diversity of Chinese and Global Pea (Pisum sativum L.) Collections

“…association studies but are still limited in number and polymorphism (Cheng et al, 2015;Diapari et al, 2015). Single nucleotide polymorphism markers at present are therefore of less use than SSRs for germplasm studies.…”

“…The USDA core collection has also been evaluated for yield components (McPhee and Muehlbauer, 2001), mineral nutrients (Grusak et al, 2004), and seed protein content (Coyne et al, 2005). In a later study, 256 SNP markers were used to group pea accessions and identify marker ´ trait associations with 25 traits measured on single-plant-derived lines from this same collection (Cheng et al, 2015). In a later study, 256 SNP markers were used to group pea accessions and identify marker ´ trait associations with 25 traits measured on single-plant-derived lines from this same collection (Cheng et al, 2015).…”

Association of SNP markers with agronomic and quality traits of field pea in Italy

“…Single nucleotide polymorphisms (SNP) have now become the preferred markers due to their abundance and uniform distribution throughout genomes (Gupta et al 2008), as confirmed by molecular linkage maps produced by Aubert et al (2006), Deulvot et al (2010), Duarte et al (2014) and Sindhu et al (2014). However, investigations on the linkage of SNP markers with pea production, phenology or grain quality traits are relatively few (Timmerman-Vaughan et al 2005;Burstin et al 2007;Klein et al 2014;Cheng et al 2015;Jha et al 2015), and the QTL ability to explain sufficient phenotypic variation for use in MAS is controversial. One reason for that is the complex and polygenic control of most of these traits, which results in only moderate cumulative QTL effect (Tar'an et al 2004;Burstin et al 2007;Klein et al 2014).…”