Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)

Krishna K Gali; Yong Liu; Anoop Sindhu; Marwan Diapari; Arun S K Shunmugam; Gene Arganosa; Ketema Daba; Carolyn Caron; Reddy V B Lachagari; Bunyamin Tar'an; Thomas D Warkentin

doi:10.1186/s12870-018-1368-4

Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)

BMC Plant Biol. 2018 Aug 16;18(1):172. doi: 10.1186/s12870-018-1368-4.

Authors

Affiliations

¹ Crop Development Centre, Department of Plant Sciences, 51 Campus Drive, University of Saskatchewan, Saskatoon, SK, Canada.
² CHS, Inc, 220 Clement Ave., Grandin, ND, 58038, USA.
³ Agriculture and Agri-Food Canada, London Research and Development centre, 1391 Sandford Street, London, ON, N5V 4T3, Canada.
⁴ National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
⁵ AgriGenome Labs Pvt Ltd., BTIC, MN iHub, Genome Valley, Shamirpet, Hyderabad, 500 078, India.
⁶ Crop Development Centre, Department of Plant Sciences, 51 Campus Drive, University of Saskatchewan, Saskatoon, SK, Canada. tom.warkentin@usask.ca.

Abstract

Background: The objective of this research was to map quantitative trait loci (QTLs) of multiple traits of breeding importance in pea (Pisum sativum L.). Three recombinant inbred line (RIL) populations, PR-02 (Orb x CDC Striker), PR-07 (Carerra x CDC Striker) and PR-15 (1-2347-144 x CDC Meadow) were phenotyped for agronomic and seed quality traits under field conditions over multiple environments in Saskatchewan, Canada. The mapping populations were genotyped using genotyping-by-sequencing (GBS) method for simultaneous single nucleotide polymorphism (SNP) discovery and construction of high-density linkage maps.

Results: After filtering for read depth, segregation distortion, and missing values, 2234, 3389 and 3541 single nucleotide polymorphism (SNP) markers identified by GBS in PR-02, PR-07 and PR-15, respectively, were used for construction of genetic linkage maps. Genetic linkage groups were assigned by anchoring to SNP markers previously positioned on these linkage maps. PR-02, PR-07 and PR-15 genetic maps represented 527, 675 and 609 non-redundant loci, and cover map distances of 951.9, 1008.8 and 914.2 cM, respectively. Based on phenotyping of the three mapping populations in multiple environments, 375 QTLs were identified for important traits including days to flowering, days to maturity, lodging resistance, Mycosphaerella blight resistance, seed weight, grain yield, acid and neutral detergent fiber concentration, seed starch concentration, seed shape, seed dimpling, and concentration of seed iron, selenium and zinc. Of all the QTLs identified, the most significant in terms of explained percentage of maximum phenotypic variance (PV_max) and occurrence in multiple environments were the QTLs for days to flowering (PV_max = 47.9%), plant height (PV_max = 65.1%), lodging resistance (PV_max = 35.3%), grain yield (PV_max = 54.2%), seed iron concentration (PV_max = 27.4%), and seed zinc concentration (PV_max = 43.2%).

Conclusion: We have identified highly significant and reproducible QTLs for several agronomic and seed quality traits of breeding importance in pea. The QTLs identified will be the basis for fine mapping candidate genes, while some of the markers linked to the highly significant QTLs are useful for immediate breeding applications.

Keywords: Pea; Pisum sativum L.; Quantitative trait loci.

MeSH terms

Ascomycota / physiology*
Chromosome Mapping*
Disease Resistance / genetics
Genetic Linkage*
Genotype*
Phenotype
Pisum sativum / genetics*
Pisum sativum / physiology
Plant Diseases / microbiology
Polymorphism, Single Nucleotide
Quantitative Trait Loci*