QTLs Associated with Agronomic Traits in the Cutler × AC Barrie Spring Wheat Mapping Population Using Single Nucleotide Polymorphic Markers

Enid Perez-Lara; Kassa Semagn; Hua Chen; Muhammad Iqbal; Amidou N'Diaye; Atif Kamran; Alireza Navabi; Curtis Pozniak; Dean Spaner

doi:10.1371/journal.pone.0160623

QTLs Associated with Agronomic Traits in the Cutler × AC Barrie Spring Wheat Mapping Population Using Single Nucleotide Polymorphic Markers

PLoS One. 2016 Aug 11;11(8):e0160623. doi: 10.1371/journal.pone.0160623. eCollection 2016.

Authors

Enid Perez-Lara¹, Kassa Semagn¹, Hua Chen¹, Muhammad Iqbal^{1

2}, Amidou N'Diaye³, Atif Kamran⁴, Alireza Navabi⁵, Curtis Pozniak³, Dean Spaner¹

Affiliations

¹ Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada.
² National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan.
³ Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.
⁴ Seed Centre, Department of Botany, The University of Punjab, New Campus, Lahore, 54590, Pakistan.
⁵ Department of Plant Agriculture, Crop Science Building, University of Guelph, Guelph, ON N1G 2W1, Canada.

Abstract

We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars 'Cutler' and 'AC Barrie' using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study using microsatellite and DArT markers. Results from this study provide additional information to wheat researchers developing early maturing and short stature spring wheat cultivars.

MeSH terms

Chromosome Mapping
Chromosomes, Plant
Genotype
Phenotype
Plant Development / genetics
Polymorphism, Single Nucleotide
Quantitative Trait Loci*
Triticum / genetics*
Triticum / growth & development

Grants and funding

This research was supported by grants to the University of Alberta wheat breeding program from the Alberta Crop Industry Development Fund, Alberta Wheat Commission, Agriculture and Agri-Food Canada, Western Grains Research Foundation Endowment Fund and Core Program check-off funds, and an NSERC Collaborative Grant to DS. This work was conducted in part within the project “Canadian Triticum Advancement Through Genomics (CTAG).” The authors would like to acknowledge CTAG funding provided by the Saskatchewan Ministry of Agriculture, Western Grains Research Foundation, Agriculture and Agri-Food Canada, Genome Canada, Genome Prairie, Genome Alberta and Alberta Innovates. The study was also supported by a Canadian Wheat Board fellowship (CWB) to the sixth (AK), and a Chinese Government Scholarship to the third (HC) author, and Pakistani Government Fellowships to the fourth (MI) and sixth (AK) authors.