Physical Mapping of QTL in Four Spring Wheat Populations under Conventional and Organic Management Systems. I. Earliness.

Amidou N’Diaye,Atif Kamran,Curtis Pozniak,Darcy H Bemister,Dean Spaner,Jun Zou,Kassa Semagn,Enid Perez-Lara,Muhammad Asif,Harpinder Randhawa,Rongrong Xiang,Hua Chen,Muhammad Iqbal

doi:10.3390/plants10050853

Abstract

In previous studies, we reported quantitative trait loci (QTL) associated with the heading, flowering, and maturity time in four hard red spring wheat recombinant inbred line (RIL) populations but the results are scattered in population-specific genetic maps, which is challenging to exploit efficiently in breeding. Here, we mapped and characterized QTL associated with these three earliness traits using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map. Our data consisted of (i) 6526 single nucleotide polymorphisms (SNPs) and two traits evaluated at five conventionally managed environments in the ‘Cutler’ × ‘AC Barrie’ population; (ii) 3158 SNPs and two traits evaluated across three organic and seven conventional managements in the ‘Attila’ × ‘CDC Go’ population; (iii) 5731 SilicoDArT and SNP markers and the three traits evaluated at four conventional and organic management systems in the ‘Peace’ × ‘Carberry’ population; and (iv) 1058 SNPs and two traits evaluated across two conventionally and organically managed environments in the ‘Peace’ × ‘CDC Stanley’ population. Using composite interval mapping, the phenotypic data across all environments, and the IWGSC RefSeq v2.0 physical maps, we identified a total of 44 QTL associated with days to heading (11), flowering (10), and maturity (23). Fifteen of the 44 QTL were common to both conventional and organic management systems, and the remaining QTL were specific to either the conventional (21) or organic (8) management systems. Some QTL harbor known genes, including the Vrn-A1, Vrn-B1, Rht-A1, and Rht-B1 that regulate photoperiodism, flowering time, and plant height in wheat, which lays a solid basis for cloning and further characterization.

Highlights

The application of nitrogen (N), phosphorus (P), and potassium (K) nutrients through the application of chemical fertilizers have become a standard conventional practice for increasing yield and yield components
Our study was based on a total of 698 recombinant inbred line (RIL) from four biparental populations, which were evaluated under conventional and organic management systems and genotyped either with the wheat 90K iSelect single nucleotide polymorphisms (SNPs) array or the DArT-based genotyping by sequencing (DArTseq) technology (Table 1)
Using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq 2.0 physical map and phenotype data of four RIL mapping populations evaluated under conventional and organic management systems, we mapped and characterized a total of 44 quantitative trait loci (QTL) associated with a heading (11), flowering (10), and maturity (23) dates in hard red spring wheat

Summary

Introduction

The application of nitrogen (N), phosphorus (P), and potassium (K) nutrients through the application of chemical fertilizers have become a standard conventional practice for increasing yield and yield components. Excess use of chemical fertilizers under the conventional management system (high-N) increases the costs of crop production and reduces nitrogen use efficiency (NUE) and causes environmental damage, which is shifting the wheat (Triticum aestivum L.) breeding programs towards low input agricultural practices [1]. The wheat breeding group at the University of Alberta has been conducting extensive research in the Canada Western Red Spring (CWRS) wheat class, including (i) developing several improved cultivars [7,8,9,10], (ii) evaluating the phenotypic performance of diverse cultivars under conventional and/or organic managements [11,12,13,14,15,16], (iii) understanding the genetics of earliness that serves as baseline data for developing early maturing cultivars to avoid frost damage [17,18,19,20], and (iv) mapping genes and QTL associated with diverse traits using biparental populations [19,21,22,23,24,25,26,27] and a genomewide association mapping panel [28,29]. That study uncovered 19 QTL associated with four traits, including six QTL for flowering and five QTL for maturity [23]

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Conclusion