Phenotypic performance and associated QTL of ‘Peace’ × ‘CDC Stanley’ mapping population under conventional and organic management systems

Abstract

Identification of consistent QTL in both conventional and organic management systems is a prerequisite for improving spring wheat (Triticum aestivum) through marker‐assisted selection. The objectives of the present study were to continue investigating the effect of management systems on agronomic and end‐use quality traits, and map associated quantitative trait loci (QTL) in a hard red spring wheat population. We evaluated 165 recombinant inbred lines derived from ‘Peace’ × ‘CDC Stanley’ for nine agronomic and end‐use quality traits under conventional and organic management systems for 2 yr and genotyped them with the wheat 90K iSelect array. Using inclusive composite interval mapping on phenotypic data across two environments per management and the International Wheat Genome Sequence Consortium (IWGSC) RefSeq v2.0 physical map of 1,058 informative single nucleotide polymorphisms, we uncovered 32 QTL (17 under conventional and 15 under organic) associated with nine traits of which five QTL were common in both managements. The remaining QTL were specific either to the conventional (12) or organic (10) managements. Each QTL explained from 1.2 to 19.2% and together accounted for 3.0 to 28.4% and 3.3 to 21.9% of the total phenotypic variance of each trait evaluated under conventional and organic management systems, respectively. We found three coincident genomic regions on chromosomes 1B, 3B, and 4B associated with two and three traits. All QTL identified in the present study were not reported in any of our previous mapping populations and would provide more data to wheat researchers conducting similar studies under conventional and organic management systems.

Genome‐wide association mapping of agronomic traits and grain characteristics in spring wheat under conventional and organic management systems

“…Test weight is a measure of grain density, which is expressed as the weight of the grain packed in a specified volume, while TKW refers to the weight of 1,000 randomly sampled grains (kernels). The detailed phenotyping method has been described in our previous study (Xiang et al., 2021). Briefly, the conventionally and organically managed fields were about 500 m apart.…”

“…The wheat breeding program of the University of Alberta conducted mapping studies in biparental populations (Chen et al., 2015; Chen et al., 2016; Zou et al., 2017a; Semagn et al., 2021b, ; Xiang et al., 2021) and an association mapping panel (Chen et al., 2017; Perez‐Lara et al., 2017b). In one of our previous studies, we evaluated 81 diverse Canadian spring wheat cultivars for six traits (heading, plant maturity, plant height, test weight, grain yield, and GPC) across six environments.…”

Genomic Prediction Accuracy of Stripe Rust in Six Spring Wheat Populations by Modeling Genotype by Environment Interaction

“…The present study was conducted on six Canadian spring wheat populations (Table S4) that consisted of an association mapping (diversity) panel of 196 historical and modern spring wheat varieties and unregistered lines [53], 208 RILs derived from the cross Peace/Carberry [54], 167 RILs derived from Attila/CDC Go [55], 153 RILs from Peace/CDC Stanley [56], 190 RILs from AAC Cameron/P2711 [57], and 190 DH lines from AAC Innova/AAC Proclaim [58]. The RILs were advanced to F 6 using the single seed descent method, while the DH lines were developed from F 1 s at the Agriculture and Agri-Food Canada (AAFC) Research and Development Center in Lethbridge, AB, CA, using the wheat-maize hybridization method [59].…”

“…The diversity panel, Attila/CDC Go, and Peace/CDC Stanley populations were genotyped with the Wheat 90 K iSelect single nucleotide polymorphisms (SNPs) arrays at the University of Saskatchewan Wheat Genomics lab, Saskatoon, Canada, as described in the previous studies [22,56]. The Peace/Carberry population was genotyped with a total of 36,626 markers (22,741 SilicoDArT markers with present/absent variation and 13,885 SNPs) using the DArTseq technology (https://www.diversityarrays.com (accessed on 28 June 2022)), Canberra, Australia.…”

Identification of Spring Wheat with Superior Agronomic Performance under Contrasting Nitrogen Managements Using Linear Phenotypic Selection Indices

“…The five breeding methods employed to develop cultivars for organic agriculture are the following: (i) indirect selection under conventional management, (ii) direct selection under organic management in all generations, (iii) selection under conventional management in early generations, followed by selection under organic management in advanced generations, (iv) marker-assisted selection (MAS), and (iv) genomic selection [ 4 , 14 , 15 ]. The University of Alberta Wheat Program, Edmonton, AB, has studied the pros and cons of these methods in diverse spring wheat lines and cultivars evaluated under both conventional and organic management systems, including comparing yield components [ 16 , 17 , 18 ], the performance of sole crop with mixtures [ 19 , 20 ], weed and nutrient competitive abilities [ 8 , 9 , 21 ], breadmaking quality [ 22 ], mapping genes and quantitative trait loci (QTL) associated with agronomic traits [ 23 , 24 , 25 , 26 , 27 , 28 , 29 ], and comparing the prediction accuracies of different genomic selection models [ 30 , 31 ]. Recently, we reported the physical positions of 44 QTLs associated with heading, flowering, and maturity [ 26 ] and 152 QTLs associated with nine agronomic and end-use quality traits in four recombinant inbred line (RIL) populations, which were evaluated under conventional and organic management systems [ 25 ].…”