Abstract
Recently, we investigated the effect of the wheat 90K single nucleotide polymorphic (SNP) array and three gene-specific (Ppd-D1, Vrn-A1 and Rht-B1) markers on quantitative trait loci (QTL) detection in a recombinant inbred lines (RILs) population derived from a cross between two spring wheat (Triticum aestivum L.) cultivars, ‘Attila’ and ‘CDC Go’, and evaluated for eight agronomic traits at three environments under organic management. The objectives of the present study were to investigate the effect of conventional management on QTL detection in the same mapping population using the same set of markers as the organic management and compare the results with organic management. Here, we evaluated 167 RILs for number of tillers (tillering), flowering time, maturity, plant height, test weight (grain volume weight), 1000 kernel weight, grain yield, and grain protein content at seven conventionally managed environments from 2008 to 2014. Using inclusive composite interval mapping (ICIM) on phenotypic data averaged across seven environments and a subset of 1203 informative markers (1200 SNPs and 3 gene specific markers), we identified a total of 14 QTLs associated with flowering time (1), maturity (2), plant height (1), grain yield (1), test weight (2), kernel weight (4), tillering (1) and grain protein content (2). Each QTL individually explained from 6.1 to 18.4% of the phenotypic variance. Overall, the QTLs associated with each trait explained from 9.7 to 35.4% of the phenotypic and from 22.1 to 90.8% of the genetic variance. Three chromosomal regions on chromosomes 2D (61–66 cM), 4B (80–82 cM) and 5A (296–297 cM) harbored clusters of QTLs associated with two to three traits. The coincidental region on chromosome 5A harbored QTL clusters for both flowering and maturity time, and mapped about 2 cM proximal to the Vrn-A1 gene, which was in high linkage disequilibrium (0.70 ≤ r2 ≤ 0.75) with SNP markers that mapped within the QTL confidence interval. Six of the 14 QTLs (one for flowering time and plant height each, and two for maturity and kernel weight each) were common between the conventional and organic management systems, which suggests issues in directly utilizing gene discovery results based on conventional management to make in detail selection (decision) for organic management.
Highlights
More than 85% of wheat in Canada is produced in the western Canadian prairie provinces of Alberta, Saskatchewan and Manitoba, with a small proportion in British Columbia and eastern Canada [1]
In one of the recent studies [9], we evaluated a recombinant inbred line (RIL) population developed from a cross between ‘Attila’ (CM8583650Y-0M-0Y-3M-0Y) [18] and ‘CDC Go’ in 2008, 2009 and 2010 under conventionally and organically managed field conditions and genotyped the population with 579 diversity arrays technology (DArT) and the Rht-B1 gene specific markers
Using the averaged phenotypic data across three environments, (i) we uncovered three quantitative trait loci (QTL) under conventional management that were associated with plant height, grain yield and test weight, but none for tillering, kernel weight, grain protein content, days to flowering and maturity; (ii) we found five QTLs under organic management that were associated with plant height, test weight, grain protein content and kernel weight, but none for flowering time, maturity, number of tillers and grain yield; and (iii) only a single QTL for plant height on 4B was common between the conventional and organic management systems
Summary
More than 85% of wheat in Canada is produced in the western Canadian prairie provinces of Alberta, Saskatchewan and Manitoba, with a small proportion in British Columbia and eastern Canada [1]. Wheat breeders in western Canada primarily develop short stature cultivars that are early maturing, high yielding with high protein content and elevated dough strength. Wheat cultivars to be registered in western Canada must have at least intermediate resistance to leaf rust Most wheat breeders in western Canada develop semi-dwarf cultivars, which require high inputs (high nitrogen fertilizers, high pesticides and herbicides) to produce high grain yield and attain satisfactory protein content, but such cultivars types often produce lower grain yield in organic management due to weaker weed competitiveness [5]. Taller plants exhibit better competitive ability against weeds in organic management than shorter ones, mainly due to better light interception [6,7,8], but suffer lodging under high input demanding conventional management. Most traits of interest in breeding for conventional management are similar to organic management, some of the traits relevant to the high-input demanding conventional farming may have negative effects in organic systems
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