QTLs associated with agronomic traits in the Attila × CDC Go spring wheat population evaluated under conventional management

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.

Uncovering the Genetic Architecture of Fruiting Efficiency in Bread Wheat: A Viable Alternative to Increase Yield Potential

“…The marker Kukri_ rep_c68594_530 (12.7 Mb) on 4D associated with FE in our study was also reported in the same region linked to Rht-D1 (Sun et al, 2017). In addition, the marker Kukri_ C12384_430 associated with Vrn-A1 reported by Zou et al (2017) was close to the marker BobWhite_c8266_227 (698.5 Mb) linked to FE on 5A in the present study. Regarding SW, to our knowledge, this is the first study to provide evidence of its genetic basis in bread wheat.…”

“…Related genomic regions associated with grain yield, GNS, and TKW have been previously reported in almost the entire wheat genome (Deng et al, 2011; Cui et al, 2012; Deng et al, 2017; Guo et al, 2017; Sun et al, 2017; Zou et al, 2017; Liu et al, 2018; Su et al, 2018; Yu et al, 2018; Zhai et al, 2018). In this study, we found significant SNPs markers on 2A, 2B, and 7A for GWS; on 1B, 2A, 2B, and 7A for TKW; and on 1A, 2B, and 2D for GNS.…”

Mapping quantitative trait loci associated with leaf rust resistance in five spring wheat populations using single nucleotide polymorphism markers

“…The best order of markers was generated using both "AutoCheckInversions" and "AutoRipple" commands. Then, we built a consensus map based on fourteen hexaploid wheat mapping populations including the five QTL populations (Carberry/AC Cadillac, Carberry/Vesper, Vesper/ Lillian, Stettler/Vesper and Stettler/Red fife) used in the current leaf rust resistance mapping study and nine others, namely: 8021V2/AC Karma [30], AAC Concord/CDC Hughes, Attila/ CDC Go [31], Carberry/Thatcher, Cutler/AC Barrie [28], Norstar/Capelle Despres [29], Norstar/Manitou [29], Norstar/Winter Manitou [29] and RL4452/AC Domain. In addition to SNP markers, 8021V2/AC Karma was genotyped with 529 microsatellite or simple sequence repeat (SSR) [32][33][34] markers.…”

Grain Protein Content QTLs Identified in a Durum × Wild Emmer Wheat Mapping Population Tested in Five Environments

“…Taking into account that the cultivated parental line Svevo is a semi-dwarf cultivar carrying the dwarf allele of this gene (De Santis et al 2018) and Y12-3 is a tall WEW (Peleg et al 2005), we assume that this gene may exhibit a strong effect on all agronomical traits. Moreover, other studies in wheat also showed a possible effect of this gene on GPC, which makes Rht-B1 a strong CG for the detected QTL (Fowler et al 2016; Zou et al 2017). Members of NRT1/PTR family of proton-coupled transporters, which are involved in nitrogen metabolism in different plant species (Fang et al 2013; Naz et al 2017; Castro-Rodriguez et al 2017; Corratge-Faillie and Lacombe 2017) and, hence, influencing protein accumulation, were identified within five QTL intervals in the S×Y population and were selected as promising CGs.…”