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

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.

Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array

“…We filtered the genotype data using a minor allele frequency (MAF) of 0.01, maximum heterozygosity of 50%, and missing data points of 20%, which resulted in 28,798 polymorphic SNPs for statistical analyses (Table 1 , Supplementary Table S2 ). For each SNP, we obtained the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map in two steps as described in our previous study 32 . First, we used the marker name to retrieve at least 100 bp of the original sequence at http://download.txgen.tamu.edu/shichen/flanking_v2.html .…”

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

“…The remaining were detected either in the conventional managements (29 regions), organic managements (31 regions), and all seven environments regardless of the managements system (8 regions). Using four RIL populations, we recently reported a total of 44 QTLs associated with three earliness traits (Semagn et al., 2021c) and 152 QTLs associated with nine other agronomic and end‐use quality traits (Semagn et al., 2021b), of which only 22% of the QTLs were common between the conventional and organic management systems. Two of those common QTL had a major effect, each accounting for up to 37 and 58% of the phenotypic variation in sedimentation volume and plant height, respectively.…”

“…Cultivars were considered fixed, while managements, environments, replications, and blocks were considered random effects. For each marker, we obtained the IWGSC RefSeq v2.0 physical map as described in our previous study (Semagn et al, 2021c). All markers that had a minor allele frequency of <5%, a missing data of > 30%, and those that were not assigned to any chromosome based on IWGSC RefSeq v2.0 were excluded, which resulted in a total of 23,342 polymorphic markers for statistical analysis (Table 1, Supplementary Table S2).…”

“…Although QTL mapping in biparental populations is the most widely used method since the early 1990s, it has major drawbacks, including (a) the time and cost in developing the mapping populations, (b) low resolution due to a limited number of recombination events, (c) the use of old populations developed 5+ yr before the discovery studies, and (d) biparental mapping populations capture only alleles originated from their two parents. Besides, a substantial proportion of adjacent markers that differ by <1 cM are discarded due to the inability of QTL mapping software's in handling multicollinearity among tightly linked markers (Semagn et al., 2006; Wang et al., 2006), which can be avoided if physical maps are used instead of population‐specific or consensus genetic maps (Semagn et al., 2021b; Semagn et al., 2021c).…”

“…In biparental populations, we recently used IWGSC RefSeq v2.0 physical map to uncover QTL associated with agronomic and end‐use quality traits using a set of 1,058‐6,526 SNPs and Silico DArT markers scored across four RIL populations. Those studies identified a total of 44 QTLs associated with three earliness traits (Semagn et al., 2021c) and 152 QTLs associated with nine agronomic and end‐use quality traits (Semagn et al., 2021b) evaluated under low N (organic) and high N (conventional) management systems. Nearly 78% of the 196 QTLs were uncovered either in the conventional or organic management systems, which restricts the use of the QTL information for indirect selection using MAS to develop improved cultivars for both management systems.…”