Mapping genomic regions controlling agronomic traits in spring wheat under conventional and organic managements

Abstract

Identification of quantitative trait loci (QTL) associated with important traits is one of the first steps towards deploying marker-assisted selection, but the lack of stability and consistency in identifying QTL across environments and populations remains a limitation. We conducted this study to identify QTL associated with agronomic traits in wheat (Triticum aestivum L.) across management-specific environments. A total of 204 wheat lines derived from the 'Peace' × 'Carberry' cross were evaluated in 2016 and 2017 under conventional and organic managements in Edmonton, Canada, and genotyped with diversity arrays technology markers. Using the leastsquares means for each management system, 53 QTL were identified for nine agronomic traits, 14 of which were consistently identified in both managements. The largest QTL we identified was associated with plant height (QPht.dms-4B), which might be the plant height-reducing gene Rht-B1b from 'Carberry'. It explained 54 and 49% of the phenotypic variation in conventional and organic management, respectively. The second largest QTL was associated with gluten strength (QSds.dms-1A) in both managements. We identified consistent QTL across both organic and conventional managements, even though they were generally minor-effect QTL. Twelve organic management-specific QTL were found for grain yield, days to heading and maturity, plant height, test weight, and thousand-kernel weight, but most explained relatively low amount of phenotypic variation. The QTL identified across managements, especially the gluten strength QTL (QSds.dms-1A), may serve as useful markers in selection. The QSds.dms-1A region needs to be investigated further to confirm whether it is the Gli-1 storage protein gene.

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

“…Using the phenotype data of ‘Peace’ and ‘Carberry’ RIL populations evaluated for two years under conventional and organic management systems and linkage map of 4439 markers generated via DArTseq technology, we previously [ 21 ] uncovered three QTL on chromosomes 1A, 5B, and 7D for heading and six QTL on 3A, 4A, 4B, 4D, 5B and 7D for maturity ( Table S3 ). In the present study conducted using the IWGSC RefSeq v2.0 and four years phenotype, we identified eight QTL for heading and nine QTL for maturity ( Figure 3 , Table 4 ).…”

“…‘Attila’ is an early maturing cultivar as compared to ‘CDC Go’. The 208 RILs from the PAC populations and their parents were evaluated at four conventionally and organically managed field conditions in 2016–2020 as described in our recent study [ 21 ]. ‘Peace’ [ 74 ] is adapted to the shorter-season wheat-growing regions of the Canadian prairies and carries the dominant Vrn-A1a allele and the recessive vrn-B1 and vrn-D1 alleles [ 78 ], while ‘Carberry’ [ 75 ] carries the Vrn-A1a , and Rht-B1b alleles [ 77 ].…”

“…DNA samples from the ACG, CAB, and PCS populations were genotyped at the University of Saskatchewan Wheat Genomics lab, Saskatoon, Canada, with the wheat 90K iSelect array that consisted of 81,587 SNPs [ 79 ], while the PAC population was genotyped with the DArTseq™ technology by DArT Pty Ltd., Canberra, Australia [ 80 , 81 ]. In addition, we also screened the two parents of each population if they were polymorphic for a few functional markers linked to photoperiod response ( Ppd-B1 and Ppd-D1 ) [ 82 ], vernalization response ( Vrn-A1 and Vrn-B1 ) [ 51 ], and height reducing Rht-B1 [ 83 ] genes at the Agricultural Genomics and Proteomics Lab, University of Alberta, Edmonton, Canada, as described in our previous studies [ 21 , 23 , 53 ]. In cases where the two parents of each population showed polymorphism for the functional markers, we genotyped the RILs with the markers and used them for mapping.…”

“…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 ]. The development of early-maturing CWRS cultivars is of paramount importance in the northern breeding programs to provide farmers not only an option of growing the crop with minimal loss due to frost but also help to escape from the late incidence of diseases, heat, and drought as compared with their late-maturing counterparts.…”

“…Using the phenotype data of two environments per management, we found 53 QTL associated with nine agronomic traits, of which nine QTL were for heading (3) and maturity (6). Fourteen of the 53 QTL were common in both conventional and organic management systems [ 21 ]. We also mapped QTL associated with ten agronomic and end-use quality traits in ‘Peace’ × ‘CDC Stanley’ RIL population evaluated for two years (2016–2017) under conventional and organic management systems.…”