Dataset Information

Dissecting the genetic architecture of frost tolerance in Central European winter wheat.

ABSTRACT: Abiotic stress tolerance in plants is pivotal to increase yield stability, but its genetic basis is still poorly understood. To gain insight into the genetic architecture of frost tolerance, this work evaluated a large mapping population of 1739 wheat (Triticum aestivum L.) lines and hybrids adapted to Central Europe in field trials in Germany and fingerprinted the lines with a 9000 single-nucleotide polymorphism array. Additive effects prevailed over dominance effects. A two-dimensional genome scan revealed the presence of epistatic effects. Genome-wide association mapping in combination with a robust cross-validation strategy identified one frost tolerance locus with a major effect located on chromosome 5B. This locus was not in linkage disequilibrium with the known frost loci Fr-B1 and Fr-B2. The use of the detected diagnostic markers on chromosome 5B, however, does not allow prediction of frost tolerance with high accuracy. Application of genome-wide selection approaches that take into account also loci with small effect sizes considerably improved prediction of the genetic variation of frost tolerance in wheat. The developed prediction model is valuable for improving frost tolerance because this trait displays a wide variation in occurrence across years and is therefore a difficult target for conventional phenotypic selection.

SUBMITTER: Zhao Y

PROVIDER: S-EPMC3808325 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Dissecting the genetic architecture of frost tolerance in Central European winter wheat.

Zhao Yusheng Y Gowda Manje M Würschum Tobias T Longin C Friedrich H CF Korzun Viktor V Kollers Sonja S Schachschneider Ralf R Zeng Jian J Fernando Rohan R Dubcovsky Jorge J Reif Jochen C JC

Journal of experimental botany 20130904 14

Abiotic stress tolerance in plants is pivotal to increase yield stability, but its genetic basis is still poorly understood. To gain insight into the genetic architecture of frost tolerance, this work evaluated a large mapping population of 1739 wheat (Triticum aestivum L.) lines and hybrids adapted to Central Europe in field trials in Germany and fingerprinted the lines with a 9000 single-nucleotide polymorphism array. Additive effects prevailed over dominance effects. A two-dimensional genome ...[more]

PMID: 24006418

Similar Datasets

Project description:Hybrid wheat breeding is gaining prominence worldwide because it ensures higher and more static yield than conventionally bred varieties. The cleistogamous floral architecture of wheat (Triticum aestivum L.) impedes anthers inside the floret, making it largely an inbreeder. For hybrid seed production, high anther extrusion is needed to promote cross pollination and to ensure a high level of pollen availability for the seed plant. This study, therefore, aimed at the genetic dissection of anther extrusion (AE) in panels of spring (SP), and winter wheat (WP) accessions by genome wide association studies (GWAS). We performed GWAS to identify the SNP markers potentially linked with AE in each panel separately. Phenotypic data were collected for 3 years for each panel. The average levels of Pearson's correlation (r) among all years and their best linear unbiased estimates (BLUEs) within both panels were high (r(SP) = 0.75, P < 0.0001;r(WP) = 0.72, P < 0.0001). Genotypic data (with minimum of 0.05 minor allele frequency applied) included 12,066 and 12,191 SNP markers for SP and WP, respectively. Both genotypes and environment influenced the magnitude of AE. In total, 23 significant (|log10(P)| > 3.0) marker trait associations (MTAs) were detected (SP = 11; WP = 12). Anther extrusion behaved as a complex trait with significant markers having either favorable or unfavorable additive effects and imparting minor to moderate levels of phenotypic variance (R2(SP) = 9.75-14.24%; R2 (WP) = 9.44-16.98%). All mapped significant markers as well as the markers within their significant linkage disequilibrium (r2 ≥ 0.30) regions were blasted against wheat genome assembly (IWGSC1+popseq) to find the corresponding genes and their high confidence descriptions were retrieved. These genes and their orthologs in Hordeum vulgare, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor revealed syntenic genomic regions potentially involved in flowering-related traits. Moreover, the expression data of these genes suggested potential candidates for AE. Our results suggest that the use of significant markers can help to introduce AE in high yielding varieties to increase cross fertilization rates and improve hybrid-seed production in wheat.

Project description:BackgroundThe future productivity of wheat (T. aestivum L.) as the most grown crop worldwide is of utmost importance for global food security. Thousand kernel weight (TKW) in wheat is closely associated with grain architecture-related traits, e.g. kernel length (KL), kernel width (KW), kernel area (KA), kernel diameter ratio (KDR), and factor form density (FFD). Discovering the genetic architecture of natural variation in these traits, identifying QTL and candidate genes are the main aims of this study. Therefore, grain architecture-related traits in 261 worldwide winter accessions over three field-year experiments were evaluated.ResultsGenome-wide association analysis using 90K SNP array in FarmCPU model revealed several interesting genomic regions including 17 significant SNPs passing false discovery rate threshold and strongly associated with the studied traits. Four of associated SNPs were physically located inside candidate genes within LD interval e.g. BobWhite_c5872_589 (602,710,399 bp) found to be inside TraesCS6A01G383800 (602,699,767-602,711,726 bp). Further analysis reveals the four novel candidate genes potentially involved in more than one grain architecture-related traits with a pleiotropic effects e.g. TraesCS6A01G383800 gene on 6A encoding oxidoreductase activity was associated with TKW and KA. The allelic variation at the associated SNPs showed significant differences betweeen the accessions carying the wild and mutated alleles e.g. accessions carying C allele of BobWhite_c5872_589, TraesCS6A01G383800 had significantly higher TKW than the accessions carying T allele. Interestingly, these genes were highly expressed in the grain-tissues, demonstrating their pivotal role in controlling the grain architecture.ConclusionsThese results are valuable for identifying regions associated with kernel weight and dimensions and potentially help breeders in improving kernel weight and architecture-related traits in order to increase wheat yield potential and end-use quality.

Project description:BackgroundGenetic improvement of end-use quality is an important objective in wheat breeding programs to meet the requirements of grain markets, millers, and bakers. However, end-use quality phenotyping is expensive and laborious thus, testing is often delayed until advanced generations. To better understand the underlying genetic architecture of end-use quality traits, we investigated the phenotypic and genotypic structure of 14 end-use quality traits in 672 advanced soft white winter wheat breeding lines and cultivars adapted to the Pacific Northwest region of the United States.ResultsThis collection of germplasm had continuous distributions for the 14 end-use quality traits with industrially significant differences for all traits. The breeding lines and cultivars were genotyped using genotyping-by-sequencing and 40,518 SNP markers were used for association mapping (GWAS). The GWAS identified 178 marker-trait associations (MTAs) distributed across all wheat chromosomes. A total of 40 MTAs were positioned within genomic regions of previously discovered end-use quality genes/QTL. Among the identified MTAs, 12 markers had large effects and thus could be considered in the larger scheme of selecting and fixing favorable alleles in breeding for end-use quality in soft white wheat germplasm. We also identified 15 loci (two of them with large effects) that can be used for simultaneous breeding of more than a single end-use quality trait. The results highlight the complex nature of the genetic architecture of end-use quality, and the challenges of simultaneously selecting favorable genotypes for a large number of traits. This study also illustrates that some end-use quality traits were mainly controlled by a larger number of small-effect loci and may be more amenable to alternate selection strategies such as genomic selection.ConclusionsIn conclusion, a breeder may be faced with the dilemma of balancing genotypic selection in early generation(s) versus costly phenotyping later on.

Dataset Information

Dissecting the genetic architecture of frost tolerance in Central European winter wheat.

Publications

Dissecting the genetic architecture of frost tolerance in Central European winter wheat.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets