Dataset Information

Genome-Wide Association Mapping of Anther Extrusion in Hexaploid Spring Wheat.

ABSTRACT: In a number of crop species hybrids are able to outperform line varieties. The anthers of the autogamous bread wheat plant are normally extruded post anthesis, a trait which is unfavourable for the production of F1 hybrid grain. Higher anther extrusion (AE) promotes cross fertilization for more efficient hybrid seed production. Therefore, this study aimed at the genetic dissection of AE by genome wide association studies (GWAS) and determination of the main effect QTL. We applied GWAS approach to identify DArT markers potentially linked to AE to unfold its genetic basis in a panel of spring wheat accessions. Phenotypic data were collected for three years and best linear unbiased estimate (BLUE) values were calculated across all years. The extent of the AE correlation between growing years and BLUE values ranged from r = +0.56 (2013 vs 2015) to 0.91 (2014 vs BLUE values). The broad sense heritability was 0.84 across all years. Six accessions displayed stable AE >80% across all the years. Genotyping data included 2,575 DArT markers (with minimum of 0.05 minor allele frequency applied). AE was influenced both by genotype and by the growing environment. In all, 131 significant marker trait associations (MTAs) (|log10 (P)| >FDR) were established for AE. AE behaved as a quantitative trait, with five consistently significant markers (significant across at least two years with a significant BLUE value) contributing a minor to modest proportion (4.29% to 8.61%) of the phenotypic variance and affecting the trait either positively or negatively. For this reason, there is potential for breeding for improved AE by gene pyramiding. The consistently significant markers linked to AE could be helpful for marker assisted selection to transfer AE to high yielding varieties allowing to promote the exploitation of hybrid-heterosis in the key crop wheat.

SUBMITTER: Muqaddasi QH

PROVIDER: S-EPMC4871436 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Genome-Wide Association Mapping of Anther Extrusion in Hexaploid Spring Wheat.

Muqaddasi Quddoos H QH Lohwasser Ulrike U Nagel Manuela M Börner Andreas A Pillen Klaus K Röder Marion S MS

PloS one 20160518 5

In a number of crop species hybrids are able to outperform line varieties. The anthers of the autogamous bread wheat plant are normally extruded post anthesis, a trait which is unfavourable for the production of F1 hybrid grain. Higher anther extrusion (AE) promotes cross fertilization for more efficient hybrid seed production. Therefore, this study aimed at the genetic dissection of AE by genome wide association studies (GWAS) and determination of the main effect QTL. We applied GWAS approach t ...[more]

PMID: 27191600

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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:Anther extrusion (AE) is the most important male floral trait for hybrid wheat seed production. AE is a complex quantitative trait that is difficult to phenotype reliably in field experiments not only due to high genotype-by-environment effects but also due to the short expression window in the field condition. In this study, we conducted a genome-wide association scan (GWAS) and explored the possibility of applying genomic prediction (GP) for AE in the CIMMYT hybrid wheat breeding program. An elite set of male lines (n = 603) were phenotype for anther count (AC) and anther visual score (VS) across three field experiments in 2017-2019 and genotyped with the 20K Infinitum is elect SNP array. GWAS produced five marker trait associations with small effects. For GP, the main effects of lines (L), environment (E), genomic (G) and pedigree relationships (A), and their interaction effects with environments were used to develop seven statistical models of incremental complexity. The base model used only L and E, whereas the most complex model included L, E, G, A, and G × E and A × E. These models were evaluated in three cross-validation scenarios (CV0, CV1, and CV2). In cross-validation CV0, data from two environments were used to predict an untested environment; in random cross-validation CV1, the test set was never evaluated in any environment; and in CV2, the genotypes in the test set were evaluated in only a subset of environments. The prediction accuracies ranged from -0.03 to 0.74 for AC and -0.01 to 0.54 for VS across different models and CV schemes. For both traits, the highest prediction accuracies with low variance were observed in CV2, and inclusion of the interaction effects increased prediction accuracy for AC only. In CV0, the prediction accuracy was 0.73 and 0.45 for AC and VS, respectively, indicating the high reliability of across environment prediction. Genomic prediction appears to be a very reliable tool for AE in hybrid wheat breeding. Moreover, high prediction accuracy in CV0 demonstrates the possibility of implementing genomic selection across breeding cycles in related germplasm, aiding the rapid breeding cycle.

Dataset Information

Genome-Wide Association Mapping of Anther Extrusion in Hexaploid Spring Wheat.

Publications

Genome-Wide Association Mapping of Anther Extrusion in Hexaploid Spring Wheat.

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