Abstract
Revealing the genetic factors underlying yield and agronomic traits in wheat are an imperative need for covering the global food demand. Yield boosting requires a deep understanding of the genetic basis of grain yield-related traits (e.g., spikelet fertility and sterility). Here, we have detected much natural variation among ancient hexaploid wheat accessions in twenty-two agronomic traits collected over eight years of field experiments. A genome-wide association study (GWAS) using 15 K single nucleotide polymorphisms (SNPs) was applied to detect the genetic basis of studied traits. Subsequently, the GWAS output was reinforced via other statistical and bioinformatics analyses to detect putative candidate genes. Applying the genome-wide SNP-phenotype network defined the most decisive SNPs underlying the traits. Six pivotal SNPs, co-located physically within the genes encoding enzymes, hormone response, metal ion transport, and response to oxidative stress have been identified. Of these, metal ion transport and Gibberellin 2-oxidases (GA2oxs) genes showed strong involvement in controlling the spikelet sterility, which had not been reported previously in wheat. SNP-gene haplotype analysis confirmed that these SNPs influence spikelet sterility, especially the SNP co-located on the exon of the GA2ox gene. Interestingly, these genes were highly expressed in the grain and spike, demonstrating their pivotal role in controlling the trait. The integrative analysis strategy applied in this study, including GWAS, SNP-phenotype network, SNP-gene haplotype, expression analysis, and genome-wide prediction (GP), empower the identification of functional SNPs and causal genes. GP outputs obtained in this study are encouraging for the implementation of the traits to accelerate yield improvement by making an early prediction of complex yield-related traits in wheat. Our findings demonstrate the usefulness of the ancient wheat material as a valuable resource for yield-boosting. This is the first comprehensive genome-wide analysis for spikelet sterility in wheat, and the results provide insights into yield improvement.
Highlights
Revealing the genetic factors underlying yield and agronomic traits in wheat are an imperative need for covering the global food demand
Grain yield (GY), heading date (HD), FL, harvest index (HI), spike number per m2 (SN), and spike length (SL) were significantly correlated with most of the agronomic traits
The association results showed that single nucleotide polymorphisms (SNPs) array density (15 K) and genome-wide association study (GWAS) analysis strategy were strong enough to identify highly significant marker-trait associations, compared with previous associations identified using DArT11,23 and SNP7,22 markers
Summary
Revealing the genetic factors underlying yield and agronomic traits in wheat are an imperative need for covering the global food demand. Our findings demonstrate the usefulness of the ancient wheat material as a valuable resource for yield-boosting This is the first comprehensive genome-wide analysis for spikelet sterility in wheat, and the results provide insights into yield improvement. Current climate change scenarios predict more abiotic and biotic stress events in the areas of wheat production (e.g., Europe)[2] It is, necessary to develop cultivars with high yields and better adaptation to stress conditions, in order to ensure food security and social ease[3] by fine-tuning the genetically complex yield traits. Published wheat genome sequences with the high-quality annotated reference genome[12] make genome-wide analyses more beneficial that empowers researchers for deep genetic analysis, of complex traits in wheat It is helps breeders incorporate the discovered causative allele(s) efficiently in breeding programs, to improve yield and adaptation to specific regional conditions. Such progress in wheat production and acclimation is an imperative need to meet the demands of human population growth
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