Abstract
BackgroundCopy number variation was found to be a frequent type of DNA polymorphism in the human genome often associated with diseases but its importance in crops and the effects on agronomic traits are still largely unknown.ResultsHere, we employed a large worldwide panel of 1110 winter wheat varieties to assess the frequency and the geographic distribution of copy number variants at the Photoperiod-B1 (Ppd-B1) and the Vernalization-A1 (Vrn-A1) loci as well as their effects on flowering time under field conditions. We identified a novel four copy variant of Vrn-A1 and based on the phylogenetic relationships among the lines show that the higher copy variants at both loci are likely to have arisen independently multiple times. In addition, we found that the frequency of the different copy number variants at both loci reflects the environmental conditions in the varieties’ region of origin and based on multi-location field trials show that Ppd-B1 copy number has a substantial effect on the fine-tuning of flowering time.ConclusionsIn conclusion, our results show the importance of copy number variation at Ppd-B1 and Vrn-A1 for the global adaptation of wheat making it a key factor for wheat success in a broad range of environments and in a wider context substantiate the significant role of copy number variation in crops.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0258-0) contains supplementary material, which is available to authorized users.
Highlights
Copy number variation was found to be a frequent type of DNA polymorphism in the human genome often associated with diseases but its importance in crops and the effects on agronomic traits are still largely unknown
Owing to the available genotyping technologies at the time, these studies were almost exclusively based on single nucleotide polymorphisms (SNPs) and small insertions-deletions (INDELs) which were assumed to be the major types of DNA polymorphism underlying genotypic variation
An increased copy number of Vrn-1 resulted in a slower induction of expression during vernalization and in an increased period of cold required to potentiate flowering [12]. As both the photoperiod and the vernalization pathway affect flowering time, we investigated the role of copy number variation at both the Ppd-B1 and Vrn-A1 loci in the global adaptation success of wheat
Summary
Copy number variation was found to be a frequent type of DNA polymorphism in the human genome often associated with diseases but its importance in crops and the effects on agronomic traits are still largely unknown. The plethora of QTL mapping studies performed during the last decades has shown that the genotypic variation of agronomically important traits in crops is to a great extent controlled by polymorphisms in the nuclear DNA. While most CNVs occur in intergenic regions [7], this type of structural polymorphism can encompass protein-coding genes or sequences regulating the expression of genes. Such changes in the number of functional copies or regulatory elements can in turn result in altered expression levels of these genes. In contrast to humans, the effects of CNV on the phenotype of crops are just beginning to be understood [6]
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