Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice

Abstract

Vernalization, a period of low temperature to induce transition from vegetative to reproductive state, is an important environmental stimulus for many cool season grasses. A key gene in the vernalization pathway in grasses is the VRN1 gene. The objective of this study was to identify causative polymorphism(s) at the VRN1 locus in perennial ryegrass (Lolium perenne) for variation in vernalization requirement. Two allelic Bacterial Artificial Chromosome clones of the VRN1 locus from the two genotypes Veyo and Falster with contrasting vernalization requirements were identified, sequenced, and characterized. Analysis of the allelic sequences identified an 8.6-kb deletion in the first intron of the VRN1 gene in the Veyo genotype which has low vernalization requirement. This deletion was in a divergent recurrent selection experiment confirmed to be associated with genotypes with low vernalization requirement. The region surrounding the VRN1 locus in perennial ryegrass showed microcolinearity to the corresponding region on chromosome 3 in Oryza sativa with conserved gene order and orientation, while the micro-colinearity to the corresponding region in Triticum monococcum was less conserved. Our study indicates that the first intron of the VRN1 gene, and in particular the identified 8.6 kb region, is an important regulatory region for vernalization response in perennial ryegrass.

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Acknowledgments

This work was supported by a grant from the framework “Biotechnology and applied plant genetics in plant breeding” from The Directorate for Food, Fisheries and Agricultural Business under the Danish Ministry of Food, Agriculture and Fisheries. Dorthe Strue Nielsen and Kirsten Vangsgaard are acknowledged for their excellent technical assistance.

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Correspondence to Torben Asp.

Additional information

Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers JN969602 and JN969603 for the Veyo-GP and Falster-GP VRN1 alleles, respectively.

Communicated by Y. Van de Peer.

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Supplementary Fig. 1. Percent Identity Plot output of the comparison of the VRN1 locus of Lolium perenne, H. vulgare, T. monococcum, T. aestivum, T. turgidum, Ae. tauschii, and the AP1 locus of O. sativa.

Supplementary Table 1. Germplasm evaluation for Veyo-GP and Falster-GP VRN1 alleles in 380 genotypes of L. perenne. 1: presence of allele; 0: absence of allele.

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Supplementary material 2 (PDF 454 kb)

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Asp, T., Byrne, S., Gundlach, H. et al. Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice. Mol Genet Genomics 286, 433–447 (2011). https://doi.org/10.1007/s00438-011-0654-8

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Keywords

  • Lolium perenne
  • Perennial ryegrass
  • VRN1
  • Comparative genomics
  • Vernalization