Fine mapping and epistatic interactions of the vernalization gene VRN-D4 in hexaploid wheat

Abstract

Wheat vernalization requirement is mainly controlled by the VRN1, VRN2, VRN3, and VRN4 genes. The first three have been cloned and have homoeologs in all three genomes. VRN4 has been found only in the D genome (VRN-D4) and has not been cloned. We constructed a high-density genetic map of the VRN-D4 region and mapped VRN-D4 within a 0.09 cM interval in the centromeric region of chromosome 5D. Using telocentric 5D chromosomes generated from the VRN-D4 donor Triple Dirk F, we determined that VRN-D4 is located on the short arm. The VRN-D4 candidate region is colinear with a 2.24 Mb region on Brachypodium distachyon chromosome 4, which includes 127 predicted genes. Ten of these genes have predicted roles in development but we detected no functional polymorphisms associated to VRN-D4. Two recombination events separated VRN-D4 from TaVIL-D1, the wheat homolog of Arabidopsis vernalization gene VIL1, confirming that this gene is not a candidate for VRN-D4. We detected significant interactions between VRN-D4 and other four genes controlling vernalization requirement (Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3), which confirmed that VRN-D4 is part of the vernalization pathway and that it is either upstream or is part of the regulatory feedback loop involving VRN1, VRN2 and VRN3 genes. The precise mapping of VRN-D4 and the characterization of its interactions with other vernalization genes provide valuable information for the utilization of VRN-D4 in wheat improvement and for our current efforts to clone this vernalization gene.Electronic supplementary materialThe online version of this article (doi:10.1007/s00438-013-0788-y) contains supplementary material, which is available to authorized users.

Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia

“…Adaptive selection for VRN-D4 might have been favored by the absence of other alleles for spring growth habit in the T. aestivum ssp. sphaerococcum accessions from South Asia (SI Appendix, Table S5) and by the partial dominant nature of the Vrn-D4 allele for early flowering (29).…”

“…S2A). The A367C SNP was completely linked with spring growth habit in a high-density mapping population (3,182 gametes) segregating for VRN-D4 on chromosome arm 5DS (29). The six plants with the VRN-D4 closest recombination events are shown in SI Appendix, Fig.…”

“…A fourth vernalization locus, VRN-D4, has been mapped on the proximal region of the short arm of chromosome 5D (henceforth, 5DS) (28,29), but the gene underlying this locus has not been identified yet. VRN-D4 was first described in the Australian wheat variety Gabo (30), which likely inherited it from the Indian cultivar Muzaffarnagar (31).…”

“…VRN-D4 was transferred from Gabo into Triple Dirk to develop Triple Dirk "F" (TDF), which is part of a set of isogenic lines carrying different vernalization genes (35,36). Segregating populations generated from these isogenic lines revealed that VRN-D4 has strong epistatic interactions with the other vernalization genes and is part of the same vernalization pathway (29).…”

“…The VRN-D4 gene is located in a proximal region of 5DS that shows no recombination (29), limiting the use of map-based cloning to identify this gene. In this study we used alternative approaches to show that the VRN-D4 locus originated from the insertion of a large 5AL chromosome segment including the VRN-A1 gene into the proximal region of chromosome arm 5DS.…”