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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #318190
Title: Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia

Author
item KIPPES, NESTOR - University Of California
item DEBERNARDI, JUAN - University Of California
item VASQUEZ-GROSS, HANS - University Of California
item AKPINAR, BALA - Sabanci University
item BUDAK, HIKMENT - Sabanci University
item KATO, KENJI - Okayama University
item Chao, Shiaoman
item AKHUNOV, EDUARD - Kansas State University
item DUBCOVSKY, JORGE - Howard Hughes Medical Institute

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/13/2015
Publication Date: 8/31/2015
Publication URL: http://handle.nal.usda.gov/10113/62955
Citation: Kippes, N., Debernardi, J.M., Vasquez-Gross, H.A., Akpinar, B.A., Budak, H., Kato, K., Chao, S., Akhunov, E., Dubcovsky, J. 2015. Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia. PNAS. 112(39):E5401-E5410. doi: 10.1073/pnas.1514883122.

Interpretive Summary: Wheat varieties with a winter growth habit require long exposures to low temperatures (vernalization) to accelerate flowering. Natural variation in the vernalization genes regulating this requirement has favored wheat adaptation to different environments. The three main wheat vernalization genes VRN1, VRN2, and VRN3 have previously been cloned and characterized. In this study, we analyzed VRN-D4 gene located on chromosome 5D, and confirmed it was a duplicated copy of VRN-A1 gene on chromosome 5A. VRN-D4 is present at very high frequency in an ancient wheat subspecies mainly found in the Punjab region of Pakistan and India. Results also showed that VRN-D4 gene likely contributed to its adaptation to Southern Asian environments. This new gene can be used to modulate vernalization requirement, and to develop wheat varieties better adapted to changing environments.

Technical Abstract: Wheat varieties with a winter growth habit require long exposures to low temperatures (vernalization) to accelerate flowering. Natural variation in the vernalization genes regulating this requirement has favored wheat adaptation to different environments. The main wheat vernalization genes VRN1, VRN2, and VRN3 have been cloned and characterized but VRN-D4 remained unknown. Here we show that VRN-D4 originated by the insertion of a ~290-kb region from chromosome arm 5AL in the proximal region of chromosome arm 5DS. This duplicated 5AL region includes a copy of VRN-A1 that carries distinctive mutations in coding and regulatory regions. This duplicated gene co-segregates with VRN-D4 and is expressed early during development in the absence of vernalization, suggesting that it is a strong candidate for VRN-D4. This hypothesis was confirmed by the delayed flowering of two lines carrying different induced mutations in the duplicated gene. VRN-D4 is present at very high frequency in the ancient Indian subspecies T. aestivum ssp. sphaerococcum and is associated with reduced diversity in neighboring chromosome regions. Since this subspecies usually lacks other alleles for spring growth habit, VRN-D4 likely contributed to its adaptation to Southern Asia's environments. Three adjacent SNPs in VRN-D4 first intron interfere with binding of TaGRP2, a known repressor of VRN1 expression. The same SNPs were identified in VRN-A1 alleles with reduced vernalization requirement, and may contribute to VRN-D4 early expression during development. These new alleles can be used to modulate vernalization requirement and to develop wheat varieties better adapted to changing environments.