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Title: Single nucleotide polymorphisms in a regulatory site of VRN-A1 first intron are associated with differences in vernalization requirement in winter wheat

Author
item KIPPES, NESTOR - University Of California, Davis
item GUEDIRA, MOHAMMED - North Carolina State University
item LIN, LIJUAN - University Of California, Davis
item Brown-Guedira, Gina
item DUBCOVSKY, JORGE - University Of California, Davis

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/15/2018
Publication Date: 6/5/2018
Citation: Kippes, N., Guedira, M., Lin, L., Brown Guedira, G.L., Dubcovsky, J. 2018. Single nucleotide polymorphisms in a regulatory site of VRN-A1 first intron are associated with differences in vernalization requirement in winter wheat. Molecular Genetics and Genomics. 293:1231-1243.

Interpretive Summary: Winter wheats require a long exposure to cold temperatures (vernalization) to accelerate flowering. However, varieties differ in the length of the period of cold required to saturate the vernalization response. Here we show that single nucleotide polymorphisms (SNP) at the binding site of the GRP2 protein in the Vernalization-A1 (VRN-A1) gene first intron (henceforth, RIP3) are associated with significant differences in heading time after a short period of cold treatment. The ancestral winter VRN-A1 allele in wheat line ‘Triple Dirk C’ has one SNP in the RIP3 region (1_SNP) relative to the ancestral RIP3 sequence whereas the derived allele in the cultivar ‘Jagger’ allele three SNPs (3_SNPs). Both varieties have a single VRN-A1 copy encoding identical proteins. In an F2 population generated from a cross between these two varieties, plants with the 3_SNPs haplotype headed significantly earlier (P < 0.001) than those with the 1_SNP haplotype, both in the absence of vernalization (17 d difference) and after 3-weeks of vernalization (11 d difference). Plants with the 3_SNPs haplotype showed higher VRN-A1 transcript levels than those with the 1_SNP haplotype. The 3_SNPs haplotype was also associated with early heading in a panel of 127 winter wheat varieties grown in three separate controlled-environment experiments under partial vernalization (36 to 54 d, P < 0.001) and one experiment under field conditions (21 d, P < 0.0001). This information can be used to develop winter wheat varieties adapted to regions with different durations or intensities of the cold season.

Technical Abstract: Winter wheats require a long exposure to cold temperatures (vernalization) to accelerate flowering. However, varieties differ in the length of the period of cold required to saturate the vernalization response. Here we show that single nucleotide polymorphisms (SNP) at the binding site of the GRP2 protein in the VRN-A1 first intron (henceforth, RIP3) are associated with significant differences in heading time after a partial vernalization treatment. The ancestral winter VRN-A1 allele in ‘Triple Dirk C’ has one SNP in the RIP3 region (1_SNP) relative to the canonical RIP3 sequence whereas the derived ‘Jagger’ allele has three SNPs (3_SNPs). Both varieties have a single VRN-A1 copy encoding identical proteins. In an F2 population generated from a cross between these two varieties, plants with the 3_SNPs haplotype headed significantly earlier (P < 0.001) than those with the 1_SNP haplotype, both in the absence of vernalization (17 d difference) and after 3-weeks of vernalization (11 d difference). Plants with the 3_SNPs haplotype showed higher VRN-A1 transcript levels than those with the 1_SNP haplotype. The 3_SNPs haplotype was also associated with early heading in a panel of 127 winter wheat varieties grown in three separate controlled-environment experiments under partial vernalization (36 to 54 d, P < 0.001) and one experiment under field conditions (21 d, P < 0.0001). This information can be used to develop winter wheat varieties adapted to regions with different durations or intensities of the cold season.