Allelic variations of Vrn-1 and Ppd-1 genes in Japanese wheat varieties reveal the genotype-environment interaction for heading time

Abstract

The timing of heading is largely affected by environmental conditions. In wheat, Vrn-1 and Ppd-1 have been identified as the major genes involved in vernalization requirement and photoperiod sensitivity, respectively. To compare the effects of Vrn-1 and Ppd-1 alleles on heading time under different environments, we genotyped Vrn-1 and Ppd-1 homoeologues and measured the heading time at Morioka, Tsukuba and Chikugo in Japan for two growing seasons. A total of 128 Japanese and six foreign varieties, classified into four populations based on the 519 genome-wide SNPs, were used for analysis. Varieties with the spring alleles (Vrn-D1a or Vrn-D1b) at the Vrn-D1 locus and insensitive allele (Hapl-I) at the Ppd-D1 locus were found in earlier heading varieties. The effects of Vrn-D1 and Ppd-D1 on heading time were stronger than those of the other Vrn-1 and Ppd-1 homoeologues. Analysis of variance revealed that heading time was significantly affected by the genotype-environment interactions. Some Vrn-1 and Ppd-1 alleles conferred earlier or later heading in specific environments, indicating that the effect of both alleles on the timing of heading depends on the environment. Information on Vrn-1 and Ppd-1 alleles, together with heading time in various environments, provide useful information for wheat breeding.

Keywords: Ppd-1; Vrn-1; genotype-environment interaction; heading time; wheat.

Fig. 1.

Phylogenetic tree, principal component analysis (PCA), and STRUCTURE analysis of 134 wheat accessions based on 519 genome-wide SNPs. (A) Population structure of 134 common wheat varieties inferred by ADMIXTURE (K = 4). Ancestry proportions for individuals were estimated using 519 SNPs. Color codes (blue, green, yellow, and red) of bars indicate typical genotypes of the inferred subpopulations. (B) A maximum likelihood tree based on 519 SNPs. IDs of varieties was color-coded by breeding area as shown in Supplemental Table 1. Blue, green, yellow, and red branches indicate Population I, II, III, and IV, respectively. (C) Principal-component analysis (PCA) of 134 varieties of common wheat based on 519 SNPs. Graph of the first three axes (PC1, PC2, and PC3) from PCA. The proportion of variance explained by each component is given in a parentheses along each axis. Blue, green, yellow, and red indicate the varieties belonging to Population I, II, III, and IV.

Fig. 2.

Comparison of days to heading (DH) among four populations in three locations for two seasons. The top marks the 75% quantile, and the bottom, the 25% quantile. The median (50% quantile) is marked with a thick horizontal line. The lines that protrude from the box (the whiskers) respectively show the minimum and maximum values excluding outliers. Mean values with the same letters are not significantly different (P > 0.05) (Tukey-Kramer’s HSD test).

Fig. 3.

AMMI2-biplot, based on days to heading, of the 134 wheat varieties in six environments (two growing seasons at three locations), showing the effects of primary and secondary components (IPCA1 and IPCA2, respectively). IPCA1 and IPCA2 accounted for 72.2% and 11.2%, respectively, of the total genotype by environment interaction sum of squares. “spring” and “winter” indicate varieties with one or more spring allele of Vrn-1 and without spring allele of Vrn-1, respectively. “insensitive” and “sensitive” indicate varieties with one or more insensitive allele of Ppd-1 and without insensitive allele of Ppd-1, respectively.

Fig. 4.

Relationship between inter-seasonal difference in DH and vernalization requirement and photoperiod sensitivity based on the allele of Vrn-1 and Ppd-1. The y-axis indicates the DH for 2019–2020 season minus DH for 2020–2021 season. “spring” and “winter” indicate varieties with one or more spring allele of Vrn-1 and without spring allele of Vrn-1, respectively. “insensitive” and “sensitive” indicate varieties with one or more allele of Ppd-1 and without allele of Ppd-1, respectively. Top and bottom are 75% and 25% quartiles, respectively. Thick horizontal line, median (50% quartile). Whiskers represent minimum and maximum values excluding outliers. Mean values with same letters do not significantly differ (P > 0.05, Tukey-Kramer’s HSD test).

Fig. 5.

Comparison of daily mean temperature between 2019–2020 and 2020–2021 seasons in three locations. Data in Morioka (A), Tsukuba (B), and Kurume near Chikugo (C) were obtained from the Japan Meteorological Agency. Black and gray lines indicate the daily mean temperature in the 2019–2020 and 2020–2021 growing seasons, respectively. The two-headed arrows indicate days of heading in the 2019–2020 (black) and 2020–2021 (gray) growing seasons.