Allelic Variation at the Vernalization Response (Vrn-1) and Photoperiod Sensitivity (Ppd-1) Genes and Their Association With the Development of Durum Wheat Landraces and Modern Cultivars.

Wheat adaptability to a wide range of environmental conditions is mostly determined by allelic diversity within genes controlling vernalization requirement (Vrn-1) and photoperiod sensitivity (Ppd-1). We characterized a panel of 151 durum wheat Mediterranean landraces and 20 representative locally adapted modern cultivars for their allelic composition at Vrn-1 and Ppd-1 gene using diagnostic molecular markers and studied their association with the time needed to reach six growth stages under field conditions over 6 years. Compared with the more diverse and representative landrace collection, the set of modern cultivars were characterized by a reduction of 50% in the number of allelic variants at the Vrn-A1 and Vrn-B1 genes, and the high frequency of mutant alleles conferring photoperiod insensitivity at Ppd-A1, which resulted on a shorter cycle length. Vrn-A1 played a greater role than Vrn-B1 in regulating crop development (Vrn-A1 > Vrn-B1). The results suggest that mutations in the Vrn-A1 gene may have been the most important in establishing the spring growth habit of Mediterranean landraces and modern durum cultivars. The allele Vrn-A1d, found in 10 landraces, delayed development. The relative effects of single Vrn-A1 alleles on delaying the development of the landraces were vrn-A1 = Vrn-A1d > Vrn-A1b > Vrn-A1c. Allele vrn-B1 was present in all except two landraces and in all modern cultivars. The null allele at Ppd-A1 (a deletion first observed in the French bread wheat cultivar 'Capelle-Desprez') was found for the first time in durum wheat in the present study that identified it in 30 landraces from 13 Mediterranean countries. Allele Ppd-A1a (GS105) was detected in both germplasm types, while the allele Ppd-A1a (GS100) was found only in modern North American and Spanish cultivars. The relative effect of single Ppd-A1 alleles on extending phenological development was Ppd-A1(DelCD) > Ppd-A1b > Ppd-A1a (GS105) > Ppd-A1a (GS100). Sixteen Vrn-1+Ppd-1 allelic combinations were found in landraces and six in modern cultivars, but only three were common to both panels. Differences in the number of days to reach anthesis were 10 days in landraces and 3 days in modern cultivars. Interactive effects between Vrn-1 and Ppd-1 genes were detected.

Copy number variation of Ppd-B1 is the major determinant of heading time in durum wheat.

BACKGROUND: Heading time is an important adaptive trait in durum wheat. In hexaploid wheat, Photoperiod-1 (Ppd) loci are essential regulators of heading time, with Ppd-B1 conferring photoperiod insensitivity through copy number variations (CNV). In tetraploid wheat, the D-genome Ppd-D1 locus is absent and generally, our knowledge on the genetic architecture underlying heading time lacks behind that of bread wheat. RESULTS: In this study, we employed a panel of 328 diverse European durum genotypes that were evaluated for heading time at five environments. Genome-wide association mapping identified six putative QTL, with a major QTL on chromosome 2B explaining 26.2% of the genotypic variance. This QTL was shown to correspond to copy number variation at Ppd-B1, for which two copy number variants appear to be present. The higher copy number confers earlier heading and was more frequent in the heat and drought prone countries of lower latitude. In addition, two other QTL, corresponding to Vrn-B3 (TaFT) and Ppd-A1, were found to explain 9.5 and 5.3% of the genotypic variance, respectively. CONCLUSIONS: Our results revealed the yet unknown role of copy number variation of Ppd-B1 as the major source underlying the variation in heading time in European durum wheat. The observed geographic patterns underline the adaptive value of this polymorphism and suggest that it is already used in durum breeding to tailor cultivars to specific target environments. In a broader context our findings provide further support for a more widespread role of copy number variation in mediating abiotic and biotic stress tolerance in plants.

Features of Ppd-B1 expression regulation and their impact on the flowering time of wheat near-isogenic lines.

BACKGROUND: Photoperiod insensitive Ppd-1a alleles determine early flowering of wheat. Increased expression of homoeologous Ppd-D1a and Ppd-A1a result from deletions in the promoter region, and elevated expression of Ppd-B1a is determined by an increased copy number. RESULTS: In this study, using bread wheat cultivars Sonora and PSL2, which contrast in flowering time, and near-isogenic lines resulting from their cross, "Ppd-m" and "Ppd-w" with Ppd-B1a introgressed from Sonora, we investigated the putative factors that influence Ppd-B1a expression. By analyzing the Ppd-B1a three distinct copies, we identified an indel and the two SNPs, which distinguished the investigated allele from other alleles with a copy number variation. We studied the expression of the Ppd-A1, Ppd-B1a, and Ppd-D1 genes along with genes that are involved in light perception (PhyA, PhyB, PhyC) and the flowering initiation (Vrn-1, TaFT1) and discussed their interactions. Expression of Ppd-B1a in the "Ppd-m" line, which flowered four days earlier than "Ppd-w", was significantly higher. We found PhyC to be up-regulated in lines with Ppd-B1a alleles. Expression of PhyC was higher in "Ppd-m". Microsatellite genotyping demonstrated that in the line "Ppd-m", there is an introgression in the pericentromeric region of chromosome 5B from the early flowering parental Sonora, while the "Ppd-w" does not have this introgression. FHY3/FAR1 is known to be located in this region. Expression of the transcription factor FHY3/FAR1 was higher in the "Ppd-m" line than in "Ppd-w", suggesting that FHY3/FAR1 is important for the wheat flowering time and may cause earlier flowering of "Ppd-m" as compared to "Ppd-w". CONCLUSIONS: We propose that there is a positive bidirectional regulation of Ppd-B1a and PhyC with an FHY3/FAR1 contribution. The bidirectional regulation can be proposed for Ppd-A1a and Ppd-D1a. Using in silico analysis, we demonstrated that the specificity of the Ppd-B1 regulation compared to that of homoeologous genes involves not only a copy number variation but also distinct regulatory elements.

Distribution of photoperiod-insensitive alleles Ppd-B1a and Ppd-D1a and their effect on heading time in Japanese wheat cultivars.

The genotypes of photoperiod response genes Ppd-B1 and Ppd-D1 in Japanese wheat cultivars were determined by a PCR-based method, and heading times were compared among genotypes. Most of the Japanese wheat cultivars, except those from the Hokkaido region, carried the photoperiod-insensitive allele Ppd-D1a, and heading was accelerated 10.3 days compared with the Ppd-D1b genotype. Early cultivars with Ppd-D1a may have been selected to avoid damage from preharvest rain. In the Hokkaido region, Ppd-D1a frequency was lower and heading date was late regardless of Ppd-D1 genotype, suggesting another genetic mechanism for late heading in Hokkaido cultivars. In this study, only 11 cultivars proved to carry Ppd-B1a, and all of them carried another photoperiod-insensitive allele, Ppd-D1a. The Ppd-B1a/Ppd-D1a genotype headed 6.7 days earlier than the Ppd-B1b/Ppd-D1a genotype, indicating a significant effect of Ppd-B1a in the genetic background with Ppd-D1a. Early-maturity breeding in Japan is believed to be accelerated by the introduction of the Ppd-B1a allele into medium-heading cultivars carrying Ppd-D1a. Pedigree analysis showed that Ppd-B1a in three extra-early commercial cultivars was inherited from 'Shiroboro 21' by early-heading Chugoku lines bred at the Chugoku Agriculture Experimental Station.