Ppd Genes Research Articles

A comparative study on germination of wheat grains with different anthocyanin pigmentation of the pericarp in natural or induced aging.

One of promising areas of wheat breeding is the creation of varieties with a high concentration of anthocyanins in the grain for the production of functional food products. Nonetheless, the question of how these compounds affect seed viability after long-term storage has remained unexplored. A comparative study on seed viability was conducted using a set of near-isogenic lines on the background of spring wheat variety Saratovskaya 29. These sister lines carry different combinations of recombinant DNA regions (on chromosomes 2A and 7D) containing dominant and recessive alleles at loci Pp3 and Pp-D1 (Pp: Purple pericarp), which determine the anthocyanin color of coleoptiles and of the pericarp. Seeds were germinated on two layers of water-moistened filter paper in a climatic chamber at a constant temperature of 20 °C on a 12-hour daylight cycle. During long-term natural storage of the seeds for up to 9 years in a dry ventilated room in Kraft bags at 20 ± 2 °C, the tested wheat samples experienced a loss of seed germination capacity of ~50 %; anthocyanins were found to not participate in the preservation of germination capacity. Nonetheless, anthocyanins contributed to the preservation of seed viability under unfavorable short-term conditions of a temperature rise to 48 °C at 100 % humidity. The accelerated aging test did not predict poor germination capacity after long-term seed storage. The results showed a neutral role of anthocyanins in the maintenance of seed germination capacity for 6-9 years under natural storage conditions at 20 ± 2 °C. A small statistically significant increase in grain germination capacity during natural aging was associated with the presence of a recombinant region containing the Pp-D1 gene on wheat chromosome 7D.

Fine mapping and targeted genomic analyses of photoperiod‐sensitive gene (GB_PPD1) in Pima cotton (Gossypium barbadense L.)

AbstractCotton grown in the United States are day‐length insensitive annuals and are grown under long‐day summers. Photoperiod sensitivity, present in tropical wild and landraces endemic to the center of origin and diversity, is a major barrier for the introgression of tropical gene pool into the US cotton. Previously, we mapped the major photoperiod response locus Gb_Ppd1 on chromosome D06 of Pima cotton (Gossypium barbadense L.). In the current study, an F2 population of 2112 gametes was used to fine map the Gb_Ppd1 locus. Two sequence‐tagged‐site and nine kompetitive allele‐specific polymerase chain reaction (KASP) markers were developed and the Gb_Ppd1 locus was fine mapped to 1.1 cM region flanked by novel markers 17‐KASP‐8, 17‐KASP‐10, and 15‐PR‐10A. The closely linked markers identified 2.10 Mb region in the G. barbadense genome that contained 18 putative gene sequences. A candidate gene Gbar_D06G014560 showed high homology to VASCULAR PLANT ONE ZINC FINGER PROTEIN 1 involved in photoperiodism in Arabidopsis. We evaluated the diagnostic polymorphisms for the flanking markers on a diversity panel of 91 Pima accessions. These markers would be useful in marker‐assisted selection of photoperiod response in cotton breeding. Further, quantitative gene expression analysis indicated that the CONSTANS (CO)/FLOWERING LOCUS T (FT) system is conserved in the photoperiod response pathway in Pima cotton, while CO and FT are likely not the causal genes underlying flowering time at the Gb_Ppd1 locus. The Gb_Ppd1 gene may be an upstream regulatory sequence in the FT gene pathway that controls photoperiodism in photoperiod‐sensitive cotton by affecting the CO/FT interaction under long‐day‐length conditions.

Climate change enhances stability of wheat-flowering-date

The stability of winter wheat-flowering-date is crucial for ensuring consistent and robust crop performance across diverse climatic conditions. However, the impact of climate change on wheat-flowering-dates remains uncertain. This study aims to elucidate the influence of climate change on wheat-flowering-dates, predict how projected future climate conditions will affect flowering date stability, and identify the most stable wheat genotypes in the study region. We applied a multi-locus genotype-based (MLG-based) model for simulating wheat-flowering-dates, which we calibrated and evaluated using observed data from the Northern China winter wheat region (NCWWR). This MLG-based model was employed to project flowering dates under different climate scenarios. The simulated flowering dates were then used to assess the stability of flowering dates under varying allelic combinations in projected climatic conditions. Our MLG-based model effectively simulated flowering dates, with a root mean square error (RMSE) of 2.3 days, explaining approximately 88.5 % of the genotypic variation in flowering dates among 100 wheat genotypes. We found that, in comparison to the baseline climate, wheat-flowering-dates are expected to shift earlier within the target sowing window by approximately 11 and 14 days by 2050 under the Representative Concentration Pathways 4.5 (RCP4.5) and RCP8.5 climate scenarios, respectively. Furthermore, our analysis revealed that wheat-flowering-date stability is likely to be further strengthened under projected climate scenarios due to early flowering trends. Ultimately, we demonstrate that the combination of Vrn and Ppd genes, rather than individual Vrn or Ppd genes, plays a critical role in wheat-flowering-date stability. Our results suggest that the combination of Ppd-D1a with winter genotypes carrying the vrn-D1 allele significantly contributes to flowering date stability under current and projected climate scenarios. These findings provide valuable insights for wheat breeders and producers under future climatic conditions.

EFFECTS OF MUTANT ALLELES OF THE PPD-1 GENE ON THE DATE TO HEADING UNDER NATURAL AND SHORTENED DAYLENGTH CONDITIONS

The purpose of this work was to identify recombinant inbred lines from the hybrid of Orenburgskaya 48 //Cappelle Desprez/2B Chinese Spring and to evaluate the effects of recessive alleles of the Ppd-D1 and Ppd-A1 genes, as well as their interaction with the dominant allele of the Ppd-B1c gene, on heading dates under environment of natural and shortened photoperiods. The study was conducted on a population of 64 recombinant inbred lines and two parental genotypes. Five-days-old seedlings of each genotype were subjected to vernalization for 50 days and grown on the vegetation site under natural and artificially shortened to 10 hours photoperiods. During the growing season, the dates to heading (DH) of individual plants were recorded when the main spike appeared from the sheath of the flag leaf. Known allele-specific molecular markers were used for identifying carriers of Ppd-D1c, Ppd-D1d, Ppd-A1b and Ppd-A1b-del303 alleles. It was shown that mutant recessive alleles of Ppd-A1 and Ppd-D1 genes do not affect significantly the DH in winter bread wheat plants under environment of natural and reduced photoperiods. The dominant Ppd-B1c allele, regardless of the presence of certain recessive alleles of the Ppd-D1 and Ppd-A1 genes, contributes to the acceleration of the development (acceleration of DH) of plants at different day lengths compared to such carriers of the Ppd-B1b allele. The presence of the mutant recessive allele Ppd-A1b_del303 in the genotype of the line leads to a decrease in the effect of the dominant allele of the Ppd-B1c allele on the acceleration of heading. The interaction of the dominant allele Ppd-B1c in shortening the DH with the genes Ppd-A1b and Ppd-D1d revealed more effective on the reduced photoperiod, аnd with Ppd-A1b and Ppd-D1c on the natural day, and it was the least effective in both variants of the experiment for the combination of alleles Ppd-A1b Ppd -B1b Ppd-D1d. Allelic differences of the three Ppd-1 genes determined 54.2% of the diversity of RIL in terms of the DH under natural environment and 59.9% - at shortened days, it was to a greater extent observed due to allelic differences of the Ppd-B1 gene.

Analysis of the Structural Organization and Expression of the Vrn-D1 Gene Controlling Growth Habit (Spring vs. Winter) in Aegilops tauschii Coss.

The duration of the vegetative period is an important agronomic characteristic of cereal crops. It is mainly influenced by the Vrn (response to vernalization) and Ppd (response to photoperiod) genes. In this work, we searched for alleles of several known genes of these two systems of response to external conditions in 15 accessions of Aegilops tauschii Coss. (syn. Ae. squarrosa L.), with the aim of studying the impact these alleles have on the vegetative period duration and growth habit. As a result, three allelic variants have been found for the Vrn-D1 gene: (i) one intact (winter type), (ii) one with a 5437 bp deletion in the first intron and (iii) one previously undescribed allele with a 3273 bp deletion in the first intron. It has been shown that the spring growth habit of Ae. tauschii can be developed due to the presence of a new allele of the Vrn-D1 gene. Significant differences in expression levels between the new allelic variant of the Vrn-D1 gene and the intact allele vrn-D1 were confirmed by qPCR. The new allele can be introgressed into common wheat to enhance the biodiversity of the spring growth habit and vegetative period duration of plants.

Integrating biophysical crop growth models and whole genome prediction for their mutual benefit: a case study in wheat phenology.

Running crop growth models (CGM) coupled with whole genome prediction (WGP) as a CGM-WGP model introduces environmental information to WGP and genomic relatedness information to the genotype-specific parameters modelled through CGMs. Previous studies have primarily used CGM-WGP to infer prediction accuracy without exploring its potential to enhance CGM and WGP. Here, we implemented a heading and maturity date wheat phenology model within a CGM-WGP framework and compared it with CGM and WGP. The CGM-WGP resulted in more heritable genotype-specific parameters with more biologically realistic correlation structures between genotype-specific parameters and phenology traits compared with CGM-modelled genotype-specific parameters that reflected the correlation of measured phenotypes. Another advantage of CGM-WGP is the ability to infer accurate prediction with much smaller and less diverse reference data compared with that required for CGM. A genome-wide association analysis linked the genotype-specific parameters from the CGM-WGP model to nine significant phenology loci including Vrn-A1 and the three PPD1 genes, which were not detected for CGM-modelled genotype-specific parameters. Selection on genotype-specific parameters could be simpler than on observed phenotypes. For example, thermal time traits are theoretically more independent candidates, compared with the highly correlated heading and maturity dates, which could be used to achieve an environment-specific optimal flowering period. CGM-WGP combines the advantages of CGM and WGP to predict more accurate phenotypes for new genotypes under alternative or future environmental conditions.

Sense in sensitivity: difference in the meaning of photoperiod insensitivity between wheat and barley.

The description of long photoperiod sensitivity in wheat and barley is a cause of confusion for researchers working with these crops, usually accustomed to free exchange of physiological and genetic knowledge of such similar crops. Indeed, wheat and barley scientists customarily quote studies of either crop species when researching one of them. Among their numerous similarities, the main gene controlling the long photoperiod sensitivity is the same in both crops (PPD1; PPD-H1 in barley and PPD-D1 in hexaploid wheat). However, the photoperiod responses are different: (i) the main dominant allele inducing shorter time to anthesis is the insensitive allele in wheat (Ppd-D1a) but the sensitive allele in barley (Ppd-H1) (i.e. sensitivity to photoperiod produces opposite effects on time to heading in wheat and barley); (ii) the main 'insensitive' allele in wheat, Ppd-D1a, does confer insensitivity, whilst that of barley reduces the sensitivity but still responds to photoperiod. The different behaviour of PPD1 genes in wheat and barley is put in a common framework based on the similarities and differences of the molecular bases of their mutations, which include polymorphism at gene expression levels, copy number variation, and sequence of coding regions. This common perspective sheds light on a source of confusion for cereal researchers, and prompts us to recommend accounting for the photoperiod sensitivity status of the plant materials when conducting research on genetic control of phenology. Finally, we provide advice to facilitate the management of natural PPD1 diversity in breeding programmes and suggest targets for further modification through gene editing, based on mutual knowledge on the two crops.

CRISPR/Cas9 editing of wheat Ppd-1 gene homoeologs alters spike architecture and grain morphometric traits.

Mutations in Photoperiod-1 (Ppd-1) gene are known to modify flowering time and yield in wheat. We cloned TaPpd-1 from wheat and found high similarity among the three homoeologs of TaPpd-1. To clarify the characteristics of TaPpd-1 homoeologs in different photoperiod conditions for inflorescence architecture and yield, we used CRISPR/Cas9 system to generate Tappd-1 mutant plants by simultaneous modification of the three homoeologs of wheat Ppd-1. Tappd-1 mutant plants showed no off-target mutations. Four T0-edited lines under short-day length and three lines under long-day length conditions with the mutation frequency of 25% and 21%, respectively. These putative transgenic plants of all the lines were self-fertilized and generated T1 and T2 progenies and were evaluated by phenotypic and expression analysis. Results demonstrated that simultaneously edited TaPpd-1- A1, B1, and D1 homoeologs gene copies in T2_SDL-8-4, T2_SDL-4-5, T2_SDL-3-9, and T2_LDL-10-9 showed similar spike inflorescence, flowering time, and significantly increase in 1000-grain weight, grain area, grain width, grain length, plant height, and spikelets per spike due to mutation in both alleles of Ppd-B1 and Ppd-D1 homoeologs but only spike length was decreased in T2_SDL-8-4, T2_SDL-4-5, and T2_LDL-13-3 mutant lines due to mutation in both alleles of Ppd-A1 homoeolog under both conditions. Our results indicate that all TaPpd1 gene homoeologs influence wheat spike development by affecting both late flowering and earlier flowering but single mutant TaPpd-A1 homoeolog affect lowest as compared to the combination with double mutants of TaPpd-B1 and TaPpd-D1, TaPpd-A1 and TaPpd-B1, and TaPpd-A1 and TaPpd-D1 homoeologs for yield enhancement. Our findings further raised the idea that the relative expression of the various genomic copies of TaPpd-1 homoeologs may have an impact on the spike inflorescence architecture and grain morphometric features in wheat cultivars.

Donors of ultra-earliness for spring common wheat breeding

Knowledge of productivity and genetic control of the rate of ultra-early lines development will facilitate their use in breeding of common wheat Tritium aestivum L. for high adaptive capacity. The research focused on ultra-early lines Rico (k-65588), Rimax (k-67257) (progeny of F3 Rico × ‘Max’, k-57181), Fori 1-8 line series (progeny of F4 ‘Photon’ × Rico) and Rifor 1-13 (progeny of F7-8 Rico × ‘Forlani Roberto’), as well as on the accessions ‘Photon’ (k-55696) and ‘Forlani Roberto’ (k-42641). The varieties ‘Leningradskaya 6’ (k-64900) and ‘Leningradskaya 97’ (k-62935) were used as standards in VIR, and ‘Chelyaba 2’ (k-64379) was used in Сhelyabinsk ARI. The alleles of Vrn and Ppd genes were identified by PCR using the published allele-specific primers. Responses to vernalization (30 days at 3°C) and to a short 12-hour day were determined according to the VIR guidelines. The ultra-earliness of common wheat lines is associated with the presence of dominant alleles Vrn-A1, Vrn-B1, Vrn-D1, Ppd-B1, Ppd-D1, and possibly Eps. The shortest emergence-to-heading period at two experimental locations was noted for Rico (39.9 ± 1.49 days), which is 14.8 ± 1.22 days earlier than the development of region-adapted varieties. The Rico genotype contains Vrn-A1, Vrn-B1, Vrn-D1, Ppd-B1 and Ppd-D1. In the Rimax genotype, different alleles of the Ppd-D1 and Vrn-B1 genes were found, possibly being a result of recombination processes in Rico × ‘Max’ hybrids. Under a short photoperiod (12 hours), the Rico and Rimax genes can interact in a cumulative polymeric mode, which is not the case in long-day environments. Unlike other Rifor lines, Rifor 4 and Rifor 5, as well as ‘Forlani Roberto’, have a recessive vrn-A1a allele. However, Rifor 4 and Rifor 5 do not respond to vernalization, while ‘Forlani Roberto’ is responsive to this factor. The absence of response to vernalization in Rifor 4 and Rifor 5 possessing the recessive vrn-A1a allele is possibly provided by a complex of modifier genes along with the dominant Vrn-D1 gene, which was formed during recombination in F7-8 Rico × ‘Forlani Roberto’ hybrids. Recombinants of spring common wheat, combining ultra-earliness and relatively high ear productivity, have been identified. Grain yield per 1 m2 of new ultra-early lines in some years can reach 90% of that of the ‘Leningradskaya 97’. It is expedient to use ultra-early lines as donors of high-rate development in common wheat breeding, considering genetic peculiarities of the source lines.

Різноманіття Ppd-1 генотипів сортів ярої та озимої м’якої пшениці (Triticum aestivum L.) України

Ancient and modern 183 varieties of winter and 23 spring types of development of bread wheat (Triticum aestivum L.) selected Ukrainian state institutions and private companies are characterized by alleles of Ppd-D1, Ppd-B1, and Ppd-A1 genes. Allele-specific molecular markers, proposed in the scientific literature, were used to identify carriers of the Ppd-D1a, Ppd-D1b, Ppd-D1c, Ppd-D1d, Ppd-B1a, Ppd-B1c, Ppd-A1b alleles. According to the results of PCR analysis, the most widespread among the studied winter cultivars was observed in the dominant allele Ppd-D1a (91.9 %) with a range from 80.0 % in the sampling of varieties of the Northeast (Kharkiv, Sumy) to 95.0 % in southern cultivars (Odesa, Kherson), and in spring – recessive Ppd-D1c (43.5 %). The share of carriers of various recessive alleles of the Ppd-D1 gene among spring varieties is 73.9 %, and among winter – 8.1 % and, except for Borovitsa and Talisman consists of cultivars created by the late 60 – early 70 years of last century. The frequencies of the Ppd-B1a and Ppd-B1c alleles are quite small. The Ppd-B1a allele was found only in three spring varieties, and the Ppd-B1c allele in 5 winter varieties and spring wheat Struna Mironivska, except for the latter cultivar, in all cases found together with the Ppd-D1a allele. The Ppd-A1 gene was present in a recessive state in all studied sorts. Seven different homozygous Ppd-1 genotypes have been determined in the studied cultivars. Samples of winter and spring varieties differ significantly in the quantity and frequency of specific Ppd-1 genotypes. The presence of varieties with monogenic dominant Ppd-D1a or Ppd-B1c control of traits and digenic dominant Ppd-D1a Ppd-B1a genotypes has been marked in spring wheat, as well as monogenic dominant for Ppd-D1a and digenic dominant for Ppd-D1a in winter wheat varieties. In spring cultivars the share of carriers of recessive alleles of Ppd-1 genes is several times higher (69.6 %) than in winter varieties; conversely, the samples of winter varieties have significantly more dominant alleles (91.9 %). Such differences in genotype frequencies are due to the timing of sowing and duration of the natural day at the latitude of the growing region during the growing season of winter and spring varieties.

Vernalization and photoperiod alleles greatly affected phenological and agronomic traits in bread wheat under autumn and spring sowing conditions

The responses to temperature (vernalization) and day length (photoperiod) in wheat (Triticum aestivum L.) are mainly defined by allelic differences at the respective VRN-1 and PPD-1 loci, which greatly affect wheat phenology and adaptability. Using molecular markers, a panel of 61 diverse bread wheat varieties was genotyped for VRN-1 and PPD-1 alleles, and the traits were evaluated under two conditions by sowing in autumn and spring to investigate the impact of these genes and their alleles on phenological stages, morphological and yield traits. The results revealed that the earlier heading and flowering conferred by the dominant alleles of VRN-1 and the insensitive alleles of PPD-1 genes were consistent under both the autumn and spring sowing conditions. The effects of a single dominant allele of the three VRN-1 genes were similar whereas the effects of a single insensitive allele of the three PPD-1 genes differed, with Ppd-D1a stronger than Ppd-B1a while Ppd-A1a was the least. Varieties sown under spring conditions recorded a larger flag leaf area than those sown under autumn conditions regardless of the allelic influence at the VRN-1 and PPD-1 loci. When compared to other genes, PPD-D1 had a consistent and significant effect on flag leaf area, spike length, and plant height across both sowing conditions. Furthermore, the varieties with Ppd-D1b had larger biomass across both sowing conditions, but this did not translate into increased yield because the Ppd-D1a recorded a higher yield. The impact of PPD-D1 gene on grain yield was evident across both sowing conditions.

Genome-wide identification and expression of TIFY family in cassava (Manihot esculenta Crantz).

Plant-specific TIFY [TIF(F/Y)XG] proteins serve important roles in the regulation of plant stress responses. This family encodes four subfamilies of proteins, JAZ (JASMONATE ZIM-domain), PPD (PEAPOD), ZML (Zinc-finger Inflorescence-like), and TIFY. In this work, a total of 16 JAZ, 3 PPD, 7 ZML, and 2 TIFY genes were found in cassava (Manihot esculenta Crantz) at the genome-wide level. The phylogenetics, exon-intron structure, motif organization, and conserved domains of these genes were analyzed to characterize the members of the JAZ, PPD, and ZML subfamilies. Chromosome location and synteny analyses revealed that 26 JAZ, PPD, and ZML genes were irregularly distributed across 14 of the 18 chromosomes, and 18 gene pairs were implicated in large-scale interchromosomal segmental duplication events. In addition, JAZ, PPD, and ZML gene synteny comparisons between cassava and three other plant species (Arabidopsis, Populus trichocarpa, and rice) uncovered vital information about their likely evolution. The prediction of protein interaction network and cis-acting elements reveal the function of JAZ, PPD, and ZML genes. Subsequently, expression patterns of JAZ, PPD, and ZML genes were validated by qRT-PCR as being expressed in response to osmotic, salt, and cadmium stress. Moreover, almost all JAZ subfamily genes were responsive to jasmonic acid (JA) treatment. In particular, MeJAZ1, MeJAZ13, and MeJAZ14, were highly up-regulated by three treatments, and these genes may deserve further study. This comprehensive study lays the groundwork for future research into TIFY family genes in cassava and may be valuable for genetic improvement of cassava and other related species.

Genome-Wide Analysis of the Gene Structure, Expression and Protein Interactions of the Peach (Prunus persica) TIFY Gene Family.

The TIFY family is a plant-specific gene family involved in regulating many plant processes, such as development and growth, defense and stress responses, fertility and reproduction, and the biosynthesis of secondary metabolites. The v2.0 peach (Prunus persica) genome, which has an improved chromosome-scale assembly and contiguity, has recently been released, but a genome-wide investigation of the peach TIFY family is lacking. In this study, 16 TIFY family genes from the peach genome were identified according to the peach reference genome sequence information and further validated by cloning sequencing. The synteny, phylogenetics, location, structure, and conserved domains and motifs of these genes were analyzed, and finally, the peach TIFY family was characterized into 9 JAZ, 1 TIFY, 1 PPD and 5 ZML subfamily members. Expression profiles of peach JAZ, PPD, and ZML genes in various organs and fruit developmental stages were analyzed, and they showed limited effects with fruit ripening cues. Four TIFY members were significantly affected at the mRNA level by exogenous treatment with MeJA in the peach epicarp, and among them, PpJAZ1, PpJAZ4 and PpJAZ5 were significantly correlated with fruit epicarp pigmentation. In addition, the TIFY family member protein interaction networks established by the yeast two-hybrid (Y2H) assay not only showed similar JAZ-MYC2 and JAZ homo- and heterodimer patterns as those found in Arabidopsis but also extended the JAZ dimer network to ZML-ZML and JAZ-ZML interactions. The PpJAZ3-PpZML4 interaction found in this study suggests the potential formation of the ZML-JAZ-MYC complex in the JA-signaling pathway, which may extend our knowledge of this gene family’s functions in diverse biological processes.

Molecular labeling of <i>Vrn</i>, <i>Ppd</i> genes and vernalization response of the ultra-early lines of spring bread wheat <i>Triticum aestivum</i> L.

Background. The knowledge of genetic control of vernalization response in the ultra-early accessions can facilitate bread wheat breeding for a high adaptive capacity. Materials and methods. The study involved the ultra-early lines Rico (k-65588) and Rimax (k-67257) as the earliest maturing lines in the VIR bread wheat collection, as well as 10 Rifor lines (k-67120, k-67121, k-67250-67256) with a high rate of development before heading. A late ripening accession ‘Forlani Roberto’ (k-42641) and ‘Leningradskaya 6’ variety (k-64900), regionally adapted to Northwestern Russia, were also studied. The alleles of the Vrn and Ppd genes were identified by the PCR analysis using the allele-specific primers published in literature sources. The response to vernalization (30 days at 3°C) and a short 12-hour day were determined using a methodology accepted at VIR. Results. The ultra-early lines respond to a short 12-hour day and 30-day vernalization very poorly. The genotype of ultra-early wheat lines is mainly represented by three genes, Vrn-A1, Vrn-B1a, and Vrn-D1, which ensure insensitivity to vernalization alongside with the expression of Ppd-D1a, which controls the response to photoperiod. The ultra-early lines Rifor 4 and Rifor 5 have a recessive allele vrn-A1a, like the original ‘Forlani Roberto’ accession. The lines Rifor 4 and Rifor 5 are vernalization-insensitive under the long day and have a very weak response under the short day (3.5±0.42 days and 4.0±0.61 days, respectively). However, ‘Forlani Roberto’ with the vrn-A1a gene responds to vernalization in the same way under any photoperiod (12.3±1.58 days and 12.2±0.74 days). Conclusion The ultra-early lines of bread wheat Rifor 4 and Rifor 5 with the vrn-A1a gene can have no response to vernalization or have a low level response. This effect can be a reason for the formation of a complex of modifier genes along with the dominant gene Vrn-D1, which forms during the hybridization of F7-8 Rico × Forlani Roberto. The ultra-early lines of bread wheat Rico, Rimax and Rifor (k-67120, k-67121, k-67250-67256) can serve as effective sources of genes for earliness in common wheat breeding.

Functional Analysis of the "Green Revolution" Gene Photoperiod-1 and Its Selection Trends During Bread Wheat Breeding.

Flowering is central to the transformation of plants from vegetative growth to reproductive growth. The circadian clock system enables plants to sense the changes in the external environment and to modify the growth and development process at an appropriate time. Photoperiod-1 (Ppd-1), which is controlled by the output signal of the circadian clock, has played an important role in the wheat “Green Revolution.” In the current study, we systematically studied the relationship between Ppd-1 haplotypes and both wheat yield- and quality-related traits, using genome-wide association analysis and transgenic strategies, and found that highly appropriate haplotypes had been selected in the wheat breeding programs. Genome-wide association analysis showed that Ppd-1 is associated with significant differences in yield-related traits in wheat, including spike length (SL), heading date (HD), plant height (PH), and thousand-grain weight (TGW). Ppd-1-Hapl-A1 showed increased SL by 4.72–5.93%, whereas Ppd-1-Hapl-B1 and Ppd-1-Hapl-D1 displayed earlier HD by 0.58–0.75 and 1.24–2.93%, respectively, decreased PH by 5.64–13.08 and 13.62–27.30%, respectively, and increased TGW by 4.89–10.94 and 11.12–21.45%, respectively. Furthermore, the constitutive expression of the Ppd-D1 gene in rice significantly delayed heading date and resulted in reduced plant height, thousand-grain weight, grain width (GW), and total protein content. With reference to 40years of data from Chinese wheat breeding, it was found that the appropriate haplotypes Ppd-1-Hapl-A1, Ppd-1-Hapl-B1, and Ppd-1-Hapl-D1 had all been subjected to directional selection, and that their distribution frequencies had increased from 26.09, 60.00, and 52.00% in landraces to 42.55, 93.62, and 96.23% in wheat cultivars developed in the 2010s. A Ppd-B1 methylation molecular marker was also developed to assist molecular wheat breeding. This research is of significance for fully exploring the function of the Ppd-1 gene and its genetic resource diversity, to effectively use the most appropriate haplotypes and to improve crop yield and sustainability.

Comparative analysis of the inheritance of a high development rate in the Rimax and Rico lines of spring bread wheat (Triticum aestivum L.)

Background. Development of early-ripening spring bread wheat (Triticum aestivum L.) cultivars is an important task for Russian breeders. Knowledge of the genetics of ultraearly varieties – sources of valuable genes that determine an earlier-maturing type of plant development –will be used to work out methods for obtaining source material for breeding.Materials and methods. The ultra-early lines Rico (k65588, var. erythrospermum Koern.) and Rimax (k-67257, var. lutescens (Alef.) Mansf.), and cvs. ‘Max’ (k-57181, var. lutescens) and ‘Leningradskaya 6’ (k-64900, var. lutescens) were studied. Alleles of the Vrn and Ppd genes were identified by PCR according to known publications, and genomic DNA was isolated from 3-day-old seedlings by the CTAB method.Results. In the environments of Northwest Russia, the Rimax and Rico lines are characterized by the highest rate of development before heading among the spring wheat accessions from the VIR collection. In the Rimax and Rico genotypes, the Vrn-A1, Vrn-B1, Vrn-D1 and Ppd-D1 genes were found. Genotypes with different alleles of Ppd-D1 and Vrn-B1 were identified in the Rimax line. Under conditions of a long day (18 hours), in the population of F2 (F3 ) Rico × Rimax hybrids, the ratio of phenotypes with a high development rate to all others was observed as 1 : 15 (χ2 1: 15 = 0.64). Under a short day (12 hours), 5 clearly tested groups were identified in F2 with the ratio 1 : 4 : 6 : 4 : 1 (χ2 = 3.03; χ2 0.05 = 9.48), which indicates the manifestation of cumulative polymerization.Conclusion. Each of the Rimax and Rico lines has two pairs of independent duplicated genes that determine a high development rate. Under short-day conditions, these genes can interact like cumulative polymers. The Rimax and Rico lines, due to their high development rate, are valuable source material to be used in breeding for earliness.

Allele frequencies of Ppd-D1a, Ppd-B1a, and Ppd-B1c of photoperiodic sensitivity genes in spring bread wheat varieties (Triticum aestivum L.) of various origin

Aim. To identify and evaluate allele frequencies of Ppd-D1a, Ppd-B1a, Ppd-B1c and Ppd-1 of the genotypes of spring bread wheat varieties from various climatic zones. Methods. DNA isolation, allele-specific PCR, electrophoresis in agarose and polyacrylamide gel, statistical analysis. Results. 137 varieties of spring bread wheat of various origin were detected to identify Ppd-1 genotypes of Ppd-D1a, Ppd-B1a and Ppd-B1c allele carriers. The results for the total sampling of the varieties under investigation and the sampling of Asian varieties yielded six different Ppd-1 genotypes in each. As for samplings of other regions, there were from two (Mexico) to four (Europe, the USA, Canada, Ukraine) Ppd-1 genotypes. In the total sampling of varieties, there was a high incidence (20.5 %) of genotypes, dominant only in allele Ppd-D1a, varying from 0 (Russia) to 85.0 % (Mexico). The incidence of the genotypes with monogenically dominant Ppd-B1a (7.3 %) or Ppd-B1c (5.1 %) in the total sampling, was considerably lower. These genotypes were most common for the sampling of the varieties from the USA and Canada (25.0 and 16.7 % respectively). Digenically dominant Ppd-D1a Ppd-B1a genotypes were found in the total sampling with relatively low incidence (7.3 %), and were notable for the varieties from Asia (33.4 %), Mexico (15.0 %), Ukraine (13.1 %), and Europe (3.1 %). The di genically dominant genotype Ppd-D1a Ppd-B1с was found only in the Japanese variety Konosu-25. Gene Ppd-A1 was present in all the spring varieties under investigation in its recessive state. Conclusions. Out of three dominant alleles in the studied sampling, the highest incidence was noted for allele Ppd-D1a (28.5 %). All the varieties from Mexico, present in the set, carry this allele. At the same time, it was not found in any variety from Russia. Allele Ppd-B1a was detected in the varieties from all the regions with the incidence of 7.7 (Russia) – 44.4 % (Asia). Allele Ppd-B1c was sporadically present in the varieties from Russia, Ukraine, the USA, Japan, and Brazil, and its incidence in the total sampling was insignificant (5.8 %). The varieties, identified by the allelic status of Ppd-1 genes, may be used as donors for selection and determination of the influence of alleles for each gene by the development rate and related economically valuable traits of bread wheat.

Vernalization (VRN) and Photoperiod (PPD) Genes in Spring Hexaploid Wheat Landraces

The heading time in wheat and some other cereals is mainly determined by the genetic system of VRN (vernalization response) and PPD (photoperiod response) genes. Using diagnostic DNA markers, we analyzed VRN-A1, VRN-B1, VRN-D1, and PPD-D1 allelic diversity in a set of landraces representing seven hexaploid spring wheat species from several regions of Eurasia. The determination of the spring growth habit was found to be variable: in 55.3% accessions, it was controlled monogenically by a VRN gene; in 30.3% accessions, by a combination of two VRN genes; and in 2.6% accessions, trigenically. The dominant Ppd-D1a allele was almost completely absent (only 2.6%) in the landraces, which suggests it being secondary to the recessive ppd-D1b allele as well as increase in its frequency during the recent “green revolution.” In species T. aestivum, Т. compactum, T. petropavlovskyi, and T. tibetanum, the Vrn-D1a frequency was shown to increase eastward with maximum concentration in the regions of Afghanistan, India, and China. In species with a compact ear (T. antiquorum, T. sphaerococcum, and Asian forms of Т. compactum), the spring growth habit is controlled by a single Vrn-B1a allele, which indicates their possible initial distribution in the same gene pool. The European and Asian T. spelta subspecies, despite the very fragmented distribution range, have the same Vrn-A1b and Vrn-B1c alleles, which genetically unites these subspecies. A common set of alleles of the VRN genes in landraces and modern cultivars have provided the adaptability of wheat to diverse environmental conditions during the long period of its cultivation. The newly detected DNA fragments in the first intron of VRN-D1 and PPD-D1 loci may mark new alleles and be of interest for further examination and use in breeding programs.

Alleles of Ppd-1 genes that control sensitivity to photoperiod in a number of bread winter wheat genotypes

Purpose. Analysis of the allelic state of Ppd-1 genes, which control sensitivity to photoperiod, in varieties and lines of bread winter wheat, and comparison of the results obtained with field observations on the duration of periods before heading and flowering, whose originators were the Nosivska Breeding and Research Station of the V. M. Remeslo Myronivka Institute of Wheat National Academy of Agrarian Sciences of Ukraine and Poltava State Agrarian Academy of the Ministry of Education and Science of Ukraine.Methods. The following methods were used in the work: DNA extraction, allele-specific PCR, agarose and polyacrylamide gel electrophoresis, analysis of variance.Results. It was revealed that ‘Yuvivata 60’ variety has a recessive Ppd-1 genotype and belongs to the III haplotype by a combination of mutations in the structure of Ppd-D1 gene. Line ‘L41/95’ was heterogeneous by alleles of Ppd-D1 gene, which corresponded to the presence of haplotypes III and VII. All other tested cultivars and lines were characterized by alleles Ppd-A1b, Ppd-B1b and Ppd-D1a, and assigned to haplotype VII. According to the results of statistical data processing, the duration of the period from May, 1 to heading was the smallest for the variety ‘Donskaya polukarlikovaya’ in the conditions of both the Forest-Steppe and Polissia-Forest-Steppe regions of Ukraine, the longest – in the varieties ‘Yuvivata 60’, ‘Myronivska 61’ and ‘L41/95’. The differences between these groups were significant and amounted to 10 days.Conclusions. A breeding material with a high adaptive ability for growing conditions in Polissia-Forest-Steppe zone was studied by the allelic state of the Ppd-1 genes. A low level of polymorphism in the studied varieties and lines was revealed by the alleles of Ppd-1 genes [12.5% – Ppd-D1b (²²²), 12.5% – Ppd-D1à/b (²²²/VII), 75% – Ppd-D1a (VII)], that agrees with the hypothesis that breeders gave a greater preference for the photoperiod-insensitive wheat genotype under Ukrainian conditions. The genotypes with the dominant Ppd-D1a (VII) gene almost completely dominate in the south of Ukraine. At the same time, in northern latitudes, weather conditions negate the advantages of the genotypes with Ppd-D1a gene

Interaction of VRN and PPD genes in the regulation of the development of winter wheat (Triticum aestivum L.)

Aim. To reveal the effects of the VRN and PPD genes on the rate of development of winter wheat in absence of vernalization and after its completion with different durations of the photoperiod. Methods. Winter-type development lines of the Mironovskaya 808 variety, isogenic with respect to the PPD genes. VRN genes are recessive in all lines. Plants were grown under the conditions of a growing experiment from non-vernalized seeds (1 group of all lines), and also after vernalization (2 group of all lines) at 20-22°C. Both groups were grown under long (18 hours) and short (9 hours) photoperiods. The pace of development was determined by the timing of the transition of plants to spiking. Results. In the absence of vernalization on a short day, isogenic lines with dominant genes PPD-D1a and PPD-B1a and cultivar (all genes are PPD recessive) passed to earing, and the line with the dominant PPD-A1a gene remained in the tillering phase until the end of the experiment. On a long day, all investigated lines and cultivar did not spike until the end of the experiment (200 days). After vernalization was completed, all the studied lines under the conditions of a short photoperiod were earing later than on a long day, but the line with the dominant PPD-B1a gene was the latest. Conclusions. The VRN and PPD genes interact in the regulation of winter wheat development - they are “interchangeable” in terms of developmental effects depending on a combination of temperature and photoperiodic conditions.
 Keywords: winter wheat, (Triticum aestivum L.), vernalization, photoperiod, development rates, VRN and PPD genes.