Identification, Structural and Functional Characterization of Dormancy Regulator Genes in Apricot (Prunus armeniaca L.)

Perspectives on the adaptation of Japanese plum-type cultivars to reduced winter chilling in two regions of Spain

Japanese plum, like other temperate fruit tree species, has cultivar-specific temperature requirements during dormancy for proper flowering. Knowing the temperature requirements of this species is of increasing interest due to the great genetic variability that exists among the available Japanese plum-type cultivars, since most of them are interspecific hybrids. The reduction of winter chilling caused by climate change is threatening their cultivation in many regions. In this work, the adaptation perspectives of 21 Japanese plum-type cultivars were analyzed in two of the main plum-growing regions in Spain, Badajoz and Zaragoza, to future climate conditions. Endodormancy release for subsequent estimation of chilling and heat requirements was determined through empirical experiments conducted during dormancy at least over two years. Chill requirements were calculated using three models [chilling hours (CH), chilling units (CU) and chilling portions (CP)] and heat requirements using growing degree hours (GDH). Chilling requirements ranged 277-851 CH, 412-1,030 CU and 26-51 CP, and heat requirements ranged from 4,343 to 9,525 GDH. The potential adaption of the cultivars to future warmer conditions in both regions was assessed using climate projections under two Representative Concentration Pathways (RCP), RCP4.5 (effective reduction of greenhouse gas emissions) and RCP8.5 (continuous increase in greenhouse gas emissions), in two time horizons, from the middle to the end of 21st century, with temperature projections from 15 Global Climate Models. The probability of satisfying the estimated cultivar-specific chilling requirements in Badajoz was lower than in Zaragoza, because of the lower chill availability predicted. In this region, the cultivars analyzed herein may have limited cultivation because the predicted reduction in winter chill may result in the chilling requirements not being successfully fulfilled.

The study of the characteristics of the secondary flowering of Cerasus subhirtella 'Autumnalis'

The short flowering period of ornamental cherry trees is the main factor limiting their use in gardens. Determining the secondary flowering characteristics of ornamental cherry trees is required to prolong their flowering period. In this experiment, Cerasus subhirtella 'Autumnalis' was used as the experimental material. The phenological differences in their annual growth cycle were observed using the BBCH coding system. The cooling requirements of the flower buds were evaluated by the chilling hours model (temperature between 0 and 7.2 °C) and the Utah model. The expression of the core gene involved in bud dormancy regulation DAM (dormancy-associated MADS-box) from the completion of flower bud differentiation in one year until the following year was measured by performing real-time fluorescence-based quantitative PCR. The results showed that the flowering duration of C. subhirtella 'Autumnalis' from November to December was longer than that of C. yedoensis 'Somei Yoshino', which was from March to April. The progress from seed bud-break to flower bud opening took about 10 days for C. subhirtella 'Autumnalis', while the same stage for C. yedoensis 'Somei Yoshino' took around 20 days. Additionally, the flower buds of C. subhirtella 'Autumnalis' needed only the chilling temperature unit of 54.08 to satisfy the chilling requirement, while C. yedoensis 'Somei Yoshino' required a chilling temperature unit of 596.75. After the completion of flower bud differentiation, during low-temperature storage, the expression of DAM4 and DAM5 genes first increased and then decreased, whereas, the expression of the DAM6 gene continued to decrease, and the expression of DAM4, DAM5, and DAM6 in C. yedoensis 'Somei Yoshino' increased rapidly and was maintained at a high level. This showed that the upregulation of the expression of the DAM4, DAM5, and DAM6 genes can inhibit the flower bud germination of Cherry Blossom. The relative expression of the DAM gene of C. subhirtella 'Autumnalis' was significantly lower than that of the DAM gene of C. yedoensis 'Somei Yoshino' from the end of October to the beginning of December, leading to its secondary flowering in autumn. These results might elucidate why the flower buds of C. subhirtella 'Autumnalis' can break their internal dormancy and bloom in the autumn and then again in the following year. Our findings might provide a reference for conducting further studies on the mechanisms of secondary flowering and bud dormancy in cherries.

Evolutionary origin and functional specialization of Dormancy-Associated MADS box (DAM) proteins in perennial crops

BACKGROUND

Bud dormancy is a phenological adaptation of temperate perennials that ensures survival under winter temperature conditions by ceasing growth and increasing cold hardiness. SHORT VEGETATIVE PHASE (SVP)-like factors, and particularly a subset of them named DORMANCY-ASSOCIATED MADS-BOX (DAM), are master regulators of bud dormancy in perennials, prominently Rosaceae crops widely adapted to varying environmental conditions.

RESULTS

SVP-like proteins from recently sequenced Rosaceae genomes were identified and characterized using sequence, phylogenetic and synteny analysis tools. SVP-like proteins clustered in three clades (SVP1-3), with known DAM proteins located within SVP2 clade, which also included Arabidopsis AGAMOUS-LIKE 24 (AthAGL24). A more detailed study on these protein sequences led to the identification of a 15-amino acid long motif specific to DAM proteins, which affected protein heteromerization properties by yeast two-hybrid system in peach PpeDAM6, and the unexpected finding of predicted DAM-like genes in loquat, an evergreen species lacking winter dormancy. DAM gene expression in loquat trees was studied by quantitative PCR, associating with inflorescence development and growth in varieties with contrasting flowering behaviour.

CONCLUSIONS

Phylogenetic, synteny analyses and heterologous overexpression in the model plant Arabidopsis thaliana supported three major conclusions: 1) DAM proteins might have emerged from the SVP2 clade in the Amygdaloideae subfamily of Rosaceae; 2) a short DAM-specific motif affects protein heteromerization, with a likely effect on DAM transcriptional targets and other functional features, providing a sequence signature for the DAM group of dormancy factors; 3) in agreement with other recent studies, DAM associates with inflorescence development and growth, independently of the dormancy habit.

Male Meiosis as a Biomarker for Endo- to Ecodormancy Transition in Apricot

Dormancy is an adaptive strategy in plants to survive under unfavorable climatic conditions during winter. In temperate regions, most fruit trees need exposure to a certain period of low temperatures to overcome endodormancy. After endodormancy release, exposure to warm temperatures is needed to flower (ecodormancy). Chilling and heat requirements are genetically determined and, therefore, are specific for each species and cultivar. The lack of sufficient winter chilling can cause failures in flowering and fruiting, thereby compromising yield. Thus, the knowledge of the chilling and heat requirements is essential to optimize cultivar selection for different edaphoclimatic conditions. However, the lack of phenological or biological markers linked to the dormant and forcing periods makes it difficult to establish the end of endodormancy. This has led to indirect estimates that are usually not valid in different agroclimatic conditions. The increasing number of milder winters caused by climatic change and the continuous release of new cultivars emphasize the necessity of a proper biological marker linked to the endo- to ecodormancy transition for an accurate estimation of the agroclimatic requirements (AR) of each cultivar. In this work, male meiosis is evaluated as a biomarker to determine endodormancy release and to estimate both chilling and heat requirements in apricot. For this purpose, pollen development was characterized histochemically in 20 cultivars over 8 years, and the developmental stages were related to dormancy. Results were compared to three approaches that indirectly estimate the breaking of dormancy: an experimental methodology by evaluating bud growth in shoots collected periodically throughout the winter months and transferred to forcing chambers over 3 years, and two statistical approaches that relate seasonal temperatures and blooming dates in a series of 11-20 years by correlation and partial least square regression. The results disclose that male meiosis is a possible biomarker to determine the end of endodormancy and estimate AR in apricot.

The genome of low-chill Chinese plum 'Sanyueli' (Prunus salicina Lindl.) provides insights into the regulation of the chilling requirement of flower buds

Chinese plum (Prunus salicina Lindl.) is a stone fruit that belongs to the Prunus genus and plays an important role in the global production of plum. In this study, we report the genome sequence of the Chinese plum 'Sanyueli', which is known to have a low-chill requirement for flower bud break. The assembled genome size was 282.38 Mb, with a contig N50 of 1.37 Mb. Over 99% of the assembly was anchored to eight pseudochromosomes, with a scaffold N50 of 34.46Mb. A total of 29,708 protein-coding genes were predicted from the genome and 46.85% (132.32 Mb) of the genome was annotated as repetitive sequence. Bud dormancy is influenced by chilling requirement in plum and partly controlled by DORMANCY ASSOCIATED MADS-box (DAM) genes. Six tandemly arrayed PsDAM genes were identified in the assembled genome. Sequence analysis of PsDAM6 in 'Sanyueli' revealed the presence of large insertions in the intron and exon regions. Transcriptome analysis indicated that the expression of PsDAM6 in the dormant flower buds of 'Sanyueli' was significantly lower than that in the dormant flower buds of the high chill requiring 'Furongli' plum. In addition, the expression of PsDAM6 was repressed by chilling treatment. The genome sequence of 'Sanyueli' plum provides a valuable resource for elucidating the molecular mechanisms responsible for the regulation of chilling requirements, and it is also useful for the identification of the genes involved in the control of other important agronomic traits and molecular breeding in plum.

Downregulation of lncRNA PpL-T31511 and Pp-miRn182 Promotes Hydrogen Cyanamide-Induced Endodormancy Release through the PP2C-H2O2 Pathway in Pear (Pyrus pyrifolia)

Bud endodormancy is an important, complex process subject to both genetic and epigenetic control, the mechanism of which is still unclear. The endogenous hormone abscisic acid (ABA) and its signaling pathway play important roles in the endodormancy process, in which the type 2C protein phosphatases (PP2Cs) is key to the ABA signal pathway. Due to its excellent effect on endodormancy release, hydrogen cyanamide (HC) treatment is considered an effective measure to study the mechanism of endodormancy release. In this study, RNA-Seq analysis was conducted on endodormant floral buds of pear (Pyrus pyrifolia) with HC treatment, and the HC-induced PP2C gene PpPP2C1 was identified. Next, software prediction, expression tests and transient assays revealed that lncRNA PpL-T31511-derived Pp-miRn182 targets PpPP2C1. The expression analysis showed that HC treatment upregulated the expression of PpPP2C1 and downregulated the expression of PpL-T31511 and Pp-miRn182. Moreover, HC treatment inhibited the accumulation of ABA signaling pathway-related genes and hydrogen peroxide (H₂O₂). Furthermore, overexpression of Pp-miRn182 reduced the inhibitory effect of PpPP2C1 on the H₂O₂ content. In summary, our study suggests that downregulation of PpL-T31511-derived Pp-miRn182 promotes HC-induced endodormancy release in pear plants through the PP2C-H₂O₂ pathway.

Identification and Characterization of DAMs Mutations Associated With Early Blooming in Sweet Cherry, and Validation of DNA-Based Markers for Selection

Dormancy release and bloom time of sweet cherry cultivars depend on the environment and the genotype. The knowledge of these traits is essential for cultivar adaptation to different growing areas, and to ensure fruit set in the current climate change scenario. In this work, the major sweet cherry bloom time QTL qP-BT1.1 ^m (327 Kbs; Chromosome 1) was scanned for candidate genes in the Regina cv genome. Six MADS-box genes (PavDAMs), orthologs to peach and Japanese apricot DAMs, were identified as candidate genes for bloom time regulation. The complete curated genomic structure annotation of these genes is reported. To characterize PavDAMs intra-specific variation, genome sequences of cultivars with contrasting chilling requirements and bloom times (N = 13), were then mapped to the 'Regina' genome. A high protein sequence conservation (98.8-100%) was observed. A higher amino acid variability and several structural mutations were identified in the low-chilling and extra-early blooming cv Cristobalina. Specifically, a large deletion (694 bp) upstream of PavDAM1, and various INDELs and SNPs in contiguous PavDAM4 and -5 UTRs were identified. PavDAM1 upstream deletion in 'Cristobalina' revealed the absence of several cis-acting motifs, potentially involved in PavDAMs expression. Also, due to this deletion, a non-coding gene expressed in late-blooming 'Regina' seems truncated in 'Cristobalina'. Additionally, PavDAM4 and -5 UTRs mutations revealed different splicing variants between 'Regina' and 'Cristobalina' PavDAM5. The results indicate that the regulation of PavDAMs expression and post-transcriptional regulation in 'Cristobalina' may be altered due to structural mutations in regulatory regions. Previous transcriptomic studies show differential expression of PavDAM genes during dormancy in this cultivar. The results indicate that 'Cristobalina' show significant amino acid differences, and structural mutations in PavDAMs, that correlate with low-chilling and early blooming, but the direct implication of these mutations remains to be determined. To complete the work, PCR markers designed for the detection of 'Cristobalina' structural mutations in PavDAMs, were validated in an F₂ population and a set of cultivars. These PCR markers are useful for marker-assisted selection of early blooming seedlings, and probably low-chilling, from 'Cristobalina', which is a unique breeding source for these traits.

Elucidation of molecular and hormonal background of early growth cessation and endodormancy induction in two contrasting Populus hybrid cultivars

BACKGROUND

Over the life cycle of perennial trees, the dormant state enables the avoidance of abiotic stress conditions. The growth cycle can be partitioned into induction, maintenance and release and is controlled by complex interactions between many endogenous and environmental factors. While phytohormones have long been linked with dormancy, there is increasing evidence of regulation by DAM and CBF genes. To reveal whether the expression kinetics of CBFs and their target PtDAM1 is related to growth cessation and endodormancy induction in Populus, two hybrid poplar cultivars were studied which had known differential responses to dormancy inducing conditions.

RESULTS

Growth cessation, dormancy status and expression of six PtCBFs and PtDAM1 were analyzed. The 'Okanese' hybrid cultivar ceased growth rapidly, was able to reach endodormancy, and exhibited a significant increase of several PtCBF transcripts in the buds on the 10th day. The 'Walker' cultivar had delayed growth cessation, was unable to enter endodormancy, and showed much lower CBF expression in buds. Expression of PtDAM1 peaked on the 10th day only in the buds of 'Okanese'. In addition, PtDAM1 was not expressed in the leaves of either cultivar while leaf CBFs expression pattern was several fold higher in 'Walker', peaking at day 1. Leaf phytohormones in both cultivars followed similar profiles during growth cessation but differentiated based on cytokinins which were largely reduced, while the Ox-IAA and iP7G increased in 'Okanese' compared to 'Walker'. Surprisingly, ABA concentration was reduced in leaves of both cultivars. However, the metabolic deactivation product of ABA, phaseic acid, exhibited an early peak on the first day in 'Okanese'.

CONCLUSIONS

Our results indicate that PtCBFs and PtDAM1 have differential kinetics and spatial localization which may be related to early growth cessation and endodormancy induction under the regime of low night temperature and short photoperiod in poplar. Unlike buds, PtCBFs and PtDAM1 expression levels in leaves were not associated with early growth cessation and dormancy induction under these conditions. Our study provides new evidence that the degradation of auxin and cytokinins in leaves may be an important regulatory point in a CBF-DAM induced endodormancy. Further investigation of other PtDAMs in bud tissue and a study of both growth-inhibiting and the degradation of growth-promoting phytohormones is warranted.

VvDAM-SVPs genes are regulated by FLOWERING LOCUS T (VvFT) and not by ABA/low temperature-induced VvCBFs transcription factors in grapevine buds

In deciduous fruit trees in which dormancy is induced by low temperatures, the expression of DORMACY-ASSOCIATED MADS-BOX genes (DAM) is regulated by CBF/DREB1 transcription factors. In Vitis vinifera, in which dormancy is induced by the photoperiod, VvDAM-SVPs gene expression is regulated by FLOWERING LOCUS T (VvFT). Using the sequences of the six peach (Prunus persica) DORMACY-ASSOCIATED MADS-box genes (DAM) as query, eight putative DAM genes belonging to the family of MADS-box transcription factors and related to the Arabidopsis floral regulators SHORT VEGETATIVE PHASE (SVP) and AGAMOUS LIKE 24 (AGL24) were identified in the V. vinifera genome. Among these, five belong to the subfamily SVP-like genes which have been associated with the regulation of flowering and dormancy in annual and perennial plants, respectively. It has been proposed that they play a direct role in the induction and maintenance of endodormancy (ED) through the regulation of the FLOWERING LOCUS T (FT) gene. In the present study, it is demonstrated that in V. vinifera: (1) VvDAM-SVPs genes are not regulated by ABA/low temperature-induced VvCBFs transcription factors as described for other species of deciduous fruit trees. (2) A contrasting expression pattern between VvDAM3-SVP and VvFT was found under different experimental conditions related to the entry and exit of grapevine buds from ED. (3) Overexpression of VvFT in somatic grapevine embryos (SGE) repressed the expression of VvDAM3-SVP and VvDAM4-SVP. Taken together, the results suggest that VvDAM3-SVP could be associated with ED in grapevine buds, and that its expression could be regulated by VvFT.

The study of multivariance in realization of the plum graft and rootstock combinations adaptivity systems to the changing conditions of environment in the Krasnodar region with the use of digital technologies

The study of rootstocks group, providing the average vigor of growth for the grafted fruit plants, discovered their significant influence on the frost hardiness of the “graft-rootstock” system. The adaptivity of the plum varieties in the different graft and rootstock combinations was studied according to the “frost hardiness” criterion in the stages of the winter and spring development of the flower buds. The computer maps of the plum efficient allocation were created on the studied rootstocks, permitting to lay down the plantings with the lesser risks in the terms of climate fluctuation. It was established, that in the south of Russia the climatic conditions to cultivate Stanley variety on PK SK 1 rootstock, as compared with the rootstock of cherry plum seedling, mostly often used in industrial plantings of plum are mostly favorable. The conducted research contributes to isolation and allocation of the most adaptive graft and rootstock combinations based on their frost hardiness and, consequently, regularity of fruit-bearing and yielding capacity.

Integrating Genome-Wide Association Analysis With Transcriptome Sequencing to Identify Candidate Genes Related to Blooming Time in Prunus mume

Prunus mume is one of the most important woody perennials for edible and ornamental use. Despite a substantial variation in the flowering phenology among the P. mume germplasm resources, the genetic control for flowering time remains to be elucidated. In this study, we examined five blooming time-related traits of 235 P. mume landraces for 2 years. Based on the phenotypic data, we performed genome-wide association studies, which included a combination of marker- and gene-based association tests, and identified 1,445 candidate genes that are consistently linked with flowering time across multiple years. Furthermore, we assessed the global transcriptome change of floral buds from the two P. mume cultivars exhibiting contrasting bloom dates and detected 617 associated genes that were differentially expressed during the flowering process. By integrating a co-expression network analysis, we screened out 191 gene candidates of conserved transcriptional pattern during blooming across cultivars. Finally, we validated the temporal expression profiles of these candidates and highlighted their putative roles in regulating floral bud break and blooming time in P. mume. Our findings are important to expand the understanding of flowering time control in woody perennials and will boost the molecular breeding of novel varieties in P. mume.

Structure and Expression of Bud Dormancy-Associated MADS-Box Genes (DAM) in European Plum

Bud dormancy in temperate perennials ensures the survival of growing meristems under the harsh environmental conditions of autumn and winter, and facilitates an optimal growth and development resumption in the spring. Although the molecular pathways controlling the dormancy process are still unclear, DORMANCY-ASSOCIATED MADS-BOX genes (DAM) have emerged as key regulators of the dormancy cycle in different species. In the present study, we have characterized the orthologs of DAM genes in European plum (Prunus domestica L.). Their expression patterns together with sequence similarities are consistent with a role of PdoDAMs in dormancy maintenance mechanisms in European plum. Furthermore, other genes related to dormancy, flowering, and stress response have been identified in order to obtain a molecular framework of these three different processes taking place within the dormant flower bud in this species. This research provides a set of candidate genes to be genetically modified in future research, in order to better understand dormancy regulation in perennial species.

Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach

Dormancy is a physiological state that plants enter for winter hardiness. Environmental-induced dormancy onset and release in temperate perennials coordinate growth cessation and resumption, but how the entire process, especially chilling-dependent dormancy release and flowering, is regulated remains largely unclear. We utilized the transcriptome profiles of floral buds from fall to spring in apricot (Prunus armeniaca) genotypes with contrasting bloom dates and peach (Prunus persica) genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy. We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. During the transition from endo- to eco-dormancy, 1,367 and 2,102 genes changed in expression in apricot and peach, respectively. Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box (DAM) genes (DAM4, DAM5, and DAM6). Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. Gene expression analyses between two Prunus species highlighted the conserved transcriptional control of physiological activities in endodormancy and ecodormancy and revealed genes that may be involved in the transition between the two stages.

The evaluation of adaptation systems for apricot culture in the phases of its development for selection improvement and location of the future varieties in conditions of climate fluctuation

Apricot is one of the most valuable fruit cultures. This is a minor culture in Russia and other countries primarily because of irregular fruit-bearing by the reason of its flower buds death in the winter and spring period, caused by the low temperatures. The increased regularity of its fruit-bearing may be achieved in two primary ways: the creation of new varieties, more resistant to the temperature fluctuations of the winter and spring period and their rational allocation in the zones and microzones of the growing territories. The solution of both set tasks calls for the knowledge of protective and adaptive reactions of genotypes in the stages of their development. The investigations of the last years showed the levels of agricultural plants productivity to be determined not only by the genes of quantitative characters, but to significant extent by the effects of their interaction with environment at the different stages of the plants development. As a new factor of outdoor environment, limiting the growth and development of plants becomes evident, the spectrum and number of genes, determining one and the same quantitative character (freezing tolerance in this case) is changed at the particular stage of development on a particular territory. The climatic change permits to analyze more profoundly the regularities in manifestation of genotype peculiarities in phenotype. The response of apricot culture (Armeniaca vulgaris) to display of the winter temperature stresses in the different stages of temporal (1990-2019) and spatial - Krasnodar and Stavropol Territory, Kabardino-Balkar Republic and Kazakhstan - development was studied. The analysis was undertaken for the new terms of deadly temperatures occurrence at the different stages of development. There was studied mechanism of the apricot culture biological potential realization in the new temperature conditions in the phases of winter and spring period, permitting to open the more efficient process of apricot selection for freezing tolerance and its rational location.