Potato tubers can be dormant for 1–15 weeks after harvest, and the germination of tuber eye-buds is suppressed by cold. Genetic mechanisms regulating bud dormancy at low temperatures are not completely understood. We performed RNA-seq to compare gene expression in tubers after 0.5, 3.5, and 6.5 months of cold storage. Differentially expressed genes (DEGs) in non-dormant (3.5/6.5 months) vs. dormant (0.5 months) tubers were associated with transcriptional and translational activation, cell growth, metabolism, hormonal signaling, meristem development, dormancy break, and reproduction, confirming the non-dormant state of the meristem in the middle of storage. DEGs encoding transcription factors (TFs) (CBF1, FLC, SVP, HY5, GI, CO, FT, SOC1, CDF1, POTM1) were associated with the regulation of dormancy, flowering, and tuberization. TF DEGs upregulated (78) or downregulated (224) over four times in non-dormant vs. dormant tubers are considered potential coordinators of the endo- to non-dormancy transition and upcoming tuber sprouting during cold storage. RT-qPCR analysis of non-dormant and germinating buds revealed the upregulation of tuberigens (StSP3D, StFTL1-1, StFTL1-2), anti-tuberigens (StSP5G-like), and TF genes positively associated with tuberization or flowering/germination (StFDL1, StFDL, StCDF1, StCO-like). Our results should further investigation of the mechanisms underlying tuber meristem dormancy release and sprouting during long-term cold storage.

α-Amylases are involved in starch breakdown, thereby influencing plant development. Information on the α-amylase genes in soybean is limited. Here, we identified five soybean α-amylase genes from subfamilies AtAMY1 (GmaAMY5), AtAMY2 (GmaAMY4), AtAMY3 (GmaAMY1, GmaAMY3), and AMY6 (GmaAMY2). In silico analysis indicated that all five genes were actively expressed in leaves, flowers, and pods but weakly in roots. GmaAMY1–GmaAMY5 mRNAs were predicted to be targets of miRNAs associated with stress response, organ development, and nitrogen fixation. Putative GmaAMY1–GmaAMY5 proteins contained α-amylase-specific catalytic domain, signatures, and active sites. Short-term abiotic stresses (100 mM NaCl, 2.5–20% PEG, and 4 °C cold) applied to the cv. Doka affected both GmaAMY1–GmaAMY5 expression and the content of starch and soluble sugars in leaves. GmaAMY1 gene expression increased in response to NaCl and PEG, GmaAMY2 in response to PEG, and GmaAMY5 in response to NaCl. Salt stress suppressed the expression of the GmaAMY2–GmaAMY4 genes. The mRNA levels of all five genes increased after 2 h of cold exposure. Under salinity stress, there was inverse correlation of starch content with GmaAMY4 expression (r = −0.5135, p = 0.0293) and overall GmaAMY1–GmaAMY5 expression (r = −0.6318, p = 0.0049), suggesting a possible role of GmaAMY genes in protecting soybean from salinity by maintaining the starch/soluble sugars balance. Our results may aid in the breeding of stress-tolerant soybean varieties.

The content of hexoses (fructose, glucose) essential for the fruit of the tomato (Solanum lycopersicum L.) is regulated by the joint activity of sucrose hydrolysis enzymes (including invertases), invertase inhibitors, and sugar transporters. In addition to fruit taste, soluble sugars are closely related to the stress resistance of the tomato plant. In this work, we determined the diurnal dynamics of the content of soluble sugars (sucrose, fructose and glucose) and the expression of genes for sucrose hydrolysis enzymes (vacuolar invertase TAI, cell wall invertase LIN6) and the hexose transporter (STP1) in the leaves of the tomato variety Korneevsky. It was shown that both the amount of sugars and the level of transcripts of the TAI, LIN6 and STP1 genes depend on the circadian rhythm and correspond to the biological processes occurring in the plant at different periods of the day. The content of sucrose and hexoses changes in a similar way during the day. At the beginning of the light phase, the concentration of sugars is minimal, at the end it has the highest daily values; at the beginning of the dark phase, it shows a residual increase and then decreases towards the end of the phase. In silico analysis of organ-specific expression of TAI, LIN6 and STP1 in S. lycopersicum cv. Micro-Tom showed the presence of mRNA of all three genes in all tissues. The TAI gene was expressed most strongly in ripe fruits, while the level of LIN6 and STP1 transcripts was extremely low. The level of TAI mRNA in the leaves was ~2 times higher than that of LIN6 and ~27 times higher than that of STP1. Analysis using qRT-PCR of the diurnal dynamics of TAI, LIN6 and STP1 expression in the cv. Korneevsky leaves showed that all three genes were expressed at all points analyzed. Fluctuations in their expression levels occur in a similar manner: mRNA levels reach peak values in the middle of the light and dark phases. The results obtained are important for understanding the functions of invertases and sugar transporters in the tomato plant, and can be used in predicting the stress resistance of plants in tomato breeding.

The plant circadian system, as a result of adaptive evolution, is closely related to sensitivity to photoperiod. Zea mays L. originally belongs to the short-day species, while modern cultivated maize accessions are considered neutral with respect to photoperiod. The work analyzes the impact of changing the long-day regime to ultrashort days and long nights on the level of transcripts of key circadian rhythm (GIGZ1A, GIGZ1B), photosystem I (psaA), photosystem II (psbA), and carotenoid biosynthesis (ZmPSY1, ZmPSY2, ZmLCYE, ORANGE-GREEN) genes in the leaves of two mid-late ripening inbred lines of corn (L-5580-1 and L-5739), similar in morphophysiological characteristics. In the same leaves, the content of chlorophylls and carotenoids was determined. It was found that the studied lines differ significantly in the dynamics of the gene transcript level and pigment content in response to a change in photoperiod. GIGZ1a and GIGZ1b expression increases 1 h after the end of the ultrashort day in both lines, and is then characterized by an increase or decrease depending on the line. Expression of photosystem psaA and psbA genes differs between lines, both in the level and dynamics of the response to a change in photoperiod. Activity of carotenogenesis genes ZmPSY1, ZmPSY2, ZmLCYE, and ORANGE-GREEN increases in both lines when day changes to night (except ZmPSY2 in L‑5580-1) and decreases to varying degrees depending on the line towards the end of the night period. The content of pigments 1 h after changing the regime increases in L-5580-1 and does not change in L-5739, and it decreases in both lines by the end of the night. The obtained data indicate the preservation of the circadian rhythm in L-5580-1 and increased adaptability of L-5739 and can be used to search for donors of the trait of high adaptability to changes in photoperiod among maize accessions.

Eggplant (Solanum melongena L.) ranks fifth in importance among vegetable crops of the Solanaceae family, in part due to the high antioxidant properties and polyphenol content of the fruit. Along with the popular purplefruited varieties of S. melongena, there are cultivars, the fruits of which are rich in phenolic compounds, but are whitecolored due to the lack of anthocyanin biosynthesis. Determination of the amount of anthocyanins and other phenolic compounds, as well as carotenoids and sugars, is included in the assessment of the quality of eggplant fruits of commercial (technical) ripeness. In addition to antioxidant and taste properties, these metabolites are associated with fruit resistance to various stress factors. In this study, a comparative analysis of the content of anthocyanins, carotenoids and soluble sugars (sucrose, glucose, fructose) in the peel and pulp of the fruit of both technical and biological ripeness was carried out in purple-fruited (cv. Vlas) and white-fruited (cv. Snezhny) eggplant accessions of domestic selection. The peel and pulp of biologically ripe fruits of the cvs Vlas and Snezhny were used for comparative transcriptomic analysis. The key genes of the flavonoid and carotenoid metabolism, sucrose hydrolysis, and soluble sugar transport were shown to be differentially expressed between fruit tissues, both within each cultivar and between them. It has been confirmed that the purple color of the peel of the cv. Vlas fruit is due to substantial amounts of anthocyanins. Flavonoid biosynthesis genes showed a significantly lower expression level in the ripe fruit of the cv. Vlas in comparison with the cv. Snezhny. However, in both cultivars, transcripts of anthocyanin biosynthesis genes (DFR, ANS, UFGT) were not detected. Additionally, the purple fruit of the cv. Vlas accumulated more carotenoids and sucrose and less glucose and fructose than the white fruit of the cv. Snezhny. Biochemical data corresponded to the differential expression pattern of the key genes encoding the structural proteins of metabolism and transport of the compounds analyzed.

Метаболизм крахмала регулируется сложной каталитической сетью, одним из ключевых ферментов которой является пластидная крахмалфосфорилаза PHO1. В нашем исследовании с использованием системы CRISPR-Cas9 были получены растения табака (Nicotiana tabacum L.) с неполным нокаутом гена NtPHO1-L1 за счет делеционных вариантов каталитического домена белка NtPHO1-L1, приводящих к формированию нефункциональных форм фермента. Редактированные линии отличались от растений дикого типа повышенным накоплением крахмала и пониженным содержанием сахаров, хлорофиллов и каротиноидов в ткани листа. Показано, что в сравнении с контролем редактированные растения характеризовались дифференциальной экспрессией генов метаболизма крахмала (NtPHO1-L1, NtGWD, NtBAM1, NtBAM9, NtAI) и каротиноидов (NtPSY2, NtPDS, NtZDS, NtCRTISO, NtVDE), а также генов, кодирующих MADS-доменные транскрипционные факторы (NtFUL1, NtSEP1, NtSEP2, NtSEP3), которые предположительно участвуют в регуляции транскрипции исследуемых генов метаболизма. Предположено, что неполный нокаут NtPHO1-L1 приводит к изменению функциональной активности крахмалфосфорилазы табака. Это, в свою очередь, может влиять на скоординированную работу ферментов катаболизма крахмала, а также синтеза хлорофиллов и каротиноидов, возможно, за счет дифференциальной экспрессии MADS-box генов. Наши результаты подчеркивают критическую регуляторную роль пластидной крахмалфосфорилазы в метаболизме транзиторного крахмала, а также в стимулирующем влиянии на фотосинтез растения.

Invertases are involved in plant growth, development, and stress adaptation; however, invertase-encoding genes have not yet been reported in Allium species. In this study, we identified 23 invertase izogenes in garlic (Allium sativum L.): 11 encoding putative neutral/alkaline (AsN/AINV1–11) and 12 acid (6 cell-wall—AsCWINV1–6 and 6 vacuolar—AsVINV1–6) enzymes. Among them, AsN/AINV1, 3, 8–10, AsCWINV2–5, and AsVINV2–6 showed significant transcription in garlic organs (roots, bulbs, pseudostems, leaves, sprouts, and reproductive parts) in a tissue-specific manner, whereas the AsN/AINV4–6, 11, AsCWINV1, 6, and AsVINV1 genes had weak or no detectable expression. Gene promoters contained nine, nine, and sixteen hormone-, stress-, and light-responsive cis-regulatory elements, respectively, and fifteen sites related to transcription factor binding and plant development. Expression analysis revealed that 12 invertase genes strongly transcribed in the roots of A. sativum cv. Ershuizao showed differential expression in the roots and leaves of A. sativum cv. Sarmat exposed to abiotic stresses (low temperature, high salinity, and drought) and phytohormones (abscisic acid and methyl jasmonate), which was significantly correlated with glucose, fructose, and sucrose contents. Our results should further functional analysis of invertases from Allium crops and contribute to the breeding of stress-tolerant varieties.

Corn plants Zea mays L. are sensitive to many stress factors that cause excessive formation of reactive oxygen species, the elimination mechanism of which includes the monodehydroascorbate reductase (MDHAR; EC 1.6.5.4), which catalyzes the reduction of monodehydroascorbic acid to ascorbate. There are four known genes in the maize genome, ZmMDHAR1–ZmMDHAR4, differing in the intracellular localization of the encoded MDHAR proteins. In this work, a novel gene of the family was identified, ZmMDHAR5 (Zm00001d017786; LOC100193942), encoding a close structural homolog of peroxisomal ZmMDHAR3. It has been assumed that ZmMDHAR5 may function similarly to chloroplast-mitochondrial MDHARs. Differential expression of ZmMDHAR1–ZmMDHAR5 genes in maize seedlings in response to various stress factors also suggested the important role of ZmMDHAR4 and ZmMDHAR5 in response to exogenous abscisic acid, low temperature, and dehydration; ZmMDHAR1 and ZmMDHAR3 to salt stress; and ZmMDHAR2 to salt and water stresses.

The structure and phylogeny of the Solanum tuberosum L. phytoene synthase genes StPSY1, StPSY2, and StPSY3 were characterized. Their expression was studied in potato seedlings exposed to cold stress in the dark phase of the diurnal cycle to simulate night cooling. All of the three genes were activated as the temperature decreased, and the greatest response was observed for StPSY1. StPSY3 was for the first time shown to respond to cold stress and photoperiod. A search for cis-regulatory elements was carried out in the promoter regions and 5'-UTRs of the StPSY genes, and the regulation of all three genes proved associated with the response to light. A high level of cold-induced activation of StPSY1 was tentatively attributed to the presence of cis elements associated with sensitivity to cold and ABA.

Starch metabolism is regulated by a complex catalytic network, one of the key enzymes of which is the plastid starch phosphorylase PHO1. In this study, using the CRISPR-Cas9 system, we obtained tobacco (Nicotiana tabacum L.) plants with a partial knockout of the NtPHO1-L1 gene due to deletion variants of the catalytic domain of the NtPHO1-L1 protein, leading to the formation of nonfunctional forms of the enzyme. The edited lines differed from wild-type plants by increased starch accumulation and decreased content of sugars, chlorophylls, and carotenoids in the leaves. It was shown that, compared to the control, the edited plants were characterized by differential expression of starch (NtPHO1-L1, NtGWD, NtBAM1, NtBAM9, NtAI) and carotenoid (NtPSY2, NtPDS, NtZDS, NtCRTISO, NtVDE) metabolism genes, as well as genes encoding MADS-domain transcription factors (NtFUL1, NtSEP1, NtSEP2, NtSEP3), which are presumably involved in the regulation of transcription of the studied metabolic genes. These data suggest that partial knockout of NtPHO1-L1 alters the functional activity of tobacco starch phosphorylase. This, in turn, may influence the coordinated activity of starch catabolism enzymes, as well as chlorophyll and carotenoid synthesis enzymes, possibly through differential expression of MADS-box genes. The results highlight the critical regulatory role of plastid starch phosphorylase in transient starch metabolism and in stimulating plant photosynthesis.

Растения кукурузы Zea mays L. чувствительны ко многим стрессовым факторам, вызывающим избыточное образование активных форм кислорода, механизм нивелирования воздействия которых на организм включает фермент монодегидроаскорбатредуктазу (MDHAR; EC 1.6.5.4), катализирующий восстановление монодегидроаскорбиновой кислоты до аскорбата. В геноме кукурузы известно четыре гена ZmMDHAR1–ZmMDHAR4, различающихся внутриклеточной локализацией кодируемых белков MDHAR. В данной работе был идентифицирован новый ген семейства – ZmMDHAR5 (Zm00001d017786; LOC100193942), кодирующий близкий структурный гомолог пероксисомального ZmMDHAR3. Сделано предположение, что ZmMDHAR5 может иметь функции, близкие к хлоропласт-митохондриальным MDHAR. Дифференциальная экспрессия генов ZmMDHAR1–ZmMDHAR5 в проростках кукурузы в ответ на различные стрессовые факторы позволила также предположить важное участие ZmMDHAR4 и ZmMDHAR5 в ответе на экзогенную абсцизовую кислоту, низкие температуры и обезвоживание; ZmMDHAR1 и ZmMDHAR3 – на солевой стресс; ZmMDHAR2 – на избыток соли и дефицит воды.

The yellow and orange color of Zea mays L. grain is determined by the presence of carotenoids; the first enzyme of the carotenoid biosynthesis pathway is phytoene synthase PSY. In this study, we analyzed allelic variants of the ZmPSY1 gene in accessions of yellow-grain and white-grain maize domestic inbred lines. In four lines with different grain colors, full-length ZmPSY1 cDNAs were amplified and sequenced, and their variability was characterized. In the ZmPSY1 cDNA sequence from white-grain lines, nonsynonymous SNPs were found that lead to substitutions of four amino acid residues (L47I, W52S, E53D and A54V) in the N-terminal transit peptide responsible for the plastid localization of the enzyme. A primer system has been developed for PCR identification of the ZmPSY1 allele type in maize accessions. Testing of primers on 44 maize lines showed the presence of the wild-type ZmPSY1 allele and the absence of the mutant allele in the genome of all 22 yellow-grain lines analyzed. The mutant ZmPSY1 allele was detected in the genome of 41

Tomato Solanum lycopersicum L. is an important agricultural crop and, at the same time, a model for studying the ontogeny of the succulent fruit. The decisive role in the ripening of the fruit is played by abscisic acid, which is formed as a result of the oxidative cleavage of epoxycarotenoids 9-cis-epoxycarotenoid dioxygenases NCED. Gene-expression profiles of SINCED1 and SINCED2 and the content of carotenoids in fruits at different stages of development were determined in three varieties of tomato with different color of ripe fruit. It was shown that transcripts of both genes are present in all organs. Transcript level of SINCED1 was approximately four to six times higher than the level of SINCED2 transcripts; peak activity of SINCED1 occurs in the late stages of ripening, while that of SINCED2 is at the initial stage. Ripe fruits are characterized by the highest amount of carotenoids; lycopene was found only in the fruits of late stages in red-fruited varieties, the highest content of β-carotene was found in ripe fruits of the yellow-fruited variety. The precursor of abscisic acid, violaxanthin, is present only in the immature fruit; the other precursor, neoxanthin, decreases with ripening and is absent at the ripeness stage. In red-fruited varieties, a correlation was found between the level of SINCED1 and SINCED2 transcripts with the content of β-carotene. Findings suggest the coparticipation of SINCED1 and SINCED2 in the biosynthesis of abscisic acid during the development and ripening of tomato fruit. In this case, the key role belongs to the gene SINCED1, the peak of activity of which falls on the stage of changing the color of the fruit. Lower levels of SINCED2 transcripts and its peak activity in the early stages of fruit development suggests a division of NCED functions between the two enzymes.

Phenophase durations, including the timing of flowering and ripeness, were characterized in 20 inbred lines of the maize Zea mays L. Expression of key flowering initiation genes (CONZ1, GIGZ1a, GIGZ1b, ZmFKF1a, and ZmFKF1b) under long-photoperiod conditions was studied in seedlings of six maize lines that differed in ripeness time. Significantly lower transcription levels of all of the five genes were found in early-ripening lines compared with late-ripening lines. Similar expression patterns were observed for the GIGZ1a and GIGZ1b paralogous genes, while ZmFKF1a significantly predominated in expression over its paralog ZmFKF1b.

Carotenoids are essential participants in photosynthesis and photo protection as well as growth, development, and stress response in plants. Phytoene desaturase (PDS; EC 1.3.5.5) is an enzyme that catalyzes the first stage of desaturation of 15- cis -phytoene (a precursor to all carotenoids). In this work, we examined for the first time the effect of PDS knockout in the genome of Nicotiana tabacum L. using the CRISPR-Cas9 system on activity of downstream genes involved in biosynthesis of carotenoids. Nine transgenic lines of tobacco were obtained with a mosaic editing of gene NtPDS ; three versions of indels (350^351→ins^g#, 350^351→ins^t#, and t351→del(1nt)#) in the exon II resulting in the synthesis of a shortened non-functional version of the protein. The lines were characterized by spotted, green-white pigmentation of the leaves, altered flowering time and morphology as well as a reduced content of carotenoids and chlorophylls in the leaf tissue. A rise in the level of transcripts of phytoene synthase gene NtPSY2 was shown in late-flowering lines as compared to control material. Edited line L29 with the latest flowering showed a considerable increase in the level of transcripts of downstream structural genes of carotenogenesis. A reduction in the carotenoid content in the leaves with mosaic editing was accompanied by a decrease in the level of expression of MADS-box gene NtSEP1 , the product of which presumably participates in regulation of transcription of the carotenoid biosynthesis genes. The obtained results may be used for further studies of regulation of biosynthesis of carotenoids and apocarotenoids in Solanaceae.

In this study, the content of anthocyanins and the expression profile of regulatory ( CaMYB113 , CaMYB1 , and CaMYB1 - like ) and structural ( CaCHS , CaCHI , CaF3H , CaDFR , CaANS , CaUFGT1 , and CaGSTF12 ) genes of the anthocyanin biosynthesis pathway were characterized in leaves, flower petals, and peel of unripe fruits of Capsicum frutescens L. pepper cultivars (Samotsvet, Rozhdestvenskii buket, and Evrika), which differ in the pattern of anthocyanin-mediated pigmentation of aboveground organs. A positive correlation of the CaCHS , CaF3H , CaDFR , CaANS , and CaCSTF12 transcript levels with the amount of anthocyanins in the leaves of these cultivars was found. It was shown that only CaMYB113 out of the three regulatory genes is expressed. The presence of a 5'-UTR in CaMYB113 mRNA was confirmed based on the example of ten cultivars of three pepper Capsicum species. The second variant of the CaMYB113 allele with the insertion of the LINE-1 retrotransposon in intron I was found in the genome of cv. Rozhdestvenskii buket and Samotsvet with purple coloring of the analyzed organs.

In this study, the content of anthocyanins and the expression pattern of regulatory (CaMYB113, CaMYB1, and CaMYB1-like) and structural (CaCHS, CaCHI, CaF3H, CaDFR, CaANS, CaUFGT1, and CaGSTF12) genes of the anthocyanin biosynthesis pathway in leaves, flower petals, and peel of unripe fruits of pepper Capsicum frutescens L. cultivars (Samotsvet, Rozhdestvenskii buket and Eureka), which differ in the pattern of anthocyanin-mediated pigmentation of aboveground organs. A positive correlation was found between the levels of CaCHS, CaF3H, CaDFR, CaANS, and CaCSTF12 transcripts with the amount of anthocyanins in the leaves of these cultivars. It was shown that out of three regulatory genes only CaMYB113 is expressed. Using ten cultivars of three Capsicum species as an example, the presence of 5'-UTR in CaMYB113 mRNA was confirmed. The second variant of the CaMYB113 allele with the insertion of the LINE-1 retrotransposon in intron I was found in the genome of cv. Rozhdestvensky buket and Samotsvet with purple color of the analyzed organs.

Tomato ( Solanum lycopersicum L.) is an important crop and, due to the existence of wild related species ( Solanum section Lycopersicon), a model for studying the development of the fleshy fruit. In the study, expression analysis of sugar uniporter genes SWEET1а , 1b , 1e , 3 , 7a , 10a , 12c , 14, and 15 in tomato species and cultivars was carried out. In cv. Heinz ( S. lycopersicum ), genes that are most active in roots ( SWEET1e , 3 , 10a , and 12c ), leaves ( SWEET1a , 1e , 3 , 10a , and 12c ) and flowers ( SWEET1a , 1b , 7a , 10a , 12s , 14 , and 15 ) were revealed. The growth of the fruit is accompanied by an increase in the level of the SWEET 110a and 12c transcripts; maturation of the fruit is accompanied by an increase in the level of the SWEET 1a and 15 transcripts. Differential expression of the SWEET1a , 1b , 12c, and 15 genes in the ripe fruit of inbred lines obtained from crossing of S. lycopersicum cv. M82 × S. pennellii was demonstrated. qRT-PCR analysis showed that the expression of the SWEET1a and 12c genes is common for ripe fruit of the analyzed tomato species, while the expression of the SWEET1b and 10a genes is common for S. pennellii , S. habrochaites, and S. cheesmaniae . It was determined that the fructose : glucose ratio is equimolar in the accessions except for cv. Black Jack and White Beauty (fructose : glucose ≥ 1.10). Correlations between the level of SWEET gene transcripts and the ratio of hexoses was not revealed.

Proteins of the SWEET (Sugar Will Eventually be Exported Transporters) family play an important role in plant development, adaptation, and stress response by functioning as transmembrane uniporters of soluble sugars. However, the information on the SWEET family in the plants of the Allium genus, which includes many crop species, is lacking. In this study, we performed a genome-wide analysis of garlic (Allium sativum L.) and identified 27 genes putatively encoding clade I-IV SWEET proteins. The promoters of the A. sativum (As) SWEET genes contained hormone- and stress-sensitive elements associated with plant response to phytopathogens. AsSWEET genes had distinct expression patterns in garlic organs. The expression levels and dynamics of clade III AsSWEET3, AsSWEET9, and AsSWEET11 genes significantly differed between Fusarium-resistant and -susceptible garlic cultivars subjected to F. proliferatum infection, suggesting the role of these genes in the garlic defense against the pathogen. Our results provide insights into the role of SWEET sugar uniporters in A. sativum and may be useful for breeding Fusarium-resistant Allium cultivars.