Plant Molecular Biology Reporter

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Number of SNP markers distributed across the 10 chromosomes
Heterozygosity rate among the 151 inbred lines and the 10,940 SNP markers
Neighbor-joining tree for 151 maize inbred lines based on Roger’s genetic distance
a Population structure among individuals with ΔK = 2. b Population structure among individuals with ΔK = 3. c Population structure among individuals with ΔK = 4. Each subpopulation is represented by a different color
Principal component analysis for the 151 inbred lines
The use of molecular markers allows for precise estimates of genetic diversity, which is an important parameter that enables breeders to select parental lines and designing breeding systems. We assessed the level of genetic diversity and population structure in a panel of 151 tropical maize inbred lines using 10,940 SNP (single nucleotide polymorphism) markers generated through the DArTseq genotyping platform. The average gene diversity was 0.39 with expected heterozygosity ranging from 0.00 to 0.84, and a mean of 0.02. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual inbred lines within the populations while only 3% was distributed among the populations. Both neighbor-joining clustering and STRUCTURE analysis classified the inbred lines into four major groups. The crosses that involve inbred lines from most divergent subgroups are expected to generate maximum heterosis and produce wide variation. The results will be beneficial for breeders to better understand and exploit the genetic diversity available in the set of maize inbred lines we studied.
 
Phenotypic distribution of wheat internode and plant height component indices in KJ-RILs under different environments. Parent value of KN9204 and J411 are shown by black and gray arrows, respectively. FIITCI, the first internode component index; SITCI, the second internode component index; TITCI, the third internode component index; FOITCI, the fourth internode component index; PHCI, the plant height component index
Location of QTLs for internode and plant height component indices identified in four different environments based on a population of 187 KJ-RILs derived from a cross between ‘KN9204’ and ‘J411’. The chromosome number is marked at the top of each chromosome. The positions of markers are listed on the left of the bars, and the names of markers and QTLs are listed on the right of the corresponding chromosomes. The colored segments on the chromosome indicate the confidence interval of the corresponding QTL, and the segment of red, green, black, fluorescent green, and pink colors represent the traits for the first internode component index (FIITCI), the second internode component index (SITCI), the third internode component index (TITCI), the fourth internode component index (FOITCI), the plant height component index (PHCI), respectively. The environments where the corresponding QTLs detected are shown in parenthesis
Epistatic QTL analysis for the first internode component index (FIITCI) and the third internode component index (TITCI). The values on the line represent the phenotypic variance explained by the two interacting QTLs, and the values in the ellipse represent the physical position (Mb) on the ‘KN9204’ genome
Single-marker QTL analysis for TKW, KNPS, SNPP, and YPP on chromosome 4B (KN4B:15–36 Mb) based on phenotypic values in eight environments in Cui et al. (2016, 2017). The left-hand figures show the LOD scores of the corresponding traits in eight different environments; the right-hand figures show the additive effect values of the corresponding traits in eight different environments. Of the eight scatter diagrams, a and b, c and d, e and f, and g and h indicate the QTL LOD profiles and additive effects for kernel number per spike (KNPS), thousand-kernel weight (TKW), spike number per plant (SNPP), and yield per plant (YPP), respectively
Plant height (PH) is one of the most important traits related to plant architecture in wheat. Together, the lengths of individual internodes determine plant height and have a great influence on lodging resistance. To specify the genetic basis of wheat internode characteristics, we identified quantitative trait loci (QTLs) for each internode component index (ICI) and plant height component index (PHCI) using a recombinant inbred line (RIL) mapping population derived from ‘Kenong 9204’ (‘KN9204’) × ‘Jing 411’ (‘J411’). Up to 57 putative additive QTLs for the four ICIs and PHCI were detected, which together covered 20 of the 21 wheat chromosomes, with the exception of chromosome 1B. Among them, eight QTLs were major, stable QTLs with a logarithm-of-odds (LOD) score of ≥ 3.0 and a phenotypic variance explained (PVE) of ≥ 7.0%. In the epistatic analysis, only one pair of epistatic QTLs was identified for the first internode component index (FIITCI) and three pairs of epistatic QTLs for the third internode component index (TITCI). A total of 20 of the 57 detected QTLs (35.1%) were co-localized QTLs for PH, spike length, and internode lengths, indicating that those traits have their own individual genetic basis in most cases. Moreover, 12 QTL clusters for PHCI/ICIs and yield-related traits were identified, indicating that plant architecture plays a potential role in the formation of yield in wheat. The plant architecture with gradually bottom-up shortened internode lengths tends to be high-yielding potential, especially for the uppermost internode. This study may provide useful information for understanding the genetic basis of plant height components and to accelerate the genetic improvement of plant ideotypes designed to increase yield.
 
Dendrogram derived from cluster analysis of 120 barley genotypes based on simple sequence repeat markers data
Dendrogram derived from cluster analysis of 120 barley genotypes based on phenotypic data under cold stress conditions
In the present study, the genetic diversity of 120 barley genotypes was investigated through 14 phenologic and agronomic traits as well as 50 SSR markers that cover the seven chromosomes of barley. In addition, the relationships between these marker loci and the studied traits were assessed via multiple regressions in two conditions. The field experiment was conducted in two planting dates, namely before the ideal time of the region planting date and the ideal planting date of the region in the experimental field of the Faculty of Agriculture and Natural Resources, Gonbad-e-Kavous University. A randomized complete block design with two replications was laid out for both planting dates. The results of cluster analysis based on SSR data classified the studied barley genotypes into six groups. For all the traits, except for spike length, more than one informative marker was detected. The results of stepwise regression analysis revealed significant associations between the traits and 60 SSR marker alleles under cold stress conditions. Under normal conditions, 63 SSR marker alleles showed a significant correlation with the studied traits. Among the 50 SSR markers, particular attention should be paid to a number of them, including the Bmag0211 marker with the highest coefficient of determination (R²) in regression analyses of grain yield, 1000-kernel weight under non-stress conditions, and grain width and days to maturity under cold stress conditions as well as HVBM5A marker associated with spike length, 1000-kernel weight, and days to flowering under cold stress conditions. These markers may be a novel finding and relatively more reliable than the other identified markers. The informative markers could be suitable for marker-assisted breeding in barley after confirming them in other experiments.
 
Mango is flavour-rich fruit and considered as king of fruit in India. About 578 volatile compounds have so far been identified in various cultivars. These are believed to accumulate differentially during the course of ripening. In order to understand the molecular mechanism of aroma in mango, de novo transcriptome assembly and analysis of Mangifera indica (Dashehari) were performed by Illumina sequencing. Mining of transcriptome data led to identification of major genes related to most of the genes of terpenoid, carotenoid, flavonoid, lactone, lipoxygenase, aromatic amino acid, alkaloid, and phenylpropanoid pathways, which are potentially involved in aroma biosynthesis. Comparative mRNA expression analysis in five Mango varieties (Dashehari, Banganpalli, Ratna, Mallika, and Alphonso) revealed varietal and ripening-related differences. To gain further insight into the terpenoid pathway, these genes were further studied in different tissues and developmental stages in Dashehari mango. This study is stepping stone to understand aroma pathways in different varieties of mango fruit.
 
A Chromosomal localization of different alpha-gliadins genes. B Domain organization of different alpha-gliadins genes. C Phylogenetic tree showing relatedness among different alpha-gliadin genes
Graphical representation of number of epitopes in different wheat genotypes. A Number of epitopic sequence of DQ2-glia-α1 in different wheat genotypes. B Number of epitopic sequence of DQ2-glia-α2 in different wheat genotypes. C Number of epitopic sequence of DQ2-glia-α3 in different wheat genotypes. D Number of epitopic sequence of DQ8-glia-α1 in different wheat genotypes. E Number of epitopic sequence of DQ8-glia-α1 in different wheat genotypes. F Total number of immunogenic, non-immunogenic, and toxic epitopes in different wheat genotypes
Graphical representation of cumulative RPKM expression of different wheat genotypes. A Graphical representation of cumulative RPKM expression of different wheat genotypes. B Ratio of immunogenic to non-immunogenic RPKM expression. C Total RPKM expression of all alpha-gliadin genes in all wheat genotypes with respect to specific chromosome 6A, 6B, and 6D. D Total RPKM expression of all alpha-gliadin genes in tetraploid and hexalpod wheat with respect to specific chromosome 6A, 6B, and 6D
Expression pattern of identified alpha-gliadin genes in different wheat genotypes
Celiac disease (CD) is an inflammatory disorder that damages the lining of the small intestine. The allergic reaction to the alpha (α)-gliadin class of gluten proteins present in wheat leads to this autoimmune response. α-Gliadin proteins of the wheat gluten form a multigene family with different number and type of CD-eliciting epitopes. The present experiment was planned to study the relative variations in the α-gliadin proteins and their CD-eliciting epitopes in the eight Triticum genotypes including three tetraploid (PDW 274, PBW34, Bansi162) and five hexaploid cultivars (C591, C273, K78, PBW 54, and 9D). Reference-based annotation followed by detailed analysis of unassigned gliadins for domain organization, epitope frequency, and phylogeny relatedness; out of total 43 gliadin genes, 8 were assigned to chromosome 6A, 26 to chromosome 6B, and 9 to 6D. Relative expression analysis revealed that durum wheat genotypes have lower expression of immunogenic epitopes than hexaploid. Chromosome 6A-specific T-cell stimulatory epitope combination was highyly expressed in all the cultivars followed by those from chromosome 6D and least from 6B. The lower proportion of T-cell stimulatory epitopes in PBW54 was due to the lower expression of the 6A encoded epitopic combination that was compensated by the relatively higher expression of non-immunogenic variants forms of 6B. This study is the initial step towards developing wheat that is less immunogenic for celiac disease patients.
 
Twenty-one quantitative trait loci were discovered across six environments, including three (NS), seven (LS) and eleven (VLS) conditions. The linkage groups 1A, 1B, 2A, 2B, 2D, 3B, 4A, 6A, 6B and 7D spanned quantitative trait loci (QTLs). For canopy temperature (CT), a stable QTL (Qct_rpcau_4A) in the environment E6 has shown a phenotypic variance (PVE) up to 17.85%. The QTL, Qspad_rpcau_2D, was found to be stable for SPAD value, explaining the PVE of 15.05%. Whereas, three stable QTLs viz. Qgy_rpcau_3B, Qgy_rpcau_4A and Qgy_rpcau_6A were associated with the chromosomes 3B, 4A and 6B explaining a PVE of 20.85%, 17.43% and 17.37% respectively for the trait GY. The interaction of genotype and environment has been shown to be useful in determining the best lines for heat-stressed environments. In addition, G X E analysis was performed on the population. In the ranking of genotypes for both mean yield and mean vs. stability, GGE biplot across the six environments, DH 146, 195, 60, 202, 65, 155, 124, 5, 201, 169, 15 and 170 were ranked closest to ideal and winning genotype; these were highly adapted and most stable lines. The goal of the current investigation was to find the best suitable double haploid lines which can withstand heat stress and to find those QTLs which are influential to heat stress for the studied traits.
 
Methionine (Met), including the free and protein-bound forms, can easily be oxidized in the presence of excess reactive oxygen species (ROS) under conditions of abiotic stress to form Met sulfoxide (MetO). This reaction can be reversed by MetO reductases (MSRs), which are known to be involved in a variety of stress response mechanisms in plants, but the functions of their maize MSRA homologs have not been reported to date. Cytoplasmic ZmMSRA2 and secretary ZmMSRA5.1, previously shown to be induced under salinity or drought stress, belong to the MSRA subfamily. In the present study, their constitutive expression in Arabidopsis resulted in notable increases in MSR enzymatic activity; virus-induced gene silencing (VIGS) analysis in maize indicated that the silencing expression of ZmMSRA2 or ZmMSRA5.1 decreased the tolerance of seedlings to osmotic or salinity, respectively; the ectopic expression of ZmMSRA2 in Arabidopsis increased the tolerance of seedlings to mannitol, H2O2, and ABA, and that of ZmMSRA5.1 enhanced the tolerance to NaCl and H2O2. Compared with that of the wild-type, the germination rates of seeds overexpressing ZmMSRA2 or ZmMSRA5.1 were higher under osmotic or salinity stress, respectively. The effect of active ZmMSRA2 in Arabidopsis was the suppression of ROS accumulation and the increase in intracellular proline content; ZmMSRA5.1 led to improved ion transport and decreased ROS content. The expression of the maize MSRA homologs in Arabidopsis resulted in no observed changes in the transcription of Arabidopsis MSRA subfamily members, while genes of the MSRB subfamily were downregulated overall. Together, our findings suggest that ZmMSRA2 participates in osmotic stress tolerance by decreasing the ROS content, and enhancing the proline and ABA pathways, whereas ZmMSRA5.1 is involved in tolerance to salinity by reducing ROS accumulation and modifying ion transportation. Characterization of these two genes contributes to the understanding of redox metabolism in maize.
 
Mature pear fruit lose water rapidly, and the later the harvest, the more the water loss, severely limiting the fruit quality and economic benefits of pears. However, the molecular mechanism of pear fruit water loss is complicated and still far from being understood. In this study, the flesh of juice pear fruit (JP) and water loss pear fruit (WP) were used for proteomic analyses. Compared WP with JP, we obtained 159 differentially expressed proteins, especially cell wall metabolic and endomembrane transport proteins. Moreover, the cell membrane permeability and polygalacturonase (PG) activity were increased in WP compared with JP, illustrating that water loss of pear fruit may be related to the composition and metabolism of the cell wall. Furthermore, aquaporin coding genes AQPs and the cell wall metabolic gene PbPG were cloned, and sequence analysis indicated their important roles in fruit water loss. We then verified the function of PbPG in fruit water loss and further suggested that PbPG accelerated water loss of pear fruit was achieved by degrading cell wall polysaccharides, increasing intercellular layer and AQP-encoding gene expression. These findings will provide novel insights into the molecular mechanisms behind pear fruit water loss.
 
A comprehensive analysis based on Cerasus humilis genome data was used to investigate the implications of amino acid/auxin permease (AAAP) genes on fruit growth and development. A total of 45 ChAAAP genes were identified based on their phylogenetic relationship, and they were further classified into eight types: GAT, ProT, LHT, AUX, ANT, ATLb, ATLa, and AAP, with 7, 3, 10, 3, 4, 9, 8, and 1 ChAAAP genes, respectively. The motif composition and gene structure analysis showed that motif 1 (YFSVAVFGYWAFGBKVLSQIL) was the most conserved motif, whereas no motif was found in ChAAAP11 and ChAAAP12. The numbers of introns and exons varied widely between ChAAAP genes: both ChAAAP30 and ChAAAP32 had 13 exons was the most; ChAAAP26, ChAAAP35, ChAAAP38, and ChAAAP39 had only one exon. Promoter analysis showed that ChAAAP genes play an important role in plant growth and development. The ChAAAP genes were distributed unevenly on eight chromosomes, and 9 gene duplication fragments were observed, which were all segmental, whereas there was no tandem duplication type. These genes contributed to the expansion of the ChAAAP genes in C. humilis. Gene duplication with the other species showed ChAAAP had more orthologous genes with Prunus persica. According to the transcriptome data, the expression level of ChAAAP17 was the highest in fruit, followed by ChAAAP22 and ChAAAP23. However, ChAAAP11 and ChAAAP12 were only expressed in the root. Furthermore, we utilized qPCR to evaluate the 19 candidate genes during fruit development and predicted seven ChAAAP genes (ChAAAP08, ChAAAP16, ChAAAP17, ChAAAP19, ChAAAP32, ChAAAP33, and ChAAAP40) to further explore their involvement in fruit development. Our findings provide a comprehensive understanding of the ChAAAP gene family’s functions and could be employed to validate gene function in the future.
 
Pinus massoniana (P. massoniana) is an important fast-growing tree species in China. To explore photosynthesis-related gene resources and find possible targets for high photosynthetic-efficiency breeding of P. massoniana, we cloned two full-length cDNAs with conserved sequences of RubisCO activase (RCA) genes from P. massoniana. The RCA enzyme is important in maintaining the activity of RubisCO in vivo. Two genes, named PmRCA1 and PmRCA2, showed high similarity to RCA genes from other species and were identical to each other except for a 137 bp intervening sequence in the open reading frame (ORF) of PmRCA1, which led to different protein products, herein referred to as PmRCA1 and PmRCA2, respectively. PmRCA1 and PmRCA2 showed high homology to RCA of Pinus halepensis, and PmRCA1 had two cysteine residues in its carboxyl-terminal extension that were unique to the large RCA isoform. To characterize the function of PmRCA1 and PmRCA2, plant expression vectors driven by the constitutive 35S promoter were transformed in tobacco plants. Transgenic plants of PmRCA2 were grown better than wild tobacco plants and had significantly more leaves. Overexpression of PmRCA2 increased the maximum net photosynthetic rate and dark respiration rate of tobacco by 16.49% and 81.85%, respectively. Overexpression of PmRCA1 increased the maximum net photosynthetic rate and dark respiration rate of tobacco more than overexpression of PmRCA2, but it simultaneously enhanced photoinhibition of photosynthesis.
 
Growth of Arabidopsis is controlled by the activity of a set of bHLH and bZIP transcription factors of which phytochrome interacting factor4 ( PIF4) , BRASSINAZOLE-RESISTANT 1 ( BZR1 ), and elongated hypocotyl 5 ( HY5) have been most extensively studied. Defense responses are controlled by a set of MYC transcription factors of which MYC2 is best characterized. Moreover, hundreds of additional proteins (here named co-factors) have been identified which (in)directly may affect the expression or activity of these TFs. Thus, regulation of expression of genes encoding these co-factors becomes an integral part of understanding the molecular control of growth and defense. Here, we review RNA-seq data related to PIF, BZR1, HY5, or MYC activity, which indicate that 125 co-factor genes affecting PIFs, HY5, BZR1, or MYCs are themselves under transcriptional control by these TFs, thus revealing potential feedback regulation in growth and defense. The transcriptional feedback on co-factor genes related to PIF4 , BZR1 , and MYC2 by PIFs, BZR1, or MYCs, mostly results in negative feedback on PIF4 , BZR1 , or MYC2 activity . In contrast, transcription feedback on co-factor genes for HY5 by HY5 mostly results in positive feedback on HY5 activity . PIF4 and BZR1 exert a balanced regulating of photoreceptor-gene expression, whose products directly or indirectly affect PIF4, HY5, and MYC2 protein stability as a function of light. Growth itself is balanced by both multiple positive and multiple negative feedback on PIF4 and BZR1 activity. The balance between growth and defense is mostly through direct cross-regulation between HY5 and MYC2 as previously described, but also through potential transcriptional feedback on co-factor genes for MYC2 by PIF4, BZR1, and HY5 and through transcriptional feedback of co-factors for PIF4 and BZR1 by MYC2. The interlocking feed-forward and feed-backward transcriptional regulation of PIF4 , BZR1 , HY5 , and MYC2 co-factors is a signature of robust and temporal control of signaling related to growth and defense.
 
Tea plant (Camellia sinensis) has very long history of cultivation and abundant germplasm resources in China. Purple bud is a characteristic variety, which has attracted the attention of breeding researchers because it accumulated a large number of anthocyanins naturally. In many species, R2R3-MYB transcription factors (TFs) were proved to be involved in the regulation of anthocyanin biosynthesis. Research on anthocyanin metabolism has been relatively clear in some species, but that needs to be further elucidated in tea plants. In this research, an R2R3-MYB transcription factor CsMYB113 related to the anthocyanin accumulation regulation was identified from tea plants. Spatial and temporal expression analysis revealed differential expression of CsMYB113 among different tissues and organs, with highest expression occurring in the roots. Subcellular localization assays showed that CsMYB113 localized in the nucleus. Ectopic expression of CsMYB113 increased pigmentation and anthocyanin contents by the upregulation of the expression levels of genes in anthocyanin biosynthesis pathway among different tissues of Arabidopsis. Moreover, transient overexpression of 35S::CsMYB113 in tea plant increased the anthocyanin contents in the leaves. Our results indicated that CsMYB113 plays important role in the anthocyanin biosynthesis regulation in tea plants. It will also provide useful candidate gene for the modification of anthocyanin metabolism by genetic engineering in plants.
 
Soil salinization–alkalization is a major hindrance to agricultural development globally. Tea crabapple is widely used in China. However, little remains known regarding the molecular mechanisms used to withstand mixed saline–alkali stress (MSAS). Herein, we exposed tea crabapple seedlings to MSAS, and RNA-seq was performed for the transcriptome analysis of roots. Between 43.26 million and 43.37 million clean reads were thus obtained. In comparison with the control group (day 0), 2931, 2335, and 3746 genes were differentially expressed at day 1, day 3, and day 6 of MSAS exposure, respectively, and 1022 genes were common in the three comparison groups. On functional annotation, we observed that numerous differentially expressed genes were involved in “global and overview maps”; “carbohydrate metabolism”; “folding, sorting, and degradation”; “biosynthesis of other secondary metabolites”; “environmental adaptation”; and “signal transduction.” Heat shock proteins, cytochrome P450s, disease-resistant proteins, non-specific lipid-transfer proteins, pectate lyase, and beta-glucosidases were also induced in response to MSAS, in addition to nitrogen, phosphorus, and potassium absorption and metabolism-related genes. Transcription factor-coding genes appear to regulate the response of tea crabapple roots to MSAS by participating in, for example, plant hormone signal transduction and heat shock response. We also performed quantitative real-time PCR to validate the expression of six differentially expressed genes. Our findings provide new insights into the molecular mechanisms used by tea crabapple to cope with MSAS.
 
Sources of heavy metal accumulation in soil and water bodies
Crosstalk mechanism of different MAPK cascades in response to heavy metal stress and their regulation as well as possible downstream responses. This figure narrates the involvement of several signalling components working during metal stress. ROS production is a common phenomenon between different stresses. An intracellular and intercellular signalling molecule i.e., H2O2 (reactive oxygen species) is responsible for the activation of MAPK cascades. MAPK signalling cascades induce the expression of metal responsive genes through the activation of transcription factors which ultimately helping the plants to counteract in stressed condition. The genes expressed and induced by MAPK cascades are mainly metal transporters, phytochelatins, metallothionine, antioxidative, or pre-oxidative enzymes
In recent years, as a result of anthropogenic activities, a rise in environmental stresses has been observed. Sessile organisms such as plants make use of signalling in order to interpret and respond appropriately to environmental changes. An evolutionary conserved signal transduction module i.e., mitogen-activated protein kinase (MAPK) is a component of kinase module engaged in different cellular signalling responses in eukaryotes including plants. They receive the extracellular signal and transmitted it to the nucleus for maintenance of cellular homeostasis. The cascade of MAPK is based on 3 components i.e., MAPK kinase kinase (MAPKKK), MAPK kinase (MAPKK), and MAPK; they are connected with each other by phosphorylation mechanism and finally transmit the signals to a particular transcription factor/s (TxFs). In plants, MAPK-based signalling can be regulated by different phytohormones. Not only cell division and differentiation, MAPK signalling plays a crucial role in various biotic and abiotic stress by generating antioxidative mechanism within the cell. Rampant industrialization and subsequent use of various agrochemicals make soil polluted by piling the soil with different kinds of heavy metals which is not essential to human beings as well as for the plants to survive. The present review is based on the signalling mechanism of MAPK cascade of plants in response to heavy metal stress (HMs).
 
Intraspecific genetic diversity study is a helpful tool for genetic improvement and germplasm conservation initiatives. In this context, the current study analyzed the population genetic diversity and structure of 89 accessions collected from 11 populations in four different northern Iraqi provinces using conserved DNA-derived polymorphism (CDDP) and inter-simple sequence repeats (ISSR) molecular markers. CDDP and ISSR revealed 105 and 179 polymorphic bands, respectively, with an average of 10.50 bands per primer for CDDP and 8.52 fragments per primer for ISSR. All the primers exhibited polymorphic information content values greater than 0.50. Shannon’s information index (0.43) and expected heterozygosity (0.28) were both the highest in the KNOX-1 primer. Based on CDDP, ISSR, and CDDP + ISSR data, dendrogram analysis of populations revealed the presence of two genetic clusters, which were subsequently sub-clustered. The slight similarity between the geographic distribution of Q. aegilops populations and their clustering pattern was stated. The genetic dissimilarity among populations ranged from 0.13 to 0.34 for CDDP, 0.11 to 0.39 for the ISSR, and 0.13 to 0.36 for the CDDP + ISSR combination. In the model-based structure analysis, both markers and their combinations showed a similar clustering trend, with two major genetic clusters. A moderate relationship was observed between the structure and cluster patterns in terms of the distribution of populations within the clusters. The highest fixation index values (0.43 for CDDP markers and 0.39 for ISSR markers) were recorded by the second cluster. The analysis of molecular variance revealed high genetic variation within regions than between them, as well as significant gene exchange between regions. The Sulaimani-Sharbazher (SSH) and Erbil-Shaqlawa (ESH) populations had the highest values of Shannon’s information index (0.36 for SSH and 0.35 for ESH, according to CDDP data) and expected heterozygosity (0.23 for SSH and 0.24 for ESH, according to ISSR data). There was a significant association between CDDP and ISSR dissimilarity matrices. The supplied data can be used by producers and scientists to improve the preservation and rational use of wild Q. aegilops populations. By selecting a small number of individuals from diverse populations, ex and in situ conservation may be an appropriate method for adequately capturing the total genetic diversity.
 
Calmodulin (CaM) and calmodulin-like (CML) proteins, a group of Ca²⁺ sensors, play an important role in a large number of different biological processes, including plant growth and development, as well as the biotic and abiotic stress responses. However, CaM/CML genes have not been identified in sacred lotus (Nelumbo nucifera), an important horticultural plant, and the expressional patterns of these genes are yet to be elucidated. In this study, thirty-four CaM/CML genes from Nelumbo nucifera were identified. Phylogenetic analysis showed that they could be divided into nine groups. Gene structure and conserved motif analyses demonstrated the conservation and divergence of CaMs/CMLs in Nelumbo nucifera. Cis-acting elements analysis indicated that they might be related to plant growth and development, abiotic stress, and plant hormones. In addition, expression analysis showed that NNU-CaMs/CMLs were differentially expressed in various tissues and responded to calcium treatments in roots. Moreover, weighted gene co-expression network analysis of public transcriptome data of lotus wild variety “China Antique” with different tissues presented the expression connectivity of NNU-CaMs/CMLs, which were divided into 11 modules. Gene ontology analysis of the genes in each module demonstrated that NNU-CaMs/CMLs may be involved in extensive biological processes, such as synthesis and processing of DNA and RNA, and protein post-translational modification, and each module specifically correlated with the phenotypes including the development of leaves’ petiole and lotus seed, implying the wide regulation of NNU-CaMs/CMLs in lotus. Taken together, our results will enhance the understanding and lay a foundation for further study of the functions of the NNU-CaMs/CMLs.
 
Soybean seeds are easily affected by high temperature and humidity (HTH) stress during growth and development period, which usually results in serious seed deterioration in field before harvest. In our previous study, GmCDPKSK5 was found to be highly related to the formation of seed vigor under HTH stress in soybean sown in spring in South China, and GmFAD2-1B was preliminarily screened as a candidate GmCDPKSK5-interacting protein by yeast two-hybrid assay. In this study, subcellular localization results indicated that GmFAD2-1B was localized on the cell membrane. GmFAD2-1B showed higher expression levels in young seeds and mature seeds. Expression level of GmFAD2-1B was induced by HTH stress in soybean seed. The interaction between GmCDPKSK5 and GmFAD2-1B was further confirmed by yeast two-hybrid assay and bimolecular fluorescence complementation (BiFC). The overexpression of GmCDPKSK5 and GmFAD2-1B in Arabidopsis enhanced the tolerance of developing seed to HTH stress and improved seed vitality. Our results indicated that GmFAD2-1B interacts with GmCDPKSK5, which may participate in seed vigor formation under HTH stress in soybean.
 
Kiwifruit (Actinidia chinensis) is rich in dietary fiber and vitamin C and has high commercial value. However, it is susceptible to Botrytis cinerea pathogenesis. This fungus causes gray mold rot which negatively impacts kiwifruit quality. It also induces changes in superoxide dismutase, peroxidase, and catalase activity. Peroxidase and superoxide dismutase activities were detected at 1 dpi, increased till 4 dpi, and decreased by 5 dpi. Catalase was activated at 2 dpi, increased thereafter, and declined by 5 dpi. RNA-seq identified 2726 unique differentially expressed genes. The fold change was at least two, and the false discovery rate was less than 0.01. The 233 genes relevant to B. cinerea response were modulated in the first three infection stages. A weighted gene co-expression network analysis identified genes and modules in the transcriptome datasets that were responsive to B. cinerea. A network analysis disclosed the families “Plant-pathogen interactions”, “Lipid metabolism”, “Phytohormone signaling”, “Transcription factor”, “Cell wall biogenesis” and “Phenylpropanoid biosynthesis” possibly regulating B. cinerea response. The hub genes identified here are potential targets for breeding kiwifruit with improved biotic stress tolerance. This work lays an empirical foundation for investigating the proteins in kiwifruit that are modulated in response to B. cinerea pathogenesis.
 
Agarose gel images of two sets of consensus primers for S-genotyping sweet cherry cultivars grown in Estonia. S-allele consensus primers SI-19 + SI-20 and SI-31 + SI-32 determine S-alleles S1-S6 and S9. S-allele consensus primers PaConsI-F + PaConsI-R and PaConsII-F + PaConsII-R determine S1-S16. S17 can be detected and is distinct from all other alleles with each consensus primer set. Agarose gel images of PCR products amplified by a SI-19 and SI-20 primers, b SI-31 and SI-32 primers, c PaConsI-F and PaConsI-R primers, and d PaConsII-F and PaConsII-R primers. Cultivars ‘Lapins’ S1|S4, ‘Kompaktnaja’ S2|S4, ‘Anne’ S3|S6, ‘Krupnoplodnaya’ S5|S9, ‘Madissoni roosa’ S4|S13 and ‘Irma’ S3|S17 were selected to represent all S-alleles detected in this study
S-allele frequencies of 32 Estonian sweet cherry cultivars (blue bars) and 18 foreign sweet cherry cultivars (green bars) grown in Estonia in comparison to 545 European cultivars shown with gray bars in the background (Schuster 2012). The most common S-allele among both groups was S17
Comparison of two S17-specific primer pairs. New S17-specific primers amplify 398 bp long fragment specifically from the second intron of S-RNase of the S17 allele, whereas previously published S17-specific reverse primer combined with EM-PC2consFD amplifies also other S-locus alleles of different sizes. a Primers EM-PC2consFD (Sutherland et al. 2004) and PavS17R2 (Szikriszt et al. 2012) amplify S17 (505 bp), but also S3 (613 bp) and S4 (796 bp). b Primers PaS17_F3 and PaS17_R3 designed within this study amplify specifically only S17
Schematic overview of sweet cherry blossom and the role of S-alleles in self-incompatibility. a Pollination in self-incompatible sweet cherry can only occur when pollen is of a different S-allele than either of the alleles of the pistil. b Pollen with self allele triggers matching S-RNase to become cytotoxic and does not allow pollen tube to form. c Several sweet cherry cultivars grown in Estonia were found to be pollinated by (♀) or to pollinate (♂) other cultivars carrying the same S-alleles (Table 2). Some cultivars belong to both groups
The pollination of self-incompatible diploid sweet cherry is determined by the S-locus alleles. We resolved the S-alleles of 50 sweet cherry cultivars grown in Estonia and determined their incompatibility groups, which were previously unknown for most of the tested cultivars. We used consensus primers SI-19/20, SI-31/32, PaConsI, and PaConsII followed by allele-specific primers and sequencing to identify sweet cherry S-genotypes. Surprisingly, 48% (24/50) of the tested cultivars, including 17 Estonian cultivars, carry the rare S-allele S 17 , which had initially been described in wild sweet cherries in Belgium and Germany. The S 17 -allele in Estonian cultivars could originate from ‘Leningradskaya tchernaya’ (S 6 |S 17 ), which has been extensively used in Estonian sweet cherry breeding. Four studied cultivars carrying S 17 are partly self-compatible, whereas the other 20 cultivars with S 17 have not been reported to be self-compatible. The recommended pollinator of seven self-incompatible sweet cherries is of the same S-genotype, including four with S 17 -allele, suggesting heritable reduced effectiveness of self-infertility. We classified the newly genotyped sweet cherry cultivars into 15 known incompatibility groups, and we proposed four new incompatibility groups, 64–67, for S-locus genotypes S 3 |S 17 , S 4 |S 17 , S 5 |S 17 , and S 6 |S 17 , respectively, which makes them excellent pollinators all across Europe. Alternatively, the frequency of S 17 might be underestimated in Eastern European populations and some currently unidentified sweet cherry S-alleles might potentially be S 17 .
 
Heat map and cluster analysis based on principal component analysis (P < 0.05) using 18,344 genes from RNAseq analysis with FPKM ≥ 5 in all replicates of at least one treatment. The standard score is indicated in the color key at the top left, where positive values are red, means are black, and negative values are green
Regulation of CBF signaling pathway. The CBF regulon plays an important role in cold acclimation of evolutionarily diverse plant species. CCA1 and LHY directly bind to the CBF promoters to upregulate their expression (Dong et al. 2011). Both SOC1 and PRRs (PRR5/7/9) are negative regulators of CBFs. The expression of SOC1 is positively regulated by FT. SOC1 directly binds to the CBF promoters to repress their expression (Seo et al. 2009), whereas PRRs repress CBF expression by inhibiting the expression of CCA1 and LHY (Nakamichi et al. 2009, 2010). However, although PRR proteins are known to play negative roles in regulating the cold stress response (Nakamichi et al. 2009), the transcript abundance of PRR5, 7, and 9 was increased after vernalization in this study. PIFs are known to negatively regulate plant freezing tolerance by inhibiting the CBF pathway (Leivar and Quail 2011; Lee and Thomashow 2012; Jiang et al. 2020). However, the increased expression of PIF5 and PIF7 observed post-acclimation is contradictory to the concurrent increased expression of CBFs, and thus, these PIFs may have a functional role in vernalization. FLC is a master regulator of flowering; during vernalization, FLC expression is repressed possibly via VIN3 (Wood et al. 2006). The repression of FLC facilitates the activation of downstream floral activators, FT and SPL15 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE15), to initiate flowering. The transcript abundance of FT and SPL15 was low (FPKM values < 5) pre- and post-acclimation for both Joelle and CO46 in this study. FLC also directly represses the transcription of SOC1 (Searle et al. 2006; Deng et al. 2011), which may reverse CBF repression. A microRNA, MIR172A, was identified as a central hub among upregulated genes in Joelle pre- and post-acclimation relative to CO46. MIR172A is known to play positive roles in flowering (Wang et al. 2016) possibly via the regulation of SPL15 (Wu et al. 2009) and through its target genes (such as TARGET OF EAT) to upregulate the expression of FT (Teotia and Tang 2015)
Camelina (Camelina sativa L. Crantz) is a short-season oilseed crop of the Brassicaceae family that consists of both summer and winter annual biotypes. Winter biotypes require non-freezing cold conditions for acquiring freezing tolerance (cold acclimation) and floral initiation (vernalization). Transcriptome profiles of a summer (CO46) biotype with poor freezing tolerance after acclimation and a winter (Joelle) biotype with excellent freezing tolerance after acclimation were compared prior to and after an 8-week cold treatment to identify key molecular pathways and genes responsive to cold acclimation and vernalization and potentially associated with freezing tolerance. Gene-set enrichment analyses identified AraCyc pathways involved in photosynthesis and lipid and hormone biosynthesis that were different between the two biotypes. Sub-network enrichment analyses identified hubs of molecular networks such as circadian clock, flowering, and hormone and stress responsive genes that were likely involved in vernalization but may also overlap with cold-induced freezing tolerance. A microRNA involved in floral initiation (MIR172A) was identified as a central hub for microRNA targets among upregulated genes for Joelle post-acclimation. Combined results are generally consistent with many previously identified molecular pathways and genes acting together to control vernalization, cold acclimation, and freezing tolerance. Our research provides new insights into the regulation of cold acclimation and molecular genetic mechanisms underlying cold tolerance and floral induction for the winter biotype Joelle.
 
Recent studies have shown that a variety of cytokines are involved in cell cycle regulation and that the E2F-DP transcription factor (TF) family is one of the important regulatory links. However, little is known about E2F-DP gene family members and their evolutionary and functional characteristics in plants, especially under stress conditions. Their characterization has not been performed in bread wheat (Triticum aestivum). In this study, 27 E2F-DP genes were identified from the wheat genome (TaE2F-DP). The phylogenetic analysis split these 27 genes into three groups. Five typical conserved motifs of TaE2F-DP protein ranging in length from 28 to 50 amino acid residues had been found. Using chromosome location, we found that the E2F-DP gene family members were distributed on all 21 chromosomes of wheat. Conjoint analysis indicated the association between E2F-DP genes in wheat and its three ancestors (T. urartu, T. dicoccoides, and Aegilops tauschii). Transcriptome analysis showed that in several genes, expression was stress related. To uncover the reason for induction expression patterns of TaE2F-DPs during abiotic and biotic stresses in wheat, the cis-regulatory elements functionally associated with stress responding and hormones in the promoter region of TaE2F-DPs were analyzed. In addition, qRT-PCR results further confirmed that these TaE2F-DP genes are involved in wheat stress response. In summary, this study provided evolutionary and functional information of TaE2F-DP gene family members and revealed the gene expression of different members under different stress treatments. These findings provide comprehensive insights into the E2F-DP family members in wheat and offer candidate E2F-DP genes for further researches on their roles in stress resistance and potential for improving wheat breeding programs.
 
Rue plants (R. graveolens) treated with different levels of CuSO4, micromaterials (MMs) and nanomaterials (NMs) CuO for 21 days in hydroponic culture. The control was 0.5 µM CuSO4
Effects of different levels of CuSO4, micromaterials (MMs) and nanomaterials (NMs) CuO on a CAT enzyme activity; b CAT relative gene expression in shoots of rue plants (R. graveolens) in hydroponic culture for 3 weeks. The control was 0.5 µM CuSO4. The data are the mean ± StD
Effects of different levels of CuSO4, micromaterials (MMs) and nanomaterials (NMs) CuO on a shoot Cu, b root Cu, and c root to shoot transition (RST) of rue (R. graveolens) plants in hydroponic culture for 3 weeks. The control was 0.5 µM CuSO4. The data are the mean ± StD
Effects of different levels of CuSO4, micromaterials (MMs) and nanomaterials (NMs) CuO on aIRT1 relative gene expression in shoot; bIRT1 relative gene expression in root of rue plants (R. graveolens) in hydroponic culture for 3 weeks. The control was 0.5 µM CuSO4. The data are the mean ± StD
Background Copper oxide nanomaterials’ (NMs) are important for the critical roles of Cu as a micronutrient that its improper concentration could cause toxicity or deficiency in plant. The Nano form of CuO could amplify the effects due to special characteristic of nano materials. Method Treatments of 0.1, 0.5, and 2.5 μM and NM of copper with three replications were applied to plants under hydroponic conditions. Physiological parameters and expression of IRT1 and CAT genes were investigated. Results Copper absorption decreased according to MMs-CuO ˂ NMs-CuO ˂˂ CuSO4 pattern. The positive effects of MMs-CuO on plant copper content were higher than those of nanomaterials and CuSO4. MMs-CuO effect was more significant on plant biomass increase compared to the control. Rue plant needed lower amounts of copper for better plant growth. The treatments increased protein and carotenoids content in leaves compared with control. Changes in total chlorophyll content under three copper forms were very low and were only increased in leaves at 0.1 μM CuSO4. The NMs-CuO and MMs-CuO similarly reduced leaves’ Cu, MDA and ROS contents, and SOD activities. CAT enzyme activity had a similar pattern in three copper forms. CAT enzyme activity was only induced under the lowest level of three forms, while at other levels of Cu, it was reduced. NMs-CuO had a more negative effect on IRT1 relative gene expression in root compared with other iron forms. The IRT1 relative gene expression in shoots was positively affected under 2.5 μM CuSO4, 0.5 μM MMs-CuO, and 0.1 and 2.5 μM NMs CuO treatments. Conclusion The effect of micro- and nano-CuO on physiology and gene expression mechanisms in rue plants is shown to be does-dependent.
 
The basic-helix-loop-helix (bHLH) transcription factors superfamily is present in eukaryotes and has been widely characterized in several species. The study of these proteins has focused on processes involved in plant growth and development. However, it has also been shown that bHLH plays a relevant role in processes of response to abiotic stress. In this study, the bHLH family in Eucalyptus was systematically characterized for the first time, using the Eucalyptus grandis genome. 153 bHLH genes in the E. grandis genome were identified, which were characterized phylogenetically and structurally. Then, a cold-tolerant hybrid of Eucalyptus (Eucalyptus nitens × Eucalyptus globulus) to generate a reference assembly was used to study the alternative splicing events produced in the cold response. 44 bHLH candidate genes to generate alternative splicing events in the hybrid were identified. These genes had exons differentially expressed in cold acclimation conditions. The splicing event prediction was further validated by qRT-PCR in three bHLH genes. Through this experiment was possible to determine that two of them were differentially expressed, so that new isoforms of these genes were being produced under cold acclimation conditions.
 
The modification of proteins by malonylation plays an important regulatory role in multiple biological processes. Protein malonylation is the reversible addition of malonyl groups to lysine residues to regulate protein localization, enzyme activity, protein stability, and many other biochemical processes. However, little information was available on the malonylation of lysine in Eucommia ulmoides, an important traditional Chinese herb with multiple active substances. In this study, we analyzed the malonylation of lysine to determine the potential regulatory role of lysine malonylation in the growth and development of E. ulmoides using LC–MS/MS combined with immune-based purification. A total of 388 lysine malonylation sites distributed in 256 proteins were identified. A gene ontology (GO) analysis showed that the proteins in which lysine is malonylated are related to a wide range of cellular functions ranging from metabolic processes to responses to stimuli. A bioinformatic analysis showed that malonylated proteins are primarily distributed in the chloroplast (108 proteins, 42.19%), cytoplasm (90 proteins, 35.16%), and nucleus (27 proteins, 10.55%). They are primarily involved in energy metabolism, including photosynthesis, carbon metabolism, glycolysis, and the biosynthesis of secondary metabolites. Our research suggests that the malonylation of lysine is necessary for the life cycle of plants, which are primarily involved in the process of converting solar energy to biomass energy that is stored and converting the energy stored by plants into energy (ATP) available for direct use in E. ulmoides. To our knowledge, this is the first posttranslational malonylation modification of E. ulmoides proteins, which was conducted simultaneously to explore the mechanism of modification groups in protein functions, protein interactions, and biological metabolism, so as to provide a theoretical basis for the production and breeding of E. ulmoides.
 
Subcellular localization and substrate specificity of ZmMSRB1. a Images of A. thaliana mesophyll protoplasts with transient expression of ZmMSRB1-GFP, showing the subcellular localization of the protein in the chloroplasts. GFP indicates the control vector lacking the protein sequence (p35S::GFP). b Image of a gel with the recombinant protein indicated by the red arrow. c Reduction of dabsyl-Met-R-SO by ZmMSRB1; the quantity of Met-R-SO decreased, compared with the negative control, and a peak corresponding to Met appeared. GFP, green fluorescent protein; Met, methionine; MetSO, methionine sulfoxide; MSR, methionine sulfoxide reductase
The effect of salt or oxidative stress on A. thaliana constitutively expressing ZmMSRB1. a Appearance of 1-week-old wild-type Col-0, transgenic and msrb1 mutant A. thaliana seedlings grown under conditions of no stress or 100 or 200 mM NaCl. b The root length and c fresh weight of these seedlings. d Appearance of 1-week-old Col-0, transgenic and msrb1 mutant A. thaliana grown under conditions of no stress or 1 or 2 mM H2O2. e The root length and (f) fresh weight of these seedlings. Data are presented as the mean ± SE (n = 3). *P < 0.05 and **P< 0.01 vs Col-0, using Student’s t-test. CK indicates the no stress control conditions. AtOE, Arabidopsis line overexpressing the ZmMSRB1 gene; MSR, methionine sulfoxide reductase
Effect of ZmMSRB1 expression on ROS-scavenging ability in A. thaliana. a Images of DAB- and NBT-stained leaves of 4-week-old wild-type Col-0, transgenic and msrb1 mutant seedlings exposed to 100 mM NaCl for 48 h. b H2O2 content, c SOD activity, d POD activity, e CAT activity, and f MDA content in the aforementioned leaves. Data are presented as the mean ± SE (n = 3). *P < 0.05 and **P < 0.01 vs Col-0, using Student’s t-test. AtOE, Arabidopsis line overexpressing the ZmMSRB1 gene; CAT, catalase; DAB, diaminobenzidine tetrahydrochloride; FW, fresh weight; MSR, methionine sulfoxide reductase; NBT, nitroblue tetrazolium; POD, peroxidase; SOD, superoxide dismutase
Effect of ZmMSRB1 expression on K⁺/Na⁺ and sugar balance. Leaves of 4-week-old wild-type Col-0, transgenic AtOE and msrb1 mutant A. thaliana seedlings were used to measure a the K⁺/Na⁺ ratio and b soluble sugar content. Relative expression levels of genes associated with c ion transport and d sugar synthesis. Data are presented as the mean ± SE (n = 3). *P < 0.05 and **P < 0.01 vs Col-0, using Student’s t-test. AtOE, Arabidopsis line overexpressing the ZmMSRB1 gene; FW, fresh weight; HKT, high-affinity K⁺ transporter; INV, invertase; MSR, methionine sulfoxide reductase; NHX, Na⁺/H⁺ exchanger; SOS, Salt Overly Sensitive; SPS, sucrose-phosphate synthase
Relationship between ZmMSRB1 and ZmGSTF8. Images from a yeast-2-hybrid assay revealing the interaction between a plastidic ZmMSRB1 and ZmGSTF8, and b cytoplasmic ZmMSRB5 and ZmGSTF3. Protein interactions were monitored on both SD/-L-T and SD/-L-T-H plus 5 mM 3-AT media. Larget/P53, or AD/BD are positive and negative controls, respectively. Appearance of 1-week-old wild-type Col-0, transgenic and msrb1 mutant A. thaliana seedlings grown under conditions of c no stress, d 1 mM BSO, e 100 mM NaCl, or f 100 mM NaCl plus 1 mM BSO. g Root lengths of the plants in c, d. h Root lengths of the plants in e, f. i Measurement of total GST activity and j relative expression levels of AtGSTF8, following treatment with 100 mM NaCl. Data are presented as the mean ± SE (n = 3). *P < 0.05 and **P < 0.01 vs Col-0, using Student’s t-test or two-way ANOVA. AtOE, Arabidopsis line overexpressing the ZmMSRB1 gene; BSO, butyrylamine sulfoxide; FW, fresh weight; GST, glutathione S-transferase; MSR, methionine sulfoxide reductase; ns, no statistically significant
Plant methionine sulfoxide reductases (MSRs) can repair oxidative damage done to intracellular proteins and, therefore, play an active role in the response to abiotic stress. However, the function of MSR homologs in maize has not been reported, to the best of our knowledge. In a previous study, we reported that ZmMSRB1 can be induced by salinity stress. In this study, we revealed that ZmMSRB1 is localized to chloroplasts and belongs to the MSRB sub-family. Characterization of an Arabidopsis thaliana msrb1 mutant and lines with ectopic expression of MSRB1 indicated that MSRB1 contributes to tolerance of salinity stress. Overexpression of ZmMSRB1 in Arabidopsis seedlings significantly decreased reactive oxygen species (ROS) accumulation by leading to the downregulation of ROS-generating genes and upregulation of ROS-scavenging genes, which resulted in a significant increase in ROS-scavenging protein activity. ZmMSRB1 overexpression was also found to enhance the expression of Salt Overly Sensitive genes, which maintain intracellular K⁺/Na⁺ balance. Furthermore, it resulted in the promotion of expression of key genes involved in glucose metabolism, increasing the soluble sugar content in the leaves. The ZmMSRB1 protein was observed to physically interact with glutathione S-transferase ZmGSTF8 in a yeast two-hybrid assay. GST catalyzes the conjugation of glutathione (GSH) to other compounds, counteracting oxidative damage to cells in vivo. When GSH synthesis was disrupted, the ZmMSRB1-induced response to salinity stress was partially impaired. Together, the findings of the present study indicate that maize MSRB1 promotes resistance to salinity stress by regulating Na⁺/K⁺ transport, soluble sugar content, and ROS levels in A. thaliana.
 
Valsa canker is a destructive fungal disease that results in a serious loss of production. The pathogen Valsa pyri (Vp) usually infiltrates the bark and xylem via the wound. ‘Duli’ (Pyrus betulifolia), a rootstock with high tolerance to this disease and multiple other stresses, is widely planted in northern China. We found that wound healing plays a crucial role in the resistance of ‘Duli’ against Vp infection. Nevertheless, elucidation of the molecular mechanism of this process has been largely limited. Using RNA sequencing (RNA-seq), we investigated dynamic gene expression profiles of ‘Duli’ and ‘Zaosu’ (Pyrus bretschneideri, susceptible) phloem tissues which 0–3 mm around the wounded site that were cultured for 1, 3, and 7 days after wounding. Quantitative real-time PCR (qRT-PCR) was used to confirm data veracity. After wounding at 1, 3, and 7 days, 4930, 4652, and 6279 differentially expressed genes (DEGs) were found from ‘Duli’, compared to 1641, 1968, and 3347 in ‘Zaosu’, respectively. Functional enrichment analysis revealed that the DEGs associated with “cell wall organization and biogenesis”, “biosynthesis of secondary metabolites” and “cell wall organization. pectin” were enriched both in ‘Duli’ and ‘Zaosu’. Additionally, expressions of DEGs encoding receptor-like kinase (RLK) subfamily Extensin, LRR-III, LRR-IV, LRR-IX, LRR-XI-1, LRR-XII-1, RLCK-IXa and RLCK-V, and transcription factor CRE1, TF, ABF, TGA, and MYC2 were rapidly activated in ‘Duli’, but only a subtle induction in ‘Zaosu’. In conclusion, DEGs related to cell wall thickening are rapidly and continuously induced in ‘Duli’, which plays a positive role in the formation of protective tissues. Notably, JA-, SA-, LRR-, RLCK-, and Extensin-related DEGs probably participated in the regulation of multiple molecular networks and contributed to the quick wound healing of ‘Duli’.
 
In rice, moderate leaf rolling improves photosynthesis and crop yield. However, the molecular mechanisms underlying this important agronomic trait remain incompletely understood. Here, we investigated a dominant rolled leaf mutant (RL-D) developed from Nipponbare rice (WT). From the six-leaf stage, the leaves of the mutant rolled inward, and abnormal sclerenchyma tissues developed on the abaxial side of the leaf midribs. Additionally, leaf length, plant height, grain weight, and chlorophyll content were significantly greater in the mutant as compared to the WT. Genetic mapping analysis suggested that the leaf-rolling trait in the RL-D mutant was controlled by a single dominant gene, which was located in a 743-kb region on rice chromosome 3. Re-sequencing analysis showed that one gene in the mapped region encoding a protein phosphatase, Os03g0395100 (herein designated OsPP2C), had base mutations in the first exon. These mutations may have produced a truncated form of the OsPP2C protein in RL-D. Further transcriptomic analysis revealed that several biological processes, especially secondary cell wall formation and protein phosphorylation, were overrepresented among the differentially expressed genes (DEGs) between the mutant and the wild type. qRT-PCR verification also demonstrated that specific genes associated with leaf polarity and secondary cell wall formation were differentially expressed in the mutant. This study presents a novel dominant rolled-leaf germplasm that may help to improve rice leaf morphology in the future. The results also suggested that the RL-D phenotype might result from abnormal sclerenchyma tissue development, possibly regulated by OsPP2C via the dephosphorylation pathway. This may present a novel mechanism underlying leaf-rolling in rice.
 
Melia dubia, a fast-growing tree species with multi-various uses, is suitable species for agro and farm forestry. In an extensive survey in eight districts of Karnataka, India, it was observed that the majority of M. dubia natural populations are fragmented and tree number is very less. Sixty trees were selected to assess the genetic variability using SSR markers. Analysis revealed a moderate level of genetic diversity (Ho = 0.47; He = 0.69) and inbreeding as evinced by overall positive fixation index of 0.30. Mean Fst observed was 0.16 indicating moderate genetic differentiation among populations. The analysis of molecular variance ascribed 99% of total genetic diversity to within population variation. Cluster analysis by unweighted pair group method and genetic differentiation through structure analysis did not differentiate 10 populations as per geographic location, showing that moderate genetic diversity was not due to geographic distance. As genetic diversity was more within population, selection of individual plants would be more effective for genetic improvement to capture the natural variation within the population. An understanding of genetic diversity and differentiation of M. dubia natural populations will help in exploiting the genetic resource for tree improvement and also in formulating management and conservation strategies for this species.
 
Flavonoids from Ginkgo biloba have antioxidant and free radical scavenging activity. In the present study, we used different concentrations of OS (organic selenium), NS (nano-selenium), and IS (inorganic selenium) to treat the 2-year-old Ginkgo seedlings and studied the effects of different concentrations of selenium treatment on the physiological indexes and flavonoid content of Ginkgo at different growth stages. Our results showed that the content of chlorophyll, soluble sugar, and total flavonoid glycosides in the 1.6-mM NS treatment group increased significantly in July and September (by 43.87%, 59.92%, and 43.99% and 13.86%, 18.60%, and 35.04%), compared to the control respectively, all P < 0.05. To further analyze the changes of flavonoid content and gene expression levels in Ginkgo leaves, transcriptome sequencing analysis was performed on the treated seedlings. Sequencing analysis results showed that NS could promote PAL, COMT, CAD, and F6H gene expression levels in the flavonoid synthesis pathway; OS up-regulates the CCR and HCT genes. IS promotes the expression of C3'H, CCoAOMT, CYP, DFR, and HCT genes. Furthermore, the increase of key genes and enzyme levels promotes the increase of total flavonoid content. These data suggest that the appropriate concentration of OS and NS can promote the expression level of flavonoid synthesis genes and further promote the increase of total flavonoid content in Ginkgo leaves, which is beneficial to the medicinal value of Ginkgo extract.
 
Population structure of 287 maize inbred lines inferred by ADMIXTURE analysis using 18,497 SNPs. Each individual is represented by a thin vertical bar with the length of each segment representing the proportion of the individual’s genome when k = 8 groups
Dendrogram based on neighbor-joining clustering from genetic distance matrix consisting of 18,497 SNPs across 287 maize inbred lines. Individuals are colored based on potential heterotic groups
The first three principal components of a multidimensional scaling plot from the genetic distance matrix containing 18,497 SNPs of 287 maize inbred lines. Individuals are colored based on their majority admixture membership. a PCA for the entire set of maize lines. b PCA for regular tropical maize. c PCA for popcorn lines
Differentiation of allele frequencies between maize germplasm. a Allele frequency difference between maize germplasm collections: popcorn versus waxy maize, popcorn versus regular tropical maize, and popcorn versus regular temperate maize. b Distribution of allele frequency difference of SNP markers on 10 maize chromosomes for three pairwise comparisons. The marker density is indicated by different bar colors, and each bar represents 1-Mb window size
Whole-genome distribution of Tajima’s D a and nucleotide diversity b with 2 Mb windows, as revealed by 18,497 SNPs and 287 maize inbred lines
Specialty maize is widely used for human and animal consumption. It is therefore important to conduct a genome-wide comparison of regular and specialty maize. In the present study, a total of 20,000 SNP markers were generated using genotyping by target sequencing (GBTS) approach, of which 18,497 high-quality SNPs were used to explore the population structure and genetic diversity of both regular (163) and specialty (124) maize resources. Neighbor-joining clustering analysis classified the 287 tested maize inbred lines into three major groups, in which popcorn and other types of maize clustered into separate groups. The regular temperate maize was further divided into five heterotic subgroups, while the waxy maize and regular tropical maize were divided into two separate subgroups. However, the quality protein maize (QPM) could not be distinguished from regular tropical maize. The highest difference in allele frequency (P < 0.05) was observed between popcorn and waxy maize (28.2%), while 26.0% SNPs between popcorn and regular tropical maize, and 25.4% SNPs between popcorn and regular temperate maize. The information generated in this study is helpful for incorporating identified genetic variation into hybrid breeding programs for specialty maize improvement and also for genome-wide association mapping in specialty maize.
 
The morphological traits of Korla pear fruit. a to c The phenotypic traits of the fruit at 20, 50, and 80 DAF, respectively. d to f The Safranin staining of stone cells in the fruit pulp at 20, 50, and 80 DAF, respectively
The phylogenetic relations of the NAC family genes in P. bretschneideri and A. thaliana. Full-length amino acid sequences were aligned with MUSCLE program; the phylogenetic tree was constructed using MEGA-X software package. The phylogenetic trees were derived using the neighbor-joining (NJ) method with bootstrap value of 1000 replicates. The tree divided the PbNAC genes into 13 subgroups on differently colored clusters (C1–C13) within the tree. The NAC family genes annotated as associated with SCW biogenesis in pear labeled with blue circles; the SCW master switch NACs in A. thaliana labeled with red circles on gene ids in the figure
The phylogenetic relationship, gene structure, and architecture of conserved protein motifs in SCW-related NACs in A. thaliana and P. bretschneideri. a The phylogenetic tree that constructed by MEGA-X using NJ method. Eight subgroups on the phylogenetic tree were highlighted with different background colors. b The structures of NAC genes; green boxes indicated UTR regions, yellow boxes indicate exons, and black lines indicate introns. c The motif distribution of NAC proteins. Different motifs were indicated by different colors for motifs 1–20. The sequence information of each motif is provided in Table S4
The expression clustering of NAC family genes in Korla pear transcriptomes at different development stages. a The dendrogram of clustering FPKM values of NAC family genes; the vertical axis represents for the height of the dendrogram; the horizontal axis represents for the genes in the cluster. b Gene expression heat map; the vertical axis represents for 11 branches after cutting the dendrogram; the horizontal axis represents for samples from different fruit developmental stages; the red and green colors in the heat map stand for high and low level of expression of genes, respectively
Quantification of expression levels of 10 SCW related NAC family genes in rough-skinned pear fruit. The blue and red colors represent the fold changes of each gene in both the skin and pulp of rough-skinned fruits relative to normal fruits. Bar represents the mean expression value of three replicates ± standard deviation (SD)
Korla pear (Pyrus sinkiangensis Yü) is a native species of Xinjiang, China. Nowadays, the formation of rough-skinned fruits is becoming one of the main factors that adversely affect the fruit quality. The rough-skin phenotype is caused by an excessive accumulation of stone cells in pear fruits. Like fibers, the stone cells are formed by secondary thickening of cell walls, which is regulated by NAC and MYB family transcription factors (TFs) as master switches. In this work, we have mainly investigated NAC family genes in pear genome and found 158 TFs that belong to this family. Among them, nineteen genes were highly homologous with secondary cell wall (SCW) master switches in Arabidopsis. By analyzing transcriptome data from different stages of fruit development (early, late, and stationary stage of stone cell differentiation), twenty-three NAC members were found to be differentially expressed. Among them, nine genes were homologs of Arabidopsis SCW master switches and the rest were clustered in expression patterns with these genes. Among these nine genes, five of them were VND genes which regulate the vessel development, and the rest were annotated as NST2 and SND2 that involve in the fiber differentiation. In other 14 genes, five of them were the homologs of NAC83 and NAC104 that represses VNDs, and the rest of them were the homologs of membrane-bound NACs (NTM1, NTL6, and NTL8) that involve in plant responses to diverse stresses and developmental signals. The gene expression quantification indicated that fiber-specific SNDs and negative regulators of VNDs were upregulated in rough-skinned fruits.
 
Cinnamomum camphora linalool type ( C. camphora linalool type) is an economically important plant that contains abundant linalool. To explore the optimal concentration of exogenously applied indole-3-butyric acid (IBA) for root formation and development, morphological analyses were performed with plants after a 1-min soaking treatment with five different concentrations of IBA. When grown on the medium (laterite with plant ash) for 60 days after treatment with 3000 mg/L IBA, the root ratio and the number of roots were significantly higher than those obtained with 0, 1000, 2000, or 4000 mg/L IBA treatment. After soaking with 3000 mg/L IBA, the stem bases at five key stages of root development (0, 14, 21, 28, and 42 days) were selected for global transcriptome analyses. IBA treatment modified the expression of genes related to the auxin, brassinosteroid, and abscisic acid signalling transduction pathways. The rooting process reduced the accumulation of starch and the synthesis of linalool but promoted the metabolism of D-glucose. Our study identified the optimum concentration of IBA for a short treatment of C. camphora linalool type stem segments to regulate root formation and development at the transcriptional level.
 
The APETALA2/ethylene responsive AP2/ERF element-binding factors (AP2/ERFs), as a class of transcription factors (TFs), play an important role in plant growth and development as well as various biotic and/or abiotic stresses responses. AP2/ERF gene families have been widely identified in a lot of plants, but there was little known about this gene family in strawberry. To investigate the characteristics and functions of strawberry FvAP2/ERF gene family in abiotic stresses, a total of 139 FvAP2/ERF genes were identified in this study. The sequence alignment and phylogenetic analysis clustered AP2/ERF gene family into four subfamilies (AP2, RAV, ERF, and DREB). Chromosome location analysis revealed that the tandem duplication and the whole-genome duplications (WGDs) may result in the expansion of FvAP2/ERF gene family. The qRT-PCR (quantitative real-time PCR) indicated 14 FvAP2/ERFs underwent up- or down-regulated expression in response to abiotic stresses. In summary, these results offered vital information for further evolutionary and functional characterization of FvAP2/ERF genes, and it also gave some guidance for improving the resistance of strawberry in the growth process. Ultimately, this study may contribute to the selection and breeding of high-yield, high-quality, and highly resistant strawberry varieties.
 
Classification of transposable elements (Bourque et al. 2018; Wicker et al. 2007; Feschotte et al. 2002). Created with BioRender.com
Transpositions difference between class I and II transposons in host cell. Created with BioRender.com
Mechanisms of transpositions of LTR retrotransposons in host cell
Total class I and class II transposons in the total genome of different plant species
Overview of ATAC-Seq (assay for transposase-accessible chromatin using next-generation and third-generation sequencing. Hyperactive Tn5 transposase is used to capture the open chromatin regions. Created with BioRender.com
Transposable elements (TEs) have long been considered junk DNA; however, the availability of genome sequences and the growth of omics databases have accelerated the study of TEs, and they are now considered evolutionary signatures. TEs, essential genetic elements in plant genomes, can move around the genome by either “cut-paste” (DNA transposons) or “copypaste” mechanisms (RNA transposons). TEs often affect host genome size and interact with host genes, resulting in altered gene expression and regulatory networks. Several genes have been identified to be influenced/modified by the action of TEs. TEs have diverse structures and functions. Plants are capable of using TEs as promoters and enhancers to drive epigenetic mechanisms in a tissue-specific manner. However, our knowledge about TEs remains poor despite extensive research in plants. Plant physiological functions associated with TEs have been challenging to analyse due to a lack of focused research. Another limitation is the lack of sufficient genetic information. The different functions displayed by plant genomes are genetically regulated, which opens up opportunities in areas such as genomic evolution and epigenetic modification. Indeed, understanding the contribution of TEs in the plant genome is indispensable to assess the diversity of evolutionary adaptability in plant taxa. In this study, we review the applications of TEs and discuss the value of genetic information in the plant genome. Genomic information about TEs has a significant value in high throughput research, including forward and reverse genetics. We discuss current strategies in using TEs for the genetic dissection of plant genomes. This review covers opportunities to use different TEs databases to increase the productivity of economically important plants for sustainable development
 
Protein phosphatase 2Cs (PP2Cs) are negative regulators in the classic abscisic acid (ABA)-mediated drought stress signaling network. However, some members of PP2Cs can regulate the resistant to abiotic stresses positively, which provided a new way to solve the problem of low yield under severe environment. PP2C genes have been studied in many plants, but not been reported in Tibetan hulless barley, which survived from harsh environment and can be used as a good subject for analyzing drought tolerance mechanism. Fifty-four PP2C genes were identified in hulless barley under dehydration stress from our previous RNA-Seq data. Of these PP2Cs, 12 were significantly induced under dehydration stress and may be considered drought resistance candidate genes. Phylogenetic study showed that these HvPP2Cs can be classified into 12 major clusters (group A-I, K-M). HvPP2C59, which belongs to group F, showed remarkable continuously upregulated pattern during dehydration stress, was cloned in this study. Bioinformatics analysis identified motifs such as ABRE, MeJA, and G-box (light responsiveness) within its promoter region. Expression analysis indicated that HvPP2C59 can be promoted under drought, NaCl, and polyethylene glycol (PEG) 6000 stress, suppressed under dark, but was almost unaffected with ABA treatment. HvPP2C59-silenced plants had higher leaf water loss rate (WLR) and lower survival rate (SR) compared with controls under dehydration stress. The silenced plants also showed retarded vegetative growth under normal condition. Silencing of HvPP2C59 resulted in restrained expression of cold-regulated gene, LEA genes, and JA bio-synthesis key gene AOC. The study of PP2C genes in hulless barley will provide practical support to further expound the specific mechanism of plant response to drought stress.
 
Soil salinity is a major environmental stress that adversely affects the growth, development, productivity, and quality of crop species, in particular, in arid and semi-arid regions. Identification of chromosomal regions associated with agronomic traits under salinity stress is crucial for improving salinity tolerance in wheat. Genome-wide association study (GWAS) was employed to evaluate 289 elite lines of the Wheat Association Mapping Initiative (WAMI) population under low (LS) and high (HS) salinity conditions using 15,737 SNP markers for seven agronomical traits. The genotypes responded differently to the different environments for all traits, highlighting genetic diversity within the WAMI population in response to salt stress, where the heritability ranged from moderate (37%) to high (88%). GWAS identified 118 and 120 significant marker-trait associations (MTAs) under LS and HS conditions, respectively. Significant association of some markers with more than one phenotypic trait was observed, indicating possible pleiotropic or indirect effects. A high degree of significant linkage disequilibrium (> 52%) was observed among SNPs on different chromosomes, indicating epistatic interaction. The salt stress index (STI) exhibited a positive significant correlation to grain yield per plant (GYP) under both LS and HS conditions (R² = 0.851–0.856). Linear regression analysis between STI and GYP under HS conditions indicated that STI is the best tolerance index for predicting high-yielding genotypes. The results present the WAMI population as a valuable source for improving yield potential for salt tolerance in wheat. Furthermore, our findings emphasize that GWAS is a powerful tool in promoting wheat breeding through accurate identification of molecular markers significantly associated with agronomic traits, which is essential for marker-assisted breeding.
 
Unweighted Neighbor-Joining dendrogram depicting the grouping pattern of Indian mustard germplasm accessions based on agro-morphological traits
UPGMA-dendrogram generated from 182 SSR markers showing the genetic relationship among 145 Indian mustard accessions
Structure bar plot assigning 145 Indian mustard accessions into three subpopulations (K = 3) based on SSR markers
Analysis of molecular variance (AMOVA) among and within Indian mustard germplasm accessions using SSR markers
Indian mustard is an economically important oilseed crop in India; therefore, exploring the genetic diversity of various germplasm collections is quite relevant for its genetic improvement. In the present study, we investigated genetic diversity and population structure among a panel of 145 Indian mustard germplasm accessions using 11 agro-morphological traits and 182 SSR markers. The result of variance analysis exhibited significant differences among the tested genotypes inferring the presence of a high degree of variability. The phenotypic coefficient of variation for seed yield (CV = 28.26%) was the highest among all the studied traits followed by biological yield (CV = 25.72%). Days to maturity ranged from 130 to 141 days (CV = 1.88%), which was the minimum variation exhibited by Indian mustard genotypes. Out of 235 SSR primer pairs evaluated, 182 (77.45%) SSRs resulted in polymorphic amplicons, while 53 (22.55%) SSRs amplified monomorphic loci. Allele number varied from 2 to 7 with 3.97 average number of alleles per SSR marker. PIC value varied from 0.03 (SJ1668I) to 0.71 (EJU4) with an average value of 0.39 per SSR marker. Gene diversity in the present study ranged from 0.03 (SJ1668I) to 0.75 (EJU4) with an average value of 0.46. Cluster analysis using morphological traits and SSR markers grouped all 145 accessions into two major clusters each, respectively. Population structure analysis grouped all the genotypes into three subpopulations with varying degrees of admixture genotypes. Analysis of molecular variance inferred that 88% of the total variation resides within the groups. The resulting estimates of genetic diversity and population structure may be useful for the effective management of Indian mustard germplasm resources and for future mustard breeding programs.
 
Dendrogram showing relationships among Hippophae rhamnoides collections from Leh (red) and Lahaul (blue) derived using hierarchical unweighted cluster analysis of morphological characters. The collections from two geographical regions are clustered in separate groups
a, b Dendrogram showing relationships among Hippophae rhamnoides collections from Leh (red) and Lahaul (blue), derived using hierarchical unweighted cluster analysis based on microsatellite marker data
Dendrogram prepared using combined data on morphometric and microsatellite data on Hippophae rhamnoides collections from Leh (red) and Lahaul (blue), using hierarchical unweighted cluster analysis. Regrouping of some collections from one geographical region in the other region is visible
Seabuckthorn (Hippophae rhamnoides L.), an upcoming superfood plant, has attracted researchers' attention worldwide for its medicinal, nutritional, and socio-economic value, along with its characteristic features to sustain extreme climatic conditions. We have studied microsatellite marker-based genetic and morphometric diversity in 93 collections of H. rhamnoides from different geographic sites representing two regions, namely Leh and Lahaul of the Indian Himalayas. Microsatellite markers were isolated using two different approaches, including screening of microsatellite-enriched genomic library, and in silico screening of in-house developed seabuckthorn EST database and whole transcriptome assembly. In Leh and Lahaul collections, 32 and 30 microsatellite markers were found polymorphic, respectively. All the markers developed for H. rhamnoides showed cross-species transferability to H. salicifolia and H. tibetana. Two to six alleles were recorded in the two sets of collections with an average of 3.71 and 3.53 alleles per locus in Leh and Lahaul collections, respectively. Mean polymorphic information content (PIC) values for microsatellite markers were 0.39 and 0.41 for Leh and Lahaul collections, respectively. The average expected heterozygosity was less than the observed heterozygosity. Wright's fixation index (F IS) varied from (-)0.2045 to 1.0 and (-)0.1688 to 1.0 for Leh and Lahaul collections, respectively. Shannon's informative index (I) remained in the range of 0.6745 to 1.8621, and 0.6824 to 1.6308 for Leh and Lahaul collections, respectively. The UPGMA-based combined dendrogram showed clear demarcation between Leh and Lahaul collections, although a few ecotypes were regrouped with collections from the other region. No significant relationship was observed between the morphological distance matrix and molecular marker distance matrix. The findings of the present study may prove helpful in future breeding and conservation strategies aiming for seabuckthorn improvement. Supplementary information: The online version contains supplementary material available at 10.1007/s11105-022-01338-6.
 
Seed dormancy is an important breeding trait for the development of certain types of peanut cultivars. Peanut cultivars with seed dormancy can inhibit preharvest sprouting in which the sprouting may increase susceptibility to preharvest aflatoxin contamination. The recombinant inbred line (RIL) mapping population derived from a cross of Tifrunner, a dormant Runner type, and GT-C20, a non-dormant Spanish type, were planted in the field for 2 years, and the freshly harvested seeds were used for seed dormancy tests at 7, 14, 21, and 28 days during germination. There were three RILs from 2-year tests with no dormancy (T48, T83, T160) and two lines with strong dormancy (T11, T163). This RIL population was genotyped using peanut SNP array ‘Axiom_Arachis’ 58 K, and two major seed dormancy QTLs were anchored on chromosome A04 and A05 with 43.16% and 51.61% of the phenotype variation explained (PVE), respectively. The QTL mapped on chromosome A05 had been anchored on a physical map interval of 98 kb (157.538–157.636 Mb) from which a possible candidate gene (Arahy.KB746A, ethylene-responsive transcription factor) was identified. Reference to the peanut physical map and flanking sequences, DNA markers can be developed for these two QTLs and used in marker-assisted breeding selection for seed dormancy in peanut.
 
Inorganic phosphate (Pi) deficiency is a main limiting factor on crops growth and to select low-Pi tolerant breeding lines is very significant for crop breeding. Here, two contrasting maize ( Zea mays L.) breeding lines showed different physiological response to Pi deficiency. The low-Pi tolerant QXN233 maintained normal growth, including high fresh weight, green leaves, strong shoots, and numerous roots relative to that of the sensitive MH05-4, mainly due to QXN233’ high Pi content in shoots under Pi deficiency. Importantly, some Pi-responsive genes were detected, and among them, Pi transporters ZmPHT1;1 and ZmPHT1;9 as well as phytase gene Zmphytase 2 were expressed increasingly in QXN233 compared to MH05-4 under Pi deprivation or Pi resupply. Moreover, QXN233 had higher proline content, soluble sugar content, and SOD activity than MH05-4, related with its tolerance. Taken together, this study enriches the understanding of the mechanism of maize responding to Pi deficiency.
 
Phenotypic comparison of five homozygous PfAGL28–transgenic Arabidopsis lines (35S::PfAGL28), wild-type Arabidopsis plants (WT), and Arabidopsis plants transformed with the empty vector (Mock) (A) under long-day (B) and short-day (C) conditions. Photos were taken 12, 27, and 46 days after transplanting under long-day conditions, and 28, 95, and 123 days after transplanting under short-day conditions
Morphological differences in various structures parts of PfAGL28–transgenic Arabidopsis plants (35S::PfAGL28), wild-type Arabidopsis plants (WT), and Arabidopsis plants transformed with the empty vector (Mock). A Leaves, 4 days after transplanting. B Single flowers and inflorescences. C Pods. D Seeds
Relative expression levels of PfAGL28 and other related genes in PfAGL28-–transgenic Arabidopsis plants (35S::PfAGL28), wild-type Arabidopsis plants (WT), and Arabidopsis plants transformed with the empty vector (Mock). A RT–qPCR quantification of the relative expression levels of PfAGL28 and other flowering-related genes in above–ground plant materials at the flowering stage. B RT–qPCR quantification of the relative expression levels of other type I MADS genes in flowers and pods. The ACTIN8 gene was used as the internal standard, and the mRNA expression levels of all genes were normalized to the WT. **p < 0.01. FT, flowering locus T; SOC1, suppressor of overexpression of CO1; CO, constans; AP1, APETALA1; LFY, LEAFY; FLC, flowering locus C; FPF1, flowering promoting factor 1; LD, lumindependens
RT-qCR quantification of PfAGL28 expression in the Polypogon fugax populations. SS, susceptible plants at the seedling stage; SR, resistant plants at the seedling stage; TS, susceptible plants at the tillering stage; TR, resistant plants at the tillering stage; HS, susceptible plants at the heading stage; FR, resistant plants at the flowering stage. **p < 0.01
Herbicide-driven selective pressures on weeds promote genetic changes in various physiological traits, including flowering time and fructification, allowing weeds to evade control techniques. Previously, we showed that early flowering was associated with resistance to acetyl coenzyme A carboxylase (ACCase) inhibitor herbicides in a population of Polypogon fugax. Here, we isolated the type I–like MADS-box gene PfAGL28 from ACCase inhibitor-resistant P. fugax, and showed that this gene was strongly upregulated in the resistant compared to susceptible populations at the flowering stage. Overexpression of PfAGL28 in Arabidopsis thaliana resulted in the early-flowering phenotype and early seed formation likely due to the upregulation of FLOWERING LOCUS T (FT), and AGMOUS-LIKE 23 (AGL23), AGMOUS-LIKE 61 (AGL61), and AGMOUS-LIKE 80 (AGL80). These results indicate that PfAGL28 gene is likely involved in the regulation of early flowering and pod formation in P. fugax. Our study thus provides a reference for future explorations of the flowering mechanisms of herbicide-resistant weeds.
 
Read length distribution of PacBio sequence data
K-mer spectra of KDH19-17, F1 (KDH13 × KDH19-17), and KDH13
Plot of genome variation in KDH13, KDH19-17, and F1 (KDH13xKDH19-17) relative to the Beta vulgaris EL10.1 genome
Hierarchical clustering based on relationship coefficients determined between KDH13, KDH19-17, and F1 (KDH13 × KDH17-19) relative to other sequenced genomes representing the cultivated lineages of Beta vulgaris
Beet curly top disease scores for F1 (KDH13 × KDH19-17) and parental lines KDH13 and KDH19-17
Beet Curly Top (BCT) is a viral disease which negatively impacts crop productivity for sugar beet growers and the sugar beet industry in the western USA and dry regions worldwide. Current varieties exhibit little genetic resistance to the Beet Curly Top Virus (BCTV), suggesting there is a large potential for improvement. KDH13 (PI 663862) is a double-haploid line created from a population (C762-17/PI 560130) which segregates for resistance to BCTV and was identified as genetic stock for the improvement of sugar beet varieties. PacBio sequences were generated and assembled to better define the content and organization of variation within the KDH13 genome and to provide resources to identify specific variation underpinning durable genetic resistance. Using ab initio predicted proteins as anchors, the assembled KDH13 contigs were placed in a more contiguous order using the EL10.1 reference genome, which leveraged Bio-Nano optical maps and Hi-C proximity information for chromosome level scaffolding. In total, 4681 (75%) of the 6245 contigs were placed in the order and orientation of the EL10.1 genome. The anchored contigs represented 502,929,268 bp (87.7%), the KDH13 genome assembly. An F 1 hybrid and parental lines KDH13 (resistant) and KDH19-17 (susceptible) were sequenced using Illumina technology in order to characterize the SNP, indel, and structural variation between parental lines and allow for a more detailed investigation into causal variation linked to important phenotypes. In total, 3,086,720 variants were detected, including 2,259,324 single-nucleotide polymorphisms, 191,448 insertions, 198,057 deletions, 268,090 complex substitutions, 90,004 multi allelic variants, and 79,797 structural variants. Of the total variation, 1,158,491 were informative in the F1 and were able to discriminate between the two parents. This information represents a high-density marker dataset distributed globally across the sugar beet genome and can be used to track genomic segments in populations where KDH13 is used as parental material to improve BCTV resistance.
 
Gibberellin (GA) is a crucial hormone that drives parthenocarpy and fruit set progression. However, it remains unknown whether GA participates in the parthenocarpy and fruit set in jujube (Ziziphus jujuba Mill.). In this study, we observed the morphology and effect of parthenocarpy in jujube flowers with GA3 treatment. Liquid chromatography tandem-mass spectrometry analysis was performed to detect the levels of endogenous hormones in sepal spread (H), filament wilting (S), and ovary inflation (G) stages of jujube flowers, and the GA3-induced differentially expressed genes (DEGs) were identified by RNA sequencing. We found that GA3 improved jujube parthenocarpic fruit set and that the morphology and size of flowers after GA3 treatment were superior to those in control flowers. GA3 treatment increased the levels of gibberellin, ABA, auxins, and cytokinins in jujube flowers. RNA sequencing revealed that GA3-induced DEGs expressed in the H, S, and G stages. Functional and pathway analyses demonstrated that these DEGs belong to plant development, including glucan metabolic processes and plant hormone signal transduction. Moreover, quantitative reverse transcription polymerase chain reaction validated the reliability of the sequencing data. Fruit set–related genes were significantly induced in the H, S, and G stages of jujube flowers. Our study confirmed that GA3 induced phytohormone production and fruit set by regulating the expression of endogenous hormones and related genes.
 
SQUAMOSA promoter binding protein (SBP)-box proteins are plant-specific transcription factors (TFs) and play crucial roles in a variety of physiological processes, including plant growth and development, signal transduction, and stress response. However, SBP-box family genes have not been well characterized in tea plant. In the present study, we identified 16 CsSBP genes in tea plant based on the tea plant genomic data. Phylogenetic analysis of SBP-box proteins from tea plant, Arabidopsis, and rice divided these proteins into nine groups (A–I). The number of exon–intron varied among the groups. The SBP-box genes in a same group shared similar exon–intron structures and motif locations. Prediction of miRNA target sites revealed that six CsSBPs genes contained a miR156 target site, while seven were targeted by miR157. RT-qPCR analysis revealed tissue/organ-specific expression patterns of CsSBP genes. In addition, their expression patterns in response to different phytohormone treatments and abiotic stresses were also investigated. This work provides base foundation for understanding the crucial roles of CsSBP genes in plant development and other biological processes.
 
Distribution of sampling locations for genetic study of Arachis hypogaea
UPGMA dendrogram based on SM similarity coefficient representing the relationships among Algerian Peanut cultivars
The second-order rate change for K ranging from 1 to 10 (Delta K)
A Bayesian clustering analysis based on 11 SSR marker data for Algerian Peanut populations performed using STRUCTURE at K = 2. Each individual is represented by a single vertical bar. B Bayesian sub-clustering analysis for the south region of the Algerian peanut performed with STRUCTURE at K = 3
The principal components analysis (PCA) of 11 SSR marker data of the 68 Algerian peanut accessions
Peanut (Arachis hypogaea L) is one of the wide cultivated plants with a narrow genetic base, hence the interest in prospecting, rescuing, and characterizing germplasm of this species is continuously carried out. In this work, eleven microsatellite markers were used to assess the genetic diversity and population structure of 68 Algerian peanut accessions originated from four geographic regions in the north and south of Algeria. A total of 83 alleles were amplified with a mean number of 7.545 alleles per locus and polymorphic information content (PIC) ranged from 0.625 to 0.874. The observed and expected heterozygosity varied from 0.31 to 1.00 and from 0.61 to 0.84 with a mean of 0.704 and 0.732, respectively. Genetic structure analysis showed a strong population at K = 2, separating accessions according to their subspecies affiliation (hypogeae ssp. and fastigiata ssp.). It was also able to quantify the genetic correlations between genotypes using principal component analysis (PCA) and the method of groups of unweighted pairings with arithmetic means (UPGMA). Analysis of molecular variance (AMOVA) revealed high genetic variation within individuals (90.7%) and low genetic differentiation between subspecies (10.3%) and among populations (8.9%) from different geographical origin. Genetic diversity analysis in this study provides useful information for the exploration and utilization of these peanut cultivars.
 
DNA replication, repair, and recombination (DRRR) are the fundamental processes required for faithful transmission of genetic information within and between generations. The DRRR genes protect the cells from potential mutations and damage during the developmental phases and stress conditions. Thus, these genes indirectly regulate diverse important agronomic traits in a crop plant. A genome-wide survey of six DRRR pathway genes, namely, DNA replication, Base Excision Repair, Nucleotide Excision Repair, Homologous Recombination, Mismatch Excision Repair, and Non-Homologous End-Joining, identified 157 DRRR genes in chickpea. Phylogenetic analysis of these genes within the legume clades and model plant Arabidopsis identified 42 conserved DRRR genes exhibiting clade-specific evolutionary patterns. Integrating the gene-based association mapping with differential expression profiling identified the natural alleles of the potential DRRR genes, primarily regulating flowering and maturation time and involved in drought tolerance of chickpea. Identifying and understanding DRRR genes’ roles in regulating yield and stress tolerance traits in a vital grain legume like chickpea is requisite for its future crop improvement endeavors. Manipulation of promising functionally relevant DRRR genes will pave the way for simultaneous improvement in multiple beneficial agronomic traits in chickpea.
 
a Genome map of CaMV; blue circle represents the dsDNA genome. The arcs represent the ORFS (green arc—ORF with known function; red arc—unknown function). b Pictorial representation of the genome of different genera of the family Caulimoviridae. Genera are arranged in ascending order of the number of their open reading frames (ORFs). ORFs are represented by different colour blocks. ORFs encode different functional proteins which are indicated by different shapes within them. Numbers below the genus name indicate the total number of accepted species by ICTV 2019 Master Species List (MSL35). The genome sizes are mentioned on the right side of the figure
Plant pararetroviruses (PRVs; family Caulimovirida) are non-enveloped double-stranded DNA viruses having either isometric or bacilliform virion. According to the current taxonomy, the family Caulimoviridae consists of ten genera with two newly added genera Dioscovirus and Vaccinivirus. PRVs have a genome size between 7 and 9 kilobase pairs and differ mainly based on the number of open reading frames (ORFs; 1 to 8) in each genus. These ORFs encode many functional proteins that help the virus to survive within the host cell. They are transmitted by aphids, mealy bugs, or leafhoppers. These viruses have a wide geographical distribution and infect a broad range of monocotyledonous and dicotyledonous plant species, making their early detection and control a paramount requirement. The transcriptional unit (promoter) of the PRV genome has become an interesting “modular cassette” to the molecular biologist worldwide for fine-tuning of gene expression in plants. The present review highlights the current taxonomy, genome structure, transmission, and diagnosis of pararetroviruses and how the “modular cassette” would help the modern biotechnology-based translational research.
 
Background MicroRNAs (miRNAs) have emerged as key regulators of post-transcriptional degradation and/or translational repression in both plants and animals. Increasing evidence has pointed to the important role of intergenic miRNAs in response to environmental stresses; however, detailed information about intronic miRNAs in plants is not clear.ResultsHere, we performed quantitative real-time PCR (qRT-PCR) analysis using transgenic plants to investigate the relationship between intronic miRNAs and their respective host genes in Arabidopsis. Here, we found that three Arabidopsis thaliana intronic miRNAs (miR400, miR838, and miR848) were co-transcribed with their host genes in different organs. Intriguingly, both miR400 and its host gene (At1g32583) were up-regulated during cold stress. Unlike intronic miRNAs in animals, the change of expression levels of plant intronic miRNAs in transgenic lines did not affect the transcriptional levels of their host genes. This result indicates that there is no feedback regulation loop between the intronic miRNAs and their host genes in Arabidopsis. In miRNAs-cropping mutants, the mature miRNAs were significantly reduced, while the expression levels of host genes did not change, suggestting the microprocessor also play roles in intronic miRNA processing.Conclusions Together, these results provide the evidence that there is an independent relationship between the processing of intronic miRNAs and their host genes in Arabidopsis.
 
Introduction Terpene trilactones (TTLs) are one of the main active ingredients of Ginkgo biloba. Owing to TTL’s unique chemical structure, it is difficult to increase TTL content through chemical and biological methods. Studying its regulatory mechanism is important in the G. biloba industry.ResultsThe effect of exogenous methyl jasmonate (MeJA) on the physiological and molecular mechanism of TTL biosynthesis was studied. These results showed that MeJA treatment could improve the TTL contents, soluble sugar, starch, soluble protein, endogenous hormones (ZT, GA3, IAA, and ABA), antioxidant enzymes (catalase, peroxidase, and superoxide dismutase), and the efficiency of photosynthesis in G. biloba leaves. A total of 100 differentially expressed genes (DEGs) were identified between the control group and MeJA treatment through RNA-seq analysis. The results indicated that exogenous MeJA treatment upregulated the expression levels of the following genes: BMY (beta-amylase) in the starch and sucrose metabolic pathway; PEX7 (peroxin-7) in the peroxisome pathway; psbA (photosystem II reaction center D1 protein), psbC (photosystem II CP43 chlorophyll apoprotein), psaA (photosystem I P700 chlorophyll a apoprotein A1), and petF (photosynthetic electron transport ferredoxin) in the photosynthesis pathway; and CYP450 (Gb-16765) (cytochromeP450).Conclusions Exogenous MeJA treatment can promote physiological indexes (photosynthetic efficiency, starch, sucrose, antioxidant enzyme activities, etc.) and then regulating differential genes, thus controlling the synthesis of TTLs.
 
Top-cited authors
Awais Khan
  • Cornell University
Junichi Obokata
  • Kyoto Prefectural University
Fumio Takaiwa
  • Institute of Agrobiological Sciences, NARO, Tsukuba, Japan
Julapark Chunwongse
  • Kasetsart University
Mamoru Sugita
  • Nagoya University