Molecular insights into OPR gene family in Saccharum identified a ScOPR2 gene could enhance plant disease resistance.

12-Oxo-phytodienoic acid reductases (OPRs) perform vital functions in plants. However, few studies have been reported in sugarcane (Saccharum spp.), and it is of great significance to systematically investigates it in sugarcane. Here, 61 ShOPRs, 32 SsOPRs, and 36 SoOPRs were identified from R570 (Saccharum spp. hybrid cultivar R570), AP85-441 (Saccharum spontaneum), and LA-purple (Saccharum officinarum), respectively. These OPRs were phylogenetically classified into four groups, with close genes similar structures. During evolution, OPR gene family was mainly expanded via whole-genome duplications/segmental events and predominantly underwent purifying selection, while sugarcane OPR genes may function differently in response to various stresses. Further, ScOPR2, a tissue-specific OPR, which was localized in cytoplasm and cell membrane and actively response to salicylic acid (SA), methyl jasmonate, and smut pathogen (Sporisorium scitamineum) stresses, was cloned from sugarcane. In addition, both its transient overexpression and stable overexpression enhanced the resistance of transgenic plants to pathogen infection, most probably through activating pathogen-associated molecular pattern/pattern-recognition receptor-triggered immunity, producing reactive oxygen species, and initiating mitogen-activated protein kinase cascade. Subsequently, the transmission of SA and hypersensitive reaction were triggered, which stimulated the transcription of defense-related genes. These findings provide insights into the function of ScOPR2 gene for disease resistance.

A novel system with robust compatibility and stability for detecting Sugarcane yellow leaf virus based on CRISPR-Cas12a.

Sugarcane yellow leaf virus (SCYLV) can reduce sugarcane productivity. A novel detection system based on reverse transcription-multienzyme isothermal rapid amplification (RT-MIRA) combined with CRISPR-Cas12a, named RT-MIRA-CRISPR-Cas12a, was developed. This innovative approach employs crude leaf extract directly as the reaction template, streamlining the extraction process for simplicity and speed. Combining RT-MIRA and CRISPR-Cas12a in one reaction tube increases the ease of operation while reducing the risk of aerosol contamination. In addition, it exhibits sensitivity equivalent to qPCR, boasting a lower detection limit of 25 copies. Remarkably, the entire process, from sample extraction to reaction completion, requires only 52-57 minutes, just a thermostat water bath. The result can be observed and judged by the naked eye.IMPORTANCESugarcane yellow leaf disease (SCYLD) is an important viral disease that affects sugarcane yield. There is an urgent need for rapid, sensitive, and stable detection methods. The reverse transcription-multienzyme isothermal rapid amplification combined with CRISPR-Cas12a (RT-MIRA-CRISPR-Cas12a) method established in this study has good specificity and high sensitivity. In addition, the system showed good compatibility and stability with the crude leaf extract, as shown by the fact that the crude extract of the positive sample could still be stably detected after 1 week when placed at 4°C. RT-MIRA-CRISPR-Cas12a, reverse transcription polymerase chain reaction (RT-PCR), and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) were used to detect SCYLV on 33 sugarcane leaf samples collected from the field, and it was found that the three methods reached consistent conclusions. This Cas12a-based detection method proves highly suitable for the rapid on-site detection of the SCYLV.

The first complete mitochondrial genome of Grossulariaceae: Molecular features, structure recombination, and genetic evolution.

BACKGROUND: Mitochondria play crucial roles in the growth, development, and adaptation of plants. Blackcurrant (Ribes nigrum L.) stands out as a significant berry species due to its rich nutritional profile, medicinal properties, and health benefits. Despite its importance, the mitochondrial genome of blackcurrant remains unassembled. RESULTS: This study presents the first assembly of the mitochondrial genome of R. nigrum in the Grossulariaceae family. The genome spans 450,227 base pairs (bp) and encompasses 39 protein-coding genes (PCGs), 19 transfer RNAs (tRNAs), and three ribosomal RNAs (rRNAs). Protein-coding regions constitute 8.88% of the entire genome. Additionally, we identified 180 simple sequence repeats, 12 tandem repeats, and 432 pairs of dispersed repeats. Notably, the dispersed sequence R1 (cotig3, 1,129 bp) mediated genome recombination, resulting in the formation of two major conformations, namely master and double circles. Furthermore, we identified 731 C-to-U RNA editing sites within the PCGs. Among these, cox1-2, nad1-2, and nad4L-2 were associated with the creation of start codons, whereas atp6-718 and rps10-391 were linked to termination codons. We also detected fourteen plastome fragments within the mitogenome, constituting 1.11% of the total length. Phylogenetic analysis suggests that R. nigrum might have undergone multiple genomic reorganization and/or gene transfer events, resulting in the loss of two PCGs (rps2 and rps11) during its evolutionary history. CONCLUSIONS: This investigation unveils the molecular characteristics of the R. nigrum mitogenome, shedding light on its evolutionary trajectory and phylogenetic implications. Furthermore, it serves as a valuable reference for evolutionary research and germplasm identification within the genus.

Pathogen resistance was negatively regulated by the NAC transcription factor ScATAF1 in sugarcane.

The NAC (NAM, ATAF, and CUC) is one of the largest transcription factor gene families in plants. In this study, 180, 141, and 131 NAC family members were identified from Saccharum complex, including S. officinarum, S. spontaneum, and Erianthus rufipilus. The Ka/Ks ratio of ATAF subfamily was all less than 1. Besides, 52 ATAF members from 12 representative plants were divided into three clades and there was only a significant expansion in maize. Surprisingly, ABA and JA cis-elements were abundant in hormonal response factor, followed by transcriptional regulator and abiotic stressor. The ATAF subfamily was differentially expressed in various tissues, under low temperature and smut pathogen treatments. Further, the ScATAF1 gene, with high expression in leaves, stem epidermis, and buds, was isolated. The encoded protein, lack of self-activation activity, was situated in the cell nucleus. Moreover, SA and JA stresses down-regulated the expression of this gene, while ABA, NaCl, and 4°C treatments led to its up-regulation. Interestingly, its expression in the smut susceptible sugarcane cultivars was much higher than the smut resistant ones. Notably, the colors presented slight brown in tobacco transiently overexpressing ScATAF1 at 1 d after DAB staining, while the symptoms were more obvious at 3 d after inoculation with Ralstonia solanacearum, with ROS, JA, and SA signaling pathway genes significantly up-regulated. We thus speculated ScATAF1 gene could negatively mediate hypersensitive reactions and produce ROS by JA and SA signaling pathways. These findings lay the groundwork for in-depth investigation on the biological roles of ATAF subfamily in sugarcane.

Sugarcane ScOPR1 gene enhances plant disease resistance through the modulation of hormonal signaling pathways.

KEY MESSAGE: Transgenic plants stably overexpressing ScOPR1 gene enhanced disease resistance by increasing the accumulation of JA, SA, and GST, as well as up-regulating the expression of genes related to signaling pathways. 12-Oxo-phytodienoate reductase (OPR) is an oxidoreductase that depends on flavin mononucleotide (FMN) and catalyzes the conversion of 12-oxophytodienoate (12-OPDA) into jasmonic acid (JA). It plays a key role in plant growth and development, and resistance to adverse stresses. In our previous study, we have obtained an OPR gene (ScOPR1, GenBank Accession Number: MG755745) from sugarcane. This gene showed positive responses to methyl jasmonate (MeJA), salicylic acid (SA), abscisic acid (ABA), and Sporisorium scitamineum, suggesting its potential for pathogen resistance. Here, in our study, we observed that Nicotiana benthamiana leaves transiently overexpressing ScOPR1 exhibited weaker disease symptoms, darker 3,3-diaminobenzidine (DAB) staining, higher accumulation of reactive oxygen species (ROS), and higher expression of hypersensitive response (HR) and SA pathway-related genes after inoculation with Ralstonia solanacearum and Fusarium solanacearum var. coeruleum. Furthermore, the transgenic N. benthamiana plants stably overexpressing the ScOPR1 gene showed enhanced resistance to pathogen infection by increasing the accumulation of JA, SA, and glutathione S-transferase (GST), as well as up-regulating genes related to HR, JA, SA, and ROS signaling pathways. Transcriptome analysis revealed that the specific differentially expressed genes (DEGs) in ScOPR1-OE were significantly enriched in hormone transduction signaling and plant-pathogen interaction pathways. Finally, a functional mechanism model of the ScOPR1 gene in response to pathogen infection was depicted. This study provides insights into the molecular mechanism of ScOPR1 and presents compelling evidence supporting its positive involvement in enhancing plant disease resistance.

Theory to practice: a success in breeding sugarcane variety YZ08-1609 known as the King of Sugar.

Sugarcane, a significant cash crop in tropical and subtropical regions, contributes to 80% of sugar production and 40% of bioethanol production in the world. It is a key sugar crop, accounting for 85% of sugar production in China. Developing new varieties with high yield, high sugar, and better stress resistance is crucial for the sustainable growth of sugar industry. Hybrid breeding is the most widely used and effective method, with over 98% of Chinese sugarcane varieties resulting from this approach. Over the past two decades, Chinese breeders have developed the theory of high-heterogeneous composite high-sugar breeding, leading to the successful breeding of the fifth-generation sugarcane varieties. Among them, YZ08-1609, a complex hybrid of Saccharum spp., was developed by Sugarcane Research Institute (YSRI) of Yunnan Academy of Agricultural Sciences. The average cane yield of YZ08-1609 was 14.4% higher than ROC22. It is highly resistant to mosaic disease, and highly tolerant to drought stress, but moderately susceptible to smut disease. Notably, YZ08-1609 stands out with a sucrose content of 20.3%, setting an international record, earning the reputation as "King of Sugar". To summarize experience and inspire breeding, we provided here the detailed insights into the selection of parents, breeding process, and characteristics of YZ08-1609. Besides, the biological mechanisms underlying its high yield and high sugar was excavated at both transcriptional and metabolic levels. The challenges and prospects in breeding sugarcane varieties especially with high sugar were also discussed, offering a foundation for the future development of high-sugar varieties.

Key Factors of Quality Formation in Wuyi Black Tea during Processing Timing.

As the most consumed tea in the world, all kinds of black tea are developed from Wuyi black tea. In this study, quality components, regulatory gene expression, and key enzyme activity during the processing were analyzed to illustrate the taste formation of WBT. Withering mainly affected the content of amino acids, while catechins and tea pigments were most influenced by rolling and the pre-metaphase of fermentation. Notably, regulatory gene expression was significantly down-regulated after withering except for polyphenoloxidase1, polyphenoloxidase2, leucoanthocyanidin dioxygenase, chalcone isomerase, and flavonoid 3', 5'-hydroxylase. Co-expression of flavonoid pathway genes confirmed similar expression patterns of these genes in the same metabolic pathway. Interestingly, rolling and fermentation anaphase had a great effect on polyphenol oxidase, and fermentation pre-metaphase had the greatest effect on cellulase. Since gene regulation mainly occurs before picking, the influence of chemical reaction was greater during processing. It was speculated that polyphenol oxidase and cellulase, which promoted the transformation of quality components, were the key factors in the quality formation of WBT. The above results provide theoretical basis for the processing of WBT and the reference for producing high-quality black tea.

Sugarcane ScCAX4 is a Negative Regulator of Resistance to Pathogen Infection.

Calcium (Ca2+) is a second messenger in various physiological processes within plants. The significance of the Ca2+/H+ exchanger (CAX) has been established in facilitating Ca2+ transport in plants; however, disease resistance functions of the CAX gene remain elusive. In this study, we conducted sequence characterization and expression analysis for a sugarcane CAX gene, ScCAX4 (GenBank Accession Number: MW206380). In order to further investigate the disease resistance functions, this gene was then transiently overexpressed in Nicotiana benthamiana leaves, which were subsequently inoculated with Fusarium solani var. coeruleum. Results showed that ScCAX4 overexpression increased the susceptibility of N. benthamiana to pathogen infection by regulating the expression of genes related to salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) pathways, suggesting its negative role in disease resistance. Furthermore, we genetically transformed the ScCAX4 gene into N. benthamiana and obtained three positive T2 generation lines. Interestingly, the symptomatology of transgenic plants was consistent with that of transient overexpression after pathogen inoculation. Notably, the JA content in transgenic overexpression lines was significantly higher than that in the wild-type. RNA-seq revealed that ScCAX4 could mediate multiple signaling pathways, and the JA signaling pathway played a key role in modulating disease resistance. Finally, a regulatory model was depicted for the increased susceptibility to pathogen infection conferred by the ScCAX4 gene. This study provides genetic resources for sugarcane molecular breeding and the research direction for plant CAX genes.

Transcriptional Regulation of SugarCane Response to Sporisorium scitamineum: Insights from Time-Course Gene Coexpression and Ca2+ Signaling.

Sugarcane response to Sporisorium scitamineum is determined by multiple major genes and numerous microeffector genes. Here, time-ordered gene coexpression networks were applied to explore the interaction between sugarcane and S. scitamineum. Totally, 2459 differentially expressed genes were identified and divided into 10 levels, and several stress-related subnetworks were established. Interestingly, the Ca2+ signaling pathway was activated to establish the response to sugarcane smut disease. Accordingly, two CAX genes (ScCAX2 and ScCAX3) were cloned and characterized from sugarcane. They were significantly upregulated under ABA stress but inhibited by MeJA treatment. Furthermore, overexpression of ScCAX2 and ScCAX3 enhanced the susceptibility of transgenic plants to the pathogen infection, suggesting its negative role in disease resistance. A regulatory model for ScCAX genes in disease response was thus depicted. This work helps to clarify the transcriptional regulation of sugarcane response to S. scitamineum stress and the function of the CAX gene in disease response.

Sugarcane breeding: a fantastic past and promising future driven by technology and methods.

Sugarcane is the most important sugar and energy crop in the world. During sugarcane breeding, technology is the requirement and methods are the means. As we know, seed is the cornerstone of the development of the sugarcane industry. Over the past century, with the advancement of technology and the expansion of methods, sugarcane breeding has continued to improve, and sugarcane production has realized a leaping growth, providing a large amount of essential sugar and clean energy for the long-term mankind development, especially in the face of the future threats of world population explosion, reduction of available arable land, and various biotic and abiotic stresses. Moreover, due to narrow genetic foundation, serious varietal degradation, lack of breakthrough varieties, as well as long breeding cycle and low probability of gene polymerization, it is particularly important to realize the leapfrog development of sugarcane breeding by seizing the opportunity for the emerging Breeding 4.0, and making full use of modern biotechnology including but not limited to whole genome selection, transgene, gene editing, and synthetic biology, combined with information technology such as remote sensing and deep learning. In view of this, we focus on sugarcane breeding from the perspective of technology and methods, reviewing the main history, pointing out the current status and challenges, and providing a reasonable outlook on the prospects of smart breeding.

Molecular identification and functional characterization of a transcription factor GeRAV1 from Gelsemium elegans.

BACKGROUND: Gelsemium elegans is a traditional Chinese medicinal plant and temperature is one of the key factors affecting its growth. RAV (related to ABI3/VP1) transcription factor plays multiple roles in higher plants, including the regulation of plant growth, development, and stress response. However, RAV transcription factor in G. elegans has not been reported. RESULTS: In this study, three novel GeRAV genes (GeRAV1-GeRAV3) were identified from the transcriptome of G. elegans under low temperature stress. Phylogenetic analysis showed that GeRAV1-GeRAV3 proteins were clustered into groups II, IV, and V, respectively. RNA-sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) analyses indicated that the expression of GeRAV1 and GeRAV2 was increased in response to cold stress. Furthermore, the GeRAV1 gene was successfully cloned from G. elegans leaf. It encoded a hydrophilic, unstable, and non-secretory protein that contained both AP2 and B3 domains. The amino acid sequence of GeRAV1 protein shared a high similarity of 81.97% with Camptotheca acuminata CaRAV. Subcellular localization and transcriptional self-activation experiments demonstrated that GeRAV1 was a nucleoprotein without self-activating activity. The GeRAV1 gene was constitutively expressed in the leaves, stems, and roots of the G. elegans, with the highest expression levels in roots. In addition, the expression of the GeRAV1 gene was rapidly up-regulated under abscisic acid (ABA), salicylic acid (SA), and methyl jasmonate (MeJA) stresses, suggesting that it may be involved in hormonal signaling pathways. Moreover, GeRAV1 conferred improved cold and sodium chloride tolerance in Escherichia coli Rosetta cells. CONCLUSIONS: These findings provided a foundation for further understanding on the function and regulatory mechanism of the GeRAV1 gene in response to low-temperature stress in G. elegans.

Complete mitogenome assembly of Selenicereus monacanthus revealed its molecular features, genome evolution, and phylogenetic implications.

BACKGROUND: Mitochondria are the powerhouse of the cell and are critical for plant growth and development. Pitaya (Selenicereus or Hylocereus) is the most important economic crop in the family Cactaceae and is grown worldwide, however its mitogenome is unreported. RESULTS: This study assembled the complete mitogenome of the red skin and flesh of pitaya (Selenicereus monacanthus). It is a full-length, 2,290,019 bp circular molecule encoding 59 unique genes that only occupy 2.17% of the entire length. In addition, 4,459 pairs of dispersed repeats (≥ 50 bp) were identified, accounting for 84.78% of the total length, and three repeats (394,588, 124,827, and 13,437 bp) mediating genomic recombination were identified by long read mapping and Sanger sequencing. RNA editing events were identified in all 32 protein-coding genes (PCGs), among which four sites (nad1-2, nad4L-2, atp9-copy3-223, and ccmFC-1309) were associated with the initiation or termination of PCGs. Seventy-eight homologous fragments of the chloroplast genome were identified in the mitogenome, the longest having 4,523 bp. In addition, evolutionary analyses suggest that S. monacanthus may have undergone multiple genomic reorganization events during evolution, with the loss of at least nine PCGs (rpl2, rpl10, rps2, rps3, rps10, rps11, rps14, rps19, and sdh3). CONCLUSIONS: This study revealed the genetic basis of the S. monacanthus mitogenome, and provided a scientific basis for further research on phenotypic traits and germplasm resource development.

Deep learning-empowered crop breeding: intelligent, efficient and promising.

Crop breeding is one of the main approaches to increase crop yield and improve crop quality. However, the breeding process faces challenges such as complex data, difficulties in data acquisition, and low prediction accuracy, resulting in low breeding efficiency and long cycle. Deep learning-based crop breeding is a strategy that applies deep learning techniques to improve and optimize the breeding process, leading to accelerated crop improvement, enhanced breeding efficiency, and the development of higher-yielding, more adaptive, and disease-resistant varieties for agricultural production. This perspective briefly discusses the mechanisms, key applications, and impact of deep learning in crop breeding. We also highlight the current challenges associated with this topic and provide insights into its future application prospects.

Assembly and analysis of the first complete mitochondrial genome of Punica granatum and the gene transfer from chloroplast genome.

Pomegranate (Punica granatum L.) is one of the oldest fruits with edible, medicinal and ornamental values. However, there is no report on the mitochondrial genome of pomegranate. In this study, the mitochondrial genome of P. granatum was sequenced, assembled and analyzed in detail, while the chloroplast genome was assembled using the same set of data. The results showed that the P. granatum mitogenome had a multi branched structure, using BGI + Nanopore mixed assembly strategy. The total genome length was 404,807 bp, with the GC content of 46.09%, and there were 37 protein coding genes, 20 tRNA genes and three rRNA genes. In the whole genome, 146 SSRs were identified. Besides, 400 pairs of dispersed repeats were detected, including 179 palindromic, 220 forward and one reverse. In the P. granatum mitochondrial genome, 14 homologous fragments of chloroplast genome were found, accounting for 0.54% of the total length. Phylogenetic analysis showed that among the published mitochondrial genomes of related genera, P. granatum had the closest genetic relationship with Lagerstroemia indica of Lythraceae. The 580 and 432 RNA editing sites were predicted on 37 protein coding genes of mitochondrial genome using BEDTools software and online website PREPACT respectively, but all were from C to U, of which ccmB and nad4 gene were most frequently edited, with 47 sites. This study provides a theoretical basis for understanding the evolution of higher plants, species classification and identification, and will also be useful for further utilization of pomegranate germplasm resources.

Deciphering the Atlas of Post-Translational Modification in Sugarcane.

In plants, lysine acetylation (Kac), 2-hydroxyisobutyrylation (Khib), and lysine lactylation (Kla), the three new types of post-translational modification (PTM), play very important roles in growth, development, and resistance to adverse environmental stresses. Herein, we report the first global acetylome, 2-hydroxyisobutyrylome, and lactylome in sugarcane. A total of 8573 Kac, 4637 Khib, and 215 Kla sites across 3903, 1507, and 139 modified proteins were identified. Besides, homology analyses revealed the Kac, Khib, and Kla sites on histones were conserved between sugarcane and rice or poplar. Functional annotations demonstrated that the Kac, Khib, and Kla proteins were mainly involved in energy metabolism. In addition, a number of modified transcription factors and stress-related proteins, which were constitutively expressed in different tissues of sugarcane and induced by drought, cold or Sporisorium scitamineum stress, were identified. Finally, a proposed working mode on how PTM functions in sugarcane was depicted. We thus concluded that PTM should play a role in sugarcane growth, development, and response to biotic and abiotic stresses, but the mechanisms require further investigation. The present study provided the all-new comprehensive profile of proteins Kac, Khib, and Kla and a new perspective to understand the molecular mechanisms of protein PTMs in sugarcane.

Grapevine double cropping: a magic technology.

Grapevine is one of the most important fruit trees in the world, but it is often threatened by various biotic and abiotic stresses in production, resulting in decreased yield and quality. Grapevine double cropping in one year is a kind of preparatory and artificial control technology, which can not only save the loss of natural disasters, but also plays an important role in staggering the peak to market, thus increasing yield and improving the quality of grape fruit. This perspective provides a concise discussion of the physiological basis, the main determinants, and their impacts on yield and fruit quality of grapevine double cropping. We also highlight the current challenges around this theme and prospect its application in the future.

Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors.

Sugarcane, a C4 plant, provides most of the world's sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the potential to be grown in arid and semi-arid regions if its stress tolerance can be improved. Modern sugarcane cultivars which exhibit a greater extent of polyploidy and agronomically important traits, such as high sugar concentration, biomass production, and stress tolerance, are regulated by complex mechanisms. Molecular techniques have revolutionized our understanding of the interactions between genes, proteins, and metabolites, and have aided in the identification of the key regulators of diverse traits. This review discusses various molecular techniques for dissecting the mechanisms underlying the sugarcane response to biotic and abiotic stresses. The comprehensive characterization of sugarcane's response to various stresses will provide targets and resources for sugarcane crop improvement.

Dissecting the features of TGA gene family in Saccharum and the functions of ScTGA1 under biotic stresses.

Sugarcane is an important sugar and energy crop and smut disease caused by Sporisorium scitamineum is a major fungal disease which can seriously reduce the yield and quality of sugarcane. In plants, TGACG motif binding (TGA) transcription factors are involved in the regulation of salicylic acid (SA) and methyl jasmonate (MeJA) signaling pathways, as well as in response to various biotic and abiotic stresses. However, no TGA-related transcription factor has been reported in Saccharum. In the present study, 44 SsTGA genes were identified from Saccharum spontaneum, and were assorted into three clades (I, II, III). Cis-regulatory elements (CREs) analysis revealed that SsTGA genes may be involved in hormone and stress response. RNA-seq data and RT-qPCR analysis indicated that SsTGAs were constitutively expressed in different tissues and induced by S. scitamineum stress. In addition, a ScTGA1 gene (GenBank accession number ON416997) was cloned from the sugarcane cultivar ROC22, which was homologous to SsTGA1e in S. spontaneum and encoded a nucleus protein. It was constitutively expressed in sugarcane tissues and up-regulated by SA, MeJA and S. scitamineum stresses. Furthermore, transient overexpression of ScTGA1 in Nicotiana benthamiana could enhance its resistance to the infection of Ralstonia solanacearum and Fusarium solani var. coeruleum, by regulating the expression of immune genes related to hypersensitive response (HR), ethylene (ET), SA and jasmonic acid (JA) pathways. This study should contribute to our understanding on the evolution and function of the SsTGA gene family in Saccharum, and provide a basis for the functional identification of ScTGA1 under biotic stresses.

Identification and Expression Analysis of Hexokinases Family in Saccharum spontaneum L. under Drought and Cold Stresses.

In plants, the multi-gene family of dual-function hexokinases (HXKs) plays an important role in sugar metabolism and sensing, that affects growth and stress adaptation. Sugarcane is an important sucrose crop and biofuel crop. However, little is known about the HXK gene family in sugarcane. A comprehensive survey of sugarcane HXKs, including physicochemical properties, chromosomal distribution, conserved motifs, and gene structure was conducted, identifying 20 members of the SsHXK gene family that were located on seven of the 32 Saccharum spontaneum L. chromosomes. Phylogenetic analysis showed that the SsHXK family could be divided into three subfamilies (group I, II and III). Motifs and gene structure were related to the classification of SsHXKs. Most SsHXKs contained 8-11 introns which was consistent with other monocots. Duplication event analysis indicated that HXKs in S. spontaneum L. primarily originated from segmental duplication. We also identified putative cis-elements in the SsHXK promoter regions which were involved in phytohormone, light and abiotic stress responses (drought, cold et al.). During normal growth and development, 17 SsHXKs were constitutively expressed in all ten tissues. Among them, SsHXK2, SsHXK12 and SsHXK14 had similar expression patterns and were more highly expressed than other genes at all times. The RNA-seq analysis showed that 14/20 SsHXKs had the highest expression level after cold stress for 6 h, especially SsHXK15, SsHXK16 and SsHXK18. As for drought treatment, 7/20 SsHXKs had the highest expression level after drought stress for 10 days, 3/20 (SsHKX1, SsHKX10 and SsHKX11) had the highest expression level after 10 days of recovery. Overall, our results revealed the potential biological function of SsHXKs, which may provide information for in-depth functional verification.

Identification of QTLs and critical genes related to sugarcane mosaic disease resistance.

Mosaic viral diseases affect sugarcane productivity worldwide. Mining disease resistance-associated molecular markers or genes is a key component of disease resistance breeding programs. In the present study, 285 F1 progeny were produced from a cross between Yuetang 93-159, a moderately resistant variety, and ROC22, a highly susceptible variety. The mosaic disease symptoms of these progenies, with ROC22 as the control, were surveyed by natural infection under 11 different environmental conditions in the field and by artificial infections with a mixed sugarcane mosaic virus (SCMV) and sorghum mosaic virus (SrMV) inoculum. Analysis of consolidated survey data enabled the identification of 29 immune, 55 highly resistant, 70 moderately resistant, 62 susceptible, and 40 highly susceptible progenies. The disease response data and a high-quality SNP genetic map were used in quantitative trait locus (QTL) mapping. The results showed that the correlation coefficients (0.26~0.91) between mosaic disease resistance and test environments were significant (p< 0.001), and that mosaic disease resistance was a highly heritable quantitative trait (H2 = 0.85). Seven mosaic resistance QTLs were located to the SNP genetic map, each QTL accounted for 3.57% ~ 17.10% of the phenotypic variation explained (PVE). Furthermore, 110 pathogen response genes and 69 transcription factors were identified in the QTLs interval. The expression levels of nine genes (Soffic.07G0015370-1P, Soffic.09G0015410-2T, Soffic.09G0016460-1T, Soffic.09G0016460-1P, Soffic.09G0017080-3C, Soffic.09G0018730-3P, Soffic.09G0018730-3C, Soffic.09G0019920-3C and Soffic.03G0019710-2C) were significantly different between resistant and susceptible progenies, indicating their key roles in sugarcane resistance to SCMV and SrMV infection. The seven QTLs and nine genes can provide a certain scientific reference to help sugarcane breeders develop varieties resistant to mosaic diseases.