Abstract Background Saccharum spontaneumL. is a closely related species of sugarcane and has become an important genetic component of modern sugarcane cultivars. Stem development is one of the important factors for affecting the yield, while the molecular mechanism of stem development remains poorly understanding in S. spontaneum. Phenylalanine ammonia-lyase (PAL) is a vital component of both primary and secondary metabolism, contributing significantly to plant growth, development and stress defense. However, the current knowledge about PAL genes in S. spontaneum is still limited. Thus, identification and characterization of the PAL genes by transcriptome analysis will provide a theoretical basis for further investigation of the function of PAL gene in sugarcane. Results In this study, 42 of PAL genes were identified, including 26 SsPAL genes from S. spontaneum, 8 ShPAL genes from sugarcane cultivar R570, and 8 SbPAL genes from sorghum. Phylogenetic analysis showed that SsPAL genes were divided into three groups, potentially influenced by long-term natural selection. Notably, 20 SsPAL genes were existed on chromosomes 4 and 5, indicating that they are highly conserved in S. spontaneum. This conservation is likely a result of the prevalence of whole-genome replications within this gene family. The upstream sequence of PAL genes were found to contain conserved cis-acting elements such as G-box and SP1, GT1-motif and CAT-box, which collectively regulate the growth and development of S. spontaneum. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that SsPAL genes of stem had a significantly upregulated than that of leaves, suggesting that they may promote the stem growth and development, particularly in the + 6 stem (The sixth cane stalk from the top to down) during the growth stage. Conclusions The results of this study revealed the molecular characteristics of SsPAL genes and indicated that they may play a vital role in stem growth and development of S. spontaneum. Altogether, our findings will promote the understanding of the molecular mechanism of S. spontaneum stem development, and also contribute to the sugarcane genetic improving.

Plant flowering is a crucial phenomenon affecting crop yield and crossbreeding. Saccharum spontaneum is the closest wild relative sugarcane species widely used in sugarcane genetic improvement. However, the molecular interactions among the components of the flowering regulatory network of S. spontaneum are still unclear. In this study, we conducted a transcriptome sequencing approach to analyze the expressed genes on four developmental stages of panicle samples in S. spontaneum. The weighted gene co-expression network analysis (WGCNA) results suggested that genes from the MEred (p = 3 x 10(-4)) module were significantly enriched in pathways of ABC transporters, photosynthesis, and circadian rhythm-plant. Thus, 23 genes associated with flower development-related genes were screened, including 7 AGL24, 1 FLC, 3 VIN3, 3 GA20ox, and 9 ELF3. In the gibberellic acid (GA) synthesis pathway, GA20ox, GA3ox, and GA2ox were the three enzymes that catalyzed later reactions of GA biosynthesis and belong to the 2-oxoglutarate Fe (II) oxygenase (2OG) superfamily. Flavonoid synthesis was promoted by 2-oxoglutarate Fe (II) oxygenase genes, a flowering hormone, which catalyzed and oxidized naringenin to dihydrokaempferol, an important precursor of florigen. Genome-wide analysis revealed that 122 Ss2OG genes were identified in S. spontaneum, of which 99 genes were enriched in the panicle transcriptome. Furthermore, a quantitative reverse transcription polymerase chain reaction analysis showed that Ss2OG-FeII_Oxy90, Ss2OG-FeII_Oxy47, and Ss2OG-FeII_Oxy89 could introduce the flower development, while Ss2OG-FeII_Oxy34, Ss2OG-FeII_Oxy37, and Ss2OG-FeII_Oxy50 inhibited it. These findings provide new clues and resources for exploring the molecular mechanism of flowering regulation in S. spontaneum and promoting sugarcane breeding.

Leaf scald, caused by Xanthomonas albilineans, is a severe disease affecting sugarcane worldwide. One of the most practical ways to control it is by developing resistant sugarcane cultivars. It is essential to identify genes associated with the response to leaf scald. A panel of 170 sugarcane genotypes was evaluated for resistance to leaf scald in field conditions for 2 years, followed by a 1-year greenhouse experiment. The phenotypic evaluation data showed a wide continuous distribution, with heritability values ranging from 0.58 to 0.84. Thirteen single nucleotide polymorphisms (SNPs) were identified, significantly associated with leaf scald resistance. Among these, eight were stable across multiple environments and association models. The candidate genes identified and validated based on RNA-seq and qRT-PCR included two genes that encode NB-ARC leucine-rich repeat (LRR)-containing domain disease-resistance protein. These findings provide a basis for developing marker-assisted selection strategies in sugarcane breeding programs.

甘蔗(Saccharum officinarum)是重要的糖料和生物能源作物,其产量受到各种生物胁迫和非生物胁迫的影响.割手密(S.spontaneum)是甘蔗栽培育种过程中的重要亲本之一.GRAS(GAI-RGA-SCR)转录因子在植物光形态建成、种子萌发、根系生长及防御应答等过程中起重要调控作用.本研究利用GRAS结构域的隐马尔科夫模型(Hidden Markov Model,HMM)配置文件,从割手密基因组中鉴定出173个GRAS基因家族成员,分布于割手密30条染色体.利用最大似然法进行系统发育分析,结果显示,173个割手密GRAS家族基因可分为8个亚家族;基因结构分析显示,GRAS家族基因在C端含有至少1个保守的GRAS结构域,61.2%的GRAS家族基因存在至少1个内含子;GRAS家族基因上游2000 bp序列启动子顺式作用元件分析显示,所有GRAS启动子区域存在应答生物和非生物胁迫的顺式作用元件,表明其可能涉及多种逆境胁迫的调控过程.转录组数据分析显示,割手密GRAS家族成员在茎和叶的不同发育时期存在较大的表达差异,qRT-PCR验证9个基因在成熟茎叶组织的表达,其结果与转录组数据一致,推测GRAS家族成员在割手密生长发育调控中发挥不同作用;胁迫分析表明,SsPAT1.8-1和SsDELLA6-2受甘蔗梢腐病病原菌胁迫诱导表达;SsPAT1.8-2、SsPAT1.9、SsPAT1.10、SsDELLA2、SsSCR2、SsDELLA1-2、SsSCL3.1-2和SsHAM9受甘蔗花叶病毒(Sugarcane mosaic virus,ScMV)胁迫诱导表达;SsSCL3.2-1受干旱胁迫诱导表达.以ScMV侵染抗病品种'B48',qRT-PCR检测结果显示,SsSCR2在+1叶中上调表达,SsHAM9在+1和-3叶中均上调表达,SsLISCL11-1在-3叶中下调表达.上述结果提示,GRAS家族基因可能在甘蔗对不同胁迫的响应中发挥调节功能.本研究为进一步解析甘蔗GRAS家族基因的功能提供基础资料,为甘蔗抗逆育种提供潜在的基因资源.

分子指纹图谱直接反映生物个体在DNA水平上的差异,可有效鉴别植物品种,保护品种权.甘蔗是无性繁殖作物,在生产上更容易造成品种混杂.本文概述了指纹图谱的分类、概念和作用,近年来国内外常见的DNA分子指纹图谱方法(RFLP、RAPD、AFLP、SSR、ISSR、SNP)在甘蔗中的研究进展,以及指纹图谱在甘蔗品种鉴别与育种研究中的应用,探讨了我国甘蔗分子指纹图谱研究中存在的问题,并由此指出构建甘蔗标准指纹图谱库和分子身份证的必要性与迫切性.

Sugarcane is a major crop for sugar production around the world. The complexity of the sugarcane genome creates challenges for the use of both conventional and molecular breeding methods to improve sugarcane at a genetic level. DNA sequencing is an important tool to assess how the genus Saccharum and the genera of the Saccharum complex are interrelated. Here, we identify the kinship of Nepal2013-6 (Saccharum spontaneum, x = 10) using a tetra-primer amplification refractory mutation system (ARMS) PCR. Based on rDNA-ITS sequence analysis, the accession Nepal2013-6 falls within a single cluster with S. spontaneum (Yunnan82-114 and SES208), which is consistent with the previous results. Moreover, fluorescence in situ hybridization (FISH) results indicate that the 5S rDNA spots are consistent with the chromosomal ploidy in the analytical Saccharum materials, whereas 35S rDNA has similar or fewer sites than the ploidy. Therefore, 5S rDNA FISH patterns would be more suitable than 35S rDNA for chromosomal ploidy analysis in S. spontaneum with varied basic chromosome number x = 8, 9, 10. Altogether, these results indicate that the rDNA sequences will be a useful marker for further rapidly identifying the relationship and ploidy of S. spontaneum in sugarcane breeding.

Drought is the main abiotic stress that constrains sugarcane growth and production. To understand the molecular mechanisms that govern drought stress, we performed a comprehensive comparative analysis of physiological changes and transcriptome dynamics related to drought stress of highly drought-resistant (ROC22, cultivated genotype) and weakly drought-resistant (Badila, wild genotype) sugarcane, in a time-course experiment (0 h, 4 h, 8 h, 16 h and 32 h). Physiological examination reviewed that ROC22, which shows superior drought tolerance relative to Badila, has high performance photosynthesis and better anti-oxidation defenses under drought conditions. The time series dataset enabled the identification of important hubs and connections of gene expression networks. We identified 36,956 differentially expressed genes (DEGs) in response to drought stress. Of these, 15,871 DEGs were shared by the two genotypes, and 16,662 and 4423 DEGs were unique to ROC22 and Badila, respectively. Abscisic acid (ABA)-activated signaling pathway, response to water deprivation, response to salt stress and photosynthesis-related processes showed significant enrichment in the two genotypes under drought stress. At 4 h of drought stress, ROC22 had earlier stress signal transduction and specific up-regulation of the processes response to ABA, L-proline biosynthesis and MAPK signaling pathway–plant than Badila. WGCNA analysis used to compile a gene regulatory network for ROC22 and Badila leaves exposed to drought stress revealed important candidate genes, including several classical transcription factors: NAC87, JAMYB, bHLH84, NAC21/22, HOX24 and MYB102, which are related to some antioxidants and trehalose, and other genes. These results provide new insights and resources for future research and cultivation of drought-tolerant sugarcane varieties.

A genetic diversity analysis and identification of plant germplasms and varieties are important and necessary for plant breeding. Deoxyribonucleotide (DNA) fingerprints based on genomic molecular markers play an important role in accurate germplasm identification. In this study, Specific-Locus Amplified Fragment Sequencing (SLAF-seq) was conducted for a sugarcane population with 103 cultivated and wild accessions. In total, 105,325 genomic single nucleotide polymorphisms (SNPs) were called successfully to analyze population components and genetic diversity. The genetic diversity of the population was complex and clustered into two major subpopulations. A principal component analysis (PCA) showed that these accessions could not be completely classified based on geographical origin. After filtration, screening, and comparison, 192 uniformly-distributed SNP loci were selected for the 32 chromosomes of sugarcane. An SNP complex genotyping detection system was established using the SNaPshot typing method and used for the precise genotyping and identification of 180 sugarcane germplasm samples. According to the stability and polymorphism of the SNPs, 32 high-quality SNP markers were obtained and successfully used to construct the first SNP fingerprinting and quick response codes (QR codes) for sugarcane. The results provide new insights for genotyping, classifying, and identifying germplasm and resources for sugarcane breeding.

[目的]通过对不同甘蔗群体进行遗传多样性和选择性清除分析,了解甘蔗基因组中受人工选择的区域及优良基因,以期为甘蔗分子育种提供参考.[方法]对83份甘蔗栽培种和24份细茎野生种共107份材料进行简化基因组测序,以甘蔗割手密基因组为参考,获得基因组SNP基因型数据,分析群体遗传多样性、不同群组的分化系数(Fst),并以此为基础进行选择信号扫描分析.[结果](1)栽培种与细茎野生种群体之间的Fst=0.216,栽培种群体的核苷酸多样性(π=8.93×10-6)高于细茎野生种群体(π=6.11×10-6).(2)选择性清除分析得到72个基因组区域,对前5％的基因组区域进一步分析,共检测到439个基因.对候选基因进行基因功能注释,发现受选择基因主要富集在泛素蛋白转移酶活性过程、核苷酸结合过程和热反应过程等,包括抗病蛋白RGA2、谷胱甘肽S-转移酶、钾转运蛋白等抗性基因.[结论]107份甘蔗材料可分为两个亚群,且抗性基因在甘蔗育种过程中得到了强烈的选择.

甘蔗是我国重要的糖料作物.宿根蔗在甘蔗种植中占据极其重要的地位,选育宿根性强的品种是提高宿根蔗产量和品质的重要途径.本文综述了甘蔗的宿根性评价指标为:宿根能力与产量性状及效益相结合,综述了影响甘蔗宿根性内在因素主要有品种(基因型)和亲本(血缘),外在因素主要有土壤条件、肥水情况、收获时间、栽培措施和机械化收割等.介绍了适宜机械化生产的强宿根品种的选育情况,并对未来甘蔗宿根性的研究提出了:加强野生种质资源的开发利用、在逆境和机械收获条件下评价选育强宿根品种、加强全基因组选择评价及发株相关基因的研究挖掘等新技术新方法的应用研究.

Additional file 1 List of the 218 SsAP2/ERF genes identified in this study.

Additional file 15. Sequences of the primers used in this study.

Additional file 9. One-to-one orthologous relationships between sugarcane and other five plant species.

Abstract Background: APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play important roles in plant growth, development, metabolism, as well as in biotic and abiotic stress responses. However, there are few studies concerning AP2/ERF genes in sugarcane, which is the most critical sugar and energy crop worldwide. Results: A total of 218 AP2/ERF genes were identified in the Saccharum spontaneum genome. Phylogenetic analysis showed that these genes could be divided into four groups, including 43 AP2s, 160 ERFs, and Dehydration-responsive element-binding (DREB) factors, 11 ABI3/VPs (RAV) and 4 Soloist genes. These genes were unevenly distributed on 32 chromosomes. Analysis of the structural of SsAP2/ERF genes showed that 91 SsAP2/ERFs lacked introns. Sugarcane and sorghum have a collinear relationship between 168 SsAP2/ERF genes and sorghum AP2/ERF genes that reflects their similarity. Multiple cis-regulatory elements (CREs) are present in the SsAP2/ERF promoter, and many are related to abiotic stresses, suggesting that SsAP2/ERF activity could contribute to the adaptation of sugarcane crops to environmental changes. The tissue-specific analysis showed spatiotemporal expression of SsAP2/ERF in the stems and leaves of sugarcane at different stages of development. In 10 sugarcane samples, 39 SsAP2/ERFs were not expressed at all, whereas 58 SsAP2/ERFs were expressed in all samples. Quantitative PCR experiments showed that SsERF52 expression was up-regulated under salt stress, but suppressed under drought stress. SsSoloist4 had the most considerable upregulation in response to treatment with the exogenous hormones ABA and GA. Within 3 hours of ABA or PEG6000 treatment, SsSoloist4 expression was up-regulated, indicating that this gene could play a role in ABA and GA-associated drought stress response mechanisms. Analysis of AP2/ERF gene expression patterns under different treatments indicated that SsAP2/ERF genes play an important role in drought and salt stress responses of S. spontaneum. Conclusions: In this study, a total of 218 members of the AP2 / ERF superfamily were identified in sugarcane, and their genetic structure, evolution characteristics, and expression patterns were studied and analyzed. The results of this study provide a foundation for future analyses to elucidate the importance of AP2/ERF transcription factors in the function and molecular breeding of sugarcane.

BackgroundAPETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play essential roles in plant growth, development, metabolism, and responses to biotic and abiotic stresses. However, few studies concerning AP2/ERF genes in sugarcane which are the most critical sugar and energy crops worldwide.ResultsA total of 218 AP2/ERF genes were identified in the Saccharum spontaneum genome. Phylogenetic analysis showed that these genes could be divided into four groups, including 43 AP2s, 160 ERFs and Dehydration-responsive element-binding (DREB) factors, 11 ABI3/VPs (RAV), and four Soloist genes. These genes were unevenly distributed on 32 chromosomes. The structural analysis of SsAP2/ERF genes showed that 91 SsAP2/ERFs lacked introns. Sugarcane and sorghum had a collinear relationship between 168 SsAP2/ERF genes and sorghum AP2/ERF genes that reflected their similarity. Multiple cis-regulatory elements (CREs) present in the SsAP2/ERF promoter were related to abiotic stresses, suggesting that SsAP2/ERF activity could contribute to sugarcane adaptation to environmental changes. The tissue-specific analysis showed spatiotemporal expression of SsAP2/ERF in the stems and leaves of sugarcane at different development stages. In ten sugarcane samples, 39 SsAP2/ERFs were not expressed, whereas 58 SsAP2/ERFs were expressed in all samples. Quantitative PCR experiments showed that SsERF52 expression was up-regulated under salt stress, but suppressed under dehydration stress. SsSoloist4 had the most considerable upregulation in response to treatment with the exogenous hormones ABA and GA. Within 3h of ABA or PEG6000 treatment, SsSoloist4 expression was up-regulated, indicating that this gene could play a role in the responses to ABA and GA-associated dehydration stress. Analysis of AP2/ERF gene expression patterns under different treatments indicated that SsAP2/ERF genes played an essential role in dehydration and salt stress responses of S. spontaneum.ConclusionsIn this study, a total of 218 members of the AP2 / ERF superfamily were identified in sugarcane, and their genetic structure, evolution characteristics, and expression patterns were studied and analyzed. The results of this study provide a foundation for future analyses to elucidate the importance of AP2/ERF transcription factors in the function and molecular breeding of sugarcane.