Tropical Plant Biology

Wang, Jiang; Li, Yaxin; Zhu, Fan; Ming, Ray; Chen, Li-Qing

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09220-8

Nitrate is the predominant nitrogen source for plant growth and development. However, sugarcane, globally used as the primary sugar crop and biofuel feedstock, displays a low nitrate use efficiency due to a low capacity in storing nitrate in shoots. It is well studied that the nitrate transporter (NRT/NPF) family functions as the gatekeeper in governing nitrogen uptake and distribution, and optimizing nitrogen utilization in plants. This makes it a promising target for improving nitrogen use efficiency in sugarcane. Here, we carried out a comprehensive analysis of NRT/NPF genes at a genome-wide scale in Saccharum spontaneum. A BLAST search of NRT/NPF genes was initially performed against recently released sugarcane genome, followed by phylogenetic, gene structure and protein motif analysis. Additionally, NRT/NPF gene expression profile from various tissues was obtained from RNA-seq data analysis. As a result, we identified 178 NPF, 20 NRT2, and 6 NRT3 genes which spread across all 8 monoploid chromosomes. NPF and NRT3 exhibit high levels of genetic diversities as opposed to NRT2 which is more evolutionarily conserved. Interestingly, several SsNPF genes are products of gene fusions of several tandem duplications, which provide valuable structural resources for functional characterization of nitrate transporters. Moreover, several genes are tissue-specific expressed, indicating roles in tissue-specific nitrate translocations. A substantial number of NRT/NPF genes are heterogeneous in terms of their gene structures and mRNA abundance. Taken together, our work provides a genetic foundation for future investigations of molecular and physiological functions of sugarcane nitrate transporters.

Nelson, David

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09226-2

The Cytochrome P450 gene family is one of the largest in plants. Cytochrome P450 sequences have been annotated in the Saccharum spontaneum genome and they make up 1.3% of the known alleles. 394 genes have been identified in this family after mining two releases of the S. spontaneum AP85–441 genome. The P450 sequences are most similar to those of sorghum. The 45 CYP families in sugarcane have been compared to sorghum P450s. CYP51 was the most similar sequence at 98.6%. Average percent identity to the best plant blast match was 86%. Three of the 45 CYP families show modest gene expansion. CYP71 has 15 more genes CYP76 has 12 more genes and CYP81 has 6 more genes than sorghum. The other families are identical or within 4 genes, showing a strong similarity between P450s in the two species. Alleles have been assigned for this tetraploid genome. Only 32% of the genes still have four alleles.

Ma, Panpan; Yuan, Yuan; Shen, Qiaochu; Jiang, Qing; Hua, Xiuting; Zhang, Qing; Zhang, Muqing; Ming, Ray; Zhang, Jisen

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09225-3

Starch is one of two crucial products of photosynthetic carbon-assimilation and mainly functions as the unit of energy storage in most crops such as rice, maize and sorghum, whereas interestingly in sugarcane that unit of energy storage is sucrose. Mature sugarcane stalk tissue has a very large apoplastic volume and contains nearly 700 mM sucrose—which is among the highest recorded sucrose concentrations in plant tissue. We identified 9 genes of starch synthases (SSs) related to the starch synthesis pathway in the genome of S. spontaneum. Based on gene structure and phylogenetic analysis, SSs genes were clustered into five clades and were relatively conserved. In S. spontaneum, the SS is a very ancient gene family, in which, SSIIIa and SSIIIb originated from the ρ-whole genome duplications (WGDs), SSIIb and SsIIc originated from gene duplication after the split of monocots and dicots; GBSSI and GBSSII in Clade V and SSIIa in Clade II were retained from the ε-WGD, and the remaining two SSs (SSI and SSIV) were retained from the very ancient gene duplication event about 355–389 million year ago (Mya). In addition, we found all SS genes were under the influence of strong purification with a Ka/Ks ratio of less than 0.5 in S. spontaneum. In the 5 families, SSIIIa, SSIIb and GBSSII had relatively predominant expression levels in all the examined tissues from the two Saccharum species, indicating the three genes were the fundamental members in the non-storage tissues, leaf or stem, which is in agreement with previous studies. Interestingly, the expression levels of SSs in stems showed significantly higher values in S. spontenum than in S. officinarum at pre-mature and mature stages. These results were negatively correlated with the sucrose levels between the two Saccharum species. At the pre-mature and mature stages, the sucrose contents in stems from S. officinarum were much higher than in stems from S. spontenum, suggesting that SSs involved in the differential of carbohydrate metabolism between the two Saccharum species. Besides, the expression of SSs displayed a clearly consistent trend in line with normal distribution under the diurnal rhythms of S. spontaneum. Moreover, the expression pattern of SSIIIa, SSIIb and GBSSII displayed a clearly consistent trend in both Saccharum species and in maize, rice, which was in accordance with photosynthetic intensity across leaf gradients. This result suggested the functional constraints for the SSs gene family in Gramineae. Our results are valuable for further functional analysis of SSs genes and provided the foundation for carbohydrate metabolism in sugarcane.

Shi, Yan; Xu, Huimin; Shen, Qiaochu; Lin, Jingxian; Wang, Yongjun; Hua, Xiuting; Yao, Wei; Yu, Qingyi; Ming, Ray; Zhang, Jisen

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09230-6

Sugarcane is a major sugar-producing crop, which contributed 80% of the world’s sugar in 2010. Saccarhum officinarum is a domestic species with high sugar content, while, Saccarhum spontaneum is a wild species with stress tolerance. The highly complex polyploid genome of modern sugarcane cultivars arose from the interspecific hybridization between S. officinarum and S. spontaneum. Sucrose synthase (SUS) is a key enzyme for sucrose metabolism in plants, where activity is bidirectional: both synthetic and separate. In this study, nine genomic sequences of S. officinarum and eight genomic sequences of S. spontaneum for five SUS genes were identified. Phylogenetic analysis showed that the Saccharum SUS3 and SUS5 genes were generated from ρ duplication, SUS1 and SUS2 were duplicated after the split of dicot and monocot species, and SUS4 was retained from the last common ancestor before the origination of Angiospermae. The gene structure and Ka/Ks analysis suggested the functional constraint of SUS genes in the two Saccharum species. Gene expression based on RNA-seq analysis revealed that SUS1was dominantly expressed in source tissues including the internodes and the basal zone of the leaves, SUS2 was detectable in all tissues examined, and the remaining three SUS genes were expressed at low levels in the examined tissues, indicating SUS1 is the key member involved in sucrose accumulation. In addition, SUS genes were observed to be present at higher expression levels in S. officinarum than in S. spontaneum, while SUS2 presented different expression patterns during the circadian rhythm in S. spontaneum and S. officinarum, suggesting the two SUS genes contribute to the differential sugar levels in these species. Our comprehensive study in Saccharum provides the foundations for further functional studies of the SUS gene family.

Marquardt, Annelie; Henry, Robert; Botha, Frederik

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09221-7

Sucrose accumulation and decreased photosynthesis are early symptoms of yellow canopy syndrome (YCS) in sugarcane (Saccharum spp.), and precede the visual yellowing of the leaves. To investigate broad-scale gene expression changes during YCS-onset, transcriptome analyses coupled to metabolome analyses were performed. Across leaf tissues, the greatest number of differentially expressed genes related to the chloroplast, and the metabolic processes relating to nitrogen and carbohydrates. Five genes represented 90% of the TPM (Transcripts Per Million) associated with the downregulation of transcription during YCS-onset, which included PSII D1 (PsbA). This differential expression was consistent with a feedback regulatory effect upon photosynthesis. Broad-scale gene expression analyses did not reveal a cause for leaf sugar accumulation during YCS-onset. Interestingly, the midrib showed the greatest accumulation of sugars, followed by symptomatic lamina. To investigate if phloem loading/reloading may be compromised on a gene expression level – to lead to leaf sucrose accumulation - sucrose transport-related proteins of SWEETs, Sucrose Transporters (SUTs), H+-ATPases and H+-pyrophosphatases (H+-PPases) were characterised from a sugarcane transcriptome and expression analysed. Two clusters of Type I H + -PPases, with one upregulated and the other downregulated, were evident. Although less pronounced, a similar pattern of change was observed for the H + -ATPases. The disaccharide transporting SWEETs were downregulated after visual symptoms were present, and a monosaccharide transporting SWEET upregulated preceding, as well as after, symptom development. SUT gene expression was the least responsive to YCS development. The results are consistent with a reduction of photoassimilate movement through the phloem leading to sucrose build-up in the leaf.

Lin, Jishan; Zhu, Mengting; Cai, Mingxing; Zhang, Wenping; Fatima, Mahpara; Jia, Haifeng; Li, Feifei; Ming, Ray

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09238-y

The TCP family genes have been under selection during domestication in maize and related andropogoneae crops. They encode plant-specific transcription factors involved in growth and development, especially in shaping the plant morphology and architecture. Sugarcane (Saccharum spp.) is the most productive in harvesting tonnage and 5th economically valuable crops worldwide for supporting world’s sugar and fuel ethanol production. Based on recently published sugarcane genome, we performed a genome-wide analysis of this gene family in the sugarcane genome and identified 22 TCP genes (SsTCPs), with 1–4 alleles each. They distributed across 28 chromosomes of S. spontaneum. Phylogenetic analysis showed that all 22 SsTCP genes can be classifed into two major groups: class I and class II. All 22 groups of SsTCPs showed species-specific clustering with TCPs of sorghum which indicate close relationship between sorghum and Saccharum. Structural organization of SsTCP genes showed that 37 SsTCPs are intronless and of the 22 SsTCPs with introns exist in coding region, which are different with TCPs of sorghum and wheat that located in UTR region. Expression study showed that transcripts of class I SsTCPs were more abundant than transcripts of class II SsTCPs. Moreover, the expression of SsTCP5–4, SsTCP6–2, SsTCP8–1, SsTCP12, SsTCP13, SsTCP15–1, SsTCP17–1 and SsTCP17–6 displayed significant change after plant hormones treatments, which suggest their function related to plant hormones. Cis-element analysis of SsTCPs’s promoter suggests that subfunctionalization may have occurred for homoeologous genes. Taken together, our analysis of TCPs in S. spontaneum provide a good starting for further studies to elucidate their specific function in sugarcane.

Zhang, Wenping; Lin, Jishan; Dong, Fei; Ma, Qing; Wu, Songlin; Ma, Xinyi; Fatima, Mahpara; Jia, Haifeng; Ming, Ray

2019 Tropical Plant Biology

doi: 10.1007/s12042-019-09239-x

Laccases play crucial roles in catalyzing lignin and flavonoid biosynthesis in plants, and are predominantly involved in lignin breakdown of bacteria and fungi. Lignin distributes in all parts of plant and is a key component in plant morphogenesis. The complex sugarcane genome limited the study of laccase genes, but our completed reference genome of tetraploid S. spontaneum AP85–441 makes it possible to study this gene family. We identified 29 laccase genes, and 10 genes with 4 alleles, 9 genes with 3 alleles, 5 genes with 2 alleles, 5 genes with 1 allele in sugarcane. Among them 4 genes have tandemly dupicated paralogs; and 12 genes have dispersely distributed paralogs. They distributed unevenly among 27 of 32 chromosomes, and 9 (31.03%) genes located in Chromosome 3. Phylogeny and conserved domain suggested sugarcane laccase genes had the highest similarity with sorghum, and laccase10 was the most conserved gene in monocots and dicotyledons. We found sugarcane laccase genes were regulated by light signal, phytohormones, abiotic stress and some tissue-specific transcription factors by predicted cis-elements in the promoters. Nine laccase genes had miR397 and miR528 target sites, which have been reported as post-transcriptionally regulated laccase genes. Four laccase genes had 4 new miRNA target sites, including stem specific miRNA. Analysis of RNA-seq data of different developmental stages of leaves and stems showed that 27 genes had expression of those tissues, and most of them mainly express in stems. Among them laccase 4 and laccase10 showed the highest expression level in mature stems, while laccase27 showed the highest expression in seedling leaves. Our results show the potential function of sugarcane laccase genes in catalyzing lignin biosynthesis, stress resistance, and morphogenesis. These findings and genomic resources will facilitate research on improving stress tolerance, lignin content, and biomass yield in sugarcane.