Xiuting Hua

Guangxi University

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Jisen Zhang

Fujian Agriculture and Forestry University

Ray Ming

Fujian Agriculture and Forestry University

Qing Zhang

Fujian Normal University

Qingyi Yu

Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center

Yongjun Wang

Fujian Agriculture and Forestry University

Xingtan Zhang

Agricultural Genomics Institute at Shenzhen

Muqing Zhang

Guangxi University

Haibao Tang

Fujian Agriculture and Forestry University

Qiaochu Shen

Fujian Agriculture and Forestry University

Wei Yao

Guangxi University

Cooperative Institutions

Fujian Agriculture and Forestry University

126

Guangxi University

Chinese Academy of Sciences

Ministry of Agriculture and Rural Affairs

University of Illinois Urbana-Champaign

State Key Laboratory For Conservation and Utilization of Subtropical Agro-Bioresources

Fujian Normal University

University of Chinese Academy of Sciences

Chinese Academy of Agricultural Sciences

Zhejiang University

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Identification and Functional Analysis of Strigolactone Pathway Genes Regulating Tillering Traits in Sugarcane

Plant and Cell Physiology (2024)

Yiying Qi Xiaoxi Feng Hongyan Ding Dadong Lin Yuhong Lan

Saccharum officinarum (S. officinarum) and Saccharum spontaneum (S. spontaneum) are two fundamental species of modern sugarcane cultivars, exhibiting divergent tillering patterns crucial for sugarcane architecture and yield. Strigolactones (SLs), a class of plant hormones, are considered to play a central role in shaping plant form and regulating tillering. Our study highlights the distinct tillering patterns observed between S. officinarum and S. spontaneum, and implicates significant differences in SL levels in root exudates between the two species. Treatment with rac-GR24 (an artificial strigolactone analog) suppressed tillering in S. spontaneum. Based on transcriptome analysis, we focused on two genes, TRANSCRIPTION ELONGATION FACTOR 1 (TEF1) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1), which show higher expression in S. spontaneum or S. officinarum, respectively. While the overexpression of SoCCA1 did not lead to significant phenotypic differences, overexpression of SsTEF1 in rice stimulated tillering and inhibited plant height, demonstrating its role in tillering regulation. However, the overexpression of suggesting that SoCCA1 may not be the key regulator of sugarcane tillering. Yeast one-hybrid (Y1H) assays identified four transcription factors (TFs) regulating SsTEF1, four and five TFs regulating SsCCA1 and SoCCA1. This study provides a theoretical foundation for deciphering the molecular mechanisms underlying the different tillering behaviors between S. officinarum and S. spontaneum, providing valuable insights for the molecular-based design of sugarcane breeding strategies.

Saccharum officinarum

Strigolactone

10.1093/pcp/pcae146

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Genomic insights into the recent chromosome reduction and polyploidization of complex autopolyploid sugarcane S. spontaneum

Research Square (Research Square) (2021)

Jisen Zhang Qing Zhang Yiying Qi Haoran Pan Gang Wang

Abstract S. spontaneum is a founding Saccharum species that contributes stress resistance to the genetic background of modern sugarcane cultivars. Here, we have assembled the autopolyploid S. spontaneum Np-X genome with ancestral form into 40 pseudo-chromosomes in 10 homologous groups, revealing the recent chromosome reduction and polyploidization that occurred in Saccharum . The paleo-duplicated chromosomal pairs exhibit functional redundancy in Saccharum and underwent fission followed by fusion accompanied by centromeric spreading around 0.80 million years ago (Mya) before evolving into their current forms with basic chromosome numbers x = 9 and x = 8 in S. spontaneum , likely in a stepwise manner. WGDs occurred independently in Saccharum species around 1.5 Mya. Highly diverse chromatin structures exist among homologous chromosomes despite their high collinearity, and the re-structuring of NpChr5 and NpChr8 might have suppressed switching of chromatin structure from inactive to active. Resequencing of 116 sugarcane accessions elucidated that the S. spontaneum originated from North India and that the basic chromosome numbers x = 8, x = 9, and x = 10 originated independently, indicating that recent chromosome reduction rather than polyploidization has driven the adaptive evolution of Saccharum . Our study provides genomic resources and suggests new directions for accelerating sugarcane improvement and advances our knowledge of the evolution of auto-polyploids.

Saccharum

Polyploid

10.21203/rs.3.rs-494691/v1

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Additional file 5: of Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum

Figshare (2019)

Yongjun Wang Xiuting Hua Jingsheng Xu Zhichang Chen Tianqu Fan

Amino acid sequences of 16 species. (FASTA 133 kb)

Saccharum

Divergence (linguistics)

10.6084/m9.figshare.7628036

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Additional file 10: of Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum

Figshare (2019)

Yongjun Wang Xiuting Hua Jingsheng Xu Zhichang Chen Tianqu Fan

The non-synonymous (Ka) and synonymous (Ks) substitution ratios of each MGTs from 10 representative plants. (XLSX 804 kb)

Saccharum

Functional divergence

Divergence (linguistics)

10.6084/m9.figshare.7627922

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A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis

Plant Communications (2023)

Huakun Zheng Baiyu Wang Xiuting Hua Ruiting Gao Yuhao Wang

JUJUNCAO (Cenchrus fungigraminus; 2n = 4x = 28) is a Cenchrus grass with the highest biomass production among cultivated plants, and it can be used for mushroom cultivation, animal feed, and biofuel production. Here, we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated ∼2.7 million years ago (mya). Its genome consists of two subgenomes, and subgenome A shares high collinear synteny with pearl millet. We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO. Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes, which was a further indication of asymmetric DNA methylation. The three types of centromeric repeat in the JUJUNCAO genome (CEN137, CEN148, and CEN156) may have evolved independently within each subgenome, with some introgressions of CEN156 from the B to the A subgenome. We investigated the photosynthetic characteristics of JUJUNCAO, revealing its typical C4 Kranz anatomy and high photosynthetic efficiency. NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO, which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield. Taken together, our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies, as well as genetic improvement of Cenchrus grasses.

Synteny

10.1016/j.xplc.2023.100633

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Additional file 1: of New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics

Figshare (2018)

Weichang Hu Xiuting Hua Qing Zhang Jianping Wang Qiaochu Shen

The SWEET gene alleles in S. spontaneum. (XLSX 12 kb)

Saccharum

Divergence (linguistics)

Comparative Genomics

Functional Genomics

10.6084/m9.figshare.7313660

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Comparative analysis of sucrose phosphate synthase (SPS) gene family between Saccharum officinarum and Saccharum spontaneum

BMC Plant Biology (2020)

Panpan Ma Xingtan Zhang Lanping Chen Qian Zhao Qing Zhang

Abstract Background Sucrose phosphate synthase (SPS) genes play vital roles in sucrose production across various plant species. Modern sugarcane cultivar is derived from the hybridization between the high sugar content species Saccharum officinarum and the high stress tolerance species Saccharum spontaneum , generating one of the most complex genomes among all crops. The genomics of sugarcane SPS remains under-studied despite its profound impact on sugar yield. Results In the present study, 8 and 6 gene sequences for SPS were identified from the BAC libraries of S. officinarum and S. spontaneum , respectively. Phylogenetic analysis showed that SPSD was newly evolved in the lineage of Poaceae species with recently duplicated genes emerging from the SPSA clade. Molecular evolution analysis based on Ka/Ks ratios suggested that polyploidy reduced the selection pressure of SPS genes in Saccharum species. To explore the potential gene functions, the SPS expression patterns were analyzed based on RNA-seq and proteome dataset, and the sugar content was detected using metabolomics analysis. All the SPS members presented the trend of increasing expression in the sink-source transition along the developmental gradient of leaves, suggesting that the SPSs are involved in the photosynthesis in both Saccharum s pecies as their function in dicots. Moreover, SPSs showed the higher expression in S. spontaneum and presented expressional preference between stem ( SPSA ) and leaf ( SPSB ) tissue, speculating they might be involved in the differentia of carbohydrate metabolism in these two Saccharum species, which required further verification from experiments. Conclusions SPSA and SPSB genes presented relatively high expression and differential expression patterns between the two Saccharum species, indicating these two SPSs are important in the formation of regulatory networks and sucrose traits in the two Saccharum species. SPSB was suggested to be a major contributor to the sugar accumulation because it presented the highest expressional level and its expression positively correlated with sugar content. The recently duplicated SPSD2 presented divergent expression levels between the two Saccharum species and the relative protein content levels were highest in stem, supporting the neofunctionalization of the SPSD subfamily in Saccharum .

Saccharum officinarum

Saccharum

Sucrose-phosphate synthase

RNA-Seq

10.1186/s12870-020-02599-7

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Citations (37)

Additional file 4: of Evolution and expression of the fructokinase gene family in Saccharum

Yihong Chen Qing Zhang Weichang Hu Xingtan Zhang Liming Wang

Fructokinase

Saccharum

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