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Genomic and Allelic Analyses of Laccase Genes in Sugarcane (Saccharum spontaneum L.)

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Abstract

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.

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Acknowledgements

This project was supported by startup fund from Fujian Agriculture and Forestry University, the International Consortium for Sugarcane Biotechnology project #35 to R.M., US DOE DE-SC0010686, and EBI BP2012OO2J17.

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Authors and Affiliations

  1. FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

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

  2. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Ray Ming

  3. College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China

    Fei Dong, Qing Ma & Xinyi Ma

  4. College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Songlin Wu & Haifeng Jia

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  1. Wenping Zhang
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  2. Jishan Lin
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  3. Fei Dong
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  4. Qing Ma
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  7. Mahpara Fatima
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  8. Haifeng Jia
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  9. Ray Ming
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Correspondence to Ray Ming.

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Communicated by: Paulo Arruda

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Zhang, W., Lin, J., Dong, F. et al. Genomic and Allelic Analyses of Laccase Genes in Sugarcane (Saccharum spontaneum L.). Tropical Plant Biol. 12, 219–229 (2019). https://doi.org/10.1007/s12042-019-09239-x

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  • DOI: https://doi.org/10.1007/s12042-019-09239-x

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