Welcome to Chinese Journal of Tropical Crops,

Chinese Journal of Tropical Crops ›› 2021, Vol. 42 ›› Issue (10): 2841-2848.DOI: 10.3969/j.issn.1000-2561.2021.10.013

• Omics & Biotechnology • Previous Articles     Next Articles

Bioinformatic Analysis and Identification of Genes Contributing to Sugarcane Defoliation via BSR-Seq

YUE Qu1, SHANG Heyang1, ZHANG Pin2, CHEN Baoshan1,3,*(), HUANG Youzong1,3,*()   

  1. 1. College of Agriculture, Guangxi University / State Key Laboratory of Conservation and Utilization of Subtropical Aro-bioresources, Nanning, Guangxi 530005, China
    2. College of Agronomy, Hebei Agricultural University, Baoding, Hebei 071001, China
    3. Agri-animal Industrial Development Institute, Guangxi University / Guangxi Key Laboratory of Sugarcane Biology, Nanning, Guangxi 530005, China
  • Received:2020-12-28 Revised:2021-03-02 Online:2021-10-25 Published:2021-11-25
  • Contact: CHEN Baoshan,HUANG Youzong


Sugarcane (Saccharam spp.), a C4 tropical grass mainly for sugar production, is commercially cultivated in over 100 countries. One of the main barriers to mechanical or manual harvesting of whole sugarcane stalk is the high percentage of impurities, mainly the debris of leaves and sheathes that results in increase of harvest time and cost. The most efficient solution for this issue is to develop sugarcane cultivars that are easy to defoliate in sugarcane breeding program. In order to investigate the genes responsible to sugarcane defoliation, BSR-Seq technology was employed in the current study to analyze pools of the leaves at +6 position of extremely hard-to-defoliate and easy-to-defoliate sugarcane plants derived from the cross of ‘ROC25’ × ‘Yunzhe 89-7’, together with the two parental lines with contrast defoliation phenotypes. A total of 60 Gb of clean reads were obtained and the Q30 values of the four samples were greater than 93% with GC content of 51%. Using R570 genome as reference, the alignment rate was greater than 41%. A total of 4085 differential expressed genes were detected in the 4 samples. The candidate regions were found to locate at 4 loci on chromosome 9, covering a total length of 1.40 Mb in which 86 genes were annotated. There were 15 non-synonymous mutations annotated between the parental lines, and two significant differentially expressed genes (Sh09_g020620, Sh09_g020080) were identified. The expression level of Sh09 g020080 in the easy-to-defoliate genotype was higher than that of the hard-to-defoliate genotype and consistent with the parents but that of Sh09_g020620 was opposite between the offspring pools and the parental lines, suggesting that only Sh09 g020080 may contributing to the phenotype of easy defoliation. Quantitation of Sh09 g020080 gene expression in leaves from position +1 to +7 from the extremely easy-to-defoliate representative accession 40-159 and the extremely hard-to-defoliate accession 5-94 confirmed the BSR-seq results of the two pools. In analysis of another genetic population derived from the cross of ‘B35-9’ × ‘CP08-1553’, Sh09 g020080 was also found to express in a higher level in the extremely easy-to-defoliate accession 16-226 than in the extremely hard-to-defoliate accession 16-224 in +4 to +6 leaves. Analysis of the deduced Sh09_g020080 protein revealed that this protein has four domains conserved in σ factor-like proteins that may function in in red, far red and blue light reactions and accumulation of chlorophyll. Overall, this study shed a new light into the endeavor of exploring essential genes for defoliation in sugarcane.

Key words: sugarcane, BSR-Seq, defoliation

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