An Improved Suppression Subtractive Hybridization Technique to Develop Species-specific Repetitive Sequences from Erianthus Arundinaceus (Saccharum Complex)

Overview

Journal BMC Plant Biol

Publisher Biomed Central

Specialty Biology

Date 2018 Nov 8

PMID 30400857

Citations 4

Authors

Fan Yu

Yongji Huang

Ling Luo

Xueting Li

Jiayun Wu

Rukai Chen

Muqing Zhang

Zuhu Deng

Affiliations

Soon will be listed here.

Abstract

Background: Sugarcane has recently attracted increased attention for its potential as a source of bioethanol and methane. However, a narrow genetic base has limited germplasm enhancement of sugarcane. Erianthus arundinaceus is an important wild genetic resource that has many excellent traits for improving cultivated sugarcane via wide hybridization. Species-specific repetitive sequences are useful for identifying genome components and investigating chromosome inheritance in noblization between sugarcane and E. arundinaceus. Here, suppression subtractive hybridization (SSH) targeting E. arundinaceus-specific repetitive sequences was performed. The five critical components of the SSH reaction system, including enzyme digestion of genomic DNA (gDNA), adapters, digested gDNA concentrations, primer concentrations, and LA Taq polymerase concentrations, were improved using a stepwise optimization method to establish a SSH system suitable for obtaining E. arundinaceus-specific gDNA fragments.

Results: Specificity of up to 85.42% was confirmed for the SSH method as measured by reverse dot blot (RDB) of an E. arundinaceus subtractive library. Furthermore, various repetitive sequences were obtained from the E. arundinaceus subtractive library via fluorescence in situ hybridization (FISH), including subtelomeric and centromeric regions. EaCEN2-166F/R and EaSUB1-127F/R primers were then designed as species-specific markers to accurately validate E. arundinaceus authenticity.

Conclusions: This is the first report that E. arundinaceus-specific repetitive sequences were obtained via an improved SSH method. These results suggested that this novel SSH system could facilitate screening of species-specific repetitive sequences for species identification and provide a basis for development of similar applications for other plant species.

Citing Articles

Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants.

Harun A, Liu H, Song S, Asghar S, Wen X, Fang Z Plants (Basel). 2023; 12(15).

PMID: 37570972 PMC: 10420648. DOI: 10.3390/plants12152816.

Efficient Anchoring of Erianthus arundinaceus Chromatin Introgressed into Sugarcane by Specific Molecular Markers.

Wu J, Zhang M, Liu J, Huang Y, Xu L, Deng Z Int J Mol Sci. 2022; 23(16).

PMID: 36012702 PMC: 9408830. DOI: 10.3390/ijms23169435.

Chromosomal Characterization of Revealed by Oligo-FISH.

Yu F, Chai J, Li X, Yu Z, Yang R, Ding X Int J Mol Sci. 2021; 22(16).

PMID: 34445245 PMC: 8395171. DOI: 10.3390/ijms22168539.

What Has Been the Focus of Sugarcane Research? A Bibliometric Overview.

Figueroa-Rodriguez K, Hernandez-Rosas F, Figueroa-Sandoval B, Velasco-Velasco J, Aguilar Rivera N Int J Environ Res Public Health. 2019; 16(18).

PMID: 31509963 PMC: 6765814. DOI: 10.3390/ijerph16183326.

References

Li T, Wang J, Bai Y, Sun X, Lu Z . A novel method for screening species-specific gDNA probes for species identification. Nucleic Acids Res. 2004; 32(4):e45. PMC: 390316. DOI: 10.1093/nar/gnh041. View

Lamar E, Palmer E . Y-encoded, species-specific DNA in mice: evidence that the Y chromosome exists in two polymorphic forms in inbred strains. Cell. 1984; 37(1):171-7. DOI: 10.1016/0092-8674(84)90312-x. View

Lengauer C, Speicher M, Popp S, Jauch A, Taniwaki M, Nagaraja R . Chromosomal bar codes produced by multicolor fluorescence in situ hybridization with multiple YAC clones and whole chromosome painting probes. Hum Mol Genet. 1993; 2(5):505-12. DOI: 10.1093/hmg/2.5.505. View

Yang S, Li X, Huang F, Huang Y, Liu X, Wu J . A new method based on SNP of nrDNA-ITS to identify Saccharum spontaneum and its progeny in the genus Saccharum. PLoS One. 2018; 13(5):e0197458. PMC: 5955562. DOI: 10.1371/journal.pone.0197458. View

DHont A, Rao P, Feldmann P, Grivet L, Islam-Faridi N, Taylor P . Identification and characterisation of sugarcane intergeneric hybrids, Saccharum officinarum x Erianthus arundinaceus, with molecular markers and DNA in situ hybridisation. Theor Appl Genet. 2013; 91(2):320-6. DOI: 10.1007/BF00220894. View

Devos K, Gale M . The use of random amplified polymorphic DNA markers in wheat. Theor Appl Genet. 2013; 84(5-6):567-72. DOI: 10.1007/BF00224153. View

Girio F, Fonseca C, Carvalheiro F, Duarte L, Marques S, Bogel-Lukasik R . Hemicelluloses for fuel ethanol: A review. Bioresour Technol. 2010; 101(13):4775-800. DOI: 10.1016/j.biortech.2010.01.088. View

DHont A, Paulet F, Glaszmann J . Oligoclonal interspecific origin of 'North Indian' and 'Chinese' sugarcanes. Chromosome Res. 2002; 10(3):253-62. DOI: 10.1023/a:1015204424287. View

Svitashev S, Bryngelsson T, Li X, Wang R . Genome-specific repetitive DNA and RAPD markers for genome identification in Elymus and Hordelymus. Genome. 1998; 41(1):120-8. View

10.

Jiang L, You W, Zhang X, Xu J, Jiang Y, Wang K . Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization. Mar Biotechnol (NY). 2015; 18(1):49-56. DOI: 10.1007/s10126-015-9666-4. View

11.

Kato A, Lamb J, Birchler J . Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci U S A. 2004; 101(37):13554-9. PMC: 518793. DOI: 10.1073/pnas.0403659101. View

12.

Rabelo S, Carrere H, Maciel Filho R, Costa A . Production of bioethanol, methane and heat from sugarcane bagasse in a biorefinery concept. Bioresour Technol. 2011; 102(17):7887-95. DOI: 10.1016/j.biortech.2011.05.081. View

13.

Piperidis G, Christopher M, Carroll B, Berding N, DHont A . Molecular contribution to selection of intergeneric hybrids between sugarcane and the wild species Erianthus arundinaceus. Genome. 2001; 43(6):1033-7. View

14.

Zhang H, Bian Y, Gou X, Zhu B, Xu C, Qi B . Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat. Proc Natl Acad Sci U S A. 2013; 110(9):3447-52. PMC: 3587266. DOI: 10.1073/pnas.1300153110. View

15.

Stocki S, Babiuk L, Rawlyk N, Potter A, Allan B . Identification of genomic differences between Escherichia coli strains pathogenic for poultry and E. coli K-12 MG1655 using suppression subtractive hybridization analysis. Microb Pathog. 2002; 33(6):289-98. DOI: 10.1006/mpat.2002.0536. View

16.

Dai Z, Mao X, Magnuson J, Lasure L . Identification of genes associated with morphology in Aspergillus niger by using suppression subtractive hybridization. Appl Environ Microbiol. 2004; 70(4):2474-85. PMC: 383145. DOI: 10.1128/AEM.70.4.2474-2485.2004. View

17.

Humann F, Hartfelder K . Representational Difference Analysis (RDA) reveals differential expression of conserved as well as novel genes during caste-specific development of the honey bee (Apis mellifera L.) ovary. Insect Biochem Mol Biol. 2011; 41(8):602-12. DOI: 10.1016/j.ibmb.2011.03.013. View

18.

Straus D, Ausubel F . Genomic subtraction for cloning DNA corresponding to deletion mutations. Proc Natl Acad Sci U S A. 1990; 87(5):1889-93. PMC: 53589. DOI: 10.1073/pnas.87.5.1889. View

19.

Sagerstrom C, Sun B, Sive H . Subtractive cloning: past, present, and future. Annu Rev Biochem. 1997; 66:751-83. DOI: 10.1146/annurev.biochem.66.1.751. View

20.

Wu J, Huang Y, Lin Y, Fu C, Liu S, Deng Z . Unexpected inheritance pattern of Erianthus arundinaceus chromosomes in the intergeneric progeny between Saccharum spp. and Erianthus arundinaceus. PLoS One. 2014; 9(10):e110390. PMC: 4195721. DOI: 10.1371/journal.pone.0110390. View