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

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2022 Aug 26

PMID 36012702

Authors

Jiayun Wu

Mingxiao Zhang

Jiarui Liu

Yongji Huang

Liangnian Xu

Zuhu Deng

Xinwang Zhao

Affiliations

Soon will be listed here.

Abstract

Erianthus arundinaceus is a valuable gene reservoir for sugarcane improvement. However, insufficient molecular markers for high-accuracy identification and tracking of the introgression status of E. arundinaceus chromatin impede sugarcane breeding. Fortunately, suppression subtractive hybridization (SSH) technology provides an excellent opportunity for the development of high-throughput E. arundinaceus-specific molecular markers at a reasonable cost. In this study, we constructed a SSH library of E. arundinaceus. In total, 288 clones of E. arundinaceus-specific repetitive sequences were screened out and their distribution patterns on chromosomes were characterized by fluorescence in situ hybridization (FISH). A subtelomeric repetitive sequence Ea086 and a diffusive repetitive sequence Ea009, plus 45S rDNA-bearing E. arundinaceus chromosome repetitive sequence EaITS were developed as E. arundinaceus-specific molecular markers, namely, Ea086-128, Ea009-257, and EaITS-278, covering all the E. arundinaceus chromosomes for high-accuracy identification of putative progeny. Both Ea086-128 and Ea009-257 were successfully applied to identify the authenticity of F1, BC1, BC2, BC3, and BC4 progeny between sugarcane and E. arundinaceus. In addition, EaITS-278 was a 45S rDNA-bearing E. arundinaceus chromosome-specific molecular marker for rapid tracking of the inherited status of this chromosome in a sugarcane background. Three BC3 progeny had apparently lost the 45S rDNA-bearing E. arundinaceus chromosome. We reported herein a highly effective and reliable SSH-based technology for discovery of high-throughput E. arundinaceus-specific sequences bearing high potential as molecular markers. Given its reliability and savings in time and efforts, the method is also suitable for development of species-specific molecular markers for other important wild relatives to accelerate introgression of wild relatives into sugarcane.

References

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

Diatchenko L, Lau Y, Campbell A, Chenchik A, Moqadam F, Huang B . Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci U S A. 1996; 93(12):6025-30. PMC: 39182. DOI: 10.1073/pnas.93.12.6025. View

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

Pachakkil B, Terajima Y, Ohmido N, Ebina M, Irei S, Hayashi H . Cytogenetic and agronomic characterization of intergeneric hybrids between Saccharum spp. hybrid and Erianthus arundinaceus. Sci Rep. 2019; 9(1):1748. PMC: 6370852. DOI: 10.1038/s41598-018-38316-6. View

Villano C, Miraglia V, Iorizzo M, Aversano R, Carputo D . Combined Use of Molecular Markers and High-Resolution Melting (HRM) to Assess Chromosome Dosage in Potato Hybrids. J Hered. 2015; 107(2):187-92. PMC: 5994968. DOI: 10.1093/jhered/esv094. View

Phung N, Mai C, Mournet P, Frouin J, Droc G, Ta N . Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes. BMC Plant Biol. 2014; 14:371. PMC: 4279583. DOI: 10.1186/s12870-014-0371-7. View

Mehrotra S, Goyal V . Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function. Genomics Proteomics Bioinformatics. 2014; 12(4):164-71. PMC: 4411372. DOI: 10.1016/j.gpb.2014.07.003. View

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

He Q, Cai Z, Hu T, Liu H, Bao C, Mao W . Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.). BMC Plant Biol. 2015; 15:105. PMC: 4417506. DOI: 10.1186/s12870-015-0480-y. View

10.

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

11.

Cai Z, Liu H, He Q, Pu M, Chen J, Lai J . Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping. BMC Genomics. 2014; 15:1025. PMC: 4256728. DOI: 10.1186/1471-2164-15-1025. View

12.

Yao F, Zhang X, Ye X, Li J, Long L, Yu C . Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces. BMC Genet. 2019; 20(1):38. PMC: 6434810. DOI: 10.1186/s12863-019-0736-x. View

13.

Piperidis N, Chen J, Deng H, Wang L, Jackson P, Piperidis G . GISH characterization of Erianthus arundinaceus chromosomes in three generations of sugarcane intergeneric hybrids. Genome. 2010; 53(5):331-6. DOI: 10.1139/g10-010. View

14.

Hsieh W, Pan M . Identification Leptospira santarosai serovar shermani specific sequences by suppression subtractive hybridization. FEMS Microbiol Lett. 2004; 235(1):117-24. DOI: 10.1016/j.femsle.2004.04.024. View

15.

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

16.

Naito K, Zhang F, Tsukiyama T, Saito H, Hancock C, Richardson A . Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature. 2009; 461(7267):1130-4. DOI: 10.1038/nature08479. View

17.

Harakava R, Gabriel D . Genetic differences between two strains of Xylella fastidiosa revealed by suppression subtractive hybridization. Appl Environ Microbiol. 2003; 69(2):1315-9. PMC: 143624. DOI: 10.1128/AEM.69.2.1315-1319.2003. View

18.

Biscotti M, Olmo E, Heslop-Harrison J . Repetitive DNA in eukaryotic genomes. Chromosome Res. 2015; 23(3):415-20. DOI: 10.1007/s10577-015-9499-z. View

19.

He J, Zhao X, Laroche A, Lu Z, Liu H, Li Z . Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci. 2014; 5:484. PMC: 4179701. DOI: 10.3389/fpls.2014.00484. View

20.

Yu F, Huang Y, Luo L, Li X, Wu J, Chen R . An improved suppression subtractive hybridization technique to develop species-specific repetitive sequences from Erianthus arundinaceus (Saccharum complex). BMC Plant Biol. 2018; 18(1):269. PMC: 6220460. DOI: 10.1186/s12870-018-1471-6. View