Mycological Progress

, Volume 13, Issue 2, pp 247–255 | Cite as

Haplotype variation and phylogeography of Rhizoctonia solani AG1-IA strains based on rDNA5.8S-ITS and ß-actin gene sequence analyses

  • Yong Wei
  • Jiandong Bao
  • Huijuan Cao
  • Jing Zhai
  • Chatchawan Jantasuriyarat
  • Shimin Zuo
  • Xuebiao Pan
  • Hua Wang
  • Bo Zhou
Original Article
First Online:
Received:
Revised:
Accepted:

Abstract

The haplotype variation and phylogeography of Rhizoctonia solani AG1-IA strains were estimated using rDNA5.8S-ITS and ß-actin gene sequences. Two haplotypes of ITS sequences were revealed, designated as ITSa and ITSb. Thirty-four SNPs from the ß-actin gene, which displayed more allele discriminations than rDNA-ITS, were identified. The SNPs were used to classify R. solani into 12 haplotypes, designated as H1–H12. Most SNPs occurred at the third codon position and resulted as silent mutations. Three SNPs occurred at the first codon position and one SNP occurred at the second position, which these four SNPs causing non-synonymous mutations. According to the translational amino acid sequences, the 12 nucleotide-inferred haplotypes were further classified into 5 groups, designated as ITRL, VARI, VARL, VTRI, and VAMI. Analysis of the geographical distribution of 12 haplotypes, showed that H1 and H9 were widely distributed in all studied locations and existed simultaneously in the strains collected in most areas. The results lead to the speculation that H1 and H9 could be the founder haplotypes of ß-actin gene, and other haplotypes might be derived from them.

Keywords

Single nucleotide polymorphism SNP Rice sheath blight rDNA-ITS ß-actin 
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Notes

Acknowledgments

We thank Mr. Robert Harman II for critically reviewing this manuscript. This project was supported by National Transgenic Breeding Program of China (2012ZX08009001-002) and National Basic Research Program of China (2012CB722504).

Supplementary material

11557_2013_909_MOESM1_ESM.doc (144 kb)
Figure S1 Neighbor-joining tree of different Rhizoctonia solani AG 1-IA isolates based on the nucleotide sequences of the rDNA ITS-5.8S. All the sequences within the same subgroup of AG1-IA collected from rice are clustered together and cannot be differentiated. The sequences described in this study were designated as either ITSa or ITSb. Other sequences were retrieved from NCBI with respective accession numbers (DOC 144 kb)
11557_2013_909_MOESM2_ESM.docx (12 kb)
Table S1 Frequency of different SNP types in ß-actin sequence of R. solani AG1-IA strains (DOCX 12 kb)
11557_2013_909_MOESM3_ESM.docx (12 kb)
Table S2 Groups based on the deduced amino acids and haplotypes based on SNPs in ß-actin sequence of R. solani AG1-IA strains (DOCX 11 kb)

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Copyright information

© German Mycological Society and Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Yong Wei
    • 1
    • 2
  • Jiandong Bao
    • 1
  • Huijuan Cao
    • 2
  • Jing Zhai
    • 2
  • Chatchawan Jantasuriyarat
    • 3
    • 4
  • Shimin Zuo
    • 5
  • Xuebiao Pan
    • 5
  • Hua Wang
    • 1
  • Bo Zhou
    • 1
    • 2
    • 6
  1. 1.State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
  2. 2.Institute of BiotechniquesZhejiang UniversityHangzhouChina
  3. 3.Department of Genetics, Faculty of ScienceKasetsart UniversityBangkokThailand
  4. 4.Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU)Kasetsart UniversityBangkokThailand
  5. 5.Key Lab for Crop Genetics and Physiology of Jiangsu ProvinceYangzhou UniversityYangzhouPeople’s Republic of China
  6. 6.International Rice Research InstituteMetro ManilaPhilippines

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