Czech J. Genet. Plant Breed., 2018, 54(4):154-160 | DOI: 10.17221/25/2017-CJGPB

Identification of molecular markers associated with genic male sterility in tetraploid cotton (Gossypium hirsutum L.) through bulk segregant analysis using a cotton SNP 63K arrayOriginal Paper

Dharmalingam RAJA*,1, Marappan SARVANA KUMAR1, Ponnuswamy RENUKA DEVI2, Sankaran LOGANATHAN1, Kamalasekharan RAMYA1, Nallathambi KANNAN1, Vaidyanathan SUBRAMANIAN1
1 Rasi Research and Development Center, Rasi Seeds (P) Ltd., Attur, Tamil Nadu, India
2 Department of Biotechnology, Anna University, Coimbatore, Tamil Nadu, India

Genic male sterility (GMS) is one of the most important economic traits for cotton (Gossypium hirsutum L.) hybrid seed production. The GMS trait conferred by two recessive alleles ms5 and ms6 in homozygous constitution is widely used for cotton hybrid seed production in India. Identification of molecular markers closely linked to the ms5 and ms6 alleles would be useful in effective transferring in a short time male-sterility genes into cultivars or elite lines using marker-assisted backcrossing. Here, we describe a quick method to identify markers for GMS genes using bulk segregant analysis (BSA) in the interspecific (G. hirsutum × G. hirsutum) biparental population. The parents and bulks were genotyped with a cotton single nucleotide polymorphism (SNP) 63K array that contains 63 058 SNP markers including 45 104 intraspecific and 17 954 interspecific SNP markers. Four SNP markers were found to be linked with the Ms5 and Ms6 genes. The markers i23493Gh and i46470Gh linked with the Ms5 gene, and other two markers i08605Gh and i08573Gh linked with the Ms6 gene are located on chromosome 12 and 26, respectively. A simple and cost effective tetra-primer amplification refractory mutation system PCR (tetra-primer ARMS-PCR) assay was optimized for screening a large number of breeding samples with the identified SNP markers in a short time. The molecular markers developed in this study will facilitate the marker-assisted selection (MAS) and accelerate the development of new GMS lines to use in cotton hybrid seed production.

Keywords: Gossypium hirsutum; hybrid; male-fertility; polymorphism; test cross

Published: December 31, 2018  Show citation

ACS AIP APA ASA Harvard Chicago Chicago Notes IEEE ISO690 MLA NLM Turabian Vancouver
RAJA D, SARVANA KUMAR M, RENUKA DEVI P, LOGANATHAN S, RAMYA K, KANNAN N, SUBRAMANIAN V. Identification of molecular markers associated with genic male sterility in tetraploid cotton (Gossypium hirsutum L.) through bulk segregant analysis using a cotton SNP 63K array. Czech J. Genet. Plant Breed. 2018;54(4):154-160. doi: 10.17221/25/2017-CJGPB.
Share...
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)
    • Open full article

    References

    1. Chen D., Ding Y., Guo W., Zhang T. (2009): Molecular mapping of genic male-sterile genes ms15, ms5 and ms6 in tetraploid cotton. Plant Breeding, 128: 193-198. Go to original source...
    2. Collins A., Ke X. (2012): Primer1: primer design web service for tetra-primer ARMS-PCR. Open Bioinformatics Journal, 6: 55-58. Go to original source...
    3. Feng X., Keim D., Wanjugi H., Coulibaly I., Fu.Y Schwarz J., Huesgen S., Cho S. (2015): Development of molecular markers for genetic male sterility in Gossypium hirsutum. Molecular Breeding, 35: 141. Go to original source... Go to PubMed...
    4. Hulse-Kemp A.M., Lemm J., Plieske J., Ashrafi H., Buyyarapu R., Fang D.D., Frelichowski J., Giband M., Hague S., Hinze L.L., Kochan K.J., Riggs P.K., Scheffler J.A, Udall J.A., Ulloa M., Wang S.S., Zhu Q.H., Bag S.K., Bhardwaj A., Burke J.J., Byers R.L., Claverie M., Gore M.A., Harker D.B., Islam M. S., Jenkins J.N., Jones D.C., Lacape J.M., Llewellyn D.J., Percy R.G., Pepper A.E., Poland J.A., Rai K.M., Sawant S.V., Singh S.K., Spriggs A., Taylor J.M., Wang F., Yourstone S.M., Zheng X., Lawley C.T., Ganal M.W., Allen Van Deynze., Wilson L.W., Stelly D.M. (2015): Development of a 63K SNP array for cotton and high-density mapping of intra-specific and inter-specific populations of Gossypium spp. G3: Genes, Genomes, Genetics, 5: 1187-1209. Go to original source... Go to PubMed...
    5. Lakshmi Praba M., Thangaraj M. (2005): Effect of growth regulators chemicals on pollen sterility in TGMS lines of rice. Plant Growth Regulation, 46: 117-124. Go to original source...
    6. Mandaliya V.B., Thaker V.S. (2016): Molecular markers in male sterility: step towards crop improvement. International Journal of Molecular Biology & Biochemistry, 4: 1-12.
    7. Michelmore R.W., Paran I., Kesseli R.V.(1991): Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proceedings of the Natural Academy of Sciences, 88: 9828-9832. Go to original source... Go to PubMed...
    8. Okayama N., Fujimura K., Nakamura J., Suehiro Y., Hamanaka Y., Hinoda Y. (2004): Evaluation of a new efficient procedure for single-nucleotide polymorphism genotyping: tetra-primer amplification refractory mutation system-polymerase chain reaction. Clinical Chemistry and Laboratory Medicine, 42: 13-16. Go to original source... Go to PubMed...
    9. Oliphant A., Barker D.L., Stuelpnagel J.R., Chee M.S. (2002): Bead array technology: enabling an accurate cost-effective approach to high-throughput genotyping. Biotechniques, 32: S56-S61. Go to original source...
    10. Paroda R.S., Basu A.K. (1993): Cotton scenario with particular reference to hybrid cotton in India. In: Proc. FAO-ICAR Reg. Expert Consult. Hybrid Cotton, Nagpur, Oct 22-25, 1990: 21-40.
    11. Paterson A.H., Brubaker C.L., Wendel J.F. (1993): A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Molecular Biolology Report, 11: 122-127. Go to original source...
    12. Rhyne C.L. (1991): Male-sterile ms5ms5ms6ms6 and ms8ms8ms9ms9. In: Proc. Beltwide Cotton Conferences, San Antonio, Jan 6-10, 1991: 532-533.
    13. Steemers F.J., Gunderson K.L. (2007): Whole genome genotyping technologies on the bead array platform. Biotechnology Journal, 2: 41-49. Go to original source... Go to PubMed...
    14. Tiwari S., Sl K., Kumar V., Singh B., Rao A., Mithra S.V.A., Rai V., Sigh A.K., Singh N.K. (2016): Mapping QTLs for salt tolerance in rice (Oryza sativa L.) by bulked segregant analysis of recombinant inbred lines using 50K SNP chip. PLoS ONE, 11: e0153610. Go to original source... Go to PubMed...
    15. Wang Z., Jia Y., Rutzer J.N., Xia Y. (2007): Rapid survey for presence of a blast resistance gene pi-ta in rice cultivars using the dominant DNA markers derived from portions of the Pi-ta gene. Plant Breeding, 126: 36-42. Go to original source...
    16. Wang F., Feng C., Stewart J., McD., O'Connell M.A., ZhangJ. (2010): RFLP analysis of mitochondrial DNA in two cytoplasmic male sterility systems (CMS-D2 CMS-D8) of cotton. Euphytica, 172: 93-99. Go to original source...
    17. Ye S., Sahar D., Xiayi K., Andrew R.C., Day I.N.M. (2001): An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Research, 29: 88-94. Go to original source... Go to PubMed...
    18. Yu H., Xie W., Li J., Zhou F., Zhang Q. (2014): A wholegenome SNP array (RICE 6K) for genomic breeding in rice. Plant Biotechnology Journal, 12: 28-37. Go to original source... Go to PubMed...
    19. Zhou W., Kolb F.L., Domier L.L., Wang S. (2005): SSR markers associated with fertility restoration genes against Triticum timopheevii cytoplasm in Triticum aestivum. Euphytica, 141: 33-40. Go to original source...

    This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY NC 4.0), which permits non-comercial use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.


    Return to the content