Development and validation of EST derived SSR markers with relevance to downy mildew (Sclerospora graminicola Sacc.) resistance in pearl millet [Pennisetum glaucum (L.) R. Br.]

• Published in: Journal of plant biochemistry and biotechnology 2017-07, Vol.26 (3), p.356-365
• Main Authors: Zala, Harshvardhan N., Kulkarni, Kalyani S., Bosamia, Tejas C., Shukla, Yogesh M., Kumar, Sushil, Fougat, Ranbir S., Patel, Ankita
• Format: Article
• Language: English
• Subjects: Airborne microorganisms; Biomedical and Life Sciences; Breeding; Cell Biology; Downy mildew; Fungi; Gene expression; Gene polymorphism; Genotypes; Harvest; Life Sciences; Mapping; Marker-assisted selection; Markers; Millet; Nucleotides; Original Article; Parents; Peroxidase; Plant Biochemistry; Polymorphism; Primers; Protein Science; Receptors; Transcription factors; Wounds; Zinc; Zinc finger proteins
• ISSN: 0971-7811; 0974-1275
• DOI: 10.1007/s13562-017-0398-6

Molecular markers associated or linked with a particular trait are immensely essential for marker-assisted selection. Downy mildew is a severe disease in pearl millet causing huge production losses annually. There is a need to develop reliable functional markers associated with downy mildew resistance. In this study, expressed sequence tag-SSR (EST-SSRs) markers were developed from transcriptome data of downy mildew inoculated resistant and susceptible pearl millet genotypes. The high quality pearl millet reads were assembled by Trinity into 26,690 transcripts and 3586 (13.4%) transcripts harbored 4510 SSR motifs with the frequency of one SSR per 5.73 kb. The distribution of SSR motifs in different repeat type classes highlighted tri-nucleotide repeats as the highest (54.6% with CCG/CGG) followed by hexa-nucleotide (16.1% with CCGGCG/CCGGCG), penta-nucleotide (14.5% with CCGCG/CGCGG), tetra-nucleotides (8.0% with AGGG/CCCT) and di-nucleotide (6.8% with AG/CT) repeats. Total of 2419 EST-SSRs markers were developed and 230 markers based on their function in downy mildew-pearl millet interaction were validated in 12 pearl millet genotypes which are parents of mapping population. A total of 33 (20.62%) EST-SSR markers displayed polymorphism with a polymorphism information content (PIC) value ranging from 0.188 to 0.375 with an average of 0.354 and 2.2 alleles. The highest polymorphism was displayed by tri-nucleotide repeat EST-SSR markers followed by hexa-nucleotide, penta-nucleotide and di-nucleotide. The EST-SSR primers designed from eight transcripts coding for peroxidase 16-like, transcription factor myc7e, wound stress protein precursor, peroxidase 16-like, zinc finger ccch domain-containing, wrky transcription factor, beta purothionin were found to be more polymorphic than rest of the transcripts. The newly developed EST-SSR markers have added to the repository of molecular markers for pearl millet and can be employed for downy mildew resistance breeding.