Exploration of Markers associated with Heat Stress Tolerance in Pennisetum Glaucum (L.) R. Br.
Sunil Nigombam1, Reetika Mahajan1, Avijit Tarafdar1, Albert Maibam1, Satish Kumar1, Monika Dalal1, SV Amitha CR Mithra1, Sumer Pal Singh2 and Jasdeep Chatrath Padaria1*
1ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
2ICAR-Division of Genetics, IARI, Pusa Campus, New Delhi, India
*Corresponding Author:Jasdeep Chatrath Padaria, ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India.
December 14, 2022; Published: February 20, 2023
Development of high-temperature stress-tolerant Pennisetum glaucum (L.) R. Br. genotypes are essential for growing these as an irrigated summer crop for enhanced production. Identification of molecular markers associated with heat stress tolerance is a prerequisite for developing tolerant P. glaucum through molecular breeding strategies. In the present research, 59 expressed sequence tag (EST) derived microsatellite markers [50 EST-Simple Sequence Repeats (SSR) + 9 Sequence Tagged Sites (STS)] were developed from the available heat stress-responsive transcriptome data in pearl millet and validated in 24 diverse genotypes of pearl millet. Among them, four EST-SSRs markers (15.38%) and one STS markers (16.66%) displayed polymorphism respectively. The polymorphic information content (PIC) of newly developed EST-SSRs was in the range from 0.207 to 0.662 with an average value of 0.435. Based on the five polymorphic markers, the 24 pearl millet genotypes were clustered into 5 main and 11 sub-clusters. Annotation of the five transcripts for which polymorphism was detected, was found to code for genes related to stress response and signaling pathway. The EST-SSRs and STS markers thus analyzed would augment the existing SSR marker resource and find their applications in diversity assessment and marker-aided breeding programs for genetic improvement of pearl millet.
Keywords: Pearl Millet; Abiotic Stress Tolerance; SSR Markers; Validation; Polymerase Chain Reaction
- Bidinger FR., et al. “Assessment of drought resistance in pearl millet [Pennisetum americanum (L.) Leeke]. Factors affecting yield under stress”. Austrailain Journal of Crop Science and Agricultural Research 38 (1987): 37-48.
- Adeoti K., et al. “Nutritional value and physicochemical composition of pearl millet (Pennisetum glaucum) produced in Benin”. Journal of Microbiology, Biotechnology and Food Sciences 7 (2017): 92-96.
- Qi X. “An integrated genetic map and a new set of simple sequence repeat markers for pearl millet, Pennisetum glaucum”. Theoretical and Applied Genetics 109 (2004): 1485-1493.
- Supriya A., et al. “Development of molecular linkage map of pearl millet integrating DArT and SSR markers”. Theoretical and Applied Genetics 123 (2011): 239-250.
- Devos KM., et al. “Comparative mapping reveals a complex relationship between the pearl millet and those of foxtail millet and rice”. Theoretical and Applied Genetics 100 (2000): 190-198.
- Yadav R S., et al. “Quantitative trait loci associated with traits determining grain and stover yield in pearl millet under terminal drought stress conditions”. Theoretical and Applied Genetics 104 (2002): 67-83.
- Bidinger FR., et al. “Quantitative trait loci for grain yield in pearl millet under variable post flowering moisture conditions”. Crop Science 4 (2007): 969-980.
- Kholová J., et al. “Water saving traits co-map with a major terminal drought tolerance quantitative traitlocus in pearl millet (Pennisetum glaucum (L.) R. Br.)”. Molecular Breeding 30 (2012): 1337-1353.
- Punnuri SM. “Development of a highdensity linkage map and tagging leaf spot resistance in pearl millet using genotyping-by-sequencing markers”. Plant Genome 09 (2016): 1-13.
- Devran Z., et al. “Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing”. Molecular Breeding 35 (2015): 101-109.
- Varshney RK., et al. “A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum)”.BMC Genomics 10 (2009): 523-540.
- Fougat R., et al. “Rapid development of microsatellite markers for Plantago ovate using next generation sequencing and their cross-species transferability”. Agriculture 2 (2014): 199-216; 199.
- Howarth CJ., et al. “Development of laboratory based methods for assessing seedling thermotolerance in pearl millet”. New Phytologist 137 (1997): 129-139.
- Untergasser A., et al. “Primer3-new capabilities and interfaces”. Nucleic Acids Research 40 (2012): 115-126.
- Perrier X and Jacquemoud-Collet J P. “DARwin software”.
- Liu K and Muse S V. “PowerMarker: Integrated analysis environment for genetic marker data”. Bioinformatics 21 (2005): 2128-2129.
- Padaria JC., et al. “An efficient protocol for genomic DNA isolation from field grown mature leaves of Pennisetum glaucum (L.) R.Br”. Research Journal of Biotechnology 8 (2013): 30-34.
- Vishwakarma H., et al. “Isolation and characterization of stress inducible protein (Tasti/Hop) from heat-tolerant wheat cultivar C306”. Research Journal of Biotechnology 14 (2018): 111-121.
- Nei M. “Genetic distance between populations”. The American Naturalist 106 (1972): 283-
- Conesa A and Gotz S. “Blast2GO: A comprehensive suite for functional analysis in plant genomics”. International Journal of Plant Genomics 619832 (2008): 12.
- Smith JSC., et al. “Genetic diversity among elite sorghum inbred lines assessed with simple sequence repeats”. Crop Science 40 (2000): 226-232.
- Sankar SM., et al. “Genetic diversity analysis for high temperature stress tolerance in pearl millet [Pennisetum glaucum (L.) R. Br]”. Indian Journal of Plant Physiology 19 (2014): 324-329.
- Satyavathi CT., et al. “Genetic diversity analysis in a novel set of restorer lines of pearl millet [Pennisetum glaucum (L.) R. Br] using SSR markers”. Vegetos 26 (2013): 72-82.
- Senthilvel S., et al. “Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags”. BMC Plant Biology 8 (2008): 119-127.
- Rajaram V., et al. “Pearl millet [Pennisetum glaucum (L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST-SSRs”. BMC Genomics 14 (2013): 159-173.
- Gupta PK and Varshney RK. The development and use of microsatellite markers for genetic analysis and plant breeding with the emphasis on bread wheat. Euphytica 113 (2000): 163-185.
- Caniato FF., et al. “Genetic diversity for aluminum tolerance in sorghum”. Theoretical and Applied Genetics 114 (2007): 863-876.
- Varshney RK. “Exciting journey of 10 years from genomes to ﬁelds and markets: some success stories of genomics-assisted breeding in chickpea pigeonpea and groundnut”. Plant Science 242 (2016): 98-107.
- Li YY. et al. “De novo assembly and characterization of the fruit transcriptome of Chinese jujube (Ziziphus jujuba) using 454 pyrosequencing and the development of novel tri-nucleotide SSR markers”. PLoS One 9.9 (2014): 1-17. e106438.
- Zhang K., et al. “Development and Identification of SSR Markers Associated with Starch Properties and β-Carotene Content in the Storage Root of Sweet Potato (Ipomoea batatas)”. Frontiers in Plant Sciences 7 (2016): 223-243.
- Afzal AJ., et al. “Plant receptor-like serine threonine kinases: roles in signaling and plant defense”. Molecular Plant-Microbe Interaction 21 (2008): 507-5