Molecular Characterization and Genetic Diversity Analysis of Released Hybrids and Varieties of Pearl Millet [Pennisetum glaucum (L.) R. Br.]

Main Article Content

Supriya Ambawat
C. Tara Satyavathi
Rajbala Meena
Vikas Khandelwal
R. C. Meena

Abstract

Pearl millet is a climate-resilient crop which is most widely grown in the arid and semi-arid tropics of Asia and Africa over 26 mha. It is a highly nutritious cereal crop and rightly termed as nutricereal. This crop requires low inputs and delivers high cost-effective benefits. Development of high yielding hybrids is the major target of pearl millet researchers globally. The understanding of genetic diversity is very important and must for developing superior hybrids and crop improvement programs. In the present study, we evaluated the diversity among 30 different released hybrids and varieties of pearl millet using 125 Simple Sequence Repeat (SSR) markers. Out of these, 61 polymorphic SSRs were reported giving 191 alleles with an average of 3.13 alleles per primer. Polymorphic Information Content (PIC) varied from 0.33 to 0.76 with an average of 0.55 PIC value. The cluster analysis based on these SSR markers categorized the genotypes into four major clusters viz., I, II, III, IV with similarity coefficient ranging from 0.58 to 0.73. The results depicted that sufficient genetic variability exists among the different hybrids and varieties used in the study which can further prove useful for pearl millet improvement programs. The study also reveals that SSR markers are proficient and may be used efficiently for genetic diversity studies in pearl millet. It is also anticipated that findings of this study may be further used for DNA fingerprinting and varietal identification.

Keywords:
Diversity estimation, microsatellites, molecular analysis, pearl millet, varietal identification

Article Details

How to Cite
Ambawat, S., Satyavathi, C. T., Meena, R., Khandelwal, V., & Meena, R. C. (2020). Molecular Characterization and Genetic Diversity Analysis of Released Hybrids and Varieties of Pearl Millet [Pennisetum glaucum (L.) R. Br.]. Current Journal of Applied Science and Technology, 39(31), 92-104. https://doi.org/10.9734/cjast/2020/v39i3130994
Section
Original Research Article

References

Taylor JR, NBTRM. In Millet FS: Pearl. In reference module in food science. Elsevier; 2016.

Yadav OP, Rai KN. Genetic improvement of pearl millet in India. Agri. Res. 2013; 2(4):275-292.

Singh AK, Rana MK, Singh S, Kumar S, Durgesh K, Arya L. Assessment of genetic diversity among pearl millet [Pennisetum glaucum (L.) R Br.] cultivars using SSR markers. Range Manag Agrofor. 2013; 34(1):77-81.

Waddington S, Li X, Dixon J, Hyman G, de Vicente MC. Getting the focus right: Production constraints for six major food crops in Asian and African farming systems. Food Secur. 2010;2(1): 27-48.

Brar DS, Khush GS. Rice breeding in the genomics era: Perspectives. Agric. Res. J. 2017;54(4):612-619.

Kumar S, Parekh MJ, Patel CB, Zala HN, Sharma R, Kulkarni KS, et al. Development and validation of EST-derived SSR markers and diversity analysis in cluster bean (Cyamopsis tetragonoloba), J. Plant Biochem. Biotechnol. 2016;25(3):263.

Singh BK, Choudhary SB, Yadav S, Malhotra EV, Rani R, Supriya A, et al. Genetic structure identification and assessment of interrelationships between Brassica and allied genera using newly developed genic-SSRs of Indian mustard (Brassica juncea L.). Industrial Crops and Products. 2018;113: 111–120.

Bharti R, Kumar S, Parekh MJ. Development of genomic simple sequence repeat (gSSR) markers in cumin and their application in diversity analyses and cross-transferability. Ind. Crops Prod. 2018;111: 158-64.

Singh S, Gupta SK. Formation of heterotic pools and understanding relationship between molecular divergence and heterosis in pearl millet [Pennisetum glaucum (L.) R. Br.], PLoS One. 2019; 14(5):0207463.

Serba DD, Yadav RS. Genomic tools in pearl millet breeding for drought tolerance: Status and prospects. Front Plant Sci. 2016;7:1724.

Mohammed HI, Hamza NB. Genetic diversity analysis of forty pearl millet (Pennisetum glaucum (L.) R. Br) Accessions from Sudan Using Agronomical Descriptors and DNA Molecular Markers Advances in Bioscience and Biotechnology. 2018;9:322-37.

Mariac C, Luong IV, Kapran A, Mamadou F, Sagnard M, Deu J, et al. Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers, Theor. Appl. Genet. 2006;114:49–58.

Govindaraj M, Selvi B, Arun Prabhu D, Rajarathinam S. Genetic diversity analysis of pearl millet (Pennisetum glauccum [L.] R. Br.) accessions using molecular markers. African Journal of Biotechnology. 2009; 8(22):6046-6052.

Supriya A, Senthilvel S, Nepolean T, Eshwar K, Rajaram V, Shaw R, et al. Development of a molecular linkage map of pearl millet integrating DArT and SSR markers. Theor Appl Genet. 2011;123(2): 239-50. DOI: 10.1007/s00122-011-1580

Radhika Ramya A, Ahamed ML, Srivastava RK. Genetic diversity analysis among inbred lines of pearl millet [Pennisetum glaucum (L.) R. Br.] based on grain yield and yield component characters. Int. J. Curr. Microbiol. App. Sci. 2017;6(6):2240-2250. DOI:https://doi.org/10.20546/ijcmas.2017.606.266

Waghmode BT, Sharma KM, Pawar GS, Salunke VD, Kal SP. Genetic diversity and hybrid purity analysis of pearl millet using molecular markers Int. J. Curr. Microbiol. App. Sci. 2018;6:772-79.

Kanfany G, D-Serba D, Rhodes D, St. Amand P, Bernardo A, I-Gangashetty P, et al. Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties BMC Genomics. 2020; 21:469.

Nadeem MA, Nawaz MA, Shahid MQ, Doğan Y, Comertpay G, Yıldız M, et al. DNA molecular markers in plant breeding: Current status and recent advancements in genomic selection and genome editing. Biotechnol. Biotechnol. Equip. 2018;32(2): 261–85.

Abdurakhmonov IY. Introduction to Microsatellites: Basics, trends and highlights: in: Abdurakhmonov IY. (Ed.), microsatellite markers. In Tech Publisher, London, EC3R 6AF, UK. 2016;1-16. Available:http://dx.doi.org/10.5772/62560

Amelework B, Abakemal D, Shimelis H, Laing M. Application of microsatellites in genetic diversity analysis and Heterotic grouping of Sorghum and maize in: Abdurakhmonov IY. (Ed.), Microsatellite markers, In Tech Publisher, London, EC3R 6AF, UK. 2016:117-138 Available:http://dx.doi.org/10.5772/65078

Supriya A, Kumar R, Singh S, Yadav R. An easy, quick and cost effective method of high quality dna extraction from mungbean [Vigna radiata (L.) Wilczek] without liquid Nitrogen. Int. J. Curr. Microbiol. App.Sci. 2017;6(9):2695-703.

Allouis S, Qi X, Lindup S, Gale MD, Devos KM. Construction of a BAC library of pearl millet, [Pennisetum glaucum (L.) R. Br.]. Theor. Appl. Genet. 2001;102: 1200-1205.

Qi X, Lindup S, Pittaway TS, Allouis S, Gale MD, Devos KM. Development of simple sequence repeat markers from bacterial artificial chromosomes without subcloning. Biotechniques. 2001;31:355-358.

Qi X, Pittaway TS, Lindup S, Liu H, Waterman E, Padi FK, et al. An integrated genetic map and a new set of simple sequence repeat markers for pearl millet [Pennisetum glaucum (L.) R. Br.]. Theor. Appl. Genet. 2004;109:485-1493.

Shaikh TR. Assessment of hybrid purity in Sorghum by using molecular markers, submitted to Vasantrao Naik Marathwada Krishi Vidyapeeth Parbhani-431402 (M.S.) India; 2015.

Senthilvel S, Jayashree B, Mahalakshmi V, Kumar PS, Nakka S, Nepolean T, et al. Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biology. 2008;8:119.

Kumar S, Hash CT, Singh G, Basava RK, Srivastava RK. Identification of polymorphic SSR markers in elite genotypes of pearl millet and diversity analysis Ecological Genetics and Genomics. 2020;14:100051.

Oumar I, Mariac C, Pham JL, Vigouroux Y. Phylogeny and origin of pearl millet (Pennisetum glaucum [L.] R. Br) as revealed by microsatellite loci. Theor. Appl. Genet. 2008;117:489–497. DOI: 10.1007/s00122-008-0793-4

Kapila RK, Yadav RS, Plaha P, Rai KN, Yadav OP, Hash CT, et al. Genetic diversity among pearl millet maintainers using microsatellite markers, Plant Breed. 2008;127:33–37.

Narshimulu G, Jamaloddin M, Vemireddy LR, Anuradha G, Siddiq E. Potentiality of evenly distributed hyper-variable microsatellite markers in marker-assisted breeding of rice. Plant Breed. 2011;130: 314–320. DOI: 10.1111/j.1439-0523.2010.01834.x

Singh S, Singh VV, Supriya A, Dubey M, Singh D. Screening and estimation of allelic differentiation in Indian Mustard (Brassica juncea L.) genotypes based on SSR Markers for background selection. Int. J. Curr. Microbiol. App. Sci. 2017;6(9): 2506-16.

Gonzaga ZJ, Aslam K, Septiningsih EM, Collard BCY. Evaluation of SSR and SNP markers for molecular breeding in rice. Plant Breed. Biotechnol. 2015;3:139–52. DOI: 10.9787/PBB.2015.3.2.139

Vieira ML, Santini L, Diniz AL, Munhoz CF. Microsatellite markers: What they mean and why they are so useful. Genet Mol Biol. 2016;39:312–328.

Shete S, Tiwari H, Elston RC. On estimating heterozygosity and polymorphism information content value. Theor Popul Biol. 2000;57:265-71.

Yadav S, Singh AK, Singh MR, Goel N, Vinod KK, Mohapatra T. Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): Use of random versus trait-linked microsatellite markers. J Genet. 2013;92:545–557.

Tiwari KK, Singh A, Pattnaik S, Sandhu M, Kaur S, Jain S, et al. Identification of a diverse mini-core panel of Indian rice germplasm based on genotyping using microsatellite markers. Plant Breed. 2015; 134(2):164–171.

Mahalingam A, Sarawathi R, Ramalingam J. SSR marker diversity analysis for WA cytoplasm based fertility restorer genes of hybrid rice (Oryza sativa L.). J Innov Agric. 2016;3(1):19–27.

Salazar B, Laurentin H, Davila M, Castillo MA. Reliability of the RAPD technique for Oryza sativa analysis of sesame (Sesamum indicum L.) from Venezuela. Interciencia. 2006;31:456-460.

Shrivastava A, Mishra D, Koutu G, Singh S, Prakash V, Sohgaura N. Assessment of genetic diversity of restorer and maintainer lines of rice using SSR markers. The Ecascan. 2015;9(1–2):265–269.

Akkaya MS, Buyukunal-Bal EB. Assessment of genetic variation of bread wheat varieties using microsatellite markers. Euphytica. 2004;135:179-185.

Gupta SK, Nepolean T, Sankar SM, Rathore A, Das RR, Rai KN, Hash CT. Patterns of molecular diversity in current and previously developed hybrid parents of pearl millet [Pennisetum glaucum (L.) R. Br.]. Am. J. Plant Sci. 2015;6:1697-1712.

Sehgal, D, Skot L, Singh R, Srivastava RK, Das SP, Taunk J, et al. Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits. PLoS One. 2015;0(5): 0122165.

Satyavathi CT, Khandelwal V, Supriya A, Kumar K, Bhanwariya S, Yadav SL, Chand M. Pearl millet: Hybrids and varieties. ICAR-All India Coordinated Research Project on Pearl Millet, Mandor, Jodhpur, India. 2018;142.

Shanmuganathan M, Gopalan A, Mohanraj K. Genetic variability and multivariate analysis in pearl millet (Pennisetum glaucum (L.) R. Br.) germplasm for dual purpose. J. Agric. Sci. 2006;2(1):73-80.

Sathya M, Vinodhana NK, Sumathi P. Hierarchial clustering of pearl millet (Pennisetum glaucum (L.) R.Br) inbreds for morpho-physiological traits. Int. J. Curr. Microbiol. App. Sci. 2013;2(12):647-652.

Chaudhary S, Sagar P, Hooda BK, Arya RK. Multivariate analysis of pearl millet data to delineate genetic variation. Forage Res. 2015;40(4):201-208.