Molecular characterization of popular rice ( Oryza sativa L.) varieties of India and association analysis for blast resi
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RESEARCH ARTICLE
Molecular characterization of popular rice (Oryza sativa L.) varieties of India and association analysis for blast resistance Mawuli K. Azameti . B. Vishalakshi . B. Umakanth . Marathi Balram . M. Srinivas Prasad . Maganti Sheshu Madhav
Received: 17 November 2019 / Accepted: 8 July 2020 Ó Springer Nature B.V. 2020
Abstract Blast is a major biotic factor accountable for near-complete yield loss in rice (Oryza sativa L.). Thirty-seven leaf blast resistant lines were found out of 103 rice germplasm through phenotyping. Subsequent genotyping of the germplasm for five important blast resistance genes of India namely, Pitp, Pi1, Pi2, Pi9, and Pi54 using gene-specific markers revealed the prevalence of Pitp as more and Pi2 as least in the tested lines. An initial genetic diversity study showed the highest PIC value of 0.77 for RM234 defining its high polymorphic behaviour. Model-based and distance-based approaches showed a high correlation in displaying genetic diversity. The modelbased structural analysis based on log-likelihood (Dk) displayed three clusters and remaining accessions Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10722-020-00976-7) contains supplementary material, which is available to authorized users. M. K. Azameti M. Balram Institute of Biotechnology, College of Agriculture, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad, India B. Vishalakshi B. Umakanth M. S. Madhav (&) Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500030, India e-mail: [email protected] M. Srinivas Prasad Department of Pathology, Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
under admixture. Distance-based analysis using Unweighted Pair Group Method with Arithmetic Mean method also divided the accessions into three major clusters. Analysis of molecular variance revealed a variation of 19% among the populations, while 81% within the populations. The association analysis using 101 SSR markers revealed ten newly identified marker-trait associations by General Linear Model and two marker-trait associations using Mixed Linear Model approach. These markers can be validated in a large set of germplasm and can be used in marker-assisted selection. The identified resistant sources having known genes can be readily used in the breeding programmes. Keywords AMOVA Association mapping Blast resistance Population structure SSR marker
Introduction Blast caused by Magnaporthe oryzae is one of the most devastating diseases of rice (Oryza sativa L.), evolving in all rice-growing areas leading to a yield loss of up to 100% (Kato 2001). Every year it destroys the rice crop that could feed 60 million people, costing approximately $66 billion (Pennisi 2010). Controlling the disease using fungicides is not economical and eco-friendly in most of the developing countries, including India and Ghana. Therefore, the use of
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