Candidate-gene based gwas for identification of genomic regions associated with brittleness in rice [Oryza sativa L.]
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Date
2020-10-20
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Vasantrao Naik Marathwada Krishi Vidyapeeth, Parbhani
Abstract
Rice (Oryza sativa L.) (2n=24) is the most important cereal crop that has been referred to as “Global Grain” because of its use as a prime staple food in about 100 countries of the world. Rice straw burning has disadvantages from an environmental perspective, especially for those practicing double or triple cropping, but it could result in the loss of major nutrients. Huge scope fordevelopmentofbrittlericelinesbymodifyingthecellwallcomponentswhichcanmakesthem to easily degradable in soil. The present study was aim to assess the Brittleness trait for selected 150 lines form 3K rice panel germplasm and Genome wide association study for the brittleness trait.
The results of the experiment represents that among the 150 experimental lines there are less number of highly brittle lines and more number of partially brittle lines, analyzed by phenotyping for leaf and stem brittleness at mature stage. In phylogenetic analysis 150 rice accessions from 3K rice panel into five distinct varietal groups based on Phylogenetic clustering through neighbor-joining method and Jukes–Cantor genetic distance using the program MEGA7. Population structure analysis through principle component method results the percentage of variants in population with respect major varietal groups of rice , PC1- 11%, PC2- 8.2%, PC3- 2.8% and PC4-2.4%. In the genome wide association study for the brittleness traits results a total 28SNPsweresignificantlyassociatedwithstembrittleness.80SNPsweresignificantlyassociated with leaves brittleness. No QTLs where found in both the case for leaves and stem brittleness. A MAF are found associated with brittleness. In GWAS using smaller numbers of individuals, markers with MAF less than 0.05 are oftenexcluded.