Salsabila, Hana Azizah and Dr. Niken Kendarini, S.P., M.Si, and Dr Afifuddin Latif Adiredjo, SP, M.Sc., (2024) Genotypic and Phenotypic Variability among F7 Rice (Oryza sativa L.) Genotypes Based on Morphology and Simple Sequence Repeat (SSR) Marker. Magister thesis, Universitas Brawijaya.
Abstract
Rice is a staple food that is often consumed in Asia. However, rice production is stagnant throughout the world and unable to meet increasing demand. In Indonesia, almost 97% of the population consumes rice as a staple food, which in 2022 could reach a rice requirement of 39,99 ton per year with the productivity that reaches 31,54 million ton per year in a 10,45 hectwere field, leading to a mean where domestic production were not able to meet the population's needs. Increasing the potential for rice yields can be done through the use of plant breeding, which is the variation analysis through morphology and molecular markers by Simple Sequence Repeat (SSR). The aim of this study was to analyze the genetic variability of rice F7 and the distribution of genotypes through PCA and dendogram. The hypothesis of this research states that there is genetic variability in F7 rice as indicated by the distribution of genotypes based on the main components that contribute to genetic variability and dendogram clustering. The research were conducted from December 2023 to April 2024. Research activities was proceed in two locations, the research field of the Faculty of Agriculture Brawijaya University in Jatimulyo sub-district for planting and sampling and the Biotechnology Laboratory, Department of Agronomy, Faculty of Agriculture, Universitas Brawijaya for molecular analysis. The research will be carried out by testing 9 F7 genotypes of rice using 3 SSR primers consisting of CMAG59, CMCT505, and CMTA134a. Research methods include planting in a Randomized Block Design (RBD) with 3 replications, quantitative and qualitative morphological observation and DNA amplification. The molecular data results were analyzed by NTSYS version 2.02 and Microsoft Excel. The results of quantitative and qualitative morphological observation data were analyzed through PCA using RStudio. Correlation of morphological and molecular data were tested using Z-Mantel test. Similarity matrix results indicated that SSR markers showed higher genetic similarity than morphological traits. The result of dendrogram based on morphological traits, F7 4-21-11-23-6-2, F7 4-21-11-23-6-17, F7 4-21-11-23-3-2, and F7 4-21-11-23-3-12 has high similarity. Meanwhile, in the dendrogram of SSR markers, F7 4-21-11-23-3-11 and F7 4-21-11-23-6-11 that had high similarity. PCA revealed that leaf length and flag leaf length contributed most to genetic variability, with PC1 accounting for 65.1% of total variation. The highest polymorphism was found in CMCT505, with a PIC value of 0.6, indicating high informativeness. The correlation between morphological traits and SSR markers showed a matrix correlation (r) of 0.41483, Z = 22.3636, and P = 0.9883, suggesting a positive correlation but no significant relationship between them.
English Abstract
Rice is a staple food that is often consumed in Asia. However, rice production is stagnant worldwide and unable to meet increasing demand. In Indonesia, almost 97% of the population consumes rice as a staple food, which in 2022 could reach a rice requirement of 44,88 tons per year with a productivity that reaches 31,54 million tons per year in a 10,45 hectare field, leading to a mean where domestic production is not able to meet the population's needs. Increasing the potential for rice yields can be done through the use of plant breeding, which is the variability analysis through morphology and molecular markers by Simple Sequence Repeat (SSR). This study aimed to analyze the genetic variability of rice F7 and the distribution of genotypes through PCA. The hypothesis of this research states that there is genetic variability in F7 rice as indicated by the distribution of genotypes based on the main components that contribute to genetic variability. The research type for (RQ1 and RQ3) utilizes quantitative approaches. Meanwhile (RQ2) is conducted through quantitative and qualitative approaches. Data collection is through on-field measurements, laboratory activities, and literature studies. Data analysis for RQ1 employed similarity matrices both for morphological data and SSR data, RQ2 analyzed the clustering from PCA biplot, and RQ3 utilized the Z-Mantel test to show correlation.
| Item Type: | Thesis (Magister) |
|---|---|
| Identification Number: | 0424060097 |
| Uncontrolled Keywords: | genetic variability, genotype, morphology, molecular marker, correlation |
| Divisions: | S2/S3 > Magister Ilmu Tanaman, Fakultas Pertanian |
| Depositing User: | Unnamed user with username nova |
| Date Deposited: | 14 Oct 2024 02:50 |
| Last Modified: | 14 Oct 2024 02:50 |
| URI: | http://repository.ub.ac.id/id/eprint/229877 |
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