The classification of the Musaceae (banana) family species and their phylogenetic inter-relationships remain controversial, in part due to limited nucleotide information to complement the morphological and physiological characters. In this work the phylogenetic relationships within the Musaceae family were studied locally using 3 species. DNA sequences obtained from nine unlinked nuclear genes. Musa species grow in a wide range of environments and have varied human uses, ranging from the edible bananas and plantains of the tropics to cold-hardy fibre and ornamental plants. There are five taxonomic sections in the genus Musa, two of which contain edible bananas. For studying phylogeny of locally collected Musaceae (banana) family varieties using rbcL gene and matK gene. For this study DNA was extracted by using CTAB method. This extracted DNA was analysed by spectrophotometry method for checking purity of DNA. The samples were gel electrophoresed by 1% agarose gel electrophoresis at 80 volts. After electrophoresis the gel is examined in gel documentation system. The DNA band was observed under UV light looking florescent orange red colour. The extracted DNA was amplified by PCR method and PCR sample was applied for electrophoresis for checking DNA bands. After all this analysis PCR sample send for DNA sequencing for checking the nucleotide. Comparing the sequenced nucleotide for checking phylogeny of locally collected banana varieties. The locally collected gene sequence-based phylogeny presented here provides support for the early studies of speciation within the Musaceae. An understanding of the main phylogenetic relationships between banana species will help to fine-tune the taxonomy of Musaceae.
Table of Contents
1. Introduction
1.1 Objectives
1.2 Objectives of the study
1.3 Taxonomical classification
2. Review of literature
2.1 Uses and importance
2.2 Banana stem and flower
2.3 Banana Leaves:
2.4 Environmental status:
2.5 Molecular markers
3. Hypothesis
4. Materials and Methods
4.1 Study area
4.2 Sample collection
4.3 Description of the species
4.4 Species identification
4.3 Isolation of DNA
4.5 Quantification of DNA
4.6 PCR primers
4.7 PCR amplification
4.8 Data sequencing
4.9 Data analysis
4.11 Statistical analysis
5. Results and discussion
5.1 BLAST search for rbcL: sample A; Palayankodan
5.2 BLAST search for rbcL: sample B; Njalipoovan
5.3 BLAST search for rbcL: sample C; Robusta
5.4 BLAST search for matK: sample A; Palayankodan
5.5 BLAST search for matK : sample B; Njalipoovan
5.6 BLAST search for matK: sample C; Robusta
5.7 Multiple sequence alignment for partial rbcL gene for Musaceae
5.8 Multiple sequence alignment for partial matK gene for Musaceae
5.9 Phylogenetic tree based on partial sequence rbcL gene by UPGMA method
5.10 Phylogenetic tree based on partial sequence rbcL gene by Maximum likelihood method
5.11 Calculation of genetic distance using rbcL gene
5.12 Phylogenetic tree based on partial sequence matK gene by UPGMA method
5.13 Phylogenetic tree based on partial sequence matK gene by Maximum likelihood method
5.14 Calculation of genetic distance using matK gene
6. Conclusions
Research Objectives and Themes
The primary objective of this study is to determine the phylogenetic relationships among locally cultivated Musaceae varieties in Kerala by utilizing PCR-based amplification and sequencing of the rbcL and matK genes to analyze genetic variations. The research aims to establish a molecular basis for taxonomic classification and genetic differentiation within the collected samples.
- Phylogenetic assessment of Musaceae species using rbcL and matK markers.
- Isolation and genomic analysis of local banana varieties including Robusta, Njalipoovan, and Palayankodan.
- Evaluation of genetic diversity through sequencing and bioinformatics tools like BLAST and UPGMA.
- Examination of morphological characteristics in relation to genetic data.
- Application of statistical methods to confirm phylogenetic relationships and speciation patterns.
Excerpts from the Book
1. Introduction
Musa is a member of the monocot order Zingiberales, a lineage of Commelinids that diverged from the lineage leading to rice (Poales) in the mid Cretaceous period over 100 million years ago. The banana plant is a large perennial herb with leaf sheaths that form trunk-like pseudostems. These are tree-like, herbaceous plants that live in warm countries. They can be grown in hot houses in colder areas, or outside during the summer months for the tropical beauty of their large, paddle-shaped leaves. The "stems" of these plants are made of overlapping leaf sheaths that die after flowering.
The common Banana is Musa paradisiaca subspecies sapientum. It can grow to 15 or 20 feet tall and produce seedless, nourishing fruits. There are many different kinds; most having yellow skin, but some are red. Some of the better-known varieties are: Gros Michel, Red Jamaica, Apple, Orinoco and Champa (Lady-Finger Banana). The Plantain, M. paradisiaca, is a species of Musa that grows about 30 feet high and produces green or greenish-yellow seedless fruits that can be eaten after they have been cooked. It is grown in most tropical countries and is a part of the staple diet. It's probably a native of India (Chia, 1981).
Summary of Chapters
1. Introduction: Outlines the biological and taxonomic background of the Musaceae family, the economic importance of banana varieties, and the research objectives regarding their phylogenetic classification.
2. Review of literature: Examines the botanical significance, traditional uses, environmental requirements, and current knowledge regarding molecular markers used in phylogenetic studies of Musa spp.
3. Hypothesis: Presents the research assumptions, positing that morphological variations among local Musaceae varieties correlate with their genetic diversity, which can be elucidated via matK and rbcL genes.
4. Materials and Methods: Details the field collection of samples across Kerala, DNA extraction procedures using the CTAB method, PCR amplification parameters, and the subsequent bioinformatics analysis.
5. Results and discussion: Provides the experimental findings, including BLAST search results, sequence alignments, and the construction of phylogenetic trees based on molecular data for the studied varieties.
6. Conclusions: Summarizes the findings, noting that while rbcL markers showed minimal difference among selected samples, matK markers revealed variations that provide insights into genetic relationships and speciation.
Keywords
Musaceae, matK, rbcL, PCR, RFLP, Phylogenetics, DNA sequencing, Kerala, Musa acuminata, genetic distance, plant systematics, UPGMA, molecular markers, speciation, banana varieties.
Frequently Asked Questions
What is the core focus of this research?
This research focuses on investigating the genetic relationships and phylogenetic structure of locally cultivated Musaceae (banana) varieties in Kerala using molecular markers.
Which specific genes were targeted in this study?
The study utilized the rbcL (ribulose-1,5-bisphosphate carboxylase oxygenase) and matK (maturase K) genes as molecular targets for phylogenetic analysis.
What is the primary scientific aim of the work?
The main goal is to generate baseline information regarding the phylogenetic relatedness and variations among local Musa varieties, helping to refine their taxonomy.
Which methodology was employed for DNA analysis?
The research employed the CTAB method for DNA extraction, followed by PCR amplification, DNA sequencing, and bioinformatics analysis using ClustalW and MEGA software.
What topics are covered in the main body of the text?
The main body covers the botanical description of banana species, the review of existing phylogenetic literature, the detailed experimental protocols, and the discussion of BLAST results and tree construction.
What defines the core set of keywords for this study?
The keywords are centered on the plant family Musaceae, the specific genes used (matK, rbcL), the techniques applied (PCR, RFLP, phylogenetic reconstruction), and the study's geographical context.
How did the study distinguish between different banana varieties?
The study combined morphological observation of physical traits (stem size, leaf morphology) with molecular data obtained from sequencing chloroplast DNA genes.
What was the observed difference between rbcL and matK markers in this study?
The findings indicated that while the rbcL gene showed little variation among the locally collected samples, the matK gene revealed slight variations that were more useful for phylogenetic discrimination.
Why are matK genes considered particularly useful for this research?
The matK gene is noted for its relatively fast mutation rate compared to other chloroplast genes, making it highly effective for studying phylogeny at the family or genus level.
- Arbeit zitieren
- Dr. Prem Jose Vazhacharickal (Autor:in), Sajeshkumar N. K. (Autor:in), Jiby John Mathew (Autor:in), Mathew Sebastian (Autor:in), Betty Sebastian (Autor:in), 2016, Studies on genetic relationships among locally cultivated Musaceae varieties in Kerala employing rbcL and matK gene using PCR technique and RFLP markers, München, GRIN Verlag, https://www.grin.com/document/370768
