Abaca functional genomics: high throughput discovery of genes and molecular markers
Date
2015
Abstract
This research project is the first to establish the genomic resources of the Philippine endemic abaca. This laid down the fundamentals not just of genomics researching in the Philippines, but also answers the questions on genetic, molecular and biochemical mechanisms underlying particular traits in abaca, including fiber quality and disease resistance. The establishment of the genomic resources of abaca has been performed through three-platforms: High-throughout Genome sequencing, High-throughput Transcriptome sequencing and Sanger sequencing of abaca (cv Abuab), pacol and BC2. The first platform, High-throughput Genome sequencing of the exome-filtered whole genome of abaca (cv abuab) has been assembled and annotated. The fir st draft assembly of the abaca genome in the Philippines. From the annotated genome of abaca (cv abuab), putative functions related to fiber quality were elucidated, including 38 genes coding for polysaccharide synthases and glycosyl transferase,93 genes coding for Assembly, Architecture and Growth, 43 genes coding for differentiation and Secondary cell wall formation, and 5 genes coding for structural proteins. The second platform was High-throughput transcriptome sequencing. Three to four month old tissue-culture derived seedlings of BC2A2 hybrids were obtained through RNA-Seq and clustering analysis via K-means method, 349 genes were observed to be differentially expressed and 41 of these re specific genes that are uniquely expressed in each of the five samples relative to all the other samples. The observed occurrence in the abaca backcross hybrid of high amounts of the putative defense response genes that forms the five modes of immunity, directly supports the possibility that these molecular mechanisms play major roles to protect the hybrid against the damaging effects of ABTV infection.The third platform Sanger sequencing lead to he development o SSR-based markers and gene specific markers from the genomic data and Gene-enriched microgenomic DNA libraries. A total of 157 SSR primers were successfully designed. This technique may provide a sample but efficient mean to help find coding regions of large genome plant species and produce more sequences, more quickly, at greater resolution. Using molecular and bioinformatics tool this three-year project has generated enough genomic resources that can be used for association to the traits of economic importance.
Language
English
Document Type
Article
Recommended citation
Laurena, A. C., "Abaca functional genomics: high throughput discovery of genes and molecular markers" (2015). Report. 427.
https://www.ukdr.uplb.edu.ph/reports/427
Pages /Collation
184 leaves
En – AGROVOC descriptors
MUSA TEXTILIS; INDIGENOUS ORGANISMS; GENETIC MARKERS; GENOMES; GENES; GENETIC RESISTANCE; PLANT FIBRES; DISEASE RESISTANCE; GENE EXPRESSION