Functional genomics- and bioinformatics-assisted gene marker development for economically important traits in cacao
Abstract
© 2018 International Society for Horticultural Science. All Rights Reserved. Varietal improvement is needed in cacao for increased yield, resistance to pests and diseases, and other economically important traits. To facilitate marker-assisted breeding and selection programs, molecular markers are essential tools. Through functional genomics and bioinformatics, gene markers were generated using two approaches: genome filtering using methylation-sensitive restriction enzymes and gene mining in the cacao genome sequence database. In the genome-filtering method, genomic DNA of a number of cacao cultivars was digested with methylation-sensitive restriction enzymes for ligation, amplification, cloning, sequencing and bioinformatics analysis. From 215 library samples, a total of 578 putative simple sequence repeat (SSR) loci were predicted from the sequences, with 271 perfect loci and 307 ambiguous. The unique and perfect SSRs with primers were subjected to homology and gene ontology analysis. These SSRs were involved in 11 molecular functions, 11 cellular components, and 25 biological processes. In the gene-mining approach, genome sequences were downloaded from the database for bioinformatics analysis. Sequences were analyzed for de novo annotation, SSR prediction and deduplication, SSR marker and primer development, homology and gene ontology. A total of 4897 putative SSR locus regions were predicted from the coding DNA sequence regions of the cacao genome, with 3423 perfect loci and 1474 ambiguous loci. The unique and perfect SSRs with primers were involved in seven molecular functions, six cellular components, and 17 biological processes. SSR markers for genes of interest from both approaches were selected for amplification to assess polymorphism among cacao cultivars.
Source or Periodical Title
Acta Horticulturae
ISSN
5677572
Page
85-91
Document Type
Article
Subject
Bioinformatics, Cacao, Gene markers, Genomics, Simple sequence repeats
Recommended Citation
Barlaan, E. A.; Sales, E. K.; and Laurena, A. C., "Functional genomics- and bioinformatics-assisted gene marker development for economically important traits in cacao" (2021). Journal Article. 1051.
https://www.ukdr.uplb.edu.ph/journal-articles/1051