Issue Date
2024
Abstract
To facilitate abaca (Musa textilisNee) genotype screening, microsatellite markers developed from RNA-seq data of M. textilis cv. ‘Abuab’, M. balbisiana cv. ‘Pacol’, and ‘Abuab × Pacol’ backcross progenies were utilized. Through a modified bioinformatics pipeline for in silico SSR mining, an average of 4,611 non- redundant SSRs (94.95%) were retrieved. Trinucleotide SSRs (38.5%) were the most abundant, followed by dinucleotides (32.47%). A total of 15,305 primer pairs were designed from this study. Twenty-four polymorphic SSRs from a random set of 50 SSR markers selected for validation were successfully cross- amplified in different abaca genotypes. The average number of alleles per locus, observed heterozygosity, Shannon’s information index, and polymorphic information content were 6.11, 0.449, 1.448, and 0.738, respectively. Analysis of banding patterns and hierarchical clustering revealed distinct grouping of Pacol and backcross progenies from Abuab and other abaca genotypes. The 70.83% of the identified polymorphic SSR markers showed significant alignment with M. acuminata subsp. malaccensis transcripts, including expansin, a fiber-quality gene. More than twelve percent of the identified polymorphic SSR markers targeted unique sequences when compared to published sequences in NCBI. The identified SSR markers were also capable of discriminating between Abuab accessions and are therefore recommended for future abaca screening work.
Source or Periodical Title
UP Los Baños Journal
Volume
22
Issue
3
Page
52-72
Document Type
Article
College
College of Arts and Sciences (CAS)
Recommended Citation
Calapit-Palao, Cecilia Diana O.; Diaz, Maria Genaleen Q.; Laude, Rita P.; Mendioro, Merlyn S.; Lalusin, Antonio G.; and Laurena, Antonio C., "RNA-seq data derived microsatellite markers for polymorphism detection and profiling of abaca (Musa textilis NEE) and selected relatives" (2024). Journal Article. 6311.
https://www.ukdr.uplb.edu.ph/journal-articles/6311