Newly developed genomic SSR markersrevealed the population structure and genetic characteristicsof abaca (Musa textilis Nee)

Abaca (<i>Musa textilis</i> Nee) is the primary source of manila hemp fiber, a vital industrial product for the country. Previous studies have relied on molecular markers designed for other <i>Musa</i> species or distant genera like rice, limiting accurate genetic characterization and germplasm conservation. To address this, we developed 50 genome-specific molecular markers based on the recently released whole genome sequence assembly of Abaca var. <i>Abuab</i> by Galvez et al. (2021). Among these markers, 28 showed high polymorphism, with an average PIC value of 0.78. Population analysis revealed a heterozygosity of 0.428, indicating moderate genetic diversity, supported by an alpha value of 0.0735 and an <i>F</i> _stp value of 0.0815, which suggests moderate genetic differentiation among abaca accessions. Cluster analyses, generated by DARwin and STRUCTURE software with 91% similarity, identified four clusters. The new markers were also able to distinguish six <i>Musa</i> accessions exhibiting morphological traits of both abaca and banana. Discrepancies in sample identification due to identical or inverted names were resolved using population structure analysis. Molecular variance analysis showed a 12% variance among the four abaca subpopulations and 88% within populations, suggesting recent divergence. Our study highlights the diversity, identity, and genetic variation within the abaca collection using accurate, robust, cost-effective, and computationally simple genome-specific markers. These markers are pivotal for genetic studies of abaca, including traitmarker mapping and the differentiation of accessions even in the juvenile stage, when phenotypic differences may be subtle.