Unraveling genetic diversity and population structure of pineapple germplasm using genome-wide SNP markers

Pineapple (Ananas comosus (L.) Merr.) is one of the most important tropical fruits worldwide. It is primarily propagated clonally and exhibits high heterozygosity which can mask deleterious mutations, potentially leading to inbreeding depression and hindering breeding efforts. To address this, we conducted a comprehensive genome-wide analysis of 91 pineapple accessions and identified over 7.9 million high-quality SNPs. We utilized these SNPs to investigate the genetic structure and reproductive patterns of diverse cultivars and related varieties. Population structure analysis revealed a unique genetic makeup of A. comosus var. microstachys accessions and unidirectional gene flow from A. comosus var. microstachys into A. comosus var. comosus, A. comosus var. bracteatus, and A. comosus var. erectifolius. Among the cultivated pineapples, 'Mordilona-related' and 'Smooth Cayenne' cultivars showed unidirectional gene flow from 'Singapore Spanish', 'Queen', and the wild A. comosus var. microstachys. Heterozygosity patterns suggested predominantly asexual reproduction in 'Queen', 'Singapore Spanish', 'Smooth Cayenne', and A. comosus var. microstachys populations, while 'Mordilona-related' and A. comosus var. bracteatus populations might have experienced increased sexual reproduction or population expansion. We developed two SNP panels: one for germplasm identification and the other one for pedigree analysis. These resources will facilitate pineapple germplasm evaluation, diversity analysis, and informed breeding decisions for cultivar improvement.