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ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Plant Genetic Resources and Disease Research » Research » Publications at this Location » Publication #419366
Research Project: Conservation, Management, and Genetic Improvement of Tropical and Subtropical Fruit, Nut, and Beverage Crop Germplasm for the Pacific Region

Location: Tropical Plant Genetic Resources and Disease Research

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

Author
item LYU, HAOMIN - Hawaii Agricultural Research Center
item Matsumoto Brower, Tracie
item Yu, Qingyi

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/21/2025
Publication Date: 7/19/2025
Citation: Lyu, H., Matsumoto Brower, T.K., Yu, Q. 2025. Unraveling genetic diversity and population structure of pineapple germplasm using genome-wide SNP markers. Molecular Genetics and Genomics. 300. Article 71. https://doi.org/10.1007/s00438-025-02275-1.
DOI: https://doi.org/10.1007/s00438-025-02275-1

Interpretive Summary: Pineapples are primarily propagated clonally and exhibit strong self-incompatibility, which result in a high level of heterozygosity. High level of heterozygousity can mask unfavorable alleles and potentially cause severe inbreeding depression and hinder breeding efforts. To address this challenge, we analyzed the population structure and heterozygosity of 91 pineapple accessions. This assessment provides important information for selecting optimal breeding materials for cultivar improvement. Furthermore, we developed two SNP panels to facilitate pineapple germplasm evaluation, diversity analysis, and informed breeding decisions for breeding programs.

Technical Abstract: 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. ccomosus, A.comosus var. bracteatus, and A. comosus var. erectifolius. 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.