Genetic purity assessment of rice hybrid seeds using microsatellite markers

Abstract:

A challenge facing the Philippine hybrid rice industry is that traditional grow-out tests (GOT) for seed purity take 90-110 days, generate variable results, and cost PHP 8,500-12,800 per lot, which delays distribution and erodes grower confidence. This research evaluated microsatellite (SSR) marker-based genetic purity assessment as an alternative across six commercial rice hybrid seed lots (Sahyadri-2, KRH-4, PHB-71, PA-6444, Suruchi, 25P25) procured from certified seed production fields in wet season 2022 and 2023. Six highly polymorphic SSR markers (RM490, RM231, RM204, RM287, RM335, RM72) were selected for foreground discrimination. Each hybrid lot was tested at four sample sizes (n = 30, 60, 90, 120 plants). SSR-based purity estimates converged toward stable values at n ≥ 90 plants, with 95% confidence intervals of±1.2 percentage points. Four of the six lots passed the 98% certification threshold (Sahyadri-2: 99.2%, KRH-4: 98.7%, PA-6444: 98.4%, 25P25: 98.1%), two failed (PHB-71: 96.3%, Suruchi: 94.8%). Concordance with GOT on duplicate subsamples was 98.3%. SSR testing completed in 6 working days at PHP 4,900 per lot—about 60% cost and 5% time compared with GOT. The data support SSR-based purity assessment as a practical replacement for grow-out testing in commercial rice hybrid seed certification.