Genetic Diversity of Indigenous Rice Landraces Assessed Using SSR Markers

Abstract

Farmer-maintained rice landraces hold much of the variation that breeders and gene banks hope to use, and simple sequence repeat (SSR) markers have been the workhorse for describing it for almost two decades. This narrative review asks what an SSR survey of indigenous rice landraces can and cannot tell a reader. It draws on published work on rice domestication and population structure, on the discovery and behaviour of microsatellites, on the statistics used to summarise allelic data, and on the practical problems of sampling and scoring, and it reports no new data. SSR markers are co-dominant, multi-allelic and cheap to run, which makes them well suited to comparing many accessions at modest cost; they are also prone to scoring differences between laboratories, null alleles and size homoplasy, and a limited set of loci may say little about genes of agronomic value. Rice is largely self-pollinating, so landrace accessions are mostly homozygous and the usual heterozygosity-based summaries must be read with care. Common weaknesses in published surveys include unclear definitions of what counts as a landrace, small or uneven samples, unreported scoring rules and over-interpretation of clusters. The review concludes that SSR surveys remain a sound first step for describing and conserving landrace diversity, provided that sampling, scoring and analysis are reported openly, and it sets out a short list of reporting practices.