Association analysis of important agronomic traits in japonica rice germplasm

Abstract

For unraveling complex genetic traits and for marker-assisted selection in plant breeding, using elite germplasm for quantitative trait loci (QTL) mapping provides advantages over traditional linkage analysis. Association or linkage disequilibrium (LD) mapping revolutionized genetic mapping in humans, and is increasingly being used to examine plant genetics; it has been suggested that it is an efficient way of determining the genetic basis of complex traits. In this study, a natural population comprising 128 japonica rice varieties was investigated during two years, for eleven important agronomic traits. The population was genotyped using 152 microsatellite markers across the whole genome. A unified mixed linear model was used to identify marker-trait associations, taking into account population structure and kinship. A total of 16 significant marker-trait associations were identified. It is noteworthy that the loci exhibiting significant marker-trait associations were in genomic regions also identified as such in previous reports, and some new QTL regions for important agronomic traits were also detected in this study. Our results demonstrate that using association analysis to examine different varieties is an efficient approach and provides indicators that can be used in rice breeding.

Key words: Association mapping, linkage disequilibrium, agronomic traits, rice.