Identification of candidate markers associated with agronomic traits in rice using discriminant analysis

Abstract

Plant genetic mapping strategies routinely utilize marker genotype frequencies obtained from progeny of controlled crosses to declare presence of a quantitative trait locus (QTL) on previously constructed linkage maps. We have evaluated the potential of discriminant analysis (DA), a multivariate statistical procedure, to detect candidate markers associated with agronomic traits among inbred lines of rice (Oryza sativa L.). A total of 218 lines originating from the US and Asia were planted in field plots near Alvin, Texas, in 1996 and 1997. Agronomic data were collected for 12 economically important traits, and DNA profiles of each inbred line were produced using 60 SSR and 114 RFLP markers. Model-based methods revealed population structure among the lines. Marker alleles associated with all traits were identified by DA at high levels of correct percent classification within subpopulations and across all lines. Associated marker alleles pointed to the same and different regions on the rice genetic map when compared to previous QTL mapping experiments. Results from this study suggest that candidate markers associated with agronomic traits can be readily detected among inbred lines of rice using DA combined with other methods described in this report.

Phenotypic and QTL analyses of herbage production-related traits in perennial ryegrass (Lolium perenne L.)

“…Markers in the LG6 region flanking this QTL position corresponded to a segment between 28-31 Mb on rice pseudomolecule chromosome 2 (Table 11), consistent with earlier comparative analyses (Jones et al 2002b;Sim et al 2005). In rice, the distal end of chromosome 2 has been associated with QTL for tiller number (Yan et al 1998;Takehisa et al 2004;Zhang et al 2004) and plant biomass (Liu et al 2006). Markers flanking those QTL, including C424 (26.5 Mb) R3393 (28.4 Mb), RZ58 (28.7 Mb), C1408 (30.1 Mb), CD0686 (30.9 Mb) and RM240 (31.5 Mb), map to a physical location (www.…”

“…For example, we were able to show that the LG6 QTL for TN in both spring and autumn appears to correspond to a region of rice chromosome 2 that has been repeatedly identified as associated with tiller or biomass production in rice (Yan et al 1998;Takehisa et al 2004;Zhang et al 2004;Liu et al 2006). This genome position may therefore harbour conserved genes that regulate above-ground biomass in a range of grasses, and markers from this position could be utilised effectively in breeding for biomass outcomes in different grass species.…”

Genetic and molecular basis of grain size and grain number and its relevance to grain productivity in higher plants

“…For example, in a study conducted in bread wheat, 14 loci (6 on 2D and 4 each on 5A and 5D) showing significant association with different grain morphology traits (including grain mass, area, length, and width) were identified (Breseghello and Sorrells 2006). Similarly, a solitary locus in maize (chromosome 5) and 4 loci in rice showing association with 1000-kernel mass were identified (Buntjer et al 2005;Zhang et al 2005). Near-isogenic lines (NILs) were also developed in rice for these 2 traits, which facilitated positional cloning of the underlying genes, OsCKX2 encoding cytokinin oxidase/dehydrogenase and GS3 encoding a transmembrane protein (Ashikari et al 2005;Fan et al 2006).…”

Genetic diversity and marker-trait associations in a collection of Pak-choi (Brassica rapa L. ssp. chinensis Makino) Accessions

“…A set of novel approaches have recently been proposed, wherein QTLs are associated with traits of interest through association genetics after the phenotypic and genotypic characterization of collections of diverse materials (Lynch and Walsh, 1997;Flint-Garcia et al, 2005). Association mapping is a reliable tool in highlighting markertrait associations in different plant species (Zhang et al, 2005;Breseghello and Sorrels, 2006). Current methods for accounting for population structure are described by Yu et al, (2006), and are illustrated numerous cases (Hasan et al, 2008;Achleitner et al, 2008;Mazzucato et al, 2008;D'hoop et al, 2008).…”