Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

Abstract

Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm.

Genetic diversity, population structure, and association mapping of agronomic traits in waxy and normal maize inbred lines

“…During the past few decades, QTL mapping has been used in many studies to detect genes that control phenotypic traits (Yan et al, 2006;Ma et al, 2007;Li et al, 2009). Recently, association mapping has been used as an alternative to QTL mapping, because it is effective in detecting marker-trait associations in LD data (Zhu et al, 2008;Borba et al, 2010;Lorenz et al, 2010;Mezmouk et al, 2011;Kwon et al, 2012).…”

“…Recently, association mapping based on LD has been used to identify genes that control important traits, and has been used in human genetics (Khoury et al, 2009). These methods have successfully been applied to the analysis of many crops (Zhu et al, 2008), e.g., rice (Borba et al, 2010), maize (Mezmouk et al, 2011), barley (Lorenz et al, 2010), and pea (Kwon et al, 2012).…”

Field level evaluation of rice introgression lines for heat tolerance and validation of markers linked to spikelet fertility

“…Identification of QTLs for heat tolerance may be limited by low marker coverage and small QTL effect (Steele et al 2006;Jena and Mackill 2008). Association mapping is another approach used for identifying genes controlling important traits (Borba et al 2010). A significant number of QTL for important traits have been found by genome-wide association studies (GWAS) in rice (Courtois et al 2013;Samuel et al 2010;Zhao et al 2007).…”

Genome-Wide Consistent Molecular Markers Associated with Phenology, Plant Production and Root Traits in Diverse Rice (<i>Oryza sativa</i> L.) Accessions under Drought in Rainfed Target Populations of the Environment

“…Mapping the markers related to drought resistance traits using diverse rice accessions will help in a better understanding of the genetic basis of drought resistance and to develop drought-resistant varieties. In rice, markers associated with disease resistance 13 , stigma and spikelet fertility characteristics 14 , flowering time 15 , yield and grain quality 16 , and agronomic traits 17 have been identified using AM.…”