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

• Published in: Genetics and molecular biology Vol. 33; no. 3; pp. 515 - 524
• Main Authors: de Oliveira Borba, Tereza Cristina, Brondani, Rosana Pereira Vianello, Breseghello, Flávio, Coelho, Alexandre Siqueira Guedes, Mendonça, João Antônio, Rangel, Paulo Hideo Nakano, Brondani, Claudio
• Format: Journal Article
• Language: English
• Published: Brazil Sociedade Brasileira de Genética 01.01.2010
• Subjects: association analysis; BIOCHEMISTRY & MOLECULAR BIOLOGY; core collection; genetic structure; GENETICS & HEREDITY; Plant Genetics; core collection; association analysis; genetic structure
• ISSN: 1415-4757; 1678-4685; 1678-4685
• DOI: 10.1590/S1415-47572010005000065

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.