Dataset Information

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.

SUBMITTER: de Oliveira Borba TC

PROVIDER: S-EPMC3036121 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

de Oliveira Borba Tereza Cristina TC Brondani Rosana Pereira Vianello RP Breseghello Flávio F Coelho Alexandre Siqueira Guedes AS Mendonça João Antônio JA Rangel Paulo Hideo Nakano PH Brondani Claudio C

Genetics and molecular biology 20100701 3

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 gr ...[more]

PMID: 21637426

Similar Datasets

Project description:A core set of 190 rice landraces were used to decipher the genetic structure and to discover the chromosomal regions containing QTLs, affecting the grain micro-nutrients, fatty acids, and yield-related traits by using 148 molecular markers in this study. Landraces were categorized into three sub-groups based on population stratification study and followed by neighbor-joining tree and principal component analysis. Analysis of variance revealed abundant variations among the landraces for studied traits with less influence of environmental factors. Genome Wide Association Studies (GWAS) revealed 22 significant and consistent QTLs through marker trait association (MTAs) for 12 traits based on 2 years and pooled analysis. Out of 22 QTLs, three have been reported earlier while 19 QTLs are novel. Interestingly, 13 QTLs out of 22 were explained more than 10% phenotypic variance. Association of RM1148 and RM205 with Days to 50% flowering was comparable with flowering control genes Ghd8/qDTH8 and qDTH9, respectively. Similarly, Zn content was associated with RM44, which is situated within the QTL qZn8-1. Moreover, significant association of RM25 with oleic acid content was closely positioned with QTL qOle8. Association of RM7434 with grain yield/plant; RM184 with spikelet fertility %; R3M10, R9M42 with hundred seed weight; RM536, RM17467, RM484, RM26063 with Fe content; RM44, RM6839 with Zn content are the major outcomes of this study. In addition, association of R11M23 with days to 50% flowering, panicle length and total spikelets per panicle are explained the possible occurrence of pleiotropism among these traits. Prominent rice landraces viz., Anjani (early maturity); Sihar (extra dwarf); Gangabaru (highest grain yield/plant); Karhani (highest iron content); Byalo-2 (highest zinc content) and Kadamphool (highest oleic acid) were identified through this study. The present study will open many avenues towards utilization of these QTLs and superior landraces in rice breeding for developing nutrition-rich high yielding varieties.

Project description:Introduction Approximately 50% of irrigation water is saved during drip-irrigation of rice, which has tremendous potential for water-saving agriculture, particularly in areas where water resources are scarce. However, the grain yield and quality of drip-irrigated rice are adversely affected. Methods In this study, we investigated the effects of different irrigation strategies on the grain yield and quality of drip-irrigated rice using field experiments. Four irrigation treatments were studied: whole growing season flooding (FI), whole growing season normal drip irrigation (DI, soil relative moisture (RSM) was maintained in the range of 90-100%), pre-anthesis drip irrigation and post-anthesis water stress (SAF, the RSM was maintained in the range of 80-90% after anthesis), pre-anthesis drip irrigation, and post-anthesis flooding (FAF). Results The results showed that grain yield, harvest index, seed setting rate and 1000 grain weight in DI and SAF were significantly lower than in FI and FAF. These parameters were not significantly different between FI and FAF but were significantly greater in DI than in SAF. Compared with FI and FAF, the source capacity, source activity time, and sink activity of DI and SAF decreased, and the sink-source difference increased. The sink-source difference had a significant negative correlation with rice yield and 1000 grain weight. The activities of ADP-glucose pyrophosphorylase, starch branching enzyme, and amylopectin content in grains in the middle panicles of FAF were significantly higher than those of DI and SAF. SAF resulted in increased amylose/amylopectin ratio and total protein content in grains but decreased proportion of glutenin in total protein. Irrigation after anthesis of drip-irrigated rice narrowed the difference between sink sources in rice plants, increased the grain yield and harvest index by 29.2% and 11%, respectively, compared to DI, increased water productivity by 19% compared to FI, and improved the grain quality of drip-irrigated rice. Discussion This study highlights that post-anthesis sufficient irrigation of drip-irrigated rice plays a positive role in maintaining the source-sink balance. This study serves as a foundation for the development of more effective rice farming methods that conserve water, while increasing the grain yield and quality of drip-irrigated rice.

Project description:Microarray-based markers such as Diversity Arrays Technology (DArT) have become the genetic markers of choice for construction of high-density maps, quantitative trait loci (QTL) mapping and genetic diversity analysis based on their efficiency and low cost. More recently, the DArT technology was further developed in combination with high-throughput next-generation sequencing (NGS) technologies to generate the DArTseq platform representing a new sequencing tool of complexity-reduced representations. In this study, we used DArTseq markers to investigate genetic diversity and genome-wide association studies (GWAS) of grain quality traits in rice (Oryza sativa L.). The study was performed using 59 rice genotypes with 525 SNPs derived from DArTseq platform. Population structure analysis revealed only two distinct genetic clusters where genotypes were grouped based on environmental adaptation and pedigree information. Analysis of molecular variance indicated a low degree of differentiation among populations suggesting the need for broadening the genetic base of the current germplasm collection. GWAS revealed 22 significant associations between DArTseq-derived SNP markers and rice grain quality traits in the test genotypes. In general, 2 of the 22 significant associations were in chromosomal regions where the QTLs associated with the given traits had previously been reported, the other 20 significant SNP marker loci were indicative of the likelihood discovery of novel alleles associated with rice grain quality traits. DArTseq-derived SNP markers that include SNP12_100006178, SNP13_3052560 and SNP14_3057360 individually co-localised with two functional gene groups that were associated with QTLs for grain width and grain length to width ratio on chromosome 3, indicating trait dependency or pleiotropic-effect loci. This study demonstrated that DArTseq markers were useful genomic resources for genome-wide association studies of rice grain quality traits to accelerate varietal development and release.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets