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

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.

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

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 analysis of a local population of Oryza glumaepatula using SSR markers: implications for management and conservation programs.

Knowledge of natural diversity and population structures of wild species, which might be related to cultivated species, is fundamental for conservation and breeding purposes. In this study, a genetic characterization of a large population of Oryza glumaepatula, occurring in a 10 km(2) area located at Tamengo Basin (Paraguay River, Brazil), was performed using SSR markers. This population is annually dragged from the river to permit navigation; one goal of this study was to examine the impact of this removal on genetic variability. From 18 polymorphic SSR markers, a total of 190 alleles were detected in a sample of 126 individuals, with an average of 10.3 alleles/locus, and a H(e) of 0.67. The five QTL-related markers showed an average H(e) value of 0.56, while the remaining 13 markers detected an average estimate of 0.70. An apparent outcrossing rate of 30%, a high proportion of alleles at low frequencies (56%), and the presence of exclusive alleles (9.5%) were found, with strong evidence of the establishment of individuals from different populations upstream in the Paraguay River. For conservation purposes, the river drag has no effect on the population. However, periodical seed collection from the Corumbá population can preserve part of the genetic variability present in upstream populations reducing the need for upriver collecting expeditions.

Microsatellite marker-mediated analysis of the EMBRAPA Rice Core Collection genetic diversity.

The objectives of this study were to determine the genetic structure of 242 accessions from the EMBRAPA Rice Core Collection (ERiCC), to create a mini-core collection and to develop a multiplex panel of fluorescent labeled simple sequence repeats (SSRs). Eighty-six SSRs were used to identify 1,066 alleles, with an average number of 12.4 alleles/locus and average polymorphism information content (PIC)/locus of 0.75. A model-based clustering method recognized the structure of the accessions on two levels, according to their cultivation system and origin. The most divergent subgroup identified was the worldwide lowland accessions, with the highest values for gene diversity (0.75), average Rogers distance modified by Wright (0.80), average number of alleles/locus (11.7) and private alleles (132). A mini-core was assembled with the most divergent 24 lowland and upland accessions. This mini-core displayed an average distance of 0.86, an average number of alleles/locus of 8.4 and an average PIC/locus of 0.8. From the 86 SSRs, 24 were selected to compose six multiplex panels in order to optimize the process of rice genotyping. This set of markers distinguished all 242 accessions, and showed an average PIC of 0.80 and an average number of alleles/locus of 15.4, higher than the entire set of 86 SSRs. Since the heterogeneity found in lines and cultivars of ERiCC was higher than expected, it is necessary to analyze pooled DNA samples to get a better estimate of genetic variability. The SSR characterization of ERiCC clearly indicates that there is high genetic variability in rice accessions stored in genebanks worldwide which can be promptly explored by rice pre-breeding programs.

Comparative linkage mapping of Oryza glumaepatula and Oryza sativa interspecific crosses based on microsatellite and expressed sequence tag markers

Molecular linkage maps representing the rice genome have been an important tool for breeding programs because they allow the elucidation of polygenic traits and are an efficient tool for monitoring wild introgressions in interspecific crosses. Common markers among rice genetic maps are important in defining the homology of chromosomes and the synteny between genomic target regions. We used 148 markers (expressed sequence tags, microsatellites and single nucleotide polymorphisms) to construct a molecular linkage map based on co-dominant markers for an interspecific backcross population using a wild rice (Oryza glumaepatula) from Brazil and performed a comparative analysis with other interspecific maps. The comparative analysis revealed a Spearman correlation index of 0.86 for marker order conservation to a previous map constructed for an interspecific cross using the same wild parent. Approximately 90 percent of markers common to other interspecific maps kept the same order. These results indicate that it will be possible to generate a unique genetic map using the wild donor and that it may be a helpful tool for breeding programs because plants derived from different interspecific populations can be rapidly scanned using markers associated with useful wild traits.

Determination of genetic variability of traditional varieties of Brazilian rice using microsatellite markers

The rice (Oryza sativa) breeding program of the Rice and Bean research center of the Brazilian agricultural company Empresa Brasileira de Pesquisa Agropecuária (Embrapa) is well established and provides new cultivars every year to attend the demand for improved high yielding varieties with tolerance to biotic and abiotic stresses. However, the elite genitors used to compose new populations for selection are closely related, contributing to the yield plateau reached in the last 20 years. To overcome this limit, it is necessary to broaden the genetic basis of the cultivars using diverse germplasm such as wild relatives or traditional varieties, with the latter being more practical because they are more easily crossed with elite germplasm to accelerate the recovery of modern plant types in the breeding lines. The objective of our study was to characterize the allelic diversity of 192 traditional varieties of Brazilian rice using 12 simple sequence repeat (SSR or microsatellite) markers. The germplasm was divided into 39 groups by common name similarity. A total of 176 alleles were detected, 30 of which (from 23 accessions) were exclusive. The number of alleles per marker ranged from 6 to 22, with an average of 14.6 alleles per locus. We identified 16 accessions as a mixture of pure lines or heterozygous plants. Dendrogram analysis identified six clusters of identical accessions with different common names and just one cluster with identical accessions with the same common name, indicating that SSR markers are fundamental to determining the genetic relationship between landraces. A subset of 24 landraces, representatives of the 13 similarity groups plus the 11 accessions not grouped, was the most variable set of genotypes analyzed. These accessions can be used as genitors to increase the genetic variability available to rice breeding programs.

Transferability of microsatellite and sequence tagged site markers in Oryza species.

The genus Oryza comprises 22 species which are potentially useful as a source of genetic variability that can be introgressed into the worldwide cultivated rice, Oryza sativa. Molecular markers are useful tools for monitoring gene introgressions and for detecting polymorphism among species. In this study, cross-amplification was estimated among 28 accessions of 16 Oryza species, representing the genomes AA, BB, CC, BBCC and CCDD, using 59 microsatellite (OG, OS and RM series) and 15 STS (Sequence Tagged Sites) markers. All markers amplified at least one Oryza species, indicating different levels of transferability across species. Markers based on microsatellite sequences amplified 37 % of the accessions, with an average of 6.58 alleles per locus and an average polymorphism information content (PIC) of 70 %. For STS markers, the amplification level was 53.3 %, and the average number of alleles and PIC values were 1.6 and 10 %, respectively. These Results showed that although the STS markers detected a reduced level of genetic diversity, the transferability was higher, indicating that they can be used for genetic analysis when evaluating less genetically related species of Oryza. Among the microsatellite markers, an analysis of species with an AA genome showed that the OG markers produced the highest level of polymorphic loci (54.6 %), followed by RM markers (48 %). Highly polymorphic and transferable molecular markers in Oryza can be useful for exploiting the genetic resources of this genus, for detecting allelic variants in loci associated with important agronomic traits, and for monitoring alleles introgressed from wild relatives to cultivated rice.

Genetic structure and gene flow in Eugenia dysenterica DC in the Brazilian Cerrado utilizing SSR markers

The ''cagaita tree'' (Eugenia dysenterica) is a plant found widespread in the Brazilian Cerrado. Its fruit is used for popular consumption and for industrial purposes. This study opens a new perspective for the generation of population genetic data and parameters estimates for devising sound collection and conservation procedures for Eugenia dysenterica. A battery of 356 primer pairs developed for Eucalyptus spp. was tested on the ''cagaita tree''. Only 10 primer pairs were found to be transferable between the two species. Using a polyacrilamide gel, an average of 10.4 alleles per locus was detected, in a sample of 116 individuals from 10 natural ''cagaita tree'' populations. Seven polymorphic loci allowed estimation of genetic parameters, including expected average heterozygosity He = 0,442, among population diversity, R ST = 0,268 and gene flow Nm = 0,680. Results indicated a potential of SSR locus transferability developed for Eucalyptus to other species of different genera, such as in the case of the ''cagaita tree''. The high genetic diversity among populations detected with SSR markers indicated that these markers are highly sensitive to detect population structure. Estimated Nm values and the existence of private alleles indicated reduced gene flow and consequently possible damage to the metapopulation structure.