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Upland rice is cultivated mostly in Latin America and Africa by small farmers and in areas with risk of dry spells. This study evaluated morphophysiological mechanisms of upland rice associated to drought adaptation. A set of 25 upland rice genotypes were grown in a plant phenotyping platform during 2015 and 2017 under regular irrigation and water restriction. We evaluated morphophysiological traits in shoots (vegetative structures growth, gas exchange, water use efficiency, carboxylation efficiency, water status) and roots (length, surface area, volume and diameter), as well as agronomic traits (grain yield and its components). There was a reduction in grain yield by up to 54 % and 58 % in 2015 and 2017, respectively, under water deficit. Five upland rice genotypes with the best yield performances in both water treatments applied were recommended to the upland rice-breeding program: Bico Ganga, BRS Esmeralda, BRSMG Curinga, Guarani, and Rabo de Burro. In this study, morphophysiological traits associated to drought tolerance concerned the plant high capacity to save water in the leaves, low leaf water potential, high ability to reduce vegetative structures, high water use efficiency, high photosynthetic capacity, and improved capacity to absorb water from drying soil, either by osmotic adjustment or additional investment into the root system. Therefore, we concluded that different secondary traits contributed to drought tolerance and should be evaluated along with grain yield to improve efficiency of breeding selection. Made available in DSpace on 2020-11-10T09:17:25Z (GMT). No. of bitstreams: 1 SciAgric-2021.pdf: 1083892 bytes, checksum: 229f86b1cca0d54b92dab1a2f7b69135 (MD5) Previous issue date: 2021

Rice has extensive collections of germplasm, but a small fraction of genotypes are used in breeding programs worldwide. This aimed to assess the heterosis and the combining ability for higher grain yield and earliness, and their correlations to genetic distance among accessions belonging to the Embrapa ́s Rice Core Collection. Crosses were made in complete diallel, without the reciprocals, being phenotyped in generations F2 and F7 for grain yield (GY) and days to flowering (DTF). It were estimated the varietal effect, mean heterosis, varietal heterosis, specific combining abilityand general combining ability (GCA) of the parents in each generation. For the selection of new lines, the combinations involving the genitors with the highest magnitudes and positive effects for GCA were considered more promising for the GY, of which Canela Curta, Maninjau, Epagri 108 and Diamante stood out, and were also the most productive. For the DTF, the genitors with the largest earliness estimates were Araguaia, CT11632, Irat 122, Pratinha Branco and Tox 503. The recommended parameters for estimating GY in F7 generation from the data of the F2 generation were the mean of GY, GCA and the mean Rogers-W genetic distance coefficient. Crosses with Rogers-W distance coefficients above 0.9 showed higher GY and earliness in F7 generation, whereas in F2 the superior crosses were those that showed Rogers-W between 0.7 and 0.89. The above genotypes and the specific combinations identified may lead to new rice cultivars. Made available in DSpace on 2021-03-01T16:01:30Z (GMT). No. of bitstreams: 1 fpbj-2019.pdf: 636966 bytes, checksum: ae44eface09b14a8ad20d7f3d594327c (MD5) Previous issue date: 2019

The objective of this work was to identify and validate single-nucleotide polymorphism (SNP) markers related to grain yield in rice (Oryza sativa) core collection. The genome-wide association studies (GWAS) methodology was applied for genotyping of 541 rice accessions by 167,470 SNPs. The grain yield of these accessions was estimated through the joint analysis of nine field experiments carried out in six Brazilian states. Fifteen SNPs were significantly associated with grain yield, and out of the ten SNPs converted to TaqMan assays, four discriminated the most productive accessions. These markers were used for the screening of rice accessions with favorable alleles. The selected accessions were, then, evaluated in field experiments in target environments, in order to select the most productive ones. This screening reduces the number of accessions evaluated experimentally, making it possible to prioritize those with higher productive potential, which allows of the increase of the number of replicates and, consequently, of the experimental accuracy. Resumo: O objetivo deste trabalho foi identificar e validar marcadores de polimorfismo de nucleotídeo único (SNP) relacionados à produtividade de grãos em coleção nuclear de arroz (Oryza sativa). A metodologia de estudos de associação genômica ampla (GWAS) foi aplicada à genotipagem de 541 genótipos por 167.470 SNPs. A produtividade de grãos desses acessos foi estimada por meio da análise conjunta de nove experimentos de campo, realizados em seis estados brasileiros. Quinze SNPs foram significativamente associados à produtividade de grãos e, dos dez SNPs que foram convertidos em ensaios TaqMan, quatro discriminaram os acessos com maior produtividade. Esses marcadores foram utilizados para identificar aceessos de arroz com os alelos favoráveis. Em seguida, os acessos selecionados foram avaliados em experimentos de campo, em ambientes-alvo, para identificar os mais produtivos. Essa triagem reduz o número de acessos avaliados experimentalmente, pois torna possível priorizar aqueles com maior potencial produtivo, o que permite aumentar o número de repetições e, consequentemente, a precisão experimental.

The availability of high-density molecular markers in common bean has allowed to explore the genetic basis of important complex agronomic traits with increased resolution. Genome-Wide Association Studies (GWAS) and Regional Heritability Mapping (RHM) are two analytical approaches for the detection of genetic variants. We carried out GWAS and RHM for plant architecture, lodging and productivity across two important growing environments in Brazil in a germplasm of 188 common bean varieties using DArTseq genotyping strategies. The coefficient of determination of G × E interaction (c2int) was equal to 17, 21 and 41%, respectively for the traits architecture, lodging, and productivity. Trait heritabilities were estimated at 0.81 (architecture), 0.79 (lodging) and 0.43 (productivity), and total genomic heritability accounted for large proportions (72% to ≈100%) of trait heritability. At the same probability threshold, three marker–trait associations were detected using GWAS, while RHM detected eight QTL encompassing 145 markers along five chromosomes. The proportion of genomic heritability explained by RHM was considerably higher (35.48 to 58.02) than that explained by GWAS (28.39 to 30.37). In general, RHM accounted for larger fractions of the additive genetic variance being captured by markers effects inside the defined regions. Nevertheless, a considerable proportion of the heritability is still missing (∼42% to ∼64%), probably due to LD between markers and genes and/or rare allele variants not sampled. RHM in autogamous species had the potential to identify larger-effect QTL combining allelic variants that could be effectively incorporated into whole-genome prediction models and tracked through breeding generations using marker-assisted selection.

EnglishWe aimed to apply genomic information based on SNP (single nucleotide polymorphism) markers for the genetic evaluation of the traits “stay-green” (SG), plant architecture (PA), grain aspect (GA) and grain yield (GY) in common bean through Bayesian models. These models were compared in terms of prediction accuracy and ability for heritability estimation for each one of the mentioned traits. A total of 80 cultivars were genotyped for 377 SNP markers, whose effects were estimated by five different Bayesian models: Bayes A (BA), B (BB), C (BC), LASSO (BL) e Ridge regression (BRR). Although, prediction accuracies calculated by means of cross-validation have been similar within each trait, the BB model stood out for the trait SG, whereas the BRR was indicated for the remaining traits. The heritability estimates for the traits SG, PA, GA and GY were 0.61, 0.28, 0.32 and 0.29, respectively. In summary, the Bayesian methods applied here were effective and ease to be implemented. The used SNP markers can help in the early selection of promising genotypes, since incorporating genomic information increase the prediction accuracy of the estimated genetic merit. Key words: Phaseolus vulgaris; SNP markers; cross-validation portuguesObjetivou-se incorporar informacoes genomicas de marcadores SNP (“single nucleotide polymorphism”) na avaliacao genetica das caracteristicas “stay-green” (SG), arquitetura de planta (AP), aspecto de graos (AG) e produtividade de graos (PG) em feijoeiro-comum via modelos Bayesianos. Estes modelos foram comparados quanto a acuracia de predicao e habilidade de estimacao da herdabilidade para cada caracteristica. Utilizaram-se informacoes de 80 cultivares genotipadas para 377 marcadores SNP, cujos efeitos de substituicao alelica foram estimados por meio de cinco diferentes modelos Bayesianos: Bayes A (BA), B (BB), C (BC), LASSO (BL) e regressao “ridge” (BRR). Embora as acuracias de predicao calculadas por meio de analise de validacao cruzada tenham sido similares dentro de cada caracteristica, o modelo BB se destacou para a caracteristica SG, enquanto o modelo BRR foi indicado para as demais. As herdabilidades estimadas para SG, AP, AG e PG foram, respectivamente, 0,61, 0,28, 0,32 e 0,29. Em resumo, os metodos contemplados mostraram-se efetivos e de facil implementacao. O conjunto de marcadores utilizado pode auxiliar na selecao precoce de genotipos promissores, uma vez que a incorporacao de informacoes genomicas aumenta a acuracia de predicao do merito genetico estimado. Palavras-chave: Phaseolus vulgaris; marcadores SNP; validacao cruzada

Breeding for water-deficit tolerance is fundamental to guarantee the sustainability of upland rice production, mainly due to the possibility of an increased frequency of drought episodes due to climate change. This work aimed to identify single nucleotide polymorphism (SNP) markers, derived from RNA sequencing (RNA-Seq), genome-wide association study (GWAS) and candidate genes from Arabidopsis, with potential for use in marker-assisted selection (MAS) for drought tolerance. RNA-Seq and GWAS were efficient in identifying useful SNP markers from the data obtained from three years of field experiments for 175 upland rice accessions, which were sequenced using 32 genes by Capture-Seq. Three genes were equally able to generate SNP markers that discriminated 95% of the 20 most drought susceptible accessions in the joint analysis of the experiments. The elimination of the genotypes with the unfavourable SNP allele reduced the initial number of accessions to one third, and transferring this result in a breeding routine, would enable to conduct smaller experiments per target location, increasing the precision and reducing the cost of the drought phenotyping. Made available in DSpace on 2018-03-10T00:34:10Z (GMT). No. of bitstreams: 1 CNPAF2018gmr.pdf: 333924 bytes, checksum: 202e7a3c0bca406bccdf93cad82d91f8 (MD5) Previous issue date: 2018-03-08

This paper proposes the construction of a genetic linkage map with 376 recombinant inbred lines (RILs) derived from a cross between Mesoamerican × Andean common bean (Phaseolus vulgaris L) parents based on single nucleotide polymorphism (SNP) markers; and to detect quantitative trait loci (QTLs) associated with seven morpho-agronomic traits: number of days to flowering (DF), number of days to maturity (DM) or crop cycle; plant architecture (ARC); seed yield (YLD); degree of seed flatness (SF); seed shape (SS); and 100-seed weight (SW). A total of 3060 polymorphic SNP markers were used and 2041 segregated at a 1:1 ratio in the RIL population, as expected. These markers were subjected to linkage analysis in each chromosome. The genetic linkage analysis resulted in linkage maps with a total of 1962 markers spanning 1079.21 cM. A total of 29 QTLs associated with seven morpho-agronomic traits were detected on the 11 chromosomes, which explained between 3.83 and 32.92% of the phenotypic variation in DF. A total of 18 candidate genes associated with the detected QTLs were identified and related with biological processes, molecular functions and cellular components.

The common bean is characterized by high sensitivity to drought and low productivity. Breeding for drought resistance in this species involves genes of different genetic groups. In this work, we used a SEA 5 x AND 277 cross to map quantitative trait loci associated with drought tolerance in order to assess the factors that determine the magnitude of drought response in common beans. A total of 438 polymorphic markers were used to genotype the F8 mapping population. Phenotyping was done in two greenhouses, one used to simulate drought and the other to simulate irrigated conditions. Fourteen traits associated with drought tolerance were measured to identify the quantitative trait loci (QTLs). The map was constructed with 331 markers that covered all 11 chromosomes and had a total length of 1515 cM. Twenty-two QTLs were discovered for chlorophyll, leaf and stem fresh biomass, leaf biomass dry weight, leaf temperature, number of pods per plant, number of seeds per plant, seed weight, days to flowering, dry pod weight and total yield under well-watered and drought (stress) conditions. All the QTLs detected under drought conditions showed positive effects of the SEA 5 allele. This study provides a better understanding of the genetic inheritance of drought tolerance in common bean. Made available in DSpace on 2017-12-04T23:17:23Z (GMT). No. of bitstreams: 1 CNPAF2017gm.pdf: 1951704 bytes, checksum: c709e665fcda309878e5db6cb226845d (MD5) Previous issue date: 2017-10-27

An RNA extraction method with high integrity and purity as well as the selection of adequate reference genes are prerequisites for gene expression analysis. For common bean seeds, there is no well-defined protocol that can be used in a laboratory routine for gene expression analysis. In this study, an extraction protocol for RNA from common bean seeds, which produced material with good integrity for qPCR (RIN ≥ 6.5), was optimized. In addition, 10 reference genes were evaluated under qPCR standard conditions using different tissue samples of common beans. Gene stabilities were analyzed using the delta-CT method, Bestkeeper, NormFinder and geNorm approaches. The genes β-tubulin and T197 were ranked as the most stable among the sample sets evaluated with different tissue samples, while PvAct and Pv18S were the least stable. To our knowledge, this is the first study evaluating RNA isolation methods and reference gene selection for seeds of Phaseolus vulgaris. Made available in DSpace on 2017-09-27T10:32:00Z (GMT). No. of bitstreams: 1 CNPAF2017cbab.pdf: 460872 bytes, checksum: b7233be3c24ab77be0d94d7156f8aac4 (MD5) Previous issue date: 2017-09-26

The common bean (Phaseolus vulgaris L.) is the world?s most important legume for human consumption. Anthracnose (ANT; Colletotrichum lindemuthianum) and angular leaf spot (ALS; Pseudocercospora griseola) are complex diseases that cause major yield losses in common bean. Depending on the cultivar and environmental conditions, anthracnose and angular leaf spot infections can reduce crop yield drastically. This study aimed to estimate linkage disequilibrium levels and identify quantitative resistance loci (QRL) controlling resistance to both ANT and ALS diseases of 180 accessions of common bean using genomewide association analysis. A randomized complete block design with four replicates was performed for the ANT and ALS experiments, with four plants per genotype in each replicate. Association mapping analyses were performed for ANT and ALS using a mixed linear model approach implemented in TASSEL. A total of 17 and 11 significant statistically associations involving SSRs were detected for ANT and ALS resistance loci, respectively. Using SNPs, 21 and 17 significant statistically associations were obtained for ANT and angular ALS, respectively, providing more associations with this marker. The SSR-IAC167 and PvM95 markers, both located on chromosome Pv03, and the SNP scaffold00021_89379, were associated with both diseases. The other markers were distributed across the entire common bean genome, with chromosomes Pv03 and Pv08 showing the greatest number of loci associated with ANT resistance. The chromosome Pv04 was the most saturated one, with six markers associated with ALS resistance. The telomeric region of this chromosome showed four markers located between approximately 2.5 Mb and 4.4 Mb. Our results demonstrate the great potential of genome-wide association studies to identify QRLs related to ANT and ALS in common bean. The results indicate a quantitative and complex inheritance pattern for both diseases in common bean. Our findings will contribute to more effective screening of elite germplasm to find resistance alleles for marker-assisted selection in breeding programs. Made available in DSpace on 2017-09-27T10:34:08Z (GMT). No. of bitstreams: 1 CNPAF2016plosone.pdf: 978494 bytes, checksum: 7270612231930d2467501c7c4e087487 (MD5) Previous issue date: 2017-09-26

O objetivo deste trabalho foi identificar, por meio da análise de mapeamento associativo, os marcadores moleculares relacionados à produtividade do arroz de terras altas e aos seus caracteres componentes. Foram usadas 113 linhagens e cultivares de arroz de terras altas, da Coleção Nuclear de Arroz da Embrapa, com reduzido vínculo genético entre si. Os seguintes caracteres componentes da produtividade foram avaliados: número de panículas por metro, número de grãos por panícula e peso de 100 grãos. Dos 115 marcadores utilizados, 25 (21,7%) associaram-se significativamente a um ou mais caracteres. Entre os 29 SSR ("simple sequence repeats") colocalizados em QTL ("quantitative trait loci") de produtividade de arroz, 12 foram associados aos caracteres avaliados e considerados como candidatos para uso na seleção assistida por marcadores. Os marcadores NP914540, Q6ZGD1 e Q69JE3, associados ao número de grãos por panícula, ainda não foram anotados no arroz e podem constituir o ponto de partida para estudos de genômica funcional. Entre os marcadores derivados de sequências transcritas, NP914526 e NP914533 destacam-se por pertencer a rotas metabólicas relacionadas ao aumento do potencial produtivo de arroz. The objective of this work was to identify, through analysis of associative mapping, the molecular markers related to upland rice yield and its component traits. One hundred thirteen lines and cultivars of upland rice, with reduced admixture, from the Rice Core Collection of Embrapa, were used. The following yield component traits were evaluated: number of panicles per meter, number of grains per panicle, and weight of 100 grains. Out of the 115 used markers, 25 (21.7%) were significantly associated with one or more traits. Among the 29 SSR (simple sequence repeats) co-located in yield QTL (quantitative trait loci) in rice, 12 were associated with the evaluated traits and considered candidates for use in marker-assisted selection. The markers NP914540, Q6ZGD1, and Q69JE3, associated with the number of grains per panicle, are not yet annotated in rice and should constitute the starting point for functional genomics studies. Among the markers derived from transcribed sequences, NP914526 and NP914533 stand out for belonging to metabolic pathways related to increased yield potential of rice.

Analysis of DNA polymorphisms allows for the genetic identification and precise discrimination of species with a narrow genetic base such as common bean. The primary objectives of the present study were to molecularly characterize commercial common bean varieties developed at various research institutions using microsatellite markers and to determine the degree of genetic diversity among the bean varieties analyzed. Fifty cultivars representing 12 grain classes and 64 genitors, i.e., accessions used to develop these cultivars, were characterized. Based on an analysis of 24 simple sequence repeats, the estimates for the average number of alleles and genetic diversity were 8.29 and 0.646, respectively. The combined probability of identity was estimated at 7.05 x 10(-17), indicating a high individual discriminatory power. Thirty-two percent of the cultivars exhibited heterogeneity for multiple loci that reflected either homozygosity for different alleles of a given locus in different individuals or heterozygosity for the locus. The average genetic diversity for the groups of cultivars and genitors was 0.605 and 0.660, respectively, with no genetic differentiation (F-ST) between these groups. Although similar estimates of expected heterozygosity were observed when the cultivars were grouped by release date, a greater number of private alleles was observed in the most recent cultivars. The genetic differentiation among cultivars originating from different institutions was not different from zero (F-ST = 0.01). The molecular profile database derived from these analyses may increase the statistical power of genetic estimates and may be incorporated into breeding programs for common bean. Furthermore, the profiles obtained for the different cultivars may be used as molecular descriptors to complement traditional descriptors used in distinctiveness, uniformity and stability tests, thereby improving the traceability of samples and their derivatives and helping to protect the intellectual property rights of breeders. Made available in DSpace on 2018-01-16T23:22:02Z (GMT). No. of bitstreams: 1 CNPAF2014gmr.pdf: 525097 bytes, checksum: 45b4d58b033cdce57844eb22451466e1 (MD5) Previous issue date: 2018-01-16

The study aimed to evaluate the capacity of SSR markers to detect the gene flow between the red rice (RR) and the cultivated rice (CR). SSR is currently used in plant genomic analysis due to the high information content, to be co-dominant, and based on the PCR reaction. The field experiment was organized in ten concentric circles, 5 m to 50 m apart from a central red rice plant, assumed as the pollen donor. One hundred twenty rice CR plants, cv. BR-Irga 409, were planted in the intersections of the concentric circles and the twelve radii. From 51 SSR markers, four were selected due to their capacity to detect the polymorphism between RR and CR, aiming to identify RR alleles in seeds produced by BR-Irga 409 plants. The maximum distance found for gene flow between RR and CR plants was 10 m from the RR plant. In theory, at 0.1% cross pollination rate, this distance can generate 4,710 hybrids between RR and CR. In the next generation, about 3,532 plants would produce exclusively rice grains with red color. The SSR markers were able to identify the gene flow between RR and CR; therefore, they can be useful to increase the precision of cross pollination rate estimates in rice, mainly if used with other methodologies (e.g., herbicide tolerant plants). KEY WORDS: Cross pollination; microsatellite markers; Oryza sativa. Este trabalho objetivou avaliar a capacidade de marcadores SSR em detectar a ocorrência de fluxo gênico entre o arroz vermelho (AV) e o arroz cultivado (AC). Marcadores SSR são utilizados em análise genômica de plantas devido ao alto conteúdo informativo, serem co-dominantes e baseados na reação de PCR. O ensaio de campo foi realizado em dez círculos concêntricos de 5 m a 50 m de distância, a partir de uma planta AV central, que foi a fonte doadora de pólen. Foram semeadas 120 plantas de arroz da cultivar BR-Irga 409, distribuídas nas interseções entre os círculos e doze raios. A partir de 51 marcadores SSR, foram selecionados quatro marcadores que detectaram polimorfismo entre o AV e AC, para identificar os alelos de AV em sementes produzidas pelas plantas da cultivar BR-Irga 409. A distância máxima encontrada entre a planta AV doadora de pólen e uma planta AC que produziu sementes híbridas (AV x AC) foi de 10 m. Teoricamente, sob 0,1% de taxa de cruzamento, esta distância de polinização pode dar origem a 4.710 sementes híbridas entre AC e AV, o que, na geração seguinte, resultará em 3.532 plantas produzindo grãos vermelhos. Marcadores SSR foram capazes de identificar fluxo gênico entre AR e AC; e, portanto, podem ser empregados em associação com outras metodologias (ex. plantas tolerantes a herbicidas) para melhorar a precisão das estimativas de polinização cruzada em arroz. PALAVRAS-CHAVE: Oryza sativa; polinização cruzada; marcadores microssatélites.

Gene expression related to drought response in the leaf tissues of two Brazilian upland cultivars, the drought-tolerant Douradao and the drought-sensitive Primavera, was analyzed. RNA-seq identified 27,618 transcripts in the Douradao cultivar, with 24,090 (87.2%) homologous to the rice database, and 27,221 transcripts in the Primavera cultivar, with 23,663 (86.9%) homologous to the rice database. Gene-expression analysis between control and water-deficient treatments revealed 493 and 1154 differentially expressed genes in Douradao and Primavera cultivars, respectively. Genes exclusively expressed under drought were identified for Douradao, including two genes of particular interest coding for the protein peroxidase precursor, which is involved in three distinct metabolic pathways. Comparisons between the two drought-exposed cultivars revealed 2314 genes were differentially expressed (978 upregulated, 1336 downregulated in Douradao). Six genes distributed across 4 different transcription factor families (bHLH, MYB, NAC, and WRKY) were identified, all of which were upregulated in Douradao compared to Primavera during drought. Most of the genes identified in Douradao activate metabolic pathways responsible for production of secondary metabolites and genes coding for enzymatically active signaling receptors. Quantitative PCR validation showed that most gene expression was in agreement with computational prediction of these transcripts. The transcripts identified here will define molecular markers for identification of Cis-acting elements to search for allelic variants of these genes through analysis of polymorphic SNPs in GenBank accessions of upland rice, aiming to develop cultivars with the best combination of these alleles, resulting in materials with high yield potential in the event of drought during the reproductive phase.

The mapping population consisted of 94 F 2 generation plants derived from a cross between the CNFC 7812 and CNFC 8056 lines, with different protein contents, 24% and 19% respectively. Seven hundred and fifty-two molecular markers were tested among the parents and four individuals from the segregant population. A total of 101 loci were used to develop the genetic map. The polymorphism rate was 8.3% and 23.2% for the microsatellite and RAPD markers, respectively. The sizes of the linkage groups ranged from 6.7 to 139.0 cM , presenting a mean of 49.4 ± 36.8. The map length was 840.7 cM and the mean group length was 45.9 cM. The average distance between the framework loci was 16.1 cM. This map was compared with international reference bean maps and results were discussed. The construction of the genetic map from parents of the same center of origin and the commercial grain type were discussed. Made available in DSpace on 2011-04-09T14:42:25Z (GMT). No. of bitstreams: 1 CBABv10.pdf: 150953 bytes, checksum: d92528f695146dfbce6985a2ea995588 (MD5) Previous issue date: 2010-08-04

This study aimed to present and discuss the recurrent selection methodology used in the development of the rice cultivar SCSBRS Tio Taka. This cultivar, derived from the population CNA-IRAT 4, achieves high yields and has agronomic traits related to a better performance in the pre-germinated cultivation system used in Santa Catarina State. The molecular characterization of Tio Taka and CNA-IRAT 4 parents with 16 SSR markers showed that one of the parents, BG 90-2, was highly similar to SCSBRS Tio Taka. The most probable reason was that SCSBRS Tio Taka was extracted from CNA-IRAT 4 in the second recombination cycle, preventing the ccurrence of a high level of recombination and favoring the phenotypic selection of plants derived from crosses with BG 90-2 as parent, once this line has one of the best plant architectures and yields.

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. Made available in DSpace on 2017-11-16T23:22:34Z (GMT). No. of bitstreams: 1 CNPAF2006cb.pdf: 155864 bytes, checksum: ffd86dc387ebba5704fb19aaec91565a (MD5) Previous issue date: 2006-11-06

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, RST = 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. Made available in DSpace on 2020-05-05T04:39:47Z (GMT). No. of bitstreams: 1 CNPAF-2003-gmb.pdf: 338713 bytes, checksum: 2671ac248e5bee5e383d296465041bf1 (MD5) Previous issue date: 2003

The objective of this work was to evaluate the yield performance of two generations (BC2F2 and BC2F9) of introgression lines developed from the interspecific cross between Oryza sativa and O. glumaepatula, and to identify the SSR markers associated to yield. The wild accession RS‑16 (O. glumaepatula) was used as donor parent in the backcross with the high yielding cultivar Cica‑8 (O. sativa). A set of 114 BC2F1 introgression lines was genotyped with 141 polymorphic SSR loci distributed across the whole rice genome. Molecular analysis showed that in average 22% of the O. glumaepatula genome was introgressed into BC2F1 generation. Nine BC2F9 introgression lines had a significantly higher yield than the genitor Cica‑8, thus showing a positive genome interaction among cultivated rice and the wild O. glumaepatula. Seven QTL were identified in the overall BC2F2, with one marker interval (4879‑EST20) of great effect on yield. The alleles with positive effect on yield came from the cultivated parent Cica‑8. O objetivo deste trabalho foi avaliar o desempenho produtivo de duas gerações (RC2F2 e RC2F9) de linhagens de introgressão, desenvolvidas a partir do cruzamento interespecífico entre Oryza sativa e O. glumaepatula, bem como identificar marcadores SSR associados à produtividade. O acesso selvagem RS‑16 (O. glumaepatula) foi utilizado como doador parental no retrocruzamento com a cultivar elite Cica‑8 (O. sativa). Uma série de 114 linhagens de introgressão RC2F1 foi genotipada com 141 locos SSR polimórficos distribuídos ao longo de todo o genoma do arroz. A análise molecular indicou que, em média, 22% do genoma de O. glumaepatula foi introgredida na geração RC2F1. Nove linhagens de introgressão RC2F9 tiveram produção significativamente maior que o genitor Cica‑8, o que mostra uma interação genômica positiva entre o arroz cultivado e a espécie silvestre O. glumaepatula. Sete QTL foram identificados em toda geração RC2F2, com um intervalo de marcadores (4879‑EST20) de grande efeito sobre a produtividade. Os alelos com efeitos positivos sobre a produtividade foram provenientes do genitor cultivado Cica‑8.

An AG microsatellite-enriched genomic DNA library was constructed for Magnaporthe grisea (anamorph Pyricularia grisea), the causal agent of rice blast. Seventy-two DNA clones containing microsatellite repeats were isolated and sequenced in order to develop a series of new PCR-based molecular markers to be used in genetic studies of the fungus. Twenty-four of these clones were selected to design primer pairs for the PCR amplification of microsatellite alleles. Single spore cultures of M. grisea isolated from rice and wheat in Brazil, Colombia and China were genotyped at three microsatellite loci. Isolates from southern Brazil were predominantly monomorphic at the tested SSR loci, indicating a low level of genetic variability in these samples. However, seven alleles were observed at the MGM-1 locus in isolates from Central Brazil and at least nine alleles were detected at the same locus in a sample of Colombian isolates. Polymorphism analysis at SSR loci is a simple and direct approach for estimating the genetic diversity of M. grisea isolates and a powerful tool for studying M. grisea genetics. Uma biblioteca genômica enriquecida para seqüências microssatélites foi construída para Magnaporthe grisea (anamorfo Pyricularia grisea), o agente causal da doença brusone do arroz. Setenta e dois clones de DNA contendo unidades repetitivas microssatélites foram isolados e seqüenciados para o desenvolvimento de uma série de novos marcadores moleculares baseados em reação de PCR, para serem utilizados na análise genética do fungo. Dos 72 clones, 24 foram selecionados para o desenho dos pares de primers para amplificação dos alelos microssatélites pela técnica de PCR. Culturas monospóricas de M. grisea isoladas de plantas de arroz e trigo no Brasil, Colômbia e China foram genotipadas utilizando-se 3 locos microssatélites. Isolados do fungo provenientes do Estado do Rio Grande do Sul foram predominantemente monomórficos nos locos microssatélites testados, indicando um baixo nível de variabilidade genética destas amostras. Contudo, 7 alelos puderam ser detectados pelo marcador MGM-1 em isolados provenientes do Estado do Tocantins e no mínimo 9 alelos puderam ser detectados com o mesmo marcador em uma amostra de isolados da Colômbia. A análise com marcadores microssatélites é uma metodologia simples e direta para se estimar a diversidade genética dos isolados de M. grisea e uma poderosa ferramenta para o estudo da genética de M. grisea.

The objective of this study was to evaluate the genetic variability of rice (Oryza sativa) landraces collected in Brazilian small farms. Twelve simple sequence repeat (SSR) markers characterized 417 landraces collected in 1986, 1987 and 2003, in the state of Goiás, Brazil. The number of landraces with long and thin grain type increased in the evaluated period, probably due to market demand. Based on the molecular data, the genetic variability increased during this period and, as per to the factorial correspondence analysis, most of the accessions were grouped according to the year of collection. The incorporation of modern rice cultivars in landrace cultivation areas and the selection carried out by small farmers are the most probable factors responsible for increasing landrace genetic variability, during the evaluated period. Genotype exchange between farmers, selection practice and local environmental adaptation are able to generate novel adapted allele combinations, which can be used by breeding programs, to reinitiate the process. O objetivo deste trabalho foi avaliar a variabilidade genética de variedades locais de arroz (Oryza sativa), coletadas em pequenas propriedades rurais. Doze marcadores microssatélites (SSR) caracterizaram 417 variedades locais, coletadas em 1986, 1987 e 2003, no Estado de Goiás. O número de variedades locais com tipo de grão longo e fino aumentou no intervalo de tempo avaliado, provavelmente em razão da demanda de mercado. Conforme os dados moleculares, houve aumento na variabilidade genética e, por meio da análise fatorial de correspondência, observou-se que a maior parte dos acessos foi agrupada de acordo com o ano de coleta. A incorporação de cultivares modernas de arroz às áreas de cultivo das variedades locais e a seleção realizada pelos pequenos agricultores são, provavelmente, os fatores responsáveis pelo aumento observado na variabilidade genética, ao longo do período avaliado. O intercâmbio de genótipos entre fazendeiros, a prática da seleção e a adaptação ambiental ao local de cultivo são capazes de gerar novas combinações alélicas adaptadas que, por sua vez, podem ser usadas pelos programas de melhoramento, para reiniciar o processo.