Abstract Genes related to the response to drought stress in leaf and root tissue of drought-susceptible (DS) and tolerant (DT) genotypes were characterized by RNA-Seq. In total, 54,750 transcripts, representative of 28,590 genes, were identified; of these, 1,648 were of high-fidelity (merge of 12 libraries) and described for the first time in the Andean germplasm. From the 1,239 differentially expressed genes (DEGs), 458 were identified in DT, with a predominance of genes in categories of oxidative stress, response to stimulus and kinase activity. Most genes related to oxidation-reduction terms in roots were early triggered in DT (T75) compared to DS (T150) suggestive of a mechanism of tolerance by reducing the damage from ROS. Among the KEGG enriched by DEGs up-regulated in DT leaves, two related to the formation of Sulfur-containing compounds, which are known for their involvement in tolerance to abiotic stresses, were common to all treatments. Through qPCR, 88.64% of the DEGs were validated. A total of 151,283 variants were identified and functional effects estimated for 85,780. The raw data files were submitted to the NCBI database. A transcriptome map revealed new genes and isoforms under drought. These results supports a better understanding of the drought tolerance mechanisms in beans.

Abstract This study aimed to evaluate the tolerance to salinity and temperature, the genetic diversity and the symbiotic efficiency of rhizobia isolates obtained from wild genotypes of common bean cultivated in soil samples from the States of Goiás, Minas Gerais and Paraná. The isolates were subjected to different NaCl concentrations (0%, 1%, 2%, 4% and 6%) at different temperatures (28 °C, 33 °C, 38 °C, 43 °C and 48 °C). Genotypic characterization was performed based on BOX-PCR, REP-PCR markers and 16S rRNA sequencing. An evaluation of symbiotic efficiency was carried out under greenhouse conditions in autoclaved Leonard jars. Among 98 isolates about 45% of them and Rhizobium freirei PRF81 showed a high tolerance to temperature, while 24 isolates and Rhizobium tropici CIAT899 were able to use all of the carbon sources studied. Clustering analysis based on the ability to use carbon sources and on the tolerance to salinity and temperature grouped 49 isolates, R. tropici CIAT899 and R. tropici H12 with a similarity level of 76%. Based on genotypic characterization, 65% of the isolates showed an approximately 66% similarity with R. tropici CIAT899 and R. tropici H12. About 20% of the isolates showed symbiotic efficiency similar to or better than the best Rhizobium reference strain (R. tropici CIAT899). Phylogenetic analysis of the 16S rRNA revealed that two efficient isolates (ALSG5A1 and JPrG6A8) belong to the group of strains used as commercial inoculant for common bean in Brazil and must be assayed in field experiments.

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.

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.

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.

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.