Begomoviruses are ssDNA plant viruses that cause serious epidemics in economically important crops worldwide. Non-cultivated plants also harbour many begomoviruses, and it is believed that these hosts may act as reservoirs and as mixing vessels where recombination may occur. Begomoviruses are notoriously recombination-prone, and also display nucleotide substitution rates equivalent to those of RNA viruses. In Brazil, several indigenous begomoviruses have been described infecting tomatoes following the introduction of a novel biotype of the whitefly vector in the mid-1990s. More recently, a number of viruses from non-cultivated hosts have also been described. Previous work has suggested that viruses infecting non-cultivated hosts have a higher degree of genetic variability compared with crop-infecting viruses. We intensively sampled cultivated and non-cultivated plants in similarly sized geographical areas known to harbour either the weed-infecting Macroptilium yellow spot virus (MaYSV) or the crop-infecting Tomato severe rugose virus (ToSRV), and compared the molecular evolution and population genetics of these two distantly related begomoviruses. The results reinforce the assertion that infection of non-cultivated plant species leads to higher levels of standing genetic variability, and indicate that recombination, not adaptive selection, explains the higher begomovirus variability in non-cultivated hosts.

Brazil stands out in grain production, being the world's second-largest soya bean producer and the largest in Latin America. The area occupied by leguminous in the 2018/2019 harvest was 36 million hectares (CONAB, 2019). The Cerrado biome occupies about 44% of the country's agricultural area, which is responsible for 60% of total soya bean production (DICKIE, Magno, Giampietro, & Dolginow, 2016). The advance of agriculture in this biome is growing, which tends to further increase the percentage of crop production. In the Cerrado, the volume and frequency of rainfall is often fluctuating and insufficient, reducing the chances of adequate supply of the crop's water demand (Goes, Rodrigues, Arf, Arruda, & Vilela, 2011; Tardin et al., 2013). Therefore, it is common in Cerrado the soya bean crops to be subjected to drought stress conditions in their early stages, which can affect the germination process. The severity of the drought stress effect on soya bean depends on the

TaALMT1 and TaMATE1B promoter alleles are highly correlated with wheat growth in acidic soil with a high concentration of toxic aluminium. The aluminium (Al(3+)) resistance of 338 wheat genotypes with different geographic origins was correlated with morphological traits and TaALMT1 and TaMATE1B alleles. Both of these genes encode malate and citrate transporters associated with Al(3+) resistance mechanisms in wheat. Based on comparisons with the sensitive and resistant controls, the relative root growth was evaluated in hydroponic experiments and the plant performance was visually accessed in the field. The correlation between Al(3+) tolerance in the hydroponic and field tests was moderate (r = 0.56, P < 0.001). Higher selection pressure was observed in the field because a smaller number of genotypes was classified as resistant. The combination between the six TaALMT1 alleles and the two TaMATE1B promoters allowed the identification of 11 haplotypes that showed a high (r = 0.71, P < 0.001) correlation with Al(3+) resistance in the field, with the TaALMT1 alleles accounting for most of the correlation. The Brazilian wheat genotypes presented the best performance in soil, including eight cultivars with promoters usually associated with Al(3+) resistance and another six genotypes classified as moderately resistant but containing alleles usually associated with Al(3+) sensitivity. Although an increase in favourable alleles was observed over the past few decades, the average Al(3+) resistance in the field was not significantly different from that of older cultivars. The ease identification of the TaALMT1 and TaMATE1B alleles and their higher association with Al(3+) resistance along with the best genotypes identified here may be used for wheat-breeding programmes interested in increasing wheat Al(3+) resistance.

Repeated blocks in the TaALMT1 promoter as well as a transposon insertion in the TaMATE1B upstream region have been correlated with the level of gene expression, organic acid efflux, and ultimately aluminum (Al 3? ) resistance in wheat (Triticum aestivum L.). In this study, we investigated the allelic polymorphism related to the TaALMT1 and TaMATE1B promoter regions in 300 Brazilian wheat genotypes and the correlation of that variation with root growth on acid soil. In addition, SSR markers were used to determine the genetic variability of the genotypes. Seven TaALMT1 promoter alleles (Types I-VII) were detected based on size of PCR products. The most common alleles were Type V and Type VI (71.3 and 11.9 %, respectively), and these are generally associated with higher levels of TaALMT1 expression and Al 3? resistance. The promoter alleles Type I and Type II, which are usually associated with Al 3? sensitivity, were detected in 12.2 % of the genotypes. The insertion in the TaMATE1B promoter, associated with greater Al 3? resistance, was identified in 80 genotypes. Combination among the alleles allowed the separation in 12 haplotypes were 68 genotypes presented the TaALMT1 promoters Type V and Type VI along with the transposon insertion in the TaMATE1B promoter. However, the most represented haplotype was Type V without the insertion (176 genotypes). Short-term soil experiment, performed in 33 genotypes representing the 12 haplotypes, revealed that the higher relative root length was observed in some genotypes presenting TaALMT1 promoters Type V or Type VI and the transposon insertion in the TaMATE1B promoter. Moreover, when comparing genotypes inside the same haplotype, the transposon insertion was significantly advantageous for a few materials. However, the majority the genotypes presenting the insertion in the TaMATE1B promoter did not outperform the genotypes without the insertion but showing the same TaALMT1 promoter. Analysis using SSR markers, with an average PIC of 0.60, showed high genetic diversity among the genotypes belonging to different haplotypes. The alleles and the genetically diverse genotypes reported here should be considered for wheat-breeding programs aiming increments in wheat Al 3? resistance.

-Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that are often associated with weed plants. The aim of this study was to further characterize the diversity of begomoviruses infecting weeds (mostly Sida spp.) in Brazil. Total DNA was extracted from weed samples collected in Viçosa (Minas Gerais state) and in some municipalities of Alagoas state in 2009 and 2010. Viral genomes were amplified by RCA, cloned and sequenced. A total of 26 DNA-A clones were obtained. Sequence analysis indicated the presence of 10 begomoviruses. All viral isolates from Blainvillea rhomboidea belonged to the same species, Blainvillea yellow spot virus (BlYSV ), thereby suggesting that BlYSV may be the only begomovirus present in this weed species. Four isolates represent new species, for which the following names are proposed: Sida yellow blotch virus (SiYBV), Sida yellow net virus (SiYNV), Sida mottle Alagoas virus (SiMoAV) and Sida yellow mosaic Alagoas virus (SiYMAV). Recombination events were detected among the SiYBV isolates and in the SiYNV isolate. These results constitute further evidence of the high species diversity of begomoviruses in Sida spp. However, the role of this weed species as a source of begomoviruses infecting crop plants remains to be determined.Keywords: geminivirus, recombination, Blainvillea rhomboidea, Sida micrantha, Sida urens, Sida santaremnensis RESUMO -Begomovírus são vírus de DNA circular fita simples transmitidos por mosca branca, os quais são frequentemente associados com plantas daninhas. O objetivo deste trabalho foi caracterizar a diversidade de begomovírus infectando plantas daninhas (principalmente Sida spp.) no Brasil. DNA total foi extraído a partir de plantas daninhas coletadas em Viçosa (Minas Gerais) e em alguns municípios do estado de Alagoas em 2009 e 2010. Os genomas virais foram amplificados por RCA, clonados e sequenciados. Um total de 26 clones de DNA-A foram obtidos. A análise das sequências indicou a presença de dez diferentes begomovírus. Todos os isolados originários de Blainvillea rhomboidea pertencem a uma única espécie viral, Blainvillea yellow spot virus (BlYSV), sugerindo que o BlYSV pode ser o único begomovírus presente nesta espécie de planta invasora. Quatro isolados representam espécies novas, para as quais os seguintes nomes são propostos: Sida yellow blotch virus (SiYBV), Sida yellow net virus (SiYNV), Sida mottle Alagoas virus (SiMoAV) e Sida yellow mosaic Alagoas virus (SiYMAV). Eventos de recombinação foram detectados entre isolados de SiYBV e no isolado de SiYNV. Estes resultados constituem uma evidência adicional da alta diversidade de espécies de begomovírus em Sida spp. Contudo, o possível papel dessas plantas daninhas como fonte de begomovírus para plantas cultivadas ainda permanece indeterminado.

Bread wheat (Triticum aestivum L.) is one of the world’s most important crops. Maintaining wheat yield gains across all of its major production areas is a key target toward underpinning global food security. Brazil is a major wheat producer in South America, generating grain yields of around 6.8 million tons per year. Here, we establish and genotype a wheat association mapping resource relevant to contemporary Brazilian wheat breeding programs. The panel of 558 wheat accessions was genotyped using an Illumina iSelect 90,000 single nucleotide polymorphism array. Following quality control, the final data matrix consisted of 470 accessions and 22,475 polymorphic genetic markers (minor allele frequency ≥5%, missing data <5%). Principal component analysis identified distinct differences between materials bred predominantly for the northern Cerrado region, compared to those bred for southern Brazilian agricultural areas. We augmented the genotypic data with 26 functional Kompetitive Allele-Specific PCR (KASP) markers to identify the allelic combinations at genes with previously known effects on agronomically important traits in the panel. This highlighted breeding targets for immediate consideration – notably, increased Fusarium head blight resistance via the Fhb1 locus. To demonstrate the panel’s likely future utility, genome-wide association scans for several phenotypic traits were undertaken. Significant (Bonferroni corrected P < 0.05) marker-trait associations were detected for Fusarium kernel damage (a proxy for type 2 Fusarium resistance), identifying previously known quantitative trait loci in the panel. This association mapping panel represents an important resource for Brazilian wheat breeding, allowing future genetic studies to analyze multiple agronomic traits within a single genetically diverse population.

Drought stress, salinity and aluminium toxicity are considered the most critical abiotic factors limiting the growth of soya bean plants, accounting for the low yield of the crop in the Cerrado region. Our hypothesis is that soya bean cultivars have differential morphological responses to stressful environmental conditions. Thus, an experiment was carried out with the purpose of identifying and recommending soya bean genotypes that simultaneously combine adaptability and stability for morphological traits when subjected to stressful environmental conditions. Drought, saline and aluminium stresses were induced in seeds of 25 soya bean cultivars. Seed germination, and length and dry mass of the seedlings were measured. For each trait, adaptability and stability were evaluated by the Lin & Binns method and simultaneously considering all traits for the set of environments. There was significant GxE interaction for all traits evaluated. The genotypes 97R50 IPRO, BMX Bônus IPRO and 98R31 IPRO simultaneously combine adaptability and stability for all traits measured. These genotypes can be cultivated both under optimal and abiotic stress conditions, such as those investigated in this study. Additionally, they can be used as parents in crossing blocks aiming at obtaining genotypes resistant to drought, saline and aluminium toxicity stresses.

Begomoviruses are whitefly-transmitted single-stranded DNA viruses of great economic importance in the tropics and subtropics. Several begomovirus species have been reported in tomatoes in Brazil, but only a few predominate in the field, for unknown reasons. In this study begomovirus-infected tomato samples were collected in Viçosa, State of Minas Gerais, in Nov/2009 and Dec/2010. Viral genomes were amplified, cloned and sequenced. A total of 36 DNA-A components were obtained. Sequence comparisons indicated the presence of a single begomovirus, Tomato severe rugose virus (ToSRV), with pairwise identities between isolates ranging from 97.3 to 100%. Subdivision tests indicated the existence of a single population. The analysis of variability descriptors indicated that the ToSRV population has a genetic variability similar to other begomovirus populations described in Brazil infecting tomato. Neutrality tests suggested the occurrence of purifying selection acting upon the population. Recombination analysis identified recombination events with begomoviruses from the weed species Sida micrantha. The wide distribution of ToSRV in the field and the detection of recombination indicate that continuous monitoring of viral populations in the field will be required to enable an efficient resistance-based control strategy for begomoviruses