Biology subjects

de Souza, A. P.

Publications and source records attributed to de Souza, A. P..

At least 19 recordsLinked to original sources

bioRxiv2025

Evaluating effects of elevated and accelerated NPQ relaxation on yield, physiology and transcription in soybean

Improving photosynthetic efficiency is proposed as a means of enhancing crop productivity under rising atmospheric CO2 concentrations ([CO2]). To assess whether additive gains can be realized from simultaneous improvements in light use-efficiency and carbon assimilation, we investigated the physiological and molecular responses to elevated CO2 (e[CO2]) of a transgenic soybean line (VPZ-34A) expressing the genes violaxanthin de-epoxidase (VDE), Photosystem II subunit S (PsbS) and zeaxanthin epoxidase (ZEP) from Arabidopsis thaliana (arabidopsis) (AtVPZ). Plants were grown at a free-air CO2 enrichment facility (SoyFACE) in 2021, with physiological and transcriptomic measurements collected during vegetative (V4-5) and reproductive stages (R5-6), then compared to final biomass and seed production parameters. VPZ-34A showed increased maximum quantum photosynthetic efficiency of photosynthesis ({varphi}PSIImax) under fluctuating light during vegetative stages, but no increase in maximum efficiency of carbon assimilation ({varphi}CO2, max), and no significant increase in seed or biomass related traits under ambient or e[CO2]. Transcriptome analysis showed the VPZ construct impacted a small number of genes, among them downregulation of a mitochondrial thioredoxin (Trx o1) and up-regulation of two AP2 transcription factors in VPZ lines may suggest alterations in redox balance and seed development. In conclusion, the improvements in {varphi}PSIImax and NPQ in VPZ-34A were unaffected by e[CO2] but didnt translate to stimulation of yield. Our data highlight the complexity of VPZ manipulation on plant performance and provide avenues for future research to optimize this strategy to improve crop yields.

plant biology↗

bioRxiv2025

Exploring the genetic basis of cluster architecture-related traits in grapevine through a Genome-wide Association Study

Berry and cluster size are pivotal determinants of grapevine productivity and consumer preferences and remain major targets in grapevine breeding. However, given their complexity as quantitative traits under polygenic control, a deeper understanding of their genetic determinants is needed. The gene pool of the Brazilian grapevine has made a significant contribution to enhancing grapevine performance in tropical and subtropical regions. In this study, we conducted a genome-wide association study (GWAS) using a diverse panel of 288 Vitis spp. accessions from the Instituto Agronomico Germplasm Bank, Brazil. This panel was phenotyped for six cluster architecture traits over 12 years and genotyped using the Vitis18kSNP array. Using two different algorithms, the GWAS identified 56 significant SNPs distributed across 17 chromosomes, validating previously identified quantitative trait loci (QTLs) and revealing novel associations. Four closely spaced markers on Chr1 suggest the presence of a QTL influencing five traits simultaneously. A strong association signal, with phenotypic variance explained (PVE) values of approximately 29-35%, indicated a major QTL for berry length (BL) and width (BWi) on Chr14. Additionally, major-effect SNP loci were identified for cluster weight (CW) on Chr1, cluster length (CL) on Chr7 and 14, cluster width (CWi) on Chr6 and 18, and berry weight (BW) on Chr4, with PVE values ranging from 18-27%. Furthermore, 80 genes associated with berry traits and 52 genes associated with cluster traits were identified as putative candidate genes in the genomic regions associated with significant SNPs. These candidate genes are involved in the regulation of growth and development, hormone regulation, protein synthesis, stress response, and other physiological processes essential for cell health and functionality. Our results provide valuable insights into the genetic determinants of grape berry size and cluster architecture, offering critical data to support future functional studies and enhance the efficiency of related breeding programs.

genomics↗

bioRxiv2025

Genetic response to light and carbon source variations in Trichoderma harzianum: The key regulatory roles of env1, cre1, and blr2

In filamentous fungi, light plays a key role in regulating physiological processes such as growth, conidiation, secondary metabolism, and the expression of hydrolytic enzymes. The processes that depend on light are controlled by photoreceptors, including BLR1, BLR2, and ENV1, as well as by signaling pathways involving heterotrimeric G-proteins and cyclic adenosine monophosphate (cAMP). Trichoderma harzianum is a promising candidate for biotechnological use and is able to promote hydrolytic reactions under biomass degradation conditions. However, the genetic mechanisms underlying its response to light remain poorly understood, especially under degradative conditions. This study aimed to assess the expression of carbohydrate-active enzymes (CAZymes), transcription factors (TFs), and signaling pathway proteins under different light conditions and carbon sources. The results revealed distinct patterns of relative gene expression influenced by these environmental factors, highlighting the complex regulatory mechanisms at play in T. harzianum. Moreover, our results suggested that env1, cre1, and blr2 are critical for adjusting to different light conditions and carbon sources. This highlights the importance of both factors in regulating gene expression and supporting metabolic adaptation in T. harzianum. To our knowledge, such findings have not been previously reported in the context of cellulose degradation for this species. Overall, these results offer valuable insights into how T. harzianum responds to environmental changes, revealing a complex regulatory network that is not only crucial for optimizing fungal growth in industrial applications but also deepens our understanding of its biology and ecological interactions. Highlights{blacksquare} Trichoderma harzianum is a key candidate for biotechnology applications. {blacksquare}Light and carbon control CAZymes, photoreceptors, key regulators, and signaling. {blacksquare}T. harzianum has distinct gene expression patterns under different light conditions and carbon sources. {blacksquare}env1, cre1, and blr2 regulate metabolic adaptation in T. harzianum. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/657067v1_ufig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@8167c7org.highwire.dtl.DTLVardef@1c46f6borg.highwire.dtl.DTLVardef@16eddc8org.highwire.dtl.DTLVardef@1a2afa6_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Sugarcane yellow leaf virus impairs the transcriptomic defense responses of sugarcane to its new aphid vector Melanaphis sorghi

Sugarcane (Saccharum spp.) is a preeminent sugar and bioenergy crop and has great economic importance in tropical countries. A major disease affecting this crop is yellow leaf disease, which is caused by sugarcane yellow leaf virus (SCYLV, Polerovirus SCYLV, Solemoviridae). The sugarcane aphid Melanaphis sacchari is considered the main vector of SCYLV, and the closely related sorghum aphid Melanaphis sorghi, which has recently emerged as a pest of great relevance in sorghum, has also been suspected as a vector. Genetic resistance is an important resource for preventing yield losses caused by SCYLV and its vectors, but knowledge on the underlying molecular mechanisms is lacking. Therefore, the present work was aimed at investigating the transcriptomic responses of sugarcane to SCYLV and M. sorghi, which was reported to transmit this virus for the first time herein. Two sugarcane cultivars, one susceptible and one tolerant to SCYLV, were fed upon by aviruliferous and viruliferous aphids. The transcriptome of the plants was assessed by RNA-Seq using differential gene expression analyses and a gene coexpression network. The susceptible cultivar showed an incipient reaction to both M. sorghi and SCYLV, with very few differentially expressed genes (DEGs) identified in comparison with aphid-free plants. The response of the tolerant cultivar to aviruliferous M. sorghi involved pathways typically associated with defense against herbivory, which were also enriched in coexpression network modules in which DEGs were overrepresented. Some of these genes were hubs in their respective modules, indicating they are potential key regulators of the defense responses. However, these responses were diminished when viruliferous aphids were used, and other processes linked to infection with SCYLV were altered. These results indicated that SCYLV could affect sugarcane defense responses to its vector, similar to other viruses of the same genus. Some possible implications for the epidemiology and impact of SCYLV and M. sorghi are discussed.

plant biology↗

bioRxiv2024

Multiomic insights into sucrose accumulation in sugarcane

Sugarcane (Saccharum spp.) holds significant economic importance in sugar and biofuel production. Despite extensive research, understanding highly quantitative traits, such as sucrose content, remains challenging due to the complex genomic landscape of the crop. In this study, we conducted a multiomic investigation to elucidate the genetic architecture and molecular mechanisms governing sucrose accumulation in sugarcane. Using a biparental cross (IACSP95-3018 x IACSP93-3046) and a genetically diverse collection of sugarcane genotypes, we evaluated the soluble solids (Brix) and sucrose content (POL) across various years and environments. Both populations were genotyped using a genotyping-by-sequencing (GBS) approach, with single nucleotide polymorphisms (SNPs) identified via bioinformatics pipelines. Genotype-phenotype associations were established using a combination of traditional linear mixed-effect models and machine learning algorithms. Furthermore, we conducted an RNA sequencing (RNA-Seq) experiment on genotypes exhibiting distinct Brix and POL profiles across different developmental stages. Differentially expressed genes (DEGs) potentially associated with variations in sucrose accumulation were identified. All findings were integrated through a comprehensive gene coexpression network analysis. Strong correlations among the evaluated characteristics were observed, with estimates of modest to high heritabilities. By leveraging a broad set of SNPs identified for both populations, we identified several SNPs potentially linked to phenotypic variance. Our examination of genes close to these markers facilitated the association of such SNPs with DEGs in genotypes with contrasting sucrose levels. Through the integration of these results with a gene coexpression network, we delineated a set of genes potentially involved in the regulatory mechanisms of sucrose accumulation in sugarcane, collectively contributing to the definition of this critical phenotype. Our findings constitute a significant resource for biotechnology and plant breeding initiatives. Furthermore, our genotype-phenotype association models hold promise for application in genomic selection, offering valuable insights into the molecular underpinnings governing sucrose accumulation in sugarcane.

genetics↗

bioRxiv2024

Identifying Candidate Genes for Sugar Accumulation in Sugarcane Cultivars: From a Syntenic Genomic Region to a Gene Coexpression Network

Elucidating the intricacies of the sugarcane genome is essential for breeding superior cultivars. This economically important crop originates from hybridizations of highly polyploid Saccharum species. However, the large size (10 Gb), high polyploidy, and aneuploidy of the sugarcane genome pose significant challenges to complete genome sequencing, assembly, and annotation. One successful strategy for identifying candidate genes linked to agronomic traits, particularly those associated with sugar accumulation, leverages synteny and potential collinearity with related species. In this study, we explored synteny between sorghum and sugarcane. Genes from a sorghum Brix QTL were used to screen bacterial artificial chromosome (BAC) libraries from two Brazilian sugarcane varieties (IACSP93-3046 and SP80-3280). The entire region was successfully recovered, confirming synteny and collinearity between the species. Manual annotation identified 51 genes in the hybrid varieties that were subsequently confirmed to be present in Saccharum spontaneum. To identify candidate genes for sugar accumulation, this study employed a multifaceted approach, including retrieving the genomic region of interest, performing gene-by-gene analysis, analyzing RNA-seq data of internodes from Saccharum officinarum and S. spontaneum accessions, constructing a coexpression network to examine the expression patterns of genes within the studied region and their neighbors, and finally identifying differentially expressed genes (DEGs). This comprehensive approach led to the discovery of three candidate genes potentially involved in sugar accumulation: an ethylene-responsive transcription factor (ERF), an ABA 8-hydroxylase, and a prolyl oligopeptidase (POP). These findings could be valuable for identifying additional candidate genes for other important agricultural traits and directly targeting candidate genes for further work in molecular breeding.

genomics↗

bioRxiv2024

Molecular attributes of the tropical tree Avicennia schaueriana involved in the response and tolerance to low temperatures

Mangroves are coastal ecosystems of great socioenvironmental importance that are highly threatened by human activities. Mangrove trees live under harsh environmental conditions, which makes them sensitive to extreme weather events, particularly freezing events. Such events are unpredictable and have catastrophic consequences for mangrove trees; therefore, understanding and anticipating the impacts of such events are essential for directing future mitigation measures. Freezing cold currently limits the distribution of mangroves to tropical and subtropical latitudes worldwide. Mangrove trees are seriously affected by freezing conditions and suffer severe metabolic fluctuations due to photosystem and cellular structure damage. However, land plants more broadly have developed sophisticated mechanisms of resistance to freezing during their evolution, and the central molecular mechanisms involved in this process are consistent. However, the known information is restricted to models of herbaceous plants, such as Arabidopsis thaliana, that are native to temperate habitats, and there is a research gap regarding tropical trees such as mangroves. This work aimed to improve the understanding of the molecular aspects of the response and tolerance to freezing in mangrove trees using Avicennia schaueriana as a model. This species occurs within the colder range limits of South American mangroves and shows evidence of the existence of two functional groups that are locally adapted to the equatorial (EQ) and subtropical (ST) portions of the Brazilian coast. We investigated the transcriptional profiles of seedlings from both functional groups under freezing shock (-4{degrees}C) in a time series. We analyzed transcriptomic data by combining differential expression, coexpression network and protein interaction data. Our results allowed us to describe the profile of the molecular response of A. schaueriana to freezing and the divergence in the behavior of the EQ and ST functional groups. In EQ plants, the response strongly depended on the action of abscisic acid (ABA) and stress signals throughout the experiment. Notably, ABA negatively affects plant growth and promotes the accumulation of carotenoids, anthocyanins and lipids through chlorophyll degradation. On the other hand, in the ST, there were fewer hormones active in the process of primary growth maintenance and metabolic normalization. The accumulation of substances is mainly based on sucrose, anthocyanin and lipid levels, and lipid synthesis is not dependent on chlorophyll degradation. Based on these results, we hypothesize that susceptibility to freezing damage is greater in EQ mangroves than in ST mangroves. Therefore, we recommend that this fact be considered when managing this species, especially at higher latitudes, which are more prone to lower temperatures and extreme freezing events.

plant biology↗

bioRxiv2023

Lignocellulolytic carbohydrate-active enzyme-encoding gene clusters in novel Trichoderma atroviride and Trichoderma harzianum strains: A BAC-guided transcriptome analysis

Lignocellulosic biomass is known as a challenging substrate for enzymatic hydrolysis, increasing the processing cost in biorefineries. In nature, filamentous fungi, including those of the genus Trichoderma, naturally degrade lignocellulose by using an arsenal of hydrolytic and oxidative enzymes that act synergistically with biomass degradation. This work explored the genome organization of target genes of Trichoderma atroviride and Trichoderma harzianum that are able to promote hydrolysis by identifying regions enriched in degradative enzyme-encoding genes, namely, hydrolytic clusters. We employed bacterial artificial chromosome (BAC) methodology to target specific genomic regions to explore their genetic organization, proximal gene context, and gene expression under degradative conditions. Using this tool, it was possible to inspect the linear structure and expression data of target hydrolytic-rich genomic regions. The results offered a genomic perspective of the organization of genome regions related to carbohydrate metabolism, revealing novel genome regions and genes that are positively regulated during cellulose degradation and contributing to elucidating differences in gene organization among Trichoderma species. HighlightsO_LIHigh-quality genomic regions were selected using closely related species CAZyme targets. C_LIO_LIRNA-seq data were used to quantify BAC genes expression. C_LIO_LIRelevant regions were identified by combining functional and differential expression data. C_LIO_LINovel targets for future characterization identified via differential expression. C_LI

genomics↗

bioRxiv2023

Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits in Urochloa ruziziensis

Tropical forage grasses, especially species of the genus Urochloa, play an important role in cattle production and are the main food source for animals in tropical/subtropical regions. Most of the species are apomictic and tetraploid, which gives special importance to U. ruziziensis, a sexual diploid species that can be tetraploidized for use in interspecific crosses with apomictic species. As a means to assist in breeding programs, this study investigates the applicability of genome-wide family prediction (GWFP) in U. ruziziensis half-sibling families to predict growth and biomass production. Machine learning and feature selection algorithms were used to reduce the necessary number of markers for prediction and to enhance the predictive ability across the phenotypes. Beyond that, to investigate the regulation of agronomic traits, the positions of the markers with more importance for the prediction were considered putatively associated to quantitative trait loci (QTLs), and in a multiomic approach, genes obtained in the species transcriptome were mapped and linked to those markers. Furthermore, a gene coexpression network was modeled, enabling the investigation of not only the mapped genes but also their coexpressed genes. The functional annotation showed that the mapped genes are mainly associated with auxin transport and biosynthesis of lignin, flavonol and folic acid, while the coexpressed genes are associated with DNA metabolism, stress response and circadian rhythm. The results provide a viable marker-assisted breeding approach for tropical forages and identify target regions for future molecular studies on these agronomic traits.

genetics↗

bioRxiv2023

Advances in genomic characterization of Urochloa humidicola: exploring polyploid inheritance and apomixis

Tropical forage grasses are an important food source for animal feeding, with Urochloa humidicola, also known as Koronivia grass, being one of the main pasture grasses for poorly drained soils in the tropics. However, genetic and genomic resources for this species are lacking due to its genomic complexity, including high heterozygosity, evidence of segmental allopolyploidy, and reproduction by apomixis. These complexities hinder the application of marker-assisted selection (MAS) in breeding programs. Here, we developed the highest-density linkage map currently available for the hexaploid tropical forage grass U. humidicola. This map was constructed using a biparental F1 population generated from a cross between the female parent H031 (CIAT 26146), the only known sexual genotype for the species, and the apomictic male parent H016 (BRS cv. Tupi). The linkage analysis included 4,873 single nucleotide polymorphism (SNP) markers with allele dosage information. It allowed mapping of the apospory locus and phenotype to linkage group 3, in a region syntenic with chromosome 3 of Urochloa ruziziensis and chromosome 1 of Setaria italica. We also identified hexaploid haplotypes for all individuals, assessed the meiotic configuration, and estimated the level of preferential pairing in parents during the meiotic process, which revealed the autopolyploid origin of sexual H031 in contrast to H016, which presented allopolyploid behavior in preferential pairing analysis. These results provide new information regarding the genetic organization, mode of reproduction, and allopolyploid origin of U. humidicola, potential SNPs markers associated to apomixes for MAS and resources for research on polyploids and tropical forage grasses. Key messageWe present the highest-density genetic map for the hexaploid Urochloa humidicola. SNP markers expose genetic organization, reproduction, and species origin, aiding polyploid and tropical forage research.

genomics↗

bioRxiv2023

Uncovering the molecular signatures of russet skin formation in Niagara grapevine (Vitis vinifera x Vitis labrusca)

Grape breeding programs are mostly focused on developing new varieties with high production volume, sugar contents, and phenolic compound diversity combined with resistance and tolerance to the main pathogens under culture and adverse environmental conditions. The Niagara variety (Vitis labrusca x Vitis vinifera) is one of the most widely produced and commercialized table grapes in Brazil. In this work, we selected three Niagara somatic variants with contrasting berry phenotypes and performed morphological and transcriptomic analyses of their berries. Histological sections of the berries were also performed to understand anatomical and chemical composition differences of the berry skin between the genotypes. An RNA-Seq pipeline was implemented, followed by global coexpression network modeling. Niagara Steck, an intensified russet mutant with the most extreme phenotype, showed the largest difference in expression and showed selection of coexpressed network modules involved in the development of its russet-like characteristics. Enrichment analysis of differently expressed genes and hub network modules revealed differences in transcription regulation, auxin signaling and cell wall and plasmatic membrane biogenesis. Cutin- and suberin-related genes were also differently expressed, supporting the anatomical differences observed with microscopy.

bioinformatics↗

bioRxiv2022

Unraveling growth molecular mechanisms in Pinus taeda with GWAS, machine learning and gene coexpression networks

Pinus taeda (loblolly pine [LP]) is a long-lived tree species and one of the most economically significant forest species. Among growth traits, volume is the most widely considered trait in tree improvement programs. However, deciphering the genetic variants responsible for growth trait variations in conifers, such as LP, is particularly challenging due to the vast size and intricate complexity of Pinus genomes. We present a comprehensive genetic analysis of LP, focusing on markers associated with stem volume variation, to elucidate the molecular mechanisms governing high-performance phenotypes. We used a population of 1,692 individuals phenotyped for stem volume and genotyped these individuals using sequence capture probes. To conduct genome-wide associations, we utilized both genome-wide association study (GWAS) analysis and machine learning (ML) approaches. The markers identified in association with volume were found to be linked with the genes assembled from three distinct transcriptomes. These genes were subsequently used to construct gene coexpression networks, and through topological evaluations, we identified key genes with potential regulatory roles within stem volume configurations. Using a set of 31,589 SNPs, we defined 7 GWAS-associated SNPs and 128 ML-associated markers, all of which were correlated with multiple genes involved in diverse biological functions. Gene coexpression analysis revealed a group of 270 genes potentially associated with the regulation of genetic material. Key genes directly implicated in the regulation of growth and response to stress were identified, and inferences about their impact on pine development were subsequently elucidated. Our study not only offers insights into SNPs associated with stem volume but also elucidates a subset of genes characterized by unique regulatory features. These findings significantly advance our understanding of the genetic factors influencing growth traits, reveal candidate genes for future functional studies, and contribute to a broader comprehension of the genetic architecture underlying volume traits in LP.

genetics↗

bioRxiv2022

The rubber tree kinome: genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

The protein kinase (PK) superfamily constitutes one of the largest and most conserved protein families in eukaryotic genomes, comprising core components of signaling pathways in cell regulation. Despite its remarkable relevance, only a few kinase families have been studied in Hevea brasiliensis. A comprehensive characterization and global expression analysis of the PK superfamily, however, is currently lacking. In this study, with the aim of providing novel inferences about the mechanisms associated with the stress response developed by PKs and retained throughout evolution, we identified and characterized the entire set of PKs, also known as the kinome, present in the Hevea genome. A total of 1,809 PK genes were identified using the current reference genome assembly at the scaffold level, and 1,379 PK genes were identified using the latest chromosome-level assembly and combined into a single set of 2,842 PKs. These proteins were further classified into 20 different groups and 122 families, exhibiting high compositional similarities among family members and with two phylogenetically close species (Manihot esculenta and Ricinus communis). Different RNA-sequencing datasets were employed to identify tissue-specific expression patterns and potential correspondences between different rubber tree genotypes. In addition, coexpression networks under several abiotic stress conditions, such as cold, drought and latex overexploitation, were employed to elucidate associations between families and tissues/stresses. Through the joint investigation of tandemly duplicated kinases, transposable elements, gene expression patterns, and coexpression events, we provided insights into the understanding of the cell regulation mechanisms in response to several conditions, which can often lead to a significant reduction in rubber yield.

plant biology↗

bioRxiv2022

Multiomic investigation of sugarcane mosaic virus resistance in sugarcane

Sugarcane mosaic virus (SCMV) is the main etiological agent of sugarcane mosaic disease, which affects sugarcane, maize and other economically important grass species. Despite the extensive characterization of quantitative trait loci controlling resistance to SCMV in maize, the genetic basis of this trait is largely unexplored in sugarcane. Here, a genome-wide association study was performed and machine learning coupled to feature selection was used for the genomic prediction of resistance to SCMV in a diverse panel of sugarcane accessions. This ultimately led to the identification of nine single nucleotide polymorphisms (SNPs) explaining up to 29.9% of the phenotypic variance and a 73-SNP set that predicted resistance with high accuracy, precision, recall, and F1 scores. Both marker sets were validated in additional sugarcane genotypes, in which the SNPs explained up to 23.6% of the phenotypic variation and predicted resistance with a maximum accuracy of 69.1%. Synteny analyses showed that the gene responsible for the major SCMV resistance in maize is probably absent in sugarcane, explaining why such a major resistance source is thus far unknown in this crop. Lastly, using sugarcane RNA sequencing data, markers associated with the resistance to SCMV in sugarcane were annotated and a gene coexpression network was constructed to identify the predicted biological processes involved in SCMV resistance. This allowed the identification of candidate resistance genes and confirmed the involvement of stress responses, photosynthesis and regulation of transcription and translation in the resistance to this virus. These results provide a viable marker-assisted breeding approach for sugarcane and identify target genes for future molecular studies on resistance to SCMV.

plant biology↗

bioRxiv2022

Genome-wide characterization of the common bean kinome: catalog and insights into expression patterns and genetic organization

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinome of common bean (Phaseolus vulgaris) has not been profiled yet. Here, we identified and characterised the complete set of kinases of common bean, performing an in-depth investigation with phylogenetic analyses and measurements of gene distribution, structural organization, protein properties, and expression patterns over a large set of RNA-Sequencing data. Being composed of 1,203 PKs distributed across all P. vulgaris chromosomes, this set represents 3.25% of all predicted proteins for the species. These PKs could be classified into 20 groups and 119 subfamilies, with a more pronounced abundance of subfamilies belonging to the receptor-like kinase (RLK)-Pelle group. In addition to provide a vast and rich reservoir of data, our study supplied insights into the compositional similarities between PK subfamilies, their evolutionary divergences, highly variable functional profile, structural diversity, and expression patterns, modeled with coexpression networks for investigating putative interactions associated with stress response.

plant biology↗

bioRxiv2022

Genetic Diversity, Population Structure and Parentage Analysis in Brazilian Grapevine Hybrids after Half a Century of Genetic Breeding

In the 1940s, the Agronomic Institute of Campinas (IAC) started a grapevine breeding program to develop new cultivars adapted to the tropical and subtropical regions of Brazil. More than 2,000 crosses were carried out over 50 years, using 850 varieties as parents. However, among the thousands of hybrids developed by the program, only 130 are still maintained in the IAC grapevine germplasm collection. Little is known about their genetic makeup and usefulness for current breeding programs. In this study, we genotyped 130 Brazilian grape hybrids at 21 polymorphic microsatellite markers to evaluate the genetic diversity and population structure of the hybrids and verified their disclosed pedigrees. The results showed that the hybrid collection is highly diverse, with an expected heterozygosity (HE) of 0.80 and an observed heterozygosity (Ho) of 0.78. Strong structure in three subgroups based mainly on the usage and combination of parental groups was revealed by STRUCTURE software and confirmed by discriminant analysis of principal components (DAPC). Through molecular profiling analysis, fourteen synonyms, one homonym and one duplicate were identified. Parentage analysis confirmed 24 full parentages, as well as 33 half-kinships. In addition, 18 pedigrees were invalidated, and seven mislabeling events were identified. No compatible parent was identified for 33% of the IAC hybrids, highlighting severe genetic erosion in the IAC germplasm. The molecular characterization of the breeding hybrid bank collection contributes to our understanding of the genetic basis of the varieties, guiding the efficient utilization of available genetic diversity. Together, our results could be applied to other breeding programs and assist in the selection of parents, management of the breeding collection, and conservation of grapevine genetic resources.

molecular biology↗

bioRxiv2022

Taxonomically Restricted Genes are Associated with Responses to Biotic and Abiotic Stresses in Sugarcane (Saccharum spp.)

Orphan genes (OGs) are protein-coding genes that are restricted to particular clades or species and lack homology with genes from other organisms, making their biological function difficult to predict. OGs can rapidly originate and become functional; consequently, they may support rapid adaptation to environmental changes. Extensive spread of mobile elements, and whole genome duplication, occurred in the Saccharum group, which may have contributed to the origin and diversification of OGs in the sugarcane genome. Here, we identified and characterized OGs in sugarcane, examined their expression profiles across tissues and genotypes, and investigated their regulation under varying conditions. We identified 319 OGs in the Saccharum spontaneum genome without detected homology to protein-coding genes in green plants, except those belonging to Saccharinae. Transcriptomic analysis showed 288 sugarcane OGs with detectable expression levels in at least one tissue or genotype. We observed similar expression patterns of OGs in sugarcane genotypes originating from the closest geographical locations. We also observed tissue-specific expression of some OGs, possibly indicating a complex regulatory process for maintaining diverse functional activity of these genes across sugarcane tissues and genotypes. Sixty-six OGs were differentially expressed under stress conditions, especially cold and osmotic stresses. Gene co-expression network and functional enrichment analyses suggested that sugarcane OGs may be involved in several biological mechanisms, including stimulus response and defence mechanisms. These findings provide a valuable genomic resource for sugarcane researchers, especially those interested in selecting stress-responsive genes.

plant biology↗

bioRxiv2022

A joint learning approach for genomic prediction in polyploid grasses

Poaceae, among the most abundant plant families, includes many economically important polyploid species, such as forage grasses and sugarcane (Saccharum spp.). These species have elevated genomic complexities and limited genetic resources, hindering the application of marker-assisted selection strategies. Currently, the most promising approach for increasing genetic gains in plant breeding is genomic selection. However, due to the polyploidy nature of these polyploid species, more accurate models for incorporating genomic selection into breeding schemes are needed. This study aims to develop a machine learning method by using a joint learning approach to predict complex traits from genotypic data. Biparental populations of sugarcane and two species of forage grasses (Urochloa decumbens, Megathyrsus maximus) were genotyped, and several quantitative traits were measured. High-quality markers were used to predict several traits in different cross-validation scenarios. By combining classification and regression strategies, we developed a predictive system with promising results. Compared with traditional genomic prediction methods, the proposed strategy achieved accuracy improvements exceeding 50%. Our results suggest that the developed methodology could be implemented in breeding programs, helping reduce breeding cycles and increase genetic gains.

bioinformatics↗