Sugarcane mosaic disease (SMD) caused by sugarcane mosaic virus, is one of the main diseases in sugarcane production areas in Brazil. Thus, the identification of new sources of resistance for use in ...future introgression crosses is key for reliable economic gains. Here, we aimed to screen a diversity panel of 98 sugarcane genotypes for SMD under natural infection conditions, to investigate virus-specific amplicons from SCMV coat protein gene (CP), and identify marker-trait associations via association mapping using Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeats (SSR). The highest SMD incidence (26.53%) was observed eight months after planting, with significant differences (p<0.01) among genotypes and a means-based broad-sense heritability of 62.49% with a noticeable contribution of
Saccharum spontaneum
to SMD resistance. The CP sequence analysis revealed no variation among the four selected plant samples, which phylogenetic analysis revealed clustering with the RIB-1 strain while putative amino acid substitutions indicate a new SCMV isolate. From a subset of 135 SSR and 663 AFLP markers, selected after quality control, 91 markers were associated with response to SCMV (
p
<0.05) by simple linear regression, and 24 were significant at
p
<0.01. Four out these 24 fit in a stepwise regression at
p
<0.05, all contributing for the resistance to SMD, and are present in thirteen genotypes showing no SMD symptoms. These four markers collectively explain 29.95% of trait variation, while individually explain from 5.51 to 14.02%, and may correspond to new genomic regions conferring genetic resistance to SMD which investigation is worthwhile.
Dirigent (DIR) proteins, encoded by
DIR
genes, are referred to as “dirigent” because they direct the outcome of the coupling of the monolignol coniferyl alcohol into (+) or (−) pinoresinol, the first ...intermediates in the enantiocomplementary pathways for lignan biosynthesis. DIR domain-containing or DIR-like proteins are, thus, termed for not having a clear characterization. A transcriptome- and genome-wide survey of DIR domain-containing proteins in sugarcane was carried out, in addition to phylogenetic, physicochemical and transcriptional analyses. A total of 120 non-redundant sequences containing the DIR domain were identified and classified into 64 groups according to phylogenetic and sequence alignment analyses. In silico analysis of transcript abundance showed that these sequences are expressed at low levels in leaves and genes in the same phylogenetic clade have similar expression patterns. Expression analysis of
ShDIR1
-
like
transcripts in the culm internodes of sugarcane demonstrates their abundance in mature internodes, their induction by nitrogen fertilization and their predominant expression in cells that have a lignified secondary cell wall, such as vascular bundles of young internodes and parenchymal cells of the pith of mature internodes. Due to the lack of information about the functional role of DIR in plants, a possible relationship is discussed between the
ShDIR1
-
like
transcriptional profile and cell wall development in parenchyma cells of sugarcane culm, which typically accumulates large amounts of sucrose. The number of genes encoding the DIR domain-containing proteins in sugarcane is intriguing and is an indication per se that these proteins may have an important metabolic role and thus deserve to be better studied.
Yellow leaf disease (YLD), caused by sugarcane yellow leaf virus (SCYLV), has been reported to infect sugarcane worldwide causing significant yield losses and is considered a major disease of this ...crop. A panel composed of 98 genotypes encompassing basic germplasm, commercial cultivars, and elite clones was assayed in the nursery and a replicated field for resistance to SCYLV, combining symptom expression and virus quantification. Virus symptom intensity was evaluated using a diagrammatic scale while virus titer was estimated by DAS-ELISA (Double Antibody Sandwich-ELISA) and RT-qPCR (Reverse Transcription Quantitative PCR) in the nursery and field trials, respectively. Resistance was evaluated alongside symptom development kinetics. Based on the symptom intensity, 52 (53.06%) genotypes were classified as resistant in the nursery and 42 (42.86%) in the field. Twenty-nine (29.59%) genotypes showed no symptoms in the nursery and field trial. Moderately resistant genotypes showed a low correlation between virus titer and symptom intensity. The kinetics of symptom development increased over time in moderately susceptible and susceptible genotypes. The SCYLV incidence assessed by RT-qPCR was 92.55%, which was detected in 83% of the asymptomatic genotypes. The broad-sense heritability based on symptom expression and relative quantification was 52.62% and 68%, respectively. The virus quantification assays allowed for the identification of potential genotypes immune to SCYLV.
•Resistance evaluation combining symptom expression and virus quantification.•83% of asymptomatic but SCYLV infected genotypes.•Five potential SCYLV immune genotypes identified by DAS-ELISA and RT-qPCR.•Combination of RT-qPCR and symptom expression proven suitable for parental selection.•Moderate to high broad-sense heritability for symptom expression (52.62%) and virus titer (68%).
Sugarcane mosaic disease (SMD) caused by sugarcane mosaic virus, is one of the main diseases in sugarcane production areas in Brazil. Thus, the identification of new sources of resistance for use in ...future introgression crosses is key for reliable economic gains. Here, we aimed to screen a diversity panel of 98 sugarcane genotypes for SMD under natural infection conditions, to investigate virus-specific amplicons from SCMV coat protein gene (CP), and identify marker-trait associations via association mapping using Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeats (SSR). The highest SMD incidence (26.53%) was observed eight months after planting, with significant differences (p<0.01) among genotypes and a means-based broad-sense heritability of 62.49% with a noticeable contribution of Saccharum spontaneum to SMD resistance. The CP sequence analysis revealed no variation among the four selected plant samples, which phylogenetic analysis revealed clustering with the RIB-1 strain while putative amino acid substitutions indicate a new SCMV isolate. From a subset of 135 SSR and 663 AFLP markers, selected after quality control, 91 markers were associated with response to SCMV (p <0.05) by simple linear regression, and 24 were significant at p <0.01. Four out these 24 fit in a stepwise regression at p <0.05, all contributing for the resistance to SMD, and are present in thirteen genotypes showing no SMD symptoms. These four markers collectively explain 29.95% of trait variation, while individually explain from 5.51 to 14.02%, and may correspond to new genomic regions conferring genetic resistance to SMD which investigation is worthwhile.
Abstract
Sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV) is a major disease affecting sugarcane, a leading sugar and energy crop. Despite damages caused by SCYLV, the ...genetic base of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic base of SCYLV resistance using dominant and codominant markers and genotypes of interest for sugarcane breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them and demonstrated their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.
The increasing demand of strawberry (Fragaria×ananassa Duch) fruits is associated mainly with their sensorial characteristics and the content of antioxidant compounds. Nevertheless, the strawberry ...production has been hampered due to its sensitivity to abiotic stresses. Therefore, to understand the molecular mechanisms highlighting stress response is of great importance to enable genetic engineering approaches aiming to improve strawberry tolerance. However, the study of expression of genes in strawberry requires the use of suitable reference genes. In the present study, seven traditional and novel candidate reference genes were evaluated for transcript normalization in fruits of ten strawberry cultivars and two abiotic stresses, using RefFinder, which integrates the four major currently available software programs: geNorm, NormFinder, BestKeeper and the comparative delta-Ct method. The results indicate that the expression stability is dependent on the experimental conditions. The candidate reference gene DBP (DNA binding protein) was considered the most suitable to normalize expression data in samples of strawberry cultivars and under drought stress condition, and the candidate reference gene HISTH4 (histone H4) was the most stable under osmotic stresses and salt stress. The traditional genes GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and 18S (18S ribosomal RNA) were considered the most unstable genes in all conditions. The expression of phenylalanine ammonia lyase (PAL) and 9-cis epoxycarotenoid dioxygenase (NCED1) genes were used to further confirm the validated candidate reference genes, showing that the use of an inappropriate reference gene may induce erroneous results. This study is the first survey on the stability of reference genes in strawberry cultivars and osmotic stresses and provides guidelines to obtain more accurate RT-qPCR results for future breeding efforts.
•The expression stability of reference genes for RT-qPCR in strawberry was evaluated.•Cultivars and plants cultivated under abiotic stresses were included in the study.•DBP was the most stable gene along cultivars and under drought stress condition.•HISTH4 was the considered the most suitable under osmotic stresses and salt stress.•This study provides guidelines to obtain more accurate RT-qPCR results.
•Prebiotic based on β-glucans, glucomannans and MOS, at lower levels, showed an analogous effect to chlorohydroxyquinoline (positive control).•The antimicrobial treatment provided a better feed ...conversation.•Chlorohydroxyquinoline and β-glucans, glucomannans and MOS increased spleen weight.•The higher level of the prebiotic (3000 mg/kg) reduced the jejunal villus density.
This study proposes to evaluate the addition a prebiotic product based on beta-glucans (β-glucans), glucomannans, and mannan oligosaccharides (MOS), replacing an antimicrobial growth promoters in diets for newly weaned piglets, on their performance, occurrence of diarrhea (OD), hematological parameters, organ morphometry, pH of the digestive content, and intestinal epithelium morphology. The experiment involved 120 piglets weaned at 21 days of age, with an initial weight of 6.35 ± 0.10 kg, which were allotted to five treatments in a completely randomized block design with six replicates and four piglets per experimental unit. The following treatments were: 0 – basal diet; 1000, 2000, or 3000 mg/kg of a prebiotic; and ANT – basal diet with 120 mg/kg chlorohydroxyquinoline. The inclusion of prebiotic levels in the diet caused a worsening (P < 0.05) in feed conversion (FC). Hematological analysis revealed that prebiotic levels in the diet provided a quadratic effect (P < 0.05) in eosinophil count. The antimicrobial treatment provided a better FC (P < 0.05). Prebiotic levels elicited a quadratic response from villus density (VD) in the duodenum and, in the jejunum, VD decreased linearly (P < 0.05). The ANT treatment led to a lower VD (P < 0.05), in duodenum, compared with treatment 3000 mg/kg. In the jejunum, VD increased (P < 0.05) in ANT when compared with 1000 and 3000 mg/kg of prebiotic. Based on the present results, 3000 mg/kg of a prebiotic are not a viable alternative to performance-enhancing antimicrobials in the diet of piglets.
Sugarcane (Saccharum spp.) is currently one of the most efficient crops in the production of first-generation biofuels. However, the bagasse represents an additional abundant lignocellulosic resource ...that has the potential to increase the ethanol production per plant. To achieve a more efficient conversion of bagasse into ethanol, a better understanding of the main factors affecting biomass recalcitrance is needed. Because several studies have shown a negative effect of lignin on saccharification yield, the characterization of lignin biosynthesis, structure, and deposition in sugarcane is an important goal. Here, we present, to our knowledge, the first systematic study of lignin deposition during sugarcane stem development, using histological, biochemical, and transcriptional data derived from two sugarcane genotypes with contrasting lignin contents. Lignin amount and composition were determined in rind (outer) and pith (inner) tissues throughout stem development. In addition, the phenolic metabolome was analyzed by ultra-high-performance liquid chromatography-mass spectrometry, which allowed the identification of 35 compounds related to the phenylpropanoid pathway and monolignol biosynthesis. Furthermore, the Sugarcane EST Database was extensively surveyed to identify lignin biosynthetic gene homologs, and the expression of all identified genes during stem development was determined by quantitative reverse transcription-polymerase chain reaction. Our data provide, to our knowledge, the first in-depth characterization of lignin biosynthesis in sugarcane and form the baseline for the rational metabolic engineering of sugarcane feedstock for bioenergy purposes.
ABSTRACT The objective of this study was to examine the effects of replacement of an antibiotic (ANT, chlorohydroxyquinoline) in the diet of weaned piglets with a prebiotic composed of β-glucans, ...glucomannans, and mannan-oligosaccharides on growth performance, diarrhea occurrence (DO), hematological parameters, pH of digestive content, organ weights, intestinal epithelium morphology, and intestinal bacterial counts. A total of 120 piglets (weaned at 21 d old; 6.32±0.10 kg BW) were allocated in a randomized block design, with six pens replicates and four piglets per pen as experimental unit. Treatments consisted of diets with 0, 1,000, 2,000, or 3,000 mg kg−1 of prebiotic and a basal diet with 120 mg kg−1 ANT. No differences of treatments were observed on performance, DO, pH of digestive content, organ weights, and hematological parameters. Duodenal villus density (VD) increased linearly with the prebiotic levels. In the jejunum, the prebiotic level of 2,000 mg kg−1 resulted in a greater VD compared with the ANT. Enterobacteriaceae count in the ileum and total and lactic acid bacteria counts in the cecum responded quadratically to increasing prebiotic levels. The equations estimated the prebiotic levels of 2,125, 1,167, and 1,500 mg kg−1 to provide reduced counts of the respective bacteria (ileal enterobacteria: 6.47 log CFU g−1; total cecal bacteria: 6.70 log CFU g−1; and cecal lactic acid: 7.29 log CFU g−1). Salmonella spp. was not detected, whereas Escherichia coli and Lactobacillus spp. gene copies were unaffected by the treatments. Prebiotic levels or ANT do not enhance performance or health of weanling pigs, but the effects observed on VD and microbiota profile might be an indication of the potential benefits of these products in commercial farming conditions.
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