Phenotypic Variation Research Articles

Distinct prophage gene profiles of Staphylococcus aureus strains from atopic dermatitis patients and healthy individuals.

Through a nuanced exploration of Staphylococcus aureus strains obtained from atopic dermatitis (AD) patients and healthy controls (HE), our research unveils pivotal genetic determinants influencing their pathogenic associations. Utilizing a random forest classifier, we illuminate distinct marker genes, with phage holin emerging as a critical differential factor, revealing the profound impact of prophages on genetic and pathogenic profiles. HE strains exhibited a diverse gene content, notably shaped by unique, heightened prophages. Conversely, AD strains emphasized a pronounced enrichment of virulence factors within prophages, signifying their key role in AD pathogenesis. This work crucially highlights prophages as central architects of the genetic and functional attributes of S. aureus strains, providing vital insights into pathogenic mechanisms and phenotypic variations, thereby paving the way for targeted AD therapeutic approaches and management strategies by demystifying specific genetic and pathogenic mechanisms.

Scans for Signatures of Selection in Genomes of Wagyu and Buryat Cattle Breeds Reveal Candidate Genes and Genetic Variants for Adaptive Phenotypes and Production Traits

Past and ongoing selection shapes the genomes of livestock breeds. Identifying such signatures of selection allows for uncovering the genetic bases of affected phenotypes, including economically important traits and environmental adaptations, for the further improvement of breed genetics to respond to climate and economic challenges. Turano-Mongolian cattle are a group of taurine breeds known for their adaptation to extreme environmental conditions and outstanding production performance. Buryat Turano-Mongolian cattle are among the few breeds adapted to cold climates and poor forage. Wagyu, on the other hand, is famous for high productivity and unique top-quality marbled meat. We used hapFLK, the de-correlated composite of multiple signals (DCMS), PBS, and FST methods to search for signatures of selection in their genomes. The scans revealed signals in genes related to cold adaptation (e.g., STAT3, DOCK5, GSTM3, and CXCL8) and food digestibility (SI) in the Buryat breed, and growth and development traits (e.g., RBFOX2 and SHOX2) and marbling (e.g., DGAT1, IQGAP2, RSRC1, and DIP2B) in Wagyu. Several putatively selected genes associated with reproduction, immunity, and resistance to pathogens were found in both breed genomes. The results of our work could be used for creating new productive adapted breeds or improving the extant breeds.

Combining high-throughput deep learning phenotyping and GWAS to reveal genetic variants of fruit branch angle in upland cotton

Cotton (Gossypium spp.), an economically and strategically significant crop in China, faces challenges such as rising cultivation costs and conflicts between grain and cotton cultivation. These challenges underscore the need for enhancing yields per unit area. In response, this study employs deep learning techniques, combined with high-throughput angle detection, to conduct genome-wide association studies (GWAS) on 355 upland cotton accessions, identify key SNPs and candidate genes for plant architecture by fruit branch angle (FBA) influences planting density, yield, and mechanized harvesting. A convolutional neural network (CNN)-based software was developed for rapid and accurate branch angle detection, showing high correlation with both AutoCAD and manual measurements. Significant phenotypic variation in FBA was observed across various cotton planting regions, with the Northwest Inland Region (NIR) exhibiting notably smaller angles. In total, 107 significant Single Nucleotide Polymorphisms (SNPs) were detected across 45 quantitative trait loci (QTL), and three potential candidate genes (Ghir_A11G034910, Ghir_D05G007790, and Ghir_D05G031350) were identified, providing insights into the genetic basis of FBA and presenting valuable genetic resources for cotton breeding programs.

Phenotypic Expansion of Autosomal Dominant LZTR1-Related Disorders with Special Emphasis on Adult-Onset Features

Leucine zipper-like transcription regulator 1 (LZTR1) acts as a negative factor that suppresses RAS function and MAPK signaling; mutations in this protein may dysregulate RAS ubiquitination and lead to impaired degradation of RAS superfamily proteins. Germline LZTR1 variants are reported in Noonan syndrome, either autosomal dominant or autosomal recessive, and in susceptibility to schwannomatosis. This article explores the genetic and phenotypic diversity of the autosomal dominant LZTR1-related disorders, compiling a cohort of previously published patients (51 with the Noonan phenotype and 123 with schwannomatosis) and presenting two additional adult-onset cases: a male with schwannomatosis and Parkinson’s disease and a female with Noonan syndrome, generalized joint hypermobility, and breast cancer. This review confirms that autosomal dominant LZTR1-related disorders exhibit an extreme phenotypic variability, ranging from relatively mild manifestations to severe and multi-systemic involvement, and offers updated frequences of each clinical feature. The aim is to precisely define the clinical spectrum of LZTR1-related diseases, using also two new emblematic clinical cases. Gaining insight into the mechanisms underneath this variability is crucial to achieve precision diagnostics and the development of therapeutic interventions.

Ontogenetic variation in the marine foraging of Atlantic salmon functionally links genomic diversity with a major life history polymorphism.

The ecological role of heritable phenotypic variation in free-living populations remains largely unknown. Knowledge of the genetic basis of functional ecological processes can link genomic and phenotypic diversity, providing insight into polymorphism evolution and how populations respond to environmental changes. By quantifying the marine diet of Atlantic salmon, we assessed how foraging behaviour changes along the ontogeny, and in relation to genetic variation in two loci with major effects on age at maturity (six6 and vgll3). We used a two-component, zero-inflated negative binomial model to simultaneously quantify foraging frequency and foraging outcome, separately for fish and crustaceans diets. We found that older salmon forage for both prey types more actively (as evidenced by increased foraging frequency), but with a decreased efficiency (as evidenced by fewer prey in the diet), suggesting an age-dependent shift in foraging dynamics. The vgll3 locus was linked to age-dependent changes in foraging behaviour: Younger salmon with vgll3LL (the genotype associated with late maturation) tended to forage crustaceans more often than those with vgll3EE (the genotype associated with early maturation), whereas the pattern was reversed in older salmon. Vgll3 LL genotype was also linked to a marginal increase in fish acquisition, especially in younger salmon, while six6 was not a factor explaining the diet variation. Our results suggest a functional role for marine feeding behaviour linking genomic diversity at vgll3 with age at maturity among salmon, with potential age-dependent trade-offs maintaining the genetic variation. A shared genetic basis between dietary ecology and age at maturity likely subjects Atlantic salmon populations to evolution induced by bottom-up changes in marine productivity.

Long-Term Outcomes of Cochlear Implantation in Usher Syndrome.

Usher syndrome (USH), characterized by bilateral sensorineural hearing loss (SNHL) and retinitis pigmentosa (RP), prompts increased reliance on hearing due to progressive visual deterioration. It can be categorized into three subtypes: USH type 1 (USH1), characterized by severe to profound congenital SNHL, childhood-onset RP, and vestibular areflexia; USH type 2 (USH2), presenting with moderate to severe progressive SNHL and RP onset in the second decade, with or without vestibular dysfunction; and USH type 3 (USH3), featuring variable progressive SNHL beginning in childhood, variable RP onset, and diverse vestibular function. Previous studies evaluating cochlear implant (CI) outcomes in individuals with USH used varying or short follow-up durations, while others did not evaluate outcomes for each subtype separately. This study evaluates long-term CI performance in subjects with USH, at both short-term and long-term, considering each subtype separately. This retrospective, observational cohort study identified 36 CI recipients (53 ears) who were categorized into four different groups: early-implanted USH1 (first CI at ≤7 years of age), late-implanted USH1 (first CI at ≥8 years of age), USH2 and USH3. Phoneme scores at 65 dB SPL with CI were evaluated at 1 year, ≥2 years (mid-term), and ≥5 years postimplantation (long-term). Each subtype was analyzed separately due to the significant variability in phenotype observed among the three subtypes. Early-implanted USH1-subjects (N = 23 ears) achieved excellent long-term phoneme scores (100% [interquartile ranges {IQR} = 95 to 100]), with younger age at implantation significantly correlating with better CI outcomes. Simultaneously implanted subjects had significantly better outcomes than sequentially implanted subjects (p = 0.028). Late-implanted USH1 subjects (N = 3 ears) used CI solely for sound detection and showed a mean phoneme discrimination score of 12% (IQR = 0 to 12), while still expressing satisfaction with ambient sound detection. In the USH2 group (N = 23 ears), a long-term mean phoneme score of 85% (IQR = 81 to 95) was found. Better outcomes were associated with younger age at implantation and higher preimplantation speech perception scores. USH3-subjects (N = 7 ears) achieved a mean postimplantation phoneme score of 71% (IQR = 45 to 91). This study is currently one of the largest and most comprehensive studies evaluating CI outcomes in individuals with USH, demonstrating that overall, individuals with USH benefit from CI at both short- and long-term follow-up. Due to the considerable variability in phenotype observed among the three subtypes, each subtype was analyzed separately, resulting in smaller sample sizes. For USH1 subjects, optimal CI outcomes are expected with early simultaneous bilateral implantation. Late implantation in USH1 provides signaling function, but achieved speech recognition is insufficient for oral communication. In USH2 and USH3, favorable CI outcomes are expected, especially if individuals exhibit sufficient speech recognition with hearing aids and receive ample auditory stimulation preimplantation. Early implantation is recommended for USH2, given the progressive nature of hearing loss and concomitant severe visual impairment. In comparison with USH2, predicting outcomes in USH3 remains challenging due to the variability found. Counseling for USH2 and USH3 should highlight early implantation benefits and encourage hearing aid use.

What we know about Turkey oak (Quercus cerris L.) — from evolutionary history to species ecology

Abstract Turkey oak (Quercus cerris L.) is a deciduous tree species of the genus Quercus section Cerris (Fagaceae), widely distributed in Europe and Asia Minor. Throughout its vast distribution range, the species carries high phenotypic and genetic variability. Due to its high drought tolerance, Turkey oak may have great potential to be a key tree species in Central and Western Europe under climate change conditions. However, more detailed information on its phylogeny, phylogeography, phenotypic, and genetic variability is still needed for a more careful and reliable assessment of the species’ adaptation potential. To this end, based on 41 reviewed articles, we collected detailed information to support the evaluation of Turkey oak’s adaptation potential under climate change. In the reviewed articles, we observed a significantly lower number of genetic studies of the members of the section Cerris (especially the Euro-Mediterranean species) relative to the subgenus Quercus. We also identified research gaps with respect to the functional and population genetics of the species that should be addressed in the future. Nevertheless, the different evolutionary background and adaptation strategies of Turkey oak as compared to Central European white oaks, as well as its high phenotypic and genetic variability, may indeed represent a great potential for this species to support the climate adaptation of forestry in Central and Western Europe.

Identification and characterization of a new species of Taxus — Taxus qinlingensis by multiple taxonomic methods

BackgroundThe taxonomy of Taxus Linn. remains controversial due to its continuous phenotypic variation and unstable topology, thus adversely affecting the formulation of scientific conservation strategies for this genus. Recently, a new ecotype, known as Qinling type, is mainly distributed in the Qinling Mountains and belongs to a monophyletic group. Here, we employed multiple methods including leaf phenotype comparison (leaf shapes and microstructure), DNA barcoding identification (ITS + trnL-trnF + rbcL), and niche analysis to ascertain the taxonomic status of the Qinling type.ResultsMultiple comparisons revealed significant differences in the morphological characters (length, width, and length/width ratio) among the Qinling type and other Taxus species. Leaf anatomical analysis indicated that only the Qinling type and T. cuspidata had no papilla under the midvein or tannins in the epicuticle. Phylogenetic analysis of Taxus indicated that the Qinling type belonged to a monophyletic group. Moreover, the Qinling type had formed a relatively independent niche, it was mainly distributed around the Qinling Mountains, Ta-pa Mountains, and Taihang Mountains, situated at an elevation below 1500 m.ConclusionsFour characters, namely leaf curvature, margin taper, papillation on midvein, and edges were put forward as primary indexes for distinguishing Taxus species. The ecotype Qingling type represented an independent evolutionary lineage and formed a unique ecological niche. Therefore, we suggested that the Qingling type should be treated as a novel species and named it Taxus qinlingensis Y. F. Wen & X. T. Wu, sp. nov.

Beyond the standard GWAS - a guide for plant biologists.

Classic genome-wide association studies (GWAS) look for associations between individual SNPs and phenotypes of interest. With the rapid progress of high-throughput genotyping and phenotyping technologies, GWAS have become increasingly powerful for detecting genetic determinants and their molecular mechanisms underpinning natural phenotypic variation. However, GWAS frequently yield results with neither expected nor promising loci, nor any significant associations. This is often because associations between SNPs and a single phenotype are confounded, for example with the environment, other traits, or complex genetic structures. Such confounding can mask true genotype-phenotype associations, or inflate spurious associations. To address these problems, numerous methods have been developed that go beyond the standard model. Such advanced GWAS models are flexible and can offer improved statistical power for understanding the genetics underlying complex traits. Despite this advantage, these models have not been widely adopted and implemented compared to the standard GWAS approach, partly because this literature is diverse and often technical. In this review, our aim is to provide an overview of the application and the benefits of various advanced GWAS models for handling complex traits and genetic structures, targeting plant biologists who wish to carry out GWAS more effectively.

Genome-wide analysis of histone modifications can contribute to the identification of candidate cis-regulatory regions in the threespine stickleback fish

BackgroundCis-regulatory mutations often underlie phenotypic evolution. However, because identifying the locations of promoters and enhancers in non-coding regions is challenging, we have fewer examples of identified causative cis-regulatory mutations that underlie naturally occurring phenotypic variations than of causative amino acid-altering mutations. Because cis-regulatory elements have epigenetic marks of specific histone modifications, we can detect cis-regulatory elements by mapping and analyzing them. Here, we investigated histone modifications and chromatin accessibility with cleavage under targets and tagmentation (CUT&Tag) and assay for transposase-accessible chromatin-sequencing (ATAC-seq).ResultsUsing the threespine stickleback (Gasterosteus aculeatus) as a model, we confirmed that the genes for which nearby regions showed active marks, such as H3K4me1, H3K4me3, and high chromatin accessibility, were highly expressed. In contrast, the expression levels of genes for which nearby regions showed repressive marks, such as H3K27me3, were reduced, suggesting that our chromatin analysis protocols overall worked well. Genomic regions with peaks of histone modifications showed higher nucleotide diversity within and between populations. By comparing gene expression in the gills of the marine and stream ecotypes, we identified several insertions and deletions (indels) with transposable element fragments in the candidate cis-regulatory regions.ConclusionsThus, mapping and analyzing histone modifications can help identify cis-regulatory elements and accelerate the identification of causative mutations in the non-coding regions underlying naturally occurring phenotypic variations.

Genetic analysis of efficiency-related traits in Boer x Central Highland goats.

This study aimed to identify important non-genetic factors and estimate genetic parameters for efficiency-related traits in Boer x Central Highland goats. The genetic parameters were estimated using the Average Information Restricted Maximum Likelihood algorithm using the WOMBAT program fitting animal model. The least-squares means for growth efficiency from birth to 3 months (GE1), 3-6 months (GE2), 6-12 months (GE3), relative growth rate from birth to 3 months (RGR1), 3-6 months (RGR2) and 6-12 month (RGR3) were 294.0 ± 5.06, 36.6 ± 1.20, 44.9 ± 1.81, 1.46 ± 0.01, 0.32 ± 0.01 and 0.19 ± 0.01, respectively. Birth type, blood level, sex of the kid, and year of kidding had a sizable effect on efficiency-related traits. About 18, 3.0, 23, 20, and 12% of the phenotypic variation in GE2, GE3, RGR1, RGR2, and RGR3 was explained by the direct additive genetic effect. Except for RGR3, all investigated traits were under the influence of maternal genetic effect, and maternal heritability ranged from 0.09 to 0.17. The total heritability estimate depicts that slow genetic progress would be expected from selection. Nevertheless, even with this level of heritability, selection for efficiency-related traits would improve the efficiency of chevon production as these traits are economically important traits. Nearly six-months of age was when farmers sold Boer crossbred goats. Therefore, improving the growth efficiency till the marketing age (GE2) in such a scenario could increase the production efficiency.

Natural variation of domestication-related genes contributed to latitudinal expansion and adaptation in soybean

Soybean is a major source of protein and edible oil worldwide. Originating from the Huang-Huai-Hai region, which has a temperate climate, soybean has adapted to a wide latitudinal gradient across China. However, the genetic mechanisms responsible for the widespread latitudinal adaptation in soybean, as well as the genetic basis, adaptive differentiation, and evolutionary implications of theses natural alleles, are currently lacking in comprehensive understanding. In this study, we examined the genetic variations of fourteen major gene loci controlling flowering and maturity in 103 wild species, 1048 landraces, and 1747 cultivated species. We found that E1, E3, FT2a, J, Tof11, Tof16, and Tof18 were favoured during soybean improvement and selection, which explained 75.5% of the flowering time phenotypic variation. These genetic variation was significantly associated with differences in latitude via the LFMM algorithm. Haplotype network and geographic distribution analysis suggested that gene combinations were associated with flowering time diversity contributed to the expansion of soybean, with more HapA clustering together when soybean moved to latitudes beyond 35°N. The geographical evolution model was developed to accurately predict the suitable planting zone for soybean varieties. Collectively, by integrating knowledge from genomics and haplotype classification, it was revealed that distinct gene combinations improve the adaptation of cultivated soybeans to different latitudes. This study provides insight into the genetic basis underlying the environmental adaptation of soybean accessions, which could contribute to a better understanding of the domestication history of soybean and facilitate soybean climate-smart molecular breeding for various environments.

Cold tolerance SNPs and candidate gene mining in the soybean germination stage based on genome-wide association analysis.

Three QTLs associated with low-temperature tolerance were identified by genome-wide association analysis, and 15 candidate genes were identified by haplotype analysis and gene expression analyses. Low temperature is a critical factor affecting the geographical distribution, growth, development, and yield of soybeans, with cold stress during seed germination leading to substantial productivity loss. In this study, an association panel comprising 260 soybean accessions was evaluated for four germination traits and four cold tolerance index traits, revealing extensive variation in cold tolerance. Genome-wide association study (GWAS) identified 10 quantitative trait nucleotides (QTNs) associated with cold tolerance, utilizing 30,799 single nucleotide polymorphisms (SNPs) and four GWAS models. Linkage disequilibrium (LD)analysis positioned these QTNs within three cold-tolerance quantitative trait loci (QTL) and, with QTL19-1, was positioned by three multi-locus models, underscoring its importance as a key QTL. Integrative haplotype analysis, supplemented by transcriptome analysis, uncovered 15 candidate genes. The haplotypes within the genes Glyma.18G044200, Glyma.18G044300, Glyma.18G044900, Glyma.18G045100, Glyma.19G222500, and Glyma.19G222600 exhibited significant phenotypic variations, with differential expression in materials with varying cold tolerance. The QTNs and candidate genes identified in this study offer substantial potential for marker-assisted selection and gene editing in breeding cold-tolerant soybeans, providing valuable insights into the genetic mechanisms underlying cold tolerance during soybean germination.

Cold tolerance SNPs and candidate gene mining in the soybean germination stage based on genome-wide association analysis.

Three QTLs associated with low-temperature tolerance were identified by genome-wide association analysis, and 15 candidate genes were identified by haplotype analysis and gene expression analyses. Low temperature is a critical factor affecting the geographical distribution, growth, development, and yield of soybeans, with cold stress during seed germination leading to substantial productivity loss. In this study, an association panel comprising 260 soybean accessions was evaluated for four germination traits and four cold tolerance index traits, revealing extensive variation in cold tolerance. Genome-wide association study (GWAS) identified 10 quantitative trait nucleotides (QTNs) associated with cold tolerance, utilizing 30,799 single nucleotide polymorphisms (SNPs) and four GWAS models. Linkage disequilibrium (LD)analysis positioned these QTNs within three cold-tolerance quantitative trait loci (QTL) and, with QTL19-1, was positioned by three multi-locus models, underscoring its importance as a key QTL. Integrative haplotype analysis, supplemented by transcriptome analysis, uncovered 15 candidate genes. The haplotypes within the genes Glyma.18G044200, Glyma.18G044300, Glyma.18G044900, Glyma.18G045100, Glyma.19G222500, and Glyma.19G222600 exhibited significant phenotypic variations, with differential expression in materials with varying cold tolerance. The QTNs and candidate genes identified in this study offer substantial potential for marker-assisted selection and gene editing in breeding cold-tolerant soybeans, providing valuable insights into the genetic mechanisms underlying cold tolerance during soybean germination.

COMPARISON OF THE CHEMICAL COMPOSITION AND MORPHOLOGICAL CHARACTERISTICS OF DIFFERENT CARROT VARIETIES

Carrot (Daucus carota L.) is a globally significant root vegetable, rich in bioactive and nutritional compounds. Carrot is a crop with a wide range of phenotypic variability including colour, shape, size, and other characteristics. The aim of this work was to determine and compare selected morphological traits and chemical composition of 24 carrot varieties grown under open field conditions in Slovakia. Altogether, 11 qualitative characteristics and 6 quantitative parameters were evaluated. The carrot roots were also analysed for essential chemical constituents including reducing sugars (fructose, glucose, saccharose), carotenoids, dietary fibre, dry matter, ash, and mineral compounds. A wide range of diversity in morphological characteristics and chemical composition indicates a high variability of studied varieties. The root length ranged from 59 to 205 mm, root diameter varied from 17.7 to 39.0 mm and root weight ranged from 21.0 to 74.8 g. Based on the measurement results, saccharose was the dominant sugar ranging from 1.89 to 4.67 g.100 g-1 of fresh weight, carotenoid content varied from 85.94 to 374.24 µg.g-1 of fresh weight, the amount of dietary fibre ranged from 25.67 to 36.02% of dry matter. Considerable differences were also observed in the content of macro and microelements [mg.100 g-1] ranging as follows: P (17.5 - 52.0), K (110.0 – 337.0), Na (65.9 – 186.0), Fe (0.324 – 3.340), Cu (0.042 – 0.126), Zn (0.152 – 0.945) and Mn (0.062 – 0.189). The presented results can provide useful information for carrot growers and consumers in terms of morphological characteristics as well as the chemical composition of individual carrot varieties.

Root system of Coffea canephora cv. Robusta genotypes cultivated in the Brazilian Amazon

The root system distribution of coffee, especially Coffea canephora cv. Robusta, remains poorly characterized. The aim of this study were: (i) to analyze the distribution of the root system in various genotypes of C. canephora cv. Robusta cultivated in the Amazon region; (ii) to evaluate genetic variability based on root traits; and (iii) to test the correlation between root traits, aboveground part, and production capacity. Roots were collected up to a depth of 60 cm and 30 cm away from the stems. The roots were washed, scanned, and processed to quantify root volume (mm3 cm−3), surface area (mm2 cm−3), diameter (mm), and length (mm cm−3). The variations in root systems reveled phenotypic variability among different genotypes of C. canephora cv. Robusta. Most roots were concentrated in the surface layer of the soil (0–30 cm), with LB015 standing out. At a depth of 50–60 cm, AS10, AS4, A106, and GJ08 had more roots than other genotypes, suggesting a promising capacity to avoid drought. There were significant negative correlations between root traits, aboveground part, and production capacity. This study provides valuable information for the selection of genotypes with desirable root traits for different environmental conditions, contributing to the improvement of management practices and breeding programs for Robusta coffee.

COMPARISON OF THE CHEMICAL COMPOSITION AND MORPHOLOGICAL CHARACTERISTICS OF DIFFERENT CARROT VARIETIES

Carrot (Daucus carota L.) is a globally significant root vegetable, rich in bioactive and nutritional compounds. Carrot is a crop with a wide range of phenotypic variability including colour, shape, size, and other characteristics. The aim of this work was to determine and compare selected morphological traits and chemical composition of 24 carrot varieties grown under open field conditions in Slovakia. Altogether, 11 qualitative characteristics and 6 quantitative parameters were evaluated. The carrot roots were also analysed for essential chemical constituents including reducing sugars (fructose, glucose, saccharose), carotenoids, dietary fibre, dry matter, ash, and mineral compounds. A wide range of diversity in morphological characteristics and chemical composition indicates a high variability of studied varieties. The root length ranged from 59 to 205 mm, root diameter varied from 17.7 to 39.0 mm and root weight ranged from 21.0 to 74.8 g. Based on the measurement results, saccharose was the dominant sugar ranging from 1.89 to 4.67 g.100 g-1 of fresh weight, carotenoid content varied from 85.94 to 374.24 µg.g-1 of fresh weight, the amount of dietary fibre ranged from 25.67 to 36.02% of dry matter. Considerable differences were also observed in the content of macro and microelements [mg.100 g-1] ranging as follows: P (17.5 - 52.0), K (110.0 – 337.0), Na (65.9 – 186.0), Fe (0.324 – 3.340), Cu (0.042 – 0.126), Zn (0.152 – 0.945) and Mn (0.062 – 0.189). The presented results can provide useful information for carrot growers and consumers in terms of morphological characteristics as well as the chemical composition of individual carrot varieties.

Root system of Coffea canephora cv. Robusta genotypes cultivated in the Brazilian Amazon

The root system distribution of coffee, especially Coffea canephora cv. Robusta, remains poorly characterized. The aim of this study were: (i) to analyze the distribution of the root system in various genotypes of C. canephora cv. Robusta cultivated in the Amazon region; (ii) to evaluate genetic variability based on root traits; and (iii) to test the correlation between root traits, aboveground part, and production capacity. Roots were collected up to a depth of 60 cm and 30 cm away from the stems. The roots were washed, scanned, and processed to quantify root volume (mm3 cm−3), surface area (mm2 cm−3), diameter (mm), and length (mm cm−3). The variations in root systems reveled phenotypic variability among different genotypes of C. canephora cv. Robusta. Most roots were concentrated in the surface layer of the soil (0–30 cm), with LB015 standing out. At a depth of 50–60 cm, AS10, AS4, A106, and GJ08 had more roots than other genotypes, suggesting a promising capacity to avoid drought. There were significant negative correlations between root traits, aboveground part, and production capacity. This study provides valuable information for the selection of genotypes with desirable root traits for different environmental conditions, contributing to the improvement of management practices and breeding programs for Robusta coffee.

Screening of CIMMYT and South Asian Bread Wheat Germplasm Reveals Marker–Trait Associations for Seedling Resistance to Septoria Nodorum Blotch

Wheat (Triticum aestivum L.) production is adversely impacted by Septoria nodorum blotch (SNB), a fungal disease caused by Parastagonospora nodorum. Wheat breeders are constantly up against this biotic challenge as they try to create resistant cultivars. The genome-wide association study (GWAS) has become an efficient tool for identifying molecular markers linked with SNB resistance. This technique is used to acquire an understanding of the genetic basis of resistance and to facilitate marker-assisted selection. In the current study, a total of 174 bread wheat accessions from South Asia and CIMMYT were assessed for SNB reactions at the seedling stage in three greenhouse experiments at CIMMYT, Mexico. The results indicated that 129 genotypes were resistant to SNB, 39 were moderately resistant, and only 6 were moderately susceptible. The Genotyping Illumina Infinium 15K Bead Chip was used, and 11,184 SNP markers were utilized to identify marker–trait associations (MTAs) after filtering. Multiple tests confirmed the existence of significant MTAs on chromosomes 5B, 5A, and 3D, and the ones at Tsn1 on 5B were the most stable and conferred the highest phenotypic variation. The resistant genotypes identified in this study could be cultivated in South Asian countries as a preventative measure against the spread of SNB. This work also identified molecular markers of SNB resistance that could be used in future wheat breeding projects.

Unveiling New Genetic Variants Associated with Age at Onset in Alzheimer’s Disease and Frontotemporal Lobar Degeneration Due to C9orf72 Repeat Expansions

Alzheimer’s disease (AD) and Frontotemporal lobar degeneration (FTLD) represent the most common forms of neurodegenerative dementias with a highly phenotypic variability. Herein, we investigated the role of genetic variants related to the immune system and inflammation as genetic modulators in AD and related dementias. In patients with sporadic AD/FTLD (n = 300) and GRN/C9orf72 mutation carriers (n = 80), we performed a targeted sequencing of 50 genes belonging to the immune system and inflammation, selected based on their high expression in brain regions and low tolerance to genetic variation. The linear regression analyses revealed two genetic variants: (i) the rs1049296 in the transferrin (TF) gene, shown to be significantly associated with age at onset in the sporadic AD group, anticipating the disease onset of 4 years for each SNP allele with respect to the wild-type allele, and (ii) the rs7550295 in the calsyntenin-1 (CLSTN1) gene, which was significantly associated with age at onset in the C9orf72 group, delaying the disease onset of 17 years in patients carrying the SNP allele. In conclusion, our data support the role of genetic variants in iron metabolism (TF) and in the modulation of the calcium signalling/axonal anterograde transport of vesicles (CLSTN1) as genetic modulators in AD and FTLD due to C9orf72 expansions.