Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa.

BackgroundPopulus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation.ResultsWe identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value < 6.1479E-8) in association with diameter, height, leaf carbon and nitrogen contents, and δ15N. The number of significant SNPs ranged from 2 to 220 per trait. Additionally, multiple-marker analyses by sliding-windows tests detected between 6 and 192 significant windows for the analyzed traits. The significant SNPs resided within genes that encode proteins belonging to different functional classes as such protein synthesis, energy/metabolism and DNA/RNA metabolism, among others.ConclusionsSNP-markers within genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture of P. trichocarpa biomass required to support the development and application of marker breeding technologies

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).

Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers

Presence of Middle Cerebellar Peduncle Sign in FMR1 Premutation Carriers Without Tremor and Ataxia

Here we report five cases of male FMR1 premutation carriers who present without clinical symptoms of the fragile X-associated tremor/ataxia syndrome (FXTAS), but who on MRI demonstrate white matter hyperintensities in the middle cerebellar peduncles (MCP sign) and other brain regions, a rare finding. MCP sign is the major radiological feature of FXTAS; it is therefore remarkable to identify five cases in which this MRI finding is present in the absence of tremor and ataxia, the major clinical features of FXTAS. Subjects underwent a detailed neurological evaluation, neuropsychological testing, molecular testing, and MRI evaluation utilizing T2 imaging described here. Additional white matter disease was present in the corpus callosum in four of the five cases. However, all cases were asymptomatic for motor signs of FXTAS

Identification of a male with fragile X syndrome through newborn screening

A pilot newborn screening (NBS) study for fragile X syndrome was recently conducted at the University of California, Davis Medical Center. The screening study identified a case of a male with the full mutation completely methylated and no detectable expression of the fragile X mental retardation-1 (FMR1) gene. The patient was initially seen in clinic at the MIND Institute, for medical follow-up and a genetic counseling session at the chronological age of 3 months. Since then, he has been seen in clinic every six months for follow up, medical examination and developmental assessments. Longitudinally administered developmental testing of the infant has revealed persistent delays in development, consistent with fragile X syndrome. Cascade testing revealed that the patient's mother and two siblings also have the full mutation. The patient has been receiving speech and language therapy, combined with physical and occupational therapies on a weekly basis since the age of one year. He is currently being treated with 2.5 mg of sertraline, which has been demonstrated to be helpful for improving language in young children with the syndrome

Neuropsychological changes in FMR1 premutation carriers and onset of fragile X-associated tremor/ataxia syndrome.

BackgroundCarriers of the FMR1 premutation are at increased risk of developing a late-onset progressive neurodegenerative disease, fragile X-associated tremor/ataxia syndrome (FXTAS), characterized by intention tremor, gait ataxia, and cognitive decline. Cross-sectional studies to date have provided evidence that neuropsychological changes, such as executive function alterations, or subtle motor changes, may precede the onset of formal FXTAS, perhaps characterizing a prodromal state. However, the lack of longitudinal data has prevented the field from forming a clear picture of progression over time within individuals, and we lack consensus regarding early markers of risk and measures that may be used to track response to intervention.MethodsThis was a longitudinal study of 64 male FMR1 premutation carriers (Pm) without FXTAS at study entry and 30 normal controls (Nc), aged 40 to 80 years (Pm M = 60.0 years; Nc M = 57.4 years). Fifty of the Pm and 22 of the Nc were re-assessed after an average of 2.33 years, and 37 Pm and 20 Nc were re-assessed a third time after an average of another 2.15 years. Eighteen of 64 carriers (28%) converted to FXTAS during the study to date. Neuropsychological assessments at each time point, including components of the Cambridge Neuropsychological Test Automated Battery (CANTAB), tapped domains of episodic and working memory, inhibitory control, visual attention, planning, executive control of movement, and manual speed and dexterity. Age-based mixed models were used to examine group differences in change over time on the outcomes in the full sample, and differences were further evaluated in 15 trios (n = 45; 15 Pm "converters," 15 Pm "nonconverters," 15 Nc) that were one-one matched on age, education, and socioeconomic status.ResultsCompared to Nc, Pm showed significantly greater rates of change over time in visual working memory, motor dexterity, inhibitory control, and manual movement speed. After multiple comparison correction, significant effects remained for motor dexterity. Worsening inhibitory control and slower manual movements were related to progression in FXTAS stage, but these effects became statistically non-significant after correcting for multiple comparisons. Higher FMR1 mRNA correlated with worsening manual reaction time but did not survive multiple comparisons and no other molecular measures correlated with neuropsychological changes. Finally, trio comparisons revealed greater rate of decline in planning and manual movement speed in Pm converters compared to Pm nonconverters.ConclusionsAccelerated decline in executive function and subtle motor changes, likely mediated by frontocerebellar circuits, may precede, and then track with the emergence of formal FXTAS symptoms. Further research to develop and harmonize clinical assessment of FMR1 carriers across centers is needed to prepare for future prophylactic and treatment trials for this disorder

GWAS on the Attack by Aspen Borer <i>Saperda calcarata</i> on Black Cottonwood Trees Reveals a Response Mechanism Involving Secondary Metabolism and Independence of Tree Architecture

Black cottonwood (Populus trichocarpa) is a species of economic interest and an outstanding study model. The aspen borer (Saperda calcarata) causes irreversible damage to poplars and other riparian species in North America. The insect can produce multiple effects ranging from the presence of some galleries in the stem to tree death. Despite the ecological and commercial importance of this tree–insect interaction, the genetic mechanisms underlying the response of P. trichocarpa to S. calcarata are scarcely understood. In this study, a common garden trial of P. trichocarpa provenances, established in Davis, California, was assessed at the second year of growth, regarding the infestation of S. calcarata from a natural outbreak. A genome-wide association study (GWAS) was conducted using 629k of exonic SNPs to assess the relationship between genomic variation and insect attack. Tree architecture, in terms of stem number per plant, and the wood metabolome were also included. Insect attack was independent of the number of stems per tree. The performed GWAS identified three significantly associated SNP markers (q-value < 0.2) belonging to the same number of gene models, encoding proteins involved in signal transduction mechanisms and secondary metabolite production, including that of R-mandelonitrile lyase, Chromodomain-helicase-DNA-binding family protein, and Leucine-rich repeat protein. These results are aligned with the current knowledge of defensive pathways in plants and trees, helping to expand the understanding of the defensive response mechanisms of black cottonwood against wood borer insects

Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry.

The development of strawberry (Fragaria × ananassa Duchesne ex Rozier) cultivars resistant to Phytophthora crown rot (PhCR), a devastating disease caused by the soil-borne pathogen Phytophthora cactorum (Lebert &amp; Cohn) J. Schröt., has been challenging partly because the resistance phenotypes are quantitative and only moderately heritable. To develop deeper insights into the genetics of resistance and build the foundation for applying genomic selection, a genetically diverse training population was screened for resistance to California isolates of the pathogen. Here we show that genetic gains in breeding for resistance to PhCR have been negligible (3% of the cultivars tested were highly resistant and none surpassed early 20th century cultivars). Narrow-sense genomic heritability for PhCR resistance ranged from 0.41 to 0.75 among training population individuals. Using multivariate genome-wide association studies (GWAS), we identified a large-effect locus (predicted to be RPc2) that explained 43.6-51.6% of the genetic variance, was necessary but not sufficient for resistance, and was associated with calcium channel and other candidate genes with known plant defense functions. The addition of underutilized gene bank resources to our training population doubled additive genetic variance, increased the accuracy of genomic selection, and enabled the discovery of individuals carrying favorable alleles that are either rare or not present in modern cultivars. The incorporation of an RPc2-associated single-nucleotide polymorphism (SNP) as a fixed effect increased genomic prediction accuracy from 0.40 to 0.55. Finally, we show that parent selection using genomic-estimated breeding values, genetic variances, and cross usefulness holds promise for enhancing resistance to PhCR in strawberry

Multi-dimensional machine learning approaches for fruit shape phenotyping in strawberry

Shape is a critical element of the visual appeal of strawberry fruit and is influenced by both genetic and non-genetic determinants. Current fruit phenotyping approaches for external characteristics in strawberry often rely on the human eye to make categorical assessments. However, fruit shape is an inherently multi-dimensional, continuously variable trait and not adequately described by a single categorical or quantitative feature. Morphometric approaches enable the study of complex, multi-dimensional forms but are often abstract and difficult to interpret. In this study, we developed a mathematical approach for transforming fruit shape classifications from digital images onto an ordinal scale called the Principal Progression of k Clusters (PPKC). We use these human-recognizable shape categories to select quantitative features extracted from multiple morphometric analyses that are best fit for genetic dissection and analysis. We transformed images of strawberry fruit into human-recognizable categories using unsupervised machine learning, discovered 4 principal shape categories, and inferred progression using PPKC. We extracted 68 quantitative features from digital images of strawberries using a suite of morphometric analyses and multivariate statistical approaches. These analyses defined informative feature sets that effectively captured quantitative differences between shape classes. Classification accuracy ranged from 68% to 99% for the newly created phenotypic variables for describing a shape. Our results demonstrated that strawberry fruit shapes could be robustly quantified, accurately classified, and empirically ordered using image analyses, machine learning, and PPKC. We generated a dictionary of quantitative traits for studying and predicting shape classes and identifying genetic factors underlying phenotypic variability for fruit shape in strawberry. The methods and approaches that we applied in strawberry should apply to other fruits, vegetables, and specialty crops

Presence of Middle Cerebellar Peduncle Sign in FMR1 Premutation Carriers Without Tremor and Ataxia

Here we report five cases of male FMR1 premutation carriers who present without clinical symptoms of the fragile X-associated tremor/ataxia syndrome (FXTAS), but who on MRI demonstrate white matter hyperintensities in the middle cerebellar peduncles (MCP sign) and other brain regions, a rare finding. MCP sign is the major radiological feature of FXTAS; it is therefore remarkable to identify five cases in which this MRI finding is present in the absence of tremor and ataxia, the major clinical features of FXTAS. Subjects underwent a detailed neurological evaluation, neuropsychological testing, molecular testing, and MRI evaluation utilizing T2 imaging described here. Additional white matter disease was present in the corpus callosum in four of the five cases. However, all cases were asymptomatic for motor signs of FXTAS