Search

Abstract Verticillium wilt (VW), a devastating vascular wilt disease of strawberry (Fragaria × ananassa), has caused economic losses for nearly a century. This disease is caused by the soil‐borne pathogen Verticillium dahliae, which occurs nearly worldwide and causes disease in numerous agriculturally important plants. The development of VW‐resistant cultivars is critically important for the sustainability of strawberry production. We previously showed that a preponderance of the genetic resources (asexually propagated hybrid individuals) preserved in public germplasm collections were moderately to highly susceptible and that genetic gains for increased resistance to VW have been negligible over the last 60 years. To more fully understand the challenges associated with breeding for increased quantitative resistance to this pathogen, we developed and phenotyped a training population of hybrids (n=564) among elite parents with a wide range of resistance phenotypes. When these data were combined with training data from a population of elite and exotic hybrids (n=386), genomic prediction accuracies of 0.47–0.48 were achieved and were predicted to explain 70%–75% of the additive genetic variance for resistance. We concluded that breeding values for resistance to VW can be predicted with sufficient accuracy for effective genomic selection with routine updating of training populations.

Abstract Genomic prediction in breeding populations containing hundreds to thousands of parents and seedlings is prohibitively expensive with current high‐density genetic marker platforms designed for strawberry. We developed mid‐density panels of molecular inversion probes (MIPs) to be deployed with the “DArTag” marker platform to provide a low‐cost, high‐throughput genotyping solution for strawberry genomic prediction. In total, 7742 target single nucleotide polymorphism (SNP) regions were used to generate MIP assays that were tested with a screening panel of 376 octoploid Fragaria accessions. We evaluated the performance of DArTag assays based on genotype segregation, amplicon coverage, and their ability to produce subgenome‐specific amplicon alignments to the FaRR1 assembly and subsequent alignment‐based variant calls with strong concordance to DArT's alignment‐free, count‐based genotype reports. We used a combination of marker performance metrics and physical distribution in the FaRR1 assembly to select 3K and 5K production panels for genotyping of large strawberry populations. We show that the 3K and 5K DArTag panels are able to target and amplify homologous alleles within subgenomic sequences with low‐amplification bias between reference and alternate alleles, supporting accurate genotype calling while producing marker genotypes that can be treated as functionally diploid for quantitative genetic analysis. The 3K and 5K target SNPs show high levels of polymorphism in diverse F. × ananassa germplasm and UC Davis cultivars, with mean pairwise diversity (π) estimates of 0.40 and 0.32 and mean heterozygous genotype frequencies of 0.35 and 0.33, respectively.

Abstract 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 & 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.

Abstract Reliable phenotyping methods that are simple to operate and inexpensive to deploy are critical for studying quantitative traits in plants. Traditional fruit shape phenotyping relies on human raters or 2D analyses to assess form, e.g., size and shape. Systems for 3D imaging using multi‐view stereo have been implemented, but frequently rely on commercial software and/or specialized hardware, which can lead to limitations in accessibility and scalability. We present a complete system constructed of consumer‐grade components for capturing, calibrating, and reconstructing the 3D form of small‐to‐moderate sized fruits and tubers. Data acquisition and image capture sessions are 9 seconds to capture 60 images. The initial prototype cost was $1600 USD. We measured accuracy by comparing reconstructed models of 3D printed ground truth objects to the original digital files of those same ground truth objects. The R2 between length of the primary, secondary, and tertiary axes, volume, and surface area of the ground‐truth object and the reconstructed models was >0.97 and root‐mean square error (RMSE) was < 3 mm for objects without locally concave regions. Measurements from 1 mm and 2 mm resolution reconstructions were consistent (R2 > 0.99). Qualitative assessments were performed on 48 fruit and tubers, including 18 strawberries, 12 potatoes, five grapes, seven peppers, and four Bosc and two red Anjou pears. Our proposed phenotyping system is fast, relatively low cost, and has demonstrated accuracy for certain shape classes, and could be used for the 3D analysis of fruit form.

Abstract Understanding the genetic basis of plant traits requires comprehensive and quantitative descriptions of the phenotypic variation that exists within populations. Cameras and other sensors have made high‐throughput phenotyping possible, but image‐based phenotyping procedures involve a step where a researcher selects the traits to be measured. This feature selection step is inherently prone to human biases. Recently, a set of phenotyping approaches, which are referred to collectively as latent phenotyping techniques, have arisen in the literature. Latent phenotyping techniques isolate a latent source of variance in the data, such as stress or genotype, and then quantify the effect of this latent source of variance using latent variables without defining any conventional traits. In this review, we discuss the differences between, and challenges of, both traditional and latent phenotyping.

Males comprise a minority of patients with eating disorders (ED). However, men who have sex with men, males with gender identity disorder, and transsexual (TS) males are at increased risk for ED. Little has been published about the unique treatment needs of TS patients with ED. A 19-year-old male-to-female TS patient presented with restrictive eating, purging, and weight loss. History revealed that her ED ideation and behaviors were strongly intertwined with her gender identity. She was admitted and during her hospitalization both her ED and TS status were addressed medically. Physicians treating patients with ED should be aware of patients' gender identities and the ways in which gender identity may impact management and recovery. When appropriate, providers should consider addressing medical treatment toward gender transition concurrently with treatment for ED to facilitate medical stabilization and weight restoration in the manner most consistent with the patient's identified gender., (Copyright © 2013 Wiley Periodicals, Inc.)