Genotype-by-environment interactions and local adaptation shape selection in the US National Chip Processing Trial.

KEY MESSAGE: We find evidence of selection for local adaptation and extensive genotype-by-environment interaction in the potato National Chip Processing Trial (NCPT). We present a novel method for dissecting the interplay between selection, local adaptation and environmental response in plant breeding schemes. Balancing local adaptation and the desire for widely adapted cultivars is challenging for plant breeders and makes genotype-by-environment interactions (GxE) an important target of selection. Selecting for GxE requires plant breeders to evaluate plants across multiple environments. One way breeders have accomplished this is to test advanced materials across many locations. Public potato breeders test advanced breeding material in the National Chip Processing Trial (NCPT), a public-private partnership where breeders from ten institutions submit advanced chip lines to be evaluated in up to ten locations across the country. These clones are genotyped and phenotyped for important agronomic traits. We used these data to interrogate the NCPT for GxE. Further, because breeders submitting clones to the NCPT select in a relatively small geographic range for the first 3 years of selection, we examined these data for evidence of incidental selection for local adaptation, and the alleles underlying it, using an environmental genome-wide association study (envGWAS). We found genomic regions associated with continuous environmental variables and discrete breeding programs, as well as regions of the genome potentially underlying GxE for yield.

Selection for high levels of resistance to double-stranded RNA (dsRNA) in Colorado potato beetle (Leptinotarsa decemlineata Say) using non-transgenic foliar delivery.

Insecticidal double-stranded RNAs (dsRNAs) silence expression of vital genes by activating the RNA interference (RNAi) mechanism in insect cells. Despite high commercial interest in insecticidal dsRNA, information on resistance to dsRNA is scarce, particularly for dsRNA products with non-transgenic delivery (ex. foliar/topical application) nearing regulatory review. We report the development of the CEAS 300 population of Colorado potato beetle (Leptinotarsa decemlineata Say) (Coleoptera: Chrysomelidae) with > 11,100-fold resistance to a dsRNA targeting the V-ATPase subunit A gene after nine episodes of selection using non-transgenic delivery by foliar coating. Resistance was associated with lack of target gene down-regulation in CEAS 300 larvae and cross-resistance to another dsRNA target (COPI ß; Coatomer subunit beta). In contrast, CEAS 300 larvae showed very low (~ 4-fold) reduced susceptibility to the Cry3Aa insecticidal protein from Bacillus thuringiensis. Resistance to dsRNA in CEAS 300 is transmitted as an autosomal recessive trait and is polygenic. These data represent the first documented case of resistance in an insect pest with high pesticide resistance potential using dsRNA delivered through non-transgenic techniques. Information on the genetics of resistance and availability of dsRNA-resistant L. decemlineata guide the design of resistance management tools and allow research to identify resistance alleles and estimate resistance risks.

The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. 'Atlantic'-derived F1 population.

There are many challenges involved with the genetic analyses of autopolyploid species, such as the tetraploid potato, Solanum tuberosum (2n = 4x = 48). The development of new analytical methods has made it valuable to re-analyze an F1 population (n = 156) derived from a cross involving 'Atlantic', a widely grown chipping variety in the USA. A fully integrated genetic map with 4285 single nucleotide polymorphisms, spanning 1630 cM, was constructed with MAPpoly software. We observed that bivalent configurations were the most abundant ones (51.0~72.4% depending on parent and linkage group), though multivalent configurations were also observed (2.2~39.2%). Seven traits were evaluated over four years (2006-8 and 2014) and quantitative trait loci (QTL) mapping was carried out using QTLpoly software. Based on a multiple-QTL model approach, we detected 21 QTL for 15 out of 27 trait-year combination phenotypes. A hotspot on linkage group 5 was identified with co-located QTL for maturity, plant yield, specific gravity, and internal heat necrosis resistance evaluated over different years. Additional QTL for specific gravity and dry matter were detected with maturity-corrected phenotypes. Among the genes around QTL peaks, we found those on chromosome 5 that have been previously implicated in maturity (StCDF1) and tuber formation (POTH1). These analyses have the potential to provide insights into the biology and breeding of tetraploid potato and other autopolyploid species.

Genetic Variance Partitioning and Genome-Wide Prediction with Allele Dosage Information in Autotetraploid Potato.

As one of the world's most important food crops, the potato (Solanum tuberosum L.) has spurred innovation in autotetraploid genetics, including in the use of SNP arrays to determine allele dosage at thousands of markers. By combining genotype and pedigree information with phenotype data for economically important traits, the objectives of this study were to (1) partition the genetic variance into additive vs. nonadditive components, and (2) determine the accuracy of genome-wide prediction. Between 2012 and 2017, a training population of 571 clones was evaluated for total yield, specific gravity, and chip fry color. Genomic covariance matrices for additive (G), digenic dominant (D), and additive × additive epistatic (G#G) effects were calculated using 3895 markers, and the numerator relationship matrix (A) was calculated from a 13-generation pedigree. Based on model fit and prediction accuracy, mixed model analysis with G was superior to A for yield and fry color but not specific gravity. The amount of additive genetic variance captured by markers was 20% of the total genetic variance for specific gravity, compared to 45% for yield and fry color. Within the training population, including nonadditive effects improved accuracy and/or bias for all three traits when predicting total genotypic value. When six F1 populations were used for validation, prediction accuracy ranged from 0.06 to 0.63 and was consistently lower (0.13 on average) without allele dosage information. We conclude that genome-wide prediction is feasible in potato and that it will improve selection for breeding value given the substantial amount of nonadditive genetic variance in elite germplasm.

Linkage map construction and QTL analysis for internal heat necrosis in autotetraploid potato.

KEY MESSAGE: A tetraploid potato population was mapped for internal heat necrosis (IHN) using the Infinium ® 8303 potato SNP array, and QTL for IHN were identified on chromosomes 1, 5, 9 and 12 that explained 28.21% of the variation for incidence and 25.3% of the variation for severity. This research represents a significant step forward in our understanding of IHN, and sets the stage for future research focused on testing the utility of these markers in additional breeding populations. Internal heat necrosis (IHN) is a significant non-pathogenic disorder of potato tubers and previous studies have identified AFLP markers linked to IHN susceptibility in the tetraploid, B2721 potato mapping population. B2721 consists of an IHN susceptible×resistant cross: Atlantic×B1829-5. We developed a next-generation SNP-based linkage map of this cross using the Infinium® 8303 SNP array and conducted additional QTL analyses of IHN susceptibility in the B2721 population. Using SNP dosage sensitive markers, linkage maps for both parents were simultaneously analyzed. The linkage map contained 3427 SNPs and totaled 1397.68 cM. QTL were detected for IHN on chromosomes 1, 5, 9, and 12 using LOD permutation thresholds and colocation of high LOD scores across multiple years. Genetic effects were modeled for each putative QTL. Markers associated with a QTL were regressed in models of effects for IHN incidence and severity for all years. In the full model, the SNP markers were shown to have significant effects for IHN (p < 0.0001), and explained 28.21% of the variation for incidence and 25.3% of the variation for severity. We were able to utilize SNP dosage information to identify and model the effects of putative QTL, and identify SNP loci associated with IHN resistance that need to be confirmed. This research represents a significant step forward in our understanding of IHN, and sets the stage for future research focused on testing the utility of these markers in additional breeding populations.

Effectiveness of the women's lacrosse protective eyewear mandate in the reduction of eye injuries.

BACKGROUND: In an effort to minimize the risk of catastrophic eye injury, US Lacrosse initiated mandatory use of protective eyewear in women's lacrosse in the 2004-2005 season. PURPOSE: The authors compared eye injury rates in girls' scholastic lacrosse before and after implementation of protective eyewear. They also compared head/face injury rates, concussion rates, and overall injury rates before and after the rule change to assess possible unintended consequences of the change. STUDY DESIGN: Cohort study; Level of evidence, 3. METHODS: The study group included female scholastic lacrosse players in the 25 public high schools in Fairfax County, Virginia, during the 2004-2009 spring seasons. Injury rates were compared with those from the same data source for the 2000-2003 seasons. Premandate versus postmandate injury rates were adjusted for athlete exposures, or total opportunities for injury throughout the season. RESULTS: The rate of eye injuries was reduced from 0.10 injuries per 1000 athlete exposures (AEs) in 2000 through 2003 before the use of protective eyewear to 0.016 injuries per 1000 AEs in 2004 through 2009 (incident rate ratio [IRR], 0.16; 95% confidence interval [CI], 0.06-0.42). The rate ratio of head/face injuries excluding concussion also decreased (IRR, 0.44; 95% CI, 0.26-0.76). There was no change in the rate ratio of total injuries involving all body parts (IRR, 0.93; 95% CI, 0.82-1.1) after introduction of protective eyewear. However, the rate ratio of concussion increased (IRR, 1.6; 95% CI, 1.1-2.3). CONCLUSION: The use of protective eyewear in women's lacrosse was associated with a reduction in the number of eye injuries. The number of head/face injuries decreased in this study group after introduction of protective eyewear, and there was no change in overall injury rates. The reason for the increase in concussion rate cannot be determined conclusively based on this study, but the authors speculate that this increase resulted largely from increased recognition and diagnosis because overall injury rates do not indicate rougher play with introduction of protective equipment.

Males with familial idiopathic scoliosis: a distinct phenotypic subgroup.

STUDY DESIGN: Statistical analysis of genomic screening and fine mapping data. OBJECTIVE: The goals of this study were to analyze a region on chromosome 17 and to identify specific genetic determinants within this region linked to familial idiopathic scoliosis (FIS) in a subgroup of families in which affected males have undergone surgery. SUMMARY OF BACKGROUND DATA: The high prevalence and variability of FIS is indicative of genetic heterogeneity. To localize genes related to scoliosis, identification of groups of families with common clinical characteristics is a strategy that reduces genetic heterogeneity. Two independent studies have implicated a region on chromosome 17 as related to FIS. METHODS: With approval of the Institutional Review Board, the initial study population consisted of 202 families (1198 individuals), each of which had 2 or more affected individuals; 17 of those families had an affected male who had surgery. Individuals underwent genomic screening and subsequent fine mapping. Results were obtained using model-independent linkage analysis, with scoliosis set as a qualitative and as a quantitative trait, as implemented in SIBPAL (S.A.G.E., v4.5). The level of significance was set at P < or = 0.05. RESULTS: The initial study population had significant results at markers d17s975 and d17s2196. Analyses of a subgroup of families with males having undergone surgery using a customized single nucleotide polymorphism panel resulted in increased significance of this region. CONCLUSION: The data confirm a previously reported genetic locus on chromosome 17 as statistically significant in the etiology of FIS within a subgroup of families in which an affected male had spinal surgery.

Clinical assessment of three common tests for traumatic anterior shoulder instability.

BACKGROUND: Although traumatic anterior shoulder instability is common, the usefulness of various physical examination tests as tools for the diagnosis of this condition has been studied infrequently. We hypothesized that (1) such tests would be specific but not sensitive for this condition, (2) the usefulness of the anterior drawer test would be limited because of pain during the test, and (3) an anterior drawer test would be a useful adjunct for making the diagnosis if it reproduced the instability symptoms. METHODS: Between 2000 and 2004, 363 patients underwent a physical examination followed by shoulder arthroscopy. Forty-six patients with traumatic anterior shoulder instability that had been noted arthroscopically or documented radiographically after the trauma were included in our study group, and the remaining patients served as controls. The clinical usefulness of three tests (anterior apprehension, relocation, and anterior drawer tests) performed during the physical examination to make a diagnosis of traumatic anterior instability then was evaluated with statistical methods to assess their sensitivity, specificity, and likelihood ratios. RESULTS: If demonstration (or relief) of apprehension was used as the diagnostic criterion for a positive test, the sensitivity, specificity, and likelihood ratio were 72%, 96%, and 20.2, respectively, for the apprehension test and 81%, 92%, and 10.4, respectively, for the relocation test. If pain (or relief of pain) was used as the diagnostic criterion for a positive test, the values for the sensitivity, specificity, and likelihood ratio of both tests were lower. The anterior drawer test could be performed successfully in the physician's office for 87% of the patients. If reproduction of instability symptoms was used as the criterion for a positive anterior drawer test, the sensitivity, specificity, and likelihood ratio values of that test were 53%, 85%, and 3.6, respectively. CONCLUSIONS: The three physical examination tests for traumatic anterior shoulder instability are specific but not sensitive. Apprehension is a better criterion than pain for a positive apprehension or relocation test. The anterior drawer test (when pain does not prevent it from being performed) is helpful for diagnosing traumatic anterior instability. LEVEL OF EVIDENCE: Diagnostic Level I. See Instructions to Authors for a complete description of levels of evidence.