Characterizing introgression-by-environment interactions using maize near isogenic lines.

KEY MESSAGE: Significant introgression-by-environment interactions are observed for traits throughout development from small introgressed segments of the genome. Relatively small genomic introgressions containing quantitative trait loci can have significant impacts on the phenotype of an individual plant. However, the magnitude of phenotypic effects for the same introgression can vary quite substantially in different environments due to introgression-by-environment interactions. To study potential patterns of introgression-by-environment interactions, fifteen near-isogenic lines (NILs) with > 90% B73 genetic background and multiple Mo17 introgressions were grown in 16 different environments. These environments included five geographical locations with multiple planting dates and multiple planting densities. The phenotypic impact of the introgressions was evaluated for up to 26 traits that span different growth stages in each environment to assess introgression-by-environment interactions. Results from this study showed that small portions of the genome can drive significant genotype-by-environment interaction across a wide range of vegetative and reproductive traits, and the magnitude of the introgression-by-environment interaction varies across traits. Some introgressed segments were more prone to introgression-by-environment interaction than others when evaluating the interaction on a whole plant basis throughout developmental time, indicating variation in phenotypic plasticity throughout the genome. Understanding the profile of introgression-by-environment interaction in NILs is useful in consideration of how small introgressions of QTL or transgene containing regions might be expected to impact traits in diverse environments.

Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor.

Determining the genetic control of root system architecture (RSA) in plants via large-scale genome-wide association study (GWAS) requires high-throughput pipelines for root phenotyping. We developed Core Root Excavation using Compressed-air (CREAMD), a high-throughput pipeline for the cleaning of field-grown roots, and Core Root Feature Extraction (COFE), a semiautomated pipeline for the extraction of RSA traits from images. CREAMD-COFE was applied to diversity panels of maize (Zea mays) and sorghum (Sorghum bicolor), which consisted of 369 and 294 genotypes, respectively. Six RSA-traits were extracted from images collected from >3,300 maize roots and >1,470 sorghum roots. Single nucleotide polymorphism (SNP)-based GWAS identified 87 TAS (trait-associated SNPs) in maize, representing 77 genes and 115 TAS in sorghum. An additional 62 RSA-associated maize genes were identified via expression read depth GWAS. Among the 139 maize RSA-associated genes (or their homologs), 22 (16%) are known to affect RSA in maize or other species. In addition, 26 RSA-associated genes are coregulated with genes previously shown to affect RSA and 51 (37% of RSA-associated genes) are themselves transe-quantitative trait locus for another RSA-associated gene. Finally, the finding that RSA-associated genes from maize and sorghum included seven pairs of syntenic genes demonstrates the conservation of regulation of morphology across taxa.

Correction: Genotype-by-environment interactions affecting heterosis in maize.

[This corrects the article DOI: 10.1371/journal.pone.0191321.].

Validation of a Model for Identification of Patients With Compensated Cirrhosis at High Risk of Decompensation.

BACKGROUND & AIMS: It is important to rapidly identify patients with advanced liver disease. Routine tests to assess liver function and fibrosis provide data that can be used to determine patients' prognoses. We tested the validated the ability of combined data from the ALBI and FIB-4 scoring systems to identify patients with compensated cirrhosis at highest risk for decompensation. METHODS: We collected data from 145 patients with compensated cirrhosis (91% Child A cirrhosis and median MELD scores below 8) from a cohort in Nottingham, United Kingdom, followed for a median 4.59 years (development cohort). We collected baseline clinical features and recorded decompensation events. We used these data to develop a model based on liver function (assessed by the ALBI score) and extent of fibrosis (assessed by the FIB-4 index) to determine risk of decompensation. We validated the model in 2 independent external cohorts (1 in Dublin, Ireland and 1 in Menoufia, Egypt) comprising 234 patients. RESULTS: In the development cohort, 19.3% of the patients developed decompensated cirrhosis. Using a combination of ALBI and FIB-4 scores, we developed a model that identified patients at low vs high risk of decompensation (hazard ratio [HR] for decompensation in patients with high risk score was 7.10). When we tested the scoring system in the validation cohorts, the HR for decompensation in patients with a high-risk score was 12.54 in the Ireland cohort and 5.10 in the Egypt cohort. CONCLUSION: We developed scoring system, based on a combination of ALBI and FIB-4 scores, that identifies patients at risk for liver decompensation. We validated the scoring system in 2 independent international cohorts (Europe and the Middle East), so it appears to apply to diverse populations.

Genotype-by-environment interactions affecting heterosis in maize.

The environment can influence heterosis, the phenomena in which the offspring of two inbred parents exhibits phenotypic performance beyond the inbred parents for specific traits. In this study we measured 25 traits in a set of 47 maize hybrids and their inbred parents grown in 16 different environments with varying levels of average productivity. By quantifying 25 vegetative and reproductive traits across the life cycle we were able to analyze interactions between the environment and multiple distinct instances of heterosis. The magnitude and rank among hybrids for better-parent heterosis (BPH) varied for the different traits and environments. Across the traits, a higher within plot variance was observed for inbred lines compared to hybrids. However, for most traits, variance across environments was not significantly different for inbred lines compared to hybrids. Further, for many traits the correlations of BPH to hybrid performance and BPH to better parent performance were of comparable magnitude. These results indicate that inbred lines and hybrids show similar trends in environmental response and both are contributing to observed genotype-by-environment interactions for heterosis. This study highlights the degree of heterosis is not an inherent trait of a specific hybrid, but varies depending on the trait measured and the environment where that trait is measured. Studies that attempt to correlate molecular processes with heterosis are hindered by the fact that heterosis is not a consistent attribute of a specific hybrid.

Nightly Home Hemodialysis: Fifteen Months of Experience in Lynchburg, Virginia.

What constitutes adequate dialysis has been debated in the nephrology literature over the past eight years. The mortality rate of patients on dialysis in the United States is about 20% per year. We believed that short and infrequent dialysis sessions contributed to poor outcomes. To improve the results, Lynchburg Nephrology started the nightly home hemodialysis (NHHD) program in September 1997. Ten patients were trained in the first 15 months of the program. Patients dialyzed 7 - 9 hours, 6 nights/week, using the Fresenius 2008H machine. A standard dialysis solution with 2.0 mEq/L potassium, calcium concentration of 3.0 - 3.5 mEq/L was used. Dialysis solution flow rates were 200 - 300 mL/min. Serum phosphate levels were maintained above 2.5 mg/dL by adding 0 - 45 mL Fleet's Phosphosoda to the bicarbonate bath. Patients had marked improvement in quality of life as measured with the SF-36. Blood pressure was better controlled with fewer medications. All phosphate binders were eliminated. Caloric intake and protein intake increased to normal levels as measured by three-day dietary histories pre-NHHD, and at 3, 6, and 12 months on NHHD. Epoetin alfa dosages were reduced by about 50%. Nightly home hemodialysis should be considered as a valuable modality option for end-stage renal disease patients; it is potentially superior to conventional thrice-weekly hemodialysis.