Joint Effect of Unlinked Genotypes: Application to Type 2 Diabetes in the EPIC-Potsdam Case-Cohort Study

Bulked Segregant Analysis and Association Analysis Identified the Polymorphisms Related to the Intermuscular Bones in Common Carp (Cyprinus carpio)

Simple Summary

Many widely cultured freshwater fish species, such as common carp, belong to the Cyprinidae family. However, most cyprinids have numerous and complex intermuscular bones (IBs), resulting in an adverse effect on cyprinid fish meat processing and consumption. Numerous studies have been trying to understand the development mechanism of IBs and to identify the SNPs associated with the total IB number. However, the SNPs associated with different forms of IBs have been studied less thoroughly. The joint effects of the SNPs on IB development also remain poorly understood. The common carp has numerous geographical populations and domesticated strains, diversifying its phenotypes. The question of whether consensus IB-related SNPs or genes exist among multiple strains of common carp has also not yet been answered. Selective breeding of IB-reduced common carp has been hindered due to a lack of effective molecular markers. To answer these questions, we performed bulked segregant analysis (BSA) to detect the consensus SNPs in three strains. The consensus BSA-SNPs and the other SNPs in their flanking regions were validated in additional individuals. The SNPs associated with the frequency of different IB types were identified. We examined the joint effects of significant SNPs on the numbers of different types of IBs. The identified genetic markers may benefit future selective breeding and reduce the IB number in common carp.

Abstract

The allotetraploid common carp is one of the most important freshwater food fish. However, the IBs found in allotetraploid common carp increase the difficulty in fish meat processing and consumption. Although candidate genes associated with the total IB number have been identified, the SNPs associated with the numbers of the total IBs and different forms of IBs have not yet been identified, hindering the breeding of IB-reduced common carp. Herein, the numbers of different types of IBs in three common carp strains were measured. Using whole-genome resequencing and bulked segregant analysis in three pairs of IB-more and IB-less groups, we identified the consensus nonsynonymous SNPs in three strains of common carp. Screening the flanking regions of these SNPs led to the detection of other SNPs. Association study detected 21 SNPs significantly associated with the number of total IBs, epineural-IBs, and ten detailed types of IBs. We observed the joint effects of multiple SNPs on each associated IB number with an improved explained percentage of phenotypic variation. The resulting dataset provides a resource to understand the molecular mechanisms of IB development in different common carp strains. These SNPs are potential markers for future selection to generate IB-reduced common carp.

Joint Analysis of SNP-SNP-Environment Interactions for Chronic Dialysis by an Improved Branch and Bound Algorithm

In previous studies, both single-nucleotide polymorphism (SNP)-SNP or gene-gene (G × G) interactions and SNP-environmental factor (G × E) interactions were reported to partially account for "missing" heritability. However, (G × G) × E interactions were less commonly addressed. The purpose of this study was to develop a novel strategy to evaluate possible (G × G) × E interactions in D-loop-based chronic dialysis association. Using values from our previously published data set (704 controls and 193 cases) of 77 D-loop SNPs and 7 environmental factors (coronary heart disease, hypertension, diabetes mellitus, triglyceride, cholesterol, blood thiol, and TBARS levels), we compared the performances of G, G × G, G × E, and (G × G) × E. We found that the interactions of four individual SNPs previously associated with a significantly high risk of chronic dialysis [odds ratio (OR) = 1.56-4.93] with environmental factors (G × E) increased the risk of chronic dialysis (maximum OR = 35.43). We then used an improved branch and bound algorithm to identify combinations of two to four SNPs that were most highly associated with chronic dialysis (OR = 9.27-34.39). When the interactions of the two- and three-SNP combinations with environmental factors were evaluated, we found that the (G × G) × E effects increased the risk of chronic dialysis (maximum OR = 8.32-57.54 and OR = 12.52-57.81, respectively; adjusted OR = 8.67-81.81 and OR = 12.29-81.95, respectively). Taken together, the (G × G) × E interactions identified chronic dialysis-associated SNPs that would not have been found using G × G or G × E interactions, suggesting that (G × G) × E interactions may be helpful to solve the problems of missing heritability in association studies.