Visual Integration of Genome-Wide Association Studies and Differential Expression Results with the Hidecan R Package.

Background/objectives: We present hidecan, an R package for generating visualisations that summarise the results of one or more genome-wide association studies (GWAS) and differential expression analyses, as well as manually curated candidate genes, e.g., extracted from the literature.

Molecular breeding of flower load related traits in dioecious autotetraploid .

Unlabelled: Flowering plants exhibit a wide range of sexual reproduction systems, with the majority being hermaphroditic. However, some plants, such as (kiwiberry), have evolved into dioecious species with distinct female and male vines. In this study, we investigated the flower load and growth habits of female kiwiberry genotypes to identify the genetic basis of high yield with low maintenance requirements.

Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry ().

Unlabelled: In dioecious crops such as (kiwiberries), some of the main challenges when breeding for fruit characteristics are the selection of potential male parents and the long juvenile period. Currently, breeding values of male parents are estimated through progeny tests, which makes the breeding of new kiwiberry cultivars time-consuming and costly. The application of best linear unbiased prediction (BLUP) would allow direct estimation of sex-related traits and speed up kiwiberry breeding.

Investigating the genetic components of tuber bruising in a breeding population of tetraploid potatoes.

Background: Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economic importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still much to learn about this complex phenotype.

Alcohol acyl transferase genes at a high-flavor intensity locus contribute to ester biosynthesis in kiwifruit.

Volatile esters are key compounds contributing to flavor intensity in commonly consumed fruits including apple (Malus domestica), strawberry (Fragaria spp.), and banana (Musa sapientum). In kiwifruit (Actinidia spp.

Kinetics of Colour Development during Frying of Potato Pre-Treated with Pulsed Electric Fields and Blanching: Effect of Cultivar.

The current research aimed to investigate the effect of pulsed electric fields (1 kV/cm; 50 and 150 kJ/kg) followed by blanching (3 min., 100 °C) on the colour development of potato slices during frying on a kinetic basis. Four potato cultivars 'Crop77', 'Moonlight', 'Nadine', and 'Russet Burbank' with different content of glucose and amino acids were used.

sismonr: simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R.

Summary: We present sismonr, an R package for an integral generation and simulation of in silico biological systems. The package generates gene regulatory networks, which include protein-coding and non-coding genes along with different transcriptional and post-transcriptional regulations. The effect of genetic mutations on the system behaviour is accounted for via the simulation of genetically different in silico individuals.

TriPoly: haplotype estimation for polyploids using sequencing data of related individuals.

Motivation: Knowledge of haplotypes, i.e. phased and ordered marker alleles on a chromosome, is essential to answer many questions in genetics and genomics.

Somatic cell selection for chlorsulfuron-resistant mutants in potato: identification of point mutations in the acetohydroxyacid synthase gene.

Background: Somatic cell selection in plants allows the recovery of spontaneous mutants from cell cultures. When coupled with the regeneration of plants it allows an effective approach for the recovery of novel traits in plants. This study undertook somatic cell selection in the potato (Solanum tuberosum L.

FLOWERING LOCUS T genes control onion bulb formation and flowering.

Onion (Allium cepa L.) is a biennial crop that in temperate regions is planted in the spring and, after a juvenile stage, forms a bulb in response to the lengthening photoperiod of late spring/summer. The bulb then overwinters and in the next season it flowers and sets seed.

Genetic analyses of bolting in bulb onion (Allium cepa L.).

We present the first evidence for a QTL conditioning an adaptive trait in bulb onion, and the first linkage and population genetics analyses of candidate genes involved in photoperiod and vernalization physiology. Economic production of bulb onion (Allium cepa L.) requires adaptation to photoperiod and temperature such that a bulb is formed in the first year and a flowering umbel in the second.

A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.).

Background: Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers.

Results: We report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.

AlliumMap-A comparative genomics resource for cultivated Allium vegetables.

Background: Vegetables of the genus Allium are widely consumed but remain poorly understood genetically. Genetic mapping has been conducted in intraspecific crosses of onion (Allium cepa L.), A.

Quantitative, small-scale, fluorophore-assisted carbohydrate electrophoresis implemented on a capillary electrophoresis-based DNA sequence analyzer.

Fluorophore-assisted carbohydrate electrophoresis (FACE) is an analytical method for characterizing carbohydrate chain length that has been applied to neutral, charged, and N-linked oligosaccharides and that has been implemented using diverse separation platforms, including polyacrylamide gel electrophoresis and capillary electrophoresis. In this article, we describe three substantial improvements to FACE: (i) reducing the amount of starch and APTS required in labeling reactions and systematically analyzing the effect of altering the starch and 8-amino-1,3,6-pyrenetrisulfonic acid (APTS) concentrations on the reproducibility of the FACE peak area distributions; (ii) implementing FACE on a multiple capillary DNA sequencer (an ABI 3130xl), enabling higher throughput than is possible on other separation platforms; and (iii) developing a protocol for producing quantitative output of peak heights and areas using genetic marker analysis software. The results of a designed experiment to determine the effect of decreasing both the starch and fluorophore concentrations on the sensitivity and reproducibility of FACE electrophoregrams are presented.

Rapid analysis of seed size in Arabidopsis for mutant and QTL discovery.

Background: Arabidopsis thaliana is a useful model organism for deciphering the genetic determinants of seed size; however the small size of its seeds makes measurements difficult. Bulk seed weights are often used as an indicator of average seed size, but details of individual seed is obscured. Analysis of seed images is possible but issues arise from variations in seed pigmentation and shadowing making analysis laborious.

Towards disease resistance in potatoes using intragenic approaches.

Disease resistance is an important objective of global potato breeding programmes. The use of resistant cultivars is a significant tool for disease management. Recent advances in plant molecular genetics have identified several genes for resistance to potato diseases from within the germplasm pool available to potato breeders.

Large-scale identification of polymorphic microsatellites using an in silico approach.

Background: Simple Sequence Repeat (SSR) or microsatellite markers are valuable for genetic research. Experimental methods to develop SSR markers are laborious, time consuming and expensive. In silico approaches have become a practicable and relatively inexpensive alternative during the last decade, although testing putative SSR markers still is time consuming and expensive.