RESUMEN
JBrowse 2 is a next-generation genome browser that can be run as a web or desktop application. We describe a new plugin, the Linkout Plugin, that enables users to link features to external databases based on their IDs and the remote URLs on JBrowse 2 desktop or web. As a result, genome analysis time and effort are reduced, enabling researchers to gain insights more quickly. The Linkout Plugin fills a common need scientists have: looking for more information on a gene. Overall, the Linkout Plugin is a valuable and practical addition to the JBrowse functionality.
RESUMEN
Hybrid breeding employs heterosis, which could potentially improve the yield and quality of a crop. Genomic selection (GS) is a promising approach for the selection of quantitative traits in plant breeding. The main objectives of this study are to (i) propose a GS-based approach to identify potential parental lines and superior hybrid combinations from a breeding population, which is composed of hybrids produced by a half diallel mating design; (ii) develop a software package for users to carry out the proposed approach. An R package, designated EHPGS, was generated to facilitate the employment of the genomic best linear unbiased model considering additive plus dominance marker effects for the hybrid performance evaluation. The R package contains a Bayesian statistical algorithm for calculating genomic estimated breeding value (GEBVs), GEBV-based specific combining ability, general combining ability, mid-parent heterosis, and better-parent heterosis. Three datasets that have been published in literature, including pumpkin (Cucurbita maxima), maize (Zea mays), and wheat (Triticum aestivum L.), were reanalyzed to illustrate the use of EHPGS.
