geneHapR: an R package for gene haplotypic statistics and visualization

BACKGROUND

Together with application of next-generation sequencing technologies and increased accumulation of genomic variation data in different organism species, an opportunity for effectively identification of superior alleles of functional genes to facilitate marker-assisted selection is emerging, and the clarification of haplotypes of functional genes is becoming an essential target in recent study works.

RESULTS

In this paper, we describe an R package 'geneHapR' developed for haplotypes identification, statistics and visualization analysis of candidate genes. This package could integrate genotype data, genomic annotating information and phenotypic variation data to clarify genotype variations, evolutionary-ship, and morphological effects among haplotypes through variants visualization, network construction and phenotypic comparison. 'geneHapR' also provides functions for Linkage Disequilibrium block analysis and visualizing of haplotypes geo-distribution.

CONCLUSIONS

The R package 'geneHapR' provided an easy-to-use tool for haplotype identification, statistic and visualization for candidate gene and will provide useful clues for gene functional dissection and molecular-assistant pyramiding of beneficial alleles of functional locus in future breeding programs.

Current and Potential Future Global Distribution of the Raisin Moth Cadra figulilella (Lepidoptera: Pyralidae) under Two Different Climate Change Scenarios

Global trade facilitates the introduction of invasive species that can cause irreversible damage to agriculture and the environment, as well as stored food products. The raisin moth (Cadra figulilella) is an invasive pest that poses a significant threat to fruits and dried foods. Climate change may exacerbate this threat by expanding moth's distribution to new areas. In this study, we used CLIMEX and MaxEnt niche modeling tools to assess the potential global distribution of the raisin moth under current and future climate change scenarios. Our models projected that the area of suitable distribution for the raisin moth could increase by up to 36.37% by the end of this century under high emission scenario. We also found that excessive precipitation decreased the probability of raisin moth establishment and that the optimum temperature range for the species during the wettest quarter of the year was 0-18 °C. These findings highlight the need for future research to utilize a combined modeling approach to predict the distribution of the raisin moth under current and future climate conditions more accurately. Our results could be used for environmental risk assessments, as well as to inform international trade decisions and negotiations on phytosanitary measures with regards to this invasive species.