Biology subjects

Zheya Sheng

Publications and source records attributed to Zheya Sheng.

3 recordsLinked to original sources

bioRxiv2016

Wide genome involvement in response to long-term selection for antibody response in an experimental population of White Leghorn chickens

Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation. They allow researchers to uncover the targets of selection and how these contribute to the mode and tempo of adaptation. Here we report results from a pooled genome re-sequencing study to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells. We observed wide genome involvement in response to this selection regime, with over 200 candidate sweep regions characterised by spans of high genetic differentiation (FST). These sweep signatures, encompassing almost 20% of the chicken genome (208.8 Mb), are primarily the result from bidirectional selection on haplotypes present in the base population. These extensive genomic changes highlight both the extent of standing genetic variation at immune loci available at the onset of selection, as well as how the long-term selection response results from selection on a highly polygenic genetic architecture. Furthermore, we present three examples of strong candidate genes that may have contributed to the profound phenotypic response to selection.\n\nData AvailabilityPooled genome data generated for this study will become available via SRA upon acceptance of manuscript

Genomics↗

bioRxiv2015

Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment

Artificial selection has, for decades, provided a powerful approach to study the genetics of adaptation. Using selective-sweep mapping, it is possible to identify genomic regions in populations where the allele-frequencies have diverged during selection. To avoid misleading signatures of selection, it is necessary to show that a sweep has an effect on the selected trait before it can be considered adaptive. Here, we confirm candidate selective-sweeps on a genome-wide scale in one of the longest, on-going bi-directional selection experiments in vertebrates, the Virginia high and low body-weight selected chicken lines. The candidate selective-sweeps represent standing genetic variants originating from the common base-population. Using a deep-intercross between the selected lines, 16 of 99 evaluated regions were confirmed to contain adaptive selective-sweeps based on their association with the selected trait, 56-day body-weight. Although individual additive effects were small, the fixation for alternative alleles in the high and low body-weight lines across these loci contributed at least 40% of the divergence between them and about half of the additive genetic variance present within and between the lines after 40 generations of selection. The genetic variance contributed by the sweeps corresponds to about 85% of the additive genetic variance of the base-population, illustrating that these loci were major contributors to the realised selection-response. Thus, the gradual, continued, long-term selection response in the Virginia lines was likely due to a considerable standing genetic variation in a highly polygenic genetic architecture in the base-population with contributions from a steady release of selectable genetic variation from new mutations and epistasis throughout the course of selection.

Genetics↗

bioRxiv2014

Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality

As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation. Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites. We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele. This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods. Sixteen novel loci were found, including an association between Chromomethylase 2 (CMT2) and temperature seasonality where the genome-wide CHH methylation was different for the group of accessions carrying the plastic allele. Cmt2 mutants were shown to be more tolerant to heat-stress, suggesting genetic regulation of epigenetic modifications as a likely mechanism underlying natural adaptation to variable temperatures, potentially through differential allelic plasticity to temperature-stress.\n\nAUTHOR SUMMARYA central problem when studying adaptation to a new environment is the interplay between genetic variation and phenotypic plasticity. Arabidopsis thaliana has colonized a wide range of habitats across the world and it is therefore an attractive model for studying the genetic mechanisms underlying environmental adaptation. Here, we study two collections of A. thaliana accessions from across Eurasia to identify loci associated with differences in climates at the sampling sites. A new genome-wide association analysis method was developed to detect adaptive loci where the alleles tolerate different climate ranges. Sixteen novel such loci were found including a strong association between Chromomethylase 2 (CMT2) and temperature seasonality. The reference allele dominated in areas with less seasonal variability in temperature, and the alternative allele existed in both stable and variable regions. Our results thus link natural variation in CMT2 and epigenetic changes to temperature adaptation. We showed experimentally that plants with a defective CMT2 gene tolerate heat-stress better than plants with a functional gene. Together this strongly suggests a role for genetic regulation of epigenetic modifications in natural adaptation to temperature and illustrates the importance of re-analyses of existing data using new analytical methods to obtain deeper insights into the underlying biology from available data.

Genomics↗