Evolution of color phenotypes in two distantly related species of stick insect: different ecological regimes acting on similar genetic architectures

Recurrent (e.g. parallel or convergent) evolution is widely cited as evidence for natural selection’s central role in evolution but can also highlight constraints affecting evolution. Here we describe the evolution of green and melanistic color phenotypes in two species of stick insect: Timema podura and T. cristinae. We show that similar color phenotypes of these species (1) cluster in phenotypic space and (2) confer crypsis on different plant microhabitats. We then use genome-wide association mapping to determine the genetic architecture of color in T. podura, and compare this to previous results in T. cristinae. In both species, color is under simple genetic control, dominance relationships of melanistic and green alleles are the same, and SNPs associated with color phenotypes colocalize to the same genomic region. These results differ from those of ‘typical’ parallel phenotypes because the form of selection acting on color differs between species: a balance of multiple sources of selection acting within host species maintains the color polymorphism in T. cristinae whereas T. podura color phenotypes are under divergent selection between hosts. Our results highlight how different adaptive landscapes can result in the evolution of similar phenotypic variation, and suggest the same genomic region is involved.

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Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽

10.3390/agronomy11010027 ◽

2020 ◽

Vol 11 (1) ◽

pp. 27

Author(s):

Archana Khadgi ◽

Courtney A. Weber

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genomic Region ◽

Rubus Idaeus ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Red Raspberry ◽

Genome Wide ◽

A Genome ◽

Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

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A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽

10.1186/s12864-020-07288-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Shenping Zhou ◽

Rongrong Ding ◽

Fanming Meng ◽

Xingwang Wang ◽

Zhanwei Zhuang ◽

...

Keyword(s):

Candidate Genes ◽

Growth And Development ◽

Genetic Architecture ◽

Association Studies ◽

Meta Analysis ◽

Average Daily Gain ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

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A combination of genome-wide association study and selection signature analysis dissects the genetic architecture underlying bone traits in chickens

animal ◽

10.1016/j.animal.2021.100322 ◽

2021 ◽

Vol 15 (8) ◽

pp. 100322

Author(s):

Y.D. Li ◽

X. Liu ◽

Z.W. Li ◽

W.J. Wang ◽

Y.M. Li ◽

...

Keyword(s):

Association Study ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Signature Analysis ◽

Selection Signature ◽

Genome Wide

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Genetic architecture of common bunt resistance in winter wheat using genome-wide association study

BMC Plant Biology ◽

10.1186/s12870-018-1435-x ◽

2018 ◽

Vol 18 (1) ◽

Cited By ~ 10

Author(s):

Amira M. I. Mourad ◽

Ahmed Sallam ◽

Vikas Belamkar ◽

Ezzat Mahdy ◽

Bahy Bakheit ◽

...

Keyword(s):

Winter Wheat ◽

Association Study ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Common Bunt ◽

Genome Wide ◽

Bunt Resistance

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Faculty Opinions recommendation of Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.733105041.793567849 ◽

2019 ◽

Author(s):

Benjamin Neale

Keyword(s):

Major Depression ◽

Genetic Architecture ◽

Genome Wide Association ◽

Association Analyses ◽

Risk Variants ◽

Genome Wide

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Faculty Opinions recommendation of Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.733105041.793546400 ◽

2018 ◽

Author(s):

Holger Lerche ◽

Mahmoud Koko Musa

Keyword(s):

Major Depression ◽

Genetic Architecture ◽

Genome Wide Association ◽

Association Analyses ◽

Risk Variants ◽

Genome Wide

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A New Polygenic Model for Nonfamilial Colorectal Cancer Inheritance Based on the Genetic Architecture of the Azoxymethane-Induced Mouse Model

Genetics ◽

10.1534/genetics.119.302833 ◽

2019 ◽

Vol 214 (3) ◽

pp. 691-702

Author(s):

Anika C. Bissahoyo ◽

Yuying Xie ◽

Lynda Yang ◽

R. Scott Pearsall ◽

Daekee Lee ◽

...

Keyword(s):

Colorectal Cancer ◽

Mouse Model ◽

Genetic Architecture ◽

Inbred Strains ◽

Genome Wide Association ◽

Polygenic Resistance ◽

Genetic Studies ◽

Polygenic Model ◽

Genome Wide ◽

Dominant Characteristic

The azoxymethane model of colorectal cancer (CRC) was used to gain insights into the genetic heterogeneity of nonfamilial CRC. We observed significant differences in susceptibility parameters across 40 mouse inbred strains, with 6 new and 18 of 24 previously identified mouse CRC modifier alleles detected using genome-wide association analysis. Tumor incidence varied in F1 as well as intercrosses and backcrosses between resistant and susceptible strains. Analysis of inheritance patterns indicates that resistance to CRC development is inherited as a dominant characteristic genome-wide, and that susceptibility appears to occur in individuals lacking a large-effect, or sufficient numbers of small-effect, polygenic resistance alleles. Our results suggest a new polygenic model for inheritance of nonfamilial CRC, and that genetic studies in humans aimed at identifying individuals with elevated susceptibility should be pursued through the lens of absence of dominant resistance alleles rather than for the presence of susceptibility alleles.

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