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The impact of genetic adaptation on chimpanzee subspecies differentiation

Joshua M. Schmidt, Marc de Manuel, Tomas Marques-Bonet, Sergi Castellano, Aida M. Andrés

PLoS Genet. 2019 Nov; 15(11): e1008485. Published online 2019 Nov 25. doi: 10.1371/journal.pgen.1008485

PMCID:: PMC6901233

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Genetic architecture of complex traits and disease risk predictors

Soke Yuen Yong, Timothy G. Raben, Louis Lello, Stephen D. H. Hsu

Sci Rep. 2020; 10: 12055. Published online 2020 Jul 21. doi: 10.1038/s41598-020-68881-8

PMCID:: PMC7374622

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Temporal and genomic analysis of additive genetic variance in breeding programmes

Letícia A. de C. Lara, Ivan Pocrnic, Thiago de P. Oliveira, R. Chris Gaynor, Gregor Gorjanc

Heredity (Edinb) 2022 Jan; 128(1): 21–32. Published online 2021 Dec 15. doi: 10.1038/s41437-021-00485-y

PMCID:: PMC8733024

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Genic and non-genic SNP contributions to additive and dominance genetic effects in purebred and crossbred pig traits

Mahshid Mohammadpanah, Ahmad Ayatollahi Mehrgardi, Hélène Gilbert, Catherine Larzul, Marie-José Mercat, Ali Esmailizadeh, Mehdi Momen, Llibertat Tusell

Sci Rep. 2022; 12: 3795. Published online 2022 Mar 9. doi: 10.1038/s41598-022-07767-3

PMCID:: PMC8907311

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Quantitative genetics of breeding coloration in sand lizards; genic capture unlikely to maintain additive genetic variance

Willow R. Lindsay, Badreddine Bererhi, Gabriella Ljungström, Erik Wapstra, Mats Olsson

Heredity (Edinb) 2023 May; 130(5): 329–334. Published online 2023 Mar 20. doi: 10.1038/s41437-023-00607-8

PMCID:: PMC10162981

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Assessment of morphological and genetic variability through genic microsatellite markers for essential oil in Sandalwood (Santalum album L.)

Tanzeem Fatima, Ashutosh Srivastava, P. V. Somashekar, Vageeshbabu S. Hanur, M. Srinivasa Rao, Surendra Singh Bisht

3 Biotech. 2019 Jul; 9(7): 252. Published online 2019 Jun 7. doi: 10.1007/s13205-019-1758-9

PMCID:: PMC6555841

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rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo

Gregory J Bedwell, Sooin Jang, Wen Li, Parmit K Singh, Alan N Engelman

Nucleic Acids Res. 2021 Jul 21; 49(13): 7330–7346. Published online 2021 Jun 24. doi: 10.1093/nar/gkab514

PMCID:: PMC8287940

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Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

Jinyu Wang, Xianran Li, Kyung Do Kim, Michael J. Scanlon, Scott A. Jackson, Nathan M. Springer, Jianming Yu

Genome Biol. 2019; 20: 74. Published online 2019 Apr 25. doi: 10.1186/s13059-019-1683-6

PMCID:: PMC6482504

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Patterns of genic intolerance of rare copy number variation in 59,898 human exomes

Douglas M. Ruderfer, Tymor Hamamsy, Monkol Lek, Konrad J. Karczewski, David Kavanagh, Kaitlin E. Samocha, Exome Aggregation Consortium, Mark J. Daly, Daniel G. MacArthur, Menachem Fromer, Shaun M. Purcell

Nat Genet. Author manuscript; available in PMC 2017 Feb 17.

Published in final edited form as: Nat Genet. 2016 Oct; 48(10): 1107–1111. Published online 2016 Aug 17. doi: 10.1038/ng.3638

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Polysome-CAGE of TCL1-driven chronic lymphocytic leukemia revealed multiple N-terminally altered epigenetic regulators and a translation stress signature

Ariel Ogran, Tal Havkin-Solomon, Shirly Becker-Herman, Keren David, Idit Shachar, Rivka Dikstein

eLife. 2022; 11: e77714. Published online 2022 Aug 8. doi: 10.7554/eLife.77714

PMCID:: PMC9359700

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Moderate Genetic Diversity and Genetic Differentiation in the Relict Tree Liquidambar formosana Hance Revealed by Genic Simple Sequence Repeat Markers

Rongxi Sun, Furong Lin, Ping Huang, Yongqi Zheng

Front Plant Sci. 2016; 7: 1411. Published online 2016 Sep 21. doi: 10.3389/fpls.2016.01411

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The long-term effects of genomic selection: 1. Response to selection, additive genetic variance, and genetic architecture

Yvonne C. J. Wientjes, Piter Bijma, Mario P. L. Calus, Bas J. Zwaan, Zulma G. Vitezica, Joost van den Heuvel

Genet Sel Evol. 2022; 54: 19. Published online 2022 Mar 7. doi: 10.1186/s12711-022-00709-7

PMCID:: PMC8900405

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Species diversity and phylogeography of Cornus kousa (Asian dogwood) captured by genomic and genic microsatellites

Marcin Nowicki, Logan C. Houston, Sarah L. Boggess, Anthony S. Aiello, Miriam Payá‐Milans, Margaret E. Staton, Mitsuhiro Hayashida, Masahiro Yamanaka, Shigetoshi Eda, Robert N. Trigiano

Ecol Evol. 2020 Aug; 10(15): 8299–8312. Published online 2020 Jul 11. doi: 10.1002/ece3.6537

PMCID:: PMC7417245

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Assortative mating can help adaptation of flowering time to a changing climate: Insights from a polygenic model

Claire Godineau, Ophélie Ronce, Céline Devaux

J Evol Biol. 2022 Apr; 35(4): 491–508. Published online 2021 May 14. doi: 10.1111/jeb.13786

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Genetic and molecular dissection of ginseng (Panax ginseng Mey.) germplasm using high-density genic SNP markers, secondary metabolites, and gene expressions

Sizhang Liu, Yue Jiang, Yanfang Wang, Huimin Huo, Mustafa Cilkiz, Ping Chen, Yilai Han, Li Li, Kangyu Wang, Mingzhu Zhao, Lei Zhu, Jun Lei, Yi Wang, Meiping Zhang

Front Plant Sci. 2023; 14: 1165349. Published online 2023 Jul 28. doi: 10.3389/fpls.2023.1165349

PMCID:: PMC10416250

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The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data

Vince Buffalo, Graham Coop

Genetics. 2019 Nov; 213(3): 1007–1045. Published online 2019 Sep 26. doi: 10.1534/genetics.119.302581

PMCID:: PMC6827383

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Functional Partitioning of Genomic Variance and Genome-Wide Association Study for Carcass Traits in Korean Hanwoo Cattle Using Imputed Sequence Level SNP Data

Mohammad S. A. Bhuiyan, Dajeong Lim, Mina Park, Soohyun Lee, Yeongkuk Kim, Cedric Gondro, Byoungho Park, Seunghwan Lee

Front Genet. 2018; 9: 217. Published online 2018 Jun 22. doi: 10.3389/fgene.2018.00217

PMCID:: PMC6024024

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The Impact of Genomic and Traditional Selection on the Contribution of Mutational Variance to Long-Term Selection Response and Genetic Variance

Herman A. Mulder, Sang Hong Lee, Sam Clark, Ben J. Hayes, Julius H. J. van der Werf

Genetics. 2019 Oct; 213(2): 361–378. Published online 2019 Aug 20. doi: 10.1534/genetics.119.302336

PMCID:: PMC6781905

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Natural variation in DNA methylation homeostasis and the emergence of epialleles

Yinwen Zhang, Jered M. Wendte, Lexiang Ji, Robert J. Schmitz

Proc Natl Acad Sci U S A. 2020 Mar 3; 117(9): 4874–4884. Published online 2020 Feb 18. doi: 10.1073/pnas.1918172117

PMCID:: PMC7060739

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Molecular evidence supports a genic capture resolution of the lek paradox

Robert J. Dugand, Joseph L. Tomkins, W. Jason Kennington

Nat Commun. 2019; 10: 1359. Published online 2019 Mar 25. doi: 10.1038/s41467-019-09371-y

PMCID:: PMC6433924

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PMC Images search for genic variance

Figure 2Partitioning of genomic variation by genic annotation.

(a) Estimates of variance explained by genic and intergenic regions (GRM<0.025). The genic region is defined as ±20 kb from the 3′ and 5′ UTRs. (b) Estimates of variance explained by genic and intergenic regions. The genic region is defined by the LD-weighted genic annotation scheme. *P<0.05, **P<0.004. Error bars represent the s.e. of the estimates. Estimates were tested for significantly different from zero by likelihood ratio test.

Large-scale genomics unveil polygenic architecture of human cortical surface area

Nat Commun. 2015;6:7549.
Fig. 3Estimates of the variance explained by all SNPs in genic (intergenic) regions for 3 traits (a, b, and c indicate milk yield, fat, and protein, respectively) against length of genic (intergenic) DNA. Shown in panels (A), (C), and (E) are the results for the genic SNPs, and shown on panels (B), (D), and (F) are the results for intergenic SNPs, under the assumption that genic regions is Wor0 Kb of UTRs. (A) Milk yield, genic region (slope = 7.89 E-04, S.E = 3.30 E-04, p-value = 3.56 E-02). (B) Milk yield, intergenic region (slope = 9.11 E-04, S.E = 6.70 E-04, p-value = 2.07 E-01). (C) Milk fat, genic region (slope = 4.04 E-04, S.E = 2.20 E-04, p-value = 8.01 E-02). (D) Milk fat, intergenic region (slope = 5.23 E-04, S.E = 1.78 E-04, p-value = 7.02 E-03). (E) Milk protein, genic region (slope = 3.66 E-04, S.E = 2.24 E-04, p-value = 1.34 E-01). (F) Milk protein, intergenic region (slope = 7.53 E-04, S.E = 2.24 E-04, p-value = 7.20 E-03).

Heritability Estimated Using 50K SNPs Indicates Missing Heritability Problem in Holstein Breeding

Genomics Inform. 2015 Dec;13(4):146-151.
Fig. 6Statistical analysis.

The empirical Bayesian approach versus the full Bayesian approach for posterior mean of genetic variance (A), posterior mean of genic variance (B), posterior standard deviation of genetic variance (C) and posterior standard deviation of genic variance (D); equal value is represented by the dashed red line.

Temporal and genomic analysis of additive genetic variance in breeding programmes

Heredity (Edinb). 2022 Jan;128(1):21-32.
Figure 6

Genetic and genic additive variances for different cross-selection indices in the TRUE scenario (PM: parental mean, UC: usefulness criterion, OCS-He*: optimal cross-selection, and UCPC-He*: UCPC-based optimal cross-selection) according to the generations. (A) Additive genic variance () measured on the whole progeny, (B) additive genetic variance () measured on the whole progeny, and (C) ratio of genetic over genic variance () reflecting the Bulmer effect.

Improving Short- and Long-Term Genetic Gain by Accounting for Within-Family Variance in Optimal Cross-Selection

Front Genet. 2019;10:1006.