Article
Biology
Claire Burny, Viola Nolte, Marlies Dolezal, Christian Schloetterer
Summary: Experimental evolution combined with whole-genome sequencing is a powerful method to study the adaptive architecture of selected traits. This study shows that the presence of a second stressor affects the genomic selection response, and the combination of temperature and laboratory adaptation results in widespread synergistic effects.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Evolutionary Biology
Baohua Chen, Zhixiong Zhou, Yue Shi, Jie Gong, Chengyu Li, Tao Zhou, Yun Li, Dianchang Zhang, Peng Xu
Summary: Considering the importance of thermal adaptation in evolutionary biology and climate-change biology, the genetic structure and adaptive evolution of the spotted sea bass (Lateolabrax maculatus) were investigated. The study revealed significant genetic differentiation among populations and identified genes related to growth, muscle contraction, and vision that are under positive natural selection.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Agriculture, Dairy & Animal Science
Xing Guo, Chao-Hui Xing, Wei Wei, Xue-Fang Zhang, Zheng-Yu Wei, Lei-Lei Ren, Jin-Jin Jiang, Min Li, Jiang-Xian Wang, Xin-Xin He, Ming-Shan Wang, Run-Shen Jiang
Summary: Heat stress is a major challenge for the poultry industry, and this study identified genes associated with heat tolerance in chickens by analyzing the genomes of indigenous chicken populations from tropical and temperate regions. The researchers found a mutation in the TSHR gene that may enhance heat tolerance in chickens and facilitate adaptation to higher ambient temperatures in tropical climates. This study provides potential candidate genes for molecular breeding of heat-tolerant chickens.
Article
Multidisciplinary Sciences
Reid S. Brennan, James A. DeMayo, Hans G. Dam, Michael Finiguerra, Hannes Baumann, Vince Buffalo, Melissa H. Pespeni
Summary: This study reveals that the copepod Acartia tonsa adapts to ocean warming, acidification, and combined warming and acidification by a polygenic response involving multiple adaptive mechanisms. It demonstrates that warming is the dominant driver of selection in combined warming and acidification, while acidification has a weaker effect. The study also highlights the nonadditive effects of multiple stressors on genetic selection targets.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Demissew Sertse, Frank M. You, Valentyna Klymiuk, Jemanesh K. Haile, Amidou N'Diaye, Curtis J. Pozniak, Sylvie Cloutier, Sateesh Kagale
Summary: Wheat, a crop domesticated in the Fertile Crescent region approximately 10,000 years ago, is now grown in over 130 countries and accounts for a quarter of the world's cereal production. Its success can be attributed to its broad genetic diversity, allowing it to thrive in different environments. Genome scans and genome-environment association analysis identified important genetic markers and environmental factors associated with adaptations in the wheat genome. These findings provide insight into the historical selection and hybridization events that shaped the wheat's genetic structure and can aid in breeding and conservation efforts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Ying-Hui Li, Chao Qin, Li Wang, Chengzhi Jiao, Huilong Hong, Yu Tian, Yanfei Li, Guangnan Xing, Jun Wang, Yongzhe Gu, Xingpeng Gao, Delin Li, Hongyu Li, Zhangxiong Liu, Xin Jing, Beibei Feng, Tao Zhao, Rongxia Guan, Yong Guo, Jun Liu, Zhe Yan, Lijuan Zhang, Tianli Ge, Xiangkong Li, Xiaobo Wang, Hongmei Qiu, Wanhai Zhang, Xiaoyan Luan, Yingpeng Han, Dezhi Han, Ruzhen Chang, Yalong Guo, Jochen C. Reif, Scott A. Jackson, Bin Liu, Shilin Tian, Li-juan Qiu
Summary: This study analyzed the genome sequences of soybeans and revealed the evolutionary history and domestication process of soybean. The expansion and breeding of soybean were accompanied by positive selection of flowering time genes, and genetic introgression in soybean landraces mostly derived from sympatric wild populations.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Multidisciplinary Sciences
M. E. Lopez, M. Cadiz, E. B. Rondeau, B. F. Koop, J. M. Yanez
Summary: This study aims to identify selection signatures involved in adaption to culture conditions and traits of productive interest in coho salmon through genotyping and analysis, detecting several signatures of selection on different chromosomal regions. This can contribute to understanding the genetic mechanisms of phenotypic diversity in coho salmon.
SCIENTIFIC REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
Peng Zuo, Chaoxin Zhang, Yupeng Gao, Lijunyi Zhao, Jiaxu Guo, Yonglin Yang, Qian Yu, Yunna Li, Zhipeng Wang, Hua Yang
Summary: Epistatic effects, an important part of the genetic effect in livestock, were studied in synthetic ewes from China. Genome-wide single nucleotide polymorphisms (SNPs) were used to identify SNP-SNP interactions associated with birth weight and weaning weight. Significant interactions were found for weaning weight, but not for one-yearling weight. The interactions of sheep body weight were dynamic and time-dependent. Transcription factors were found to play a role in explaining epistatic effects, and the target genes of transcription factors were also identified. The study provides insights into the genetic mechanism of weight development.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yulong Wang, Conghui Jiang, Xingtan Zhang, Huimin Yan, Zhigang Yin, Xingming Sun, Fenghua Gao, Yan Zhao, Wei Liu, Shichen Han, Jingjing Zhang, Yage Zhang, Zhanying Zhang, Hongliang Zhang, Jinjie Li, Xianzhi Xie, Quanzhi Zhao, Xiaoning Wang, Guoyou Ye, Junzhou Li, Ray Ming, Zichao Li
Summary: This study investigates the genetic and genomic basis for the drought-aerobic adaptation of upland rice, a highly resistant drought stress variety. By assembling the genome of one typical upland rice variety, the study reveals the distinct ecotype differentiation between upland and lowland rice within the japonica subgroup. Comparative genomic analyses suggest that natural variation in promoter regions, formation of specific genes, and expansion of gene families contribute to the adaptive differentiation of lowland and upland rice. The study also identifies key genes associated with drought resistance, providing valuable insights for drought-resistant rice breeding and revolutionizing agriculture.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Microbiology
Changlong Chen, Shu Che, Zhou Dong, Jiayi Sui, Yu Tian, Yanyan Su, Meng Zhang, Wangwang Sun, Jiaqin Fan, Jianbo Xie, Hua Xie
Summary: Genome-wide association studies (GWAS) were conducted to identify the genetic basis of Pectobacterium spp. pathogenicity by analyzing genomic data and phenotypic measurements. The analysis revealed multiple loci associated with virulence and cellulase activity, as well as epistasis effects. This study provides valuable insights into the genetic mechanisms underlying Pectobacterium spp. pathogenicity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Changlong Chen, Shu Che, Zhou Dong, Jiayi Sui, Yu Tian, Yanyan Su, Meng Zhang, Wangwang Sun, Jiaqin Fan, Jianbo Xie, Hua Xie
Summary: This study used genome-wide association studies to identify genetic basis of pathogenicity in Pectobacterium spp. by integrating genomic data with virulence and cellulase activity phenotypes. The analysis discovered significant loci associated with Pectobacterium virulence and cellulase activity, as well as identified epistasis loci pairs. Furthermore, the study confirmed the epistasis effects of AraC transcriptional regulator and nutrient transport-related genes in contributing to the virulence phenotype.
MICROBIOLOGY SPECTRUM
(2023)
Article
Plant Sciences
Guogen Zhang, Zhiyuan Bi, Jing Jiang, Jingbing Lu, Keyang Li, Di Bai, Xinchen Wang, Xueyu Zhao, Min Li, Xiuqin Zhao, Wensheng Wang, Jianlong Xu, Zhikang Li, Fan Zhang, Yingyao Shi
Summary: By utilizing genome-wide association and epistasis analysis (GWAES), the genetic basis of rice saline-alkali tolerance was studied. A total of 165 main-effect quantitative trait nucleotides (QTNs) and 124 additional epistatic QTNs were identified, explaining a significant portion of the phenotypic variation of saline-alkali tolerance. Most of these QTNs were located in genomic regions associated with saline-alkali tolerance or known genes. The finding of candidate genes and favorable haplotypes provides valuable information for genetic improvement of rice saline-alkali tolerance.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Environmental Sciences
Nora Hanson, James Ounsley, Stuart J. J. Middlemas, John Gilbey, Christopher D. D. Todd
Summary: This study successfully tracked and reconstructed the migration patterns of individual wild Atlantic salmon at sea using high resolution stable isotope sampling, genetic assignment, growth increment analyses, and a simple movement model. These techniques offer a powerful tool for understanding the movement and survival processes of individual fish during their largely unobservable life-stage in the oceanic environment.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Microbiology
Chanenath Sriaporn, Kathleen A. Campbell, Martin J. Van Kranendonk, Kim M. Handley
Summary: This study analyzed the genomes of Acidithiobacillus strains from hot springs in the Taupo Volcanic Zone of New Zealand, revealing four distinct species, including three novel ones. The findings suggest that these Acidithiobacillus have undergone genome streamlining to adapt to high temperatures in geothermal environments.
Article
Plant Sciences
Hanne De Kort, Tuomas Toivainen, Filip Van Nieuwerburgh, Javier Andres, Timo P. Hytonen, Olivier Honnay
Summary: By studying the genomic and epigenomic variation of wild strawberry plants, it was found that covariation between SNPs and DMCs is independent of genomic proximity, but associated with fitness-related processes. Drought-induced DMCs frequently co-vary with multiple SNPs, suggesting high genomic redundancy as a potential basis for polygenic adaptation of gene expression.
Article
Biology
Christopher L. Owen, Heather Bracken-Grissom, David Stern, Keith A. Crandall
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2015)
Article
Ecology
David B. Stern, Jesse Breinholt, Carlos Pedraza-Lara, Marilu Lopez-Mejia, Christopher L. Owen, Heather Bracken-Grissom, James W. Fetzner, Keith A. Crandall
Article
Multidisciplinary Sciences
David B. Stern, Eduardo Castro Nallar, Jason Rathod, Keith A. Crandall
Article
Zoology
David B. Stern, Keith A. Crandall
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
David B. Stern, Keith A. Crandall
MOLECULAR BIOLOGY AND EVOLUTION
(2018)
Article
Ecology
David Ben Stern, Carol Eunmi Lee
NATURE ECOLOGY & EVOLUTION
(2020)
Article
Zoology
Daniel P. Johnson, David B. Stern, Keith A. Crandall
Summary: This study provides a detailed description of the crayfish genus Creaserinus in Texas, including six species in total, with one species previously misidentified and five newly described species. The taxonomic acts are supported by data from genetics, morphology, ecology, etc., and each species is extensively described with illustrations, along with a key to the species based on form I males in the state.
Letter
Gastroenterology & Hepatology
Lydia Nashed, Jyoti Mani, Sahel Hazrati, David B. Stern, Poorani Subramanian, Lisa Mattei, Kyle Bittinger, Weiming Hu, Shira Levy, George L. Maxwell, Suchitra K. Hourigan
Article
Biochemistry & Molecular Biology
Paul Bastide, Charlotte Soneson, David B. Stern, Olivier Lespinet, Melina Gallopin
Summary: This study develops and implements a new simulation framework to generate interspecies gene expression count datasets based on the RNA-Seq and phylogenetic comparative methods. Through a simulation study, the usefulness of this framework is demonstrated and several approaches for differential expression analysis are compared. The tool has been integrated in the R package compcodeR, which is freely available on Bioconductor.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)