Article
Plant Sciences
Vinay Sharma, Sunil S. Gangurde, Spurthi N. Nayak, Anjan S. Gowda, B. S. Sukanth, Supriya S. S. Mahadevaiah, Surendra S. Manohar, Rakeshkumar S. Choudhary, T. Anitha, Sachin S. Malavalli, S. N. Srikanth, Prasad Bajaj, Shailendra Sharma, Rajeev K. Varshney, Putta Latha, Pasupuleti Janila, Ramesh S. Bhat, Manish K. Pandey
Summary: Rising temperatures in semi-arid environments hinder groundnut productivity and quality. Understanding the molecular mechanisms of heat stress tolerance will help address yield losses. QTL analysis identified three QTL clusters that harbor most of the major QTLs for heat tolerant traits, and several candidate genes with potential roles in seed development, plant architecture regulation, yield, plant growth and flowering time regulation, and photosynthesis were also identified. These findings provide a platform for further mapping, gene discovery, and marker development for genomics-assisted breeding of heat-tolerant groundnut varieties.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agronomy
Tengkui Chen, Lixin Luo, Zhe Zhao, Hui Wang, Chun Chen, Yongzhu Liu, Xinchang Li, Tao Guo, Wuming Xiao
Summary: Grain size affects rice yield and quality. This study constructed a near-isogenic line LB3 with long grain size and identified a major QTL, qGL10, located on chromosome 10, for grain length. Candidate gene analysis suggested LOC_Os10g39130 (OsMADS56). Sequence comparison revealed SNPs in the promoter and coding regions of OsMADS56 in 02428 and LB3. Haplotype analysis indicated that the SNP9 (G/A) in the TGTCACA motif may contribute to the differential expression of OsMADS56. These findings provide a foundation for the molecular breeding of new rice varieties using qGL10.
Article
Plant Sciences
Dennis N. Lozada, Guillermo Nunez, Phillip Lujan, Srijana Dura, Danise Coon, Derek W. Barchenger, Soumaila Sanogo, Paul W. Bosland
Summary: A genetic linkage map was constructed using GBS-derived SNP markers in a RIL population, identifying genomic regions associated with P. capsici resistance and candidate genes. The study revealed the genetic complexity of the P. capsici-Capsicum pathosystem and the potential role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response were identified, providing a deeper understanding of Phytophthora root rot resistance in chile pepper.
Article
Plant Sciences
Xin Zhang, Xiaoji Zhang, Luhuan Wang, Qimei Liu, Yuying Liang, Jiayu Zhang, Yunyun Xue, Yuexia Tian, Huiqi Zhang, Na Li, Cong Sheng, Pingping Nie, Suping Feng, Boshou Liao, Dongmei Bai
Summary: This study successfully located and identified the genomic region and genes related to cold tolerance in peanut germination using a recombinant inbred line (RIL) population, high density SNP-based genetic linkage map, and KASP genotyping. The results provide valuable information for future breeding and molecular research in improving cold tolerance in peanuts.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Junnan Zhang, Zhongyi Duan, Xiqiong Wang, Fengning Li, Jiajing Chen, Xingfu Lai, Liang Qu, Congjiao Sun, Guiyun Xu
Summary: Eggs with different yolk weights despite the same total weight have varying nutritional values and consumer preferences. Investigating the genetic factors of yolk quantity in chicken eggs is crucial for scientific and practical purposes. Studying the molecular mechanisms of high yolk percentage traits can optimize breeding strategies for altering yolk percentage in eggs.
Article
Agriculture, Dairy & Animal Science
Wei Li, Maiqing Zheng, Guiping Zhao, Jie Wang, Jie Liu, Shunli Wang, Furong Feng, Dawei Liu, Dan Zhu, Qinghe Li, Liping Guo, Yuming Guo, Ranran Liu, Jie Wen
Summary: Background feed contributes to the majority of costs in poultry meat production, making feed efficiency a critical factor. This study identified genetic parameters and QTL for feed efficiency in purebred broilers through a genome-wide association study. Candidate genes related to mitochondrial function and behavioral regulation were identified, suggesting their potential role in growth and feed efficiency in poultry.
GENETICS SELECTION EVOLUTION
(2021)
Article
Genetics & Heredity
Gaofeng Zhou, Huaan Yang, Daniel Renshaw, Meilin Zou, Geoff Thomas, Chengdao Li
Summary: The study revealed that resistance against gray leaf spot (GLS) in lupin is controlled by a single major gene, with markers identified through MFLP linked to GLS. Through QTL analysis and fine mapping, the gene was narrowed down to a 241kb region containing two disease resistance genes. Further analysis identified a SNP in the TMV resistance protein N-like gene region as potentially associated with GLS resistance.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Takayuki Ochiai, Marina Sakaguchi, Shin-Ichi Kawakami, Akira Ishikawa
Summary: An integrated approach of transcriptome, haplotype frequency, and association analyses was used to identify candidate genes for the QTL affecting innate fear behavioral traits in chickens. The initial QTL interval on chromosome 4 contained 333 genes, but through further analysis, the number of candidate genes was reduced to 11, with NPY5R and LOC101749214 identified as strong candidates for innate fear behavior.
G3-GENES GENOMES GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Hanpeng Luo, Lirong Hu, Luiz F. Brito, Jinhuan Dou, Abdul Sammad, Yao Chang, Longgang Ma, Gang Guo, Lin Liu, Liwei Zhai, Qing Xu, Yachun Wang
Summary: This study aimed to identify QTL regions associated with heat stress response in Holstein dairy cattle and investigate candidate genes through RNA-seq analysis. The results showed that physiological indicators of heat stress are heritable and have polygenic nature. The identified candidate genes will contribute to optimizing genomic evaluation models and designing SNP panels for heat tolerance improvement.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Xiurong Zhao, Changsheng Nie, Jinxin Zhang, Xinghua Li, Tao Zhu, Zi Guan, Yu Chen, Liang Wang, Xue Ze Lv, Weifang Yang, Yaxiong Jia, Zhonghua Ning, Haiying Li, Changqing Qu, Huie Wang, Lujiang Qu
Summary: This study utilized genome-wide association study to identify 148 SNPs associated with egg number traits and 32 candidate genes related to hormone regulation, follicle development, and reproductive system development. The study also highlighted a genomic region on GGA5 as a potential candidate region underlying egg number traits.
Article
Genetics & Heredity
Ahmed A. Easa, Marina Selionova, Magomet Aibazov, Tatiana Mamontova, Alexander Sermyagin, Anna Belous, Alexandra Abdelmanova, Tatiana Deniskova, Natalia Zinovieva
Summary: The objective of this study was to identify SNPs and candidate genes associated with body weight and body conformation traits in Karachai goats. A total of 241 SNPs and 238 candidate genes were found to be significantly associated with these traits, suggesting their potential use as molecular markers for genetic improvement.
Article
Biochemistry & Molecular Biology
Lieqiong Kuang, Nazir Ahmad, Bin Su, Lintao Huang, Keqi Li, Hanzhong Wang, Xinfa Wang, Xiaoling Dun
Summary: Marker-assisted selection was used to study root-related and shoot biomass traits in a new recombinant inbred line population. A high-density linkage map was constructed and 86 quantitative trait loci were detected. Using fine mapping and comparative sequencing, important candidate genes for root development were identified.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
N. D. Vinay, Hideo Matsumura, Anilabha Das Munshi, Ranjith Kumar Ellur, Viswanathan Chinnusamy, Ankita Singh, Mir Asif Iquebal, Sarika Jaiswal, Gograj Singh Jat, Ipsita Panigrahi, Ambika Baladev Gaikwad, A. R. Rao, Shyam Sundar Dey, Tusar Kanti Behera
Summary: This study investigated the inheritance and genomic regions associated with gynoecious sex expression in bitter gourd, and identified possible candidate genes through QTL-seq. The results revealed that a 1.31 Mb region on chromosome 1 is associated with gynoecious sex expression in bitter gourd, and twelve genes related to male and female gametophyte development were identified. The findings provide insights into sex expression in bitter gourd and will aid in the identification of candidate genes through functional validation.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Ophthalmology
Zhiwei Ma, Daniel Chauss, Joshua Disatham, Xiaodong Jiao, Lisa Ann Brennan, A. Sue Menko, Marc Kantorow, J. Fielding Hejtmancik
Summary: This study identified the expression patterns of crystallin genes during the transition from lens epithelial cells to lens fiber cells in embryonic day 13 chicken lenses. Three distinct expression patterns of crystallin genes were discovered, each highly correlated with specific transcription factors. These findings provide quantitative evidence for understanding the mechanisms that govern crystallin expression during fiber cell differentiation for achieving lens transparency.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Article
Agriculture, Multidisciplinary
Ke-xin Chen, Dong-yang Dai, Ling Wang, Li-min Yang, Dan-dan Li, Chao Wang, Peng Ji, Yun-yan Sheng
Summary: This study crossed a soft fruit melon and a hard fruit melon to generate F2 and recorded the flesh firmness (FF) and fruit-related traits for two years. Using QTL-SLAF sequencing and molecular marker-linkage analysis, they identified 112,844 SLAF markers and constructed a genetic linkage map. Ten QTLs related to FF and fruit traits were found.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Gastroenterology & Hepatology
Sarra Smati, Arnaud Polizzi, Anne Fougerat, Sandrine Ellero-Simatos, Yuna Blum, Yannick Lippi, Marion Regnier, Alexia Laroyenne, Marine Huillet, Muhammad Arif, Cheng Zhang, Frederic Lasserre, Alain Marrot, Talal Al Saati, JingHong Wan, Caroline Sommer, Claire Naylies, Aurelie Batut, Celine Lukowicz, Tiffany Fougeray, Blandine Tramunt, Patricia Dubot, Lorraine Smith, Justine Bertrand-Michel, Nathalie Hennuyer, Jean-Philippe Pradere, Bart Staels, Remy Burcelin, Francoise Lenfant, Jean-Francois Arnal, Thierry Levade, Laurence Gamet-Payrastre, Sandrine Lagarrigue, Nicolas Loiseau, Sophie Lotersztajn, Catherine Postic, Walter Wahli, Christophe Bureau, Maeva Guillaume, Adil Mardinoglu, Alexandra Montagner, Pierre Gourdy, Herve Guillou
Summary: The study found that different diets induced more severe NAFLD in male mice, characterized by lipid accumulation and inflammation/fibrosis. Sex-biased hepatic gene signatures showed different responses to various dietary challenges, with Peroxisome proliferator-activated receptor alpha (PPAR alpha) playing a key role in gender-specific and NAFLD pathophysiology.
Article
Dermatology
Pierre-Francois Roux, Thierry Oddos, Georgios Stamatas
Summary: The advent of 16S RNA profiling and shotgun metagenomics has allowed for a comprehensive study of the skin microbiome composition. Analysis of skin surface samples from healthy infants revealed the coexistence of different microbiome and metabolome clusters, highlighting the diverse roles of various microorganisms and metabolites in skin physiology.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
Article
Dermatology
Claire Mangez, Pierre-Francois Roux, Georgios Stamatas, Thierry Oddos, Cecilia Brun
Summary: Despite starting development early in utero, neonatal skin is still immature at birth compared to adult skin, undergoing a maturation process in the first years of life. The differences between the two include thinner and dryer stratum corneum, less natural moisturizing factors and lipids in newborns. Baby skin shows a higher epidermal cellular turnover, with specific molecular and metabolic characteristics still poorly understood.
EXPERIMENTAL DERMATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ming Wen, Qiaowei Pan, Elodie Jouanno, Jerome Montfort, Margot Zahm, Cedric Cabau, Christophe Klopp, Carole Iampietro, Celine Roques, Olivier Bouchez, Adrien Castinel, Cecile Donnadieu, Hugues Parrinello, Charles Poncet, Elodie Belmonte, Veronique Gautier, Jean-Christophe Avarre, Remi Dugue, Rudhy Gustiano, Tran Thi Thuy Ha, Marc Campet, Kednapat Sriphairoj, Josiane Ribolli, Fernanda L. de Almeida, Thomas Desvignes, John H. Postlethwait, Christabel Floi Bucao, Marc Robinson-Rechavi, Julien Bobe, Amaury Herpin, Yann Guiguen
Summary: This study generated novel genomic resources for 12 Pangasiids, characterized their sex determination system, and identified a conserved master sex-determining gene. The findings contribute to a better understanding of the dynamics of sex determination systems.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Andrew J. Jasonowicz, Anna Simeon, Margot Zahm, Cedric Cabau, Christophe Klopp, Celine Roques, Carole Iampietro, Jerome Lluch, Cecile Donnadieu, Hugues Parrinello, Daniel P. Drinan, Lorenz Hauser, Yann Guiguen, Josep Planas
Summary: This study reports the first generation of a high-quality chromosome-level assembly of the Pacific halibut genome, providing an essential resource for future studies on population structure, evolutionary history, and responses to environmental and anthropogenic influences in Pacific halibut.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Genetics & Heredity
Emilie Dordet-Frisoni, Celine Vandecasteele, Rachel Contarin, Eveline Sagne, Eric Baranowski, Christophe Klopp, Laurent-Xavier Nouvel, Christine Citti
Summary: DNA methylation plays a crucial role in the biology of bacteria, affecting bacterial evolution by interfering with horizontal gene transfer events. In this study, DNA methylations were detected in Mycoplasma agalactiae strains using single molecule real-time (SMRT) and bisulphite sequencing, leading to the identification of methylated motifs associated with methyltransferases (MTases) and restriction modification (RM) systems. The study also revealed the dynamic epigenomic landscape of M. agalactiae, influenced by genetic events such as DNA shuffling, frameshift mutations, gene duplication, erosion, and horizontal gene transfer.
MICROBIAL GENOMICS
(2022)
Article
Environmental Sciences
Audrey Barranger, Christophe Klopp, Barbara Le Bot, Gaelle Saramito, Lise Dupont, Stephanie Llopis, Claudia Wiegand, Francoise Binet
Summary: Diffuse pollution of the environment by pesticides has led to a decline in non-target organisms such as earthworms. However, some earthworm species have developed tolerance to long-term exposure to pesticides in intensively cultivated fields. This study investigated the tolerance of Aporrectodea caliginosa earthworm populations from conventionally managed and organically managed fields by studying differentially expressed molecular pathways and physiological traits. The results showed distinct gene expression pathways related to metabolism in the population exposed to high levels of pesticides, providing insights into the long-term impact of chronic pesticide exposure on soil engineers.
ENVIRONMENTAL POLLUTION
(2023)
Article
Multidisciplinary Sciences
Camille Eche, Carole Iampietro, Clement Birbes, Andreea Dreau, Claire Kuchly, Arnaud Di Franco, Christophe Klopp, Thomas Faraut, Sarah Djebali, Adrien Castinel, Matthias Zytnicki, Erwan Denis, Mekki Boussaha, Cecile Grohs, Didier Boichard, Christine Gaspin, Denis Milan, Cecile Donnadieu
Summary: Inspired by the Genome in a Bottle project, we sequenced a Charolais heifer using various technologies and generated high quality reference genomes. The PacBio HiFi assembly reached a larger size than the ARS-UCD1.2 reference, and the consensus assembly had a high BUSCO score and identified numerous structural variants. This assembly contributes to the bovine pangenome and provides valuable resources for SNP calling, variant analysis, and de novo assembly.
Article
Microbiology
Ayman Sabra, Nicolas Biteau, Jean-William Dupuy, Christophe Klopp, Thierry Noel, Karine Dementhon
Summary: In this study, it was found that a dpp3 Delta mutants of Candida lusitaniae were impaired in cell separation, pseudohyphal growth, and mating. The defective phenotypes were not restored even after wild-type DPP3 locus reconstruction, indicating the presence of an additional mutation, which was identified as MED15. The inactivation of MED15 was confirmed to be responsible for the defective phenotypes and its role in regulating hyphal growth, cell separation, and mating pathways was revealed.
Article
Plant Sciences
Nico Nouwen, Marjorie Pervent, Franck El M'Chirgui, Frederique Tellier, Maelle Rios, Natasha Horta Araujo, Christophe Klopp, Frederic Gressent, Jean-Francois Arrighi
Summary: This study reveals the essential role of AeORM1 in nodulation, as well as lateral root development, in legume species. AeORM1 regulates sphingolipid homeostasis, which is crucial for rhizobial infection and nodule organogenesis.
Article
Cell Biology
Ricardo Ivan Martinez-Zamudio, Alketa Stefa, Jose Americo Nabuco Leva Ferreira Freitas, Themistoklis Vasilopoulos, Mark Simpson, Gregory Dore, Pierre-Francois Roux, Mark A. Galan, Ravi J. Chokshi, Oliver Bischof, Utz Herbig
Summary: This study uncovers the regulatory mechanisms underlying the escape from oncogene-induced senescence (OIS) and identifies senescence-associated chromatin scars (SACSs) as an epigenetic memory of OIS that can be detected during colorectal cancer progression. Increased expression of POU2F2 is associated with the escape from OIS and decreased patient survival.
Article
Dermatology
Takahiro Sato, Janet Nikolovski, Russell Gould, Imane Lboukili, Pierre-Francois Roux, Gabriel Al-Ghalith, Jeremy Orie, Richard Insel, Georgios N. Stamatas
Summary: This study aimed to predict atopic dermatitis (AD) in children across a broad age range using non-invasive methods. The results showed that children who developed AD had increased levels of skin immune markers before disease onset, along with skin lesions. These findings help in identifying susceptible children for early intervention.
SKIN RESEARCH AND TECHNOLOGY
(2023)
Meeting Abstract
Dermatology
Georgios N. Stamatas, Imane Lboukili, Pierre-Francois Roux, Thierry Oddos
JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY
(2022)
Article
Cell Biology
Ana Guerrero, Andrew J. Innes, Pierre-Francois Roux, Sonja C. Buisman, Johannes Jung, Laura Ortet, Victoria Moiseeva, Verena Wagner, Lucas Robinson, Albertina Ausema, Anna Potapova, Eusebio Perdiguero, Ellen Weersing, Marieke Aarts, Nadine Martin, Torsten Wuestefeld, Pura Munoz-Canoves, Gerald de Haan, Oliver Bischof, Jesus Gil
Summary: 3-Deazaadenosine (3DA) is a promising drug that enhances the efficiency of cellular therapies by restraining senescence.
Article
Plant Sciences
Johan Quilbe, Nico Nouwen, Marjorie Pervent, Remi Guyonnet, Julie Cullimore, Frederic Gressent, Natasha Horta Araujo, Djamel Gully, Christophe Klopp, Eric Giraud, Jean-Francois Arrighi
Summary: Characterization of Aeschynomene evenia mutants altered in nodulation provides insights into the mechanisms of Nod-independent symbiosis and contributes to the understanding of rhizobium-legume symbiosis.