Article
Biology
Mahdi Moradi Marjaneh, Edwin P. Kirk, Ralph Patrick, Dimuthu Alankarage, David T. Humphreys, Gonzalo Del Monte-Nieto, Paola Cornejo-Paramo, Vaibhao Janbandhu, Tram B. Doan, Sally L. Dunwoodie, Emily S. Wong, Chris Moran, Ian C. A. Martin, Peter C. Thomson, Richard P. Harvey
Summary: Unlike single-gene mutations leading to Mendelian conditions, common human diseases are likely to be emergent phenomena arising from multilayer, multiscale, and highly interconnected interactions. This study provides the first high-resolution picture of genetic complexity and network liability underlying common congenital heart disease, with relevance to human ASD and PFO.
Article
Agronomy
Shilei Liu, Wenli Zou, Xiang Lu, Jianmin Bian, Haohua He, Jingguang Chen, Guoyou Ye
Summary: The study identified QTLs associated with Zn2+ concentrations in both shoots and grains of rice, with some QTLs affecting Zn2+ concentration in both tissues. Candidate gene analysis suggested that LOC_Os02g06010 may play a crucial role in zinc accumulation in indica rice.
Article
Biochemistry & Molecular Biology
Jae-Ryoung Park, Yoon-Hee Jang, Eun-Gyeong Kim, Sang-Sun Hur, Kyung-Min Kim, Deyong Ren
Summary: In this study, QTLs and candidate genes related to rice plant height regulation were identified, which can provide information and foundation for marker-assisted selection and breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Yuefeng Ruan, Bianyun Yu, Ron E. Knox, Wentao Zhang, Asheesh K. Singh, Richard Cuthbert, Pierre Fobert, Ron DePauw, Samia Berraies, Andrew Sharpe, Bin Xiao Fu, Jatinder Sangha
Summary: In the genetic study of durum wheat in Canada, QTL mapping was conducted to identify loci associated with grain protein concentration (GPC). Several major and minor QTL were discovered on different chromosomes, with some being consistently detected across multiple years and showing potential for improving both GPC and grain yield. The results of traditional and conditional mapping provide valuable insights for the development of high GPC and high yielding durum cultivars.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Jianing You, Hang Liu, Surong Wang, Wei Luo, Lulu Gou, Huaping Tang, Yang Mu, Mei Deng, Qiantao Jiang, Guoyue Chen, Pengfei Qi, Yuanying Peng, Liwei Tang, Ahsan Habib, Yuming Wei, Youliang Zheng, Xiujin Lan, Jian Ma
Summary: The study identified QTL for spike density in wheat, providing a genetic basis for optimizing spike structure. Major and stable QTL were discovered, along with analyses of QTL x environment effects and epistatic interactions for spike density. Pyramiding analysis revealed additive effects between specific QTL, and correlations with agronomic traits such as spike length and kernel length were observed. Several genes related to spike development within major or stable QTL intervals were predicted. Overall, the research broadened the genetic basis of spike density and identified QTL with potential applications in modern wheat breeding.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
C. Pawan K. Patro, Darryl Nousome, Rose K. Lai
Summary: The study revealed the complex regulation of the transcriptome by glioma risk alleles, with potential for both eQTL and sQTL to jointly influence gliomagenesis in risk loci. Many loci's QTLs involved multiple target genes, some of which were specific to alternative splicing.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Jing Wu, Lili Mao, Jincai Tao, Xiuxiu Wang, Haijun Zhang, Ming Xin, Yongqi Shang, Yanan Zhang, Guihua Zhang, Zhongting Zhao, Yiming Wang, Mingshuo Cui, Liming Wei, Xianliang Song, Xuezhen Sun
Summary: This study used a genetic map and phenotype data to analyze the QTL of plant height in cotton, identifying several stable and unconditional QTL and revealing the dynamic expression characteristics of genes related to plant height development. Additionally, through functional annotation and transcriptome analysis, candidate genes potentially involved in plant height development were predicted.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Francesca Taranto, Salvatore Esposito, Pasquale De Vita
Summary: In recent years, the genetic basis of yield and yield components in durum wheat has been studied extensively using linkage mapping and genome-wide association studies. The reductionist approach of dissecting yield into individual components appears insufficient for significant yield increases due to limited resources, land loss, and climate change. Polyploidy in durum wheat makes it challenging to identify genes and chromosomal regions controlling grain yield. Next-generation sequencing, improved wheat genome assembly, high-throughput genotyping platforms, and genome editing technology offer great potential for revolutionizing plant breeding. Genomic selection can model optimal allelic combinations to maximize phenotypic potential under specific environments.
Article
Biochemical Research Methods
Jing Chen, Lindsey J. Leach, Zewei Luo
Summary: Mapping quantitative trait loci (QTL) in autotetraploid species is a timely and challenging task. Two papers by Wu and his colleagues proposed statistical methods for QTL mapping in these species, but have been criticized for fundamental conceptual errors from statistical and genetic perspectives.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Agronomy
Ankit Malik, Aruna Kumar, Ranjith Kumar Ellur, Subbaiyan Gopala Krishnan, Kunnummal Kurungara Vinod, Deepshikha Dixit, Mariappan Nagarajan, Prolay Kumar Bhowmick, Haritha Bollinedi, Nagendra Kumar Singh, Ashok Kumar Singh
Summary: A population of 352 RILs was generated through the single seed descent method, and 12 QTLs governing yield and yield-related traits were mapped. Among them, a key QTL controlling plant height and panicle length was identified on chromosome 1. These findings contribute to the development of Basmati rice varieties with higher yield through marker-assisted selection.
Article
Biochemical Research Methods
Nora Scherer, Peggy Sekula, Peter Pfaffelhuber, Pascal Schlosser
Summary: A new R package has been developed to determine study-specific critical values for quantitative trait loci. The package allows for user-friendly simulations and integration of an interpolation functionality for extensive multiple testing scenarios.
Article
Agronomy
Miguel Angel Raffo, Pernille Sarup, Xiangyu Guo, Huiming Liu, Jeppe Reitan Andersen, Jihad Orabi, Ahmed Jahoor, Just Jensen
Summary: The inclusion of additive-by-additive epistasis in the genomic prediction model improves the predictive ability for wheat grain yield, but does not achieve orthogonal partitioning of genetic variances.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Agronomy
Siti Hazirah Zolkafli, Ngoot-Chin Ting, Nik Shazana Nik Mohd Sanusi, Maizura Ithnin, Sean Mayes, Festo Massawe, Ravigadevi Sambanthamurthi, Ismanizan Ismail, Mohd Isa Zainol Abidin, Siti Habsah Roowi, Yang Ping Lee, Nurul Fatiha Farhana Hanafi, Rajinder Singh
Summary: By analyzing QTLs associated with YCs in oil palm, this study revealed potential genetic factors influencing yield. A comparison of QTLs from different genetic backgrounds identified common chromosomes that may play a role in regulating YCs. The use of genome data also facilitated the discovery of candidate genes related to oil palm yield.
Article
Plant Sciences
Tao Yao, Jin Zhang, Timothy B. Yates, Him K. Shrestha, Nancy L. Engle, Raphael Ployet, Cai John, Kai Feng, William Patrick Bewg, Margot S. S. Chen, Haiwei Lu, Scott A. Harding, Zhenzhen Qiao, Sara S. Jawdy, Mengjun Shu, Wenya Yuan, Khadijeh Mozaffari, Anne E. Harman-Ware, Renee M. Happs, Larry M. York, Brad M. Binder, Yuko Yoshinaga, Christopher Daum, Timothy J. Tschaplinski, Paul E. Abraham, Chung-Jui Tsai, Kerrie Barry, Anna Lipzen, Jeremy Schmutz, Gerald A. Tuskan, Jin-Gui Chen, Wellington Muchero
Summary: This study identified PtrXB38 as an expression quantitative trait loci (eQTL) hotspot, with predicted target genes involved in plant hormone responses and root development. Overexpression of PtrXB38 led to increased callusing and the formation of stem-born and base-born adventitious roots in Populus. Omics studies revealed the involvement of genes and proteins controlling auxin transport and signaling in PtrXB38-mediated root formation. Protein-protein interaction assays indicated that PtrXB38 interacts with components of the endocytosis pathway.
Article
Plant Sciences
Guozhong Zhu, Sen Hou, Xiaohui Song, Xing Wang, Wei Wang, Quanjia Chen, Wangzhen Guo
Summary: This study identified numerous QTLs and candidate genes associated with yield-related traits in cotton through phenotype data analysis and genetic analysis under multiple field environments. LP and SI were identified as more suitable traits for genetic improvement, while GN and BW had lower heritability estimates. Additionally, NET genes related to fiber development stages and stable QTL regions were discovered, providing insights into the regulatory mechanisms of yield components in cotton.
Article
Genetics & Heredity
Muhammed Walugembe, Francesca Bertolini, Chandraratne Mahinda B. Dematawewa, Matheus P. Reis, Ahmed R. Elbeltagy, Carl J. Schmidt, Susan J. Lamont, Max F. Rothschild
FRONTIERS IN GENETICS
(2019)
Article
Genetics & Heredity
Ahmed R. Elbeltagy, Francesca Bertolini, Damarius S. Fleming, Angelica Van Goor, Chris M. Ashwell, Carl J. Schmidt, Donald R. Kugonza, Susan J. Lamont, Max F. Rothschild
FRONTIERS IN GENETICS
(2019)
Article
Biotechnology & Applied Microbiology
Allen H. Hubbard, Xiaoke Zhang, Sara Jastrebski, Abhyudai Singh, Carl Schmidt
Article
Agriculture, Dairy & Animal Science
Nathaniel W. Barrett, Kaylee Rowland, Carl J. Schmidt, Susan J. Lamont, Max F. Rothschild, Chris M. Ashwell, Michael E. Persia
Article
Physiology
Chelsea A. Phillips, Benjamin J. Reading, Matthew Livingston, Kimberly Livingston, Chris M. Ashwell
FRONTIERS IN PHYSIOLOGY
(2020)
Article
Multidisciplinary Sciences
Allen Hubbard, Matthew Bomhoff, Carl J. Schmidt
Article
Zoology
Karen G. Burnett, David S. Durica, Donald L. Mykles, Jonathon H. Stillman, Carl Schmidt
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Heidi A. Van Every, Carl J. Schmidt
Summary: This study investigates the metabolic reprogramming in the liver between Day 4 and Day 20 post-hatch, revealing differences in metabolic pathways and important metabolites during different stages of metabolism. At Day 4, metabolic flexibility allows for rapid liver growth efficiency under oxygen-limiting conditions, while at Day 20, the liver's metabolism shifts to process a carbohydrate-rich diet that supports the rapid overall growth of modern broilers.
Article
Genetics & Heredity
Janet E. Fulton, Wiola Drobik-Czwarno, Ashlee R. Lund, Carl J. Schmidt, Robert L. L. Taylor Jr
Summary: The chicken D blood system is one of the alloantigen systems found on chicken red blood cells. The candidate gene for this system, CD99, was identified through genome sequencing and DNA analysis. The CD99 gene is involved in various cellular processes and plays a role in peripheral immune responses.
Article
Biochemistry & Molecular Biology
Elizabeth M. M. Pritchett, Angelica Van Goor, Blair K. K. Schneider, Meaghan Young, Susan J. J. Lamont, Carl J. J. Schmidt
Summary: This study investigated the response of the pituitary gland in chickens to acute heat stress through transcriptome analysis. The results showed that the pituitaries of heat-stressed birds exhibited altered gene expression in response to hyperthermia, affecting chaperones, cell cycle regulators, cholesterol synthesis, transcription factors, as well as peptide hormones secretion.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Agriculture, Dairy & Animal Science
Shelly J. Nolin, Robert L. Taylor Jr, Frank W. Edens, Paul B. Siegel, Christopher M. Ashwell
Summary: Since the 1970s, two lines of White Leghorn chickens, referred to as HAS and LAS, have been selectively bred based on their antibody response to injection with sheep red blood cells (SRBC) for 5 days after injection. By analyzing the gene expression in the jejunum of these chickens, the study found differences in ATP production and cellular processes between the two lines and after SRBC injection. The gene expression pattern suggests that HAS chickens maintain a primed system with higher ATP production, while LAS chickens require increased ATP production when exposed to the antigen. Overall, this study provides insights into the energetic resource needs and allocations in the jejunum due to genetic selection and antigen exposure, which may explain the observed phenotypic differences in antibody response.
Article
Multidisciplinary Sciences
Carl. J. J. Schmidt, Dong Kyun Kim, G. Ken Pendarvis, Behnam Abasht, Fiona. M. M. McCarthy
Summary: Chicken domestication began for divination, cockfighting, and food purposes around 3,500 years ago. Later, industrial scale chicken production selected larger birds with increased egg production. In the mid-20(th) century, intensive selection for growth traits in the broiler industry led to specific cellular and biochemical changes in the modern broiler line compared to the legacy line.
Article
Agriculture, Dairy & Animal Science
Yanghua He, Robert L. Taylor Jr, Hao Bai, Christopher M. Ashwell, Keji Zhao, Yaokun Li, Guirong Sun, Huanmin Zhang, Jiuzhou Song
Summary: This study analyzed genome-wide DNA methylation patterns in chickens and found a strong association between DNA methylation and Marek's disease incidence. It also revealed that DNA methylation plays a vital role in MD tumorigenesis and other immune responses, with specific methylated regions being important modulators of general immunity.
Article
Agriculture, Dairy & Animal Science
McCaide T. Wooten, Zachary S. Lowman, Christopher M. Ashwell
Summary: Previous studies have shown a link between maternal condition or resource availability and offspring sex ratio in avian species. This study found that the sex ratio of avian offspring was not influenced by parental diet, but a sudden change in diet may have an effect. Further research is needed to assess the efficacy of diet alteration in sex allocation manipulation.
POULTRY SCIENCE JOURNAL
(2021)
Article
Agriculture, Dairy & Animal Science
Kaylee Rowland, Chris M. Ashwell, Michael E. Persia, Max F. Rothschild, Carl Schmidt, Susan J. Lamont
GENETICS SELECTION EVOLUTION
(2019)