Article
Biology
Jean-Marc Aury, Stefan Engelen, Benjamin Istace, Cecile Monat, Pauline Lasserre-Zuber, Caroline Belser, Corinne Cruaud, Helene Rimbert, Philippe Leroy, Sandrine Arribat, Isabelle Dufau, Arnaud Bellec, David Grimbichler, Nathan Papon, Etienne Paux, Marion Ranoux, Adriana Alberti, Patrick Wincker, Frederic Choulet
Summary: Here, we present an optimized procedure using long reads produced on the Oxford Nanopore Technology PromethION device to assemble the genome of the French bread wheat cultivar Renan. This study provides the most contiguous chromosome-scale assembly of a bread wheat genome to date. The assembly, coupled with RNA-sequencing based annotation, will be valuable for the crop community and facilitate the rapid selection of agronomically important traits. We also propose a framework to generate high-quality assemblies of complex genomes using ONT.
Article
Biotechnology & Applied Microbiology
Zsolt Banfai, Erzsebet Koevesdi, Katalin Suemegi, Gergely Bueki, Andras Szabo, Lili Magyari, Valerian adam, Ferenc Palos, Attila Miseta, Miklos Kasler, Bela Melegh
Summary: This study provides the first analysis of the genetic composition of the Danube Swabians based on genome-wide autosomal data. The results suggest that they have significant German and other West European ancestry, with a prominent Hungarian ancestry.
Article
Agriculture, Dairy & Animal Science
Abbas Hajihosseinlo, Ardeshir Nejati-Javaremi, Seyed Reza Miraei-Ashtiani
Summary: This research measured the extent of linkage disequilibrium, effective population size, haplotype block structure, and runs of homozygosity in several cattle populations using SNP genotypes. The results showed a decrease in genetic diversity with increasing distance between SNP pairs. The Iranian Holstein population had the lowest level of genomic inbreeding, while the French Holstein population had the highest. The number of runs of homozygosity decreased with increasing distance due to the increased recombination rate. This is concerning as it leads to a reduction in the effective population size.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Gizem Levent, Ashlynn Schlochtermeier, Samuel E. Ives, Ken N. Norman, Sara D. Lawhon, Guy H. Loneragan, Robin C. Anderson, Javier Vinasco, Henk C. den Bakker, H. Morgan Scott
Summary: Our study reveals that clonal expansion of Salmonella strains in cattle is mainly influenced by the randomization of block and pen, as well as the origin/source of the cattle, regardless of sampling time and sample type (i.e., feces, lymph node, or hide). Further research is needed concerning the role of the feedlot pen environment prior to cattle placement to better understand carryover contributions of existing strains of Salmonella and their bacteriophages.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Lining Wang, Baosheng Liao, Lu Gong, Shuiming Xiao, Zhihai Huang
Summary: This study investigated the genetic diversity, heat adaptation mechanisms, and allele-specific expression of HSP20 genes in Coriolopsis trogii, providing insights into the molecular mechanisms of high-temperature adaptation in this thermotolerant fungus. The unique structural and expression profiles of HSP20 genes revealed by the haplotype-resolved genomes offer a more thorough understanding of the genetic background of C. trogii, with implications for future strain selection and breeding.
MICROBIOLOGY SPECTRUM
(2021)
Article
Agriculture, Dairy & Animal Science
P. A. S. Fonseca, F. S. Schenkel, A. Canovas
Summary: This study investigated the genetic basis of stillbirth in dairy cattle and identified 31 potential functional candidate genes associated with reproductive performance.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Multidisciplinary Sciences
Fan Feng, Yuan Yao, Xue Qing David Wang, Xiaotian Zhang, Jie Liu
Summary: While large-scale 3D genome architecture is well studied, the authors developed a deep learning model CAESAR to map 1D epigenomic profiles to fine-scale 3D chromatin structures, accurately predicting structures that were missed by Hi-C datasets. They successfully imputed high-resolution 3D chromatin contact maps for 91 human tissues and cell lines, demonstrating the potential of CAESAR in coupling transcriptional regulation with 3D chromatin organization at high resolution.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Yanlei Yue, Jiawen Li, Xuegang Sun, Zhen Li, Bingjun Jiang
Summary: By analyzing the polymorphisms of chloroplasts and mitochondria in 2580 soybean accessions, it was found that the chloroplast genome is more variable than the mitochondrial genome. There were 44 chloroplast haplotypes and 30 mitochondrial haplotypes. The distribution of these haplotypes was extremely uneven, with the top two haplotypes accounting for a large proportion of cultivated soybean accessions. Wild soybeans exhibited more diversity in organelle genomes, but only a small percentage of cultivated soybeans shared cytoplasm with wild soybeans. Evaluating the impact of cytoplasm on soybean performance is important for breeding.
Article
Biochemistry & Molecular Biology
Daria Shipilina, Arka Pal, Sean Stankowski, Yingguang Frank Chan, Nicholas H. H. Barton
Summary: The term haplotype block is commonly used in haplotype-based inference methods. The structure of the Ancestral Recombination Graph (ARG) should be used to define the term. Simulated examples demonstrate the relationship between haplotype blocks and ancestral structure, showing the stochasticity of the processes that generate them. Novel methods for inferring haplotype structure, based on the full ARG or a sequence of trees, are highlighted and their application to define haplotype blocks using empirical data is illustrated. Understanding and applying the concept of haplotype blocks will be essential for exploiting long and linked-read sequencing technologies.
Article
Biotechnology & Applied Microbiology
Claire Oget-Ebrad, Naveen Kumar Kadri, Gabriel Costa Monteiro Moreira, Latifa Karim, Wouter Coppieters, Michel Georges, Tom Druet
Summary: This study evaluates several population-based haplotype phasing methods in a Holstein cattle pedigree using whole-genome sequence data. The results show that ShapeIT4.1 and Beagle5.2 are the most accurate methods, particularly for phasing long segments and in the first scenario.
Article
Genetics & Heredity
Andre C. Araujo, Paulo L. S. Carneiro, Amanda B. Alvarenga, Hinayah R. Oliveira, Stephen P. Miller, Kelli Retallick, Luiz F. Brito
Summary: Behavior is a complex trait, and understanding its genetic architecture is crucial for effective breeding strategies. This study utilized haplotypes for genome-wide association studies and found that yearling temperament in Angus cattle is highly polygenic, with genes and QTL distributed across the entire genome. When conducting association studies with LD-based haplotypes, inclusion of non-LD-clustered SNPs and different LD thresholds can increase the likelihood of identifying relevant genomic regions affecting the trait.
Article
Biochemistry & Molecular Biology
Zhengyu Luo, Ran Zhang, Tengfei Hu, Yuting Zhu, Yueming Wu, Wenfei Li, Zhi Zhang, Xuebiao Yao, Haiyi Liang, Xiaoyuan Song
Summary: The study introduces a new method called NicE-C, which allows for the detection of open chromatin interactions, particularly enhancer-promoter interactions, at a high resolution, with stability and cost-effectiveness. Using this method, the researchers revealed characteristics of dynamic enhancer-promoter interactions in TNF stimulation and mouse kidney aging models.
Article
Biochemistry & Molecular Biology
Zhigui Bao, Canhui Li, Guangcun Li, Pei Wang, Zhen Peng, Lin Cheng, Hongbo Li, Zhiyang Zhang, Yuying Li, Wu Huang, Mingwang Ye, Daofeng Dong, Zhukuan Cheng, Peter VanderZaag, Evert Jacobsen, Christian W. B. Bachem, Suomeng Dong, Chunzhi Zhang, Sanwen Huang, Qian Zhou
Summary: In this study, a chromosome-scale, haplotype-resolved genome assembly of a cultivated potato was achieved using state-of-the-art sequencing technologies and polyploid graph binning. The study provides insights into the genomic architecture of autopolyploids and will guide their breeding.
Article
Plant Sciences
Anchittha Satjarak, Linda E. Graham, Marie T. Trest, Patricia Arancibia-Avila
Summary: In this study, the complete chloroplast genome of the giant species Equisetum xylochaetum was assembled and compared with two other Equisetum species. The analysis revealed conserved traits in chloroplast genome structure and protein-coding regions among Equisetum species. Phylogenetic analysis confirmed the monophyly of Equisetum and provided insights into the relationships among different species. Single-gene phylogenetic estimation and haplotype analysis also shed light on the genetic diversity and mutation rate in Equisetum species.
Article
Evolutionary Biology
Yujing Yan, Charles C. Davis, Dimitar Dimitrov, Zhiheng Wang, Carsten Rahbek, Michael Krabbe Borregaard
Summary: The tea family, Theaceae, exhibits a unique distribution pattern with species mainly found in East Asia and some in the Americas. By integrating fossil evidence and phylogenetic analysis, the study revealed the historical biogeography of Theaceae species and highlighted the significance of combining fossil and molecular data for improving the reliability of biogeographic inferences.
SYSTEMATIC BIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
M. Neupane, J. L. Hutchison, C. P. Van Tassell, P. M. VanRaden
Summary: The study found a genetic component for heifer livability differences in breeds and sire lines. Genomic evaluation for this trait can increase profitability and improve animal health and welfare. Results showed a favorable genetic trend for HLIV, suggesting that it should be emphasized in the Lifetime Net Merit index.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Veterinary Sciences
Jennifer N. Kiser, Zeping Wang, Ricardo Zanella, Erik Scraggs, Mahesh Neupane, Bonnie Cantrell, Curtis P. Van Tassell, Stephen N. White, Jeremy F. Taylor, Holly L. Neibergs
Summary: This study identified putative causal mutations for disease susceptibility in Holstein and Jersey cattle related to MAP infection, suggesting that two specific SNPs may alter transcription and consequently susceptibility to MAP infection.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Genetics & Heredity
Robert N. Vaughn, Kelli J. Kochan, Aline K. Torres, Min Du, David G. Riley, Clare A. Gill, Andy D. Herring, James O. Sanders, Penny K. Riggs
Summary: The study revealed a relationship between the expression of the ACTN3 gene in skeletal muscle and feed efficiency in crossbred steers. The inefficient group showed higher expression of ACTN3 and a maternal effect was observed in ACTN3 inheritance. Additionally, a significant breed effect was found in other genes related to feed efficiency, suggesting a possible link between muscle fiber type ratio and feed efficiency.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Liu Yang, Yahui Gao, Mingxun Li, Ki-Eun Park, Shuli Liu, Xiaolong Kang, Mei Liu, Adam Oswalt, Lingzhao Fang, Bhanu P. Telugu, Charles G. Sattler, Cong-Jun Li, John B. Cole, Eyal Seroussi, Lingyang Xu, Lv Yang, Yang Zhou, Li Li, Hongping Zhang, Benjamin D. Rosen, Curtis P. Van Tassell, Li Ma, George E. Liu
Summary: This study conducted the first large-scale whole-genome sequencing of single sperm in livestock, revealing the distribution patterns of meiotic recombination in cattle sperm genomes. The findings provide valuable information for future studies on meiotic recombination, genome instability, and male infertility.
Article
Biotechnology & Applied Microbiology
Liu Yang, Yahui Gao, Adam Oswalt, Lingzhao Fang, Clarissa Boschiero, Mahesh Neupane, Charles G. Sattler, Cong-Jun Li, Eyal Seroussi, Lingyang Xu, Lv Yang, Li Li, Hongping Zhang, Benjamin D. Rosen, Curtis P. Van Tassell, Yang Zhou, Li Ma, George E. Liu
Summary: This study used single-cell sequencing to predict CNV events in individual sperms of two Holstein bulls and compared the results with bulk-cell sequencing. The results showed that although only some of the single sperm CNVs were validated by trio CNVs, they still had significant associations with chromosomal distribution patterns and segmental duplications.
Article
Genetics & Heredity
Gabrielle M. Becker, Joan M. Burke, Ronald M. Lewis, James E. Miller, James L. M. Morgan, Benjamin D. Rosen, Curtis P. Van Tassell, David R. Notter, Brenda M. Murdoch
Summary: Gastrointestinal nematodes pose a severe threat to sheep production. Drug resistance and environmental concerns have led to the exploration of alternative control methods. This study identified genetic variants associated with resistance to nematode infection in Katahdin sheep, providing insights into the genetic mechanisms of host response to nematodes.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Shuli Liu, Yahui Gao, Oriol Canela-Xandri, Sheng Wang, Ying Yu, Wentao Cai, Bingjie Li, Ruidong Xiang, Amanda J. Chamberlain, Erola Pairo-Castineira, Kenton D'Mellow, Konrad Rawlik, Charley Xia, Yuelin Yao, Pau Navarro, Dominique Rocha, Xiujin Li, Ze Yan, Congjun Li, Benjamin D. Rosen, Curtis P. Van Tassell, Paul M. Vanraden, Shengli Zhang, Li Ma, John B. Cole, George E. Liu, Albert Tenesa, Lingzhao Fang
Summary: Characterizing genetic regulatory variants that affect livestock gene expression is crucial for understanding the molecular mechanisms underlying economically important traits and improving genetic gain through artificial selection. In this study, we construct a Cattle Genotype-Tissue Expression atlas based on publicly available RNA-sequencing samples to provide valuable resources for the research community. We analyze the transcriptomic landscape of over 100 tissues/cell types, identify genetic associations with gene expression and alternative splicing in 23 distinct tissues, and investigate the functional implications of these regulatory effects using multiomics data. Additionally, we link gene expression in different tissues to 43 economically important traits in cattle, decoding the molecular regulatory mechanisms underlying these agronomic traits. The integration with genome-wide association studies also allows us to identify candidate genes and variants associated with these economically important traits.
Article
Materials Science, Multidisciplinary
Carlos Tamayo-Bello, Angel Sauceda-Carvajal, Rafael Villa-Angulo, Carlos Villa-Angulo
Summary: To improve the stability of perovskite solar cells, this study proposed the concept of using cadmium sulfide photoluminescent filters to downconvert UV light.
JOURNAL OF PHOTONICS FOR ENERGY
(2022)
Article
Genetics & Heredity
Xiao-Lin Wu, George R. Wiggans, H. Duane Norman, Asha M. Miles, Curtis P. Van Tassell, Ransom L. Baldwin, Javier Burchard, Joao Durr
Summary: This study evaluated the performance of various statistical methods for estimating daily milk yields (DMY) in Holstein and Jersey cows and found that the MCF and linear regression models had smaller biases and higher accuracies for estimating DMY.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Yang Zhou, Lv Yang, Xiaotao Han, Jiazheng Han, Yan Hu, Fan Li, Han Xia, Lingwei Peng, Clarissa Boschiero, Benjamin D. Rosen, Derek M. Bickhart, Shujun Zhang, Aizhen Guo, Curtis P. Van Tassell, Timothy P. L. Smith, Liguo Yang, George E. Liu
Summary: A cattle pangenome representation was created based on the genome sequences of 898 cattle representing 57 breeds. The pangenome identified novel sequence and structural variants, providing valuable insights into the diversity and evolutionary history of cattle.
Article
Multidisciplinary Sciences
M. Jennifer Woodward-Greene, Jason M. Kinser, Tad S. Sonstegard, Johann Soelkner, Iosif I. Vaisman, Curtis P. Van Tassell
Summary: Computer vision is a tool that can provide livestock producers with digital body measurements important for animal health and production. The scarcity of labeled training data sets poses a challenge in building these tools. To address this, the PreciseEdge image segmentation algorithm is introduced, which employs a standard image collection protocol and a semi-automated image labeling method for efficient and accurate body measurement extraction.
Article
Agriculture, Dairy & Animal Science
F. L. Guinan, G. R. Wiggans, H. D. Norman, J. W. Durr, J. B. Cole, C. P. Van Tassell, I. Misztal, D. Lourenco
Summary: Genomic selection accelerates genetic changes in populations by increasing accuracy and decreasing generation interval. The genetic gain and inbreeding levels of US dairy cattle breeds since the implementation of genomic evaluations in 2009 were examined. The Holstein and Jersey breeds have seen the most significant increase in genetic gain since then.
JOURNAL OF DAIRY SCIENCE
(2023)
Review
Agriculture, Dairy & Animal Science
Hafedh Ben Zaabza, Curtis P. Van Tassell, Jeremie Vandenplas, Paul VanRaden, Zengting Liu, Herwin Eding, Stephanie McKay, Katrine Haugaard, Martin H. Lidauer, Esa A. Mantysaari, Ismo Stranden
Summary: This paper provides an overview of different methods and computational approaches for calculating reliability, from the animal model era to the single-step genomic model era. It also discusses the challenges faced in reliability computation and presents efficient and accurate algorithms developed recently for large-scale genomic evaluations.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Badjibassa Akounda, Dominique Ouedraogo, Albert Soudre, Pamela A. Burger, Benjamin D. Rosen, Curtis P. Van Tassell, Johann Soelkner
Summary: This study explores the morphological differences between different goat populations in Burkina Faso using morphometric traits. The results show that there is no strict distinction between the two populations, indicating a close genetic relationship. Four groups were identified based on body size, representing the main breeds and their crosses. These different goat morphotypes are the result of farmers breeding practices. The study highlights the need for sustainable genetic improvement approaches for the use of these adapted local goat genetic resources.
Article
Multidisciplinary Sciences
Taylorlyn Stephan, Shawn M. Burgess, Hans Cheng, Charles G. Danko, Clare A. Gill, Erich D. Jarvis, Klaus-Peter Koepfli, James E. Koltes, Eric Lyons, Pamela Ronald, Oliver A. Ryder, Lynn M. Schriml, Pamela Soltis, Sue VandeWoude, Huaijun Zhou, Elaine A. Ostrander, Elinor K. Karlsson
Summary: Genomics research has primarily focused on humans and a limited number of species, resulting in a lack of understanding about the genomes of the majority of species. However, a broad view that encompasses the vast diversity of life is necessary to comprehend how genomes function and how genetic variation shapes phenotypes. Integrating comparative genomics with other fields is crucial for scientific discovery and the protection of ourselves and our world.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
