Article
Plant Sciences
Wenchong Chen, Weiwu Yu, Ang Dong, Yanru Zeng, Huwei Yuan, Bingsong Zheng, Rongling Wu
Summary: This study utilizes advanced genotyping technologies to investigate the genetic structure of Torreya grandis, a species with high economic and ornamental values. A high-density linkage map is constructed, and the results suggest that the identified QTLs are relatively young and can be better utilized through clonal propagation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Behailu Mulugeta, Kassahun Tesfaye, Rodomiro Ortiz, Eva Johansson, Teklehaimanot Hailesilassie, Cecilia Hammenhag, Faris Hailu, Mulatu Geleta
Summary: The growing global demand for wheat for food is rising due to population growth and climate change. A genome-wide association study (GWAS) using 10,045 SNP markers was conducted to identify genomic regions associated with grain yield and related traits in Ethiopian durum wheat. The study revealed high heritability estimates and identified novel marker-trait associations (MTAs) that could potentially improve durum wheat production globally. The research also highlighted the importance of the Ethiopian durum wheat gene pool in this improvement.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Friedrich Teuscher
Summary: This study improves parts of the theory underlying the use of contingency tables by introducing the linkage disequilibrium parameter as a measure of two-way interactions applied to three-way tables. It also presents a simple formula to quantify Simpson's paradox. Additionally, the study addresses the determination of fixed cells in a contingency table and the limitations of methods simulating contingency tables with given pairwise associations.
Article
Agriculture, Dairy & Animal Science
Haoqiang Ye, Zhenqiang Xu, Semiu Folaniyi Bello, Qianghui Zhu, Shaofen Kong, Ming Zheng, Xiang Fang, Xinzheng Jia, Haiping Xu, Xiquan Zhang, Qinghua Nie
Summary: In this study, the performance of haplotype models for genomic prediction in a Chinese yellow-feathered chicken population was comprehensively evaluated. It was found that haplotype methods were beneficial for genomic prediction, and the accuracy could be further increased by incorporating genomic annotation information. Moreover, using LD information would potentially improve the performance of genomic prediction.
Article
Plant Sciences
Pawan Kumar, Somveer Nimbal, Rajvir Singh Sangwan, Neeraj Budhlakoti, Varsha Singh, Dwijesh Chandra Mishra, Sagar, Raju Ram Choudhary
Summary: This study identified novel markers associated with lint yield in 96 genotypes of Gossypium hirsutum, with 38 promising marker-trait associations found across multiple environments. Detailed annotation of significant markers was conducted, with 22 novel marker-trait associations discovered. These results will be valuable for marker-assisted cotton breeding programs.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Sajal R. Sthapit, Travis M. Ruff, Marcus A. Hooker, Deven R. See
Summary: The population structure and genetic diversity of wheat varieties in the United States were examined using a panel of historical and modern varieties. The results showed that population structure was related to growth habit and kernel characteristics, which also corresponded with geographic distribution. Market class classification accounted for the greatest amount of variation. There was no evidence of decreased genetic diversity after the release of the first semidwarf wheat variety in 1961, and some varieties even showed increases in genetic diversity. The findings suggest that overall genetic diversity in wheat varieties has not declined in the long term, despite occasional fluctuations.
Article
Genetics & Heredity
Robin J. Hofmeister, Diogo M. Ribeiro, Simone Rubinacci, Olivier Delaneau
Summary: SHAPEIT5, a new phasing method, accurately processes large sequencing datasets and improves imputation accuracy by generating reference panels of haplotypes. The method was applied to UK Biobank data, which resulted in the identification of 549 genes with compound heterozygous loss-of-function events. The use of UK Biobank as a reference panel, coupled with SHAPEIT5 phasing, further enhances genotype imputation accuracy.
Article
Plant Sciences
Muluken Enyew, Tileye Feyissa, Anders S. Carlsson, Kassahun Tesfaye, Cecilia Hammenhag, Amare Seyoum, Mulatu Geleta
Summary: This study conducted a genome-wide association study (GWAS) using sorghum genetic resources in Ethiopia to identify genomic regions and candidate genes associated with major agronomic traits in sorghum. The study revealed the genetic variation in sorghum traits and identified several novel and previously known quantitative trait loci. The major findings of this study were the significant association of major effect SNP loci with traits such as panicle width, days to flowering, grain yield, and panicle length.
FRONTIERS IN PLANT SCIENCE
(2022)
Editorial Material
Microbiology
Daniel Falush
Summary: The genome of Helicobacter pylori undergoes extensive mixing through homologous recombination, resulting in significant free recombination within populations. A recent study reveals that the UvrC gene in H. pylori has evolved an additional function, allowing very short DNA tracts to be imported into the genome during natural transformation.
Article
Biochemistry & Molecular Biology
Tahere Akbarpour, Navid Ghavi Hossein-Zadeh, Abdol Ahad Shadparvar
Summary: This study investigated the impact of different rates of marker genotyping error on the accuracy of genomic prediction using stochastic simulation. The results showed that marker genotyping error can decrease the accuracy of genomic evaluations and result in biased estimates of genomic breeding values. It is recommended to minimize marker genotyping errors to zero in genomic evaluation programs in order to obtain accurate results.
MOLECULAR GENETICS AND GENOMICS
(2021)
Review
Plant Sciences
Muhammad Yasir, Hafiza Hamrah Kanwal, Quaid Hussain, Muhammad Waheed Riaz, Muhammad Sajjad, Junkang Rong, Yurong Jiang
Summary: Over the past two decades, high-density SNP arrays and DNA sequencing technology have been widely used in crop research, particularly in cotton crops. Genome-wide association studies (GWAS) have provided an important tool for uncovering the relationship between crop phenotypes and underlying genetics, helping to advance crop breeding and improvement.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Jose Marcelo Soriano Viana, Antonio Augusto Franco Garcia
Summary: Additive variance is generally the most important component of genotypic variance. LD and inbreeding have a significant effect on the magnitude of the genetic variances and covariances. In general, the additive x additive variance is the most important component of epistatic variance.
Article
Ecology
Dengcheng Yang, Fan Li, Jing Wang, Ang Dong, Rongling Wu
Summary: LD in tetraploids is studied with a specific model for different loci disequilibrium, using EM algorithm for parameter estimation and experimental verification in populations. Analysis of switchgrass genomic data reveals the importance of LD in inferring evolutionary history.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
George Sandler, Stephen Wright, Aneil F. Agrawal
Summary: Most types of mutations exhibit positive linkage disequilibrium, especially if they are predicted to be less deleterious. Through simulations, it has been shown that this pattern arises easily in a model of admixture or distance-biased mating. Additionally, loss of function mutations exhibit particularly positive LD across short distances.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Cong Liu, Casey N. Ta, Jim M. Havrilla, Jordan G. Nestor, Matthew E. Spotnitz, Andrew S. Geneslaw, Yu Hu, Wendy K. Chung, Kai Wang, Chunhua Weng
Summary: This study presents an open annotation resource, derived from real-world data, for annotating phenotypic traits related to rare genetic diseases. By leveraging ontology mapping and natural language processing methods, this resource can automatically extract concepts for rare diseases and their phenotypic traits. Compared to manual annotation, it can identify more disease-phenotype associations and can be shared across different institutions.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
