Population structure and genetic diversity of Toona sinensis revealed by whole-genome resequencing.

Authors: Wang, Lei¹ (AUTHOR), Lu, Chang² (AUTHOR), Bao, Zhi-Gang¹ (AUTHOR), Li, Meng¹ (AUTHOR), Wu, Fusheng¹ (AUTHOR), Lu, Yi-Zeng¹ (AUTHOR), Tong, Bo-Qiang¹ (AUTHOR), Yu, Mei² (AUTHOR) yumeihaidu@126.com, Zhao, Yong-Jun¹ (AUTHOR) 13305317857@163.com

Source: BMC Genomic Data. 1/3/2025, Vol. 26 Issue 1, p1-4. 4p.

Subject Terms: *GENETIC variation, *LINKAGE disequilibrium, *LIFE sciences, *PRINCIPAL components analysis, *WOODY plants

Polymorphisms of KCNJ6 Gene and Their Correlation with Immune Indicators in Yaks (Bos grunniens).

Authors: Ren, Wenwen^1,2,3 (AUTHOR) maxiaoming@caas.cn, Ma, Xiaoming^1,2 (AUTHOR) wuxiaoyun@caas.cn, Yu, Daoning^1,2 (AUTHOR) layongfu@caas.cn, Wu, Xiaoyun^1,2 (AUTHOR) guoxian@caas.cn, La, Yongfu^1,2 (AUTHOR) chumin@caas.cn, Guo, Xian^1,2 (AUTHOR) yanping@caas.cn, Chu, Min^1,2 (AUTHOR), Yan, Ping^1,2 (AUTHOR), Lan, Xianyong³ (AUTHOR) lanxianyong79@nwsuaf.edu.cn, Liang, Chunnian^1,2 (AUTHOR) lanxianyong79@nwsuaf.edu.cn

Source: Biomolecules (2218-273X). Dec2024, Vol. 14 Issue 12, p1576. 10p.

Subject Terms: *YAK, *LINKAGE disequilibrium, *GENETIC polymorphisms, *GERMPLASM, *BIOMARKERS, *SINGLE nucleotide polymorphisms

How to handle high subgenome sequence similarity in allopolyploid Fragaria x ananassa: linkage disequilibrium based variant filtering.

Authors: Koorevaar, Tim^1,2 (AUTHOR) tim.koorevaar@wur.nl, Willemsen, Johan H.¹ (AUTHOR), Hildebrand, Dominic¹ (AUTHOR), Visser, Richard G.F.² (AUTHOR), Arens, Paul² (AUTHOR), Maliepaard, Chris² (AUTHOR)

Source: BMC Genomics. 11/28/2024, Vol. 25 Issue 1, p1-15. 15p.

Subject Terms: *WHOLE genome sequencing, *LINKAGE disequilibrium, *STRAWBERRIES, *GENE mapping, *ALLELES

CYP3A4*1B but Not CYP3A5*3 as Determinant of Long-Term Tacrolimus Dose Requirements in Spanish Solid Organ Transplant Patients.

Authors: Concha, Julia¹ (AUTHOR) jconcha@usj.es, Sangüesa, Estela¹ (AUTHOR), Ribate, María Pilar¹ (AUTHOR) mpribate@usj.es, García, Cristina B.¹ (AUTHOR)

Source: International Journal of Molecular Sciences. Oct2024, Vol. 25 Issue 20, p11327. 12p.

Subject Terms: *SINGLE nucleotide polymorphisms, *LINKAGE disequilibrium, *CYTOCHROME P-450 CYP3A, *TACROLIMUS, *IMMUNOSUPPRESSIVE agents

Improving polygenic prediction from summary data by learning patterns of effect sharing across multiple phenotypes.

Authors: Kunkel, Deborah¹, dekunke@clemson.edu, Sørensen, Peter², Shankar, Vijay³, Morgante, Fabio^3,4, fabiom@clemson.edu

Source: PLoS Genetics; 1/7/2025, Vol. 1 Issue 1, p1-17, 17p

Effect of Chromosomal Localization of NGS-Based Markers on Their Applicability for Analyzing Genetic Variation and Population Structure of Hexaploid Triticale.

Authors: Leśniowska-Nowak, Justyna¹ (AUTHOR) justyna.lesniowska@up.lublin.pl, Bednarek, Piotr T.² (AUTHOR) p.bednarek@ihar.edu.pl, Czapla, Karolina³ (AUTHOR) karolina.czapla@umlub.pl, Nowak, Michał¹ (AUTHOR) michal.nowak@up.lublin.pl, Niedziela, Agnieszka² (AUTHOR) michal.nowak@up.lublin.pl

Source: International Journal of Molecular Sciences. Sep2024, Vol. 25 Issue 17, p9568. 18p.

Subject Terms: *SINGLE nucleotide polymorphisms, *LINKAGE disequilibrium, *GENETIC correlations, *GENETIC variation, *CHROMOSOMES

Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization.

Authors: Rosean, Samuel¹ (AUTHOR), Sosa, Eric A.² (AUTHOR), O'Shea, Dónal³ (AUTHOR), Raj, Srilakshmi M.² (AUTHOR), Seoighe, Cathal³ (AUTHOR), Greally, John M.² (AUTHOR) john.greally@einsteinmed.edu

Source: BMC Bioinformatics. 5/7/2024, Vol. 25 Issue 1, p1-18. 18p.

Subject Terms: *PYTHON programming language, *LINKAGE disequilibrium, *SOURCE code, *PHENOTYPES, *LOCUS (Genetics)

Association between 25(OH) vitamin D and multiple sclerosis: cohort, shared genetics, and Causality.

Authors: Yu, Xing-Hao^1,2,3,4,5, Lu, Hui-Min⁶, Li, Jun^1,2,7, Su, Ming-Zhu^1,8, Li, Xiao-Min^1,2,7, lixiaomin@wjrmyy.cn, Jin, Yi^1,2,7, jinyi@wjrmyy.cn

Source: Nutrition Journal; 11/30/2024, Vol. 23 Issue 1, p1-18, 18p

The prevalence and linkage disequilibrium of 21 genetic variations related to thrombophilia, folate cycle, and hypertension in reproductive age women of Rostov region (Russia).

Authors: Bordaeva, Oksana Yurievna¹ (AUTHOR), Derevyanchuk, Ekaterina Grigorievna¹ (AUTHOR), Alset, Dema¹ (AUTHOR) damdoum1995@gmail.com, Amelina, Maria Aleksandrovna² (AUTHOR), Shkurat, Tatiana Pavlovna^1,2 (AUTHOR)

Source: Annals of Human Genetics. Mar2024, Vol. 88 Issue 2, p171-181. 11p.

Subject Terms: *GENETIC variation, *LINKAGE disequilibrium, *FOLIC acid, *HYPERCOAGULATION disorders, *PREGNANCY complications, *HYPERTENSION

Geographic Terms: RUSSIA

Genetic Variability of SNP rs7089580 in Latin American populations and its impact on Warfarin dosage.

Alternate Title: Variabilidad Genética del SNP rs7089580 en poblaciones latinoamericanas y su impacto en la dosificación de Warfarina.

Authors: Flores, Sergio V.¹, Montaña, Román M.², Roco-Videla, Angel³, Caviedes-Olmos, Marcela⁴, Pérez-Jiménez, Sofía⁴, Aguilera Eguía, Raúl⁵

Source: Data & Metadata. 2024, Vol. 3, p1-5. 5p.

Subject Terms: *GENETIC variation, *LINKAGE disequilibrium, *LATIN Americans, *GENE frequency, *WARFARIN

Genetic admixture of Chinese Tajik people inferred from genome‐wide array genotyping and mitochondrial genome sequencing.

Authors: Zhao, Jing^1,2 (AUTHOR), Wu, Qiao¹ (AUTHOR), Bai, Xin-Hong³ (AUTHOR), Allen, Edward⁴ (AUTHOR), Wang, Meng-Ge² (AUTHOR), He, Guang-Lin² (AUTHOR), Guo, Jian-Xin² (AUTHOR), Yang, Xiao-Min² (AUTHOR), Xiong, Jian-Xue^4,5 (AUTHOR), Jiang, Zi-Xi^4,5 (AUTHOR), Ji, Xiao-Yan^4,5 (AUTHOR), Wang, Hui^4,5 (AUTHOR), Tan, Jing-Ze¹ (AUTHOR) jztan@fudan.edu.cn, Wen, Shao-Qing^1,4,5 (AUTHOR) wenshaoqing@fudan.edu.cn, Wang, Chuan‐Chao^2,6,7,8 (AUTHOR) wang@xmu.edu.cn

Source: Journal of Systematics & Evolution. Jan2024, Vol. 62 Issue 1, p181-192. 12p.

Subject Terms: *MITOCHONDRIAL DNA, *LINKAGE disequilibrium, *POPULATION genetics, *PRINCIPAL components analysis, *GENE flow, *SINGLE nucleotide polymorphisms, *NUCLEOTIDE sequencing

Geographic Terms: TAJIKISTAN, XINJIANG Uygur Zizhiqu (China)

A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize.

Authors: Andorf, Carson M^1,2 (AUTHOR), Ross-Ibarra, Jeffrey³ (AUTHOR), Seetharam, Arun S⁴ (AUTHOR), Hufford, Matthew B⁴ (AUTHOR), Woodhouse, Margaret R¹ (AUTHOR)

Source: G3: Genes | Genomes | Genetics. Feb2025, Vol. 15 Issue 2, p1-9. 9p.

Subject Terms: *GENETIC databases, *LINKAGE disequilibrium, *CORN, *RESEARCH personnel, *GENOTYPES

Finemap-MiXeR: A variational Bayesian approach for genetic finemapping.

Authors: Akdeniz, Bayram Cevdet^1,2, bayramc@uio.no, Frei, Oleksandr^1,2, Shadrin, Alexey¹, Vetrov, Dmitry³, Kropotov, Dmitry³, Hovig, Eivind^2,4, Andreassen, Ole A.¹, Dale, Anders M.⁵

Source: PLoS Genetics; 8/15/2024, Vol. 20 Issue 8, p1-21, 21p

Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration.

Authors: Crone, Bradley¹, Boyle, Alan P.^1,2, apboyle@umich.edu

Source: PLoS Genetics; 8/7/2024, Vol. 20 Issue 8, p1-18, 18p

Resistance haplotypes to green rice leafhopper (Nephotettix cincticeps Uhler) estimated in genome-wide association study in Myanmar indica rice landraces.

Authors: Nang Moe Kham¹, Hiroyuki Kanamori², Jianzhong Wu², Takashi Matsumoto³, Daisuke Fujita⁴, Hideshi Yasui¹, Atsushi Yoshimura¹, Yoshiyuki Yamagata¹, yoshiyuk@agr.kyushu-u.ac.jp

Source: Breeding Science; 2024, Vol. 74 Issue 4, p366-381, 16p

Polygenic selection to a changing optimum under self–fertilisation.

Authors: Hartfield, Matthew¹, m.hartfield@ed.ac.uk, Glémin, Sylvain^2,3

Source: PLoS Genetics; 7/17/2024, Vol. 20 Issue 7, p1-30, 30p

Optimal Structured Matrix Approximation for Robustness to Incomplete Biosequence Data

Authors: Salahub, C., Uhlmann, J.

Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics IEEE/ACM Trans. Comput. Biol. and Bioinf. Computational Biology and Bioinformatics, IEEE/ACM Transactions on. 21(6):2592-2597 Jan, 2024

cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions.

Authors: Wang, Dinghao¹ (AUTHOR), Perera, Deshan² (AUTHOR), He, Jingni² (AUTHOR), Cao, Chen² (AUTHOR), Kossinna, Pathum² (AUTHOR), Li, Qing² (AUTHOR), Zhang, William³ (AUTHOR), Guo, Xingyi^4,5 (AUTHOR), Platt, Alexander⁶ (AUTHOR), Wu, Jingjing¹ (AUTHOR), Zhang, Qingrun^1,2,7 (AUTHOR) qingrun.zhang@ucalgary.ca

Source: PLoS Genetics. 12/18/2023, Vol. 19 Issue 12, p1-21. 21p.

Subject Terms: *LINKAGE disequilibrium, *MOLECULAR evolution, *GENETIC variation, *MOLECULAR association, *PROTEIN-protein interactions

Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale.

Authors: Nisa, Fakhar un^1,2,3 (AUTHOR), Kaul, Haiba³ (AUTHOR), Asif, Muhammad^1,2 (AUTHOR), Amin, Imran^1,2 (AUTHOR), Mrode, Raphael^4,5 (AUTHOR), Mansoor, Shahid^1,2,6 (AUTHOR), Mukhtar, Zahid^1,2 (AUTHOR) zahidmukhtar@yahoo.com

Source: Mammalian Genome. Dec2023, Vol. 34 Issue 4, p602-614. 13p.

Subject Terms: *LINKAGE disequilibrium, *GENE frequency, *CATTLE genetics, *DAIRY cattle, *INBREEDING, *GENETIC variation, *GENOME-wide association studies

Geographic Terms: PAKISTAN

CoreSNP: an efficient pipeline for core marker profile selection from genome-wide SNP datasets in crops.

Authors: Dou, Tingyu¹ (AUTHOR), Wang, Chunchao¹ (AUTHOR), Ma, Yanling¹ (AUTHOR), Chen, Zhaoyan¹ (AUTHOR), Zhang, Jing¹ (AUTHOR), Guo, Ganggang¹ (AUTHOR) guoganggang@caas.cn

Source: BMC Plant Biology. 11/21/2023, Vol. 23 Issue 1, p1-10. 10p.

Subject Terms: *SINGLE nucleotide polymorphisms, *LINKAGE disequilibrium, *INTELLECTUAL property, *GENETIC variation, *GENE frequency, *PLANT protection