Article
Multidisciplinary Sciences
Jonas Schmidt, Sandro Berghaus, Frithjof Blessing, Holger Herbeck, Josef Blessing, Peter Schierack, Stefan Rodiger, Dirk Roggenbuck, Folker Wenzel
Summary: Nanopore sequencing has great potential for clinical diagnostics, but further validation and certification are required.
Article
Agriculture, Dairy & Animal Science
M. Kinukawa, M. Ito, Y. Uemoto, A. Ogino, S. Haruta, K. Kurogi, T. Watanabe, S. Sasaki, Y. Naniwa, K. Uchiyama, K. Togashi
Summary: There is considerable variation in the bull conception rate (BCR) of Japanese Black cattle, and some bulls with a low BCR have been identified. In this study, a genome-wide association study with whole-exome sequencing was conducted to identify single-nucleotide polymorphisms (SNPs) for predicting low BCR. The g.116408653G > A SNP in Bos taurus autosome 5 was found to have a significant effect on BCR.
Article
Pharmacology & Pharmacy
Chiara Casotti, Claudia Maria Hattinger, Maria Pia Patrizio, Silvia Luppi, Leonardo Fantoni, Michela Pasello, Katia Scotlandi, Toni Ibrahim, Massimo Serra
Summary: In this study, an innovative mmNGS approach was used to investigate SNPs associated with MTX resistance in HGOS cell lines. The results showed that allele changes in TP53, SLC19A1, and MTHFR were functionally involved in the development of MTX resistance. In addition, a fusion transcript of DHFR and MSH3 was identified in the cells with the highest MTX resistance level.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Genetics & Heredity
Misteru Tesfaye, Tileye Feyissa, Teklehaimanot Hailesilassie, Selvaraju Kanagarajan, Li-Hua Zhu
Summary: This study investigated the genetic diversity and population structure of Ethiopian mustard (Brassica carinata) genotypes of different origins using high-throughput single nucleotide polymorphism (SNP) markers. The results revealed two distinct subpopulations, with the majority of accessions clustered in one subpopulation mainly obtained from specific regions. The analysis showed high genetic variation within populations and low genetic differentiation between populations, indicating the presence of gene flow and weak geographical structure. The study provides important information for future breeding and conservation efforts of B. carinata.
Article
Plant Sciences
Mao Yang, Jianbo He, Shubei Wan, Weiyan Li, Wenjing Chen, Yangming Wang, Xiaomei Jiang, Pengfei Cheng, Pu Chu, Wenbiao Shen, Rongzhan Guan
Summary: Plant height is an important trait in crop yield determination. Dwarf or semi-dwarf varieties are desirable in breeding due to their benefits in increasing harvest index, planting density, and lodging resistance. A new dwarf mutant Bndwarf2 in oilseed rape was studied, and a dwarf locus BnDWARF2 was mapped to a specific chromosome interval. This study identified a dominant dwarfing gene, BnaC04.BIL1, that negatively regulates plant height and may improve lodging resistance in oilseed rape.
Article
Agricultural Engineering
Hussein Abdel-Haleem, Zinan Luo, Aaron Szczepanek
Summary: This study investigated the genetic diversity and relatedness in the USDA collection of Brassica juncea. By genotyping 340 samples, a total of 99030 high-quality SNP markers were identified. Population structure and PCA analysis revealed five distinct subpopulations, with the largest subpopulation traced back to Pakistan and India. The results demonstrated a high genetic diversity and genetic differentiation among subpopulations in the USDA collection of B. juncea.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Agriculture, Dairy & Animal Science
Congyan Li, Yuying Li, Jie Zheng, Zhiqiang Guo, Xiuli Mei, Min Lei, Yongjun Ren, Xiangyu Zhang, Cuixia Zhang, Chao Yang, Li Tang, Yang Ji, Rui Yang, Jifeng Yu, Xiaohong Xie, Liangde Kuang
Summary: This study analyzed rabbit traits using single-nucleotide polymorphism markers in genotyping-by-sequencing data. It identified genes associated with fur color and weight and provided a database for research and improvement of rabbit breeding program.
Article
Plant Sciences
Mengli Ma, Hengling Meng, En Lei, Tiantao Wang, Wei Zhang, Bingyue Lu
Summary: Amomum tsaoko is a medicinal and food dual-use crop belonging to the Zingiberaceae family. This study provides transcriptome data and newly developed EST-SSR markers for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.
Article
Biochemistry & Molecular Biology
Maria Radanova, Mariya Levkova, Galya Mihaylova, Rostislav Manev, Margarita Maneva, Rossen Hadgiev, Nikolay Conev, Ivan Donev
Summary: There is a growing interest in studying single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, as they may be associated with susceptibility, prognosis, and treatment response in colorectal cancer (CRC). These miRNA-SNPs could serve as non-invasive biomarkers for early detection of CRC. However, contradictory findings have been reported when different research groups investigated the same SNP in a gene for a specific miRNA, highlighting the need for more case-control studies involving participants from different ethnic backgrounds. According to our review, three miRNA-SNPs - miR-146a rs2910164, miR-27a rs895819, and miR-608 rs4919510 - appear to be promising prognostic, diagnostic, and predictive biomarkers for CRC.
Review
Plant Sciences
Zheng Ying, Muhammad Awais, Reshmi Akter, Fengjiao Xu, Sul Baik, Daehyo Jung, Deok Chun Yang, Gi-Young Kwak, Wenying You
Summary: Discriminating plant species, cultivars, and landraces is challenging, but SNP markers have proven to be a reliable tool for differentiating Panax ginseng and similar species. This article provides a cost-effective guide for SNP marker analysis in a traditional laboratory setting.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Dennis N. Lozada, Madhav Bhatta, Danise Coon, Paul W. Bosland
Summary: Genetic diversity among New Mexican chile peppers was assessed using GBS-derived SNP markers, revealing genetic relatedness among different populations. Introducing novel alleles from other breeding programs or wild species could help increase diversity in the current germplasm. Valuable information for future association mapping and genomic selection for genetic improvement through marker-assisted breeding in New Mexican chile peppers was presented.
Article
Cardiac & Cardiovascular Systems
Matthew R. Alexander, Samuel Hank, Bethany L. Dale, Lauren Himmel, Xue Zhong, Charles D. Smart, Daniel J. Fehrenbach, Yuhan Chen, Nitin Prabakaran, Brian Tirado, Megan Centrella, Mingfang Ao, Liping Du, Yu Shyr, Daniel Levy, Meena S. Madhur
Summary: Research suggests that the Trp encoding allele of rs3184504 may be causal for hypertension and renal dysfunction, in part due to the loss of SH2B3-mediated repression of T cell IL-12 signaling leading to enhanced IFNg production.
CIRCULATION RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Qi Zhou, Peng-Yan Zhou, Wen-Tao Zou, Yin-Gang Li
Summary: High-throughput sequencing of the Phoebe bournei transcriptome led to the identification of novel SSR markers, and genetic analyses revealed significant genetic differences among populations, with the YS population from Jiangxi province showing the highest genetic diversity.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Catalina Molina, Natalia Cristina Aguirre, Pablo Alfredo Vera, Carla Valeria Filippi, Andrea Fabiana Puebla, Susana Noemi Marcucci Poltri, Norma Beatriz Paniego, Alberto Acevedo
Summary: The study optimized the identification of SNPs in sugarcane and recommended the use of long read size and paired-end reads, medium sequencing coverage, and Illumina NovaSeq6000 platform. Functional analysis showed that most of the SNPs landed within regulatory regions. The protocol demonstrated robustness in analyzing replicated genotypes.
PLANT MOLECULAR BIOLOGY
(2023)
Article
Genetics & Heredity
Wei Cui, Man Chen, Yan Yang, Meiming Cai, Qiong Lan, Tong Xie, Bofeng Zhu
Summary: In this study, a panel of 1993 SNP loci was evaluated for kinship identification. The results showed that this panel can effectively identify paternity, full siblings, second-degree kinships, and first cousin kinships. The panel can also distinguish first-degree and second-degree pairs from unrelated individuals. The system power of recommended thresholds for identifying first cousin kinships was 0.9470.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
