Article
Chemistry, Applied
Li Lin, Lejing Lin, Zhiyong Zhu, Yulong Ding, Xiaohong Xie, Jianjun Zhu
Summary: This study conducted restriction site-associated DNA sequencing (RAD-seq) on the genus Acer, and used high-quality SNP data for genotyping, clustering, and phylogenetic tree construction. It confirmed the systematic relationships among some taxonomic groups and discussed the origin, evolution, and distribution of Acer. Furthermore, it demonstrated the feasibility of using RAD-seq-generated SNP data for species identification and phylogenetic analysis.
JOURNAL OF BIOBASED MATERIALS AND BIOENERGY
(2022)
Article
Biotechnology & Applied Microbiology
Adam Nunn, Christian Otto, Mario Fasold, Peter F. Stadler, David Langenberger
Summary: This study presents a computational pre-processing approach to enable downstream analysis on a per-strand basis using conventional variant calling software. The method improves precision and sensitivity compared to specialized tools, and is applicable to both human and model plant variants.
Letter
Biotechnology & Applied Microbiology
Emel Ozcan Gokcek, Raziye Isik, Bilge Karahan, Kutsal Gamsiz
Summary: This study investigated MSTN polymorphisms in the European sea bass population reared in Turkey. Nine SNPs and two indels were identified in MSTN, and they were significantly associated with growth traits such as standard length, total weight, and fillet weight. Haplotype analysis also revealed potential associations between haplogroup 2 and all measured growth traits.
MARINE BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Neethu Francis, Ravikesavan Rajasekaran, Veera Ranjani Rajagopalan, S. Vinothini Bakya, Raveendran Muthurajan, Ashwini Girish Kumar, Senthil Alagarswamy, Iyanar Krishnamoorthy, Chitdeshwari Thiyagarajan
Summary: The aim of this study was to develop and characterize high-yielding mutants and generate functional genomic information for proso millet. Mutant populations induced by gamma irradiation were screened, and one high-yielding mutant and one low-yielding mutant were selected. Sequencing and genomic analysis revealed functional single nucleotide polymorphisms associated with yield. This information can be used to identify genes related to metabolic processes in proso millet and design useful genetic markers.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Tianyu Deng, Pengfei Zhang, Dorian Garrick, Huijiang Gao, Lixian Wang, Fuping Zhao
Summary: Genotype imputation is a crucial step prior to genome-wide association studies or genomic predictions, and its accuracy is influenced by several factors. This simulation-based study investigated the impact of factors such as target marker proportion, SNP density, genetic relationship, and imputation method. Results revealed that target marker proportion or SNP density had the greatest effect on imputation accuracy. Beagle5.1 outperformed Minimac4 in most cases, particularly when imputing from low-coverage whole-genome sequencing data. Overall, low-coverage whole-genome sequencing provided more accurate imputation compared to SNP chip data.
FRONTIERS IN GENETICS
(2022)
Review
Plant Sciences
Hilde Nybom, Gunars Lacis
Summary: Recent national and international projects have focused on large-scale genotyping of vegetatively propagated crops, aiming to identify true-to-type plant material, detect synonyms, investigate genetic diversity, and create sustainable databases for research and breeding. Different DNA markers and next-generation sequencing methods have their advantages and disadvantages, with large-scale phenotyping methods lagging behind but crucial for understanding commercially important traits. Collaborative projects with broad-scale data collection are likely to produce more reliable results in the analysis of gene action and development of robust DNA markers.
Article
Fisheries
Hao Wang, Jia Lv, Qifan Zeng, Yaran Liu, Qiang Xing, Shi Wang, Jingjie Hu, Lisui Bao
Summary: The bay scallop is an economically important bivalve species in aquaculture industry in China, with the highest annual yield. Through whole genomic resequencing analysis, researchers found that the selective breeds of bay scallop have lower levels of genomic polymorphism and increased linkage disequilibrium compared to the hatchery reference population. Selective sweep analysis revealed genes under selection in the two breeds, potentially contributing to improved growth and immunity performance.
Article
Biochemical Research Methods
Zenaida V. Magbanua, Chuan-Yu Hsu, Olga Pechanova, Mark Arick II, Corrinne E. Grover, Daniel G. Peterson
Summary: We present an improved ddRAD-Seq protocol for identifying SNPs that increases efficiency and decreases time compared to known methods. Our protocol was validated by comparing SNPs with whole genome resequencing data, showing clustering with the corresponding genotype and high discovery rate for homozygous loci. Our method is reliable and cost-effective for phylogenetic and association genetic studies.
ANALYTICAL BIOCHEMISTRY
(2023)
Article
Forestry
Bartosz Ulaszewski, Joanna Meger, Jaroslaw Burczyk
Summary: The study evaluated different genomic sequencing methods and found that SNP identification based on ddRAD provided the best results in population genetics research. Additionally, the study showed that more than 80% of SNP loci should be considered reliable markers in GBS and ddRAD.
Article
Fisheries
Chun Hui Ai, Zong Xian Zhu, Dan Dan Huang, Gan Yang, Tong De Liu, Ying Bai, Xue Ying Liang, Ying Ying Xiong, Yi Long Lin, Hao Ran Lin, Shui Sheng Li, Jun Hong Xia
Summary: In this study, the genetic architecture of early growth-related traits in the orange-spotted grouper was dissected using a genomewide association study. A total of 11 significantly associated SNPs located on three chromosomes were identified, explaining a proportion of phenotypic variance ranging from 5.15% to 6.89% for body weight, body length, and body height.
Article
Plant Sciences
Priscila Sousa, Henrique Vieira, Eileen Santos, Alexandre Viana, Marcela Boaechat, Fabio Partelli
Summary: This study molecularly characterized Coffea canephora using microsatellite markers, revealing a high level of polymorphism and genetic diversity in the population, making it suitable for breeding efforts.
Article
Plant Sciences
James Friel, Aureliano Bombarely, Carmen Dorca Fornell, Francisco Luque, Ana Maria Fernandez-Ocana
Summary: Olive, a tree species of great economic and cultural importance in the Mediterranean region, has numerous cultivars that can be characterized using different genetic methods. Both whole-genome sequencing (WGS) and genotype by sequencing (GBS) yield similar results in olive genotyping, with GBS being a cost-effective option for characterizing genetic relationships between different accessions. The study also suggests that variants from GBS and WGS datasets can be combined, enabling the reuse of publicly available data.
Article
Genetics & Heredity
Jongan Lee, Yong-Jun Kang, Yoo-Kyung Kim, Jae-Young Choi, Sang-Min Shin, Moon-Cheol Shin
Summary: The influences of diet and environmental factors on gut microbial profiles have been acknowledged, but the specific roles of host genetics remain uncertain. To study host genetic effects, 47 Jeju crossbred foals with higher genetic diversity were raised under identical conditions. Microbial composition revealed predominance of Firmicutes, Bacteroidetes, and Spirochaetes. Host-microbiome associations were identified using single nucleotide polymorphisms (SNPs) and taxa associated with horse growth, revealing functional links to metabolism and the influence of specific SNP genotypes on microbial abundances.
Article
Engineering, Civil
Shouliang Huo, Zhe Xiao, Xiaochuang Li, Hanxiao Zhang, Jingtian Zhang, Fengchang Wu
Summary: This study investigated the decade-long successional patterns of Microcystis genotypes in Lake Chaohu using high-throughput sequencing. The results showed that Microcystis populations exhibited high overall genetic diversity and remained relatively stable over the last 70 years. The successional patterns were influenced by dam construction and nutrient enrichment.
JOURNAL OF HYDROLOGY
(2022)
Article
Entomology
Fairuz Farhana Mohd Rodzik, Nurshazwani Amalina Sudirman, Chee-Keng Teh, Ai-Ling Ong, Huey-Ying Heng, Salmah Yaakop, Norfarhan Mohd-Assaad, Meilina Ong-Abdullah, Nabeel Ata, Samsudin Amit, Burhanuddin Saragih, David Ross Appleton, Harikrishna Kulaveerasingam
Summary: This study developed a set of robust nuclear DNA markers specific to the African oil palm-pollinating weevil (Elaeidobius kamerunicus) to directly assess the genetic diversity of the weevil populations. These markers can be used to confirm the weevil's origin and provide useful information for genetic monitoring and conservation planning.