The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help sol...
A safe and efficacious live-attenuated vaccine for porcine epidemic diarrhea virus (PEDV) is not commercially available in the United States yet. Two major PEDV strains are currently circulating in US swine: highly virulent non-S-INDEL strain and mil...
The effects of amino acid insertions and deletions (InDels) remain a rather under-explored area of structural biology. These variations oftentimes are the cause of numerous disease phenotypes. In spite of this, research to study InDels and their stru...
Pleomorphic adenoma gene 1 (PLAG1) belongs to the PLAG family of zinc finger transcription factors. In cattle, a 19-bp insertion/deletion (indel) was identified in intron 1 of the PLAG1 gene (GenBank Accession No. AC_000171.1). Researches showed that...
Distant hybridization, such as between apple (Malus domestica Borkh.) and pear (Pyrus communis L.), can introduce unique genetic traits that aren’t possible through traditional hybridization methods. However, these hybrids often display materna...
Lung cancer arises from the accumulation of genetic mutations, usually in exons. A recent study identified indel mutations in the noncoding region of surfactant-encoding genes in lung adenocarcinoma cases. In this study, we recruited 94 patients with...
Background and objectives: Over the last two decades, human DNA identification and kinship tests have been conducted mainly through the analysis of short tandem repeats (STRs). However, other types of markers, such as insertion/deletion polymorphisms...
A molecular marker is a valuable tool in genetic research. Insertions–deletions (InDels) are commonly used polymorphisms in gene mapping, analysing genetic diversity, marker-assisted breeding, and phylogenetics. The 3000 Rice Genome Project, a re-seq...
The aim of this work was to select InDel markers sufficient for human identification and to create a routine method for their genotyping. We analyzed the allele distribution of all known InDels in European, East Asian, South Asian, African, and Ameri...
The wax gourd is commonly grown in many countries because of its high nutritional and economic value. While the genes for the fruit shape and peel colour of wax gourd have been reported, the InDel markers linked to these genes remain undeveloped. In...
Golgin subfamily B member 1 (GOLGB1) gene encodes the coat protein 1 vesicle inhibiting factor, giantin. Previous study showed that mutations of the GOLGB1 gene are associated with dozens of human developmental disorders and diseases. However, the bi...
To address the challenges of narrow genetic backgrounds and low phenotypic selection efficiency in tomato breeding, comparative genomics was applied. Based on the genomic sequences of five tomato varieties (‘Micro-Tom’, ‘Moneymaker&...
The FBLN1 gene encodes the fibulin-1 protein, the first member of the ECM glycoprotein family, and is crucial for embryonic development and organ tissue formation in mammals. Our previous transcriptome analysis identified the FBLN1 gene and suggested...
Myostatin (MSTN) gene, also known as growth differentiation factor 8 (GDF8), is a member of the transforming growth factor-beta super-family and plays a negative role in muscle development. It acts as key points during pre- and post-natal life of amn...
Although DNA barcoding has become a useful tool for species identification and biodiversity surveys in plant sciences, there remains little consensus concerning appropriate sampling strategies and the treatment of indels. To address these two issues,...
Molecular markers play a crucial role in marker-assisted breeding and varietal identification. However, the application of insertion/deletion markers (InDels) in grapevines has been limited by the low throughput and separability of gel electrophoresi...
Accurate genotyping of small insertions and deletions (InDels; <5 bp) remains technically challenging in routine molecular breeding, largely due to the limited resolution of agarose gel electrophoresis and the labor-intensive nature of polyacrylam...
The GH growth axis plays an important role in the growth and development of animals and runs through the whole life of animals. Many studies have shown that molecular mutations in key genes of the GH axis will affect the growth and development of ani...
Sex determination is a fundamental biological process governing animal reproduction. Although substantial progress has been made in elucidating its genetic basis, the genetic architecture underlying complex sex determination systems remains poorly un...
The porcine monomyeloid cell line, or 3D4/21 cells, is an effective tool to study the immune characteristics and virus infection mechanism of pigs. Due to the introduction of the neomycin resistance gene and the SV40 large T antigen gene, its genome...
Powdery mildew (PM) is a fungal disease occurring in both field and greenhouse conditions worldwide. It infects many plant species and reduces both the productivity and quality of crops. Melon (Cucumis melo L.) is an economically important crop. In o...
Gastric cancer (GC) is a multifactorial, complex, and aggressive disease with a prevalence of one million new cases and high global mortality. Factors such as genetic, epigenetic, and environmental changes contribute to the onset and progression of t...
Porcine epidemic diarrhea virus (PEDV) continues to circulate globally, causing substantial economic losses to the swine industry. Historically, PEDV strains are classified into the classical G1, epidemic G2, and S-INDEL genotypes. Among these...
With the development and improvement of indica–japonica hybrid rice breeding technologies, it has become possible to directly utilize the heterosis between indica and japonica subspecies to cultivate high-yielding rice varieties. Precisely anal...
Diversity surveys of germplasm are important for gaining insight into the genomic basis for crop improvement; especially InDels, which are poorly understood in hexaploid common wheat. Here, we describe a map of 89,923 InDels from exome sequencing of...
Gypsophila paniculata is the only species in the genus Gypsophila that has been used as cut flowers, and the sequencing of its genome has just been completed, opening a new chapter in its molecular genetic breeding. The molecular marker system is the...
This study aimed to identify insertion–deletion (InDel) variants in key genes of the Hippo signaling pathway in four Chinese sheep breeds: Tong sheep (TS), Hu sheep (HS), Small Tail Han sheep (STHS), and Lanzhou large-tailed sheep (LLTS). InDel...
Caragana acanthophylla Kom. is an ecologically important drought-tolerant shrub in Xinjiang, China, but species-specific molecular markers for germplasm characterization remain limited. We sampled 93 individuals from 11 localities representing the cu...
The use of zebrafish in functional genomics and disease modeling has become popular due to the ease of targeted mutagenesis with genome editing nucleases, i.e., zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), a...
The tuber of Cynanchum wilfordii (Baekshuoh Radix in Korean) is an important medicinal herb in Korea and China; however, it is difficult to differentiate C. wilfordii from a related medicinal herb, C. auriculatum (Baishouwu Radix in Chinese). We soug...
A-kinase-anchoring protein 13 (AKAP13) is a member of the AKAP protein family that has been found to be associated with bone formation. Thus, we investigated the AKAP13 gene as a potential candidate gene for molecular-marker-assisted selection (MAS)...
As a “living fossil”, ginkgo (Ginkgo biloba L.) has significant ornamental, medicinal, and timber value. However, the breeding improvement of ginkgo was limited by the lack of enough excellent germplasms and suitable molecular markers. He...
Forensic DNA profiling commonly relies on polymerase chain reaction (PCR) amplification followed by capillary electrophoresis (CE) or massively parallel sequencing (MPS), which requires expensive, laboratory-based equipment that depends on a stable p...
A chromosome segment substituted line (CSSL) represents an ideal resource for studying quantitative traits like thermotolerance. To develop wheat inter-varietal CSSLs with E6015-3S (a heat-sensitive genotype) being the recipient parent, genome-wide u...
(1) Background: To assess the genetic makeup among the agro-economically important members of Euphorbiaceae, the present study was conducted to identify and characterize high-quality single-nucleotide polymorphism (SNP) markers and their comparative...
Japonica-specific markers are crucial for the analysis of genetic diversity, population structure, evolutionary traits, and genome-wide association study (GWAS) of japonica germplasm accessions. This study developed 402 insertion–deletion (InDe...
Citrus collections from extreme growing regions can be an important source of tolerant germplasms for the breeding of cold-tolerant varieties. However, the efficient utilization of these germplasms requires their genetic background information. Thus,...
In this study, whole-genome resequencing was performed on the cold-tolerant variety ND-6 and the cold-sensitive variety ‘Sorbonne’. After evaluation, the Lilium davidii var. unicolor reference genome was selected to analyze SSR distributi...
FLOWERING LOCUS T (FT) is a key integrator of flowering pathways. White lupin, a grain legume, encodes four FT homologs: LalbFTa1, LalbFTa2, LalbFTc1, and LalbFTc2. Widespread distribution of white lupin implies diverse phenological adaptations to co...
The α-gliadins of wheat, along with other gluten components, are responsible for bread viscoelastic properties. However, they are also related to human pathologies as celiac disease or non-celiac wheat sensitivity. CRISPR/Cas was successfully u...
The genetic improvement of Phalaenopsis-type Dendrobium, a valuable ornamental and medicinal orchid, is hindered by the lack of a complete reference genome. In this study, a transcriptome-based approach was employed to develop and validate insertion&...
Melon (Cucumis melo L.) is a significant horticultural crop valued for its aroma and health-promoting compounds. However, the genetic similarity among numerous varieties poses challenges for identification and breeding. ‘Dongfangmi No.4’...
The market success of any rice cultivar is exceedingly dependent on its grain appearance, as well as its grain yield, which define its demand by consumers as well as growers. The present study was undertaken to explore the contribution of nine major...
Sweetpotato (Ipomoea batatas (L.) Lam.), whose roots are rich in starch, is widely grown around the world and plays a prominent role in ensuring food security. At present, there are no reports on the genetic diversity of sweetpotato germplasm reveale...
Whole-genome sequencing (WGS) is a powerful tool for uncovering genome-wide variation, identifying selection signatures, and guiding genetic improvement in livestock. Royal White (RW) and White Dorper (WD) sheep are economically important meat-type h...
Pollen development and its fertility are obligatory conditions for the reproductive success of flowing plants. Sucrose transporter 3 (OsSUT3) is known to be preferentially expressed and may play critical role in developing pollen. A 31-bp InDel was i...
Maize(Zea mays. L) is a globally important crop, and understanding its genetic diversity is crucial for plant breeding phylogenetic analyses and comparative genetics. While nuclear markers have been extensively used for mapping agriculturally importa...
Zanthoxylum schinifolium and Zanthoxylum piperitum are the sources of the well-known traditional Korean herbal medicines “sancho” (prickly ash) and “chopi” (Korean pepper), respectively. Sancho and chopi are often indiscrimina...
We report the identification of interspecific barcoding InDel regions in Vaccinium species. We compared five complete Vaccinium chloroplast (cp) genomes (V. bracteatum, V. vitis-idaea, V. uliginosum, V. macrocarpon, and V. oldhamii) to identify regio...
Map-based gene cloning has played a key role in many genetic studies using the model plant, Arabidopsis thaliana. In the post- next generation sequencing era, identification of point mutations and their corresponding genes is increasingly becoming a...
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