scholarly journals Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1

2021 ◽  
Vol 12 ◽  
Author(s):  
Hui Zhang ◽  
Sha Tang ◽  
James C. Schnable ◽  
Qiang He ◽  
Yuanzhu Gao ◽  
...  
Keyword(s):  
Dna Polymorphism ◽  
Leaf Sheath ◽  
Forward Genetics ◽  
Polymorphism Analysis ◽  
Marker Development ◽  
High Quality ◽  
Genetics Research ◽  
Genome Wide ◽  
White Leaf ◽  
Molecular Marker Development

Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the “Yugu1” variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, “SSR41”, which is morphologically similar to, and readily cross-pollinates with, “Yugu1”. High-throughput resequencing of “SSR41” identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used “SSR41” and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.

scholarly journals Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Junjie Cui ◽  
Jiazhu Peng ◽  
Jiaowen Cheng ◽  
Kailin Hu
Keyword(s):  
Genetic Map ◽  
Average Density ◽  
Momordica Charantia ◽  
Bitter Gourd ◽  
Map Construction ◽  
Indel Markers ◽  
Genome Wide ◽  
Indel Polymorphisms ◽  
Molecular Marker Development ◽  
Development And Validation

Abstract Background The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers. Results Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Then we developed a total of 2502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines ‘47–2–1-1-3’ and ‘04–17,’ indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 ‘47–2–1-1-3’ × ‘04–17’ F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome. Conclusions This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.

scholarly journals High-Quality Genome Resource of the Pathogen of Diaporthe (Phomopsis) phragmitis Causing Kiwifruit Soft Rot

2020 ◽  
Author(s):  
Pu Liu ◽  
Wang Xiaojie ◽  
Dong Hongjie ◽  
Jianbin Lan ◽  
Kuan Liang ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Management Strategies ◽  
Soft Rot ◽  
Fruit Rot ◽  
Economic Plant ◽  
High Quality ◽  
Total Size ◽  
Genome Wide ◽  
Solid Foundation ◽  
High Quality Genome

Diaporthe spp. are critical plant pathogens that cause wood cankers, wilt, dieback, and fruit rot in a wide variety of economic plant hosts and are regarded as one of the most acute threats faced by kiwifruit industry worldwide. Diaporthe phragmitis strain NJD1 is a highly pathogenic isolate of soft rot of kiwifruit. Here, we present a high-quality genome-wide sequence of D. phragmitis NJD1 that was assembled into 28 contigs containing a total size of 58.33 Mb and N50 length of 3.55 Mb. These results lay a solid foundation for understanding host–pathogen interaction and improving disease management strategies.

Prenatal diagnosis by DNA polymorphism analysis of complete mole with coexisting twin

2003 ◽  
Vol 188 (4) ◽  
pp. 1105-1106 ◽  
Author(s):  
Joseph R. Wax ◽  
Michael G. Pinette ◽  
Renée Chard ◽  
Jacquelyn Blackstone ◽  
DO ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Dna Polymorphism ◽  
Polymorphism Analysis ◽  
Complete Mole

A pure nongestational choriocarcinoma of the ovary diagnosed with DNA polymorphism analysis

2003 ◽  
Vol 89 (3) ◽  
pp. 540-542 ◽  
Author(s):  
Hiroshi Tsujioka ◽  
Hitoshi Hamada ◽  
Takashi Miyakawa ◽  
Toru Hachisuga ◽  
Tatsuhiko Kawarabayashi
Keyword(s):  
Dna Polymorphism ◽  
Polymorphism Analysis

scholarly journals Clonal Lineages of Erysipelothrix rhusiopathiae Responsible for Acute Swine Erysipelas in Japan Identified by Using Genome-Wide Single-Nucleotide Polymorphism Analysis

2017 ◽  
Vol 83 (11) ◽  
Author(s):  
Yohsuke Ogawa ◽  
Kazumasa Shiraiwa ◽  
Yoshitoshi Ogura ◽  
Tadasuke Ooka ◽  
Sayaka Nishikawa ◽  
...  
Keyword(s):  
Polymorphism Analysis ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Erysipelothrix Rhusiopathiae ◽  
Single Nucleotide ◽  
Content Type ◽  
Genome Wide ◽  
Wide Range ◽  
Swine Erysipelas ◽  
Lineage Iv

ABSTRACTErysipelothrix rhusiopathiaecauses swine erysipelas, an important infectious disease in the swine industry. In Japan, the incidence of acute swine erysipelas due toE. rhusiopathiaeserovar 1a has recently increased markedly. To study the genetic relatedness of the strains from the recent cases, we analyzed 34E. rhusiopathiaeserovar 1a swine isolates collected between 1990 and 2011 and further investigated the possible association of the live Koganei 65-0.15 vaccine strain (serovar 1a) with the increase in cases. Pulsed-field gel electrophoresis analysis revealed no marked variation among the isolates; however, sequencing analysis of a hypervariable region in the surface-protective antigen A gene (spaA) revealed that the strains isolated after 2007 exhibited the samespaAgenotype and could be differentiated from older strains. Phylogenetic analysis based on genome-wide single-nucleotide polymorphisms (SNPs) revealed that the Japanese strains examined were closely related, showing a relatively small number of SNPs among them. The strains were classified into four major lineages, with Koganei 65-0.15 (lineage III) being phylogenetically separated from the other three lineages. The strains isolated after 2007 and the two older strains constituted one major lineage (lineage IV) with a specificspaAgenotype (M203/I257-SpaA), while the recent isolates were further divided into two geographic groups. The remaining older isolates belonged to either lineage I, with the I203/L257-SpaA type, or lineage II, with the I203/I257-SpaA type. These results indicate that the recent increased incidence of acute swine erysipelas in Japan is associated with two sublineages of lineage IV, which have independently evolved in two different geographic regions.IMPORTANCEUsing large-scale whole-genome sequence data fromErysipelothrix rhusiopathiaeisolates from a wide range of hosts and geographic origins, a recent study clarified the existence of three distinct clades (clades 1, 2, and 3) that are found across multiple continents and host species, representing both livestock and wildlife, and an “intermediate” clade between clade 2 and the dominant clade 3 within the species. In this study, we found that theE. rhusiopathiaeJapanese strains examined exhibited remarkably low levels of genetic diversity and confirmed that all of the Japanese and Chinese swine isolates examined in this study belong to clonal lineages within the intermediate clade. We report thatspaAgenotyping ofE. rhusiopathiaestrains is a practical alternative to whole-genome sequencing analysis of theE. rhusiopathiaeisolates from eastern Asian countries.

scholarly journals Genome‐Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High‐Quality Rice

2018 ◽  
Vol 11 (3) ◽  
pp. 170076 ◽  
Author(s):  
Gastón Quero ◽  
Lucía Gutiérrez ◽  
Eliana Monteverde ◽  
Pedro Blanco ◽  
Fernando Pérez de Vida ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
High Quality ◽  
Breeding Populations ◽  
Genome Wide ◽  
Genomic Regions

Bisphosphonate-related osteonecrosis of the jaw is associated with polymorphisms of the cytochrome P450 CYP2C8 in multiple myeloma: a genome-wide single nucleotide polymorphism analysis

Blood ◽  
2008 ◽  
Vol 112 (7) ◽  
pp. 2709-2712 ◽  
Author(s):  
Maria E. Sarasquete ◽  
Ramon García-Sanz ◽  
Luis Marín ◽  
Miguel Alcoceba ◽  
Maria C. Chillón ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Cytochrome P450 ◽  
Genome Wide Association Study ◽  
Osteonecrosis Of The Jaw ◽  
Bisphosphonate Therapy ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome

Abstract We have explored the potential role of genetics in the development of osteonecrosis of the jaw (ONJ) in multiple myeloma (MM) patients under bisphosphonate therapy. A genome-wide association study was performed using 500 568 single nucleotide polymorphisms (SNPs) in 2 series of homogeneously treated MM patients, one with ONJ (22 MM cases) and another without ONJ (65 matched MM controls). Four SNPs (rs1934951, rs1934980, rs1341162, and rs17110453) mapped within the cytochrome P450-2C gene (CYP2C8) showed a different distribution between cases and controls with statistically significant differences (P = 1.07 × 10−6, P = 4.231 × 10−6, P = 6.22 × 10−6, and P = 2.15 × 10−6, respectively). SNP rs1934951 was significantly associated with a higher risk of ONJ development even after Bonferroni correction (P corrected value = .02). Genotyping results displayed an overrepresentation of the T allele in cases compared with controls (48% vs 12%). Thus, individuals homozygous for the T allele had an increased likelihood of developing ONJ (odds ratio 12.75, 95% confidence interval 3.7-43.5).

scholarly journals Genome-wide polygenic analysis of multiple sclerosis markers

2021 ◽  
Vol 13 (1S) ◽  
pp. 31-38
Author(s):  
Ya. R. Timasheva ◽  
T. R. Nasibullin ◽  
I. A. Tuktarova ◽  
V. V. Erdman ◽  
T. R. Galiullin ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Ethnic Groups ◽  
Noncoding Rna ◽  
Polymorphism Analysis ◽  
Polymorphic Loci ◽  
Lectin Domain ◽  
Genome Wide ◽  
A Genome ◽  
Disease Associations ◽  
Polygenic Analysis

Objective: to perform a genome-wide polygenic analysis of multiple sclerosis (MS) markers in the ethnic groups of Bashkirs, Russians, and Tatars living in the Republic of Bashkortostan (Russian Federation).Patients and methods. Genotyping was performed using allele-specific polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism analysis of genes of the human leukocyte differentiation antigens CD6 (rs17824933), CD40 (rs6074022), CD58 (rs2300747), CD86 (rs9282641), transcription factors SOX8 (rs2744148) and ZBTB46 (rs6062314), beta-mannosidase MANBA (rs228614), C-type lectin domain CLEC16A (rs12708716), ribosomal protein S6 kinase B1 RPS6KB1 (rs180515), and long noncoding RNA gene PVT1 (rs759648) in 644 patients with MS and 1408 controls. Multilocus analysis of the disease associations with combinations of genotypes and alleles of the studied polymorphic loci was performed using the APSampler algorithm.Results and discussion. We determined the distribution of genotype and allele frequencies of the studied polymorphic loci in the ethnic groups of Bashkirs, Russians, and Tatars. We also observed disease associations with CD58 (rs2300747) and RPS6KB1 (rs180515) polymorphic loci in Russian men, CD86 (rs9282641) in Russian, PVT1 (rs759648) in Tatar women, CD40 (rs6074022) in Bashkir men, and identified 19 combinations of genotypes and/or alleles significantly associated with MS.Conclusion. Based on the genome-wide polygenic analysis of MS markers, we identified ethno- and gender-specific combined markers of the disease susceptibility.

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