scholarly journals Genetic Performance of the Semidwarfing Allele sd1 Derived from a Japonica Rice Cultivar and Minimum Requirements to Detect Its Single-Nucleotide Polymorphism by MiSeq Whole-Genome Sequencing

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Motonori Tomita ◽  
Kazuo Ishii
Keyword(s):  
Reference Genome ◽  
Green Revolution ◽  
Rice Cultivar ◽  
Chromosome 1 ◽  
Japonica Rice ◽  
Loss Of Function ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Isogenic Lines ◽  
Minimum Requirements

The influence of the semidwarfing gene sd1 derived from the rice cultivar Jukkoku (Jukkoku_sd1) and IR8 (IR8_sd1), which contributed to the Green Revolution, d60 from Hokuriku 100, as well as the combination of sd1 and d60 (Jukkoku_sd1 plus d60 and IR8_sd1 plus d60), was investigated using isogenic lines raised by backcrossing with the cultivar Koshihikari. The isogenic lines carrying Jukkoku_sd1, IR8_sd1, d60, Jukkoku_sd1 plus d60, and IR8_sd1 plus d60 had considerably shorter culm lengths than Koshihikari by 19.2%, 22.8%, 26.0%, 45.1%, and 43.4%, respectively. The sd1 plus d60 lines showed additively reduced culms, indicating that the function of d60 was different from sd1. In contrast to the culm reduction, Jukkoku_sd1 showed productive merit with a panicle length of 2.5% greater than the origin. MiSeq next-generation sequencer was used to optimize a minimum scale to detect Jukkoku_sd1 in practical breeding. Mapping with the reference genome of Nipponbare gained the average depths of Koshihikari Jukkoku_sd1 and Koshihikari being 9.17 and 7.29, respectively. Comparing the vcf files of the entire genomes of Koshihikari Jukkoku_sd1 and the virtual Koshihikari revealed a G to T SNP at position 38,382,746 in the sd1 locus on chromosome 1 of Koshihikari, causing a loss-of-function mutation of GA20-oxidase.

scholarly journals Prenatal diagnosis of 7 cases with uniparental disomy by utilization of single nucleotide polymorphism array

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Lili Zhou ◽  
Zhaoke Zheng ◽  
Yunzhi Xu ◽  
Xiaoxiao Lv ◽  
Chenyang Xu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Prenatal Diagnosis ◽  
Molecular Analysis ◽  
Correct Diagnosis ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Chromosome 1 ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Rescue Mechanism

Abstract Background The phenotypes of uniparental disomy (UPD) are variable, which may either have no clinical impact, lead to clinical signs and symptoms. Molecular analysis is essential for making a correct diagnosis. This study involved a retrospective analysis of 4512 prenatal diagnosis samples and explored the molecular characteristics and prenatal phenotypes of UPD using a single nucleotide polymorphism (SNP) array. Results Out of the 4512 samples, a total of seven cases of UPD were detected with an overall frequency of 0.16%. Among the seven cases of UPD, two cases are associated with chromosomal aberrations (2/7), four cases (4/7) had abnormal ultrasonographic findings. One case presented with iso-UPD (14), and two case presented with mixed hetero/iso-UPD (15), which were confirmed by Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as maternal UPD (15) associated with Prader-Willi syndrome (PWS). Four cases had iso-UPD for chromosome 1, 3, 14, and 16, respectively; this is consistent with the monosomy rescue mechanism. Another three cases presented with mixed hetero/isodisomy were consistent with a trisomy rescue mechanism. Conclusion The prenatal phenotypes of UPD are variable and molecular analysis is essential for making a correct diagnosis and genetic counselling of UPD. The SNP array is a useful genetic test in prenatal diagnosis cases with UPD.

Use of New Generation Single Nucleotide Polymorphism Genotyping for Rapid Development of Near-Isogenic Lines in Rice

Crop Science ◽  
2011 ◽  
Vol 51 (5) ◽  
pp. 2067-2073 ◽  
Author(s):  
Chanthakhone Boualaphanh ◽  
Venea D. Daygon ◽  
Mariafe N. Calingacion ◽  
Jarawit Sanitchon ◽  
Darunee Jothityangkoon ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Rapid Development ◽  
Near Isogenic Lines ◽  
Single Nucleotide Polymorphism Genotyping ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Isogenic Lines ◽  
New Generation

scholarly journals Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97

2017 ◽  
Vol 5 (14) ◽  
Author(s):  
Kerri M. Malone ◽  
Damien Farrell ◽  
Tod P. Stuber ◽  
Olga T. Schubert ◽  
Ruedi Aebersold ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Mycobacterium Bovis ◽  
Genome Sequence ◽  
Bovine Tuberculosis ◽  
Reference Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Coding Sequences ◽  
Content Type ◽  
Reference Genome Sequence

ABSTRACT We report here an update to the reference genome sequence of the bovine tuberculosis bacillus Mycobacterium bovis AF2122/97, generated using an integrative multiomics approach. The update includes 42 new coding sequences (CDSs), 14 modified annotations, 26 single-nucleotide polymorphism (SNP) corrections, and disclosure that the RD900 locus, previously described as absent from the genome, is in fact present.

scholarly journals Congenital sideroblastic anemia due to mutations in the mitochondrial HSP70 homologue HSPA9

Blood ◽  
2015 ◽  
Vol 126 (25) ◽  
pp. 2734-2738 ◽  
Author(s):  
Klaus Schmitz-Abe ◽  
Szymon J. Ciesielski ◽  
Paul J. Schmidt ◽  
Dean R. Campagna ◽  
Fedik Rahimov ◽  
...  
Keyword(s):  
Loss Of Function ◽  
Nucleotide Polymorphism ◽  
Sideroblastic Anemia ◽  
Single Nucleotide ◽  
Common Coding ◽  
Altered Gene Expression ◽  
Key Points ◽  
In Trans ◽  
Altered Gene ◽  
Mitochondrial Hsp70

Key Points Mutations in HSPA9 cause CSAs that may be inherited in a recessive or pseudodominant manner. HSPA9 loss-of-function alleles are often inherited in trans with a common coding single nucleotide polymorphism associated with altered gene expression.

scholarly journals Different Phenotypes, Similar Genomes: Three Newly Sequenced Fusarium fujikuroi Strains Induce Different Symptoms in Rice Depending on Temperature

2020 ◽  
Vol 110 (3) ◽  
pp. 656-665
Author(s):  
Edoardo Piombo ◽  
Pietro Bosio ◽  
Alberto Acquadro ◽  
Pamela Abbruscato ◽  
Davide Spadaro
Keyword(s):  
Gene Prediction ◽  
Illumina Miseq ◽  
Rice Cultivar ◽  
Fusarium Fujikuroi ◽  
Growth Speed ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Bakanae Disease ◽  
Gibberellin Production ◽  
Variant Analysis

Bakanae, caused by the hemibiotrophic fungus Fusarium fujikuroi, is one of the most important diseases of rice and is attributed to up to 75% of losses, depending on the strain and environmental conditions. Some strains cause elongation and thin leaves, whereas others induce stunting and chlorotic seedlings. Differences in symptoms are attributed to genetic differences in the strains. F. fujikuroi strains Augusto2, CSV1, and I1.3 were sequenced with Illumina MiSeq, and pathogenicity trials were conducted on rice cultivar Galileo, which is susceptible to bakanae. By performing gene prediction, single nucleotide polymorphism (SNP) calling, and structural variant analysis with a reference genome, we show how an extremely limited number of polymorphisms in genes not commonly associated with bakanae disease can cause strong differences in phenotype. CSV1 and Augusto2 were particularly close, with only 21,887 SNPs between them, but they differed in virulence, reaction to temperature, induced symptoms, colony morphology and color, growth speed, fumonisin, and gibberellin production. Genes potentially involved in the shift in phenotype were identified. Furthermore, we show how temperature variation may result in different symptoms even in rice plants inoculated with the same F. fujikuroi strain. Moreover, all of the F. fujikuroi strains became more virulent at higher temperatures. Significant differences were likewise observed in gibberellic acid production and in the expression of both fungal and plant gibberellin biosynthetic genes.

scholarly journals Discovery of a Novel Induced Polymorphism in SD1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1198
Author(s):  
Shivashankar Bhuvaneswari ◽  
Subbaiyan Gopala Krishnan ◽  
Ranjith Kumar Ellur ◽  
Kunnummal Kurungara Vinod ◽  
Haritha Bollinedi ◽  
...  
Keyword(s):  
Stop Codon ◽  
Spontaneous Mutation ◽  
Rice Cultivar ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Dcaps Marker ◽  
Dwarf Cultivar ◽  
Functional Single Nucleotide Polymorphism ◽  
Improvement Programs ◽  
Rice Improvement

The semi-dwarfing allele, sd1-d, has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), sd1-d, derived from a spontaneous mutation, has a 383-bp deletion in the SD1 gene. To date, as many as seven alleles of the SD1 gene have been identified and used in rice improvement, either with a functional single-nucleotide polymorphism (SNP), with insertion–deletions (InDels), or both. Here, we report discovery of a novel SNP in the SD1 gene from the rice genotype, Pusa 1652. Genetic analysis revealed that the inheritance of the semi-dwarfism in Pusa 1652 is monogenic and recessive, but it did not carry the sd1-d allele. However, response to exogenous gibberellic acid (GA3) application and the subsequent bulked segregant and linkage analyses confirmed that the SD1 gene is involved in the plant height reduction in Pusa 1652. Sequencing of the SD1 gene from Pusa 1652 revealed a novel transition in exon 3 (T/A) causing a nonsense mutation at the 300th codon. The stop codon leads to premature termination, resulting in a truncated protein of OsGA20ox2 obstructing the GA3 biosynthesis pathway. This novel recessive allele, named sd1-bm, is derived from Bindli Mutant 34 (BM34), a γ-ray induced mutant of a short-grain aromatic landrace, Bindli. BM34 is the parent of an aromatic semi-dwarf cultivar, Pusa 1176, from which Pusa 1652 is derived. The semi-dwarfing allele, sd1-bm, was further validated by developing a derived cleaved amplified polymorphic sequence (dCAPS) marker, AKS-sd1. This allele provides an alternative to the most widely used sd1-d in rice improvement programs and the functional dCAPS marker will facilitate marker-assisted introgression of the semi-dwarf trait into tall genotypes.

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