A Novel Embryo Phenotype Associated With Interspecific Hybrid Weakness in Rice Is Controlled by the MADS-Domain Transcription Factor OsMADS8

A novel hybrid weakness gene, DTE9, associated with a dark tip embryo (DTE) trait, was observed in CR6078, an introgression line derived from a cross between the Oryza sativa spp. japonica “Hwayeong” (HY) and the wild relative Oryza rufipogon. CR6078 seeds exhibit protruding embryos and flowers have altered inner floral organs. DTE9 was also associated with several hybrid weakness symptoms including decreased grain weight. Map-based cloning and transgenic approaches revealed that DTE9 is an allele of OsMADS8, a MADS-domain transcription factor. Genetic analysis indicated that two recessive complementary genes were responsible for the expression of the DTE trait. No sequence differences were observed between the two parental lines in the OsMADS8 coding region; however, numerous single nucleotide polymorphisms were detected in the promoter and intronic regions. We generated overexpression (OX) and RNA interference (RNAi) transgenic lines of OsMADS8 in HY and CR6078, respectively. The OsMADS8-OX lines showed the dark tip embryo phenotype, whereas OsMADS8-RNAi recovered the normal embryo phenotype. Changes in gene expression, including of ABCDE floral homeotic genes, were observed in the OsMADS8-OX and OsMADS8-RNAi lines. Overexpression of OsMADS8 led to decreased expression of OsEMF2b and ABA signaling-related genes including OsVP1/ABI3. HY seeds showed higher ABA content than CR6078 seeds, consistent with OsMADS8/DTE9 regulating the expression of genes related ABA catabolism in CR6078. Our results suggest that OsMADS8 is critical for floral organ determination and seed germination and that these effects are the result of regulation of the expression of OsEMF2b and its role in ABA signaling and catabolism.

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Polymorphism Detection of GDF9 Gene and Its Association with Litter Size in Luzhong Mutton Sheep (Ovis aries)

Animals ◽

10.3390/ani11020571 ◽

2021 ◽

Vol 11 (2) ◽

pp. 571

Author(s):

Fengyan Wang ◽

Mingxing Chu ◽

Linxiang Pan ◽

Xiangyu Wang ◽

Xiaoyun He ◽

...

Keyword(s):

Litter Size ◽

Tertiary Structure ◽

Novel Mutation ◽

Major Gene ◽

Ovis Aries ◽

Nucleotide Polymorphisms ◽

Economic Traits ◽

Coding Region ◽

Association Analyses ◽

Gdf9 Gene

Litter size is one of the most important economic traits in sheep. GDF9 and BMPR1B are major genes affecting the litter size of sheep. In this study, the whole coding region of GDF9 was sequenced and all the SNPs (single nucleotide polymorphisms) were determined in Luzhong mutton ewes. The FecB mutation was genotyped using the Sequenom MassARRAY®SNP assay technology. Then, the association analyses between polymorphic loci of GDF9 gene, FecB, and litter size were performed using a general linear model procedure. The results showed that eight SNPs were detected in GDF9 of Luzhong mutton sheep, including one novel mutation (g.41769606 T > G). The g.41768501A > G, g.41768485 G > A in GDF9 and FecB were significantly associated with litter size in Luzhong mutton ewes. The g.41768485 G > A is a missense mutation in the mature GDF9 protein region and is predicted to affect the tertiary structure of the protein. The results preliminarily demonstrated that GDF9 was a major gene affecting the fecundity of Luzhong mutton sheep and the two loci g.41768501A > G and g.41768485 G > A may be potential genetic markers for improving litter size.

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Haplotype analysis on correlation between transcription factor 7-like 2 gene polymorphism and breast cancer risk

BMC Cancer ◽

10.1186/s12885-021-08571-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yang Wang ◽

Xiaojuan Men ◽

Yongxue Gu ◽

Huidong Wang ◽

Zhicai Xu

Keyword(s):

Breast Cancer ◽

Transcription Factor ◽

Logistic Regression ◽

Abdominal Obesity ◽

Haplotype Analysis ◽

Environment Interaction ◽

Nucleotide Polymorphisms ◽

Chinese Han ◽

Locus Model ◽

Gene Environment

Abstract Background Up to now, limited researches focused on the association between transcription factor 7-like 2 gene (TF7L2) gene single nucleotide polymorphisms (SNPs) and breast cancer (BC) risk. The aim of this study was to evaluate the associations between TF7L2 and BC risk in Chinese Han population. Methods Logistic regression model was used to test the correlation between polymorphisms and BC risk. Strength of association was evaluated by odds ratio (OR) and 95% confidence interval (CI). Generalized multifactor dimensionality reduction (GMDR) was applied to analyze the SNP-SNP and gene-environment interaction. Results Logistic regression analysis indicated that the BC risk was obviously higher in carriers of rs1225404 polymorphism C allele than that in TT genotype carriers (TC or CC versus TT), adjusted OR (95%CI) =1.40 (1.09–1.72). Additionally, we also discovered that people with rs7903146- T allele had an obviously higher risk of BC than people with CC allele (CT or TT versus CC), adjusted OR (95%CI) =1.44 (1.09–1.82). GMDR model was used to research the effect of interaction among 4 SNPs and environmental factors on BC risk. We discovered an important two-locus model (p = 0.0100) including rs1225404 and abdominal obesity, suggesting a potential gene–environment correlation between rs1225404 and abdominal obesity. In general, the cross-validation consistency of two-locus model was 10 of 10, and the testing accuracy was 0.632. Compared with subjects with normal waist circumference (WC) value and rs1225404 TT genotype, abdominal obese subjects with rs1225404 TC or CC genotype had the highest BC risk. After covariate adjustment, OR (95%CI) was 2.23 (1.62–2.89). Haplotype analysis indicated that haplotype containing rs1225404-T and rs7903146-C alleles were associated with higher BC risk. Conclusions C allele of rs1225404 and T allele of rs7903146, interaction between rs1225404 and abdominal obesity, rs1225404-T and rs7903146-C haplotype were all related to increased BC risk.

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Sequence variants in the FcεRI alpha chain gene

Journal of Applied Physiology ◽

10.1152/japplphysiol.00993.2001 ◽

2002 ◽

Vol 93 (1) ◽

pp. 37-41 ◽

Cited By ~ 33

Author(s):

Toshiki Shikanai ◽

Eric S. Silverman ◽

Brian W. Morse ◽

Craig M. Lilly ◽

Hiroshi Inoue ◽

...

Keyword(s):

Promoter Region ◽

Population Substructure ◽

Chain Gene ◽

Polymorphism Analysis ◽

Sequence Variants ◽

Nucleotide Polymorphisms ◽

Coding Region ◽

Alpha Chain ◽

Asthmatic Patients ◽

Single Stranded Conformational Polymorphism

There is a relationship between IgE levels and expression of high-affinity IgE receptors (FcεRI). Because the alpha chain is the only portion of the receptor that binds directly to IgE, we reasoned that sequence variants in the FcεRI alpha gene may exist that alter these binding events. We screened all of the exons and the promoter region of the FcεRI alpha chain gene with genomic DNA from 389 asthmatic and 341 normal control subjects for mutations by using single-stranded conformational polymorphism analysis. No nonsynonomous single nucleotide polymorphisms (SNPs) were identified in the coding region. Three SNPs were found in the promoter region: an A/C transversion at −770 from the translation start site; a G/A transition at −664; and a T/C transition at −335. No differences in allele frequencies were detected between asthmatic subjects and controls. Homozygosity for the C variant at locus −335 was more common in Caucasian asthmatic patients with IgE levels in the lower quartile than in the upper quartile ( P = 0.032). An analysis of highly polymorphic SNPs indicated that this association is unlikely to be due to population substructure. We conclude that homozygosity for the C allele of FcεRI alpha chain variant is associated with lower IgE levels.

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Human DNA sequences homologous to a protein coding region conserved between homeotic genes of Drosophila

Cell ◽

10.1016/0092-8674(84)90261-7 ◽

1984 ◽

Vol 38 (3) ◽

pp. 667-673 ◽

Cited By ~ 121

Author(s):

Michael Levine ◽

Gerald M. Rubin ◽

Robert Tjian

Keyword(s):

Dna Sequences ◽

Homeotic Genes ◽

Coding Region ◽

Protein Coding ◽

Human Dna

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Single nucleotide polymorphisms of CBF4 locus region of Arabidopsis thaliana correspond to drought tolerance

Chinese Journal of Agricultural Biotechnology ◽

10.1079/cjb200440 ◽

2004 ◽

Vol 1 (3) ◽

pp. 181-190 ◽

Cited By ~ 1

Author(s):

Hao Gang-Ping ◽

Wu Zhong-Yi ◽

Chen Mao-Sheng ◽

Cao Ming-Qing ◽

Dominique Brunel ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Drought Tolerance ◽

World Wide ◽

Nucleotide Variation ◽

Nucleotide Polymorphisms ◽

Water Deficiency ◽

Coding Region ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Adaptation To Drought

AbstractThe levels of drought tolerance and nucleotide polymorphism at the CBF4 locus were examined in a world-wide sample of 17 core accessions of Arabidopsis thaliana. The results showed that different accessions exhibited considerable differences in adaptation to drought stress. Compared with Columbia accession, the frequency of nucleotide polymorphism at the CBF4 locus of 25av, 203av and 244av accessions, including single nucleotide polymorphism (SNP) and insertion/deletion (Indel), was high, on average 1 SNP per 35.8 bp and 1 Indel per 143 bp. No significance in all regions of Tajima's D test indicated that the neutral mutation hypothesis could explain the nucleotide polymorphism in this CBF4 gene region. The higher polymorphism was the result of purification selection. Nucleotide polymorphism in the non-coding region was three times higher than in the coding region. This might indicate a recent relaxation of selection pressures on the non-coding region of CBF4 gene. In the coding region of CBF4, SNP frequency was 1 SNP per 96.4 bp and one non-synonymous mutation was detected from 25av, 203av and 244av accessions: the amino acid variation gly↔val at position 205, caused by the nucleotide variation G↔T at position 1034 (corresponding to the nucleotide at position 19 696 of GenBank accession no. AB015478 as 1). Furthermore, four differential SNPs were discovered in haplotype 6 constituted by 203av, one of them located in the 3′ non-coding region (A↔C at position 1106) and the others in the 5′ non-coding region (A↔G, A↔C and G↔A at positions 27, 129 and 171, respectively). The drought tolerance assay indicated that accession 203av was the best at tolerating water deficiency. We propose that haplotype 6 is consistent with its drought tolerance.

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Variants in the VCAM1 gene and risk for symptomatic stroke in sickle cell disease

Blood ◽

10.1182/blood-2001-12-0306 ◽

2002 ◽

Vol 100 (13) ◽

pp. 4303-4309 ◽

Cited By ~ 52

Author(s):

James G. Taylor VI ◽

Delia C. Tang ◽

Sharon A. Savage ◽

Susan F. Leitman ◽

Seth I. Heller ◽

...

Keyword(s):

Sickle Cell ◽

Critical Role ◽

Genome Project ◽

Monogenic Disease ◽

Candidate Snps ◽

Healthy Population ◽

Nucleotide Polymorphisms ◽

Coding Region ◽

A Cell ◽

The Human Genome Project

Stroke is a major cause of morbidity and mortality in sickle cell (SS) disease. Genetic risk factors have been postulated to contribute to this clinical outcome. The human genome project has substantially increased the catalog of variations in genes, many of which could modify the risk for manifestations of disease outcome in a monogenic disease, namely SS. VCAM1 is a cell adhesion molecule postulated to play a critical role in the pathogenesis of SS disease. We identified a total of 33 single nucleotide polymorphisms (SNPs) by sequencing the entire coding region, 2134 bp upstream of the 5′ end of the published cDNA, 217 bp downstream of the 3′ end of the cDNA, and selected intronic regions of the VCAM1 locus. Allelic frequencies for selected SNPs were determined in a healthy population. We subsequently analyzed 4 nonsynonymous coding, 2 synonymous coding, and 4 common promoter SNPs in a genetic association study of clinically apparent stroke in SS disease conducted in a cohort derived from a single institution in Jamaica (51 symptomatic cases and 51 matched controls). Of the 10 candidate SNPs analyzed in this pilot study, the variant allele of the nonsynonymous SNP, VCAM1 G1238C, may be associated with protection from stroke (odds ratio [OR] 0.35, 95% confidence interval [CI] 0.15-0.83, P = .04). Further study is required to confirm the importance of this variant inVCAM1 as a clinically useful modifier of outcome in SS disease.

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The genome and transcriptome of the Phalaenopsis yield insights into floral organ development and flowering regulation

10.7287/peerj.preprints.1707v1 ◽

2016 ◽

Cited By ~ 1

Author(s):

Jian-Zhi Huang ◽

Chih-Peng Lin ◽

Ting-Chi Cheng ◽

Ya-Wen Huang ◽

Yi-Jung Tsai ◽

...

Keyword(s):

Economic Value ◽

Draft Genome ◽

Floral Organ ◽

Cool Temperature ◽

Organ Development ◽

Nucleotide Polymorphisms ◽

Protein Coding ◽

Draft Genome Assembly ◽

Genome Data ◽

Expression Of Genes

Phalaenopsis orchid is an important potted flower with high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802’, a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal the key role of PhAGL6b in the regulation of flower organ development involves alternative splicing. We also show gibberellin pathways that regulate the expression of genes control flowering time during the stage in reproductive phase change induced by cool temperature. Our work should contribute a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

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Screening of Three Different Alleles of mtDNA (G709A, G3496T, A3537G) in Subpopulation of UKM Students

Malaysian Journal of Medical and Biological Research ◽

10.18034/mjmbr.v5i1.447 ◽

2018 ◽

Vol 5 (1) ◽

pp. 37-40

Author(s):

Seri Mirianti Ishar ◽

Jeyaganesan Pillay a/l Balaraman ◽

Muhammad Jefri Mohd Yusof ◽

Khairul Osman ◽

Lee Loong Chuen

Keyword(s):

Uv Light ◽

Forensic Genetics ◽

Nucleotide Polymorphisms ◽

Coding Region ◽

Documentation System ◽

Single Nucleotide ◽

National University ◽

Pcr Products ◽

Malay Population ◽

Mutation Allele

Human DNA consists of nucleus DNA (nDNA) and mitochondrial DNA (mtDNA). Both are valuable in medicine and forensic genetics but in this project, single nucleotide polymorphisms (SNPs) in mtDNA are used to trace the mutation occurred. Mutations in the sequence of alleles can lead to haplogroup variation and also certain diseases. The purpose of this study is to screen of mutations on alleles G709A, G3496T, and A3537G in Malay population of The National University of Malaysia (UKM) students. These SNPs lie in the ND1 (nitrogen dehydrogenase subunit 1) coding region, and the reports state that these three alleles are prone to mutate. From MitoMap Web site, the mutations of these alleles are reported to have potential in causing several diseases with the collaboration of other SNPs mutation. Allele G709A is reported to have an association with hearing loss and Leber Hereditary Optic Neuropathy (LHON) while allele G3496T is associated to LHON only. Allele A3537G is related to diabetes. A total of 100 DNA samples were collected from Malay students of UKM and preserved on FTA card to be purified later. The concentration of the DNA on the purified FTA card was between 10μM to 20μM. An attempt was made by amplifying those three loci from the genomic DNA. The amplified product was detected and separated using 1% gel electrophoresis. Before sequencing, the PCR products were visualized under UV light using gel documentation system. All PCR products were sequenced to detect the mutation on every single position chosen. From the alignment of sequencing results, allele G709A and allele G3496T showed no mutation. Meanwhile four samples from alleles A3537G has the mutation. From the results obtained, it seems that mutations are rare in all selected alleles. It is recommended to increase the sample size and alleles selected in the future to increase the strength of the study. This study also should be applied to other populations in Malaysia such as Chinese and Indian.

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Nucleotide Polymorphisms in the α2 Gene Define Multiple Alleles That Are Associated With Differences in Platelet α2β1 Density

Blood ◽

10.1182/blood.v92.7.2382.2382_2382_2388 ◽

1998 ◽

Vol 92 (7) ◽

pp. 2382-2388 ◽

Cited By ~ 9

Author(s):

Marcie Kritzik ◽

Brian Savage ◽

Diane J. Nugent ◽

Sentot Santoso ◽

Zaverio M. Ruggeri ◽

...

Keyword(s):

Whole Blood ◽

Type I Collagen ◽

Type I ◽

Nucleotide Polymorphisms ◽

Coding Region ◽

Platelet Surface ◽

Multiple Alleles ◽

Increased Risk ◽

Allelic Differences

Three allelic differences in the α2 gene are associated with expression levels of the α2β1 integrin on the platelet surface. We have previously defined two linked silent polymorphisms in the α2 gene coding region at nucleotides 807 (C or T) and 873 (G or A). We have now identified one rarer nucleotide polymorphism in the coding region at nucleotide 837 (T or C) and four additional linked polymorphisms within the introns that flank these coding sequences. Moreover, we have determined that the alloantigenic Br polymorphism, which resides in a distal coding region at nucleotide 1648, is also linked to the 837 polymorphism. Thus, three α2 gene alleles, defined by eight nucleotide polymorphisms, have now been discovered. Allele 1 (807T/837T/873A/Brb) is associated with increased levels of α2β1; allele 2 (807C/837T/873G/Brb) and allele 3 (807C/837C/873G/Bra) are each associated with lower levels of α2β1. Finally, we also show here that the rate of platelet attachment to type I collagen in whole blood under conditions of high shear rate (1,500/s) is proportional to the density of α2β1 receptors on the platelet surface. Thus, the density of platelet α2β1 could have an important impact on platelet adhesion to collagen in whole blood and therefore on platelet function in vivo, contributing to an increased risk of thrombosis or to bleeding in relevant disease states.

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Genome-wide association studies of yield-related traits in high-latitude japonica rice

BMC Genomic Data ◽

10.1186/s12863-021-00995-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Guomin Zhang ◽

Rongsheng Wang ◽

Juntao Ma ◽

Hongru Gao ◽

Lingwei Deng ◽

...

Keyword(s):

Linear Model ◽

High Latitude ◽

Association Studies ◽

Genome Wide Association ◽

Japonica Rice ◽

Genome Wide Association Studies ◽

Heilongjiang Province ◽

Nucleotide Polymorphisms ◽

Coding Region ◽

Genome Wide

Abstract Background Heilongjiang Province is a high-quality japonica rice cultivation area in China. One in ten bowls of Chinese rice is produced here. Increasing yield is one of the main aims of rice production in this area. However, yield is a complex quantitative trait composed of many factors. The purpose of this study was to determine how many genetic loci are associated with yield-related traits. Genome-wide association studies (GWAS) were performed on 450 accessions collected from northeast Asia, including Russia, Korea, Japan and Heilongjiang Province of China. These accessions consist of elite varieties and landraces introduced into Heilongjiang Province decade ago. Results After resequencing of the 450 accessions, 189,019 single nucleotide polymorphisms (SNPs) were used for association studies by two different models, a general linear model (GLM) and a mixed linear model (MLM), examining four traits: days to heading (DH), plant height (PH), panicle weight (PW) and tiller number (TI). Over 25 SNPs were found to be associated with each trait. Among them, 22 SNPs were selected to identify candidate genes, and 2, 8, 1 and 11 SNPs were found to be located in 3′ UTR region, intron region, coding region and intergenic region, respectively. Conclusions All SNPs detected in this research may become candidates for further fine mapping and may be used in the molecular breeding of high-latitude rice.

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