scholarly journals WB1, a Regulator of Endosperm Development in Rice, Is Identified by a Modified MutMap Method

2018 ◽  
Vol 19 (8) ◽  
pp. 2159 ◽  
Author(s):  
Hong Wang ◽  
Yingxin Zhang ◽  
Lianping Sun ◽  
Peng Xu ◽  
Ranran Tu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
High Specificity ◽  
Endosperm Development ◽  
Grain Weight ◽  
Recessive Mutation ◽  
Related Factors ◽  
Rice Endosperm ◽  
Rice Mutant ◽  
Isolation And Characterization ◽  
White Belly

Abnormally developed endosperm strongly affects rice (Oryza sativa) appearance quality and grain weight. Endosperm formation is a complex process, and although many enzymes and related regulators have been identified, many other related factors remain largely unknown. Here, we report the isolation and characterization of a recessive mutation of White Belly 1 (WB1), which regulates rice endosperm development, using a modified MutMap method in the rice mutant wb1. The wb1 mutant develops a white-belly endosperm and abnormal starch granules in the inner portion of white grains. Representative of the white-belly phenotype, grains of wb1 showed a higher grain chalkiness rate and degree and a lower 1000-grain weight (decreased by ~34%), in comparison with that of Wild Type (WT). The contents of amylose and amylopectin in wb1 significantly decreased, and its physical properties were also altered. We adopted the modified MutMap method to identify 2.52 Mb candidate regions with a high specificity, where we detected 275 SNPs in chromosome 4. Finally, we identified 19 SNPs at 12 candidate genes. Transcript levels analysis of all candidate genes showed that WB1 (Os04t0413500), encoding a cell-wall invertase, was the most probable cause of white-belly endosperm phenotype. Switching off WB1 with the CRISPR/cas9 system in Japonica cv. Nipponbare demonstrates that WB1 regulates endosperm development and that different mutations of WB1 disrupt its biological function. All of these results taken together suggest that the wb1 mutant is controlled by the mutation of WB1, and that the modified MutMap method is feasible to identify mutant genes, and could promote genetic improvement in rice.

scholarly journals The nuclear-localized PPR protein OsNPPR1 is important for mitochondrial function and endosperm development in rice

2019 ◽  
Vol 70 (18) ◽  
pp. 4705-4720 ◽  
Author(s):  
Yuanyuan Hao ◽  
Yunlong Wang ◽  
Mingming Wu ◽  
Xiaopin Zhu ◽  
Xuan Teng ◽  
...  
Keyword(s):  
Mitochondrial Function ◽  
Endosperm Development ◽  
Pentatricopeptide Repeat ◽  
Coding Region ◽  
Rice Mutant ◽  
Ppr Protein ◽  
Isolation And Characterization ◽  
Ppr Proteins

Abstract Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants. Recent studies revealed the functions of PPR proteins in organellar RNA metabolism and plant development, but the functions of most PPR proteins, especially PPRs localized in the nucleus, remain largely unknown. Here, we report the isolation and characterization of a rice mutant named floury and growth retardation1 (fgr1). fgr1 showed floury endosperm with loosely arranged starch grains, decreased starch and amylose contents, and retarded seedling growth. Map-based cloning showed that the mutant phenotype was caused by a single nucleotide substitution in the coding region of Os08g0290000. This gene encodes a nuclear-localized PPR protein, which we named OsNPPR1, that affected mitochondrial function. In vitro SELEX and RNA-EMSAs showed that OsNPPR1 was an RNA protein that bound to the CUCAC motif. Moreover, a number of retained intron (RI) events were detected in fgr1. Thus, OsNPPR1 was involved in regulation of mitochondrial development and/or functions that are important for endosperm development. Our results provide novel insights into coordinated interaction between nuclear-localized PPR proteins and mitochondrial function.

scholarly journals Identification of sixteen novel candidate genes for late onset Parkinson’s disease

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Alessandro Gialluisi ◽  
Mafalda Giovanna Reccia ◽  
Nicola Modugno ◽  
Teresa Nutile ◽  
Alessia Lombardi ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Candidate Genes ◽  
Rare Variants ◽  
Late Onset ◽  
High Specificity ◽  
Diagnostic Tools ◽  
Multi Stage ◽  
Whole Exome ◽  
Family Based

Abstract Background Parkinson’s disease (PD) is a neurodegenerative movement disorder affecting 1–5% of the general population for which neither effective cure nor early diagnostic tools are available that could tackle the pathology in the early phase. Here we report a multi-stage procedure to identify candidate genes likely involved in the etiopathogenesis of PD. Methods The study includes a discovery stage based on the analysis of whole exome data from 26 dominant late onset PD families, a validation analysis performed on 1542 independent PD patients and 706 controls from different cohorts and the assessment of polygenic variants load in the Italian cohort (394 unrelated patients and 203 controls). Results Family-based approach identified 28 disrupting variants in 26 candidate genes for PD including PARK2, PINK1, DJ-1(PARK7), LRRK2, HTRA2, FBXO7, EIF4G1, DNAJC6, DNAJC13, SNCAIP, AIMP2, CHMP1A, GIPC1, HMOX2, HSPA8, IMMT, KIF21B, KIF24, MAN2C1, RHOT2, SLC25A39, SPTBN1, TMEM175, TOMM22, TVP23A and ZSCAN21. Sixteen of them have not been associated to PD before, were expressed in mesencephalon and were involved in pathways potentially deregulated in PD. Mutation analysis in independent cohorts disclosed a significant excess of highly deleterious variants in cases (p = 0.0001), supporting their role in PD. Moreover, we demonstrated that the co-inheritance of multiple rare variants (≥ 2) in the 26 genes may predict PD occurrence in about 20% of patients, both familial and sporadic cases, with high specificity (> 93%; p = 4.4 × 10− 5). Moreover, our data highlight the fact that the genetic landmarks of late onset PD does not systematically differ between sporadic and familial forms, especially in the case of small nuclear families and underline the importance of rare variants in the genetics of sporadic PD. Furthermore, patients carrying multiple rare variants showed higher risk of manifesting dyskinesia induced by levodopa treatment. Conclusions Besides confirming the extreme genetic heterogeneity of PD, these data provide novel insights into the genetic of the disease and may be relevant for its prediction, diagnosis and treatment.

Dissection of Closely Linked QTLs Controlling Grain Size in Rice

2021 ◽  
Author(s):  
Pao Xue ◽  
Yu-yu Chen ◽  
Xiao-xia Wen ◽  
Bei-fang Wang ◽  
Qin-qin Yang ◽  
...  
Keyword(s):  
Grain Size ◽  
Genetic Resources ◽  
Candidate Genes ◽  
Cell Expansion ◽  
Grain Weight ◽  
Cytological Observation ◽  
Yield Improvement ◽  
Transcript Levels ◽  
Grain Width ◽  
Successive Generations

Abstract Grain size is a key constituent of grain weight and appearance in rice. However, insufficient attention has been paid to the small-effect QTLs on grain size. In the present study, residual heterozygous populations were developed for mapping two genetically linked small-effect QTLs for grain size. After genotyping and phenotyping of five successive generations, qGS7.1 was dissected into three QTLs and two were selected for further analysis. qTGW7.2a was finally mapped into a 21.10-kb interval containing four annotated candidate genes. Transcript levels assay showed that the expression of candidates LOC_Os07g39490 and LOC_Os07g39500 were significantly reduced in the NIL- qTGW7.2a BG1 . Cytological observation indicated that qTGW7.2a regulated grain width through controlling cell expansion. Use the same strategy, qTGW7.2b was fine mapped into a 52.71-kb interval, showing a significant effect on grain length and width with opposite allelic directions but little on grain weight. Our study provides new genetic resources for yield improvement and fine-tunes of grain size in rice.

scholarly journals HypermethylatedFAM5CandMYLKin Serum as Diagnosis and Pre-Warning Markers for Gastric Cancer

2012 ◽  
Vol 32 (3) ◽  
pp. 195-202 ◽  
Author(s):  
Lu Chen ◽  
Liping Su ◽  
Jianfang Li ◽  
Yanan Zheng ◽  
Beiqin Yu ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Candidate Genes ◽  
Early Stage ◽  
Precancerous Lesions ◽  
Single Gene ◽  
High Specificity ◽  
Serum Samples ◽  
Promoter Regions ◽  
Gastric Cancer Cell Lines ◽  
Combined Detection

Most cases of gastric cancer (GC) are not diagnosed at early stage which can be curable, so it is necessary to identify effective biomarkers for its diagnosis and pre-warning. We have used methylated DNA immunoprecipitation (MeDIP) to identify genes that are frequently methylated in gastric cancer cell lines. Promoter regions hypermethylation of candidate genes were tested by methylation-specific polymerase chain reaction (MSP) in serum samples, including GC (n= 58), gastric precancerous lesions (GPL,n= 46), and normal controls (NC,n= 30). Eighty two hypermethylated genes were acquired by array analysis and 5 genes (BCAS4, CHRM2, FAM5C, PRACandMYLK) were selected as the candidate genes. Three genes (CHRM2, FAM5CandMYLK) were further confirmed to show methylation rates increased with progression from NC to GPL, then to GC. There was obvious decrease in detection ofFAM5CandMYLKhypermethylation, but notCHRM2, from preoperative to postoperative evaluation (P< 0.001). Combined detection of FAM5C and MYLK hypermethylation had a higher sensitivity in GC diagnosis (77.6%,45/58) and pre-warning (30.4%,14/46) than one single gene detection and also had a high specificity of 90%. The combined hypermethylated status ofFAM5CandMYLKcorrelated with tumor size (P< 0.001), tumor invasion depth (P= 0.001) and tumor-node-metastasis (TNM) stage (P= 0.003). HypermethylatedFAM5CandMYLKcan be used as potential biomarkers for diagnosis and pre-warning of GC.

scholarly journals Genome-Wide Association Mapping through 90K SNP Array for Quality and Yield Attributes in Bread Wheat against Water-Deficit Conditions

Agriculture ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 392
Author(s):  
Hafiz Ghulam Muhu-Din Ahmed ◽  
Muhammad Sajjad ◽  
Yawen Zeng ◽  
Muhammad Iqbal ◽  
Sultan Habibullah Khan ◽  
...  
Keyword(s):  
Grain Yield ◽  
Candidate Genes ◽  
Water Deficit ◽  
Bread Wheat ◽  
Genome Wide Association ◽  
Water Deficit Stress ◽  
Yield Attributes ◽  
Yield And Quality ◽  
Isolation And Characterization ◽  
Genome Wide

The decrease in water resources is a serious threat to food security world-wide. In this regard, a genome-wide association study (GWAS) was conducted to identify grain yield and quality-related genes/loci under normal and water-deficit conditions. Highly significant differences were exhibited among genotypes under both conditions for all studied traits. Water-deficit stress caused a reduction in grains yield and an increase in grains protein contents (GPC) and gluten contents (GLC). Population structure divided the 96 genotypes into four sub-populations. Out of 72 significant marker-trait associations (MTAs), 28 and 44 were observed under normal and water-deficit stress conditions, respectively. Pleiotropic loci (RAC875_s117925_244, BobWhite_c23828_341 and wsnp_CAP8_c334_304253) for yield and quality traits were identified on chromosomes 5A, 6B and 7B, respectively, under normal conditions. Under a water-deficit condition, the pleiotropic loci (Excalibur_c48047_90, Tdurum_contig100702_265 and BobWhite_c19429_95) for grain yield per plant (GYP), GPC and GLC were identified on chromosomes 3A, 4A and 7B, respectively. The pleiotropic loci (BS00063551_51 and RAC875_c28721_290) for GPC and GLC on chromosome 1B and 3A, respectively, were found under both conditions. Besides the validation of previously reported MTAs, some new MTAs were identified for flag leaf area (FLA), thousand grain weight (TGW), GYP, GPC and GLC under normal and water-deficit conditions. Twenty SNPs associated with the traits were mapped in the coding DNA sequence (CDS) of the respective candidate genes. The protein functions of the identified candidate genes were predicted and discussed. Isolation and characterization of the candidate genes, wherein, SNPs were mapped in CDS will result in discovering novel genes underpinning water-deficit tolerance in bread wheat.

scholarly journals Genetic Analysis and Related Gene Primary Mapping of Heat Stress Tolerance in Cucumber Using Bulked Segregant Analysis

HortScience ◽  
2019 ◽  
Vol 54 (3) ◽  
pp. 423-428
Author(s):  
Min Wang ◽  
Wenrui Liu ◽  
Biao Jiang ◽  
Qingwu Peng ◽  
Xiaoming He ◽  
...  
Keyword(s):  
Heat Stress ◽  
Genetic Analysis ◽  
Candidate Genes ◽  
High Temperatures ◽  
Genomic Sequence ◽  
Bulked Segregant Analysis ◽  
Recessive Gene ◽  
Chromosome 1 ◽  
Isolation And Characterization ◽  
Indel Markers

Heat stress (HS) negatively influences plant development and growth, especially production and quality. Cucumber is a widely cultivated plant in the gourd family Cucurbitaceae that is often exposed to high temperatures during summer and protected cultivation. In this study, we performed whole-genome re-sequencing of two pools, one heat-tolerant and one heat-sensitive, of the F2 population derived from L-9 (heat-resistant) and A-16 (heat-sensitive). The genetic analysis showed that the heat resistance of L-9 cucumber seedlings was controlled by a single recessive gene. By combining bulked segregant analysis (BSA) technology, the crucial gene related to HS was preliminarily mapped to a 1.08-Mb region on chromosome 1. To fine-map the locus, Indel markers were designed according to the genomic sequence. Finally, the gene was narrowed to a 550-kb region flanked by two Indel markers, namely Indel-H90 and Indel-H224, that contained 56 candidate genes. Re-sequencing results indicated that 10 candidate genes among the 56 in the candidate region showed single base pair differences in the exons. Quantitative reverse-transcription polymerase chain reaction showed that 6 genes among the 10 candidate genes were significantly decreased when exposed to high temperatures. These results not only were useful for the isolation and characterization of the key genes involved in HS but also provided a basis for understanding the mechanism of heat tolerance regulation.

scholarly journals Socio-environmental and measurement factors drive spatial variation in influenza-like illness

2017 ◽  
Author(s):  
Elizabeth C. Lee ◽  
Ali Arab ◽  
Sandra Goldlust ◽  
Cécile Viboud ◽  
Shweta Bansal
Keyword(s):  
Healthcare Access ◽  
High Specificity ◽  
Surveillance Systems ◽  
Related Factors ◽  
Influenza Like Illness ◽  
Contact Patterns ◽  
Diagnosis Codes ◽  
Influenza Activity ◽  
Measurement Biases ◽  
Access And Quality

AbstractThe mechanisms hypothesized to drive spatial heterogeneity in reported influenza activity include: environmental factors, contact patterns, population age structure, and socioeconomic factors linked to healthcare access and quality of life. Harnessing the large volume and high specificity of diagnosis codes in medical claims data for influenza seasons from 2002-2009, we estimate the importance of socio-environmental determinants and measurement-related factors on observed variation in influenza-like illness (ILI) across United States counties. We found that South Atlantic states tended to have higher ILI seasonal intensity, and a combination of transmission, environmental, influenza subtype, socioeconomic and measurement factors explained the variation in seasonal intensity across our study period. Moreover, our models suggest that sentinel surveillance systems should have fixed report locations across years for the most robust inference and prediction, and high volumes of data can offset measurement biases in opportunistic data samples.

scholarly journals Laser Microdissection Transcriptome Data Derived Gene Regulatory Networks of Developing Rice Endosperm Revealed Tissue- and Stage-specific Regulators Modulating Starch Metabolism

2021 ◽  
Author(s):  
Tsutomu Ishimaru ◽  
Sabiha Parween ◽  
Yuhi Saito ◽  
Takehiro Masumura ◽  
Motohiko Kondo ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Laser Microdissection ◽  
Critical Role ◽  
Endosperm Development ◽  
Starch Accumulation ◽  
Specific Gene ◽  
Aleurone Layer ◽  
Starch Metabolism ◽  
Starchy Endosperm ◽  
Rice Endosperm

Abstract Rice (Oryza sativa L.) filial seed tissues are heterozygous in its function, which accumulate distinct storage compounds spatially in starchy endosperm and aleurone. In this study, we identified the 18 tissue- and stage-specific gene co-regulons in the developing endosperm by isolating four fine tissues dorsal aleurone layer (AL), central starchy endosperm (CSE), dorsal starchy endosperm (DSE), and lateral starchy endosperm (LSE) at two developmental stages (7 days after flowering, DAF and 12DAF) using laser microdissection (LM) coupled with gene expression analysis of a 44K microarray. The derived co-expression regulatory networks depict that distinct set of starch biosynthesis genes expressed preferentially at first in CSE at 7 DAF and extend its spatial expression to LSE and DSE by 12 DAF. Interestingly, along with the peak of starch metabolism we noticed accumulation of transcripts related to phospholipid and glycolipid metabolism in CSE during 12 DAF. The spatial distribution of starch accumulation in distinct zones of starchy endosperm contains specific transcriptional factors and hormonal-regulated genes. Genes related to programmed cell death (PCD) were specifically expressed in CSE at 12DAF, when starch accumulation was already completed in that tissue. The aleurone layer present in the outermost endosperm accumulates transcripts of lipid, tricarboxylic acid metabolism, several transporters, while starch metabolism and PCD is not pronounced. These regulatory cascades are likely to play a critical role in determining the positional fate of cells and offer novel insights into the molecular physiological mechanisms of endosperm development from early to middle storage phase.

scholarly journals Grain Quality and Starch Physicochemical Properties of Chalky Rice Mutant

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1575
Author(s):  
Chu-Xin Wang ◽  
Cheng-Chao Zhu ◽  
Chen-Ya Lu ◽  
Yong Yang ◽  
Qian-Feng Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Grain Quality ◽  
Profile Analysis ◽  
Amylose Content ◽  
Rice Grain ◽  
Wild Type ◽  
Rice Endosperm ◽  
Rice Mutant ◽  
Apparent Amylose Content ◽  
Quality Profile

Rice mutants with altered starch components and properties are important genetic resources for grain quality and starch structure analysis. Accordingly, in the present study, two mutants of the transcription factor OsbZIP09 were generated (osbzip09a and osbzip09b), and the rice grain quality and physicochemical starch properties of the mutant and wild-type lines were compared. The OsbZIP09 mutants exhibit a chalky grain owing to loosely packed, small, spherical starch granules in the ventral region of the endosperm. Furthermore, grain-quality profile analysis showed that OsbZIP09 deficiency leads to increased apparent amylose content but decreased gel consistency. Structural analysis of the mutant starches revealed that the mutant rice lines contain more amylopectin short chains and fewer intermediate chains, leading to lower crystallinity and lower gelatinization properties than those of the wild-type rice. Moreover, the OsbZIP09 mutants rice presented a significantly higher pasting curve and corresponding parameters than the wild-type rice. The results from this work strongly indicate that the transcription factor OsbZIP09 plays an important role in rice grain quality and starch fine structure modification, and extend our understanding of starch biosynthesis in rice endosperm.

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