scholarly journals OsGRETCHENHAGEN3-2 modulates rice seed storability via accumulation of abscisic acid and protective substances

2021 ◽  
Author(s):  
Zhiyang Yuan ◽  
Kai Fan ◽  
Yuntong Wang ◽  
Li Tian ◽  
Chaopu Zhang ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Seed Viability ◽  
Seed Vigor ◽  
Negative Regulator ◽  
Artificial Ageing ◽  
Rice Seed ◽  
A Genome ◽  
Seed Storability

Abstract Seed storability largely determines the vigor of seeds during storage and is significant in agriculture and ecology. However, the underlying genetic basis remains unclear. In the present study, we report the cloning and characterization of the rice (Oryza sativa) indole-3-acetic acid (IAA)-amido synthetase gene GRETCHEN HAGEN3-2 (OsGH3-2) associated with seed storability. OsGH3-2 was identified by performing a genome-wide association study in rice germplasms with linkage mapping in chromosome substitution segment lines, contributing to the wide variation of seed viability in the populations after long periods of storage and artificial ageing. OsGH3-2 was dominantly expressed in the developing seeds and catalyzed IAA conjugation to amino acids, forming inactive auxin. Transgenic overexpression, knockout and knockdown experiments demonstrated that OsGH3-2 affected seed storability by regulating the accumulation level of abscisic acid. Overexpression of OsGH3-2 significantly decreased seed storability, while knockout or knockdown of the gene enhanced seed storability compared with the wild type. OsGH3-2 acted as a negative regulator of seed storability by modulating many genes related to the abscisic acid pathway and probably subsequently late embryogenesis-abundant proteins at the transcription level. These findings shed light on the molecular mechanisms underlying seed storability and will facilitate the improvement of seed vigor by genomic breeding and gene-editing approaches in rice.

scholarly journals Genome-Wide Association Study Reveals the QTLs for Seed Storability in World Rice Core Collections

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 812
Author(s):  
Fangxi Wu ◽  
Xi Luo ◽  
Lingqiang Wang ◽  
Yidong Wei ◽  
Jianguo Li ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Rice Genome ◽  
Genome Wide Association ◽  
Rice Seed ◽  
Core Collections ◽  
Genome Wide ◽  
A Genome ◽  
New Varieties ◽  
Seed Storability

Seed storability is a main agronomically important trait to assure storage safety of grain and seeds in rice. Although many quantitative trait loci (QTLs) and associated genes for rice seed storability have been identified, the detailed genetic mechanisms of seed storability remain unclear in rice. In this study, a genome-wide association study (GWAS) was performed in 456 diverse rice core collections from the 3K rice genome. We discovered the new nine QTLs designated as qSS1-1, qSS1-2, qSS2-1, qSS3-1, qSS5-1, qSS5-2, qSS7-1, qSS8-1, and qSS11-1. According to the analysis of the new nine QTLs, our results could well explain the reason why seed storability of indica subspecies was superior to japonica subspecies in rice. Among them, qSS1-2 and qSS8-1 were potentially co-localized with a known associated qSS1/OsGH3-2 and OsPIMT1, respectively. Our results also suggest that pyramiding breeding of superior alleles of these associated genes will lead to new varieties with improved seed storability in the future.

Effect of High Temperature Intermittent Drying on Rice Seed Viability and Vigor

2017 ◽  
Vol 13 (10) ◽  
Author(s):  
Pan Wang ◽  
Dong Li ◽  
Li-jun Wang ◽  
Benu Adhikari
Keyword(s):  
High Temperature ◽  
Ambient Temperature ◽  
Seed Viability ◽  
Seed Vigor ◽  
Drying Rate ◽  
Rice Seed ◽  
Rice Cultivars ◽  
Moisture Contents ◽  
Rice Seeds ◽  
Tempering Process

AbstractThis work aimed at determining whether high temperature intermittent drying followed by tempering at ambient temperature could preserve the seed viability and vigor.JaponicaandIndicarice seeds with 21.2 % and 22.6 % wet moisture contents (w.b.) were dried at 50 ºC and 60ºC for either 5, 10, 15 or 20 minutes, followed by tempering at 25ºC for 45 minutes. Each drying cycle was repeated until the rice seeds were dried to 12.0 % (w.b.). The drying rate was improved and the total in-dryer time was reduced in the intermittent drying when compared to continuous drying, due to the tempering process. The seed vigor was significantly reduced by intermittent drying at 60 °C with all exposure times, although the seed still kept the ability to germinate for both rice cultivars. The intermittent drying at 50 ºC for 5 minutes per drying cycle preserved the seed vigor ofJaponicarice well, while inIndicarice, the intermittent drying at 50 ºC up to 20 minutes could still be able to maintain the seed vigor.

scholarly journals Pengujian Vigor Daya Simpan dan Vigor terhadap Kekeringan pada Benih Padi Gogo dan Padi Sawah

2013 ◽  
Vol 1 (1) ◽  
pp. 67
Author(s):  
Feni Shintarika ◽  
Faiza Chairani Suwarno ◽  
. Suwarno
Keyword(s):  
Drought Stress ◽  
Upland Rice ◽  
Block Design ◽  
Seed Vigor ◽  
Lowland Rice ◽  
Rice Seed ◽  
Ethanol Vapour ◽  
Randomized Block Design ◽  
Rice Genotypes ◽  
Seed Storability

<p style="text-align: justify;">The objectives of the study were to evaluate seed storability and vigor to drought of rice genotypes from different ecologies and correlation among the characters. The experiments were conducted in the Seed Science and Technology Laboratory, Bogor Agricultural University from April to August 2011. Duration of rapid aging using ethanol vapour for testing seed storability were 87.6 and 155.4 minutes for upland and lowland rice seeds respectively. The rolled paper methods with Polyethylen Glycol (PEG 6000) at -2.0 bar was used for testing seed vigor to drought. Rice seed of 40 genotype consisting of 20 upland and 20 lowland were evaluated using Randomized Block Design with three replications. There were no correlation between seed storability and vigor to drought on all genotypes, and no similiarity of those characters on the best five genotypes. Genotypes with the highest storability were B12154D-MR-22-8 for upland rice and Aek Sibundong for lowland. Genotypes with the highest vigor to drought were B12165D-MR-8-1 and B12161D-MR-1-4-2 for upland rice, B12672-MR-19-2-PN-1-3 and Aek Sibundong for lowland.</p><p>Keywords : drought stress, Rapid aging</p>

scholarly journals Genome-Wide Association Study of H/L Traits in Chicken

Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 260 ◽  
Author(s):  
Bo Zhu ◽  
Qinghe Li ◽  
Ranran Liu ◽  
Maiqing Zheng ◽  
Jie Wen ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Immune Defense ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Presently, the heterophil-to-lymphocyte (H/L) ratio is being studied extensively as a disease resistance trait. Through intricate mechanisms to identify and destroy pathogenic microorganisms, heterophils play a pivotal role in the immune defense systems of avian species. To reveal the genetic basis and molecular mechanisms affecting the H/L ratio, phenotypic and H/L data from 1650 white feather chicken broilers were used in performing a genome-wide association study. A self-developed, chicken-specific 55K chip was used for heterophils, lymphocytes, and H/L classification, according to individual genomic DNA profiles. We identified five significant single nucleotide polymorphisms (SNPs) when the genome-wide significance threshold was set to 5% (p < 2.42 × 10−6). A total of 15 SNPs obtained seemingly significant levels (p < 4.84 × 10−5). Gene annotation indicated that CARD11 (Caspase recruitment domain family member 11), BRIX1 (Biogenesis of ribosomes BRX1), and BANP (BTG3 associated nuclear protein) play a role in H/L-associated cell regulation and potentially constitute candidate gene regions for cellular functions dependent on H/L ratios. These results lay the foundation for revealing the genetic basis of disease resistance and future marker-assisted selection for disease resistance.

scholarly journals Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana

2020 ◽  
Author(s):  
Rhonda C Meyer ◽  
Kathleen Weigelt-Fischer ◽  
Dominic Knoch ◽  
Marc Heuermann ◽  
Yusheng Zhao ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Vegetative Growth ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Temporal Dynamics ◽  
Expression Patterns ◽  
Snp Array ◽  
Relative Growth Rates ◽  
Continuous Formation ◽  
A Genome

Abstract We assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from 7 d to 18 d after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGRs). In addition, initial seed size was determined. The generated datasets were used jointly for a genome-wide association study that identified 238 marker–trait associations (MTAs) individually explaining up to 8% of the total phenotypic variation. Co-localization of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localization of MTAs for 2–9 consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasizing that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.

scholarly journals Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Huifen Cao ◽  
Dongyang Xu ◽  
Ye Cai ◽  
Xueer Han ◽  
Lu Tang ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Biological Significance ◽  
Genotoxic Stress ◽  
Cellular Adhesion ◽  
Negative Regulator ◽  
Chromatin Interactions ◽  
Multiple Genes ◽  
A Genome ◽  
Hidden Layer

Abstract Background The majority of the human genome is transcribed in the form of long non-coding (lnc) RNAs. While these transcripts have attracted considerable interest, their molecular mechanisms of function and biological significance remain controversial. One of the main reasons behind this lies in the significant challenges posed by lncRNAs requiring the development of novel methods and concepts to unravel their functionality. Existing methods often lack cross-validation and independent confirmation by different methodologies and therefore leave significant ambiguity as to the authenticity of the outcomes. Nonetheless, despite all the caveats, it appears that lncRNAs may function, at least in part, by regulating other genes via chromatin interactions. Therefore, the function of a lncRNA could be inferred from the function of genes it regulates. In this work, we present a genome-wide functional annotation strategy for lncRNAs based on identification of their regulatory networks via the integration of three distinct types of approaches: co-expression analysis, mapping of lncRNA-chromatin interactions, and assaying molecular effects of lncRNA knockdowns obtained using an inducible and highly specific CRISPR/Cas13 system. Results We applied the strategy to annotate 407 very long intergenic non-coding (vlinc) RNAs belonging to a novel widespread subclass of lncRNAs. We show that vlincRNAs indeed appear to regulate multiple genes encoding proteins predominantly involved in RNA- and development-related functions, cell cycle, and cellular adhesion via a mechanism involving proximity between vlincRNAs and their targets in the nucleus. A typical vlincRNAs can be both a positive and negative regulator and regulate multiple genes both in trans and cis. Finally, we show vlincRNAs and their regulatory networks potentially represent novel components of DNA damage response and are functionally important for the ability of cancer cells to survive genotoxic stress. Conclusions This study provides strong evidence for the regulatory role of the vlincRNA class of lncRNAs and a potentially important role played by these transcripts in the hidden layer of RNA-based regulation in complex biological systems.

scholarly journals Genome wide association study of plant height and tiller number in hulless barley

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260723
Author(s):  
Yixiong Bai ◽  
Xiaohong Zhao ◽  
Xiaohua Yao ◽  
Youhua Yao ◽  
Likun An ◽  
...  
Keyword(s):  
Association Study ◽  
Plant Height ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Tiller Number ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Hulless Barley ◽  
Genome Wide ◽  
A Genome

Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. The genome-wide specific length amplified fragment sequencing (SLAF-seq) method is a rapid deep sequencing technology that is used for the selection and identification of genetic loci or markers. In this study, we collected 300 hulless barley accessions and used the SLAF-seq method to identify candidate genes involved in plant height (PH) and tiller number (TN). We obtained a total of 1407 M paired-end reads, and 228,227 SLAF tags were developed. After filtering using an integrity threshold of >0.8 and a minor allele frequency of >0.05, 14,504,892 single-nucleotide polymorphisms (SNP) loci were screened out. The remaining SNPs were used for the construction of a neighbour-joining phylogenetic tree, and the three subcluster members showed no obvious differentiation among regional varieties. We used a genome wide association study approach to identify 1006 and 113 SNPs associated with TN and PH, respectively. Based on best linear unbiased predictors (BLUP), 41 and 29 SNPs associated with TN and PH, respectively. Thus, several of genes, including Hd3a and CKX5, may be useful candidates for the future genetic breeding of hulless barley. Taken together, our results provide insight into the molecular mechanisms controlling barley architecture, which is important for breeding and yield.

scholarly journals Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana

2020 ◽  
Author(s):  
Rhonda C. Meyer ◽  
Kathleen Weigelt-Fischer ◽  
Dominic Knoch ◽  
Marc Heuermann ◽  
Yusheng Zhao ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Association Study ◽  
Vegetative Growth ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Temporal Dynamics ◽  
Expression Patterns ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

ABSTRACTWe assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from seven to 18 days after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGR). In addition, initial seed size was determined. The generated data sets were used jointly for a genome-wide association study that identified 238 marker-trait associations (MTAs) individually explaining up to 8 % of the total phenotypic variation. Co-localisation of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localisation of MTAs for two to nine consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasising that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.HighlightA genome-wide association study including the factor time highlighted that early plant growth in Arabidopsis is governed by several medium and many small effect loci, most of which act only during short phases of two to nine days.

scholarly journals Distinct genetic bases for plant root responses to lipo-chitooligosaccharide signal molecules from distinct microbial origins

2020 ◽  
Author(s):  
Maxime Bonhomme ◽  
Sandra Bensmihen ◽  
Olivier André ◽  
Emilie Amblard ◽  
Magali Garcia ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Plant Root ◽  
Pathogenic Fungi ◽  
Signal Molecules ◽  
List Type ◽  
Root Branching ◽  
A Genome ◽  
Root Response

SummaryLipo-chitooligosaccharides (LCOs) were originally found as symbiotic signals called Nod Factors (Nod-LCOs) controlling nodulation of legumes by rhizobia. More recently LCOs were also found in symbiotic fungi and, more surprisingly, very widely in the kingdom fungi including in saprophytic and pathogenic fungi. The LCO-V(C18:1, Fuc/MeFuc), hereafter called Fung-LCOs, are the LCO structures most commonly found in fungi. This raises the question of how legume plants, such as Medicago truncatula, can perceive and discriminate between Nod-LCOs and these Fung-LCOs.To address this question, we performed a Genome Wide Association Study on 173 natural accessions of Medicago truncatula, using a root branching phenotype and a newly developed local score approach.Both Nod- and Fung-LCOs stimulated root branching in most accessions but there was very little correlation in the ability to respond to these types of LCO molecules. Moreover, heritability of root response was higher for Nod-LCOs than for Fung-LCOs. We identified 123 loci for Nod-LCO and 71 for Fung-LCO responses, but only one was common.This suggests that Nod- and Fung-LCOs both control root branching but use different molecular mechanisms. The tighter genetic constraint of the root response to Fung-LCOs possibly reflects the ancestral origin of the biological activity of these molecules.

scholarly journals O GRAU DE UMIDADE NA COLHEITA E O SISTEMA DE SECAGEM SÃO DETERMINANTES PARA O VIGOR DE SEMENTES DE ARROZ

2021 ◽  
Vol 36 (1) ◽  
pp. 28-40
Author(s):  
Jaquelini Garcia ◽  
Cileide Maria Medeiros Coelho
Keyword(s):  
Moisture Content ◽  
Seed Viability ◽  
Mechanical Damage ◽  
Accelerated Aging ◽  
Seed Vigor ◽  
Rice Seed ◽  
Randomized Design ◽  
Physiological Quality ◽  
Drying System

O GRAU DE UMIDADE NA COLHEITA E O SISTEMA DE SECAGEM SÃO DETERMINANTES PARA O VIGOR DE SEMENTES DE ARROZ   JAQUELINI GARCIA1, CILEIDE MARIA MEDEIROS COELHO1   1Programa de Pós-graduação em Produção vegetal, Universidade do Estado de Santa Catarina, Avenida Luiz de Camões, 2090, Conta Dinheiro, 88520-000, Lages, SC, Brasil, [email protected], [email protected]   RESUMO: O grau de umidade na colheita e o sistema de secagem podem ser determinantes na qualidade das sementes produzidas. Neste trabalho foi avaliado se o sistema de secagem e o grau de umidade na colheita interferem na qualidade fisiológica das sementes de arroz. Foi realizado em delineamento inteiramente casualizado em esquema fatorial triplo. Foi utilizada seis cultivares produzidas no Alto Vale do Itajaí/SC na safra 2016/17 com grau de umidade na colheita igual ou superior a 17% (19,30 - 17,30%) e inferior a 17% (16,40 - 15,03%) (base úmida). As sementes foram submetidas aos sistemas de secagem estacionário e intermitente. Realizou-se testes de germinação, viabilidade, vigor pelo envelhecimento acelerado e frio. Sementes colhidas com grau de umidade ≥ 17% apresentaram maior vigor. A cultivar foi um fator de grande relevância na sensibilidade ao dano térmico e mecânico. O sistema de secagem não afetou a viabilidade das sementes, com exceção da cultivar SCS122 Miura que foi sensível a dano térmico e mecânico. A secagem estacionária comprometeu a qualidade fisiológica. Conclui-se que a secagem intermitente e a colheita com grau de umidade igual ou superior a 17%, mantém a qualidade fisiológica das cultivares SCSBRS Tio Taka, SCS122 Miura, SCS116 Satoru e SCS121 CL.   Palavras-chaves: Secagem estacionária, secagem intermitente, qualidade fisiológica.   THE DEGREE OF MOISTURE IN THE HARVEST AND THE DRYING SYSTEM ARE DETERMINANT FOR THE RICE SEED VIGOR   ABSTRACT: The degree of moisture at harvest and the drying system can determine the quality of the seeds produced. In this work, it was evaluated whether the drying system and the degree of moisture at harvest affect the physiological quality of rice seeds. It was conducted in a completely randomized design in a triple factorial scheme. Six cultivars produced in Alto Vale do Itajaí/SC in the 2016/17 crop were used, with moisture content at harvest equal or greater than 17% (19.30 – 17.30%) and less than 17% (16,40 - 15,03%) (wet basis). Seeds were submitted to stationary and intermittent drying systems. Tests of germination, viability, vigor by accelerated aging and cold were performed. Seeds harvested with moisture content ≥ 17% showed greater vigor. The cultivar was a factor of great relevance in the sensitivity to thermal and mechanical damage. The drying system did not affect seed viability, except for the cultivar SCS122 Miura, which was sensitive to thermal and mechanical damage. Stationary drying compromised physiological quality. It was concluded that intermittent drying and harvesting with moisture content equal or greater than 17% maintain the physiological quality of the SCSBRS Tio Taka, SCS122 Miura, SCS116 Satoru and SCS121 CL cultivars.   Keywords: Stationary drying, intermittent drying, physiological quality.

Sign in / Sign up

Export Citation Format

Share Document