scholarly journals Silencing of an Ubiquitin Ligase Increases Grain Width and Weight in indica Rice

2021 ◽  
Vol 11 ◽  
Author(s):  
Ankit Verma ◽  
Geeta Prakash ◽  
Rajeev Ranjan ◽  
Akhilesh K. Tyagi ◽  
Pinky Agarwal
Keyword(s):  
Grain Size ◽  
Ubiquitin Ligase ◽  
Indica Rice ◽  
Cell Number ◽  
Negative Regulator ◽  
Functional Domain ◽  
Coding Region ◽  
Rnai Technology ◽  
Rice Genotypes ◽  
Grain Width

Many quantitative trait loci (QTLs) have been identified by molecular genetic studies which control grain size by regulating grain width, length, and/or thickness. Grain width 2 (GW2) is one such QTL that codes for a RING-type E3 ubiquitin ligase and increases grain size by regulating grain width through ubiquitin-mediated degradation of unknown substrates. A natural variation (single-nucleotide polymorphism at the 346th position) in the functional domain-coding region of OsGW2 in japonica rice genotypes has been shown to cause an increase in grain width/weight in rice. However, this variation is absent in indica rice genotypes. In this study, we report that reduced expression of OsGW2 can alter grain size, even though natural sequence variation is not responsible for increased grain size in indica rice genotypes. OsGW2 shows high expression in seed development stages and the protein localizes to the nucleus and cytoplasm. Downregulation of OsGW2 by RNAi technology results in wider and heavier grains. Microscopic observation of grain morphology suggests that OsGW2 determines grain size by influencing both cell expansion and cell proliferation in spikelet hull. Using transcriptome analysis, upregulated genes related to grain size regulation have been identified among 1,426 differentially expressed genes in an OsGW2_RNAi transgenic line. These results reveal that OsGW2 is a negative regulator of grain size in indica rice and affects both cell number and cell size in spikelet hull.

scholarly journals Characterization of Functional Genes GS3 and GW2 and their Effect on the Grain Size of Various Landraces of Rice

2021 ◽  
Author(s):  
Haroon Rasheed ◽  
Sajid Fiaz ◽  
Muhammad Abid Khan ◽  
Sultan Mehmood ◽  
Faizan Ullah ◽  
...  
Keyword(s):  
Grain Size ◽  
Grain Weight ◽  
Negative Regulator ◽  
Yield Potential ◽  
Phenotypic Traits ◽  
Dominant Allele ◽  
Diverse Range ◽  
Grain Length ◽  
Grain Width ◽  
1000 Grain Weight

Abstract Grain size is an essential factor in grain quality and yield. In the existing agricultural lands in Pakistan and even all over the world, genetics in rice works better for yield potential and quality improvement. GS3 and GW2 with functional mutation responsible for grain size in rice. In the current study, 17 different Pakistani landraces of various genetic and geographic backgrounds were evaluated for grain phenotypic traits (thousand-grain weight, length, width, and thickness) and characterized genotypes for GS3 gene (grain length) and GW2 (grain width). The two accessions JP5 and Bas370, were used as control. Phenotypic data revealed the range for grain weight from 16.86g (Lateefy) to 26.91g (PS2), grain length ranged from 7.27 mm (JP-5) to 12.18 mm (PS2), grain width ranged from 2.01 mm (Lateefy) to 3.51 mm (JP5), and grain thickness ranged from 1.79 mm to 2.19. Pearson correlation revealed a negative and significant correlation between grain width and length. There was no significant correlation between grain length and 1000-grain weight and grain width. LSD test displayed that the means of three variables grain length, grain width, and 1000-grain weight were statistically different from one another except grain width and grain breadth. GS3 is a negative regulator of grain length. Fifteen accessions GA-5015, PS-2, Swat-1, Swat-2, DR-2, Dilrosh, Malhar-346, Kashmir Basmati, Rachna Basmati, KS-282, Basmati-370, KSK-133, KSK-434, MG-Basmati, and Lateefy, carried the domesticated allele of GS3 while JP5 and Fakhr-e-Malakand carried the dominant allele. Similarly, the GW2 is a negative regulator of grain width. Fifteen accessions, i.e., Bas-370, GA-5015, PS-2, Swat-1, Swat-2, DR-2, Dilrosh, Malhar-346, Kashmir Basmati, Rachna Basmati, KS-282, KSK-133, KSK-434, MG-Basmati, and Lateefy carried the dominant allele while JP-5 and Fakhr-e-Malakand carried the mutant allele. The current phenotypic evaluation of the Germplasm revealed a diverse range of grain size of Pakistani landraces and also suggests that the selection of grain length in Pakistani landraces was independent of 1000-grain weight. The accessions with genotypic characterization will aid in marker-assisted breeding programs to break the stagnant yield prevail for the last few decades in Pakistan.

scholarly journals RING finger ubiquitin E3 ligase gene TaSDIR1-4A contributes to determination of grain size in common wheat

2020 ◽  
Vol 71 (18) ◽  
pp. 5377-5388 ◽  
Author(s):  
Jingyi Wang ◽  
Ruitong Wang ◽  
Xinguo Mao ◽  
Jialing Zhang ◽  
Yanna Liu ◽  
...  
Keyword(s):  
Grain Size ◽  
Ubiquitin Ligase ◽  
E3 Ubiquitin Ligase ◽  
Ring Finger ◽  
Wheat Breeding ◽  
Negative Regulator ◽  
Ethylene Response Factor ◽  
Wheat Varieties ◽  
Ubiquitin E3 Ligase ◽  
The Difference

Abstract Salt and drought-induced RING finger1 (SDIR1) is a RING-type E3 ubiquitin ligase that plays a key role in ABA-mediated responses to salinity and drought stress via the ubiquitination pathway in some plant species. However, its function in wheat (Triticum aestivum) is unknown. Here, we isolated a SDIR1 member in wheat, TaSDIR1-4A, and characterized its E3 ubiquitin ligase activity. DNA polymorphism assays showed the presence of two nucleotide variation sites in the promoter region of TaSDIR1-4A, leading to the detection of the haplotypes Hap-4A-1 and Hap-4A-2 in wheat populations. Association analysis showed that TaSDIR1-4A haplotypes were associated with 1000-grain weight (TGW) across a variety of different environments, including well-watered and heat-stress conditions. Genotypes with Hap-4A-2 had higher TGW than those with Hap-4A-1. Phenotypes in both gene-silenced wheat and transgenic Arabidopsis showed that TaSDIR1-4A was a negative regulator of grain size. Gene expression assays indicated that TaSDIR1-4A was most highly expressed in flag leaves, and expression was higher in Hap-4A-1 accessions than in Hap-4A-2 accessions. The difference might be attributable to the fact that TaERF3 (ethylene response factor) can act as a transcriptional repressor of TaSDIR1-4A in Hap-4A-2 but not in Hap-4A-1. Examination of modern wheat varieties shows that the favorable haplotype has been positively selected in breeding programs in China. The functional marker for TaSDIR1-4A developed in this study should be helpful for future wheat breeding.

scholarly journals Genetic diversity, population structure and allele mining of genes governing grain size related traits in rice (Oryza sativa L.)

Genetika ◽  
2020 ◽  
Vol 52 (3) ◽  
pp. 991-1007
Author(s):  
Swarajyalakshmi Bollineni ◽  
Bukya Naik ◽  
Suresh Naik ◽  
Gopalakrishnamurthy Kadambari ◽  
Eswar Reddy ◽  
...  
Keyword(s):  
Grain Size ◽  
Population Structure ◽  
Molecular Markers ◽  
Oryza Sativa L ◽  
The Novel ◽  
Allele Mining ◽  
Rice Varieties ◽  
Rice Genotypes ◽  
Grain Width ◽  
Novel Alleles

The present study was undertaken for allele mining of genes governing grain dimensions viz., grain length, grain width, grain thickness, grain size and grain weight. The molecular markers linked to the reported genes for these traits were used to screen 124 diverse rice genotypes. Thirty-two molecular markers used in this study produced a total of 86 alleles among 124 rice genotypes. The number of alleles ranged from 2 to 4 with an average of 2.58 alleles per locus. A dendrogram consisting of 124 rice genotypes revealed that all the genotypes can be divided into two groups. An analysis of the model-based population structure using simple sequence repeats (SSRs) covering all 12 chromosomes provided evidence of a significant population structure in the rice genotypes. The novel alleles identified in the study could be of great value for development of consumer-targeted rice varieties.

scholarly journals Assessing evidence for adaptive evolution in two hearing-related genes important for high-frequency hearing in echolocating mammals

2021 ◽  
Author(s):  
Hui Wang ◽  
Hanbo Zhao ◽  
Yujia Chu ◽  
Jiang Feng ◽  
Keping Sun
Keyword(s):  
Adaptive Evolution ◽  
Hair Cells ◽  
High Frequency ◽  
Phylogenetic Trees ◽  
Outer Hair Cells ◽  
Functional Domain ◽  
Coding Region ◽  
Selective Pressures ◽  
Wide Range ◽  
Different Parts

Abstract High-frequency hearing is particularly important for echolocating bats and toothed whales. Previously, studies of the hearing-related genes Prestin, KCNQ4, and TMC1 documented that adaptive evolution of high-frequency hearing has taken place in echolocating bats and toothed whales. In this study, we present two additional candidate hearing-related genes, Shh and SK2, that may also have contributed to the evolution of echolocation in mammals. Shh is a member of the vertebrate Hedgehog gene family and is required in the specification of the mammalian cochlea. SK2 is expressed in both inner and outer hair cells, and it plays an important role in the auditory system. The coding region sequences of Shh and SK2 were obtained from a wide range of mammals with and without echolocating ability. The topologies of phylogenetic trees constructed using Shh and SK2 were different; however, multiple molecular evolutionary analyses showed that those two genes experienced different selective pressures in echolocating bats and toothed whales compared to non-echolocating mammals. In addition, several nominally significant positively selected sites were detected in the non-functional domain of the SK2 gene, indicating that different selective pressures were acting on different parts of the SK2 gene. This study has expanded our knowledge of the adaptive evolution of high-frequency hearing in echolocating mammals.

scholarly journals Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Lin Zhang ◽  
Bin Ma ◽  
Zhong Bian ◽  
Xiaoyuan Li ◽  
Changquan Zhang ◽  
...  
Keyword(s):  
Grain Size ◽  
Grain Yield ◽  
Rational Design ◽  
Width Ratio ◽  
Functional Markers ◽  
Rice Breeding ◽  
Nucleotide Polymorphisms ◽  
Yield And Quality ◽  
Grain Width ◽  
Grain Yield And Quality

Abstract Background Grain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers. Result In this study, 14 genes related to grain size (GW2, GS2, qLGY3, GS3, GL3.1, TGW3, GS5, GW5, GS6, TGW6, GW6a, GLW7, GL7 and GW8) were selected for functional marker development. Twenty-one PCR-gel-based markers were developed to genotype the candidate functional nucleotide polymorphisms (FNPs) of these genes, and all markers can effectively recognize the corresponding allele types. To test the allele effects of different FNPs, a global collection of rice cultivars including 257 accessions from the Rice Diversity Panel 1 was used for allele mining, and four grain-size-related traits were investigated at two planting locations. Three FNPs for GW2, GS2 and GL3.1 were genotyped as rare alleles only found in cultivars with notably large grains, and the allele contributions of the remaining FNPs were clarified in both the indica and japonica subspecies. Significant trait contributions were found for most of the FNPs, especially GS3, GW5 and GL7. Of note, GW5 could function as a key regulator to coordinate the performance of other grain size genes. The allele effects of several FNPs were also tested by QTL analysis using an F2 population, and GW5 was further identified as the major locus with the largest contribution to grain width and length to width ratio. Conclusions The functional markers are robust for genotyping different cultivars and may facilitate the rational design of grain size to achieve a balance between grain yield and quality in future rice breeding efforts.

scholarly journals The Rho-family GTPase OsRac1 controls rice grain size and yield by regulating cell division

2019 ◽  
Vol 116 (32) ◽  
pp. 16121-16126 ◽  
Author(s):  
Ying Zhang ◽  
Yan Xiong ◽  
Renyi Liu ◽  
Hong-Wei Xue ◽  
Zhenbiao Yang
Keyword(s):  
Grain Size ◽  
Cell Division ◽  
Grain Yield ◽  
Molecular Mechanisms ◽  
Grain Filling ◽  
High Yield ◽  
Rice Grain ◽  
Rop Gtpase ◽  
Key Factor ◽  
Grain Width

Grain size is a key factor for determining grain yield in crops and is a target trait for both domestication and breeding, yet the mechanisms underlying the regulation of grain size are largely unclear. Here we show that the grain size and yield of rice (Oryza sativa) is positively regulated by ROP GTPase (Rho-like GTPase from plants), a versatile molecular switch modulating plant growth, development, and responses to the environment. Overexpression of rice OsRac1ROP not only increases cell numbers, resulting in a larger spikelet hull, but also accelerates grain filling rate, causing greater grain width and weight. As a result, OsRac1 overexpression improves grain yield in O. sativa by nearly 16%. In contrast, down-regulation or deletion of OsRac1 causes the opposite effects. RNA-seq and cell cycle analyses suggest that OsRac1 promotes cell division. Interestingly, OsRac1 interacts with and regulates the phosphorylation level of OsMAPK6, which is known to regulate cell division and grain size in rice. Thus, our findings suggest OsRac1 modulates rice grain size and yield by influencing cell division. This study provides insights into the molecular mechanisms underlying the control of rice grain size and suggests that OsRac1 could serve as a potential target gene for breeding high-yield crops.

scholarly journals SLAP2 adaptor binding disrupts c-CBL autoinhibition to activate ubiquitin ligase function

2020 ◽  
Author(s):  
Leanne E. Wybenga-Groot ◽  
Andrea J. Tench ◽  
Craig D. Simpson ◽  
Jonathan St. Germain ◽  
Brian Raught ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
Binding Site ◽  
Ubiquitin Ligase ◽  
Adaptor Proteins ◽  
Negative Regulator ◽  
Alternative Mechanism ◽  
Kinase Signaling ◽  
Tyrosine Kinase Signaling ◽  
Ligase Function

AbstractCBL is a RING type E3 ubiquitin ligase that functions as a negative regulator of tyrosine kinase signaling and loss of CBL E3 function is implicated in several forms of leukemia. The Src-like adaptor proteins (SLAP/SLAP2) bind to CBL and are required for CBL-dependent downregulation of antigen receptor, cytokine receptor, and receptor tyrosine kinase signaling. Despite the established role of SLAP/SLAP2 in regulating CBL activity, the nature of the interaction and the mechanisms involved are not known. To understand the molecular basis of the interaction between SLAP/SLAP2 and CBL, we solved the crystal structure of CBL tyrosine kinase binding domain (TKBD) in complex with SLAP2. The carboxy-terminal region of SLAP2 adopts an α-helical structure which binds in a cleft between the 4H, EF-hand, and SH2 domains of the TKBD. This SLAP2 binding site is remote from the canonical TKBD phospho-tyrosine peptide binding site but overlaps with a region important for stabilizing CBL in its autoinhibited conformation. In addition, binding of SLAP2 to CBL in vitro activates the ubiquitin ligase function of autoinhibited CBL. Disruption of the CBL/SLAP2 interface through mutagenesis demonstrated a role for this protein-protein interaction in regulation of CBL E3 ligase activity in cells. Our results reveal that SLAP2 binding to a regulatory cleft of the TKBD provides an alternative mechanism for activation of CBL ubiquitin ligase function.

scholarly journals In vitro Callus Induction and Regeneration of Popular Indica Rice Genotypes

2020 ◽  
Vol 13 (4) ◽  
Author(s):  
Aananthi. N
Keyword(s):  
Callus Induction ◽  
Callus Formation ◽  
Indica Rice ◽  
Immature Embryo ◽  
Coconut Milk ◽  
Rice Genotypes ◽  
Mist Chamber ◽  
Regenerated Plant ◽  
Better Than

Five rice cultivars viz., ASD 16, White Ponni, Pusa Basmati 1, Pusa Sugandh 4 and Pusa Sugandh 5 belonging to subspecies indica were compared for its ability in callus formation and regeneration. In this experiment, the different parameters viz., the effect of hormones (2,4-D and kinetin), organic supplement (coconut milk O1-CM 100 mll-1, O2-CM 75 mll-1, O3-CM 50 mll-1), explants (seed and immature embryo), media (MS and N6), carbon source (sucrose and maltose) using five genotypes on callus response was studied. The effect of hardening methods was also assessed. Results showed that for enhanced callus induction was with MS medium supplemented with 2.0 mgl-1 2, 4-D + 0.5 mgl-1 kinetin + 30 gl-1 maltose irrespective of explants used. Addition of 100 ml l-1 coconut milk was found have improvement in callus response. The performance of immature embryo was better than seed for callus induction, emrbyogenic callus formation, rhizogenic callus formation and regeneration. MS media provided superiority over N6. Among the genotypes Pusa Basmati 1 rendered outstanding performance in callus behavior. The treatment combination MS + 2.5 mgl-1 BAP + 0.5 mgl-1 NAA + 1.0 mgl-1 KN gave the highest organogenesis response and regeneration of plantlets. Hardening in mist chamber was recognized as the best method to give the highest per cent of regenerated plant lets.

scholarly journals Role of the 5′-untranslated region of mRNA in the synthesis of S-adenosylmethionine decarboxylase and its regulation by spermine

1994 ◽  
Vol 302 (3) ◽  
pp. 765-772 ◽  
Author(s):  
L M Shantz ◽  
R Viswanath ◽  
A E Pegg
Keyword(s):  
Secondary Structure ◽  
Untranslated Region ◽  
Fold Increase ◽  
Negative Regulator ◽  
Mrna Levels ◽  
Coding Region ◽  
Polyamine Biosynthesis ◽  
Adenosylmethionine Decarboxylase ◽  
Spermine Synthase ◽  
Synthase Inhibitor

S-Adenosylmethionine decarboxylase (AdoMetDC), a rate-limiting enzyme in polyamine biosynthesis, is regulated by polyamines at the levels of both transcription and translation. Two unusual features of AdoMetDC mRNA are a long (320 nt) 5′-untranslated region (5′UTR), which is thought to contain extensive secondary structure, and a short (15 nt) open reading frame (ORF) within the 5′UTR. We have studied the effects of altering these elements on both the expression of AdoMetDC and its regulation by n-butyl-1,3-diaminopropane (BDAP), a spermine synthase inhibitor. Human AdoMetDC cDNAs containing alterations in the 5′UTR, as well as chimaeric constructs in which the AdoMetDC 5′UTR was inserted ahead of the luciferase-coding region, were transfected into COS-7 cells. Construct pSAM320, which contains all of the 5′UTR, the AdoMetDC protein-coding region and the 3′UTR, was expressed poorly (2-fold over the endogenous activity). Deletion of virtually the entire 5′UTR, leaving nt -12 to -1, increased expression 59-fold, suggesting that 5′UTR acts as a negative regulator. The same effect was seen when the 27 nt at the extreme 5′ end were removed (pSAM293, 47-fold increase), or when the internal ORF which is present in this region was destroyed by changing the ATG to CGA (pSAM320-ATG, 38-fold increase). The expression and regulation of pSAM44 (made by deleting nt -288 to -12), which has very little predicted secondary strucutre, was very similar to that of pSAM320 indicating that the terminal 27 nt including the internal ORF rather than extensive secondary structure may be responsible for the low basal levels of AdoMetDC expression. These results, confirmed using luciferase constructs, suggest that the negative effect on expression is predominantly due to the internal ORF. Depletion of spermine by BDAP increased the expression from pSAM320 more than 5-fold without affecting AdoMetDC mRNA levels. Expression from pSAM293 was unchanged by spermine depletion, whereas that from pSAM320-ATG was increased 2.5-fold. These results indicate the presence of a spermine response element in the first 27 nt of the 5′UTR that may include but is not entirely due to the internal ORF.

The N-terminal TPR region is the functional domain of SSN6, a nuclear phosphoprotein of Saccharomyces cerevisiae

1990 ◽  
Vol 10 (9) ◽  
pp. 4744-4756
Author(s):  
J Schultz ◽  
L Marshall-Carlson ◽  
M Carlson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Function Analysis ◽  
Normal Growth ◽  
Negative Regulator ◽  
Tetratricopeptide Repeat ◽  
Functional Domain ◽  
Snf1 Kinase ◽  
C Terminus ◽  
Protein Functions

The SSN6 protein functions as a negative regulator of a variety of genes in Saccharomyces cerevisiae and is required for normal growth, mating, and sporulation. It is a member of a family defined by a repeated amino acid sequence, the TPR (tetratricopeptide repeat) motif. Here, we have used specific antibody to identify and characterize the SSN6 protein. Both SSN6 and a bifunctional SSN6-beta-galactosidase fusion protein were localized in the nucleus by immunofluorescence staining. The N-terminal one-third of the protein containing the TPR units was identified as the region that is important for SSN6 function. Analysis of four nonsense alleles, isolated as intragenic suppressors of an ssn6::URA3 insertion, revealed that polypeptides truncated after TPR unit 7 provide SSN6 function. Deletion analysis suggested that TPR units are required but that 4 of the 10 TPR units are sufficient. In addition, deletion studies indicated that three very long, homogeneous tracts of polyglutamine and poly(glutamine-alanine) are dispensable. Previous genetic evidence suggested the SSN6 protein as a possible target of the SNF1 protein kinase. Here, we show that the C terminus of SSN6 is phosphorylated in vivo and that the SNF1 kinase is not responsible for most of the phosphorylation. Finally, SSN6 has a modest effect on the maintenance of minichromosomes.

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