Loss of Function of OsFBX267 and OsGA20ox2 in Rice Promotes Early Maturing and Semi-Dwarfism in γ-Irradiated IWP and Genome-Edited Pusa Basmati-1

Targeted mutagenesis is now becoming the most favored methodology to improve traits in popular rice cultivars selectively. Understanding the genetic basis of already available mutants could be the first step in designing such experiment. Improved White Ponni (IWP), a popularly grown South Indian rice variety, was subjected to γ irradiation to develop WP-22-2, an M6 line superior in semi-dwarfism, early flowering, and high yield, and it has grain qualities similar to those of IWP. The exogenous application of gibberellic acid (GA3) on WP-22-2 resulted in the elongation of shorter internodes to a level similar to IWP. The expression profiling of six genes regulating plant height showed their differential expression pattern at different time points post GA3 treatment. Furthermore, the sequencing of WP-22-2 and IWP genomes revealed several single nucleotide polymorphisms (SNPs) and large-scale deletions in WP-22-2. The conversion of functional codons to stop codons was observed in OsGA20ox2 and OsFBX267, which have been reported to have roles in regulating semi-dwarfism and early flowering, respectively. The loss of function of OsGA20ox2 and OsFBX267 in WP-22-2 resulted in reduced plant height as well as early flowering, and the same has been confirmed by editing OsGA20ox2 in the rice variety Pusa Basmati1 (PB1) using the CRISPR-Cas9 approach. The targeted editing of OsGA20ox2 in PB1 conferred shorter plant height to the edited lines compared with the wild type. Altogether, the study provides evidence on mutating OsGA20ox2 and OsFBX267 genes to develop early maturing and semi-dwarf varieties that can be released to farmers after functional characterization and field trials.

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Auxin Efflux Transporters OsPIN1c and OsPIN1d Function Redundantly in Regulating Rice (Oryza sativa L.) Panicle Development

Plant and Cell Physiology ◽

10.1093/pcp/pcab172 ◽

2021 ◽

Author(s):

Jiajun Liu ◽

Xi’an Shi ◽

Zhongyuan Chang ◽

Yanfeng Ding ◽

Chengqiang Ding

Keyword(s):

Double Mutant ◽

Oryza Sativa L ◽

Gene Knockout ◽

Rice Variety ◽

Functional Characterization ◽

Reproductive Development ◽

Japonica Rice ◽

Loss Of Function ◽

Mild Phenotype ◽

Panicle Development

Abstract The essential role of auxin in plant growth and development is well known. Pathways related to auxin synthesis, transport, and signaling have been extensively studied in recent years, and the PIN-FORMED (PIN) protein family has been identified to be pivotal for polar auxin transport (PAT) and distribution. However, research focused on the functional characterization of PIN proteins in rice is still lacking. In this study, we investigated the expression and function of OsPIN1c and OsPIN1d in the japonica rice variety (Nipponbare) using gene knockout and high-throughput RNA sequencing (RNA-Seq) analysis. Results showed that OsPIN1c and OsPIN1d were mainly expressed in young panicles and exhibited a redundant function. Furthermore, OsPIN1c or OsPIN1d loss-of-function mutants presented a mild phenotype compared with the wild type. In addition to significantly decreased plant height and tiller number, panicle development was severely disrupted in double mutant lines of OsPIN1c and OsPIN1d. Severe defects included smaller inflorescence meristem (IM) and panicle sizes, fewer primary branches, elongated bract leaves, non-degraded hair, and no spikelet growth. Interestingly, ospin1cd-3, a double mutant line with functional retention of OsPIN1d, showed milder defects than those observed in other mutants. Additionally, several critical regulators of reproductive development, such as OsPID, LAX1, OsMADS1, and OsSPL14/IPA1, were differentially expressed in ospin1c-1 ospin1d-1, supporting the hypothesis that OsPIN1c and OsPIN1d are involved in regulating panicle development. Therefore, this study provides novel insights into the auxin pathways that regulate plant reproductive development in monocots.

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A trans-acting long non-coding RNA represses flowering in Arabidopsis

10.1101/2021.11.15.468639 ◽

2021 ◽

Author(s):

Yu Jin ◽

Maxim Ivanov ◽

Anna Nelson Dittrich ◽

Andrew Nelson ◽

Sebastian Marquardt

Keyword(s):

Gene Expression ◽

Functional Characterization ◽

Early Flowering ◽

Differentially Expressed ◽

Loss Of Function ◽

Allelic Series ◽

Non Coding Rna ◽

Genome Wide ◽

Genomic Regions ◽

Early Flowering Phenotype

Eukaryotic genomes give rise to thousands of long non-coding RNAs (lncRNAs), yet the purpose of lncRNAs remains largely enigmatic. Functional characterization of lncRNAs is challenging due to multiple orthogonal hypothesis for molecular activities of lncRNA loci. Here, we identified a flowering associated intergenic lncRNA (FLAIL) that represses flowering in Arabidopsis. An allelic series of flail loss-of-function mutants generated by CRISPR/Cas9 and T-DNA mutagenesis showed an early flowering phenotype. Gene expression analyses in flail mutants revealed differentially expressed genes linked to the regulation of flowering. A genomic rescue fragment of FLAIL introduced in flail mutants complemented gene expression defects and early flowering, consistent with trans-acting effects of the FLAIL RNA. Knock-down of FLAIL RNA levels using the artificial microRNA approach revealed an early flowering phenotype shared with genomic mutations, indicating a trans-acting role of FLAIL RNA in the repression of flowering time. Genome-wide detection of FLAIL-DNA interactions by ChIRP-seq suggested that FLAIL may directly bind genomic regions. FLAIL bound to genes involved in regulation of flowering that were differentially expressed in flail, consistent with the interpretation of FLAIL as a trans-acting lncRNA directly shaping gene expression. Our findings highlight FLAIL as a trans-acting lncRNA that affects flowering in Arabidopsis, likely through mediating transcriptional regulation of genes directly bound by FLAIL.

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Genotypic Selection for Soybean Earliness

Journal of Agricultural Science ◽

10.5539/jas.v12n11p169 ◽

2020 ◽

Vol 12 (11) ◽

pp. 169

Author(s):

Flaviane O. Ribeiro ◽

Adriano T. Bruzi ◽

Mariane C. Bianchi ◽

Igor O. Soares ◽

Karina B. Silva

Keyword(s):

Plant Height ◽

Flowering Plant ◽

High Yield ◽

Correlated Response ◽

Early Maturity ◽

Days To Flowering ◽

Lattice Design ◽

Early Maturing ◽

Superior Genotypes ◽

Selection For

Obtaining early-maturing soybean cultivars with high yield performance has long been the focus of breeding programs. Obtaining the estimates of genetic and phenotypic parameters can assist breeders at selecting the superior genotypes. Therefore, the aim was to estimate the genetic and phenotypic parameters of progenies throughout the recurrent selection for early maturity in soybeans and to select progenies with superior agronomic traits. S0:1 progenies were evaluated in one site during the 2015/2016 harvest using a 12 × 12 lattice design, with one 2-meter row plot with two replicates. The S0:2 progenies were evaluated during the 2016/2017 harvest using an 8 × 8 lattice design, with one 3-meter row plot with three replicates. The S0:3 progenies were evaluated during the 2017/2018 harvest using a 5 × 5 lattice design, with two 3-meter rows plots with three replicates. Both S0:2 and S0:3 progenies were evaluated in three different sites. The days to flowering, full maturity, first pod insertion height, plant height, lodging index and grain yield traits was evaluated. The data were analyzed using a mixed model approach. The genetic and phenotypic parameters, expected gain with selection, realized heritability, correlated response and the frequency distributions of the adjusted means were estimated. The estimates of the variance components have evidenced variability among the progenies, enabling the selection of superior genotypes. All the evaluated progenies showed good agronomic performance, combining early maturity and productive performance. When early-maturing progenies were selected, there was a reduction in days to flowering, plant height, first pod insertion height, lodging and yield.

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Actin-Related Protein 4 Interacts with PIE1 and Regulates Gene Expression in Arabidopsis

Genes ◽

10.3390/genes12040520 ◽

2021 ◽

Vol 12 (4) ◽

pp. 520

Author(s):

Wenfeng Nie ◽

Jinyu Wang

Keyword(s):

Gene Expression ◽

Plant Growth ◽

Chromatin Remodeling ◽

Leaf Size ◽

Early Flowering ◽

Physical Interaction ◽

Loss Of Function ◽

Single Nucleotide Change ◽

Chromatin Remodeling Complex ◽

Related Proteins

As essential structural components of ATP-dependent chromatin-remodeling complex, the nucleolus-localized actin-related proteins (ARPs) play critical roles in many biological processes. Among them, ARP4 is identified as an integral subunit of chromatin remodeling complex SWR1, which is conserved in yeast, humans and plants. It was shown that RNAi mediated knock-down of Arabidopsis thaliana ARP4 (AtARP4) could affect plant development, specifically, leading to early flowering. However, so far, little is known about how ARP4 functions in the SWR1 complex in plant. Here, we identified a loss-of-function mutant of AtARP4 with a single nucleotide change from glycine to arginine, which had significantly smaller leaf size. The results from the split luciferase complementation imaging (LCI) and yeast two hybrid (Y2H) assays confirmed its physical interaction with the scaffold and catalytic subunit of SWR1 complex, photoperiod-independent early flowering 1 (PIE1). Furthermore, mutation of AtARP4 caused altered transcription response of hundreds of genes, in which the number of up-regulated differentially expressed genes (DEGs) was much larger than those down-regulated. Although most DEGs in atarp4 are related to plant defense and response to hormones such as salicylic acid, overall, it has less overlapping with other swr1 mutants and the hta9 hta11 double-mutant. In conclusion, our results reveal that AtARP4 is important for plant growth and such an effect is likely attributed to its repression on gene expression, typically at defense-related loci, thus providing some evidence for the coordination of plant growth and defense, while the regulatory patterns and mechanisms are distinctive from other SWR1 complex components.

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Functional Characterization of the Adenylyl Cyclase Genesgs-1by Analysis of a Mutational Spectrum inCaenorhabditis elegans

Genetics ◽

10.1093/genetics/161.1.133 ◽

2002 ◽

Vol 161 (1) ◽

pp. 133-142 ◽

Cited By ~ 4

Author(s):

Celine Moorman ◽

Ronald H A Plasterk

Keyword(s):

Life Span ◽

Adenylyl Cyclase ◽

Neuronal Degeneration ◽

Functional Characterization ◽

Adenylyl Cyclases ◽

Loss Of Function ◽

C Elegans ◽

Larval Stages ◽

Pharyngeal Pumping

AbstractThe sgs-1 (suppressor of activated Gαs) gene encodes one of the four adenylyl cyclases in the nematode C. elegans and is most similar to mammalian adenylyl cyclase type IX. We isolated a complete loss-of-function mutation in sgs-1 and found it to result in animals with retarded development that arrest in variable larval stages. sgs-1 mutant animals exhibit lethargic movement and pharyngeal pumping and (while not reaching adulthood) have a mean life span that is >50% extended compared to wild type. An extensive set of reduction-of-function mutations in sgs-1 was isolated in a screen for suppressors of a neuronal degeneration phenotype induced by the expression of a constitutively active version of the heterotrimeric Gαs subunit of C. elegans. Although most of these mutations change conserved residues within the catalytic domains of sgs-1, mutations in the less-conserved transmembrane domains are also found. The sgs-1 reduction-of-function mutants are viable and have reduced locomotion rates, but do not show defects in pharyngeal pumping or life span.

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First genome edited poinsettias: targeted mutagenesis of flavonoid 3′-hydroxylase using CRISPR/Cas9 results in a colour shift

Plant Cell Tissue and Organ Culture (PCTOC) ◽

10.1007/s11240-021-02103-5 ◽

2021 ◽

Author(s):

Daria Nitarska ◽

Robert Boehm ◽

Thomas Debener ◽

Rares Calin Lucaciu ◽

Heidi Halbwirth

Keyword(s):

Transgenic Plants ◽

Genome Editing ◽

Ornamental Plants ◽

Targeted Mutagenesis ◽

Cloning And Expression ◽

Euphorbia Pulcherrima ◽

Loss Of Function ◽

Wild Type ◽

Promising Tool ◽

Reddish Orange

AbstractThe CRISPR/Cas9 system is a remarkably promising tool for targeted gene mutagenesis, and becoming ever more popular for modification of ornamental plants. In this study we performed the knockout of flavonoid 3′-hydroxylase (F3′H) with application of CRISPR/Cas9 in the red flowering poinsettia (Euphorbia pulcherrima) cultivar ‘Christmas Eve’, in order to obtain plants with orange bract colour, which accumulate prevalently pelargonidin. F3′H is an enzyme that is necessary for formation of cyanidin type anthocyanins, which are responsible for the red colour of poinsettia bracts. Even though F3′H was not completely inactivated, the bract colour of transgenic plants changed from vivid red (RHS 45B) to vivid reddish orange (RHS 33A), and cyanidin levels decreased significantly compared with the wild type. In the genetically modified plants, an increased ratio of pelargonidin to cyanidin was observed. By cloning and expression of mutated proteins, the lack of F3′H activity was confirmed. This confirms that a loss of function mutation in the poinsettia F3′H gene is sufficient for obtaining poinsettia with orange bract colour. This is the first report of successful use of CRISPR/Cas9 for genome editing in poinsettia.

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Performance of hybrid rice grown from separated tillers

Journal of the Bangladesh Agricultural University ◽

10.3329/jbau.v17i4.44619 ◽

2019 ◽

Vol 17 (4) ◽

pp. 507-513

Author(s):

FN Kamarum Munira ◽

Md. Parvez Anwar ◽

Sabina Yeasmin ◽

Md. Harun Or Rashid ◽

Mst Farzana Rahman ◽

...

Keyword(s):

Grain Yield ◽

Plant Height ◽

Hybrid Rice ◽

Rice Variety ◽

Field Laboratory ◽

Split Plot ◽

Rice Seeds ◽

Four Levels ◽

Plot Design

The experiment was conducted at the Agronomy Field Laboratory, Bangladesh Agricultural University, Mymensingh during July to November 2016 to investigate the performance of separated tillers of hybrid rice variety Dhani Gold. The experiment comprised three times of tiller transplantation viz. 3, 4 and 5 week aged tiller seedlings and four levels of number of tiller seedlings transplanted hill-1 viz. 2, 3, 4 and 5 tiller seedlings hill-1 laid out in a split plot design with 3 replications. The highest plant height was obtained when 3-week aged tiller seedlings were transplanted at the rate of 3 tiller seedlings hill-1. The highest number of total tillers hill-1 and number of effective tillers hill-1 were found when 3-week aged tiller seedlings were transplanted with 5 tiller seedlings hill-1. The highest grains panicle-1 was obtained when 4-week aged tiller seedlings were transplanted with 5 tiller seedlings hill-1. The highest grain yield was found when 3-week aged tiller seedlings were transplanted with 5 tiller seedlings hill-1. The lowest grain yield was found when 5-week aged tiller seedlings were transplanted with 2 tiller seedlings hill-1 in hybrid rice variety Dhani Gold. Based on the findings of the present study it may be concluded that 3-week old tiller seedlings of Dhani Gold should be transplanted at the rate of 4 or 5 tiller seedlings hill-1 for higher yield. Thus present study confirms the potentiality of growing hybrid rice from separated tillers in case of unavailability of seedlings or to minimize the seed cost of high value hybrid rice seeds. J Bangladesh Agril Univ 17(4): 507–513, 2019

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Functional characterization of a novel loss-of-function mutation of PRPS1 related to early-onset progressive nonsyndromic hearing loss in Koreans (DFNX1): Potential implications on future therapeutic intervention

The Journal of Gene Medicine ◽

10.1002/jgm.2935 ◽

2016 ◽

Vol 18 (11-12) ◽

pp. 353-358 ◽

Cited By ~ 7

Author(s):

So Young Kim ◽

Ah Reum Kim ◽

Nayoung K.D. Kim ◽

Chung Lee ◽

Jin Hee Han ◽

...

Keyword(s):

Hearing Loss ◽

Therapeutic Intervention ◽

Early Onset ◽

Functional Characterization ◽

Nonsyndromic Hearing Loss ◽

Loss Of Function

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Functional characterization of a loss-of-function mutant I324M of arginine vasopressin receptor 2 in X-linked nephrogenic diabetes insipidus

Scientific Reports ◽

10.1038/s41598-021-90736-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lixia Wang ◽

Weihong Guo ◽

Chunyun Fang ◽

Wenli Feng ◽

Yumeng Huang ◽

...

Keyword(s):

Diabetes Insipidus ◽

Arginine Vasopressin ◽

Nephrogenic Diabetes Insipidus ◽

Functional Characterization ◽

Gene Mutations ◽

Biochemical Properties ◽

Vasopressin Receptor ◽

Inherited Disease ◽

Loss Of Function ◽

Gene Encoding

AbstractX-linked nephrogenic diabetes insipidus (X-linked NDI) is a rare inherited disease mainly caused by lost-of-function mutations in human AVPR2 gene encoding arginine vasopressin receptor 2 (V2R). Our focus of the current study is on exploration of the functional and biochemical properties of Ile324Met (I324M) mutation identified in a pedigree showing as typical recessive X-linked NDI. We demonstrated that I324M mutation interfered with the conformation of complex glycosylation of V2R. Moreover, almost all of the I324M-V2R failed to express on the cell surface due to being captured by the endoplasmic reticulum control system. We further examined the signaling activity of DDAVP-medicated cAMP and ERK1/2 pathways and the results revealed that the mutant receptor lost the ability in response to DDAVP stimulation contributed to the failure of accumulation of cAMP and phosphorylated ERK1/2. Based on the characteristics of molecular defects of I324M mutant, we selected two reagents (SR49059 and alvespimycin) to determine whether the functions of I324M-V2R can be restored and we found that both compounds can significantly “rescue” I324M mutation. Our findings may provide further insights for understanding the pathogenic mechanism of AVPR2 gene mutations and may offer some implications on development of promising treatments for patients with X-linked NDI.

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