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

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.

scholarly journals The Development and Characterization of Near-Isogenic and Pyramided Lines Carrying Resistance Genes to Brown Planthopper with the Genetic Background of Japonica Rice (Oryza sativa L.)

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 498
Author(s):  
Cuong D. Nguyen ◽  
Holden Verdeprado ◽  
Demeter Zita ◽  
Sachiyo Sanada-Morimura ◽  
Masaya Matsumura ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Resistance Genes ◽  
Genetic Background ◽  
Oryza Sativa L ◽  
Rice Variety ◽  
Brown Planthopper ◽  
Nilaparvata Lugens ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Nilaparvata Lugens Stål

The brown planthopper (BPH: Nilaparvata lugens Stål.) is a major pest of rice, Oryza sativa, in Asia. Host plant resistance has tremendous potential to reduce the damage caused to rice by the planthopper. However, the effectiveness of resistance genes varies spatially and temporally according to BPH virulence. Understanding patterns in BPH virulence against resistance genes is necessary to efficiently and sustainably deploy resistant rice varieties. To survey BPH virulence patterns, seven near-isogenic lines (NILs), each with a single BPH resistance gene (BPH2-NIL, BPH3-NIL, BPH17-NIL, BPH20-NIL, BPH21-NIL, BPH32-NIL and BPH17-ptb-NIL) and fifteen pyramided lines (PYLs) carrying multiple resistance genes were developed with the genetic background of the japonica rice variety, Taichung 65 (T65), and assessed for resistance levels against two BPH populations (Hadano-66 and Koshi-2013 collected in Japan in 1966 and 2013, respectively). Many of the NILs and PYLs were resistant against the Hadano-66 population but were less effective against the Koshi-2013 population. Among PYLs, BPH20+BPH32-PYL and BPH2+BPH3+BPH17-PYL granted relatively high BPH resistance against Koshi-2013. The NILs and PYLs developed in this research will be useful to monitor BPH virulence prior to deploying resistant rice varieties and improve rice’s resistance to BPH in the context of regionally increasing levels of virulence.

Rice (Oryza sativa L.) breeding for novel black short grain associated with yield, cooking quality, high nutrition and antioxidant potential derived from indica black rice x japonica white rice

2021 ◽  
Author(s):  
Chanate Malumpong ◽  
Possawat Narumol ◽  
Uthomphon Saichompoo ◽  
Peeranut Tongyos ◽  
Aekchupong Nanta ◽  
...  
Keyword(s):  
Nutritional Value ◽  
Cooking Quality ◽  
Oryza Sativa L ◽  
Rice Variety ◽  
Japonica Rice ◽  
Black Rice ◽  
Temperate Japonica ◽  
Breeding Lines ◽  
White Rice ◽  
Pedigree Selection

Abstract The combination of the trend of Japanese food consumption with the health benefits of black rice is in high demand for rice consumers in Thailand. For this challenge, incorporation of desirable traits from temperate japonica white rice, Akitakomachi and tropical indica black rice, Riceberry was performed by pedigree selection with maker assisted selection (MAS) and these desirable traits have been presented in breeding progenies. The three candidate lines showed highly favorable agronomic characteristics and a high grain yield, with short grains and good cooking quality, similar to japonica rice, in a tropical climate. In addition, these lines showed black coloration of the pericarp, indicating high nutritional value (including Fe, Zn, Vit B6, Vit E and folate levels) and phytochemical, antioxidant and antidiabetic activities, similar to those of the Riceberry parent. In terms of the sensory testing of unpolished rice, two breeding lines (69-1-1 and 72-4-3) showed higher scores than their parents. However, only 69-1-1 was identified as japonica type according to its genetic background. Therefore, this breeding program, involving the crossing of a temperate japonica white rice with a tropical indica black rice, can create novel black short grain rice variety adapted to a tropical environment, similar to japonica-type rice.

scholarly journals 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

2021 ◽  
Vol 12 ◽  
Author(s):  
M. T. Andrew-Peter-Leon ◽  
Ramchander Selvaraj ◽  
K. K. Kumar ◽  
Mehanathan Muthamilarasan ◽  
Jeshima Khan Yasin ◽  
...  
Keyword(s):  
Plant Height ◽  
Rice Variety ◽  
Functional Characterization ◽  
Early Flowering ◽  
Targeted Mutagenesis ◽  
High Yield ◽  
Loss Of Function ◽  
South Indian ◽  
Differential Expression Pattern ◽  
Early Maturing

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.

scholarly journals Optimizing Agrobacterium-Mediated Transformation and CRISPR-Cas9 Gene Editing in the tropical japonica Rice Variety Presidio

2021 ◽  
Vol 22 (20) ◽  
pp. 10909
Author(s):  
Marco Molina-Risco ◽  
Oneida Ibarra ◽  
Mayra Faion-Molina ◽  
Backki Kim ◽  
Endang M. Septiningsih ◽  
...  
Keyword(s):  
Gene Editing ◽  
Oryza Sativa L ◽  
Rice Variety ◽  
Crop Improvement ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Tropical Japonica ◽  
Regenerated Plants ◽  
Efficient Gene ◽  
Japonica Rice Variety

Bottlenecks in plant transformation and regeneration have slowed progress in applying CRISPR/Cas-based genome editing for crop improvement. Rice (Oryza sativa L.) has highly efficient temperate japonica transformation protocols, along with reasonably efficient indica protocols using immature embryos. However, rapid and efficient protocols are not available for transformation and regeneration in tropical japonica varieties, even though they represent the majority of rice production in the U.S. and South America. The current study has optimized a protocol using callus induction from mature seeds with both Agrobacterium-mediated and biolistic transformation of the high-yielding U.S. tropical japonica cultivar Presidio. Gene editing efficiency was tested by evaluating knockout mutations in the phytoene desaturase (PDS) and young seedling albino (YSA) genes, which provide a visible phenotype at the seedling stage for successful knockouts. Using the optimized protocol, transformation of 648 explants with particle bombardment and 532 explants with Agrobacterium led to a 33% regeneration efficiency. The YSA targets had ambiguous phenotypes, but 60% of regenerated plants for PDS showed an albino phenotype. Sanger sequencing of edited progeny showed a number of insertions, deletions, and substitutions at the gRNA target sites. These results pave the way for more efficient gene editing of tropical japonica rice varieties.

scholarly journals A Mild Phenotype Caused by Two Novel Compound Heterozygous Mutations in CEP290

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1240
Author(s):  
Agnieszka Rafalska ◽  
Anna M. Tracewska ◽  
Anna Turno-Kręcicka ◽  
Milena J. Szafraniec ◽  
Marta Misiuk-Hojło
Keyword(s):  
Vision Loss ◽  
Compound Heterozygous ◽  
Loss Of Function ◽  
Mild Phenotype ◽  
Cone Function ◽  
Retinal Disorders ◽  
Molecular Inversion Probes ◽  
Disease Experience ◽  
The Individual ◽  
Inherited Retinal Disorders

CEP290 is a ciliary gene frequently mutated in ciliopathies, resulting in a broad range of phenotypes, ranging from isolated inherited retinal disorders (IRDs) to severe or lethal syndromes with multisystemic involvement. Patients with non-syndromic CEP290-linked disease experience profound and early vision loss due to cone-rod dystrophy, as in Leber congenital amaurosis. In this case report, we describe two novel loss-of-function heterozygous alterations in the CEP290 gene, discovered in a patient suffering from retinitis pigmentosa using massive parallel sequencing of a molecular inversion probes library constructed for 108 genes involved in IRDs. A milder phenotype than expected was found in the individual, which serves to prove that some CEP290-associated disorders may display preserved cone function.

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

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 133-142 ◽  
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.

scholarly journals Integrative Transcriptomic and Proteomic Analysis Reveals an Alternative Molecular Network of Glutamine Synthetase 2 Corresponding to Nitrogen Deficiency in Rice (Oryza sativa L.)

2021 ◽  
Vol 22 (14) ◽  
pp. 7674
Author(s):  
Ting Liang ◽  
Zhengqing Yuan ◽  
Lu Fu ◽  
Menghan Zhu ◽  
Xiaoyun Luo ◽  
...  
Keyword(s):  
Glutamine Synthetase ◽  
Oryza Sativa L ◽  
Alternative Pathway ◽  
Rice Variety ◽  
Nitrogen Deficiency ◽  
Primary Root ◽  
Phenotypic Characterization ◽  
Glutathione Metabolism ◽  
N Assimilation ◽  
N Deficiency

Nitrogen (N) is an essential nutrient for plant growth and development. The root system architecture is a highly regulated morphological system, which is sensitive to the availability of nutrients, such as N. Phenotypic characterization of roots from LY9348 (a rice variety with high nitrogen use efficiency (NUE)) treated with 0.725 mM NH4NO3 (1/4N) was remarkable, especially primary root (PR) elongation, which was the highest. A comprehensive analysis was performed for transcriptome and proteome profiling of LY9348 roots between 1/4N and 2.9 mM NH4NO3 (1N) treatments. The results indicated 3908 differential expression genes (DEGs; 2569 upregulated and 1339 downregulated) and 411 differential abundance proteins (DAPs; 192 upregulated and 219 downregulated). Among all DAPs in the proteome, glutamine synthetase (GS2), a chloroplastic ammonium assimilation protein, was the most upregulated protein identified. The unexpected concentration of GS2 from the shoot to the root in the 1/4N treatment indicated that the presence of an alternative pathway of N assimilation regulated by GS2 in LY9348 corresponded to the low N signal, which was supported by GS enzyme activity and glutamine/glutamate (Gln/Glu) contents analysis. In addition, N transporters (NRT2.1, NRT2.2, NRT2.3, NRT2.4, NAR2.1, AMT1.3, AMT1.2, and putative AMT3.3) and N assimilators (NR2, GS1;1, GS1;2, GS1;3, NADH-GOGAT2, and AS2) were significantly induced during the long-term N-deficiency response at the transcription level (14 days). Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that phenylpropanoid biosynthesis and glutathione metabolism were significantly modulated by N deficiency. Notably, many transcription factors and plant hormones were found to participate in root morphological adaptation. In conclusion, our study provides valuable information to further understand the response of rice roots to N-deficiency stress.

scholarly journals Loss-of-function and missense variants in NSD2 cause decreased methylation activity and are associated with a distinct developmental phenotype

2021 ◽  
Author(s):  
Paolo Zanoni ◽  
Katharina Steindl ◽  
Deepanwita Sengupta ◽  
Pascal Joset ◽  
Angela Bahr ◽  
...  
Keyword(s):  
Loss Of Function ◽  
Mild Phenotype ◽  
Psychological Issues ◽  
Missense Variants ◽  
Mild Developmental Delay ◽  
Pathogenic Variants ◽  
In Silico Modeling ◽  
And Function ◽  
Methylation Activity

Abstract Purpose Despite a few recent reports of patients harboring truncating variants in NSD2, a gene considered critical for the Wolf–Hirschhorn syndrome (WHS) phenotype, the clinical spectrum associated with NSD2 pathogenic variants remains poorly understood. Methods We collected a comprehensive series of 18 unpublished patients carrying heterozygous missense, elongating, or truncating NSD2 variants; compared their clinical data to the typical WHS phenotype after pooling them with ten previously described patients; and assessed the underlying molecular mechanism by structural modeling and measuring methylation activity in vitro. Results The core NSD2-associated phenotype includes mostly mild developmental delay, prenatal-onset growth retardation, low body mass index, and characteristic facial features distinct from WHS. Patients carrying missense variants were significantly taller and had more frequent behavioral/psychological issues compared with those harboring truncating variants. Structural in silico modeling suggested interference with NSD2’s folding and function for all missense variants in known structures. In vitro testing showed reduced methylation activity and failure to reconstitute H3K36me2 in NSD2 knockout cells for most missense variants. Conclusion NSD2 loss-of-function variants lead to a distinct, rather mild phenotype partially overlapping with WHS. To avoid confusion for patients, NSD2 deficiency may be named Rauch–Steindl syndrome after the delineators of this phenotype.

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