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 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.

scholarly journals Genetic variability for grain yield and yield associated traits in transplant Aman rice (Oryza sativa L.)

2015 ◽  
Vol 2 (2) ◽  
pp. 207-213
Author(s):  
Mashtura Begum ◽  
Md Amir Hossain ◽  
Fakir Muhammad Munawar Hossain ◽  
Ahmed Khairul Hasan
Keyword(s):  
Grain Yield ◽  
Oryza Sativa L ◽  
Rice Variety ◽  
Crop Improvement ◽  
Genetic Advance ◽  
Improvement Program ◽  
Rice Varieties ◽  
Spad Value ◽  
Crop Varieties ◽  
Planting Materials

For any crop improvement program, it is imperative to assess the grain yield progress of the existing crop varieties to find the further avenue to out yield the existing superior ones. Therefore, an experiment was conducted at the Agronomy Field Laboratory, Bangladesh Agricultural University, Mymensingh from July to December 2013 to find out the genetic variation for grain yield and their associated traits of transplant Aman rice varieties. The experiment consisted of 11 varieties viz. Bashiraj, Binadhan-7, BR10, BR11, BR22, BR23, BRRIdhan32, BRRIdhan39, BRRIdhan49, BRRIdhan57 and IR64. The high yielding Bangladeshi varieties were selected based on their releasing year with a local and one exotic T. Aman rice varieties. Among the varieties, BR10 produced the highest grain yield (3.83 t ha-1). Binadhan-7 rice variety recorded the highest chlorophyll content (39.93 SPAD value) at 29DAT, (44 SPAD value) at 39 DAT and (47.30 SPAD value) at 49 DAT. The highest phenotypic (1491.81) and genotypic (1147.26) variances and genetic advance (61.19) were obtained from spikelets panicle-1 and this parameter had greater ability to increase yield. Among the traits, the highest heritability was recorded by effective tillers hill-1 (87.91%) which influenced the grain yield. Therefore, it may be concluded that the variety BR10 of transplant Aman rice produced maximum grain yield, spikelets panicle-1, showed high phenotypic and genotypic variances and genetic advance. Bashiraj, BRRIdhan49 and BRRIdhan57 also can be considered as planting materials as their yield performance is close to BR 10. Therefore, the findings of the present study will help the breeders for further yield improvement of rice.Res. Agric., Livest. Fish.2(2): 207-213, August 2015

scholarly journals Screening and Expression of a Silicon Transporter Gene(Lsi1)in Wild-Type Indica Rice Cultivars

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Mahbod Sahebi ◽  
Mohamed M. Hanafi ◽  
M. Y. Rafii ◽  
Parisa Azizi ◽  
Rambod Abiri ◽  
...  
Keyword(s):  
Antioxidant Activities ◽  
Indica Rice ◽  
Rice Variety ◽  
Morphological Properties ◽  
Japonica Rice ◽  
Wild Type ◽  
Rice Varieties ◽  
Silicon Transporter ◽  
Chlorophyll A And B ◽  
Japonica Rice Variety

Silicon (Si) is one of the most prevalent elements in the soil. It is beneficial for plant growth and development, and it contributes to plant defense against different stresses. TheLsi1gene encodes a Si transporter that was identified in a mutant Japonica rice variety. This gene was not identified in fourteen Malaysian rice varieties during screening. Then, a mutant version ofLsi1was substituted for the native version in the three most common Malaysian rice varieties, MR219, MR220, and MR276, to evaluate the function of the transgene. Real-time PCR was used to explore the differential expression ofLsi1in the three transgenic rice varieties. Silicon concentrations in the roots and leaves of transgenic plants were significantly higher than in wild-type plants. Transgenic varieties showed significant increases in the activities of the enzymes SOD, POD, APX, and CAT; photosynthesis; and chlorophyll content; however, the highest chlorophyll A and B levels were observed in transgenic MR276. Transgenic varieties have shown a stronger root and leaf structure, as well as hairier roots, compared to the wild-type plants. This suggests thatLsi1plays a key role in rice, increasing the absorption and accumulation of Si, then alters antioxidant activities, and improves morphological properties.

scholarly journals Detection of a novel quantitative trait locus for cold tolerance at the booting stage derived from a tropical japonica rice variety Silewah

2011 ◽  
Vol 61 (1) ◽  
pp. 61-68 ◽  
Author(s):  
Masahiko Mori ◽  
Kazumitsu Onishi ◽  
Yoshiro Tokizono ◽  
Hiroshi Shinada ◽  
Toru Yoshimura ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Cold Tolerance ◽  
Quantitative Trait ◽  
Rice Variety ◽  
Japonica Rice ◽  
Booting Stage ◽  
Tropical Japonica ◽  
Trait Locus ◽  
Japonica Rice Variety

scholarly journals Genetic Diversity Analysis of 53 Indonesian Rice Genotypes using 6K Single Nucleotide Polymorphism Markers

2018 ◽  
Vol 14 (1) ◽  
pp. 1
Author(s):  
Joko Prasetiyono ◽  
Nurul Hidayatun ◽  
Tasliah Tasliah
Keyword(s):  
Genetic Diversity ◽  
Morphological Characters ◽  
Snp Markers ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Tropical Japonica ◽  
Rice Chromosomes ◽  
Improvement Programs ◽  
Rice Genotypes ◽  
Genotypic Mixtures

<p>Indonesia is rich in rice genetic resources, however, only a small number has been used in variety improvement programs. This study aimed to determine the genetic diversity of Indonesian rice varieties using 6K SNP markers. The study was conducted at ICABIOGRAD for DNA isolation and IRRI for SNP marker analysis. Genetic materials were 53 rice genotypes consisting of 49 varieties and 4 check genotypes. SNP markers used were 6K loci. Results showed that among the markers analyzed, only 4,606 SNPs (76.77%) were successfully read. The SNP markers covered all twelve rice chromosomes of 945,178.27 bp. The most common allele observed was GG, whereas the least allele was TG. Dendrograms of the 53 rice varieties analyzed with 4,606 SNPs demonstrated several small groups containing genotypic mixtures between indica and japonica rice, and no groups were found to contain firmly indica or japonica type. Structure analysis (K = 2) with value of 0.8 showed that the 53 rice varieties were divided into several groups and each group consisted of 4 japonica, 2 tropical japonica, 46 indica, and 1 aus rice type, respectively. IR64 and Ciherang proved to have an indica genome, while Rojolele has japonica one. Dupa and Hawara Bunar, usually grouped into tropical japonica rice, were classified as indica type, and Hawara Bunar has perfectly 100% indica type. The results of this study indicated that rice classification (indica-japonica) which is usually classified based only on morphological characters, e.g. grain and leaf shapes, is not enough and classification based on SNP markers should be considered for that purpose.</p>

scholarly journals Rajdeep (IET 17713): A New Rainfed Lowland High Yielding Rice Variety for Semideep Situation

2021 ◽  
Author(s):  
Indrani Dana ◽  
Sitesh Chatterjee
Keyword(s):  
West Bengal ◽  
Insect Pests ◽  
Oryza Sativa L ◽  
Rice Variety ◽  
National Level ◽  
Stem Borer ◽  
Research Station ◽  
Wet Season ◽  
Rice Varieties ◽  
Improvement Project

In eastern India, more than 13.0 million ha of rice lands are affected by excess water and periodically suffer from flash floods and complete submergence. Most of the traditional and adapted rice varieties of this situation are low yielders. To overcome these problems the high yielding rice variety (HYV), Rajdeep (IET 17713) has been developed by Rice Research Station, Government of West Bengal, Chinsurah, Hooghly as high yielding rice variety for semideep water situation. Field experiment was conducted to evaluate the performance of promising semideep water rice (Oryza sativa L.) genotypes under lowland situation during wet season of 2002-2013. Performance of Rajdeep, semideep water rice was better and therefore it was released. It is tolerant to sheath blight, sheath rot diseases and stem borer, leaf folder insect-pests. The high yielding semideep rice variety, Rajdeep exhibited superiority over national check (Sabita), regional check (Purnendu) and local check tested in different locations under All India Coordinated Rice Improvement Project (AICRIP) trials during kharif, 2002-2003 conducted by ICAR-Indian Institute of Rice Research, Hyderabed, India. This variety was also tested in multi-locational yield trials (2003-2013) along with check variety Swarna-Sub 1/ Bhudeb at different locations of West Bengal. After testing at national level as well as at state level, based on yield performance of the variety, the HYV semideep rice variety Rajdeep was released and notified by Government of India in the Gazette of India vide Notification No. S.O. 1007(E) on 30th March, 2017.

scholarly journals Screening and evaluation of upland rice (Oryza sativa L.) varieties in inundated soil

2018 ◽  
Vol 51 (2) ◽  
pp. 63-69
Author(s):  
Sunday Ojo Adigbo ◽  
Philip Joseph Osadebay ◽  
Innocent Iseghohi ◽  
Cornelius Idowu Alarima ◽  
Nnennaya Ogechi Agbenin ◽  
...  
Keyword(s):  
Upland Rice ◽  
Oryza Sativa L ◽  
Rice Variety ◽  
Rice Varieties ◽  
Inland Valley ◽  
Short Period ◽  
Maturity Period ◽  
Vigorous Growth ◽  
Number Of Leaves ◽  
Screen House

Abstract Poor germination and subsequent low grain yield of dry seeded upland rice in the existing anaerobic and short niche between lowland rice and dry season crops in the inland valley necessitate the screening of 19 rice varieties. The identification of vigorous growth and short duration upland rice variety in anaerobic condition would optimize this niche. The potted experiment was carried out in the screen house of the Department of Crop Science and Horticulture, Federal University Oye-Ekiti, Ikole campus in 2015 to screen and evaluate the performance of upland rice varieties in inundated soils with a view to selecting the suitable variety or varieties that will fit into the existing niche in the inland valley. The experiment was laid in a complete randomization design and replicated three times. The number of leaves, biomass and grain weight plant−1 of the varieties were significantly (P ≤ 0.05 %) different. The number of tillers observed in WAB 56-104, NERICA 4, NERICA 6, NERICA 3, NERICA 5, NERICA 10, NERICA 9, ARICA 4 NERICA 1, FARO 63, FARO 65 and NERICA 8 varieties were significantly (P < 0.05) lower than those of Igbemo varieties. The numbers of days to 50 % flowering of NERICA 1, NERICA 2, NERICA 10, NERICA 5, NERICA 9, NERICA 3, NERICA 7, NERICA 8, ARICA 4 and WAB 56-104 varieties were the lowest. Although Igbemo brown, Igbemo white varieties had the highest grain yields per plant, their maturity period exceeded the short period. Thus, NERICA 2 and NERICA 5 varieties which had lower number of days to flowering could be considered as candidate varieties that can be optimized in the niche in question.

scholarly journals IDENTIFICATION OF WIDE COMPATIBILITY VARIETIES IN SOME TROPICAL JAPONICA RICE

2013 ◽  
Vol 6 (1) ◽  
pp. 28 ◽  
Author(s):  
A. Hairmansis ◽  
Hajrial Aswidinnoor ◽  
Trikoesoemaningtyas Trikoesoemaningtyas ◽  
Suwarno Suwarno
Keyword(s):  
Hybrid Rice ◽  
Block Design ◽  
Hybrid Sterility ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Major Barrier ◽  
F1 Hybrid ◽  
Tropical Japonica ◽  
Wide Compatibility ◽  
Randomized Complete Block Design

The F1 hybrid sterility in indica/japonica crosses is the major barrier in developing hybrid rice varieties between these two diverse germplasm. The sterility problem in japonica/indica hybrids can be overcome by using wide compatibility genes. The objective of this study was to identify wide compatibility varieties (WCVs) in some tropical japonica rice. Twenty five tropical japonica varieties as male parents were crossed with indica (IR64) and japonica (Akitakomachi) testers as female parents. The crosses were planted following a randomized complete block design with three replications. Varieties having average spikelet fertility of more than 70% with both the indica and japonica testers were rated as WCVs. Result from this study showed that six tropical japonica varieties were classified as WCVs, i.e., Cabacu, Grogol, Kencana Bali, Klemas, Lampung Lawer, and Napa. Hybrid sterility is caused by partial sterility of male and female gametes. The WCVs from the present study can be used in hybrid rice breeding program to solve hybrid sterility in indica/japonica hybrids.

scholarly journals Identification of fgr gene and preliminary evaluation for agronomic traits of pandan sticky rice variety (Oryza sativa L.)

2019 ◽  
Vol 02 ◽  
pp. 39-48
Author(s):  
Toan D. Pham
Keyword(s):  
Oryza Sativa ◽  
Agronomic Traits ◽  
Oryza Sativa L ◽  
Rice Variety ◽  
Rice Production ◽  
Molecular Techniques ◽  
High Yield ◽  
Preliminary Evaluation ◽  
Rice Varieties ◽  
Fgr Gene

Rice (Oryza sativa L.) is the most important food crop in Vietnam particularly in the Mekong Delta. Screening of good quality and high yield rice varieties are needed for rice production in Vietnam. The purpose of this study was to use molecular techniques to identify fgr gene and to evaluate preliminarily agronomic traits of pandan sticky rice variety. The results showed that this variety contained fgr gene. The fragrant allele was amplified by ESP - IFAP primers with a product of 255 bp in size. Similarly, evaluation of agronomic traits showed that the pandan sticky rice variety displayed many desirable characteristics such as plant height of 108 cm, panicle length of 25.6 cm, seed/panicle 135, 100-grain weight 2.07 g, pandan smell, level 2 of alkali digestion, gel consistency 93 mm. These results were useful information and could be applied for improving and providing pandan sticky rice variety for rice production.

scholarly journals OsmiR396/Growth Regulating Factor modulate rice grain size through direct regulation of embryo-specific miR408

2021 ◽  
Author(s):  
Xiaofang Yang ◽  
Xiaoling Zhao ◽  
Zhengyan Dai ◽  
Feilong Ma ◽  
Xuexia Miao ◽  
...  
Keyword(s):  
Grain Size ◽  
Regulatory Networks ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Genetic Regulatory Networks ◽  
Rice Grain ◽  
Rice Varieties ◽  
Size Regulation

Abstract microRNAs (miRNAs) are promising targets for crop improvement of complex agricultural traits. Coordinated activity between/among different miRNAs may fine-tune specific developmental processes in diverse organisms. Grain size is a main factor determining rice (Oryza sativa L.) crop yield, but the network of miRNAs influencing this trait remains uncharacterized. Here we show that sequestering OsmiR396 through target mimicry (MIM396) can substantially increase grain size in several japonica and indica rice subspecies and in plants with excessive tillers and a high panicle density. Thus, OsmiR396 has a major role related to the regulation of rice grain size. The grain shape of Growth Regulating Factor8 (OsGRF8)-overexpressing transgenic plants was most similar to that of MIM396 plants, suggesting OsGRF8 is a major mediator of OsmiR396 in grain size regulation. A miRNA microarray analysis revealed changes to the expression of many miRNAs, including OsmiR408, in the MIM396 plants. Analyses of gene expression patterns and functions indicated OsmiR408 is an embryo-specific miRNA that positively regulates grain size. Silencing OsmiR408 expression (miR408KO) using CRISPR technology resulted in small grains. Moreover, we revealed the direct regulatory effects of OsGRF8 on OsMIR408 expression. A genetic analysis further showed that the large-grain phenotype of MIM396 plants could be complemented by miR408KO. Also, several hormone signaling pathways might be involved in the OsmiR396/GRF-meditated grain size regulation. Our findings suggest that genetic regulatory networks comprising various miRNAs, such as OsmiR396 and OsmiR408, may be crucial for controlling rice grain size. Furthermore, the OsmiR396/GRF module may be important for breeding new high-yielding rice varieties.

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