Progress and Prospect of Breeding Utilization of Green Revolution Gene SD1 in Rice

Rice (Oryza sativa L.) is one of the most important cereal crops in the world. The identification of sd1 mutants in rice resulted in a semi-dwarf phenotype that was used by breeders to improve yields. Investigations of sd1 mutants initiated the “green revolution” for rice and staved off famine for many people in the 1960s. The smaller plant height conferred by sd1 allele gives the plants lodging resistance even with a high amount of nitrogen fertilizer. Guang-chang-ai-carrying sd1 was the first high-yielding rice variety that capitalized on the semi-dwarf trait, aiming to significantly improve the rice yield in China. IR8, known as the miracle rice, was also bred by using sd1. The green revolution gene sd1 in rice has been used for decades, but was not identified for a long time. The SD1 gene encodes the rice Gibberellin 20 oxidase-2 (GA20ox2). As such, the SD1 gene is instrumental in uncovering the molecular mechanisms underlying gibberellin biosynthesis There are ten different alleles of SD1. These alleles are identified by genome sequencing within several donor lines in breeding for semi-dwarf rice. Apart from breeding applications and the molecular mechanism of GA biosynthesis, the SD1 gene is also involved in the molecular regulation of other important agronomic traits, like nitrogen fertilizer utilization. The dentification of new alleles of SD1 can be obtained by mutagenesis and genome editing. These new alleles will play an important role in improving the resource diversity of semi-dwarf breeding in the future.

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

The Journal of Agriculture and Development ◽

10.52997/jad.5.02.2019 ◽

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.

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OsABF1 Represses Gibberellin Biosynthesis to Regulate Plant Height and Seed Germination in Rice (Oryza sativa L.)

International Journal of Molecular Sciences ◽

10.3390/ijms222212220 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12220

Author(s):

Liqun Tang ◽

Huayu Xu ◽

Yifeng Wang ◽

Huimei Wang ◽

Zhiyong Li ◽

...

Keyword(s):

Seed Germination ◽

Plant Height ◽

Transcriptional Regulatory Network ◽

Oryza Sativa L ◽

Green Revolution ◽

Functional Characterization ◽

Gibberellin Biosynthesis ◽

Transcriptional Regulatory ◽

Repression Complex ◽

Ga Biosynthesis

Gibberellins (GAs) are diterpenoid phytohormones regulating various aspects of plant growth and development, such as internode elongation and seed germination. Although the GA biosynthesis pathways have been identified, the transcriptional regulatory network of GA homeostasis still remains elusive. Here, we report the functional characterization of a GA-inducible OsABF1 in GA biosynthesis underpinning plant height and seed germination. Overexpression of OsABF1 produced a typical GA-deficient phenotype with semi-dwarf and retarded seed germination. Meanwhile, the phenotypes could be rescued by exogenous GA3, suggesting that OsABF1 is a key regulator of GA homeostasis. OsABF1 could directly suppress the transcription of green revolution gene SD1, thus reducing the endogenous GA level in rice. Moreover, OsABF1 interacts with and transcriptionally antagonizes to the polycomb repression complex component OsEMF2b, whose mutant showed as similar but more severe phenotype to OsABF1 overexpression lines. It is suggested that OsABF1 recruits RRC2-mediated H3K27me3 deposition on the SD1 promoter, thus epigenetically silencing SD1 to maintain the GA homeostasis for growth and seed germination. These findings shed new insight into the functions of OsABF1 and regulatory mechanism underlying GA homeostasis in rice.

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‘Green revolution’ dwarf gene sd1 of rice has gigantic impact

Briefings in Functional Genomics ◽

10.1093/bfgp/elaa019 ◽

2020 ◽

Vol 19 (5-6) ◽

pp. 390-409

Author(s):

Vikram Singh Gaur ◽

Giresh Channappa ◽

Mridul Chakraborti ◽

Tilak Raj Sharma ◽

Tapan Kumar Mondal

Keyword(s):

Oryza Sativa L ◽

Green Revolution ◽

Evolutionary Relationship ◽

Climatic Conditions ◽

Cultivated Rice ◽

Dwarf Gene ◽

The World ◽

Food Grain ◽

High Yielding Varieties ◽

The 1960S

Abstract Rice (Oryza sativa L.) is one of the most important cereal that has fed the world over a longer period. Before green revolution, cultivated rice is believed to have consisted of thousands of landraces each adapted to its specific climatic conditions by surviving against different abiotic and biotic selection pressure. However, owing to the low yield, photo-period sensitivity, late maturity and sensitivity to lodging of these landraces grown world-wide, serious concerns of impending global food crisis was felt during the 1960s because of (i) unprecedented increase of the population and (ii) concomitant decline in the cultivable land. Fortunately, high-yielding varieties developed through the introgression of the semi-dwarf1 gene (popularly known as sd1) during the 1960s led to significant increments in the food grain production that averted the apprehensions of nearing famine. This historical achievement having deep impact in the global agriculture is popularly referred as ‘Green Revolution.’ In this paper, we reviewed, its genetics as well as molecular regulations, evolutionary relationship with orthologous genes from other cereals as well as pseudo-cereals and attempted to provide an up-to-date information about its introgression to different rice cultivars of the world.

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Nitrogen Use Efficiency in Rice under Abiotic Stress: Plant Breeding Approach

10.5772/intechopen.94038 ◽

2020 ◽

Author(s):

Satyen Mondal ◽

Jamil Hasan ◽

Priya Lal Biswas ◽

Emam Ahmed ◽

Tuhin Halder ◽

...

Keyword(s):

Abiotic Stress ◽

Nitrogen Use Efficiency ◽

Abiotic Stresses ◽

Molecular Mechanisms ◽

Oryza Sativa L ◽

Abiotic Stress Tolerance ◽

Rice Variety ◽

Rice Varieties ◽

Nitrogen Use ◽

Use Efficiency

Nitrogenous fertilizer has remarkably improved rice (Oryza sativa L.) yield across the world since its discovery by Haber-Bosch process. Due to climate change, future rice production will likely experience a wide range of environmental plasticity. Nitrogen use efficiency (NUE) is an important trait to confer adaptability across various abiotic stresses such as flooding, drought and salinity. The problem with the increased N application often leads to a reduction in NUE. New solutions are needed to simultaneously increase yield and maximize the NUE of rice. Despite the differences among flooding, salinity and drought, these three abiotic stresses lead to similar responses in rice plants. To develop abiotic stress tolerant rice varieties, speed breeding seems a plausible novel approach. Approximately 22 single quantitative trait loci (QTLs) and 58 pairs of epistatic QTLs are known to be closely associated with NUE in rice. The QTLs/genes for submergence (SUB1A) tolerance, anaerobic germination (AG, TPP7) potential and deepwater flooding tolerance (SK1, SK2) are identified. Furthermore, phytochrome-interacting factor-like14 (OsPIL14), or loss of function of the slender rice1 (SLR1) genes enhance salinity tolerance in rice seedlings. This review updates our understanding of the molecular mechanisms of abiotic stress tolerance and discusses possible approaches for developing N-efficient rice variety.

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Identification, genetic characterization, GA response and molecular mapping of Sdt97: a dominant mutant gene conferring semi-dwarfism in rice (Oryza sativa L.)

Genetics Research ◽

10.1017/s0016672307009020 ◽

2007 ◽

Vol 89 (4) ◽

pp. 221-230 ◽

Cited By ~ 9

Author(s):

JI-PING TONG ◽

XUE-JUN LIU ◽

SHI-YONG ZHANG ◽

SHAO-QING LI ◽

XIAO-JUE PENG ◽

...

Keyword(s):

Molecular Mapping ◽

Physical Map ◽

Oryza Sativa L ◽

Green Revolution ◽

Dominant Gene ◽

Mutant Gene ◽

Reference Sequence ◽

Lodging Resistance ◽

Dwarf Gene ◽

Ga Response

SummarySemi-dwarfism is an important agronomic trait in rice breeding programmes. sd-1, termed the ‘Green Revolution gene’, confers semi-dwarf stature, increases harvest index, improves lodging resistance, and is associated with increased responsiveness to nitrogen fertilizer. It has contributed substantially to the significant increase in rice production. In this paper, a novel semi-dwarf mutant in rice is reported. Genetic analysis revealed that only a single dominant gene locus non-allelic to sd-1, temporarily designated Sdt97, is involved in the control of semi-dwarfism of the mutant. The semi-dwarfism of the mutant could be partly restored to the tall wild-type by application of exogenous GA3, suggesting that the mutant gene Sdt97 may be involved in the gibberellin (GA) synthesis pathway and not the GA response pathway in rice. A residual heterozygous line (RHL) population derived from a recombinant inbred line (RIL) was developed. Simple sequence repeat (SSR) and bulked segregation analysis (BSA) combined with recessive class analysis (RCA) techniques were used to map Sdt97 to the long arm of chromosome 6 at the interval between two STS markers, N6 and TX5, with a genetic distance of 0·2 cM and 0·8 cM, respectively. A contig map was constructed based on the reference sequence aligned by the Sdt97 linked markers. The physical map of the Sdt97 locus was defined to a 118 kb interval, and 19 candidate genes were detected in the target region. This is the first time that a dominant semi-dwarf gene has been reported in rice. Cloning and functional analysis of gene Sdt97 will help us to learn more about molecular mechanism of rice semi-dwarfism.

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Response of Medium and Long Duration Boro Rice Variety (Oryza sativa L.) to Nitrogen Fertilizer

The Agriculturists ◽

10.3329/agric.v14i2.31347 ◽

2017 ◽

Vol 14 (2) ◽

pp. 48-60

Author(s):

Amina Khatun ◽

M K Quais ◽

A A Begum ◽

M A Saleque ◽

M S U Bhuiya

Keyword(s):

Oryza Sativa ◽

Field Experiment ◽

Grain Yield ◽

Nitrogen Fertilizer ◽

Oryza Sativa L ◽

Rice Variety ◽

Grain Yields ◽

Long Duration ◽

N Rates ◽

Boro Rice

A field experiment was conducted during November 2009-April 2010 in Bangladesh Rice Research Institute, Bangladesh to examine the response of two rice (Oryza sativa L.) varieties (BRRIdhan28 and BRRI dhan29) to six N rates of nitrogen fertilizer viz. 0, 50, 100, 150, 200 and 250 kg ha-1. The experiment was conducted in a RCB design with three replications. Grain yields of both BRRI dhan28 and BRRI dhan29 increased significantly in a quadratic fashion with N rates. The highest grain yields were obtained from 150 kg N ha-1 in both the varieties. More than 1 t ha-1 yield was obtained in BRRI dhan29 (6.34 t ha-1) at the same rate of N indicated BRRI dhan29 as a nitrogen efficient variety. However, the predicted economic optimum doses of N appeared to be 156 and 158 kg ha-1 for BRRI dhan28 and BRRI dhan29, respectively. The grain yield was mainly influenced by the number of panicles per hill, which was found to increase with the increase of N rates in both the varieties. The Agriculturists 2016; 14(2) 48-60

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Transcriptomic Analysis of Short-Term Salt-Stress Response in Mega Hybrid Rice Seedlings

Agronomy ◽

10.3390/agronomy11071328 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1328

Author(s):

Noushin Jahan ◽

Yang Lv ◽

Mengqiu Song ◽

Yu Zhang ◽

Liangguang Shang ◽

...

Keyword(s):

Salt Stress ◽

Molecular Mechanisms ◽

Oryza Sativa L ◽

Transcriptome Profiling ◽

Bhlh Transcription Factor ◽

F1 Hybrid ◽

Salt Stress Response ◽

Productivity Losses ◽

Expression Of Genes ◽

Trait Locus

Salinity is a major abiotic stressor that leads to productivity losses in rice (Oryza sativa L.). In this study, transcriptome profiling and heterosis-related genes were analyzed by ribonucleic acid sequencing (RNA-Seq) in seedlings of a mega rice hybrid, Liang-You-Pei-Jiu (LYP9), and its two parents 93–11 and Pei-ai64s (PA64s), under control and two different salinity levels, where we found 8292, 8037, and 631 salt-induced differentially expressed genes (DEGs), respectively. Heterosis-related DEGs were obtained higher after 14 days of salt treatment than after 7 days. There were 631 and 4237 salt-induced DEGs related to heterosis under 7-day and 14-day salt stresses, respectively. Gene functional classification showed the expression of genes involved in photosynthesis activity after 7-day stress treatment, and in metabolic and catabolic activity after 14 days. In addition, we correlated the concurrence of an expression of DEGs for the bHLH transcription factor and a shoot length/salinity-related quantitative trait locus qSL7 that we fine-mapped previously, providing a confirmed case of heterosis-related genes. This experiment reveals the transcriptomic divergence of the rice F1 hybrid and its parental lines under control and salt stress state, and enlightens about the significant molecular mechanisms developed over time in response to salt stress.

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Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa042 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Qian-Hao Zhu ◽

Warwick Stiller ◽

Philippe Moncuquet ◽

Stuart Gordon ◽

Yuman Yuan ◽

...

Keyword(s):

Molecular Mechanisms ◽

Agronomic Traits ◽

Gene Families ◽

Mutant Phenotype ◽

Wild Type ◽

Calcium Dependent ◽

Dependent Protein ◽

Flanking Region ◽

Comparative Transcriptomic Analysis

Abstract Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

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

International Journal of Molecular Sciences ◽

10.3390/ijms22147674 ◽

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.

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