scholarly journals Evolutional analysis of heat shock transcription factors in wild and cultivated rice (Oryza sativa L.)

2020 ◽  
Author(s):  
Huan Tao ◽  
Weifeng Wan ◽  
Jian Huang ◽  
Samuel Tareke Woldegiorgis ◽  
Yifan Xiong ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Heat Shock ◽  
Salinity Stress ◽  
Wild Rice ◽  
Oryza Sativa L ◽  
Rice Genome ◽  
Research Work ◽  
Oryza Rufipogon ◽  
Cultivated Rice ◽  
Heat Shock Transcription Factors

Abstract Background：Heat shock transcription factors (Hsfs) take part in many physiological and biochemical pathways in plants by regulating the expression of various stress-responsive genes, such as heat shock proteins (Hsps). With the development of rice genome re-sequencing projects, some researches had been carried out to identify Hsf gene family members in rice at the whole genomic scale. However, Hsfs in cultivated and wild rice genomes has not been fully studied and compared, although genetic diversity in cultivated rice is limited compared to wild rice. Results：In this research work, Hsfs genes were screened and evolutionally compared in the genomes of 6 wild rice and 1 cultivated rice varieties, including O. barthii, O. glumaepatula, O. meridionalis, O. nivara, O. punctate, O. rufipogon and O. sativa & Nipponbare. Total 22, 23, 24, 24, 25, 25 and 25 Hsf genes were identified in the tested 7 rice genomes, respectively. The different number of Hsf genes between wild and cultivated rice genotypes was due to dispersed duplication and whole genome duplication (WGD) events, reversely contributed to different stress-tolerant ability between wild and cultivated rice. The evolutional analysis on the Hsf genes confirmed that O. rufipogon was the immediate ancestral progenitors of O. sativa. The expression profile of Hsf genes in Nipponbare and O. rufipogon under different stage of salinity stress showed that 4 root Hsf genes, including HsfA3a, HsfA4d, HsfC2a and HsfC2b, were simultaneously up-regulated by salinity stress in cultivated rice and its ancestral progenitor, implying that these 4 Hsf genes played conserved roles in rice in response to salinity stress. However, a substantial number of Hsf genes were exclusively regulated only in Oryza rufipogon rice seedling, suggesting that some of genuine salinity stress tolerance genes might be missing in cultivated rice. Conclusion：The results of this study would give insight into the evolution and function of Hsf gene members in rice, and hint to the use of wild relative genes to improve rice performance.

scholarly journals SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation

2020 ◽  
Author(s):  
Wei Li ◽  
Kui Li ◽  
Ying Huang ◽  
Cong Shi ◽  
Wu-Shu Hu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Wild Rice ◽  
De Novo ◽  
Rice Genome ◽  
Gene Families ◽  
Oryza Rufipogon ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Cultivated Rice ◽  
Reproductive Process

AbstractAsian cultivated rice is believed to have been domesticated from an immediate ancestral progenitor, Oryza rufipogon, which provides promising sources of novel alleles for world rice improvement. Here we first present a high-quality de novo assembly of the typical O. rufipogon genome through the integration of single-molecule sequencing (SMRT), 10× and Hi-C technologies. This chromosome-based reference genome allows a multi-species comparative analysis of the annual selfing O. sativa and its two wild progenitors, the annual selfing O. nivara and perennial outcrossing O. rufipogon, identifying massive numbers of dispensable genes that are functionally enriched in reproductive process. Comparative genomic analyses identified millions of genomic variants, of which large-effect mutations (e.g., SVs, CNV and PAVs) may affect the variation of agronomically significant traits. We demonstrate how lineage-specific expansion of rice gene families may have contributed to the formation of reproduction isolation (e.g., the recognition of pollen and male sterility), thus brightening the role in driving mating system evolution during the evolutionary process of recent speciation. We document thousands of positively selected genes that are mainly involved in flower development, ripening, pollination, reproduction and response to biotic- and abiotic stresses. We show that selection pressures may serve as crucial forces to govern substantial genomic alterations among the three rice species that form the genetic basis of rapid evolution of mating and reproductive systems under diverse habitats. This first chromosome-based wild rice genome in the genus Oryza will become powerful to accelerate the exploration of untapped genomic diversity from wild rice for the enhancement of elite rice cultivars.

scholarly journals Rapid Accumulation of Proline Enhances Salinity Tolerance in Australian Wild Rice Oryza australiensis Domin

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2044
Author(s):  
Ha Thi Thuy Nguyen ◽  
Sudipta Das Bhowmik ◽  
Hao Long ◽  
Yen Cheng ◽  
Sagadevan Mundree ◽  
...  
Keyword(s):  
Salinity Stress ◽  
Wild Rice ◽  
Oryza Sativa L ◽  
Early Stage ◽  
Membrane Integrity ◽  
Free Proline ◽  
Cultivated Rice ◽  
Cell Membrane Integrity ◽  
Rapid Accumulation ◽  
Oryza Australiensis

Proline has been reported to play an important role in helping plants cope with several stresses, including salinity. This study investigates the relationship between proline accumulation and salt tolerance in an accession of Australian wild rice Oryza australiensis Domin using morphological, physiological, and molecular assessments. Seedlings of O. australiensis wild rice accession JC 2304 and two other cultivated rice Oryza sativa L. cultivars, Nipponbare (salt-sensitive), and Pokkali (salt-tolerant), were screened at 150 mM NaCl for 14 days. The results showed that O. australiensis was able to rapidly accumulate free proline and lower osmotic potential at a very early stage of salt stress compared to cultivated rice. The qRT-PCR result revealed that O. australiensis wild rice JC 2304 activated proline synthesis genes OsP5CS1, OsP5CS2, and OsP5CR and depressed the expression of proline degradation gene OsProDH as early as 1 h after exposure to salinity stress. Wild rice O. australiensis and Pokkali maintained their relative water content and cell membrane integrity during exposure to salinity stress, while the salt-sensitive Nipponbare failed to do so. An analysis of the sodium and potassium contents suggested that O. australiensis wild rice JC 2304 adapted to ionic stress caused by salinity by maintaining a low Na+ content and low Na+/K+ ratio in the shoots and roots. This demonstrates that O. australiensis wild rice may use a rapid accumulation of free proline as a strategy to cope with salinity stress.

scholarly journals Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

2021 ◽  
Author(s):  
Yong-Chao Xu ◽  
Jie Zhang ◽  
Dong-Yan Zhang ◽  
Ying-Hui Nan ◽  
Song Ge ◽  
...  
Keyword(s):  
Drought Stress ◽  
Stress Response ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Cultivated Rice ◽  
Antisense Transcripts ◽  
High Genetic Diversity ◽  
Natural Antisense Transcripts ◽  
Form Complex ◽  
Oryza Nivara

Abstract Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa L.), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although many rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa ssp. japonica) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1,246 lncRNAs were identified, including 1,091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1,091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes previously demonstrated to be involved in stress response; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.

scholarly journals Rescue of a developmental arrest caused by a C. elegans heat-shock transcription-factor mutation by loss of ribosomal S6-kinase activity

2018 ◽  
Author(s):  
Peter Chisnell ◽  
T. Richard Parenteau ◽  
Elizabeth Tank ◽  
Kaveh Ashrafi ◽  
Cynthia Kenyon
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Heat Shock ◽  
Heat Shock Transcription Factor ◽  
Adult Longevity ◽  
Loss Of Function ◽  
S6 Kinase ◽  
Heat Shock Transcription Factors ◽  
C Elegans ◽  
Developmental Arrest

AbstractThe widely conserved heat-shock response, regulated by heat shock transcription factors, is not only essential for cellular stress resistance and adult longevity, but also for proper development. However, the genetic mechanisms by which heat-shock transcription factors regulate development are not well understood. In C. elegans, we conducted an unbiased genetic screen to identify mutations that could ameliorate the developmental arrest phenotype of a heat-shock factor mutant. Here we show that loss of the conserved translational activator rsks-1/S6-Kinase, a downstream effector of TOR kinase, can rescue the developmental-arrest phenotype of hsf-1 partial loss-of-function mutants. Unexpectedly, we show that the rescue is not likely caused by reduced translation, nor to activation of any of a variety of stress-protective genes and pathways. Our findings identify an as-yet unexplained regulatory relationship between the heat-shock transcription factor and the TOR pathway during C. elegans’ development.

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