Comparative RFLP mapping of a wild rice, Oryza officinalis, and cultivated rice, O. sativa

Genome ◽  
1994 ◽  
Vol 37 (3) ◽  
pp. 382-389 ◽  
Author(s):  
K. K. Jena ◽  
G. S. Khush ◽  
G. Kochert
Keyword(s):  
Gene Order ◽  
High Frequency ◽  
Wild Rice ◽  
Chromosome 1 ◽  
Rflp Markers ◽  
Chromosome 11 ◽  
Cultivated Rice ◽  
Oryza Officinalis ◽  
Rflp Map ◽  
Comparative Maps

A comparative RFLP map was constructed in a wild rice, Oryza officinalis, by using 139 genomic and cDNA probes that had been used previously to map RFLPs in O. sativa. Nine of the 12 chromosomes of O. officinalis were highly homosequential to those of O. sativa. A major rearrangement of gene order was detected in chromosome 1 and small inversions were found in chromosomes 3 and 11. Fourteen translocated RFLP markers were found, and chromosome 11 contained a high frequency of such translocated segments. Results were consistent with meiotic and trisomie analysis, which suggested that the genomes of O. officinalis and O. sativa were similar. Applications of comparative maps in plant breeding and gene cloning are discussed.Key words: Oryza, rice, wild rice, RFLP, genetic map.

scholarly journals Deciphering the genetics basis of lodging resistance in wild rice O. longistaminata

2019 ◽  
Author(s):  
Weixiong Long ◽  
Dong Dan ◽  
Zhengqing Yuan ◽  
Yunping Chen ◽  
Jie Jin ◽  
...  
Keyword(s):  
Wild Rice ◽  
High Throughput Sequencing ◽  
Breaking Strength ◽  
Chromosome 8 ◽  
Stem Diameter ◽  
Chromosome 1 ◽  
Stem Length ◽  
Cultivated Rice ◽  
Lodging Resistance ◽  
Major Qtl

Abstract The abuse of fertilizer results in tall rice plants that are susceptible to lodging and reduced plant yield. Hence, it is important to identify and utilize the QTLs/genes for lodging resistance breeding. O. longistaminata exhibited a strong stem and high biomass productively, which could be the candidate gene pool for cultivars lodging resistance improvement. However, most of previous studies have focused on cultivated rice and few reports on wild rice. Here, a set of 152 BC 2 F 20 lines derived from a cross between 93-11 and O. longistaminata were evaluated for lodging resistance. QTL mapping analysis combined with SNP marker derived from high-throughput sequencing identified 12 QTLs for stem diameter (SD), 11 QTLs for stem length (SL) and 3 QTLs for breaking strength (BS). Of which, 14 QTLs were firstly identified from O. longistaminata. A major QTL, qLR1 which was delimited to a region about 80 Kb on chromosome 1, increased stem diameter, stem length and breaking strength. And another major QTL, qLR8 that was delimited in an interval about 100 Kb on chromosome 8, significantly enhanced the breaking strength. These results provide evidence that the O. longistaminata can be exploited to develop lodging resistant rice lines.

Organogenic responses in tissue culture of srd mutants of Arabidopsis thaliana

Development ◽  
1998 ◽  
Vol 125 (1) ◽  
pp. 135-142 ◽  
Author(s):  
S. Ozawa ◽  
I. Yasutani ◽  
H. Fukuda ◽  
A. Komamine ◽  
M. Sugiyama
Keyword(s):  
Tissue Culture ◽  
Arabidopsis Thaliana ◽  
High Frequency ◽  
Culture Method ◽  
Chromosome 1 ◽  
Rflp Markers ◽  
Temperature Sensitive ◽  
Root Explants ◽  
Lower Region ◽  
Hypocotyl Explants

In Arabidopsis thaliana, shoot redifferentiation and root redifferentiation can be induced at high frequency from hypocotyl and root explants by a two-step culture method. Tissues are precultured on callus-inducing medium and then transferred onto shoot-inducing medium for shoot redifferentiation or onto root-inducing medium for root redifferentiation. In an attempt to dissect these organogenic processes genetically, we characterized the responses in tissue culture of srd1, srd2 and srd3 mutants that were originally isolated as temperature-sensitive strains with defects in shoot redifferentiation (Yasutani, I., Ozawa, S., Nishida, T., Sugiyama, M. and Komamine, A. (1994) Plant Physiol. 105, 815–822). These mutants exhibited temperature sensitivity at different steps of organogenesis, which allowed the identification of three states associated with organogenic competence: IC (incompetent); CR (competent with respect to root redifferentiation); and CSR (competent with respect to shoot and root redifferentiation). Hypocotyl explants were shown to be in the IC state at the initiation of culture and to enter the CSR state, via the CR state, during preculture on callus-inducing medium, whereas root explants seemed to be in the CR state at the initiation of culture. The transition from IC to CR and that from CR to CSR appeared to require the functions of SRD2 and SRD3, respectively. It appears that explants in the CSR state redifferentiate shoots with the aid of the products of SRD1 and SRD2 when transplanted onto shoot-inducing medium. Histological examination of the srd mutants revealed that the function of SRD2 is required not only for organogenesis but also for the reinitiation of cell proliferation in hypocotyl explants during culture on callus-inducing medium. Linkage analysis using RFLP markers indicated that SRD1, SRD2, and SRD3 are located at the lower region, the central region, and the upper region of chromosome 1, respectively.

scholarly journals Transcriptomic and proteomic responses to herbivory in cultivated, Bt-transgenic and wild rice

2020 ◽  
Author(s):  
Yongbo Liu ◽  
Weiqing Wang ◽  
Yonghua Li ◽  
Fang Liu ◽  
Weijuan Han ◽  
...  
Keyword(s):  
Transgenic Rice ◽  
Wild Rice ◽  
Crop Production ◽  
Brown Planthopper ◽  
Hierarchical Cluster ◽  
Nilaparvata Lugens ◽  
Cultivated Rice ◽  
Kegg Pathways ◽  
Itraq Analysis ◽  
Go Terms

Abstract Background: Strategies are still employed to decrease insect damage in crop production, including conventional breeding with wild germplasm resources and transgenic technology with the insertion of foreign genes, while the insect-resistant mechanism of these strategies remains unclear. Results: Under the feeding of brown planthopper (Nilaparvata lugens), cultivated rice (WT) showed less DEGs (568) and DAPs (4) than transgenic rice (2098 and 11) and wild rice CL (1990 and 39) and DX (1932 and 25). Hierarchical cluster of DEGs showed gene expression of CL and DX were similar, slightly distinct to GT, and clearly different from WT. DEGs assigned to the GO terms were less in WT rice than GT, CL and DX, and “Metabolic process”, “cellular process”, “response to stimulus” were dominant. Wild rice CL significantly enriched in KEGG pathways of “Metabolic pathways”, “biosynthesis of secondary metabolites”, “plant-pathogen interaction” and “plant hormone signal transduction”. The iTRAQ analysis confirmed the results of RNA-seq, which showing the least GO terms and KEGG pathways responding to herbivory in the cultivated rice. Synthesize conclusions: This study demonstrated that similarity in the transcriptomic and proteomic response to herbivory for the wild rice and Bt-transgenic rice, while cultivated rice lack of enough pathways in response to herbivory. Our results highlighted the importance of conservation of crop wild species.

scholarly journals Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Chenna Swetha ◽  
Anushree Narjala ◽  
Awadhesh Pandit ◽  
Varsha Tirumalai ◽  
P. V. Shivaprasad
Keyword(s):  
Metabolic Pathways ◽  
Wild Rice ◽  
Regulation Of Gene Expression ◽  
Genome Integrity ◽  
Cultivated Rice ◽  
Mrna Targets ◽  
Ribonucleoprotein Complexes ◽  
The Poor ◽  
Rna Targets ◽  
Secondary Wall Formation

Abstract Background Small non-coding (s)RNAs are involved in the negative regulation of gene expression, playing critical roles in genome integrity, development and metabolic pathways. Targeting of RNAs by ribonucleoprotein complexes of sRNAs bound to Argonaute (AGO) proteins results in cleaved RNAs having precise and predictable 5` ends. While tools to study sliced bits of RNAs to confirm the efficiency of sRNA-mediated regulation are available, they are sub-optimal. In this study, we provide an improvised version of a tool with better efficiency to accurately validate sRNA targets. Results Here, we improvised the CleaveLand tool to identify additional micro (mi)RNA targets that belong to the same family and also other targets within a specified free energy cut-off. These additional targets were otherwise excluded during the default run. We employed these tools to understand the sRNA targeting efficiency in wild and cultivated rice, sequenced degradome from two rice lines, O. nivara and O. sativa indica Pusa Basmati-1 and analyzed variations in sRNA targeting. Our results indicate the existence of multiple miRNA-mediated targeting differences between domesticated and wild species. For example, Os5NG4 was targeted only in wild rice that might be responsible for the poor secondary wall formation when compared to cultivated rice. We also identified differential mRNA targets of secondary sRNAs that were generated after miRNA-mediated cleavage of primary targets. Conclusions We identified many differentially targeted mRNAs between wild and domesticated rice lines. In addition to providing a step-wise guide to generate and analyze degradome datasets, we showed how domestication altered sRNA-mediated cascade silencing during the evolution of indica rice.

scholarly journals Genetic Divergence in Indigenous Wild and Cultivated Rice Species of Manipur Valley

ISRN Genetics ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
K. Medhabati ◽  
K. Rajiv Das ◽  
M. Rohinikumar ◽  
H. Sunitibala ◽  
Th. Dikash Singh
Keyword(s):  
Genetic Divergence ◽  
Wild Rice ◽  
Flag Leaf ◽  
Cluster Formation ◽  
Leaf Length ◽  
Cultivated Rice ◽  
And Performance ◽  
Flag Leaf Length ◽  
The Individual ◽  
Hybridization Programme

Genetic divergence of 32 indigenous rice germplasms and five wild rice of which three from Manipur and two wild rice procured from IRRI, Philippines was investigated using Mahalanobis, D2 statistic. Based on twelve agromorphological characters, the thirty-seven germplasms both wild and cultivated were grouped into five clusters based on the relative magnitudes of D2 values following Tocher's method of cluster formation. Based on the rank totals, the characters which contributed maximum towards genetic divergence in the present studies were grain yield/plant, spikelet/panicle, 100 grain weight, grain length, days to 50% flowering, ear bearing tillers/plant, and flag leaf length. In the present study, maximum intercluster distance was estimated between cluster III and (D2=14.09) which was closed followed by clusters II and V (D2=12.50). On the basis of their greater intercluster distance, high value of cluster mean according to the character to be improved and performance of the individual germplasms for the character, the germplasms could be used in hybridization programme for improvement of different plant characters in the rice germplasms of Manipur.

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.

Sucrose transport and metabolism control carbon partitioning between stem and grain in rice

2021 ◽  
Author(s):  
Jyotirmaya Mathan ◽  
Anuradha Singh ◽  
Aashish Ranjan
Keyword(s):  
Grain Yield ◽  
Wild Rice ◽  
Grain Filling ◽  
Invertase Activity ◽  
Cultivated Rice ◽  
Sucrose Transport ◽  
Unit Leaf ◽  
In The Wild ◽  
Source Sink ◽  
Oryza Australiensis

Abstract The source-sink relationship is key to overall crop performance. Detailed understanding of the factors that determine source-sink dynamics is imperative for the balance of biomass and grain yield in crop plants. We investigated the differences in the source-sink relationship between a cultivated rice Oryza sativa cv. Nipponbare and a wild rice Oryza australiensis that show striking differences in biomass and grain yield. Oryza australiensis, accumulating higher biomass, not only showed higher photosynthesis per unit leaf area but also exported more sucrose from leaves than Nipponbare. However, grain features and sugar levels suggested limited sucrose mobilization to the grains in the wild rice due to vasculature and sucrose transporter functions. Low cell wall invertase activity and high sucrose synthase cleavage activity followed by higher expression of cellulose synthase genes in Oryza australiensis stem utilized photosynthates preferentially for the synthesis of structural carbohydrates, resulting in high biomass. In contrast, the source-sink relationship favored high grain yield in Nipponbare via accumulation of transitory starch in the stem, due to higher expression of starch biosynthetic genes, which is mobilized to panicles at the grain filling stage. Thus, vascular features, sucrose transport, and functions of sugar metabolic enzymes explained the differences in the source-sink relationship between Nipponbare and Oryza australiensis.

scholarly journals Segregation Distortion Observed in the Progeny of Crosses Between Oryza sativa and O. meridionalis Caused by Abortion During Seed Development

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 398
Author(s):  
Daiki Toyomoto ◽  
Masato Uemura ◽  
Satoru Taura ◽  
Tadashi Sato ◽  
Robert Henry ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Seed Development ◽  
Wild Rice ◽  
Lethal Gene ◽  
Chromosome 6 ◽  
Cultivated Rice ◽  
Substitution Lines ◽  
Putative Gene ◽  
Aa Genome ◽  
Recurrent Backcrossing

Wild rice relatives having the same AA genome as domesticated rice (Oryza sativa) comprise the primary gene pool for rice genetic improvement. Among them, O. meridionalis and O. rufipogon are found in the northern part of Australia. Three Australian wild rice strains, Jpn1 (O. rufipogon), Jpn2, and W1297 (O. meridionalis), and one cultivated rice cultivar Taichung 65 (T65) were used in this study. A recurrent backcrossing strategy was adopted to produce chromosomal segment substitution lines (CSSLs) carrying chromosomal segments from wild relatives and used for trait evaluation and genetic analysis. The segregation of the DNA marker RM136 locus on chromosome 6 was found to be highly distorted, and a recessive lethal gene causing abortion at the seed developmental stage was shown to be located between two DNA markers, KGC6_10.09 and KGC6_22.19 on chromosome 6 of W1297. We name this gene as SEED DEVELOPMENT 1 (gene symbol: SDV1). O. sativa is thought to share the functional dominant allele Sdv1-s (s for sativa), and O. meridionalis is thought to share the recessive abortive allele sdv1-m (m for meridionalis). Though carrying the sdv1-m allele, the O. meridionalis accessions can self-fertilize and bear seeds. We speculate that the SDV1 gene may have been duplicated before the divergence between O. meridionalis and the other AA genome Oryza species, and that O. meridionalis has lost the function of the SDV1 gene and has kept the function of another putative gene named SDV2.

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