RFLP mapping of the rice genome

AbstractDNA N6-methylation (6mA) in Adenine nucleotide is a post replication modification responsible for many biological functions. Automated and accurate computational methods can help to identify 6mA sites in long genomes saving significant time and money. Our study develops a convolutional neural network (CNN) based tool i6mA-CNN capable of identifying 6mA sites in the rice genome. Our model coordinates among multiple types of features such as PseAAC (Pseudo Amino Acid Composition) inspired customized feature vector, multiple one hot representations and dinucleotide physicochemical properties. It achieves auROC (area under Receiver Operating Characteristic curve) score of 0.98 with an overall accuracy of 93.97% using fivefold cross validation on benchmark dataset. Finally, we evaluate our model on three other plant genome 6mA site identification test datasets. Results suggest that our proposed tool is able to generalize its ability of 6mA site identification on plant genomes irrespective of plant species. An algorithm for potential motif extraction and a feature importance analysis procedure are two by products of this research. Web tool for this research can be found at: https://cutt.ly/dgp3QTR.

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Comparative whole-genome and proteomics analyses of the next seed bank and the original master seed bank of MucoRice-CTB 51A line, a rice-based oral cholera vaccine

BMC Genomics ◽

10.1186/s12864-020-07355-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Ai Sasou ◽

Yoshikazu Yuki ◽

Ayaka Honma ◽

Kotomi Sugiura ◽

Koji Kashima ◽

...

Keyword(s):

Seed Bank ◽

Dna Sequences ◽

Storage Proteins ◽

Oral Vaccine ◽

Rice Genome ◽

Major Allergen ◽

Selection Marker ◽

Cholera Toxin B Subunit ◽

Whole Genome ◽

Allergen Protein

Abstract Background We have previously developed a rice-based oral vaccine against cholera diarrhea, MucoRice-CTB. Using Agrobacterium-mediated co-transformation, we produced the selection marker–free MucoRice-CTB line 51A, which has three copies of the cholera toxin B subunit (CTB) gene and two copies of an RNAi cassette inserted into the rice genome. We determined the sequence and location of the transgenes on rice chromosomes 3 and 12. The expression of alpha-amylase/trypsin inhibitor, a major allergen protein in rice, is lower in this line than in wild-type rice. Line 51A was self-pollinated for five generations to fix the transgenes, and the seeds of the sixth generation produced by T5 plants were defined as the master seed bank (MSB). T6 plants were grown from part of the MSB seeds and were self-pollinated to produce T7 seeds (next seed bank; NSB). NSB was examined and its whole genome and proteome were compared with those of MSB. Results We re-sequenced the transgenes of NSB and MSB and confirmed the positions of the three CTB genes inserted into chromosomes 3 and 12. The DNA sequences of the transgenes were identical between NSB and MSB. Using whole-genome sequencing, we compared the genome sequences of three NSB with three MSB samples, and evaluated the effects of SNPs and genomic structural variants by clustering. No functionally important mutations (SNPs, translocations, deletions, or inversions of genic regions on chromosomes) between NSB and MSB samples were detected. Analysis of salt-soluble proteins from NSB and MSB samples by shot-gun MS/MS detected no considerable differences in protein abundance. No difference in the expression pattern of storage proteins and CTB in mature seeds of NSB and MSB was detected by immuno-fluorescence microscopy. Conclusions All analyses revealed no considerable differences between NSB and MSB samples. Therefore, NSB can be used to replace MSB in the near future.

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Explore the genetics of weedy traits using rice 3K database

Botanical Studies ◽

10.1186/s40529-020-00309-y ◽

2021 ◽

Vol 62 (1) ◽

Author(s):

Yu-Lan Lin ◽

Dong-Hong Wu ◽

Cheng-Chieh Wu ◽

Yung-Fen Huang

Keyword(s):

Seed Coat ◽

Coat Color ◽

Rice Genome ◽

Genome Project ◽

Weedy Rice ◽

Seed Coat Color ◽

Allele Mining ◽

Cultivated Rice ◽

Population Structure Analysis ◽

Public Data

Abstract Background Weedy rice, a conspecific weedy counterpart of the cultivated rice (Oryza sativa L.), has been problematic in rice-production area worldwide. Although we started to know about the origin of some weedy traits for some rice-growing regions, an overall assessment of weedy trait-related loci was not yet available. On the other hand, the advances in sequencing technologies, together with community efforts, have made publicly available a large amount of genomic data. Given the availability of public data and the need of “weedy” allele mining for a better management of weedy rice, the objective of the present study was to explore the genetic architecture of weedy traits based on publicly available data, mainly from the 3000 Rice Genome Project (3K-RGP). Results Based on the results of population structure analysis, we have selected 1378 individuals from four sub-populations (aus, indica, temperate japonica, tropical japonica) without admixed genomic composition for genome-wide association analysis (GWAS). Five traits were investigated: awn color, seed shattering, seed threshability, seed coat color, and seedling height. GWAS was conducted for each sub-population × trait combination and we have identified 66 population-specific trait-associated SNPs. Eleven significant SNPs fell into an annotated gene and four other SNPs were close to a putative candidate gene (± 25 kb). SNPs located in or close to Rc were particularly predictive of the occurrence of seed coat color and our results showed that different sub-populations required different SNPs for a better seed coat color prediction. We compared the data of 3K-RGP to a publicly available weedy rice dataset. The profile of allele frequency, phenotype-genotype segregation of target SNP, as well as GWAS results for the presence and absence of awns diverged between the two sets of data. Conclusions The genotype of trait-associated SNPs identified in this study, especially those located in or close to Rc, can be developed to diagnostic SNPs to trace the origin of weedy trait occurred in the field. The difference of results from the two publicly available datasets used in this study emphasized the importance of laboratory experiments to confirm the allele mining results based on publicly available data.

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Characterization of Atypical Protein Tyrosine Kinase (PTK) Genes and Their Role in Abiotic Stress Response in Rice

Plants ◽

10.3390/plants9050664 ◽

2020 ◽

Vol 9 (5) ◽

pp. 664

Author(s):

Allimuthu Elangovan ◽

Monika Dalal ◽

Gopinathan Kumar Krishna ◽

Sellathdurai Devika ◽

Ranjeet Ranjan Kumar ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Tyrosine Kinase ◽

Tyrosine Phosphorylation ◽

Rice Genome ◽

Kinase Domain ◽

Tyrosine Kinase Domain ◽

Protein Tyrosine ◽

Dual Specificity ◽

Submergence Stress

Tyrosine phosphorylation constitutes up to 5% of the total phophoproteome. However, only limited studies are available on protein tyrosine kinases (PTKs) that catalyze protein tyrosine phosphorylation in plants. In this study, domain analysis of the 27 annotated PTK genes in rice genome led to the identification of 18 PTKs with tyrosine kinase domain. The kinase domain of rice PTKs shared high homology with that of dual specificity kinase BRASSINOSTEROID-INSENSITIVE 1 (BRI1) of Arabidopsis. In phylogenetic analysis, rice PTKs clustered with receptor-like cytoplasmic kinases-VII (RLCKs-VII) of Arabidopsis. mRNAseq analysis using Genevestigator revealed that rice PTKs except PTK9 and PTK16 express at moderate to high level in most tissues. PTK16 expression was highly abundant in panicle at flowering stage. mRNAseq data analysis led to the identification of drought, heat, salt, and submergence stress regulated PTK genes in rice. PTK14 was upregulated under all stresses. qRT-PCR analysis also showed that all PTKs except PTK10 were significantly upregulated in root under osmotic stress. Tissue specificity and abiotic stress mediated differential regulation of PTKs suggest their potential role in development and stress response of rice. The candidate dual specificity PTKs identified in this study paves way for molecular analysis of tyrosine phosphorylation in rice.

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Clusters of interspersed repeated DNA sequences in the rice genome (Oryza)

Genome ◽

10.1139/g93-124 ◽

1993 ◽

Vol 36 (5) ◽

pp. 944-953 ◽

Cited By ~ 6

Author(s):

Xinping Zhao ◽

Gary Kochert

Keyword(s):

Dna Sequences ◽

Blot Hybridization ◽

Rice Genome ◽

Repeated Sequence ◽

Repeated Sequences ◽

Repeated Dna ◽

Rice Varieties ◽

Slot Blot Hybridization ◽

Repeated Dna Sequence ◽

Genus Oryza

We have characterized a repeated DNA sequence (RTL 122) from rice (Oryza sauva L.) with respect to its organization in the rice genome and its distribution among rice and other plants. The results indicate that the RTL 122 sequence is interspersed in the rice genome and limited to the genus Oryza. It is highly polymorphic and can be used to fingerprint rice varieties. A structure was observed in which several repeated sequences were clustered in DNA regions of 15–20 kb. We characterized three bacteriophage lambda clones that contained the RTL 122 sequence. Southern analysis using probes derived from restriction fragments of the three lambda clones indicated that all fragments except one are interspersed repeated sequences and belong to different repeated sequence families. Subsequent slot blot hybridization showed that most of them are only present within the genus Oryza. Some of the Oryza-specific, physically linked sequences show the same phylogenetic distribution, which suggests that these sequences might have evolved in a coordinate fashion. On the other hand, some of the repeated sequences have a different distribution even though they are physically adjacent in the genome. We speculate that such blocks of interspersed repeated sequences may serve as hotspots for rapid changes in the rice genome.Key words: rice, Oryza, repeated sequences, DNA fingerprinting, coordinated evolution.

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