Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing

Genome ◽  
2016 ◽  
Vol 59 (3) ◽  
pp. 197-207 ◽  
Author(s):  
Chong-Yun Fu ◽  
Wu-Ge Liu ◽  
Di-Lin Liu ◽  
Ji-Hua Li ◽  
Man-Shan Zhu ◽  
...  
Keyword(s):  
Oryza Sativa L ◽  
Indica Rice ◽  
Copy Number Variations ◽  
Hybrid Vigor ◽  
Dna Polymorphisms ◽  
Whole Genome ◽  
Rice Varieties ◽  
Sequencing Technologies ◽  
Hybrid Weakness ◽  
Sound Foundation

Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica ‘Nipponbare’) reference genome. A total of 2 758 740 polymorphic sites including 2 408 845 SNPs and 349 895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961 791 SNPs and 46 640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.

scholarly journals Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Prasanta K. Subudhi ◽  
Rama Shankar ◽  
Mukesh Jain
Keyword(s):  
Salt Tolerance ◽  
Dna Polymorphisms ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Salt Tolerant ◽  
Tolerance Mechanisms ◽  
Rice Varieties ◽  
Genome Wide ◽  
Rice Genotypes ◽  
Genome Level

AbstractSalinity is a major abiotic constraint for rice farming. Abundant natural variability exists in rice germplasm for salt tolerance traits. Since few studies focused on the genome level variation in rice genotypes with contrasting response to salt stress, genomic resequencing in diverse genetic materials is needed to elucidate the molecular basis of salt tolerance mechanisms. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt sensitive (Bengal, Cocodrie, and IR64) rice genotypes were analyzed. A total of 413 million reads were generated with a mean genome coverage of 93% and mean sequencing depth of 18X. Analysis of the DNA polymorphisms revealed that 2347 nonsynonymous SNPs and 51 frameshift mutations could differentiate the salt tolerant from the salt sensitive genotypes. The integration of genome-wide polymorphism information with the QTL mapping and expression profiling data led to identification of 396 differentially expressed genes with large effect variants in the coding regions. These genes were involved in multiple salt tolerance mechanisms, such as ion transport, oxidative stress tolerance, signal transduction, and transcriptional regulation. The genome-wide DNA polymorphisms and the promising candidate genes identified in this study represent a valuable resource for molecular breeding of salt tolerant rice varieties.

scholarly journals Whole-genome sequencing of three local rice varieties (Oryza sativa L.) in Vietnam

2021 ◽  
Vol 8 (3) ◽  
Author(s):  
Ky Huynh ◽  
Giang Van Quoc ◽  
Tung Nguyen Chau Thanh ◽  
Hien Nguyen Loc ◽  
Vo Cong Thanh
Keyword(s):  
Oryza Sativa ◽  
Oryza Sativa L ◽  
New Technology ◽  
Quality Data ◽  
Whole Genome ◽  
Rice Varieties ◽  
Local Varieties ◽  
Wide Range ◽  
Indel Polymorphisms ◽  
Next Generation Sequencing Ngs

Recently, a new technology, Next-generation sequencing (NGS) has been launched and providing whole-genome sequences that helps identify molecular markers across the genome. DNA markers such as single nucleotides and insertion – deletion (InDel) polymorphisms were widely used for plant breeding particularly to distinguish important traits in rice. These PCR-based markers can be used for the precision detection of polymorphisms. Moreover, PCR-based approaches are simple and effective methods for dealing with the issue of fraudulent labeling and adulteration in the global rice industry. In this study, three local varieties of Oryza sativa L. in Vietnam were sequenced with up to ten times genome depth and at least four times coverage (~83%) using the Illumina HiSeq2000™ system, with an average of 6.5 GB clean data per sample, generated after filtering low-quality data. The data was approximately mapped up to 95% to the reference genome IRGSP 1.0. The results obtained from this study will contribute to a wide range of valuable information for further investigation into this germplasm.

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.

scholarly journals Variability in Nutraceutical Lipid Content of Selected Rice (Oryza sativa L. spp. indica) Germplasms

Agronomy ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 823 ◽  
Author(s):  
Bhornchai Harakotr ◽  
Kasidid Prompoh ◽  
Supakorn Boonyuen ◽  
Bhalang Suriharn ◽  
Kamol Lertrat
Keyword(s):  
Oryza Sativa ◽  
Lipid Content ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Block Design ◽  
Added Value ◽  
Rice Varieties ◽  
Breeding Programs ◽  
Lipid Contents ◽  
Lipid Compounds

Rice (Oryza sativa L.) contains many high-value nutritional compounds, including nutraceutical lipid compounds that offer health benefits. An understanding of the genetic variability in the lipid contents of different rice germplasms is necessary to support breeding programs. The goals of this study were: i) to investigate varietal differences in levels of the nutraceutical lipid α-tocopherol, γ-oryzanol, campesterol, β-sitosterol, octacosanol, and squalene and ii) to identify clusters of rice germplasms based on their lipid contents. Eighty-three indica rice subspecies were evaluated using a randomized complete block design with three replications. Research was conducted in Thailand during the 2016 rice-growing season. Significant differences were found among genotypes across all traits. The largest variation was found for β-sitosterol, followed by campesterol, octacosanol, and α-tocopherol. Variation in squalene content was small. Four principal components were found that accounted for 93.47% of overall variability. β-sitosterol, campesterol, and squalene were the principal discriminatory constituents. No significant correlation was found between color parameters and levels of these compounds, suggesting that former are of little use as an indirect marker for selection of fat-soluble nutraceuticals. Cluster analysis sorted the germplasm into nine clusters, based on their nutraceutical lipid content. TU-010, TU-027, TU-093, and TU-244 genotypes had the highest levels, making them a potentially useful genetic resource in breeding programs for nutraceutically-improved rice. The findings of this study can support the introduction of novel rice varieties with high added-value bioactive properties.

scholarly journals Identification and Validation a Major QTL from “Sea Rice 86” Seedlings Conferred Salt Tolerance

Agronomy ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 410 ◽  
Author(s):  
Fengling Wu ◽  
Jun Yang ◽  
Diqiu Yu ◽  
Peng Xu
Keyword(s):  
Salt Tolerance ◽  
Oryza Sativa L ◽  
Bulked Segregant Analysis ◽  
Indica Rice ◽  
Chromosome 1 ◽  
Saline Stress ◽  
Salt Tolerant ◽  
Rice Varieties ◽  
Target Region ◽  
High Salt Tolerance

Saline stress severely affects rice (Oryza sativa L.) growth and development and reduces crop yield. Therefore, developing salt-tolerant and high-yielding rice using quantitative trait loci (QTLs) and linkage markers is a priority for molecular breeding. Here, the indica rice Sea Rice 86 (SR86) seedlings showed higher tolerance than ordinary rice varieties in saline soil, and a dominant effect on salinity sensitivity was demonstrated by genetic analysis. We constructed bulked segregant analysis pools using F2 populations from parents Dianjingyou 1 as the recipient and SR86 as the donor. We identified a 2.78 Mb region on chromosome 1 as the candidate region. Using simple sequence repeat markers and substitution analysis, we mapped the target region within 5.49 cM in the vicinity of markers RM8904–RM493. We speculated that this QTL, named qST1.1, might contribute significantly to the salt tolerance of SR86. The high salt tolerance of introgression lines obtained by marker assistant selection (MAS) confirmed that the qST1.1 region was associated with salinity tolerance. This newly-discovered QTL will be helpful for the analysis of the salt-tolerant mechanism of rice and breeding high-quality rice varieties using MAS.

Geographic pattern of variation among Asian native rice cultivars (Oryza sativa L.) based on fifteen isozyme loci

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 782-792 ◽  
Author(s):  
J. C. Glaszmann
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Indian Subcontinent ◽  
Indica Rice ◽  
Japonica Rice ◽  
Geographic Pattern ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Himalayan Foothills

The geographic pattern of isozyme variation among rice varieties (Oryza sativa L.) in Asia is described based on an electrophoretic survey of 1688 accessions for 15 loci. The distribution patterns are strongly determined by the existence of several varietal groups that are characterized by contrasting multilocus types with dissimilar environmental and macrogeographic distributions. The two main groups correspond to the indica and japonica subspecies. Other types are frequently found in the Indian subcontinent, especially along the Himalayan foothills. These types are predominant in the Indus River basin. They are differentiated into four groups in the eastern part of the Himalayan foothills. There is variation within the groups. Non-random allele distributions are observed, such as regional clines and narrow localization of alleles. Diversity among indica rice is evenly distributed in whole tropical Asia. Variation among japonica rice shows the hilly part of continental Southeast Asia to be the region of highest genetic diversity and its probable area of origin. All this information provides a guide for further analysis aimed at elucidating the history of cultivated rice in Asia and, subsequently, in other continents.Key words: Asian rice, genetic diversity, isozymes, geographic distributions.

scholarly journals Improving the Rice Photosynthetic Efficiency and Yield by Editing OsHXK1 via CRISPR/Cas9 System

2021 ◽  
Vol 22 (17) ◽  
pp. 9554
Author(s):  
Shaoyan Zheng ◽  
Chanjuan Ye ◽  
Jingqin Lu ◽  
Jiamin Liufu ◽  
Lin Lin ◽  
...  
Keyword(s):  
Photosynthetic Efficiency ◽  
Gene Editing ◽  
Molecular Breeding ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Rice Breeding ◽  
Phenotypic Analysis ◽  
Rice Varieties ◽  
Crop Species ◽  
Rice Yields

Rice (Oryza sativa L.) is an important food crop species in China. Cultivating high-yielding rice varieties that have a high photosynthetic efficiency is an important goal of rice breeding in China. In recent years, due to the continual innovation of molecular breeding methods, many excellent genes have been applied in rice breeding, which is highly important for increasing rice yields. In this paper, the hexokinase gene OsHXK1 was knocked out via the CRISPR/Cas9 gene-editing method in the indica rice varieties Huanghuazhan, Meixiangzhan, and Wushansimiao, and OsHXK1-CRISPR/Cas9 lines were obtained. According to the results of a phenotypic analysis and agronomic trait statistics, the OsHXK1-CRISPR/Cas9 plants presented increased light saturation points, stomatal conductance, light tolerance, photosynthetic products, and rice yields. Moreover, transcriptome analysis showed that the expression of photosynthesis-related genes significantly increased. Taken together, our results revealed that knocking out OsHXK1 via the CRISPR/Cas9 gene-editing method could effectively lead to the cultivation of high-photosynthetic efficiency and high-yielding rice varieties. They also revealed the important roles of OsHXK1 in the regulation of rice yield and photosynthesis.

scholarly journals Optimization of in vitro regeneration protocol for a popular Indica rice (Oryza sativa L. cv Swarna)

2016 ◽  
Vol 5 (08) ◽  
pp. 1395 ◽  
Author(s):  
Vijaya Naresh Juturu ◽  
Gopala Krishna Mekala ◽  
Mallikarjuna Garladinne ◽  
Puli Chandra Obul Reddy ◽  
Akila Chandra Sekhar*
Keyword(s):  
Callus Induction ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
In Vitro Regeneration ◽  
Regeneration System ◽  
Embryogenic Calli ◽  
Rice Varieties ◽  
Regenerated Plants ◽  
Rooting Medium

Though regeneration system in rice has been very well established compare to other crop plants, the fact remains that, most of the indica rice varieties are still recalcitrant for regeneration and genetic transformation. Therefore, refinement of tissue culture protocol for generation of embryogenic calli and regeneration of the fertile plants from a single cell should be a pre requisite event for development of transgenic plants. Here, in this study we reported high frequency robust regeneration protocols for a popular Indica cultivar Swarna.Mature seeds were used as initial material as explants. Highest callus induction % was observed in MSCIMP medium containing 2.0 mg-1 2,4, D + 0.5 mg-1 Kn as phytohormonal combinations. In addition, maximum regeneration was observed in 2.0 mg-l KN + 0.5 mg-l NAA. Regenerated plants were shifted to rooting medium followed by polyhouse for hardening. The callus induction and regeneration reported in this study were well suited for transformation agronomical important genes or functional genomics studies.

scholarly journals Genetic Diversity and Population Structure of Myanmar Rice (Oryza sativa L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2564
Author(s):  
Aye Aye Thant ◽  
Hein Zaw ◽  
Marie Kalousova ◽  
Rakesh Kumar Singh ◽  
Bohdan Lojka
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Oryza Sativa L ◽  
Association Studies ◽  
Plant Genetic Resources ◽  
Population Level ◽  
Dna Polymorphisms ◽  
Phenotypic Traits ◽  
Genome Wide Association Studies ◽  
Rice Varieties

Myanmar is well known as a primary center of plant genetic resources for rice. A considerable number of genetic diversity studies have been conducted in Myanmar using various DNA markers. However, this is the first report using DArTseq technology for exploring the genetic diversity of Myanmar rice. In our study, two ultra-high-throughput diversity array technology markers were employed to investigate the genetic diversity and population structure of local rice varieties in the Ayeyarwady delta, the major region of rice cultivation. The study was performed using 117 rice genotypes with 7643 SNP and 4064 silicoDArT markers derived from the DArT platform. Genetic variance among the genotypes ranged from 0 to 0.753 in SNPs, and from 0.001 to 0.954 in silicoDArT. Two distinct population groups were identified from SNP data analysis. Cluster analysis with both markers clearly separated traditional Pawsan varieties and modern high-yielding varieties. A significant divergence was found between populations according to the Fst values (0.737) obtained from the analysis of molecular variance, which revealed 74% genetic variation at the population level. These findings support rice researchers in identifying useful DNA polymorphisms in genes and pinpointing specific genes conferring desirable phenotypic traits for further genome-wide association studies and parental selection for recombination breeding to enhance rice varietal development and release.

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