Variation in seed longevity among diverse Indica rice varieties

Abstract Background and Aims Understanding variation in seed longevity, especially within closely related germplasm, will lead to better understanding of the molecular basis of this trait, which is particularly important for seed genebanks, but is also relevant to anyone handling seeds. We therefore set out to determine the relative seed longevity of diverse Indica rice accessions through storage experiments. Since antioxidants are purported to play a role in seed storability, the antioxidant activity and phenolic content of caryopses were determined. Methods Seeds of 299 Indica rice accessions harvested at 31, 38 and 45 d after heading (DAH) between March and May 2015 and differing in harvest moisture content (MC) were subsequently stored at 10.9 % MC and 45 °C. Samples were taken at regular intervals and sown for germination. Germination data were subjected to probit analysis and the resulting parameters that describe the loss of viability during storage were used for genome-wide association (GWA) analysis. Key Results The seed longevity parameters, Ki [initial viability in normal equivalent deviates (NED)], −σ−1 (σ is the time for viability to fall by 1 NED in experimental storage) and p50 [time for viability to fall to 50 % (0 NED)], varied considerably across the 299 Indica accessions. Seed longevity tended to increase as harvest MC decreased and to decrease as harvest MC increased. Eight major loci associated with seed longevity parameters were identified through GWA analysis. The favourable haplotypes on chromosomes 1, 3, 4, 9 and 11 enhanced p50 by ratios of 0.22–1.86. Conclusions This is the first study to describe the extent of variation in σ within a species’ variety group. A priori candidate genes selected based on rice genome annotation and gene network ontology databases suggested that the mechanisms conferring high seed longevity might be related to DNA repair and transcription, sugar metabolism, reactive oxygen species scavenging and embryonic/root development.

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Identification and Analysis of Micro-Exon Genes in the Rice Genome

International Journal of Molecular Sciences ◽

10.3390/ijms20112685 ◽

2019 ◽

Vol 20 (11) ◽

pp. 2685 ◽

Cited By ~ 2

Author(s):

Qi Song ◽

Fang Lv ◽

Muhammad Tahir ul Qamar ◽

Feng Xing ◽

Run Zhou ◽

...

Keyword(s):

Alternative Splicing ◽

Stop Codon ◽

Indica Rice ◽

Rice Genome ◽

Protein Structures ◽

Wide Distribution ◽

Rna Seq ◽

Rice Varieties ◽

Genome Wide ◽

Alternatively Spliced

Micro-exons are a kind of exons with lengths no more than 51 nucleotides. They are generally ignored in genome annotation due to the short length, whereas recent studies indicate that they have special splicing properties and important functions. Considering that there has been no genome-wide study of micro-exons in plants up to now, we screened and analyzed genes containing micro-exons in two indica rice varieties in this study. According to the annotation of Zhenshan 97 (ZS97) and Minghui 63 (MH63), ~23% of genes possess micro-exons. We then identified micro-exons from RNA-seq data and found that >65% micro-exons had been annotated and most of novel micro-exons were located in gene regions. About 60% micro-exons were constitutively spliced, and the others were alternatively spliced in different tissues. Besides, we observed that approximately 54% of genes harboring micro-exons tended to be ancient genes, and 13% were Oryza genus-specific. Micro-exon genes were highly conserved in Oryza genus with consistent domains. In particular, the predicted protein structures showed that alternative splicing of in-frame micro-exons led to a local structural recombination, which might affect some core structure of domains, and alternative splicing of frame-shifting micro-exons usually resulted in premature termination of translation by introducing a stop codon or missing functional domains. Overall, our study provided the genome-wide distribution, evolutionary conservation, and potential functions of micro-exons in rice.

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Genetic markers associated with seed longevity and vitamin E in diverse Aus rice varieties

Seed Science Research ◽

10.1017/s0960258520000173 ◽

2020 ◽

Vol 30 (2) ◽

pp. 133-141 ◽

Cited By ~ 1

Author(s):

Jae-Sung Lee ◽

Jieun Kwak ◽

Fiona R. Hay

Keyword(s):

Vitamin E ◽

Genetic Markers ◽

Rice Genome ◽

Seed Longevity ◽

Chromosome 1 ◽

Rna Modification ◽

Peroxy Radicals ◽

Rice Varieties ◽

Seed Moisture Content ◽

A Genome

AbstractVitamin E is known to scavenge lipid peroxy radicals and has a purported role in preventing seed deterioration during storage. In our previous studies using 20 rice varieties from different variety groups, the specific ratio of vitamin E homologues rather than total vitamin E content was associated with seed longevity. To validate this result, we extended the experiment to a rice panel composed of 185 Aus (semi-wild rice) varieties. Seed longevity values were determined through storage experiments at 45°C and 10.9% seed moisture content (MC). Eight types of vitamin E homologues (α-, β-, γ- and δ-tocopherol/tocotrienol) were quantified by ultra-performance liquid chromatography. The theoretical initial viability in NED, Ki, was positively correlated with γ- and δ-tocopherols and negatively correlated with α-tocotrienol. The time for viability to fall to 50% during storage at elevated temperature and relative humidity, p50, was positively correlated with δ-tocopherol. The harvest MC was negatively correlated with all seed longevity traits. Taking this factor into account in a genome-wide association (GWA) analysis, we were able to correct false positives. A consistent major peak on chromosome 4 associated with −σ−1 was detected with a mixed linear analysis. Based on rice genome annotation and gene network ontology databases, we suggest that RNA modification, oxidation–reduction, protein–protein interactions and abscisic acid signal transduction play roles in seed longevity extension of Aus rice. Although major GWA regions were not overlapped across traits, three genetic markers, on chromosomes 1, 3 and 4, were associated with both δ-tocopherol and Ki and two markers on chromosome 1 and 8 were associated with both δ-tocopherol and p50.

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Dynamic Insertion of Pot3 in AvrPib Prevailing in a Field Rice Blast Population in the Philippines Led to the High Virulence Frequency Against the Resistance Gene Pib in Rice

Phytopathology ◽

10.1094/phyto-06-18-0198-r ◽

2019 ◽

Vol 109 (5) ◽

pp. 870-877 ◽

Cited By ~ 1

Author(s):

Toluwase Olukayode ◽

Berlaine Quime ◽

Yin-Chi Shen ◽

Mary Jeannie Yanoria ◽

Suobing Zhang ◽

...

Keyword(s):

Resistance Gene ◽

Rice Blast ◽

Indica Rice ◽

The Philippines ◽

Avirulence Gene ◽

Rice Varieties ◽

Breeding Programs ◽

Genome Wide ◽

A Genome ◽

Polymerase Chain

The Magnaporthe oryzae avirulence gene AvrPib is required for the resistance mediated by its cognate resistance gene Pib, which has been intensively used in indica rice breeding programs in many Asian countries. However, the sequence diversity of AvrPib among geographically distinct M. oryzae populations was recently shown to be increasing. Here, we selected a field population consisting of 248 rice blast isolates collected from a disease hotspot in Philippine for the analysis of AvrPib haplotypes and their pathogenicity against Pib. We found that all of the isolates were virulent to Pib and each of them contained an insertion of Pot3 transposon in AvrPib. Moreover, Pot3 insertion was detected in different genomic positions, resulting in three different AvrPib haplotypes, designated avrPib-H1 to H3. We further conducted a genome-wide Pot2 fingerprinting analysis by repetitive element palindromic polymerase chain reaction (PCR) and identified seven different lineages out of 47 representative isolates. The isolates belonging to the same lineage often had the same AvrPib haplotype. In contrast, the isolates having the same AvrPib haplotypes did not always belong to the same lineages. Both mating types MAT1-1 and MAT1-2 were identified in the population in Bohol and the latter appeared dominant. On the host side, we found that 32 of 52 released rice varieties in the Philippines contained Pib diagnosed by PCR gene-specific primers and DNA sequencing of gene amplicons, suggesting that it was widely incorporated in different rice varieties. Our study highlights the genetic dynamics of rice blast population at both the AvrPib locus and the genome-wide levels, providing insight into the mechanisms of the mutations in AvrPib leading to the breakdown of Pib-mediated resistance in rice.

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Genome-wide Profiling of Histone Lysine Butyrylation Reveals its Role in the Positive Regulation of Gene Transcription in Rice

Rice ◽

10.1186/s12284-019-0342-6 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Shuai Liu ◽

Guanqing Liu ◽

Peifeng Cheng ◽

Chao Xue ◽

Yong Zhou ◽

...

Keyword(s):

Gene Expression ◽

Histone Modifications ◽

Rice Genome ◽

Enrichment Analysis ◽

Carbon Chain ◽

Main Body ◽

Rice Varieties ◽

Genome Wide ◽

Chromatin Immunoprecipitation Sequencing ◽

Intergenic Regions

Abstract Background Histone modifications play important roles in growth and development of rice (Oryza sativa L.). Lysine butyrylation (Kbu) with a four-carbon chain is a newly-discovered histone acylation modification in rice. Main Body In this study, we performed chromatin immunoprecipitation sequencing (ChIP-seq) analyses, the result showed that major enrichment of histone Kbu located in genebody regions of rice genome, especially in exons. The enrichment level of Kbu histone modification is positively correlated with gene expression. Furthermore, we compared Kbu with DNase-seq and other histone modifications in rice. We found that 60.06% Kub enriched region co-located with DHSs in intergenic regions. The similar profiles were detected among Kbu and several acetylation modifications such as H3K4ac, H3K9ac, and H3K23ac, indicating that Kbu modification is an active signal of transcription. Genes with both histone Kbu and one other acetylation also had significantly increased expression compared with genes with only one acetylation. Gene Ontology (GO) enrichment analysis revealed that these genes with histone Kbu can regulate multiple metabolic process in different rice varieties. Conclusion Our study showed that the lysine butyrylation modificaiton may promote gene expression as histone acetylation and will provide resources for futher studies on histone Kbu and other epigenetic modifications in plants.

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Cloning and mapping of variety-specific rice genomic DNA sequences: amplified fragment length polymorphisms (AFLP) from silver-stained Polyacrylamide gels

Genome ◽

10.1139/g96-048 ◽

1996 ◽

Vol 39 (2) ◽

pp. 373-378 ◽

Cited By ~ 59

Author(s):

Yong Gu Cho ◽

Matthew W. Blair ◽

Olivier Panaud ◽

Susan R. McCouch

Keyword(s):

Restriction Fragment ◽

Dna Sequences ◽

Fragment Length ◽

Silver Staining ◽

Indica Rice ◽

Rice Genome ◽

Polyacrylamide Gels ◽

Rice Varieties ◽

Length Polymorphisms ◽

Amplified Fragment Length Polymorphisms

An efficient technique for cloning DNA from silver-stained denaturing Polyacrylamide gels was developed to allow the isolation of specific bands obtained from selective restriction fragment amplification (SRFA). This method proved as reliable as cloning radioactively labelled SRFA bands from the same gels. Rice DNA was used as a template, both with and without [32P]dCTP, using the same PCR profiles. Amplified products were separated using denaturing polyacryamide gel electrophoresis and visualized either by silver staining of gels or by autoradiography of 32P-labelled products. We cloned specific polymorphic SRFA bands directly from the denaturing polyacrylamide gels with one round of PCR amplification and confirmed that the sequences of the bands from silver-stained gels were identical to the corresponding 32P-labelled bands. The bands that were chosen represented amplified fragment length polymorphisms (AFLPs) between japonica and indica rice varieties. We studied the ability of two cloned AFLP bands to serve as heritable genetic markers by mapping them as RFLPs in an interspecific rice population and found that they represented single-copy DNA at unique loci in the rice genome. Key words : amplified fragment length polymorphism, AFLP, selective restriction fragment amplification, SRFA, PCR cloning, silver staining.

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Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

Plant Cell Reports ◽

10.1007/s00299-017-2247-4 ◽

2018 ◽

Vol 37 (3) ◽

pp. 529-539 ◽

Cited By ~ 10

Author(s):

Mengchen Zhang ◽

Jing Ye ◽

Qun Xu ◽

Yue Feng ◽

Xiaoping Yuan ◽

...

Keyword(s):

Association Study ◽

Cold Tolerance ◽

Genome Wide Association Study ◽

Indica Rice ◽

Genome Wide Association ◽

Bud Burst ◽

Rice Varieties ◽

Genome Wide

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SNPs, InDels, and Microsatellites within and near to Rice NBS-LRR Resistance Gene Candidates

Agronomy ◽

10.3390/agronomy11112297 ◽

2021 ◽

Vol 11 (11) ◽

pp. 2297

Author(s):

Mark J. Quinton-Tulloch ◽

Katherine A. Steele

Keyword(s):

Indica Rice ◽

R Gene ◽

R Genes ◽

Rice Varieties ◽

Sequence Comparisons ◽

Bioinformatic Tools ◽

Genome Wide ◽

Resistant Varieties ◽

Resistance Gene Candidates ◽

Bioinformatics Study

Plant resistance genes (R-genes) drive the immune responses of crops against specific pathotypes of disease-causing organisms. Over time, genetic diversity in R-genes and R-pseudogenes has arisen among different rice varieties. This bioinformatics study was carried out to (i) predict the full sets of candidate nucleotide-binding site leucine-rich repeat (NLR) R-genes present in six rice genomes; (ii) detect variation within candidate R-genes; (iii) identify potential selectable markers within and near to LRR genes among 75 diverse indica rice genomes. Four high quality indica genomes, plus the standard japonica and indica reference genomes, were analysed with widely available bioinformatic tools to identify candidate R-genes and R-pseudogenes. They were detected in clusters, consistent with previous studies. BLAST analysis of cloned protein sequences of 31 R-gene loci gave confidence in this approach for detection of cloned NLR R-genes. Approximately 10% of candidate R-genes were located within 1 kb of a microsatellite (SSR) marker. Sequence comparisons among indica rice genomes detected SNPs or InDels in 334 candidate rice R-genes. There were significantly more SNPs and InDels within the identified NLR R-gene candidates than in other types of gene. The genome-wide locations of candidate R-genes and their associated markers are presented here for the potential future development of improved disease-resistant varieties. Limitations of in silico approaches used for R-gene discovery are discussed.

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Evolutionary genomics of structural variation in Asian rice (Oryza sativa) and its wild progenitor (O. rufipogon)

10.1101/2019.12.19.883231 ◽

2019 ◽

Cited By ~ 1

Author(s):

Yixuan Kou ◽

Yi Liao ◽

Tuomas Toivainen ◽

Yuanda Lv ◽

Xinmin Tian ◽

...

Keyword(s):

Oryza Sativa ◽

Population Genomics ◽

Indica Rice ◽

Rice Genome ◽

Population Sample ◽

Plant Genome ◽

Structural Variants ◽

Rice Varieties ◽

Asian Rice ◽

Long Read

ABSTRACTStructural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered structural variants (SVs) across a population sample of 358 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read dataset, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among datasets revealed different features of genome variability. For example, genome alignment identified a large (~4.3 Mb) inversion in indica rice varieties relative to an outgroup, and long-read analyses suggest that ~9% of genes from this outgroup are hemizygous. We focused, however, on the resequencing sample to investigate the population genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type -- which included inversions, duplications, deletions, translocations and mobile element insertions -- was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs are predominantly deleterious. The strength of these deleterious effects varied among SV types, with inversions especially deleterious, and across transposable element (TE) families. Among TEs SINE and mariner insertions were especially deleterious, due to stronger selection against their insertions. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ~25% more derived SVs than O. rufipogon, suggesting these deleterious SVs contribute to the cost of domestication. We also used SVs to study the effects of positive selection on the rice genome. Generally, the search for domestication genes were enriched for known candidates, suggesting some utility for SVs towards this purpose. More importantly, we detected hundreds to thousands of genes gained and lost during domestication, many of which are predicted to contribute to traits of agronomic interest.

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