scholarly journals Diversity patterns across 1,800 chloroplast genomes of wild (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.)

2016 ◽  
Author(s):  
Peter Civáň ◽  
Terence A. Brown
Keyword(s):  
Haplotype Diversity ◽  
Oryza Rufipogon ◽  
Gene Pools ◽  
Aromatic Rice ◽  
Cultivated Rice ◽  
Ecological Requirements ◽  
Asian Rice ◽  
Chloroplast Genomes ◽  
In The Wild ◽  
Taxonomic Groups

AbstractCultivated Asian rice (O. sativa L.) comprises several groups with distinct ecological requirements and culinary uses. While the two subspecies of O. sativa – indica and japonica – have been subjected to a multitude of genetic and genomic analyses, less is known about the origins and diversity of the agronomically marginal groups – aus and aromatic rice. Here we reconstructed complete chloroplast genomes of over 1,800 accessions of wild and cultivated rice, including 240 aus and 73 aromatic varieties, and analysed the haplotype diversity of the taxonomic groups. We confirm the deep phylogenetic divergence between the main chloroplast haplotypes of japonica and indica, and reveal unique profiles of chloroplast diversity in aus and aromatic rice. Our results indicate that the latter two groups are not simple derivatives of indica and japonica, respectively, but originated from independent and/or reticulate domestication processes. Absence of phylogeographic patterns in the wild distribution of chloroplast haplogroups did not allow firm conclusions about geographic origins and the role of inter-group gene flow. Nonetheless, our results suggest that the domestication of indica, japonica, aus and aromatic rice operated on genetically different gene pools and followed different dynamics.

scholarly journals Genome-Wide Analysis of CCT Transcript Factors to Identify Genes Contributing to Photoperiodic Flowering in Oryza rufipogon

2021 ◽  
Vol 12 ◽  
Author(s):  
Xin Peng ◽  
Win Tun ◽  
Shuang-feng Dai ◽  
Jia-yue Li ◽  
Qun-jie Zhang ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Functional Characterization ◽  
Oryza Rufipogon ◽  
Developmental Expression ◽  
Cultivated Rice ◽  
Functional Roles ◽  
Rhythmic Expression ◽  
Photoperiodic Flowering ◽  
In The Wild ◽  
Functional Alleles

Photoperiod sensitivity is a dominant determinant for the phase transition in cereal crops. CCT (CONSTANS, CO-like, and TOC1) transcription factors (TFs) are involved in many physiological functions including the regulation of the photoperiodic flowering. However, the functional roles of CCT TFs have not been elucidated in the wild progenitors of crops. In this study, we identified 41 CCT TFs, including 19 CMF, 17 COL, and five PRR TFs in Oryza rufipogon, the presumed wild ancestor of Asian cultivated rice. There are thirty-eight orthologous CCT genes in Oryza sativa, of which ten pairs of duplicated CCT TFs are shared with O. rufipogon. We investigated daily expression patterns, showing that 36 OrCCT genes exhibited circadian rhythmic expression. A total of thirteen OrCCT genes were identified as putative flowering suppressors in O. rufipogon based on rhythmic and developmental expression patterns and transgenic phenotypes. We propose that OrCCT08, OrCCT24, and OrCCT26 are the strong functional alleles of rice DTH2, Ghd7, and OsPRR37, respectively. The SD treatment at 80 DAG stimulated flowering of the LD-grown O. rufipogon plants. Our results further showed that the nine OrCCT genes were significantly downregulated under the treatment. Our findings would provide valuable information for the construction of photoperiodic flowering regulatory network and functional characterization of the CCT TFs in both O. rufipogon and O. sativa.

scholarly journals A Rice Ancestral Genetic Resource Conferring Ideal Plant Shapes for Vegetative Growth and Weed Suppression

2021 ◽  
Vol 12 ◽  
Author(s):  
Noritoshi Inagaki ◽  
Hidenori Asami ◽  
Hideyuki Hirabayashi ◽  
Akira Uchino ◽  
Toshiyuki Imaizumi ◽  
...  
Keyword(s):  
Vegetative Growth ◽  
Incident Light ◽  
Rice Chromosome ◽  
Oryza Rufipogon ◽  
Weed Suppression ◽  
Chromosome Segment ◽  
Recurrent Parent ◽  
Cultivated Rice ◽  
In The Wild ◽  
Grain Yield And Quality

To maximize crop growth, crops need to capture sunlight efficiently. This property is primarily influenced by the shape of the crops such as the angle, area, and arrangement of leaves. We constructed a rice (Oryza sativa L.) inbred line that displayed an ideal transition of plant shapes in terms of sunlight receiving efficiency. During vegetative growth, this line exhibited tiller spreading with increased tiller number, which formed a parabolic antenna-like structure. The architecture probably improved light reception efficiency of individuals compared with the recurrent parent. The line achieved not only acceleration of the vegetative growth, but also significant suppression of weed growth under the canopy. The increased light reception efficiency of the line has consequently reduced the amount of incident light to the ground and supplied significant competitiveness against weeds. The spread tillers became erect from the entry of the reproductive growth phase, adaptively sustaining light reception efficiency in thicker stands. The line carries a small chromosomal segment from Oryza rufipogon Griff., a putative progenitor of Asian cultivated rice. The introduced chromosome segment had little effect on grain yield and quality. Our results shed light on potentials hidden in the wild rice chromosome segment to achieve the valuable traits.

Genetic variation in the chloroplast genome suggests multiple domestication of cultivated Asian rice (Oryza sativa L.)

Genome ◽  
2007 ◽  
Vol 50 (2) ◽  
pp. 180-187 ◽  
Author(s):  
Shin-ichi Kawakami ◽  
Kaworu Ebana ◽  
Tomotaro Nishikawa ◽  
Yo-ichiro Sato ◽  
Duncan A. Vaughan ◽  
...  
Keyword(s):  
Oryza Sativa L ◽  
Wild Relatives ◽  
Oryza Species ◽  
Gene Pools ◽  
Nucleotide Substitutions ◽  
Genome Type ◽  
Asian Rice ◽  
In The Wild ◽  
Aa Genome ◽  
Cp Genome

Two hundred and seventy-five accessions of cultivated Asian rice and 44 accessions of AA genome Oryza species were classified into 8 chloroplast (cp) genome types (A–H) based on insertion–deletion events at 3 regions (8K, 57K, and 76K) of the cp genome. The ancestral cp genome type was determined according to the frequency of occurrence in Oryza species and the likely evolution of the variable 57K region of the cp genome. When 2 nucleotide substitutions (AA or TT) were taken into account, these 8 cp types were subdivided into 11 cp types. Most indica cultivars had 1 of 3 cp genome types that were also identified in the wild relatives of rice, O. nivara and O. rufipogon , suggesting that the 3 indica cp types had evolved from distinct gene pools of the O. rufipogon – O. nivara complex. The majority of japonica cultivars had 1 of 3 different cp genome types. One of these 3 was identified in O. rufipogon, suggesting that at least 1 japonica type is derived from O. rufipogon with the same cp genome type. These results provide evidence to support a polyphyletic origin of cultivated Asian rice from at least 4 principal lineages in the O. rufipogon – O. nivara complex.

Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 104-110 ◽  
Author(s):  
J. Provan ◽  
G. Corbett ◽  
W. Powell ◽  
J. W. McNicol
Keyword(s):  
Simple Sequence Repeats ◽  
Wild Rice ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Cultivated Rice ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
In The Wild ◽  
Wild Accessions ◽  
Simple Sequence

Short mononucleotide repeats analogous to nuclear microsatellites or simple sequence repeats (SSRs) have been identified in chloroplast genomes. Primers flanking mononucleotide repeats in the fully sequenced rice chloroplast genome have been used in conjunction with PCR to amplify genomic DNA from 42 wild rice accessions. The amplification products exhibited length polymorphism, which allowed the levels of chloroplast variability detected to be quantified. Seven primer pairs that amplified products from different regions of the rice chloroplast were used, five of which also amplified polymorphic products in cultivated rice (Oryza sativa). Diversity values ranged from 0.5224 ± 0.0845 (SE) to 0.8298 ± 0.0085 in the wild accessions, which was higher than that detected in the O. sativa accessions. Both intra- and inter-specific polymorphism was detected, and the extent of chloroplast genomic differentiation based on chloroplast simple sequence repeat (cpSSR) assays was quantified using the RST statistic. Primers designed to amplify cpSSRs in O. sativa can also be used to generate polymorphic chloroplast markers in related taxa. The potential of using cpSSR to trace the origin of rice polyploid species is discussed.Key words: rice, chloroplast, simple sequence repeat, microsatellites.

scholarly journals Predators as Agents of Selection and Diversification

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 415
Author(s):  
Jerald B. Johnson ◽  
Mark C. Belk
Keyword(s):  
Natural Selection ◽  
Empirical Evidence ◽  
Mortality Rates ◽  
Predator Species ◽  
Natural Systems ◽  
Evolutionary Diversification ◽  
Multiple Predator Species ◽  
In The Wild ◽  
Taxonomic Groups ◽  
Future Work

Predation is ubiquitous in nature and can be an important component of both ecological and evolutionary interactions. One of the most striking features of predators is how often they cause evolutionary diversification in natural systems. Here, we review several ways that this can occur, exploring empirical evidence and suggesting promising areas for future work. We also introduce several papers recently accepted in Diversity that demonstrate just how important and varied predation can be as an agent of natural selection. We conclude that there is still much to be done in this field, especially in areas where multiple predator species prey upon common prey, in certain taxonomic groups where we still know very little, and in an overall effort to actually quantify mortality rates and the strength of natural selection in the wild.

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.

Identifying neutral allele Sb at pollen-sterility loci in cultivated rice with Oryza rufipogon origin

2009 ◽  
Vol 54 (20) ◽  
pp. 3813-3821 ◽  
Author(s):  
LeiGang Shi ◽  
XiangDong Liu ◽  
Bo Liu ◽  
XingJuan Zhao ◽  
Lan Wang ◽  
...  
Keyword(s):  
Pollen Sterility ◽  
Oryza Rufipogon ◽  
Cultivated Rice

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.

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