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.

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 Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ai-ling Hour ◽  
Wei-hsun Hsieh ◽  
Su-huang Chang ◽  
Yong-pei Wu ◽  
Han-shiuan Chin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Indigenous Peoples ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Gene Pools ◽  
Improved Varieties ◽  
Breeding Goals

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

Characterization of indica–japonica subspecies-specific InDel loci in wild relatives of rice (Oryza sativa L. subsp. indica Kato and subsp. japonica Kato)

2016 ◽  
Vol 64 (2) ◽  
pp. 405-418 ◽  
Author(s):  
Joong Hyoun Chin ◽  
Yoo-Jin Lee ◽  
Wenzhu Jiang ◽  
Hee-Jong Koh ◽  
Michael J. Thomson
Keyword(s):  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Wild Relatives

scholarly journals Comparative Physical Mapping BetweenOryza sativa(AA Genome Type) andO. punctata(BB Genome Type)

Genetics ◽  
2007 ◽  
Vol 176 (1) ◽  
pp. 379-390 ◽  
Author(s):  
HyeRan Kim ◽  
Phillip San Miguel ◽  
William Nelson ◽  
Kristi Collura ◽  
Marina Wissotski ◽  
...  
Keyword(s):  
Physical Mapping ◽  
Genome Type ◽  
Aa Genome

scholarly journals Genetic relatedness among Ethiopian Oryza longistaminata populations and other AA genome Oryza species

2020 ◽  
Vol 91 (2) ◽  
pp. 175-183
Author(s):  
Melaku Getachew ◽  
Liyu Huang ◽  
Shilai Zhang ◽  
Guangfu Huang ◽  
Jing Zhang ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Oryza Species ◽  
Oryza Longistaminata ◽  
Aa Genome

scholarly journals Sequence Variants Linked to Key Traits in Interspecific Crosses between African and Asian Rice

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1653
Author(s):  
Hayba Badro ◽  
Marie-Noelle Ndjiondjop ◽  
Agnelo Furtado ◽  
Robert Henry
Keyword(s):  
Association Analysis ◽  
Agronomic Traits ◽  
Heading Date ◽  
Sucrose Metabolism ◽  
Interspecific Crosses ◽  
Oryza Glaberrima ◽  
Gene Pools ◽  
Synonymous Snps ◽  
African Rice ◽  
Asian Rice

Asian and African rice gene pools vary in many traits that are important in rice breeding. The genetic basis of these differences was evaluated by analysis of important agronomic traits in crosses between African and Asian rice. Trait-associated variants (TAVs) influencing three quantitative agronomic traits, heading date (Hd), tiller number at maturity (T), and 1000 grain weight (TGW), were identified by association analysis of crosses between Asian and African rice. Populations were developed by crossing WAB56-104 (Oryza sativa) and CG14 (Oryza glaberrima). DNA from plants with extremely high or low values for these phenotypes was bulked and sequenced. The reference genome of O. sativa cv Nipponbare was used in general association analysis and candidate gene analysis. A total of 5152 non-synonymous single nucleotide polymorphisms (SNPs) across 3564 genes distinguished the low and the high bulks for Hd, T, and TGW traits; 611 non-synonymous SNPs across 447 genes were found in KEGG pathways. Six non-synonymous SNPs were found in the sequences of LOC107275952, LOC4334529, LOC4326177, LOC107275432, LOC4335790, and LOC107275425 genes associated with Hd, T, and TGW traits. These genes were involved in: abscisic-acid biosynthesis, carotenoid biosynthesis, starch and sucrose metabolism, and cytokinin biosynthesis. Analysis of 24 candidate genes associated with Hd, T, and TGW traits showed seven non-synonymous variations in the sequence of Hd3a and Ehd2 from the Hd genes (not in a KEGG pathway), D10 and D53 from the T genes (strigolactones biosynthetic pathway), and Gn1a and GIF1 from the TGW genes (cytokinin biosynthetic and starch and sucrose metabolism pathways). This study identified significant differences in allele frequencies supported by high sequence depth in analysis of bulks displaying high and low values for these key traits. These trait-associated variants are likely to be useful in rice improvement.

Structure, allelic diversity and selection of Asr genes, candidate for drought tolerance, in Oryza sativa L. and wild relatives

2010 ◽  
Vol 121 (4) ◽  
pp. 769-787 ◽  
Author(s):  
Romain Philippe ◽  
Brigitte Courtois ◽  
Kenneth L. McNally ◽  
Pierre Mournet ◽  
Redouane El-Malki ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Drought Tolerance ◽  
Oryza Sativa L ◽  
Allelic Diversity ◽  
Wild Relatives ◽  
Asr Genes ◽  
Selection Of

Genetic variations of AA genome Oryza species measured by MITE-AFLP

2003 ◽  
Vol 107 (2) ◽  
pp. 203-209 ◽  
Author(s):  
K. C. Park ◽  
N. H. Kim ◽  
Y. S. Cho ◽  
K. H. Kang ◽  
J. K. Lee ◽  
...  
Keyword(s):  
Genetic Variations ◽  
Oryza Species ◽  
Aa Genome

Diagnosing genetically diverse avian malarial infections using mixed-sequence analysis and TA-cloning

Parasitology ◽  
2005 ◽  
Vol 131 (1) ◽  
pp. 15-23 ◽  
Author(s):  
J. PÉREZ-TRIS ◽  
S. BENSCH
Keyword(s):  
Dna Sequences ◽  
Accurate Method ◽  
The Other ◽  
Multiple Infections ◽  
Template Switching ◽  
Mixed Infections ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
In The Wild ◽  
Host Parasite

Birds harbouring several malarial parasites are common in the wild, and resolving such multiple infections is important for our understanding of host–parasite relationships. We propose a simple and reasonably accurate method for detecting and resolving multiple infections, based on the analysis of parasite cytochrome b DNA sequences: genetically mixed infections are first identified by double nucleotide peaks on sequence electropherograms, and later retrieved by TA-cloning. We applied this method to wild birds, and to experimentally created mixes with varying proportion of two parasites (Plasmodium spp. and Haemoproteus spp.). In general, the method was very efficient in detecting and resolving multiple infections, but some problems were encountered. Several multiple infections were erroneously scored as simple, either because one of the parasite lineages was a better target for the primers used, or because it was much more abundant in the mix. On the other hand, single nucleotide substitutions and template switching during PCR produced artificial sequences in some clones. We discuss the utility of the method, and propose a framework for its use when screening for genetically diverse avian malarial parasites.

Sign in / Sign up

Export Citation Format

Share Document