scholarly journals Segregation Distortion Observed in the Progeny of Crosses Between Oryza sativa and O. meridionalis Caused by Abortion During Seed Development

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 398
Author(s):  
Daiki Toyomoto ◽  
Masato Uemura ◽  
Satoru Taura ◽  
Tadashi Sato ◽  
Robert Henry ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Seed Development ◽  
Wild Rice ◽  
Lethal Gene ◽  
Chromosome 6 ◽  
Cultivated Rice ◽  
Substitution Lines ◽  
Putative Gene ◽  
Aa Genome ◽  
Recurrent Backcrossing

Wild rice relatives having the same AA genome as domesticated rice (Oryza sativa) comprise the primary gene pool for rice genetic improvement. Among them, O. meridionalis and O. rufipogon are found in the northern part of Australia. Three Australian wild rice strains, Jpn1 (O. rufipogon), Jpn2, and W1297 (O. meridionalis), and one cultivated rice cultivar Taichung 65 (T65) were used in this study. A recurrent backcrossing strategy was adopted to produce chromosomal segment substitution lines (CSSLs) carrying chromosomal segments from wild relatives and used for trait evaluation and genetic analysis. The segregation of the DNA marker RM136 locus on chromosome 6 was found to be highly distorted, and a recessive lethal gene causing abortion at the seed developmental stage was shown to be located between two DNA markers, KGC6_10.09 and KGC6_22.19 on chromosome 6 of W1297. We name this gene as SEED DEVELOPMENT 1 (gene symbol: SDV1). O. sativa is thought to share the functional dominant allele Sdv1-s (s for sativa), and O. meridionalis is thought to share the recessive abortive allele sdv1-m (m for meridionalis). Though carrying the sdv1-m allele, the O. meridionalis accessions can self-fertilize and bear seeds. We speculate that the SDV1 gene may have been duplicated before the divergence between O. meridionalis and the other AA genome Oryza species, and that O. meridionalis has lost the function of the SDV1 gene and has kept the function of another putative gene named SDV2.

scholarly journals Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 725
Author(s):  
Kanako Bessho-Uehara ◽  
Yoshiyuki Yamagata ◽  
Tomonori Takashi ◽  
Takashi Makino ◽  
Hideshi Yasui ◽  
...  
Keyword(s):  
Wild Rice ◽  
Comparative Sequence Analysis ◽  
Loss Of Function ◽  
Cultivated Rice ◽  
Substitution Lines ◽  
Genome Species ◽  
Wild Rice Species ◽  
Aa Genome ◽  
Genome Group ◽  
Cultivated Species

Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species Oryza sativa ssp. japonica. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, REGULATOR OF AWN ELONGATION 1 (RAE1) and RAE2. To understand the conserveness of RAE1 and RAE2 in wild rice relatives, we analyzed RAE1 and RAE2 sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional RAE1 and RAE2, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of RAE1 and RAE2 were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of RAE1 and RAE2 were selected after the speciation of O. sativa, and that two-step loss of function in RAE1 and RAE2 contributed to awnlessness in Asian cultivated rice.

Phenotypic diversity of weedy rice (Oryza sativa f. spontanea) biotypes found in California and implications for management

Weed Science ◽  
2020 ◽  
Vol 68 (5) ◽  
pp. 485-495
Author(s):  
Elizabeth Karn ◽  
Teresa De Leon ◽  
Luis Espino ◽  
Kassim Al-Khatib ◽  
Whitney Brim-DeForest
Keyword(s):  
Oryza Sativa ◽  
Chlorophyll Content ◽  
Plant Height ◽  
Wild Rice ◽  
Early Growth ◽  
Weedy Rice ◽  
Phenotypic Traits ◽  
Growth Stages ◽  
Cultivated Rice ◽  
Leaf Pubescence

AbstractWeedy rice (Oryza sativa f. spontanea Rosh.) is an emerging weed of California rice (Oryza sativa L.) that has potential to cause large yield losses. Early detection of weedy rice in the field is ideal to effectively control and prevent the spread of this weed. However, it is difficult to differentiate weedy rice from cultivated rice during early growth stages due to the close genetic and phenotypic relatedness of cultivated rice and weedy rice. The objective of this study is to examine phenotypic variation in weedy rice biotypes from California and to identify traits that could be used to visually identify weedy rice infestations at early growth stages for effective management. Greenhouse experiments were conducted in 2017 and 2018 using five phenotypically distinct biotypes of weedy rice found in California, along with diverse cultivated, weedy, and wild rice types in a randomized complete block design. We measured variation for 13 phenotypic traits associated with weedy rice and conducted principal component analysis and factor analysis to identify important weedy traits. Most weedy rice individuals within a biotype clustered together by phenotypic similarity. Pericarp color, hull color, chlorophyll content, grain length, plant height, leaf pubescence, collar color, and leaf sheath color account for most of the observed variation. California weedy rice biotypes are phenotypically distinct from wild rice and from weedy rice from the southern United States in their combinations of seed phenotypes and vegetative characteristics. In comparison with the locally grown temperate japonica cultivars, California weedy rice tends to be taller, with lower chlorophyll content and a red pericarp. Weedy rice biotypes vary in seed shattering and seed dormancy. For weedy rice management, plant height and chlorophyll content are distinct traits that could be used to differentiate weedy rice from the majority of cultivated rice varieties in California during vegetative stages of rice growth.

Extraordinarily polymorphic ribosomal DNA in wild and cultivated rice

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1109-1116 ◽  
Author(s):  
K. D. Liu ◽  
Qifa Zhang ◽  
G. P. Yang ◽  
M. A. Saghai Maroof ◽  
S. H. Zhu ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Ribosomal Dna ◽  
Wild Rice ◽  
Indica Rice ◽  
Intergenic Spacer ◽  
Oryza Rufipogon ◽  
Japonica Rice ◽  
Cultivated Rice ◽  
Spacer Length ◽  
Origin And Evolution

A collection of 481 rice accessions was surveyed for ribosomal DNA (rDNA) intergenic spacer length polymorphism to assess the extent of genetic diversity in Chinese and Asian rice germplasm. The materials included 83 accessions of common wild rice, Oryza rufipogon, 75 of which were from China; 348 entries of cultivated rice (Oryza sativa), representing almost all the rice growing areas in China; and 50 cultivars from South and East Asia. A total of 42 spacer length variants (SLVs) were detected. The size differences between adjacent SLVs in the series were very heterogeneous, ranging from ca. 21 to 311 bp. The 42 SLVs formed 80 different rDNA phenotypic combinations. Wild rice displayed a much greater number of rDNA SLVs than cultivated rice, while cultivated rice showed a larger number of rDNA phenotypes. Indica and japonica groups of O. sativa contained about equal numbers of SLVs, but the SLV distribution was significantly differentiated: indica rice was preferentially associated with longer SLVs and japonica rice with shorter ones. The results may have significant implications regarding the origin and evolution of cultivated rice, as well as the inheritance and molecular evolution of rDNA intergenic spacers in rice. Key words : rDNA, Oryza rufipogon, Oryza sativa, germplasm diversity, evolution.

Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters

Genome ◽  
2011 ◽  
Vol 54 (8) ◽  
pp. 629-638 ◽  
Author(s):  
Z. Xu ◽  
S. Rafi ◽  
W. Ramakrishna
Keyword(s):  
Oryza Sativa ◽  
Wild Rice ◽  
Evolutionary Dynamics ◽  
Genomic Sequence ◽  
Promoter Regions ◽  
Higher Plant ◽  
Wild Rice Species ◽  
History Of ◽  
Aa Genome ◽  
Rice Genotypes

Retrotransposons are ubiquitous in higher plant genomes. The presence or absence of retrotransposons in whole genome and high throughput genomic sequence (HTGS) from cultivated and wild rice was investigated to understand the organization and evolution of retrotransposon insertions in promoter regions. Approximately half of the Oryza sativa subsp. japonica ‘Nipponbare’ promoters with retrotransposons conserved in Oryza sativa subsp. indica ‘93-11’ and four wild rice species showed higher sequence conservation in retrotransposon than nonretrotransposon regions. We further investigated, in detail, the evolutionary dynamics of five retrotransposons in the promoter regions of 95 rice genotypes. Our data suggest that four of five insertions (Rp2–Rp5) occurred in the ancestor of AA genome, while the other insertion (Rp1) predates the ancestral divergence of Oryza officinalis (CC genome). Four retrotransposons (Rp2–Rp5) were present in 52% (Rp2), 29% (Rp3), 53% (Rp4), and 43% (Rp5) of the rice genotypes with AA genome type, and the fifth retrotransposon (Rp1) was present in 95% of the rice genotypes with AA, BBCC, or CC genome types. Furthermore, most of these retrotransposons were found to evolve slower than flanking promoter regions, suggesting a role in promoter function for regulating downstream genes.

Progress on Transferring Elite Genes from Non-AA Genome Wild Rice into Oryza sativa through Interspecific Hybridization

Rice Science ◽  
2008 ◽  
Vol 15 (2) ◽  
pp. 79-87 ◽  
Author(s):  
Xue-lin Fu ◽  
Yong-gen Lu ◽  
Xiang-dong Liu ◽  
Jin-quan Li
Keyword(s):  
Oryza Sativa ◽  
Interspecific Hybridization ◽  
Wild Rice ◽  
Aa Genome

scholarly journals Development of Chromosome Segment Substitution Lines (CSSLs) Derived from Guangxi Wild Rice (Oryza rufipogon Griff.) under Rice (Oryza sativa L.) Background and the Identification of QTLs for Plant Architecture, Agronomic Traits and Cold Tolerance

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 980
Author(s):  
Ruizhi Yuan ◽  
Neng Zhao ◽  
Babar Usman ◽  
Liang Luo ◽  
Shanyue Liao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Fine Mapping ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Chromosome Segment ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Genome Wide ◽  
Oryza Rufipogon Griff ◽  
Segment Substitution

Common wild rice contains valuable resources of novel alleles for rice improvement. It is well known that genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) ais a powerful tool for fine mapping of quantitative traits, new gene discovery and marker-assisted breeding. In this study, 132 CSSLs were developed from a cultivated rice (Oryza sativa) cultivar (93-11) and common wild rice (Oryza rufipogon Griff. DP30) by selfing-crossing, backcrossing and marker-assisted selection (MAS). Based on the high-throughput sequencing of the 93-11 and DP30, 285 pairs of Insertion-deletions (InDel) markers were selected with an average distance of 1.23 Mb. The length of this DP30-CSSLs library was 536.4 cM. The coverage rate of substitution lines cumulatively overlapping the whole genome of DP30 was about 91.55%. DP30-CSSLs were used to analyze the variation for 17 traits leading to the detection of 36 quantitative trait loci (QTLs) with significant phenotypic effects. A cold-tolerant line (RZ) was selected to construct a secondary mapping F2 population, which revealed that qCT2.1 is in the 1.7 Mb region of chromosome 2. These CSSLs may, therefore, provide powerful tools for genome wide large-scale gene discovery in wild rice. This research will also facilitate fine mapping and cloning of QTLs and genome-wide study of wild rice. Moreover, these CSSLs will provide a foundation for rice variety improvement.

scholarly journals Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa

2006 ◽  
Vol 103 (25) ◽  
pp. 9578-9583 ◽  
Author(s):  
J. P. Londo ◽  
Y.-C. Chiang ◽  
K.-H. Hung ◽  
T.-Y. Chiang ◽  
B. A. Schaal
Keyword(s):  
Oryza Sativa ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Cultivated Rice
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