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 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.

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.

scholarly journals Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sherry Lou Hechanova ◽  
Kamal Bhattarai ◽  
Eliza Vie Simon ◽  
Graciana Clave ◽  
Pathmasiri Karunarathne ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Wild Rice ◽  
The Other ◽  
Sequence Alignments ◽  
Rice Varieties ◽  
Genome Species ◽  
Genome Wide ◽  
Wild Rice Species ◽  
A Genome ◽  
Aa Genome

AbstractWild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a “genetic reservoir” for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.

Interspecific hybridization of cultivated rice, Oryza sativa L. with the wild rice, O. minuta Presl.

1996 ◽  
Vol 93-93 (5-6) ◽  
pp. 664-671 ◽  
Author(s):  
A. L. Mariam ◽  
A. H. Zakri ◽  
M. C. Mahani ◽  
M. N. Normah
Keyword(s):  
Oryza Sativa ◽  
Interspecific Hybridization ◽  
Wild Rice ◽  
Oryza Sativa L ◽  
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.

scholarly journals Mapping QTLs for cold tolerance at seedling stage using an Oryza sativa × O. rufipogon backcross inbred line population

2018 ◽  
Vol 54 (No. 2) ◽  
pp. 59-64 ◽  
Author(s):  
S. Yu ◽  
M. LI ◽  
Y. Xiao ◽  
D. Huang ◽  
D. Chen
Keyword(s):  
Oryza Sativa ◽  
Cold Tolerance ◽  
Inbred Line ◽  
Wild Rice ◽  
Chromosome 8 ◽  
Seedling Stage ◽  
Phenotypic Variance ◽  
Seedling Mortality ◽  
Dongxiang Wild Rice ◽  
Backcross Inbred Line

Tolerance to low temperature is an important factor affecting the growth and development of rice (Oryza sativa L.) at an early growing season in the temperate region, and at high altitudes of tropical regions. In this study, a backcross inbred line (BIL) population derived from an interspecific cross between Xieqingzao B (O. sativa L.) and an accession of Dongxiang wild rice (O. rufipogon Griff.) was used to identify quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage. Seedlings were treated with a temperature of 6°C for 2 days and seedling mortality was measured for QTL mapping. QTL analysis was performed on the whole BIL population and on one subpopulation that showed Xieqingzao B homozygous at QTL detected in the whole population. One major QTL, qSCT8, and one QTL, qSCT4.3, with smaller effect was found in the whole population. The QTLs qSCT8 and qSCT4.3 were mapped on chromosome 8 and 4, explaining 60.96% and 8.83% of the phenotypic variance, respectively. In the subpopulation, three QTLs, qSCT4.1, qSCT4.2 and qSCT12, accounting for 56.22%, 57.62% and 53.09% of the phenotypic variance, respectively, were detected on chromosome 4 and 12. At all five loci, the alleles introduced from the Dongxiang wild rice were effective in decreasing seedling mortality. Our results provide a basis for fine mapping and cloning of QTLs associated with cold tolerance, and the markers linked with QTLs could be used to improve the cold tolerance of rice varieties by marker-assisted selection.

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