Abstract
Wild rice species serve as a valuable genetic reservoir for rice improvement, and the DNA segments containing useful genes/alleles can be transferred to elite rice varieties through crosses. However, DNA markers, which are essential tools for genetic analysis and molecular breeding, are not yet well-established for harnessing wild rice species. To enable an efficient utilization of the CC-genome wild rice species in the genus Oryza , we developed a genome-wide polymorphic InDel marker (≥20 bp) set comprising 182 markers through positional sequence alignments between O. officinalis (CC-genome) and rice cultivars (AA-genome). These markers were evenly distributed across the 12 chromosomes, with ~2Mb marker intervals. For validation of marker polymorphism, all the markers were tested by using PCR-agarose gel analysis with 12 accessions of CC-genome species (four accessions each from O. eichingeri , O. officinalis , and O. rhizomatis ), two accessions of BBCC-genome species ( O. minuta ), and two cultivars, Nipponbare ( japonica ) and IR24 ( indica ). Out of 182 markers, 172 markers (94.5%) successfully amplified and exhibited polymorphism between rice and the CC-genome accessions, corresponding to an average marker interval of ~2.17Mb across the rice genome. Moreover, the marker set also showed high polymorphism (84.1-92.9%) when applied to BBCC-genome species. Based on the marker validation data, five markers were selected for species identification within the three CC-genome species. In addition, the polymorphic markers successfully detected wild rice introgressions from the wide hybridization progenies. The newly developed marker set will function as valuable genomic tools for harnessing CC-genome and CC-genome containing germplasm for rice improvement.
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Claims 6
Claim · model-written summary
A genome-wide polymorphic InDel marker set (at least 20 bp) of 182 markers was developed by positional sequence alignment between O. officinalis (CC-genome) and rice cultivars (AA-genome).
- Taxon
- O. officinalisOryza officinalise0
- Outcome
- genome-wide polymorphic InDel marker (≥20 bp) sete0
- Value
- 182 markerse0
- Comparator
- rice cultivarse0
Verbatim
e0“we developed a genome-wide polymorphic InDel marker (≥20 bp) set comprising 182 markers through positional sequence alignments between O. officinalis (CC-genome) and rice cultivars (AA-genome)”
Claim · model-written summary
The InDel markers were evenly distributed across the 12 rice chromosomes with intervals of about 2 Mb.
Verbatim
e0“These markers were evenly distributed across the 12 chromosomes, with ~2Mb marker intervals”
Claim · model-written summary
Of the 182 markers, 172 (94.5%) amplified and were polymorphic between rice and the CC-genome accessions, corresponding to an average marker interval of about 2.17 Mb across the rice genome.
- Taxon
- rice
Oryza sativae0 - Outcome
- successfully amplified and exhibited polymorphisme0
- Value
- 172 markers (94.5%)e0
- Qualifier
- average marker interval of ~2.17Mbe0
- Comparator
- the CC-genome accessionse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Out of 182 markers, 172 markers (94.5%) successfully amplified and exhibited polymorphism between rice and the CC-genome accessions, corresponding to an average marker interval of ~2.17Mb across the rice genome”
Claim · model-written summary
The marker set showed high polymorphism (84.1-92.9%) when applied to BBCC-genome species.
Verbatim
e0“the marker set also showed high polymorphism (84.1-92.9%) when applied to BBCC-genome species”
Claim · model-written summary
Five markers were selected for species identification within the three CC-genome species.
Verbatim
e0“five markers were selected for species identification within the three CC-genome species”
Claim · model-written summary
The polymorphic markers successfully detected wild rice introgressions in progenies of wide hybridization.
Not reportedComparator
Verbatim
e0“the polymorphic markers successfully detected wild rice introgressions from the wide hybridization progenies”