Abstract
Genetic improvement of rice (Oryza sativa L.) requires a clear understanding of both phenotypic and molecular diversity. This study examined 82 improved Indonesian rice varieties using grain morphological traits and three DNA-based marker systems: Simple Sequence Repeat (SSR), Subspecies-Specific Sequence-Tagged Site (SS-STS), and Start Codon Targeted (SCoT). Phenotypic evaluation revealed significant variation in grain length, width, and thickness. Principal component analysis condensed four traits into two axes explaining 94.4% of variance, separating genotypes into three clusters largely corresponding to indica and japonica types. Across 32 markers, 157 alleles were detected, with average gene diversity (He) values of 0.30 (SSR), 0.29 (SS-STS), and 0.22 (SCoT). Polymorphic information content (PIC) was generally low. SS-STS markers revealed fixation of indica-type alleles, consistent with major varieties IR64 and Ciherang, while rare alleles were scarce (1.1-1.5 per locus). Although SCoT markers generated 8.5 bands per locus, heterozygosity remained low (0.005-0.010). Analysis of molecular variance (AMOVA) showed that 90-91% of the genetic variation was distributed within subpopulations, while only 5-8% was explained by differences among subpopulations, indicating weak population structure (FST = 0.055 for SSR; 0.084 for SS-STS). STRUCTURE analysis inferred different subpopulation numbers for each marker type (K = 7 for SS-STS, K = 2 for SSR, K = 4 for SCoT). Phylogenetic clustering separated the genotypes into two to three subpopulations, which partly corresponded to grain type and inferred subspecies background. These results reveal limited molecular diversity despite observable phenotypic variation, suggesting genetic narrowing associated with the repeated use of closely related parental lines during breeding. Broader germplasm, including landraces and wild relatives, is essential for future rice breeding.
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Claims 19
Claim · model-written summary
The 82 improved Indonesian rice varieties showed significant variation in grain length, width and thickness.
- Taxon
- rice
Oryza sativat0 - Outcome
- variation in grain length, width, and thicknesse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“Phenotypic evaluation revealed significant variation in grain length, width, and thickness”
Claim · model-written summary
Principal component analysis condensed the four grain traits into two axes explaining 94.4% of variance.
- Taxon
- riceOryza sativat0
- Outcome
- variancee0
- Value
- 94.4%e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“Principal component analysis condensed four traits into two axes explaining 94.4% of variance”
Claim · model-written summary
Principal component analysis separated the genotypes into three clusters largely corresponding to indica and japonica types.
- Taxon
- riceOryza sativat0
- Outcome
- three clusters largely corresponding to indica and japonica typese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“separating genotypes into three clusters largely corresponding to indica and japonica types”
Claim · model-written summary
Across 32 markers, 157 alleles were detected in the rice varieties.
- Taxon
- riceOryza sativat0
- Outcome
- alleles were detectede0
- Value
- 157 allelese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“Across 32 markers, 157 alleles were detected”
Claim · model-written summary
Average gene diversity (He) was 0.30 with SSR markers.
- Taxon
- riceOryza sativat0
- Outcome
- gene diversity (He)e0
- Value
- 0.30 (SSR)e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“average gene diversity (He) values of 0.30 (SSR), 0.29 (SS-STS), and 0.22 (SCoT)”
Claim · model-written summary
Average gene diversity (He) was 0.29 with SS-STS markers.
- Taxon
- riceOryza sativat0
- Outcome
- gene diversity (He)e0
- Value
- 0.29 (SS-STS)e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“average gene diversity (He) values of 0.30 (SSR), 0.29 (SS-STS), and 0.22 (SCoT)”
Claim · model-written summary
Average gene diversity (He) was 0.22 with SCoT markers.
- Taxon
- riceOryza sativat0
- Outcome
- gene diversity (He)e0
- Value
- 0.22 (SCoT)e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“average gene diversity (He) values of 0.30 (SSR), 0.29 (SS-STS), and 0.22 (SCoT)”
Claim · model-written summary
Polymorphic information content was generally low.
- Taxon
- riceOryza sativat0
- Outcome
- Polymorphic information content (PIC)e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“Polymorphic information content (PIC) was generally low”
Claim · model-written summary
SS-STS markers showed fixation of indica-type alleles, consistent with the major varieties IR64 and Ciherang.
- Taxon
- riceOryza sativat0
- Material
- IR64 and Ciherange0
- Outcome
- fixation of indica-type allelese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“SS-STS markers revealed fixation of indica-type alleles, consistent with major varieties IR64 and Ciherang”
Claim · model-written summary
Rare alleles were scarce, at 1.1-1.5 per locus.
- Taxon
- riceOryza sativat0
- Outcome
- rare allelese0
- Value
- 1.1-1.5 per locuse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“rare alleles were scarce (1.1-1.5 per locus)”
Claim · model-written summary
SCoT markers generated 8.5 bands per locus.
- Taxon
- riceOryza sativat0
- Outcome
- bands per locuse0
- Value
- 8.5e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“SCoT markers generated 8.5 bands per locus”
Claim · model-written summary
Heterozygosity remained low, at 0.005-0.010.
- Taxon
- riceOryza sativat0
- Outcome
- heterozygositye0
- Value
- 0.005-0.010e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“heterozygosity remained low (0.005-0.010)”
Claim · model-written summary
AMOVA showed 90-91% of the genetic variation was distributed within subpopulations.
- Taxon
- riceOryza sativat0
- Outcome
- genetic variation was distributed within subpopulationse0
- Value
- 90-91%e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“90-91% of the genetic variation was distributed within subpopulations”
Claim · model-written summary
Only 5-8% of the genetic variation was explained by differences among subpopulations.
- Taxon
- riceOryza sativat0
- Outcome
- explained by differences among subpopulationse0
- Value
- 5-8%e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“only 5-8% was explained by differences among subpopulations”
Claim · model-written summary
Population structure was weak, with FST of 0.055 for SSR and 0.084 for SS-STS.
- Taxon
- riceOryza sativat0
- Outcome
- population structuree0
- Value
- FST = 0.055 for SSR; 0.084 for SS-STSe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“indicating weak population structure (FST = 0.055 for SSR; 0.084 for SS-STS)”
Claim · model-written summary
STRUCTURE analysis inferred different numbers of subpopulations for each marker type (K = 7 for SS-STS, K = 2 for SSR, K = 4 for SCoT).
- Taxon
- riceOryza sativat0
- Outcome
- subpopulation numberse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“STRUCTURE analysis inferred different subpopulation numbers for each marker type (K = 7 for SS-STS, K = 2 for SSR, K = 4 for SCoT)”
Claim · model-written summary
Phylogenetic clustering separated the genotypes into two to three subpopulations, partly corresponding to grain type and inferred subspecies background.
- Taxon
- riceOryza sativat0
- Outcome
- Phylogenetic clustering separated the genotypes into two to three subpopulationse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“Phylogenetic clustering separated the genotypes into two to three subpopulations, which partly corresponded to grain type and inferred subspecies background”
Claim · model-written summary
The authors conclude molecular diversity is limited despite phenotypic variation, suggesting genetic narrowing from repeated use of closely related parental lines in breeding.
- Taxon
- riceOryza sativat0
- Outcome
- limited molecular diversitye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“rice varieties”
e0“These results reveal limited molecular diversity despite observable phenotypic variation, suggesting genetic narrowing associated with the repeated use of closely related parental lines during breeding”
Claim · model-written summary
Broader germplasm, including landraces and wild relatives, is essential for future rice breeding.
- Taxon
- riceOryza sativae0
- Outcome
- Broader germplasm, including landraces and wild relativese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Broader germplasm, including landraces and wild relatives, is essential for future rice breeding”