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SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice.

Tang W, Wu T, Ye J, Sun J, Jiang Y, Yu J, Tang J, Chen G, Wang C, Wan J - BMC Plant Biol. (2016)

Bottom Line: Meanwhile, we identified polymorphic SNPs with large effects on protein-coding and miRNA genes.To validate the effect of the polymorphic SNPs, we further investigated a SNP (chr4:28,894,757) at the miRNA binding site in the 3'-UTR region of the locus Os4g48460, which is associated with rice seed size.Our study has identified the genome-wide SNPs by GBS of the parental varieties of RIL populations and identified CYP704A3, a miRNA-regulated gene that is responsible for rice seed length.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.

ABSTRACT

Background: Single-nucleotide polymorphisms (SNPs) have become the genetic markers of choice in various genetic, ecological, and evolutionary studies. Genotyping-by-sequencing (GBS) is a next-generation-sequencing based method that takes advantage of reduced representation to enable high-throughput genotyping using a large number of SNP markers.

Results: In the present study, the distribution of non-redundant SNPs in the parents of 12 rice recombination line populations was evaluated through GBS. A total of 45 Gigabites of nucleotide sequences conservatively provided satisfactory genotyping of rice SNPs. By assembling to the genomes of reference genomes of japonica Nipponbare, we detected 22,682 polymorphic SNPs that may be utilized for QTL/gene mapping with the Recombinant Inbred Lines (RIL) populations derived from these parental lines. Meanwhile, we identified polymorphic SNPs with large effects on protein-coding and miRNA genes. To validate the effect of the polymorphic SNPs, we further investigated a SNP (chr4:28,894,757) at the miRNA binding site in the 3'-UTR region of the locus Os4g48460, which is associated with rice seed size. Os4g48460 encodes a putative cytochrome P450, CYP704A3. Direct degradation of the 3'-UTR of the CYP704A3 gene by a miRNA (osa-miRf10422-akr) was validated by in planta mRNA degradation assay. We also showed that rice seeds of longer lengths may be produced by downregulating CYP704A3 via RNAi.

Conclusions: Our study has identified the genome-wide SNPs by GBS of the parental varieties of RIL populations and identified CYP704A3, a miRNA-regulated gene that is responsible for rice seed length.

No MeSH data available.


Genetic structure and population differentiation in 13 rice parental varieties. a Unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on 22,682 SNPs. b Principal component analysis for the entire set of RILs (n = 306)
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Fig2: Genetic structure and population differentiation in 13 rice parental varieties. a Unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on 22,682 SNPs. b Principal component analysis for the entire set of RILs (n = 306)

Mentions: The phylogenetic tree produced using the 22,682 SNPs revealed three distinct groups, with japonicas clustered into one group, and the other two groups together with aus and indica types (Fig. 2a). Three distinct groups were identified by principal component analysis with well-separated lines, corresponding to indica, aus, and japonica rice species (Fig. 2b). Consistent with the phenotypical classification, the varieties from China, Guichao2, Nanjing11 and Nanjing35 were grouped into the indica type, together with IR36 and IR24 from IRRI; the varieties from Japan, Sasanishiki, Koshihikari, Habataki, and Asominori were grouped into japonica, together with USSR5 from Russia; the varieties N22 and Kasalath from India were grouped into aus. Based on this classification, more SNP polymorphisms could be expected between the parental lines with distinct relationships. Thus, germplasm classification of the 12 rice varieties was properly conducted and the results were informative for further RIL or NIL construction.Fig. 2


SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice.

Tang W, Wu T, Ye J, Sun J, Jiang Y, Yu J, Tang J, Chen G, Wang C, Wan J - BMC Plant Biol. (2016)

Genetic structure and population differentiation in 13 rice parental varieties. a Unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on 22,682 SNPs. b Principal component analysis for the entire set of RILs (n = 306)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4837510&req=5

Fig2: Genetic structure and population differentiation in 13 rice parental varieties. a Unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on 22,682 SNPs. b Principal component analysis for the entire set of RILs (n = 306)
Mentions: The phylogenetic tree produced using the 22,682 SNPs revealed three distinct groups, with japonicas clustered into one group, and the other two groups together with aus and indica types (Fig. 2a). Three distinct groups were identified by principal component analysis with well-separated lines, corresponding to indica, aus, and japonica rice species (Fig. 2b). Consistent with the phenotypical classification, the varieties from China, Guichao2, Nanjing11 and Nanjing35 were grouped into the indica type, together with IR36 and IR24 from IRRI; the varieties from Japan, Sasanishiki, Koshihikari, Habataki, and Asominori were grouped into japonica, together with USSR5 from Russia; the varieties N22 and Kasalath from India were grouped into aus. Based on this classification, more SNP polymorphisms could be expected between the parental lines with distinct relationships. Thus, germplasm classification of the 12 rice varieties was properly conducted and the results were informative for further RIL or NIL construction.Fig. 2

Bottom Line: Meanwhile, we identified polymorphic SNPs with large effects on protein-coding and miRNA genes.To validate the effect of the polymorphic SNPs, we further investigated a SNP (chr4:28,894,757) at the miRNA binding site in the 3'-UTR region of the locus Os4g48460, which is associated with rice seed size.Our study has identified the genome-wide SNPs by GBS of the parental varieties of RIL populations and identified CYP704A3, a miRNA-regulated gene that is responsible for rice seed length.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.

ABSTRACT

Background: Single-nucleotide polymorphisms (SNPs) have become the genetic markers of choice in various genetic, ecological, and evolutionary studies. Genotyping-by-sequencing (GBS) is a next-generation-sequencing based method that takes advantage of reduced representation to enable high-throughput genotyping using a large number of SNP markers.

Results: In the present study, the distribution of non-redundant SNPs in the parents of 12 rice recombination line populations was evaluated through GBS. A total of 45 Gigabites of nucleotide sequences conservatively provided satisfactory genotyping of rice SNPs. By assembling to the genomes of reference genomes of japonica Nipponbare, we detected 22,682 polymorphic SNPs that may be utilized for QTL/gene mapping with the Recombinant Inbred Lines (RIL) populations derived from these parental lines. Meanwhile, we identified polymorphic SNPs with large effects on protein-coding and miRNA genes. To validate the effect of the polymorphic SNPs, we further investigated a SNP (chr4:28,894,757) at the miRNA binding site in the 3'-UTR region of the locus Os4g48460, which is associated with rice seed size. Os4g48460 encodes a putative cytochrome P450, CYP704A3. Direct degradation of the 3'-UTR of the CYP704A3 gene by a miRNA (osa-miRf10422-akr) was validated by in planta mRNA degradation assay. We also showed that rice seeds of longer lengths may be produced by downregulating CYP704A3 via RNAi.

Conclusions: Our study has identified the genome-wide SNPs by GBS of the parental varieties of RIL populations and identified CYP704A3, a miRNA-regulated gene that is responsible for rice seed length.

No MeSH data available.