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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.


Related in: MedlinePlus

Patterns of LD blocks in two genomic regions of osa-miRf10422-akr precursors and its putative target gene, LOC_Os04g48460. a No LD blocks in the osa-miRf10422-akr region (~24,872Kb) on chromosome 3 were detected. b LD block in the big black block encompassing the LOC_Os04g48460 region (~28,892 kb in small black block) on chromosome 4. Red and white spots indicate strong (r2 = 1) and weak (r2 = 0) LD, respectively
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Fig6: Patterns of LD blocks in two genomic regions of osa-miRf10422-akr precursors and its putative target gene, LOC_Os04g48460. a No LD blocks in the osa-miRf10422-akr region (~24,872Kb) on chromosome 3 were detected. b LD block in the big black block encompassing the LOC_Os04g48460 region (~28,892 kb in small black block) on chromosome 4. Red and white spots indicate strong (r2 = 1) and weak (r2 = 0) LD, respectively

Mentions: To test whether the CYP704A3 target gene and the osa-miRf10422-akr had undergone selection within the parental varieties, we calculated the linkage disequilibrium (LD) of the two genes and its flanking regions on both sides using our GBS data. LD analysis of the two genomic regions, namely, osa-miRf10422-akr and its putative target gene, CYP704A3, of these parental varieties, revealed different patterns of LD blocks (Fig. 6). The r2-values for the miRNA osa-miRf10422-akr did not show any increase in these parental varieties that are commonly used in rice breeding. No LD blocks were detected in the osa-miRf10422-akr region (~24,872 kb) on chromosome 3 (Fig. 6a). In contrast, the r2-values of the CYP704A3 gene increased in these parental varieties. A strong LD block was detected in the target gene LOC_Os04g48460 on chromosome 4 (Fig. 6b). The detection of a strong LD block in CYP704A3 compared to that in the miRNA gene indicated that the CYP704A3 target gene may have undergone selection within these parental rice varieties, although additional investigations should be performed.Fig. 6


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)

Patterns of LD blocks in two genomic regions of osa-miRf10422-akr precursors and its putative target gene, LOC_Os04g48460. a No LD blocks in the osa-miRf10422-akr region (~24,872Kb) on chromosome 3 were detected. b LD block in the big black block encompassing the LOC_Os04g48460 region (~28,892 kb in small black block) on chromosome 4. Red and white spots indicate strong (r2 = 1) and weak (r2 = 0) LD, respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig6: Patterns of LD blocks in two genomic regions of osa-miRf10422-akr precursors and its putative target gene, LOC_Os04g48460. a No LD blocks in the osa-miRf10422-akr region (~24,872Kb) on chromosome 3 were detected. b LD block in the big black block encompassing the LOC_Os04g48460 region (~28,892 kb in small black block) on chromosome 4. Red and white spots indicate strong (r2 = 1) and weak (r2 = 0) LD, respectively
Mentions: To test whether the CYP704A3 target gene and the osa-miRf10422-akr had undergone selection within the parental varieties, we calculated the linkage disequilibrium (LD) of the two genes and its flanking regions on both sides using our GBS data. LD analysis of the two genomic regions, namely, osa-miRf10422-akr and its putative target gene, CYP704A3, of these parental varieties, revealed different patterns of LD blocks (Fig. 6). The r2-values for the miRNA osa-miRf10422-akr did not show any increase in these parental varieties that are commonly used in rice breeding. No LD blocks were detected in the osa-miRf10422-akr region (~24,872 kb) on chromosome 3 (Fig. 6a). In contrast, the r2-values of the CYP704A3 gene increased in these parental varieties. A strong LD block was detected in the target gene LOC_Os04g48460 on chromosome 4 (Fig. 6b). The detection of a strong LD block in CYP704A3 compared to that in the miRNA gene indicated that the CYP704A3 target gene may have undergone selection within these parental rice varieties, although additional investigations should be performed.Fig. 6

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.


Related in: MedlinePlus