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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.


Distribution of SNPs in 12 chromosomes of different rice varieties. The x-axis represents the physical distance along each chromosome, which is split into 200-kb windows. The total size of each chromosome is shown in brackets. The y-axis indicates the number of SNPs. The regions with relatively high and low density are labeled in red and green bars, respectively
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Fig1: Distribution of SNPs in 12 chromosomes of different rice varieties. The x-axis represents the physical distance along each chromosome, which is split into 200-kb windows. The total size of each chromosome is shown in brackets. The y-axis indicates the number of SNPs. The regions with relatively high and low density are labeled in red and green bars, respectively

Mentions: We identified a total of 22,682 polymorphic SNPs in 12 parental varieties and Nipponbare in relation to the reference genome (Additional file 1: Table S1). To explore the genomic distribution of the patterns of DNA polymorphisms between the indica and japonica subspecies, the SNP count based on our sample was plotted along each chromosome (Fig. 1). SNP count (Fig. 1, solid line) was defined as the number of SNPs in a 200-kb interval. Non-random patterns of SNP distribution were observed, with highly different SNP frequencies detected on all chromosomes. These data support previous findings that polymorphisms in the rice genome (from the indica-japonica perspective) are non-randomly distributed [24]. Relatively low SNP polymorphisms were observed in the regions highlighted in green bars (Fig. 1), which could be due to stringent recombination restrictions, or lack of restriction enzyme sites or reads in these regions. More markers need to be developed in these low-density SNP regions for QTL/gene mapping.Fig. 1


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)

Distribution of SNPs in 12 chromosomes of different rice varieties. The x-axis represents the physical distance along each chromosome, which is split into 200-kb windows. The total size of each chromosome is shown in brackets. The y-axis indicates the number of SNPs. The regions with relatively high and low density are labeled in red and green bars, respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Distribution of SNPs in 12 chromosomes of different rice varieties. The x-axis represents the physical distance along each chromosome, which is split into 200-kb windows. The total size of each chromosome is shown in brackets. The y-axis indicates the number of SNPs. The regions with relatively high and low density are labeled in red and green bars, respectively
Mentions: We identified a total of 22,682 polymorphic SNPs in 12 parental varieties and Nipponbare in relation to the reference genome (Additional file 1: Table S1). To explore the genomic distribution of the patterns of DNA polymorphisms between the indica and japonica subspecies, the SNP count based on our sample was plotted along each chromosome (Fig. 1). SNP count (Fig. 1, solid line) was defined as the number of SNPs in a 200-kb interval. Non-random patterns of SNP distribution were observed, with highly different SNP frequencies detected on all chromosomes. These data support previous findings that polymorphisms in the rice genome (from the indica-japonica perspective) are non-randomly distributed [24]. Relatively low SNP polymorphisms were observed in the regions highlighted in green bars (Fig. 1), which could be due to stringent recombination restrictions, or lack of restriction enzyme sites or reads in these regions. More markers need to be developed in these low-density SNP regions for QTL/gene mapping.Fig. 1

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.