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

BMC Plant Biology

Research Article

Tingting Wu¹  Gaoming Chen¹  Jun Yu¹  Jianpeng Tang¹  Yue Jiang¹  Juan Sun¹  Chunming Wang²  Weijie Tang²  Jianmin Wan³  Jian Ye⁴ 

[1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China;State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China;Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China;State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China;National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China;

关键词: SNP;    miRNA;    Genetic diversity;    Seed size;    Rice;   

DOI  :  10.1186/s12870-016-0779-3

 received in 2015-11-30, accepted in 2016-04-13,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundSingle-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.ResultsIn 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© Tang et al. 2016