SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice.
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.
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.
Weijie
W
Tang
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
Tingting
T
Wu
State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
Jian
J
Ye
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
Juan
J
Sun
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
Yue
Y
Jiang
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
Jun
J
Yu
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
Jianpeng
J
Tang
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
Gaoming
G
Chen
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China. wangchm@njau.edu.cn.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China. wangchm@njau.edu.cn.
Chunming
C
Wang
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, Beijing, 100081, China.
Jianmin
J
Wan
D020121:5' Untranslated Regions / Q000235:genetics; D000483:Alleles; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D035683:MicroRNAs / Q000235:genetics; D012275:Oryza / Q000145:classification / Q000235:genetics* / Q000502:physiology; D010641:Phenotype; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D030821:Plants, Genetically Modified; D020641:Polymorphism, Single Nucleotide; D034622:RNA Interference; D012639:Seeds / Q000235:genetics* / Q000502:physiology
D020121:5' Untranslated Regions; D035683:MicroRNAs; D010940:Plant Proteins; D003577:Cytochrome P-450 Enzyme System
Genetic diversity; Rice; SNP; Seed size; miRNA