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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0779-3) contains supplementary material, which is available to authorized users.

The effect of gamma rays irradiation on diversity of Musa paradisiaca var. sapientum as revealed by ISSR molecular marker

“…Detection of genetic diversity using molecular markers of ISSR has been carried out in several previous studies (Wang et al, 2012;Patel et al, 2015;Taheri et al, 2013;Wang et al, 2017). Single nucleotide polymorphisms are the genetic markers of choice in various genetic, ecological and evolutionary studies (Tang et al 2016). In this study, the level of polymorphism of pisang ambon DNA bands obtained by gamma irradiation is quite high, namely, at 90%.…”

Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population

“…Defects in BR biosynthesis produce smaller seeds, but it is still uncertain how BRs promote seed growth (Hong et al, 2002(Hong et al, , 2003. It is noteworthy that several CYP family members are involved in seed size control, including the Arabidopsis CYP78A5, CYP78A6, and CYP78A9 (Adamski et al, 2009;Fang et al, 2012), and soybean CYP78A72 and CYP78A10 (Wang et al, 2015b;Zhao et al, 2016), which all act as positive regulators of grain size, whereas the rice CYP78A13 and CYP704A3 (Xu et al, 2015a;Tang et al, 2016) act as negative regulators. NAC genes have been implicated in the control of seed size via the control of various stages of seed development (Agarwal et al, 2011).…”

Genetic diversity of rice from Iran region assessed by simple sequence repeat (SSR) markers

“…Singlenucleotide polymorphisms have become the genetic markers of choice in various genetic, ecological, and evolutionary studies (Tang et al, 2016). In the present study, SSR markers were used to detect genetic variation among 24 rice genotypes; in a separate analysis (data not shown here), morphological features were combined with the SSR results, and it was found that there was general agreement between the two sets of data with respect to pair-wise genetic distances among the rice cvs.…”