Development of Genome-Wide Insertion and Deletion Polymorphism Markers from Next-Generation Sequencing Data in Rice.

Jian Liu,Jingwei Li,Jingtao Qu,Shuangyong Yan

doi:10.1186/s12284-015-0063-4

Abstract

BackgroundNext-generation sequencing technologies enable the re-sequencing of a large number of genomes and provide an unprecedented opportunity to discover numerous DNA polymorphisms throughout the genome of a species. As the second most abundant form of genetic variation, InDels, with characteristics of co-dominance, multiple alleles and high stability and density and that are easy to genotype, have received an increasing amount attention.ResultsIn this work, a total of 2,329,544 InDels were identified in 1767 rice genomes; these InDels were dispersed across all 12 rice chromosomes, with one InDel marker found, on average, every 160.22 bp. There were 162,380 highly polymorphic InDels with a polymorphism information content (PIC) ≥ 0.5, contributing 1.81 % to the unique primer set. Of these highly polymorphic InDels, we also selected InDels with major allele differences (the size difference between the most and second most frequent alleles) ≥ 3 bp or 8 bp for primer design, which provided a more flexible choice for researchers. Finally, we experimentally validated 100 highly polymorphic InDels for accuracy and polymorphism. The PCR results showed that the accuracy of the InDel markers was 95.70 %, while the average PIC value was 0.56, with a range of 0.19 to 0.78; the average allele number was 3.02, with a range of 2 to 5.ConclusionsOur genome-wide and easily used InDel markers with high polymorphism and density in both cultivated and wild rice will undoubtedly have practical implications in rice marker-assisted breeding and will also meet the need of fine-scale genetic mapping in map-based rice gene cloning.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0063-4) contains supplementary material, which is available to authorized users.

Highlights

Next-generation sequencing technologies enable the re-sequencing of a large number of genomes and provide an unprecedented opportunity to discover numerous DNA polymorphisms throughout the genome of a species
We compared the distribution of the unique primers on the 12 rice chromosomes, and the results showed that the count of unique primers on each chromosome was generally consistent with the corresponding chromosome length
Using e-PCR to align 8,995,927 unique primer pairs against publicly sequenced reads of rice varieties, the results showed that the average number of e-PCR products was 1,950,638, with a proportion of 21.68 % (Additional file 2: Table S2), which ranged from 10,631 in Bengal (0.12 %) to 8,764,237 in Omachi (97.42 %)

Summary

Introduction

Next-generation sequencing technologies enable the re-sequencing of a large number of genomes and provide an unprecedented opportunity to discover numerous DNA polymorphisms throughout the genome of a species. As the second most abundant form of genetic variation, InDels, with characteristics of co-dominance, multiple alleles and high stability and density and that are easy to genotype, have received an increasing amount attention. As the second most common type of polymorphism and the most abundant structural variant (Mullaney et al 2010), InDel markers provide a higher density than traditional SSR markers and utilize the same experimental procedure as that used for SSR markers. Because InDel markers have more practical value for laboratories without the infrastructure to perform SNP genotyping (Liu et al 2013) and because they occur more frequently than SSR markers in the rice genome and use the same experimental approaches that are routinely used for SSR markers, they have received an increasing amount of attention. InDel markers have been used for the classification of rice indica and japonica subspecies and to examine their relationships regarding evolution (Lu et al 2009; Liu et al 2012)

Methods

Results

Conclusion