Development of genome-wide insertion and deletion markers for maize, based on next-generation sequencing data

BMC Genomics

Research Article

Dengguo Tang¹  Cong Yang¹  Jingwei Li¹  Jingtao Qu¹  Jian Liu²  Hai Lan²  Tingzhao Rong² 

[1] Maize Research Institute, Sichuan Agricultural University, 611130, Chengdu, China;Maize Research Institute, Sichuan Agricultural University, 611130, Chengdu, China;Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan Agricultural University, 611130, Chengdu, China;

关键词: Maize;    Next-generation sequencing;    Insertion and deletion;    Indel;    Molecular marker;    Polymorphism;   

DOI  :  10.1186/s12864-015-1797-5

 received in 2014-11-05, accepted in 2015-07-24,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundInsertions and deletions (indels) are the most abundant form of structural variation in all genomes. Indels have been increasingly recognized as an important source of molecular markers due to high-density occurrence, cost-effectiveness, and ease of genotyping. Coupled with developments in bioinformatics, next-generation sequencing (NGS) platforms enable the discovery of millions of indel polymorphisms by comparing the whole genome sequences of individuals within a species.ResultsA total of 1,973,746 unique indels were identified in 345 maize genomes, with an overall density of 958.79 indels/Mbp, and an average allele number of 2.76, ranging from 2 to 107. There were 264,214 indels with polymorphism information content (PIC) values greater than or equal to 0.5, accounting for 13.39 % of overall indels. Of these highly polymorphic indels, we designed primer pairs for 83,481 and 29,403 indels with major allele differences (i.e. the size difference between the most and second most frequent alleles) greater than or equal to 3 and 8 bp, respectively, based on the differing resolution capabilities of gel electrophoresis. The accuracy of our indel markers was experimentally validated, and among 100 indel markers, average accuracy was approximately 90 %. In addition, we also validated the polymorphism of the indel markers. Of 100 highly polymorphic indel markers, all had polymorphisms with average PIC values of 0.54.ConclusionsThe maize genome is rich in indel polymorphisms. Intriguingly, the level of polymorphism in genic regions of the maize genome was higher than that in intergenic regions. The polymorphic indel markers developed from this study may enhance the efficiency of genetic research and marker-assisted breeding in maize.

【 授权许可】

CC BY   
© Liu et al. 2015