A cost-effective barcode system for maize genetic discrimination based on bi-allelic InDel markers

Feng Lin,Tifu Zhang,Shuaiqiang Liang,Han Zhao,Sihai Ren,Yibo Wu,Yiliang Qian,Long Ruan,Yaocheng Qi

doi:10.1186/s13007-020-00644-y

Abstract

BackgroundMaize is one of the most important cereal crop all over the world with a complex genome of about 2.3 gigabase, and exhibits tremendous phenotypic and molecular diversity among different germplasms. Along with the phenotype identification, molecular markers have been accepted extensively as an alternative tool to discriminate different genotypes.ResultsBy using previous re-sequencing data of 205 lines, bi-allelic insertions and deletions (InDels) all over maize genome were screened, and a barcode system was constructed consisting of 37 bi-allelic insertion-deletion markers with high polymorphism information content (PIC) values, large discriminative size among varieties. The barcode system was measured and determined, different maize hybrids and inbreds were clearly discriminated efficiently with these markers, and hybrids responding parents were accurately determined. Compared with microarray data of more than 200 maize lines, the barcode system can discriminate maize varieties with 1.57% of different loci as a threshold. The barcode system can be used in standardized easy and quick operation with very low cost and minimum equipment requirements.ConclusionA barcode system was constructed for genetic discrimination of maize lines, including 37 InDel markers with high PIC values and user-friendly. The barcode system was measured and determined for efficient identification of maize lines.

Highlights

Maize is one of the most important cereal crop all over the world with a complex genome of about 2.3 gigabase, and exhibits tremendous phenotypic and molecular diversity among different germplasms
Plant materials To select proper insertions and deletions (InDels) markers for barcode system, a total of 241 maize inbred lines (Additional file 1: Table S1) were used to test InDel primers, in which 227 lines were analyzed by microarray. 177 intermated recombinant inbred lines (RILs) derived from B73 and Mo17 and the parental lines were employed to assess primers. 35 hybrid lines derived from 25 inbreds were used to evaluate the barcode system for pedigree analysis
Genome sequence data and InDel marker development The generation sequence data of 205 maize inbred lines was downloaded from NCBI (Genbank accession number PRJNA82843, SRP011907 and PRJNA260788) [29,30,31]

Summary

Introduction

Maize is one of the most important cereal crop all over the world with a complex genome of about 2.3 gigabase, and exhibits tremendous phenotypic and molecular diversity among different germplasms. Along with the phenotype identification, molecular markers have been accepted extensively as an alternative tool to discriminate different genotypes. The discrimination of plant variety and cultivar is one of the most important aspects in agricultural systems. The widely used molecular marker include RAPD (random amplified polymorphism DNA), SSR (simple sequence repeat), SNP (single nucleotide polymorphism), InDel (insertion-deletion) and so forth. Most of the markers have been used for cultivar identification. Through RAPD markers, efficient identification was performed for tomato, peach and Ribes cultivars [3,4,5]. By using EST-SSR markers, red-flesh loquat cultivars were rapidly identified [6]. SNP markers were used to genotype 260 accessions of Pummelo [7]

Methods

Results

Discussion

Conclusion