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Empirical comparison of Simple Sequence Repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness.

ABSTRACT: While Simple Sequence Repeats (SSRs) are extremely useful genetic markers, recent advances in technology have produced a shift toward use of single nucleotide polymorphisms (SNPs). The different mutational properties of these two classes of markers result in differences in heterozygosities and allele frequencies that may have implications for their use in assessing relatedness and evaluation of genetic diversity. We compared analyses based on 89 SSRs (primarily dinucleotide repeats) to analyses based on 847 SNPs in individuals from the same 259 inbred maize lines, which had been chosen to represent the diversity available among current and historic lines used in breeding. The SSRs performed better at clustering germplasm into populations than did a set of 847 SNPs or 554 SNP haplotypes, and SSRs provided more resolution in measuring genetic distance based on allele-sharing. Except for closely related pairs of individuals, measures of distance based on SSRs were only weakly correlated with measures of distance based on SNPs. Our results suggest that 1) large numbers of SNP loci will be required to replace highly polymorphic SSRs in studies of diversity and relatedness and 2) relatedness among highly-diverged maize lines is difficult to measure accurately regardless of the marker system.

SUBMITTER: Hamblin MT

PROVIDER: S-EPMC2137949 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundMaize (Zea mays ssp. mays L.), as the most important plant for staple food of several million people, animal feed and bioenergy productions, is widely cultivated around the world. Simple sequence repeats (SSRs) are widely used as molecular markers in maize genetics and breeding, but only two thousands pairs of SSRs have been published currently, which hardly satisfies for the increasing needs of geneticists and breeders. Furthermore, the increasing studies have revealed that SSRs also play a vital role in functional regulation and evolution. It is fortunate that the development of sequencing technology and bio-software provides the basis for characterization and development of SSRs in maize.ResultsIn this study, MISA was applied to identify overall 179,681 SSRs in maize reference genome B73, with an average distance of 11.46 Kbp. Their distributions within the genome in different regions were non-random, and the density followed in a descending order of UTR, promotor, intron, intergenic and CDS. Meanwhile, 82,694 (46.02%) SSRs with unique flanking sequences were selected, and then applied to analyze the polymorphism of next-generation sequencing data from 345 maize inbred lines and data from maize reference genome B73. There were 58,946 SSRs with length information results in ten or more than ten genomes, accounting for 71.28% of SSRs with unique flanking sequences, while 55,621 SSRs had polymorphism, with an average PIC value of 0.498. 250 pairs of SSR primers in different genomic regions covering all maize chromosomes were randomly chosen for the experimental validation, with an average PIC value of 0.63 in 11 elite maize inbred lines.ConclusionsOur work provided insight into the non-random distribution spatterns and compositions of SSRs in different regions of maize genome, and also developed more polymorphic SSR markers using next-generation sequencing reads. The genome-wide SSRs polymorphism markers could be useful for genetic analysis and marker-assisted selection in breeding practice, and it was also proved to be high efficient for molecular marker development via next-generation sequencing reads.

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Empirical comparison of Simple Sequence Repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness.

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