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Molecular basis of off-type microsatellite markers in papaya

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Abstract

Papaya (Carica papaya L.) is a major fruit crop in the tropics and is a model system for studying sex chromosome evolution in plants. From a simple sequence repeat (SSR) mapping project in papaya, 37 SSRs displayed non-parental alleles in the F2 population, known as off-type markers. They all belong to Class I (≥20 bp, hypervariable markers). To investigate the molecular basis of these non-parental alleles, seven SSRs with off-type alleles were cloned and sequenced from two parents and selected F2 individuals. SSR repeat motif variation was the major cause for the generation of off-type alleles and single nucleotide polymorphisms (SNPs) and Insertion/deletion also contributed to off-type polymorphism. Off-type SSRs arose after one meiosis at 3 % frequency. Two of the seven markers had no polymorphisms between the parents but non-parental alleles segregated among the F2 individuals. Four of the seven markers exhibited SNPs between parents with transition and transversion at 2:1 ratio. Six markers showed additional SNPs between F2 offspring and parents with transition and transversion at about 1:1 ratio, suggesting higher than expected level of transversion mutations at the F2 population after one meiosis event between the parental genomes. These off-type SSRs were analyzed in a second F2 population and 43 % of them were conserved. The major cause of off-type SSRs in papaya is the variation of repeat length in Type I SSRs, and the underlining mechanism might be DNA replication slippage of repeat motifs. The presence and high conservation of these off-type markers demonstrated that hypervariable class I SSRs could generate genetic variation in one generation and increase genetic diversity for natural selection to enhance fitness.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

BAC:

Bacterial artificial chromosome

BES:

BAC end sequences

MSY:

Male-specific region of the Y

SSR:

Simple sequence repeat

SNP:

Single nucleotide polymorphisms

InDel:

Insertion and deletion

WGS:

Whole-genome shotgun

FISH:

Fluorescence in situ hybridization

DAPI:

4′,6-Diamidino-2-phenylindole

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Acknowledgments

This work was supported by a grant from NSF Plant Genome Research Program (Award No. DBI 0922545) and startup fund from Fujian Agriculture and Forestry University to R.M.

Authors’ contribution

RM and RC conceived the study, coordinated all research activities; JF and AW carried out wet lab experiments and conducted bioinformatics analysis; JF, RC and RM wrote the manuscript. All authors read and approved the final manuscript.

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Authors and Affiliations

  1. Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Jingping Fang & Rukai Chen

  2. FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Jingping Fang & Ray Ming

  3. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Andrew Wood & Ray Ming

Authors
  1. Jingping Fang
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Correspondence to Ray Ming.

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Fang, J., Wood, A., Chen, R. et al. Molecular basis of off-type microsatellite markers in papaya. Euphytica 209, 323–339 (2016). https://doi.org/10.1007/s10681-015-1630-x

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