Molecular basis of off-type microsatellite markers in papaya

Jingping Fang, Andrew Wood, Rukai Chen, Ray R Ming

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)323-339
Number of pages17
JournalEuphytica
Volume209
Issue number2
DOIs
StatePublished - May 1 2016

Fingerprint

Carica
papayas
Microsatellite Repeats
Alleles
microsatellite repeats
alleles
single nucleotide polymorphism
Single Nucleotide Polymorphism
Carica papaya
Meiosis
meiosis
genetic polymorphism
Population
genetic variation
Sex Chromosomes
Genetic Selection
fruit crops
sex chromosomes
DNA replication
DNA Replication

Keywords

  • Carica papaya
  • Class I/II repeat motif
  • Microsatellite
  • Off-type markers

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science
  • Horticulture

Cite this

Molecular basis of off-type microsatellite markers in papaya. / Fang, Jingping; Wood, Andrew; Chen, Rukai; Ming, Ray R.

In: Euphytica, Vol. 209, No. 2, 01.05.2016, p. 323-339.

Research output: Contribution to journalArticle

Fang, Jingping ; Wood, Andrew ; Chen, Rukai ; Ming, Ray R. / Molecular basis of off-type microsatellite markers in papaya. In: Euphytica. 2016 ; Vol. 209, No. 2. pp. 323-339.
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