Development of highly polymorphic EST-SSR markers and segregation in F₁ hybrid population of Vitis vinifera L

Genet Mol Res. 2013 Sep 23;12(3):3871-8. doi: 10.4238/2013.September.23.5.

Abstract

The objectives of this investigation were to develop and validate the expressed sequence tag (EST)-simple sequence repeat (SSR) markers from large EST sequences, and to study the segregation and distribution of SSRs within two grapevine parental lines. In total, 94 F₁ lines crossed between "Early Rose" and "Red Globe" were studied. Approximately 2100 EST-SSR sequences of Vitis vinifera L. were searched for SSRs and analyzed for the design of polymerase chain reaction (PCR) primers amplifying the SSR-rich regions. Trinucleotide repeats were found to be the most abundant, followed by other nucleotide repeats. A total of 182 SSR primer pairs were first developed for the study on the parental polymorphism. Among the 182 SSR primers, 142 primer pairs (78%) could amplify the anticipated PCR products, among which only 52 primer pairs (36.62%) showed polymorphism between the two parents. These polymorphic bands were further surveyed among the 94 F₁ lines, and the results showed that a total of 162 bands were amplified, and 98 of them were polymorphic in both parents (60.86% polymorphism), with an average of 1.88 polymorphic DNA bands for each primer pair. After testing with the chi-square test, 33 of the clearly amplified polymorphic bands followed a 3:1 ratio, and 37 followed a 1:1 ratio. The rest showed distorted segregation ratios.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping
  • DNA Primers / genetics
  • DNA, Plant / genetics
  • Expressed Sequence Tags*
  • Genetic Markers
  • Genome, Plant*
  • Microsatellite Repeats*
  • Polymerase Chain Reaction
  • Polymorphism, Genetic
  • Reproducibility of Results
  • Sequence Analysis, DNA
  • Vitis / genetics*

Substances

  • DNA Primers
  • DNA, Plant
  • Genetic Markers