Identification of sex-linked SNP markers using RAD sequencing suggests ZW/ZZ sex determination in Pistacia vera L

BMC Genomics
Salih KafkasEbru Kafkas

Abstract

Pistachio (Pistacia vera L.) is a dioecious species that has a long juvenility period. Therefore, development of marker-assisted selection (MAS) techniques would greatly facilitate pistachio cultivar-breeding programs. The sex determination mechanism is presently unknown in pistachio. The generation of sex-linked markers is likely to reduce time, labor, and costs associated with breeding programs, and will help to clarify the sex determination system in pistachio. Restriction site-associated DNA (RAD) markers were used to identify sex-linked markers and to elucidate the sex determination system in pistachio. Eight male and eight female F1 progenies from a Pistacia vera L. Siirt × Bağyolu cross, along with the parents, were subjected to RAD sequencing in two lanes of a Hi-Seq 2000 sequencing platform. This generated 449 million reads, comprising approximately 37.7 Gb of sequences. There were 33,757 polymorphic single nucleotide polymorphism (SNP) loci between the parents. Thirty-eight of these, from 28 RAD reads, were detected as putative sex-associated loci in pistachio. Validation was performed by SNaPshot analysis in 42 mature F1 progenies and in 124 cultivars and genotypes in a germplasm collection. Eight loci could distingu...Continue Reading

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Citations

Sep 16, 2015·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Qiong ZhangHongwen Huang
Dec 15, 2015·Annual Review of Plant Biology·Deborah Charlesworth
Aug 17, 2016·PloS One·Johany PeñaililloDaniela Seelenfreund
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Methods Mentioned

BETA
flow cytometry
PCR
Hi-Seq
genotyping
restriction
electrophoresis

Software Mentioned

RAD
RADseq
BatchPrimer
GeneMapper
SNaPshot

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