Construction of a high-density genetic linkage map for Phalaenopsis spp

  • 邱 尚奕

Student thesis: Master's Thesis

Abstract

Phalaenopsis orchids (2N=38) are perennial flowering plants hold a significant economic value in Taiwan agricultural industry and are the major export of ornamental crops in Taiwan Whole genome sequencing of P equestris a native species in Taiwan has been completed in 2015 However the genetic linkage map for Phalaenopsis is still unavailable The aim of this thesis is to construct a genetic linkage map for Phalaenopsis Both P aphrodite and P equestris are the only two native Phalaenopsis orchids in Taiwan For constructing the genetic map a F1 population consisting of 118 progenies from a cross between P aphrodite and P equestris was used Dr Wen-Luan Wu has being for long focused on developing simple sequence repeat (SSR) of Phalaenopsis orchids Her group had developed 5 483 SSRs from expressed sequence tags (ESTs) 454 sequenced genomic DNA and bacterial artificial chromosome (BAC)-end sequences (BESs) Among them 603 SSRs have primer sequences designed In this study 333 SSRs with primer sequences were used 241 (72 37%) SSRs can be successfully amplified and 162 (48 65%) SSRs revealed polymorphism between two parents by using a 6% polyacrylamide gel electrophoresis (PAGE) In addition 2 768 single nucleotide polymorphism (SNP) markers have been previously developed by using genotyping-by-sequencing (GBS) analysis in our lab SSR and SNP markers were filtered through chi-square test and eventually 108 SSRs and 1 798 SNPs total 1 906 markers were applied for linkage analysis The genetic linkage map was constructed by OneMap software a package from R software It is comprised of 27 linkage groups (LGs) with total 1 214 mapped markers The total length of 27 LGs is 15 192 centimorgan (cM) and the average marker density is 12 51 cM The 27 LGs then were assembled into potential 19 homologous groups (HGs) according to scaffold sequences that have already paralleled with BESs The genetic linkage map of Phalaenopsis will facilitate the access of genes that correspond to the interested traits and quantitative trait loci (QTL) incorporate with marker-assisted breeding and enhance genome assembly of P equestris
Date of Award2017 Aug 31
Original languageEnglish
SupervisorHong-Hwa Chen (Supervisor)

Cite this

Construction of a high-density genetic linkage map for Phalaenopsis spp
尚奕, 邱. (Author). 2017 Aug 31

Student thesis: Master's Thesis