The first complete pachytene FISH map of Phalaenopsis orchid

Abstract

Phalaenopsis orchid is one of the top ornamentals in global horticulture market P aphrodite (2n= 2x= 38) is an important parent in Phalaenopsis breeding and it is the specie of choice for whole genome sequencing owing to its relatively smaller genome size (2 8 pg/ 2C) in this genus However none of molecular cytogenetic map which integrates the genetic and genomic datasets to the chromosomal locations and structures was available in orchids Fluorescence in situ hybridization (FISH) has been a reliable technique for mapping DNA markers on chromosomes In this study a modified drop method for pachytene chromosome preparation was first developed Phalaenopsis meiotic pachytene chromosomes revealed up to 20 times higher resolution than their mitotic metaphase counterparts and the first pachytene-based karyotype of P aphrodite was established Second the linkage group DNA markers were FISH mapped Thus the 22 Phalaenopsis linkage groups were successfully integrated with the 19 chromosomes of P aphrodite All the orders of the FISH signals were consistent to those revealed in the genome assembly and genetic linkage map demonstrating the high quality of the physical and genetic maps Furthermore the anchored DNA markers were applied as chromosome-specific markers to facilitate chromosome identification and assisted to assign the unmapped scaffolds to the molecular cytogenetic map Last on the basis of chromosomal localizations sequence divergences and transcriptomic expression profiles of the five CHS (chalcone synthase) genes the expansion of the gene family occurred through segmental duplications followed by tandem duplications was proposed The accomplishment of this study sets a solid foundation by integrating Phalaenopsis genetic genomic and chromosomal datasets and opens the possibility for chromosome-scale comparative genomics in orchids

Date of Award	2018 Aug 2
Original language	English
Supervisor	Song-Bin Chang (Supervisor)