Construction of a high-density genetic map by RNA sequencing and eQTL analysis for stem length and diameter in Dendrobium (Dendrobium nobile × Dendrobium wardianum)

Abstract

Dendrobium nobile and Dendrobium wardianum are important orchids with high ornamental and medicinal values. The stem is the main medicinal and edible part, and thick and long stem is one of the breeding objectives. In this research, a population with 100 F1 individuals was constructed from a interspecific hybridization between D. nobile and D. wardianum. RNA sequencing (RNA-seq) was employed to identify a large number of SNP markers for parents and progeny. A total of 522.43Gb clean data was obtained from RNA-seq, and they were assembled into 177,052 transcripts and 66,153 unigenes. Among the 331,642 high-quality SNP markers that were detected, 132,747 were polymorphic. Finally, 9645 SNP markers were effective and used to construct a high-density integrated genetic map with 19 linkage groups, which covered a total length of 3612.12 cM with an average marker interval of 0.41 cM. The female map could be considered as the first high-density genetic map for D. nobile with 3608 cM in total length and an average marker interval of 0.41 cM. Three eQTLs related to stem length and diameter were identified. This study might build a foundation up for fine eQTL mapping and molecular marker-assisted breeding of Dendrobium.