High-Density Genetic Linkage Map Construction and QTLs Identification Associated with Four Leaf-Related Traits in Lady’s Slipper Orchids (Paphiopedilum concolor × Paphiopedilum hirsutissimum)

Abstract

Lady’s slipper orchids (Paphiopedilum spp.) are highly valuable within the flower industry. Recently, both Paphiopedilum concolor and Paphiopedilum hirsutissimum (2n = 2x = 26) have been widely used for hybrid parents, ornamental, and economic purposes. However, high-density genetic maps and leaf traits related to quantitative trait loci (QTLs) in these two Paphiopedilum species have been poorly studied. Herein, an interspecific F1 population of 95 individuals was developed from the cross between P. concolor and P. hirsutissimum with contrasting leaf length (LL), leaf width (LW), leaf thickness (LT), and leaf number (LN). RNA extracted from the F1 population and their parents was subjected to high-throughput RNA sequencing. Approximately 745.59 Gb of clean data were generated, and were assembled into 349,730 transcripts and 185,089 unigenes. In total, 165,196 high-resolution polymorphic single nucleotide polymorphism (SNP) markers were initially identified. Finally, 8410 SNP markers satisfied the requirements and were used to construct a genetic map. The integrated map contained 13 linkage groups (LGs) and spanned 1616.18 cM, with an average distance of 0.19 cM between adjacent markers. QTL analysis in the F1 population identified 12 QTLs linked to four leaf-related traits, including LL, LW, LT, and LN. These QTLs by composition interval mapping, explained 11.86% to 21.58% of the phenotypic variance, and were distributed on eight LGs, but not on LGs 4, 6, 8, 12, and 13. Furthermore, 25 unigenes were identified via BLAST searches between the SNP markers in the QTL regions and our assembled transcriptome, of which 11 unigenes were enriched with 59 gene ontology (GO) terms. The information generated in this study will be useful for candidate genes for further molecular regulation studies on leaf traits, future marker-assisted selection of leaf ornamental improvement breeding, genome assembly, and comparative genome analyses.