Integrative linkage mapping, GWAS, and RNA-Seq analysis unravel the genetic architecture and candidate genes for drought tolerance in <i>Chrysanthemum</i> interspecific F1 progeny

Drought stress is a major environmental constraint that severely impacts plant production. However, the genetic basis is primarily misunderstood in chrysanthemum species. The objectives of this study are to examine the genetic variation of drought tolerance in reciprocal F₁ progenies of <i>Chrysanthemum dichrum</i> (drought-tolerant) and <i>Chrysanthemum nankingense</i> (drought-sensitive) and identify candidate genes by integrating linkage mapping, genome-wide association study (GWAS), and RNA-seq analysis. The results revealed extensive variation for the investigated traits in response to drought stress and notable genetic divergence in drought tolerance between the reciprocal crosses. This confirms that the hybridization direction influenced drought tolerance phenotypes. A high-resolution genetic map containing 6677 nonredundant bin markers spanning 1859.31 cM across nine linkage groups (LGs), achieving an average marker density of 0.28 cM, was developed with a genotyping-by-sequencing (GBS) approach. The inclusive composite interval mapping (ICIM) detected 89 significant quantitative trait loci (QTLs), and GWAS identified 1360 significant quantitative trait nucleotides (QTNs) in Single_Env, 394 QTNs, and 114 quantitative epistatic interactions (QEIs) in the Multi_Env algorithm, as well as six pairs of epistatic loci (QEs) related to drought tolerance. Besides the additive effects, we observed considerable adverse dominant and epistatic effects for the significant loci, explaining why drought tolerance exhibits negative heterosis in reciprocal crosses. The integration of QTL mapping and GWAS revealed 38 colocalized loci harboring 10 known and 15 novel candidate genes, eight validated through RNA-seq and qRT-PCR analyses. Moreover, we identified elite haplotypes yielding higher drought tolerance within the candidate gene <i>Cn1062070.</i> The findings help elucidate the genetic architecture of drought tolerance in chrysanthemum species and provide valuable genetic resources for the development of drought-tolerant cultivars.