Transcriptome Analysis Reveals the Molecular Mechanisms of Carrot Adaptation to Alternaria Leaf Blight

Carrot (<i>Daucus carota</i> L.) is an important vegetable crop that is rich in carotenoids and is widely cultivated throughout the world. Alternaria leaf blight (ALB), caused by infection with <i>Alternaria dauci</i> (<i>A. dauci</i>), is the most serious fungal disease in carrot production. Although several quantitative trait loci associated with ALB resistance have been identified, the genetic mechanisms underlying this resistance remain largely unelucidated. The aim of the present study was to clarify the infection mode of <i>A. dauci</i> and examine the molecular mechanisms underlying carrot cultivar adaptation to ALB by RNA sequencing. Microscopic observation revealed that <i>A. dauci</i> invades leaf tissues by entering through stomata, and resistant germplasms may significantly inhibit the infection and colonization of <i>A. dauci</i>. In addition, transcriptomic analyses were performed to detect the key pathways and genes associated with the differential responses between ALB-resistant (HB55) and ALB-susceptible (14088) carrot cultivars. These results suggest that the secondary metabolic process, phenylpropanoid biosynthesis, and tyrosine metabolism might play important roles in the resistance of carrots to <i>A. dauci</i>. Three candidate genes (<i>LOC108208301</i>, <i>LOC108215577</i>, and <i>LOC108224339</i>) that were specifically upregulated in the resistant carrot cultivar 'HB55' after <i>A. dauci</i> infection were identified as the key resistance response genes. These findings provide insights into the resistance mechanism of carrots to ALB, as well as key candidate genes and information on expression regulation for the molecular breeding of carrot disease resistance.