Late leaf spot (LLS) is one of the most serious foliar diseases affecting peanut worldwide leading to huge yield loss. To understand the genetic basis of LLS and assist breeding in the future, we conducted quantitative trait locus (QTL) analysis for LLS and three plant-type-related traits including height of main stem (HMS), length of the longest branch (LLB) and total number of branches (TNB). Significant negative correlations were observed between LLS and the plant-type-related traits in multi-environments of a RIL population from the cross Zhonghua 5 and ICGV 86699. A total of 20 QTLs were identified for LLS, of which two QTLs were identified in multi-environments and six QTLs with phenotypic variation explained (PVE) more than 10%. Ten, seven, fifteen QTLs were identified for HMS, LLB and TNB, respectively. Of these, one, one, two consensus QTLs and three, two, three major QTLs were detected for HMS, LLB and TNB, respectively. Of all 52 unconditional QTLs for LLS and plant-type-related traits, 10 QTLs were clustered in five genetic regions, of which three clusters including five robust major QTLs overlapped between LLS and one of the plant-type-related traits, providing evidence that the correlation could be genetically constrained. On the other hand, conditional mapping revealed different numbers and different extent of additive effects of QTLs for LLS conditioned on three plant-type-related traits (HMS, LLB and TNB), which improved our understanding of interrelationship between LLS and plant-type-related traits at the QTL level. Furthermore, two QTLs, qLLSB6-7 and qLLSB1 for LLS resistance, were identified residing in two clusters of NB-LRR—encoding genes. This study not only provided new favorable QTLs for fine-mapping, but also suggested that the relationship between LLS and plant-type-related traits of HMS, LLB and TNB should be considered while breeding for improved LLS resistance in peanut.
