"A total of 67 and 35 QTL were detected under water-limited and well-watered conditions, respectively. The favorable alleles to improve the traits exhibited partial or over-dominance effects".This is a sentence picked from the paper Ref: (PDF) Progress and perspective on drought and salt stress tolerance in cotton. Available from: https://www.researchgate.net/publication/329935232_Progress_and_perspective_on_drought_and_salt_stress_tolerance_in_cotton [accessed Mar 31 2020].

The question is, how to identify the role of alleles 9partial or over-dominance etc) and the kind of gene action based on QTL anaysis for any trait. Is this built into the software and if yes, which software is the best for QTL analysis?