Development and Application of Indel Markers in Genetic Diversity Study for Cultivated Peanut (Arachis hypogaea L.).

To date, nearly 10,000 molecular markers have been identified by various research groups around the world, but only less than 14.5% showed polymorphism in peanut (Zhao et al. 2012). Low levels of polymorphism limits the application of marker-assisted selection in peanut breeding programs. Among existing assayable markers in peanut, majority are simple sequence repeat markers (SSRs). It has been reported that InDel markers are more polymorphic than SSRs in some crops. The goal of this study is to identify novel InDel markers and evaluate the potential use in peanut.  Forty-eight InDel markers were developed from conserved sequences of functional genes and tested in a diverse panel of 118 accessions covering six botanical types of cultivated peanut, 104 selected from the U.S. mini-core and an additional 14 from another two botanical types that are not present in the mini-core.  The results showed that 16 of 48 InDel markers were polymorphic, with polymorphic information content (PIC) among InDels ranged from 0.017 to 0.569.  In respect to botanical types, PICs varied from 0.176 for fastigiata var., 0.181 for hypogaea var., 0.306 for vulgaris var., 0.556 for peruviana var., 0.534 for aequatoriana var., to 0.660 for hirsuta var., implying that hirsuta var., peruviana var., and aequatoriana var. have higher genetic diversity than the other types and provide a basis for gene functional studies.  Single marker analysis was conducted to associate the marker and the trait in facilitating the discovery of functional genes.