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Research Project: Developing Strategies to Identify Useful Genes in Peanut and Breeding High Yielding Peanut Varieties and Germplasm

Location: National Peanut Research Laboratory

Title: Development and utilization of InDel markers to identify peanut (Arachis hypogaea) disease resistance

Author
item LIFENG, LIU - Agricultural University Of Hebei
item Dang, Phat
item CHEN, CHARLES - Auburn University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/29/2015
Publication Date: 11/13/2015
Publication URL: http://doi: 10.3389/fpls.2015.00988
Citation: Lifeng, L., Dang, P.M., Chen, C. 2015. Development and utilization of InDel markers to identify peanut (Arachis hypogaea) disease resistance. Frontiers in Plant Science. 6:988.

Interpretive Summary: Diseases, such as spotted wilt caused by tomato spotted wilt virus (TSWV) and leaf spots, can reduce yield and quality in peanut. Depending on the variation in the levels and severity of diseases, plants have evolved various mechanisms of resistance which can be observed in different genetic background. Molecular genetic markers provide a powerful tool for breeders to associate genetics with plant resistance. Identification and utilization of insertion and deletion (InDel) molecular markers that can be associated with disease resistance in peanut is very critical for variety development. The goals of this study were to identify novel InDel markers and evaluate the potential use in peanut breeding. 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, of which 104 were from the U.S. mini-core germplasm collection. Single marker analysis was conducted to associate specific marker to disease resistant traits. Five InDels were identified to be significantly correlated to tomato spotted wilt virus (TSWV) infection and leaf spot, which facilitated the identification of genes related to agronomic traits and marker-assisted selection in peanut breeding program.

Technical Abstract: To date, nearly 10,000 SSR-based markers have been identified by various research groups around the world, but less than 14.5% showed polymorphism in peanut and only 6.4% were mapped. Low levels of polymorphism limit the application of marker assisted selection (MAS) in peanut breeding programs. It has been reported that insertion and deletion (InDel) markers were more polymorphic than SSRs in some crops. The goals of this study were to identify novel InDel markers and evaluate the potential use in peanut breeding. 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, of which 104 were from the U.S. mini-core. The results showed that 16 InDel markers were polymorphic with polymorphic information content (PIC) among InDels ranging from 0.017 to 0.660. With respect to botanical types, PICs varied from 0.176 for fastigiata var., 0.181 for hypogaea var., 0.306 for vulgaris var., 0.534 for aequatoriana var., 0.556 for peruviana var., to 0.660 for hirsuta var., implying that aequatoriana var., peruviana var., and hirsuta var. have higher genetic diversity than the other types and provide a basis for gene functional studies. Single marker analysis was conducted to associate specific marker to disease resistant traits. Five InDels were identified to be significantly correlated to tomato spotted wilt virus (TSWV) infection and leaf spot, which facilitated the identification of genes related to agronomic traits and marker-assisted selection in peanut breeding program.