Skip to main content
ARS Home » Southeast Area » Dawson, Georgia » National Peanut Research Laboratory » Research » Publications at this Location » Publication #321168

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

Location: National Peanut Research Laboratory

Title: Evaluation of insertion-deletion markers suitable for genetic diversity studies and marker-trait correlation analyses in cultivated peanut (Arachis hypogaea L.)

Author
item MENG, S - Agricultural University Of Hebei
item YANG, X - Agricultural University Of Hebei
item Dang, Phat
item CUI, S - Agricultural University Of Hebei
item CHEN, C - Auburn University
item MU, G - Agricultural University Of Hebei
item LIU, L - Agricultural University Of Hebei

Submitted to: Genetics and Molecular Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2016
Publication Date: 8/12/2016
Citation: Meng, S., Yang, X.L., Dang, P.M., Cui, S.L., Chen, C.Y., Mu, G.J., Liu, L.F. 2016. Evaluation of insertion-deletion markers suitable for genetic diversity studies and marker-trait correlation analyses in cultivated peanut (Arachis hypogaea L.). Genetics and Molecular Research. doi:10.4238/gmr.15038207.

Interpretive Summary: Peanut is one of the most important oil crops worldwide, rich in protein and a good source of vitamins and minerals. Cultivated peanut (Arachis hypogaea) genome represents a combination of two diploids (an allotetraploid, 2n = 4x = 40, AABB). Despite the diversity in physical characteristics, growth habits, environmental requirements, and wide range of responses to disease and environmental stresses, peanut genetics show low differences according to DNA finger printing studies. Genetic variations, collected in germplasm collections, represent a wide range of breeding materials that be used to develop new varieties with desirable traits. Development of new type of genetic markers that can differentiate one genetic background from another is critical to facilitate molecular breeding. A collection of 48 Insertion-Deletion (InDel) markers were developed based on functional peanut RNA transcripts and applied to germplasm collection to evaluate their usefulness. From experimental results, InDel markers are suitable for genetic diversity and population structure analysis in peanut. Phenotypic characterization for five agronomy traits and correlation testing of 13 InDel markers provided information for further peanut breeding and genetic research.

Technical Abstract: Insertion-Deletion (InDel) marker as a genetic marker, was developed on base of genome sequence information and widely employed in crop genetic diversity and population structure. To assess genetic diversity and population structure analysis using InDel markers in cultivated peanut, we selected 54 accessions of China and genotyped them with 48 InDel markers. These markers amplified 61 polymorphic loci among the genotypes screened and amplified from 1 to 8 alleles with an average of 2.6 alleles per marker. The scale of polymorphism information content (PIC) ranged from 0.0364 to 0.9030 with an average of 0.3785. Subsequent neighbor-joining (NJ) tree and population structure analysis identified four sub-populations in this panel. All the accessions were divided into 2 groups, 4 branches (A1, A2, A3 and A4) by the Neighbour-Joining (NJ) tree analysis. In contrast, the subpopulations from STRUCTURE analysis numbered four groups (G): G1, G2, G3 and G4. Also, the results of two-dimension principal component analyses (PCA) were similar. These results indicated that InDel marker is suitable for genetic diversity and population structure analysis in peanut. Phenotypic characterization for five agronomy traits and correlation testing of 13 InDel markers provided information for further peanut breeding and genetic research.