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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND GENOMIC APPROACHES TO IMPROVE PEANUT AND CORN RESISTANCE TO DISEASE AND AFLATOXIN CONTAMINATION

Location: Crop Protection and Management Research

Title: Characterization of simple sequence repeat (SSR) markers and genetic relationships within cultivated peanut (Arachis hypogaea L.)

Authors
item Li, Yan -
item Chen, Charles
item Knapp, Steve -
item Culbreath, Albert -
item Holbrook, C
item Guo, Baozhu

Submitted to: Peanut Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 11, 2011
Publication Date: June 13, 2011
Citation: Li, Y., Chen, C.Y., Knapp, S.J., Culbreath, A.K., Holbrook Jr, C.C., Guo, B. 2011. Characterization of simple sequence repeat (SSR) markers and genetic relationships within cultivated peanut (Arachis hypogaea L.). Peanut Science. 38:1-10.

Interpretive Summary: Cultivated peanut is a tetraploid (2n = 4x = 40 chromosomes) composed of both the A and B genomes. Identification and characterization of molecular markers in cultivated peanut has lagged behind other important crops because of the limited genetic variability and the added complexity of having two genomes. The majority of SSR (simple sequence repeat) polymorphic markers detected by different research groups were collected in this study and screened with 16 cultivated peanut lines with a range of field reactions to Tomato spotted wilt virus (TSWV), Cercospora arachidicola (early leaf spot) and Cercosporidium personatum (late leaf spot). Genetic diversities and genetic distances were calculated based on genotyping using SSR markers. Two hundred thirty five (42.27%) markers showed polymorphisms in these genotypes. The average number of alleles per SSR was 2.5 with a range of 1 to 13. However, 410 SSR markers had only one allele, confirming that diversity of cultivated peanuts is very limited. The genetic relationships revealed are in agreement with the pedigrees and origins of the tested peanut genotypes, indicating that these SSR markers are useful tools for evaluation of genetic diversity in peanuts. This study will contribute to the construction of genetic linkage maps for cultivated peanut, which will be an important research goal to facilitate quantitative trait locus (QTL) analysis and gene tagging for use in marker-assisted breeding.

Technical Abstract: A total of 709 SSR markers were collected from public database and 556 SSRs passed an initial screen and were used to characterize 16 Arachis hypogaea genotypes. PIC (polymorphism information content) scores and heterozygosity indices were calculated to access the genetic diversity of SSR markers and genetic distances were estimated from shared allele distances for construction of a cladogram by the Neighbor-Joining method to illustrate the genetic relationships among the genotypes. Two hundred thirty five (42.27%) markers showed polymorphisms in these genotypes. The average heterozygosity estimated from these 556 SSRs was 0.225 with a range of 0 to 0.992 and the average PIC was 0.209. The average number of alleles per SSR was 2.5 with a range of 1 to 13. However, 410 SSR markers had only one allele, confirming that diversity of cultivated peanuts is very limited. Among the polymorphic SSR markers, 26.4 % were binucleotide GA repeat motif markers, followed by binucleotide CT (10.4%), and trinucleotide TAA (9.6%). The binucleotide and trinucleotide repeat motifs are the most abundant type of SSRs, and binucleotide GA repeat motif shows a higher polymorphism in comparison to other types. The genetic relationships revealed from the cladogram are in agreement with the pedigrees and origins of the tested peanut genotypes, indicating that these SSR markers are useful tools for evaluation of genetic diversity in peanuts.

Last Modified: 7/23/2014
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