Identification and Evaluation of Transcriptome-Derived A and B-Genome Single Nucleotide Polymorphism (SNP) Markers in Peanut (Arachis hypogaea L.)

Distinguishing homologous from homoeologous single-nucleotide polymorphisms (SNPs) poses a challenge in genotyping polyploids such as peanut. This study sought to identify and validate homologous SNPs for the purpose of constructing a genetic linkage map for a BC₁ interspecific introgression population and genotyping a BC₃ population. A-genome and B-genome SNPs were selected from a transcriptome sequence database made of A-genome parents, A. diogoi, A. cardenasii and A. duranensis, and B/K-genome parents, A. ipaënsis and A. batizocoi, and parents of the backcross population (Florunner and TxAG-6). Polymorphic SNPs were first filtered between TxAG-6 and Florunner at each contig followed by screening for sub-genome specific SNPs. Primers synthesized were validated based on KASP chemistry using the Roche LightCycler system. Validation results showed that 63% representing 49 out of 78 selected A-genome SNPs and 71% representing 91 out of the 128 selected B-genome SNPs perfectly matched the selection criteria used in targeting the SNPs. These results further emphasize the reliability of our transcriptome sequence database for selection and utilization of candidate SNPs for genotyping and construction of genetic linkage maps.