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. 2019 Dec 3;9:18246. doi: 10.1038/s41598-019-54747-1

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Workflow of identification of polymorphic co-dominant and dominant SNPs used for developing bin maps in peanut using whole genome re-sequencing data. Fastq files were aligned to the concatenated (A- and B-genome together) genomes and individually to A- and B-genomes in order to identify co-dominant and dominant SNPs. A-genome represents Arachis duranensis and B genome represents Arachis ipaensis. A total of 81,599 non-redundant SNPs was identified between the two parents using the above-mentioned approach. Individually, the co-dominant and dominant SNPs identified were used for genotyping the RIL population to identify polymorphic SNPs (alleles) present in the population. After removing the SNPs with more than 20% missing data, a total of 12,248 unique set of SNPs were obtained. Excluding the SNPs showing segregation distortion, a final set of 11,106 SNPs were used for identification of 5,816 bins used in construction of linkage maps.