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EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome

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Abstract

In a panel of seven genotypes, 437 expressed sequence tag (EST)-derived DNA fragments were sequenced. Single nucleotide polymorphisms (SNPs) that were polymorphic between the parents of three mapping populations were mapped by heteroduplex analysis and a genome-wide consensus map comprising 216 EST-derived SNPs and 4 InDel (insertion/deletion) markers was constructed. The average frequency of SNPs amounted to 1/130 bp and 1/107.8 bp for a set of randomly selected and a set of mapped ESTs, respectively. The calculated nucleotide diversities (π) ranged from 0 to 40.0 × 10−3 (average 3.1 × 10−3) and 0.52 × 10−3 to 39.51 × 10–3 (average 4.37 × 10−3) for random and mapped ESTs, respectively. The polymorphism information content value for mapped SNPs ranged from 0.24 to 0.50 with an average of 0.34. As expected, combination of SNPs present in an amplicon (haplotype) exhibited a higher information content ranging from 0.24 to 0.85 with an average of 0.50. Cleaved amplified polymorphic sequence assays (including InDels) were designed for a total of 87 (39.5%) SNP markers. The high abundance of SNPs in the barley genome provides avenues for the systematic development of saturated genetic maps and their integration with physical maps.

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Acknowledgment

We are grateful to Patrick Hayes for providing the DH lines of barley mapping populations “Steptoe” × “Morex” and “Oregon WolfeDom” × “Oregon WolfeRec” and Ulrike Beier for the excellent technical assistance. The assistance of Thomas Thiel in using the SNP2CAPS software is greatly appreciated. We thank Uwe Scholz for establishing the website featuring the supplemental data. This work was funded by the German Federal Ministry of Education and Research in conjunction with the GABI program (BMBF grants 0312270/4, 0312271A, and 0312278C).

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Correspondence to A. Graner.

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Both R. Kota and R.K. Varshney contributed equally to this work.

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This page is unfortunately not in the Publisher's archive anymore: Table ESM 1 - Details on development and characterization of SNP markers (HTML 360 kb)

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Informative set of SNP markers for haplotype analysis and CAPS assays (DOC 83 kb)

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Kota, R., Varshney, R.K., Prasad, M. et al. EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome. Funct Integr Genomics 8, 223–233 (2008). https://doi.org/10.1007/s10142-007-0060-9

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