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

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Relation http://oar.icrisat.org/3007/
http://dx.doi.org/10.1007/s10142-007-0060-9
 
Title EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome
 
Creator Kota, R
Varshney, R K
Prasad, M
Zhang, H
Stein, N
Graner, A
 
Subject Genetics and Genomics
 
Description 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.
 
Publisher Springer Verlag
 
Date 2008
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/3007/1/EST-derived_single_nucleotide_polymorphism_markers_for_assembling_genetic_and_physical_maps_of_the_barley_genome.pdf
Kota, R and Varshney, R K and Prasad, M and Zhang, H and Stein, N and Graner, A (2008) EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome. Functional & Integrative Genomics, 8 (3). pp. 223-233. ISSN 1438-7948