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EST-derived Single Nucleotide Polymorphism Markers For Assembling Genetic And Physical Maps Of The Barley Genome
| Content Provider | International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) |
|---|---|
| Author | Kota, R. Varshney, R. K. Prasad, M. Zhang, H. Stein, N. Graner, A. |
| Copyright Year | 2008 |
| 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 ((Ss(B) ranged from 0 to 40.0×103 (average 3.1×103) and 0.52×103 to 39.51×103 (average 4.37×103) 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. |
| File Format | |
| ISSN | 1438793X 14387948 |
| Journal | PeerReviewed |
| DOI | 10.1007/s10142-007-0060-9 |
| Language | English |
| Publisher | Springer Verlag |
| Publisher Date | 2008-01-01 |
| Access Restriction | One Nation One Subscription (ONOS) |
| Subject Keyword | Genetics and Genomics |
| Content Type | Text |
| Resource Type | Article |
| Subject | Genetics Medicine |
