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List of 16 barley accessions representing the western and eastern divisions of the barley gene pool, 454 pyrosequencing information, and identified single nucleotide polymorphisms (SNPs).

 
CN Origin Region Label 454 pool RLMID sequence (5′ to 3′) No. of reads NC NSP Het% MisSNP%
91147 China E ChinaE 1a ACACGACGAC 45,239 191 420 1.9 89.4
81387 India E IndiaE 1b ACACGTAGTA 145,057 930 1,834 2.0 53.9
59909 Iran E IranE 1c ACACTACTCG 142,437 986 1,862 1.8 53.2
92006 Japan E JapanE 1d ACGACACGTA 54,999 395 750 1.3 81.1
58854 Mongolia E MongoliaE 1e ACGAGTAGAC 81,011 621 1,242 1.0 68.8
81307 Nepal E NepalE 1f ACTATACGAG 199,860 1316 2,593 2.8 34.8
80536 Pakistan E PakistanE 1g ACGTACACAC 70,910 604 1,193 0.3 70.0
29118 Kyrgyzstan E KyrgyzstanE 1h ACGTACTGTG 22,540 95 180 0.0 95.5
68637 Turkey W TurkeyW 2a ACTACGTCTC 95,021 567 1,099 0.8 72.4
51205 Syria W SyriaW 2b ACACGTAGTA 182,678 1010 2,079 2.6 47.7
50729 Jordan W JordanW 2c ACACTACTCG 180,606 1055 2,129 3.7 46.5
29233 Iraq W IraqW 2d ACGACACGTA 41,578 197 410 0.5 89.7
77017 Ethiopia W EthiopiaW 2e ACGAGTAGAC 65,108 461 899 0.8 77.4
58689 Egypt W EgyptW 2f ACTATACGAG 108,165 721 1,429 2.0 64.1
68925 Greece W GreeceW 2g ACGTACACAC 36,607 161 295 0.0 92.6
94239 Lebanon W LebanonW 2h ACGTACTGTG 32,411 121 225 9.3 94.3
Average for eastern region 95,257 642 1,259 1.4 68.3
Average for western region 92,772 537 1,071 2.5 73.1
CN, Canadian National accession number at the Plant Gene Resources of Canada, Saskatoon, SK, Canada.
The cultivated barley gene pool was divided based on the distinct distribution of wild barley following Zohary and Hopf (2000) and Morrell and Clegg (2007). The eastern (E) region represents cultivated barley from the Zagros Mountains and further east, while the western (W) region includes cultivated barley from the Fertile Crescent and further west.
§RLMID, Rapid Library Multiplex Identifier.
NC, the number of contigs with SNP; NSP, the number of SNPs predicted; Het%, the percentage of the heterozygous SNPs over the predicted SNPs; MisSNP%, the percentage of the predicted SNPs that were missing for the sample due to the lack of sequence reads.



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Summary statistics of 454 pyrosequencing reads and identified contigs.

 
Read
Length
Parameter Raw Passed Total Mean Median Minimum Maximum
454 read and length
Region1 1,097,247 862,828 302,653,823 350.8 387 40 703
Region2 1,141,029 866,607 310,078,946 357.8 389 40 1,195
All 2,238,276 1,729,435 612,732,769 354.3 388 40 1,195
2578 contigs
Read 22,588 8.7 8 1 34
Length 1,057,077 410.0 423 97 540
SNP† for 2578 contigs 3,980 1.5 1 0 21
SNP for 1914 contigs with SNP 3,980 2.1 1 1 21
100 contigs for validation
Read 993 9.9 9 5 24
Length 41,614 416.1 420.5 197 503
SNP predicted 701 7 7 0 21
SNP, single nucleotide polymorphism.



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Validation results on identified contigs, putative single nucleotide polymorphisms (SNPs), and related SNP bases with Sanger sequencing (SS).

 
Feature All samples ChinaE PakistanE JordanW EthiopiaW
85 validated contigs
SNP predicted 620
SNP confirmed by SS 288
SNP not confirmed by SS 332
New SNP from SS 735
New indel from SS 39
All SNP-indels from SS 1060
SNP base match (%) 83.6%
Bases missing from 454 reads 510 458 248 463
Bases missing from SS 17 42 68 35
Total valid bases to match 94 121 305 123
Mismatched bases (%) 4 (4.3%) 31 (25.6%) 67 (22.0%) 17 (13.8%)
Matched bases (%) 90 (95.7%) 90 (74.4%) 238 (78.0%) 106 (86.2%)