View Full Table | Close Full ViewTable 1.

Names of lines in the barley CAP core, the row subpopulation they were assigned to according to their spike phenotype (two or six row), and the subpopulation label given to them for the imputation of missing marker scores (see Materials and Methods). Lines that were not assigned a row subpopulation were not used in analyses involving these subpopulations.

 
No. Line Row subpop. Label No. Line Row subpop. Label
1 2B96-5038 two 1 50 FEG66-08 six 3
2 2B98-5312 two 2 51 FEG90-31 six 3
3 6B00-1526 six 3 52 Flagship two 2
4 6B02-3394 six 3 53 Foster six 3
5 6B94-7378 six 3 54 Franklin two 2
6 6B94-8253 six 3 55 Garnett two 1
7 6B97-2245 six 3 56 Geraldine -- 4
8 88Ab536 six 3 57 Harrington two 1
9 88Ab536-B six 3 58 Haruna Nijo two 2
10 AC Metcalfe two 1 59 Haxby two 1
11 Arapiles two 2 60 Hays -- 4
12 B1202 two 2 61 Hockett two 1
13 B1215 two 2 62 Hoody -- 6
14 B1602 six 3 63 Klages two 1
15 B1614 six 3 64 Kold -- 6
16 Baronesse -- 4 65 Kompolti -- 6
17 BCD12 two 1 66 Lacey six 3
18 BCD47 two 1 67 Larker six 3
19 Belford -- 5 68 Legacy six 3
20 Bison 1H -- 4 69 M122 six 3
21 Bison 1H+4H -- 4 70 M123 six 3
22 Bison 1H+4H+5H -- 4 71 Merit two 1
23 Bison 1H+5H -- 4 72 MNBrite six 3
24 Bison 4H -- 4 73 Morex six 3
25 Bison 4H+5H -- 4 74 ND20448 six 3
26 Bison 5H -- 4 75 ND20508 six 3
27 Bison 7H -- 4 76 ND21863 two 1
28 Bowman two 1 77 NDB112 six 3
29 C-14 two 2 78 Newdale two 1
30 Canela -- 2 79 Nomini -- 6
31 CDC Copeland two 1 80 Orca two 1
32 CDC Kendall two 1 81 Pasadena two 2
33 CDC Sisler six 3 82 Price -- 6
34 CDC Stratus two 1 83 Radiant -- 4
35 Charles two 1 84 Rawson (ND19119-2) two 1
36 CIho 4196 two 2 85 Robust six 3
37 Collins two 2 86 Scarlett two 2
38 Conlon two 1 87 Shenmai 3 -- 2
39 Conrad two 2 88 Stander six 3
40 Craft two 1 89 Stellar six 3
41 Crest two 2 90 Strider -- 6
42 Dicktoo -- 6 91 Sublette two 1
43 Doyce -- 6 92 Sussex -- 6
44 Drummond six 3 93 Thoroughbred -- 6
45 Eslick -- 4 94 TR306 two 1
46 Excel six 3 95 Tradition six 3
47 Farmington two 2 96 WA1614-95 -- 6
48 FEG55-14 six 3 97 Washford -- 5
49 FEG59-09 six 3 98 Wysor -- 6



View Full Table | Close Full ViewTable 2.

ANOVA and mean percentages of markers selected as tags using Haploview's greedy method for two- and six-row subpopulations, reference panel sizes of 100 or 200 inbreds, and minimum tag selection r2 of 0.4, 0.6, and 0.8.

 
Percentage markers used as tags
Source df Mean Square
Subpopulation (S) 1 0.202
Ref. Panel Size (P) 1 0.002
Min. Tag. Sel. r2 (R) 2 0.210
S x P 1 0.000
S x R 2 0.002
P x R 2 0.000
S x P x R 2 0.000
Means by subpopulation and minimum tag selection r2 [%]
r2 = 0.4 r2 = 0.6 r2 = 0.8
Two-row 24.5 34.6 45.9
Six-row 17.1 23.6 32.7
***Significant at the 0.001 probability level.



View Full Table | Close Full ViewTable 3.

ANOVA and mean percentages of markers imputed with a prediction r2 greater than 0.5 and 0.8. Analyses were fastPHASE imputations on tag SNP (fP/tag) or on randomly selected SNP (fP/rand), and Haploview proxy test predictions on tag SNP (HV/tag).

 
Percentage markers with
Prediction r2 ≥ 0.5 Prediction r2 ≥ 0.8
Source df Mean square Mean square
Subpopulation (S) 1 0.001 0.038 *
Ref. Panel Size (P) 1 0.085 0.114
Analysis (A) 2 5.104 7.701
S x P 1 0.007 0.000
S x A 2 0.238 0.172
P x A 2 0.004 0.035 **
S x P x A 2 0.017 0.008
Means by subpopulation and analysis [%]
fP/tag fP/rand HV/tag fP/tag fP/rand HV/tag
Two-row 98.5 90.3 71.7 81.1 65.9 31.2
Six-row 97.8 85.6 79.3 77.9 66.0 40.4
***Significant at the 0.001 probability level.