As data on the specific allele present at each locus accumulate, the intercultivar chromosome crossover points can be localized in each line. Data for the 150 lines in each population are used to generate molecular maps for that population. Since linkage distances are calculated as the percentage of the 150 lines having a crossover between any two markers, only certain lines contribute the linkage estimate for adjacent markers. As the maps become more saturated with markers, only one or two lines will have a crossover point between adjacent markers. If a new marker is mapped to a given interval, only those lines having a crossover in that interval contribute information about its position.
If the cost of classifying a line for a specific trait is high, minimizing the number of lines tested is desirable. Testing of only those lines having a crossover event in the critical interval is necessary to map the new locus within that interval. However, finding the critical interval is more difficult. The crossover sites in each Steptoe X Morex and Harrington X TR306 doubled haploid line have been localized to specific intervals. If each chromosome is subdivided into a limited number of intervals (segments), mapping a new gene to a specific segment is possible using a selected subset from the 150 lines. The subsets from each mapping population can be selected to maximize the distribution of crossover points. After a new locus is mapped to a specific segment, localization within the segment can be accomplished by evaluating only lines having an exchange point in that segment.
We have chosen 15 lines as adequate subset size. A larger number would defeat the purpose of the exercise, while a smaller number would increase the probability that more than one segment is identified as the critical one. The lines chosen from the Steptoe X Morex and Harrington X TR306 populations for the subsets were selected based on visual examination of the molecular marker data. Those lines having at least one exchange point in each chromosome were identified. The 15 lines that tended to maximize the distribution of crossover points in each chromosome were chosen for inclusion in the subset. Information on the parent of origin for each chromosome segment in the selected lines in the Steptoe X Morex and Harrington X TR306 subsets are presented in Tables 1 and 2, respectively. Selection of chromosome markers and interval size were based on the molecular data available as of January, 1995.
To evaluate the effectiveness of these subsets, we selected randomly amplified polymorphic DNA (RAPD) 10-mer primers that produced few bands and were polymorphic among the parental cultivars. Using standard RAPD techniques (Williams et al., 1990), data were generated for the 15 line subset from the Steptoe X Morex population. The data obtained were organized in Table 3 in the same sequence as the selected lines in Table 1. The map position for the RAPD marker OPD01 was identified as the centromeric region of chromosome 5. Matching the data for any new marker to a specific sequence in Table 1 or Table 2 should map that marker a specific interval in the barley genome.
¹This research was partially support by an International Atomic Energy Agency (IAEA) Fellowship awarded to the senior author.
References
Kasha, K., A. Kleinhofs, and the NABGMP. 1994. Mapping of the barley cross Harringron X TR306. BGN 23:65-69.
Kleinhofs, A., A. Kilian, and the NABGMP. 1994. The NABGMP Steptoe X Morex mapping progress report. BGN 23:79-83.
Williams, J.G.K., A.R. Kubelik, K.J. Livak, J.A. Rafalski, and S.V. Tingey. 1990. DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic Acid Res. 18:6531-6535.
Table 1. Chromosome region configurations by origin for selected doubled haploid lines from the Steptoe X Morex cross in barley.
__________________________________________________________________________
Marker locus Doubled haploid line*
SM number 007 031 041 045 065 074 126 144 150 164 165 179 182 184 200
Consecutive number 7 24 29 33 47 55 86 102 107 120 121 133 136 138 150
__________________________________________________________________________
Chromosome 1 SM
Plc A** A A A B A A A B A B B B A B
ABG077 A A A A B A A A B A B A B A B
BCD129 A A A A B A A A B B B A B B B
ABG320 A A A A B A A A B B B A B B B
iEst5 A B - A B A A A B B B A B B B
ABC169A B B A A B A A A B B B A B B B
ABG380 B B B A B A B A B B B A B B B
ABC154A B B B B B B B A B B B A B B B
ABC465B B B B B B B B A B B A A B B A
MWG003 B A B - A B B A B A A A A B A
VAtp57A B A A B A B B A A A A A A B A
Ubi1 B A A B B B B A A A A A B A -
RisP103 B A A B B B B A - A B A B A A
ABC305 B A A B B B B A A A B B B A A
ABG461 B B A B B B B A A A B B B B A
WG420 B B A - B B B A A A B B B B B
Cat3 A B A B B B B A A B B B A B B
Chromosome 2 SM
ABG313A A B B B B A B B B A A B A A A
cMWG682 A B B B B A B B B A A B B A A
ABG58 A B B B B A A B B A A B B A A
ABG703B A B B B B B A B B A A B B A A
RbcS A B B B B B A B B A B B B A A
ABC156A A B B B B B A B A A B B B A A
ABG002 B B A A B B A B - A B B B A A
ABG358 B B A A A B A B A A B B B A A
Pox B B A A A B A B A A B B B A A
MWG557 A B A A A B A A A A B B B A ?
CDO537 A A A A A B A A A A B B B A A
WG996 A A A A A B A A A A B B B A B
ABC451 A A A A A B A A A A B B A A B
ABC152D A B A A A B B A A A B B A A B
MWG503 B B A A A B B A A B B A A A B
ABG072 B B B A A B B A A B B A A A B
ABC252 B B A B A B B A A B B A A A B
ABC157 A B A B A B B A A B B A A A B
ABC165 A B A B A B A A A B B A A B B
Pcr1 A A A B A B A A A B B A A B B
cMWG720 A A A B A B A A B B B A A B A
BG123A A A A B A B A A B B B A B B -
ABA005 A A A B A B A A B B B A B B A
Chromosome 3 SM
ABG316A B A B B B B A B B B B A B B A
ABC171 B A B B B B A A B B B A B B A
ABG460 B B B B B B A A - B B A B B A
ABG471 - B B B B B A A B B B A B B B
ABG398 B B B A B A A A B B B A B B B
BCD828 B B B B B A A A B B B A B B B
PSR156 B B B B B A A A B B B B B B B
MWG555B B B B B B B A A B B B B B B B
ABG453 B B B B A B A A B A B B B B B
ABR320 B B B B A B A A B A B B B B -
ABG499 B B A - - B A A A A B B B B B
His4B - - - - A B A - - A B - B A B
ABG004 A A A B A B A B A A B B A A B
ABC174 A A A B B B A B A A B B A A B
ABG495B A A A B - B A B - A A B A A B
ABC172 A A A A B B A B A A A B A A B
Chromosome 4 SM
WG622 A B B A B A A A A B B A B A A
MWG077 A A A B B A A A A B B A B A A
CDO669 A A A B B A A A A B B A B B -
BCD402B - - A B B A A A A B A A B B -
MWG635A A A A B B B A A A B A A B B A
Dhn6 A A A B B B A A A B A A B B B
Adh4 B A A B B B A A A B A A B B B
MWG058 B A A B B B B A A B A A B B B
WG464 B A A B B B B A A B A A B A B
bBE54A A A A B B B B B A B A A B A A
ABG472 A A A B A B B B A B A A B A A
iAco2 B A B B A B A B A A A A B A A
ABG366 B A B B A B A B A A A A A A -
ABG319C B B B B A B A B A A A B B A A
Bmy1 B B B B A B B B A A A B B B -
Chromosome 5 SM
Aga6 - - - B - - B A B B A A A B -
Act8 B B B A B A B A B B A A A B A
Hor1 B B B A B B B A B A A A A B A
BCD098 B B B A B B B A B A A B A B A
ABG053 - B B A B B B - B A B B - B -
Ica1 - B B A A B B A B A B B A B A
ABG500A B A A A A B B A B A B B A B B
ABC160 B A A A A B B A A A B B A A B
ABG464 B A A B A B B A A A B B A A A
ABC307A B B A B B B B B A A B A B A A
cMWG733 B B A A B B B B A A B A B A A
AtpbA A B A A B B B B A A B A B A A
ABC261 A B A A B B A B A A A A B A A
Aga7 A B A A A B A B A A A A B A -
ABG387A A B A B A B A - A A A A B A A
Chromosome 6 SM
PSR167 B A B A A A B - B A B A A B A
Nar1 B A B A A A B A A A B A B B A
MWG652A B B B A A A A A A A B B B B B
PSR106 B B B B A A A A A A B B B B B
PSR167B B B A B A A A A A A A B B B -
WG223B B B A B A A A A A A A B B A B
ABG474 B B B B A A A A A A A B B A B
ABC175 B B B B A A A B A A A B B A B
ABC170B A B B B A A A B A A A B B A B
Nar7 A B B B B - A B A B A B B A B
Amy1 A B B B B B A B A B A B B B -
MWG934 A B B B A B A B B B A B B B B
MWG684C A A B B A B A B B B A B B B B
ABC170A A A B A A B A B B B A B B B B
MWG798A A B A A A B A B B B A B B B A
Chromosome 7 SM
KFP185B B B B B A A A A B B A A B B A
ABC483 B B B B - A A A B B A A A B A
ABG705 B B B B A A A B B A A A A A B
CDO669B - - - - - A B B B A A B? A A B
Dor5 B B B B A A B B B A B A A A B
Ubi2 B B B B A A B B A A B A A A B
Ltp1 A B B B A A B B A A B A A A B
WG530 A A B B A A B B A A B A A A B
WG889 A A A B A A B B A A B A A A B
CDO348B A B A B A A B B A A B A A A B
ABC314 A B A B A A B B A A A A A A B
ABC302 A B A B A A A B A A A A A A B
mSrh A B A A A A B B B A A A A A A
MWG514B A B A B B? B B B B A B B A B A
ABG712 A B A B A B B A B A B B A B A
WG908 A B A B B B B A B A B B A B A
Cab1 A B B B B B B A B A B B B B -
ABC482 A B B B B B B A B A B B B A A
ABG391 A B B B B B B B B A B B B A A
ABG463 B B B B B B A B B A B B B A A
ABC309 B B B B B A A B A A B B B A -
MWG851C B B B B B A A B A A B B A A A
ABA304 B B B B A A A B A A B B A A A
__________________________________________________________________________
* The 150 doubled haploid lines used in the mapping population are identified
by a noncontinuous series of numbers between SM001 and SM200. Here, we also
indicate a "consecutive number" for each line to indicate its position in the
series of
lines. For example, SM031 is the 24th line in the population. In market
datasets such as those posted on Graingenes, the data for SM031 is in the 24th
position in the dataset.** Steptoe has the A allele at each locus and Morex has the B allele.
Table 2. Chromosome region configuation by origin for selected doubled haploid lines from the Harrington X TR306 cross in barley.
__________________________________________________________________________
Marker locus Doubled haploid line*
HT number 043 053 069 081 095 117 118 127 136 161 166 186 802 829 835
Consecutive number 16 23 35 42 53 67 68 74 80 101 106 121 137 146 147
__________________________________________________________________________
Chromosome 1 HT
Plc A** B B A B A B B A A A B B B A
BCD129 A B - A B A B B B A A B B B A
iEst5 A A B A B A B B B A A B B B A
ABG380 A A - A B A B A B B A A B B B
MWG836 B A A A B B B A B B A A B B B
Brz B A A B B B B A B B A A B B B
MWG003 B B A B A B B A A A A B B B B
MWG511 B A A B A A B A B A A B B B B
VAtp57A B A B B A A - A A A A B B B B
MWG571D B A A A A A B A A A A A B B B
MWG889 B A A A A A B A B A B A A B B
ABC310B B A A A A A A B B A B A A B B
ABC305 B A A A A A A B B A B A A A B
ABG461 B A A A A A A B B B B A A A B
WG380A B A A A A A A B B B B A A A A
MWG635B A A A B A A A B B B A A A B A
Chromosome 2 HT
MWG844 A A A A B A A B B A A A A A A
cMWG682 B B B B B B A B B A A - A B A
MWG684 B B - B B B A B B A A B A B A
MWG655B A B B B B B A B B A A B A A A
MWG520 A A B A B B A A A A B - B A A
Pox A A B A B A - A A A B B B A A
MWG557 A A B A A A A A A B B B B B B
MWG865 A A B A B A A A B B B B B B B
MWG503 A A B A B A A A B B - B B B B
MWG882 A B - A B A A A B B B B B A A
ABC252 B B B B B B B B B B B A B A A
ABC165 B B B B B B B A B B B A B A A
ABG609A B B B B B B B A B B B A A A A
ABG613 B B B B B B B A B B A A B A A
cMWG720 B B B B B B B A B B A A B B A
Chromosome 3 HT
ABC171 A A A B A A A A B A B A A B A
CDO395 A A - B A A A A A A B - A B A
ABG471 A B A B A A A A A A B A B B A
Ugp2 A B A B A A A A A B B A B B A
Ugp1 - - - B - A - A A B A - B B A
MWG847 B A A A B B A A - A A B A A A
ABC174 B A A A B B B B A B B B B A B
ABG709 A A A B B B B B A B B B B A B
ABG710A A A B B B B B B A B B B B A B
Prx1B A A B B B B A B A B B B B A B
WG222 A A - B B A A B B B A B B A B
iEstY A A B B B A A B B B A B B B B
ABC172 A A B B B A A B B B A A B B B
Chromosome 4 HT
WG622 B A A B A B A A B A B - A B B
ABG714 B A B B A B B A B A A - A B B
CDO669 B A B B A B B A A A A A A B B
MWG716 - A B B B B B A A A A A A B B
CDO650 B B - B B B B B A A A A A B B
dMlg B B B B B B B B A A A A A B A
ABG715 B B B B B B B A A A A - A B A
ABG472 B A B A B B B A A B A - B B A
ABG618 B A B A B A B A A B A A B B A
ABG366 A A A A B A B A A B B - B A A
ABG601 A A A A B A B A B B B A A A A
Chromosome 5 HT
Act8A B A A B A B A A A B A B B B B
OPO6 B A B B A B A A B B A B B B B
aHor2 B A A B A A A A B B A B B B B
MWG943 A A A B B A A B B B A A A B B
ABG464 A A A B B A B B B A A - A A B
AtpbA A A A A B B B B B A A A A A A
ABC261 A A B A B B A B B A B A A A A
ABG710B A B B A B B A B A A B - A A B
Aga7 A B B A B B A A A A B A A A B
MWG912 A B B A B A A A A A B A A B B
Chromosome 6 HT
PSR167 A B A B B B B A B A A B A B B
Nar1 B B A B B B B A B A A B A B B
MWG652A B B A B B A B A B A A B A B B
PSR106 B B A B B A A A A A B B A A B
MWG2065 B B A B A A A A A A B - A A B
MWG916 B B A B A A A A A A A B A A B
WG223 B B - A A A A A A B B B A B B
ABC175 B B A B A A A A A B B B A B B
vvAmy1 B A A B A A - A A B B - A B B
ABG614 B A - B A A A B A A B B A B B
ABG711 B A A A A A A B A A B - A B B
MWG934 B A A A B A A B A A B B A B B
MWG658 - A - B B A A B B A A B A B B
MWG798A A A A B A A B B B B A B A B B
Chromosome 7 HT
MWG502 B A B A B A B B A B B B A A A
ABC483 B A B A B A B B A A B - A B A
ABG705A B A A A B B A B A A B A B B A
Dor5 B A A A A B A B A A B A B B A
CDO348 B A - A B B A - A A B A B B A
MWG522 A A A A B B B B A B B B B A A
mSrh A A A A B B B B A B B B B A B
WG364 A B A A B B B B A B B B B A B
MWG914 A B B A B B B B A B B A A A B
MWG781 A B - A B B B B A B B A A A A
ABG702B B B B A B B B B A B B A A A A
ABG712 B B B A B A B B A A B - A A A
MWG740 B B B A B A A B A B B A A B A
ABC622 A B B B B A B A B B A A A B B
ABG463 A B B B B A B A B B A - B B B
MWG602 B B B B B A B A B B A A B B B
__________________________________________________________________________
* The 150 doubled haploid lines used in the mapping population are identified
by a noncontinuous series of numbers between HT003 and HT840. Here, we also
indicate a "consecutive number" for each line to indicate its position in the series of
lines. For example, HT043 is the 16th line in the population. In market
datasets such as those posted on Graingenes, the data for HT043 is in the 16th position in the dataset.** Harrington has the A allele at each locus and TR306 has the B allele.
Table 3. Data on the allele present for a RAPD marker in selected lines
from the Steptoe X Morex population of doubled haploid barley lines.
______________________________________________________________________________ Doubled haploid lines from the SM population Unknown marker SM number 007 031 041 045 065 074 126 144 150 164 165 179 182 184 200 ______________________________________________________________________________ Band pattern* Primer OPD01 B A A A A B B A A A B B A A B** ______________________________________________________________________________* A is the Steptoe and B is the Morex parental pattern of bands in the gels, respectively, for the primer sequence ACC GCG AAG G.
**The locus with a matching sequence of A and B alleles is ABC160 in the centromeric region of chromosome 5 (see Table 1.)