GrainGenes
A Database for Triticeae and Avena
Integrating Barley RFLP and Classical Marker Maps.
A. Kleinhofs
Department of Crop and Soil Sciences, Washington State University,
Pullman, WA 99164-6420, USA
Barley RFLP maps are now extensive and numerous. Most maps have a reasonable number of common markers allowing investigators to approximately locate the region of their interest. Unfortunately the morphological and physiological traits need to be better mapped. I will summarize the published information about the location of some classical loci with respect to the Steptoe x Morex (SM) skeletal RFLP map and report our preliminary results from mapping classical and RFLP markers using bulked segregant analysis (BSA) (6). Approximate locations of the classical markers with respect to the RFLP markers are presented in Fig.1 (Click here to view)on the left side of each chromosome. The loci mapped in SM are shown on the right side of the chromosome. Up to date information about the RFLP and morphological marker maps may be found in the GrainGenes database. The morphological and physiological traits positioned on the SM map are listed in Table 1. I used the current (old) nomenclature throughout this manuscript to avoid confusion. The isozyme and disease resistance loci will not be considered in this report.
Chromosome 1 (7H).
The loci br1, wx, cer-ze (gl5), nar3, f4, pmr, msg10, and Xa were associated with RFLP markers using BSA (Fig.1). The brachytic 1 (br1) trait provides an excellent marker for the most distal region of 1P with very close linkage to ABG704. The locus designated Glx or Wx is identified by the RFLP probe pcWx27 encoding starch synthase (EC 2.4.1.11) (12). This locus is almost certainly the same as the waxy endosperm (high amylopectin endosperm) locus wx (glx) as indicated by its map position and the very close linkage to the pcWx27 RFLP marker in our BSA studies. The gl5 (cer-ze) locus maps just proximal to wx and provides another excellent marker for this region. The nitrate reductase deficient molybdenum cofactor mutant nar3 and the pale green mutant pmr have not been previously mapped. The f4 and msg10 loci are positioned by BSA from n towards the distal ends of 1P and 1M, respectively, as indicated in Fig.1. This is opposite to what is indicated in the most recent morphological map from Franckowiak (personal commun.). The position of these loci need further confirmation. The xantha seedling trait Xa provides the most distal marker on 1M that has been positioned with respect to RFLP markers. However, both the RFLP and morphological marker maps extend ca. 40 cM beyond this locus.
The naked caryopsis locus n was mapped by Heun et al. in Proctor x Nudinka 2.9 cM down from Xcnl.CDO673 and cosegregating with Xcsu.BG143 (Heun et al. nomenclature, these markers are designated CDO673 and BG143 on most barley RFLP maps) (3). The marker CDO673 is mapped in SM very close to the centromere and 3.5 cM up from Amy2. Thus the n locus can be considered to approximate the barley chr. 1 (7H) centromere. The n locus was also mapped 29 cM down from MWG003 (13). This distance is ca. 15 cM in the SM map.
The low PI alpha amylase locus Amy2 was mapped in SM with the plasmid JR032 (4). It is located just distal to the centromere.
The lk2 locus was mapped 8.5 cM distal to the n locus (13).
Chromosome 2 (2H).
The two vs. six-rowed spike trait V locus has been mapped in the Igri x Franka (2) and Harrington x Morex (NABGMP, unpublished) populations. It is positioned on the SM map ca. 8 cM proximal to MWG503 based on common RFLP markers. This places it close to the centromere, but clearly on the 2M arm.
The loci msg2, yst4, Az94, fol-a, f-sh, nar4, nar6, Az86, R11301, and gp were associated with chromosome 2 markers by BSA (Fig.1). The nar4, nar6, Az86, and R11301 mutants are nitrate reductase deficient affecting molybdenum cofactor functions. They are tightly linked and may represent a single complex locus.
The msg2, fol-a, and gp loci as mapped by BSA appear to reside in similar positions as on the morphological map. Thus they, along with V, provide good references for merging the RFLP and morphological maps. The yst4 and f-sh (chlorina sh, Franckowiak, personal commun.) are not on the morphological map.
The Bmy2 locus was located in the SM RFLP map with a 0.8kb AccI fragment from the beta-amylase plasmid pcbC51 (5).
Schondelmaier et al. (13) mapped gs6 (cer-c), e, li, and wst,,k on chromosome 2 with respect to RFLP markers. Although common markers with SM are few, these loci have been approximately positioned on the SM map as shown, via the Igri x Franka map.
A photoperiod gene designated Ppd-H1, has been mapped just proximal to MWG858 (9).
Chromosome 3 (3H).
The pubescent leaf blade trait pub was mapped in the SM population 1 cM proximal to ABG389.
The loci msg5, yst2, and wst1 were associated with chromosome 3 markers using BSA (Fig.1). The msg5 and yst2 positions are inverted with respect to the morphological marker map. As noted previously, our BSA mapping data is preliminary and needs to be confirmed.
Schondelmaier et al. (13) mapped al and als with respect to RFLP markers. Unfortunately very few markers used are in common with either the SM or IF maps, thus positioning of these loci is very approximate.
The denso dwarfing gene has been mapped 12 cM proximal to WG110 (1) which is just proximal to Pub on the SM map, thus positioning this trait fairly accurately.
Chromosome 4 (4H).
The loci f9, gl4, br2, gl, and msg24 were associated with specific RFLP markers by BSA (Fig.1).
The Bmy1 locus was mapped in the SM population with a 0.8kb AccI fragment from the beta-amylase plasmid pcbC51 (5).
Schondelmaier et al. (13) mapped gl, ert-i, and yh with respect to RFLP markers. The location of gl was reported to be 13 cM distal of MWG058 and agrees very well with our positioning of this locus. The ert-i locus was reported to be 18.5 cM distal of gl. The yh locus position is very approximate due to lack of common RFLP markers, but clearly close to the end of 4M.
The vernalization response gene Sh has been shown to be associated with the Bmy1 locus (10).
Chromosome 5 (1H).
The loci msg1 and f7 were associated with the indicated RFLP markers by BSA (Fig.1). The msg1 locus appears to be very tightly linked to ABG452 which marks the approximate location of the centromere on the SM map. The f7 locus appears to be close to the end of 5M and in agreement with the Franckowiak (GrainGenes) and Jensen (BGN 25:96-99) maps.
The Hor5, Hor2 and Hor1 loci were mapped with the phorg-1, pb11 and pcP387 plasmids, respectively. These loci are also on the Jensen merged map and can be used to align with the RFLP maps.
The 1,3-1,4-B-glucanase locus Glb1 was mapped in SM with the plasmid pHGHN29A (11). Its location 9 cM proximal of ABC160 places it close to the centromere and in good agreement with the Jensen merged map.
A photoperiod response gene Ppd-H2 has been reported on 5M (10 ). Due to few common RFLP markers, this locus position on the SM map is very approximate.
The high amylose gene amo1 has been mapped (14). This locus can only be approximated on the SM map due to few common RFLP markers.
Chromosome 6 (6H).
The loci nar1, nar8, o, and sex1 were associated with specific RFLP markers by BSA (Fig.1). The nar1 locus, represented by the mutant Az12, was tightly linked to the Nar1 RFLP marker bNRp30, a cDNA clone of the barley NADH nitrate reductase. It is most likely that these are the same locus. The barley NAD(P)H nitrate reductase locus Nar7 was mapped in the SM population with a 0.44kb SphI and SacII fragment from pMJ4.1. This is most likely the same locus as detected by the mutant nar7 (15). The loci o and sex1 are very closely associated with the RFLP marker ABG474 marking the centromere location in the SM map. This is in accordance with published morphological maps.
The high PI alpha amylase locus Amy1 was mapped with the plasmid JR115 (4). The nitrate reductase locus Nir1 cosegregates with Amy1 and was mapped with the maize nitrite reductase structural gene plasmid pCIB808 (7).
Chromosome 7 (5H).
The loci cer-zp, cud, cer-zj, nar2, nar5, f6, mt2, and va1 were associated with specific RFLP markers by BSA (Fig.1). The location of cer-zp, cer-zj, cud, f6, and mt2 on the RFLP map seems to be at odds with the Franckowiak morphological map. Further work is required to clarify this situation.
The rachilla hair length locus s was mapped in the SM population.
The rough awn trait r was mapped in the Harrington x Morex population and positioned on the SM map by linkage to the common RFLP marker ABC717.
The lax-a homeotic mutant, with flowers in which lodicules are replaced by stamens giving five stamens per flower and an associated lax head phenotype, has been mapped to the centromeric portion of chromosome 7 by close linkage to the RFLP marker CDO749 (8) which is just distal to the ribosomal RNA locus Rrn2.
The vernalization locus Sh2 has been mapped close to WG644 (10 ) which is just proximal to ABG712 in the SM map, thus positioning this locus quite accurately.
Theoretically it should be possible to place many other morphological gene loci on the RFLP map based on their linkage to those presented here. However, before a complete merging of the classical and RFLP maps is attempted, the location of some of the important anchor loci must be carefully established. There are some disagreements between the maps presented here and those of Franckowiak. This map is intended to identify regions with problems so that they can be resolved in the future.
References:
1. Barua, U.M., K.J. Chalmers, W.T.B. Thomas, C.A. Hackett, V. Lea, P. Jack, B. P. Forster, R. Waugh, and W. Powell. 1993. Molecular mapping of genes determining height, time to heading, and growth habit in barley (Hordeum vulgare). Genome 36: 1080-1087.
2. Graner, A., A. Jahoor, J. Schondelmaier, H. Siedler, K. Pillen, G. Fischbeck, G. Wenzel, and R.G. Herrmann. 1991. Construction of an RFLP map of barley. Theor. Appl. Genet. 83: 250-256.
3. Heun, M., A.E. Kennedy, J.A. Anderson, N.L.V. Lapitan, M.E. Sorrells, and S.D. Tanksley. 1991. Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare ). Genome 34: 437-447.
4. Khursheed, B., and J.C. Rogers. 1988. Barley a-amylase genes. Quantitative comparison of steady-state mRNA levels from individual members of the two different families expressed in aleurone cells. J. Biol. Chem. 263: 18953-18960.
5. Kreis, M., M. Williamson, B. Buxton, J. Pywell, J. Hejgaard, and I. Svendsen. 1987. Primary structure and differential expression of B-amylase in normal and mutant barleys. Eur. J. Biochem. 169: 517-525.
6. Kudrna, D., A. Kleinhofs, A. Kilian, and J. Soule. 1996. Integrating visual markers with the Steptoe x Morex RFLP map. In: A. Slinkard, G. Scoles, and B. Rossnagel (eds.) V International Oat Conference & VII International Barley Genetics Symposium., pp. 343. University Extension Press, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
7. Lahners, K., V. Kramer, E. Back, L. Privalle, and S. Rothstein. 1988. Molecular cloning of complementary DNA encoding maize nitrite reductase. Plant Physiol. 88: 741-746.
8. Laurie, D.A., N. Pratchett, R.L. Allen, and S.S. Hantke. 1996. RFLP mapping of the barley homeotic mutant lax-a. Theor. Appl. Genet. 93: 81-85.
9. Laurie, D.A., N. Pratchett, J.H. Bezant, and J.W. Snape. 1994. Genetic analysis of a photoperiod response gene on the short arm of chromosome 2 (2H) of Hordeum vulgare (barley). Heredity 72: 619-627.
10. Laurie, D.A., N. Pratchett, J.H. Bezant, and J.W. Snape. 1995. RFLP mapping of five major genes and eight quantitative trait loci controlling flowering time in a winter x spring barley (Hordeum vulgare L.) cross. Genome 38: 575-585.
11. Litts, J.C., C.R. Simmons, E.E. Karrer, N. Huang, and R.L. Rodriguez. 1990. The isolation and characterization of a barley 1,3-1,4-B-glucanase gene. Eur. J. Biochem. 194: 831-838.
12. Rohde, W., D. Becker, and F. Salamini. 1988. Structural analysis of the waxy locus from Hordeum vulgare. Nucleic Acids Research 16: 7185-7186.
13. Schondelmaier, J., G. Fischbeck, and A. Jahoor. 1992. Linkage studies between morphological and RFLP markers in the barley genome. Barley Genetics Newsletter 22: 57-62.
14. Schondelmaier, J., A. Jacobi, G. Fischbeck, A. Jahoor. 1992. Genetical studies on the mode of inheritance and localization of the amo1 (high amylose) gene in barley. Plant Breeding 109: 274-280.
15. Warner, R.L., D.A. Kudrna, and A. Kleinhofs. 1995. Association of the NAD(P)H-bispecific nitrate reductase structural gene with the Nar7 locus in barley. Genome 38: 743-746.
Table 1. Morphological and physiological markers positioned on the SM RFLP map.
| Gene |
Phenotype |
RFLP Mapping Reference |
|---|---|---|
| Chromosome 1 (7H) |
||
| br1 |
Brachytic |
Kudrna et al. 1996 |
| wx |
Waxy endosperm |
" |
| gl5 (cer-ze) |
Glossy leaf (Eceriferum) |
" |
| nar3 |
Nitrate reductase-deficient (MoCo) |
" |
| f4 |
Chlorina seedling |
" |
| pmr |
Pale green seedling |
" |
| n |
Naked caryopsis |
Heun et al. 1991 |
| lk2 |
Short awn |
Schonde maier et al. 1992 |
| msg10 |
Male sterile genetic |
Kudrna et al. 1996 |
| Xa |
Xantha seedling |
" |
| Chromosome 2 (2H) |
||
| gs6 (cer-c) |
Glossy sheath (Eceriferum) |
Schondelmaier et al. 1992 |
| msg2 |
Male sterile genetic |
Kudrna et al. 1996 |
| Ppd-H1 |
Photoperiod response |
Laurie et al. 1994 |
| yst4 |
Yellow streak |
Kudrna et al. 1996 |
| Az94 |
Nitrate reductase-deficient (MoCo) |
" |
| e |
Elongated outer glume |
Schondelmaier et al. 1992 |
| V |
Two/six-row spike |
Graner et al. 1991 |
| fol-a |
Angustifolium |
Kudrna et al. 1996 |
| f-sh |
Clorina seedling |
" |
| li |
Liguleless |
Schondelmaier et al. 1992 |
| nar4 |
Nitrate reductase-deficient (MoCo) |
Kudrna et al. 1996 |
| wst,,k |
White streak |
Schondelmaier et al. 1992 |
| gp |
Grandpa |
Kudrna et al. 1996 |
| Chromosome 3 (3H) |
||
| al |
Albino lemma |
Schondelmaier et al. 1992 |
| msg5 |
Male sterile genetic |
Kudrna et al. 1996 |
| yst2 |
Yellow streak |
" |
| wst |
White streak |
" |
| als |
Absent lower laterals |
Schondelma ier et al.. 1992 |
| denso |
Semidwarf |
Laurie et al. 1995 |
| pub |
Pubescent leaf blade |
Kleinhofs et al. 1993 |
| Chromosome 4 (4H) | ||
| f9 |
Chlorina seedling |
Kudrna et al. 1996 |
| gl4 |
Glossy leaf |
" |
| br2 |
Brachytic |
" |
| gl |
Glossy leaf |
" |
| msg24 |
Male sterile genetic |
" |
| ert-i |
Erectoides |
Schondelmaier et al. 1992 |
| yh |
Yellow head |
" |
| Sh |
Vernalization response |
Laurie et al. 1995 |
| Chromosome 5 (1H) |
||
| amo1 |
High amylose |
Schondelmaier et al. 1992 |
| msg1 |
Male sterile genetic |
Kudrna et al. 1996 |
| Ppd-H2 |
Photoperiod response |
Laurie et al. 1995 |
| f7 |
Chlorina seedling |
Kudrna et al. 1996 |
| Chromosome 6 (6H) |
||
| nar1 |
NADH nitrate reductase-deficient |
Kudrna et al. 1996 |
| nar8 |
Nitrate reductase-deficient (MoCo) |
" |
| o |
Orange lemma |
" |
| sex1 |
Shrunken endosperm xenia |
" |
| Chromosome 7 (5H) |
||
| cer-zp |
Eceriferum |
Kudrna et al. 1996 |
| cud |
Curly dwarf |
" |
| cer-zj |
Eceriferum |
" |
| lax-a |
Laxatum (five anthers) |
Laurie et al. 1996 |
| nar2 |
Nitrate reductase-deficient (MoCo) |
Kudrna et al. 1996 |
| nar5 |
Nitrate reductase-deficient (MoCo) |
" |
| f6 |
Chlorina seedling |
" |
| s |
Short rachilla hair |
Kleinhofs et al. 1993 |
| mt2 |
Mottled leaf |
Kudrna et al. 1996 |
| va1 |
Variegated |
" |
| r |
Rough awn |
Kleinhofs (unpublished) |
| Sh2 |
Vernalization response |
Laurie et al. 1995 |