V. 3. Problems in linkage mapping in barley. (1)
T. Tsuchiya, Department of Agronomy, Colorado State University, Fort Collins, Colorado 80523. U. S. A.
(1) Supported by USDA/SEA Competitive Research Grant No. 82-CRCR-1-1020, USDA/SEA-CSU Cooperative Research Grant No. 58-9AHZ-2-.65.
Ever since the Barley Genetics Newsletter was initiated, I have been preparing linkage maps of barley each year. In 1973 the method of preparing maps (Tsuchiya, 1973) was changed based on the information on the centromere positions in genetic linkage maps obtained from telotrisomic analysis (Tsuchiya, 1972; Tsuchiya and Singh, 1973). Because the centromere positions were located in the linkage maps for 5 chromosomes (chromosome 1 through 5) it became necessary to change the method of preparing the maps. Only genes associated with a chromosome arm were mapped and others were listed as associated with chromosomes. Some genes associated with a chromosome arm have not been located in the map because of lack of sufficient information.
Some researchers have criticized my way of presenting linkage maps in the Barley Genetics Newsletter. Recently Bodil Søgaard wrote a letter to me and told me I should place all genes in linkage maps (see V. 2. P. 84). Linkage mapping is a complicated matter with various different approaches. Apparently she does not understand various aspects of linkage mapping.
Conventional methods of linkage mapping is one which has been used in barley for many years and contributed greatly for developing and establishing linkage maps in early part of history in linkage mapping (Tsuchiya, 1982, 1983b).
Cytogenetic methods such as translocation analysis and the primary trisomic method were introduced in early 1950 and also greatly contributed in establishing cytogenetic linkage maps (Kramer and Blander, 1961; Tsuchiya, 1961).
Telotrisomic analysis further contributed in improvement of linkage maps in barley by associating many genes with individual chromosome arms and locating centromere positions in the maps (Tsuchiya, 1983b; Tsuchiya and Singh, 1982). Locating centromere positions in linkage maps is one of the most important processes in linkage mapping, since the centromere is the most important marker in the map although this contribution has been ignored by some workers, for example Takahashi and Fukuyama (1977).
Before the centromeres were located in maps, development of linkage maps was based on the results of conventional genetic analysis and translocation analysis by placing the most distal gene in the short arm as the 0 point. However, once the centromere is located, the mapping procedure should be changed to improve the map, although conventional way of mapping should also be continued.
As the overall coordinator for genetic and linkage studies in barley, the major contributor for developing cytogenetic linkage maps, and sole contributor for locating centromere position in genetic linkage maps, the present author believes that the linkage maps published in Barley Gentics Newsletter are meaningful.
When the centromeres are located in the maps, it is difficult to locate
many genes which have no genetic information in relation to the centromere.
If any barley worker believes he/she can provide better maps there
is no rule or regulation to prevent them. If he/she prepared and submitted
maps to BGN, they will be published.
There was a suggestion that I should use maps prepared by Takahashi (1983) for chromosomes 3 and by J. Jensen (1983) for chromosome 5. As I mentioned above it is very difficult sometimes to place all genes studied or reported in BGN or other scientific papers. Therefore, I clearly mentioned in my report on linkage maps (Tsuchiya, 1983a) as follows: "Takahashi (1983) presented a latest linkage map of chromosome 3" (BGN 13:103), "and a detailed linkage map of chromosome 5 is presented by Jensen (1983)" (BGN 13:103).
As many readers have noticed, the map of chromosome 5 (Jensen, 1983) does not have the centromere position and it is difficult for me to deal with that in my map. The case of chromosome 3 is rather different. Takahashi believes that his results obtained mainly from conventional analysis are more reliable than cytogenetic results. As I clearly mentioned in many of my papers, I am aware of the problems in cytogenetic methods, especially trisomic analysis (Tsuchiya, 1983b; Singh and Tsuchiya, 1982; Tsuchiya and Singh, 1982 and others). Takahashi, however does not realize problems in his work. He had never conducted allelism testing until I reported allelic relations between wst and his wst 3, although I believe allelism testing is the first step in genetic studies (Tsuchiya and Haus, 1973). Also he did not accept our results on gene-chromosome arm relations in some cases. In one case of yst-uz linkage he mentioned that his results are in agreement with results of Kasha and Walker (1960). When I re-investigated the results of Kasha and Walker (1960) I found that one allele yst = ys did not segregate in a 3:1 ratio (X23:1 = 6.8547). Naturally the linkage data from that experiment are not reliable. Takahashi did not bother to check that simple aspect.
I emphasize that linkage mapping is a complicated process with many factors involved. Bodil Søgaard said that my linkage maps in 1971 contained several more genes than the recent maps (Søgaard, 1984). In linkage maps it is not "the more the better", in other words quantity or number of genes mapped is not the indication of the quality of the map. I eliminated ddt from the 1983 map for chromosome 7, though ddt was in the map in 1983 (Tsuchiya, 1984).
No method is perfect in linkage mapping. Each method has advantages and disadvantages and need to compensate each other. As a geneticist I am quite aware of the limit of cytogenetic methods as I pointed out on several occasions (Tsuchiya, 1977, 1983b; Singh and Tsuchiya, 1982; Tsuchiya and Singh, 1982). Also I know how we check problems in trisomic analysis (Tsuchiya et al., 1984 and others). Each researcher conducts research in his/her special areas.
I repeat once more that there is no rule or regulation to prevent the preparation of linkage maps and submitting them to BGN. All contributions in barley genetics are welcome in BGN.
References:
Jensen, J. 1983. BGN 13:94-97.
Kasha, K. J. and G. W. R. Walker. 1960. Can J. Genet. Cytol. 2:397-415.
Kramer, H. H. and B. A. S. Blander. 1961. Crop Sci. 1:339-342.
Singh, R. J. and T. Tsuchiya. 1982. Theor. Appl. Genet. 64:13-24.
Sogaard, B. 1984. BGN 14:84
Takahashi, R. 1983. BGN 13:89-93.
Takahashi, R. and T. Fukuyama. 1977. Plant Genetics IV. Morphogenesis and mutations (H. Yamaguchi, ed.):185-198. Shokago Co. Ltd., Tokyo (Japanese).
Tsuchiya, T. 1961. Jap. J. Genet. 36:444-451.
Tsuchiya, T. 1972. BGN 2:93-98.
Tsuchiya, T. 1973. BGN 3:99-103.
Tsuchiya, T. 1977. Plant Genetics IV. Morphogenesis and Mutations. (H. Yamaguchi, ed.):349-361. Shokago Co. Ltd., Tokyo (Japanese).
Tsuchiya, T. 1982. Linkage maps of barley (Hordeum vulgare L.). Genetic Maps 2:394-405.
Tsuchiya, T. 1983a.BGN 13:101-106.
Tsuchiya, T. 1983b. Cytogenetics of Crop Plants (M.S. Swaminathan, P. K. Gupta, U. Sinha, (eds.):251-281, MacMillan, India.
Tsuchiya, T. 1984. BGN 14:81-84.
Tsuchiya, T. and T. E. Haus. 1973. J. Hered. 64:282-284.
Tsuchiya, T. and R. J. Singh. 1973. BGN 3:75-78.
Tsuchiya, T. and R. J. Singh. 1982. Theor. App1. Genet. 61:201-208.
Tsuchiya, T., R. J. Singh, A. Shahla, A. Hang. (1984) Theor. Appl. Genet. (In press).