C. Chromosome Numbering System and Linkage Maps

Different systems for numbering chromosomes and linkage groups of rice have been proposed by different workers as shown in Table 1. During the International Rice Genetics Symposium held at IRRI in May 1985, attempts were made to adopt a unified system of numbering the chromosomes and linkage groups. For this purpose, an interim committee consisting of ten members and chaired by Prof. C.M. Rick was appointed. The membership and report of this interim committee follows this note. The consensus of the committee was that chromosomes should be numbered in order according to their pachytene length. Thus the numbering system of Shastry et al. (1960) which has been confirmed by Kurata et al. (1981) was accepted. The linkage groups were associated with respective chromosomes by Khush et al. (1984) and Iwata and Omura (1984) through trisomic tests. However, some discrepancies between these two reports remain. Dr. N. Kurata spent a couple of weeks at IRRI prior to International Rice Genetics Symposium and examined the IRRI trisomic series. Her observations indicated that there were differences in the identification of extra chromosomes of three trisomics. However, there was insufficient time to resolve these differences before the Symposium. It is hoped that Dr. N. Kurata will visit IRRI again in near future to work with Dr. G.S. Khush in resolving these differences. Due to the existing uncertainty in the association of linkage groups with respective chromosomes, the current linkage maps are not presented in this volume but will be reported in volume 3.

Table 1. Relationships among various systems of numbering linkage groups, chromosomes and trisomics.

   Linkage Groups            Chromosomes                     Trisomics
===================    ==========================        ====================
Kinoshita   Misro*     Nishimura  Shastry  Kurata         Khush    Iwata and
                                   et al.  et al.         et al.      Omura
    4         6            7         8       5             2,3          1
I             I            6         3      K6            triplo-3      B
II            II          11        12      K4            triplo-12     E
III           III          3         1      K1            triplo-1      O
IV            IV          10         7      K11           triplo-7      F
VI+IX       VI,XII         2         5      K9            triplo-5      L
V             IX           1         9      K10           triplo-9      H
VII                        1         9      K10           triplo-9      H
VIII         VIII          9        11      K8            triplo-11   G(I.J.&K)
X                          8         2      K2            triplo-2      N
XI            XI           5         4      K3            triplo-4      M
XII                        5         4      K3            triplo-4      M
fgl                        7        10      K12           triplo-10     C
d-33                       4         6      K5            triplo-6      A
su                        14         8      K7            triplo-8      D
*Groups VI, VII, and X were not correlated with Kinoshita's groups.


1. Iwata, N. and T. Omura 1984. Studies on the trisomics in rice plant (Oryza sativa L.). 6. An accomplishment of a trisomic series in japonica rice plants. Jpn. J. Genet. 59:199-204.

2. Khush, G.S., R.J. Singh, S.C. Sur and A.L. Librojo 1984. Primary trisomics of rice: origin, morphology, cytology, and use in linkage mapping. Genetics. 107(1):141-163.

3. Khush, G.S. and R.J. Singh 1985. Relationships between linkage groups and cytologically identifiable chromosomes of rice. Proceed. International Rice Genetics Symposium. (in print).

4. Kinoshita, T. 1984. Gene analysis and linkage map. p. 187-274. In S. Tsunoda and N. Takahashi, eds. Biology of Rice. Japan Scientific Societies Press, Tokyo.

5. Kurata, N., N. Iwata, and T. Omura 1981. Karyotype analysis in rice. 2. Identification of extra chromosomes in trisomic plants and banding structure on some chromosomes. Jpn. J. Genet. 56(1):41-50.

6. Misro, B. 1981. Linkage studies in rice (Oryza sativa L.). 10.Identification of linkage groups in indica rice. Oryza, Cuttack 18(4):185-195

7. Nishimura, Y. 1961. Studies on the reciprocal translocations in rice and barley (in Japanese with English summary). Bull. Natl. Inst. Agr. Sci. Ser. D9:171-235.

8. Shastry,S.V.S., D.R.R. Rao and R.N. Misra 1960. Pachytene analysis in Oryza. I. Chromosome morphology in Oryza sativa. Indian J. Genet. Plant Breed.20:15- 21.

Report of Interim Committee on Chromosome Numbering to the International Rice Genetics Symposium

May 29, 1985

In order to clarify understanding in rice genetics, a unified system of numbering rice chromosomes needs to be adopted. The chromosomes shall be assigned Arabic numbers in order according to their pachytene length (or centromere position in case of ambiguity of length) based on studies by Dr. S.V.S. Shastry et al. (1960) and confirmed by Dr. N. Kurata et al. (1981). The somatic chromosomes shall be numbered accordingly. Complete primary trisomic series have been established and the extra chromosomes identified in three laboratories but differences exist in identification of extra chromosomes of a few trisomics. These differences should be resolved as soon as possible. In this fashion all linkage groups will be identified with their respective chromosomes.
Committee members:
C. M. Rick, Chairman, G. S. Khush, N. Kurata, H. I. Oka, R. Seetharaman, N. Iwata, T. Kinoshita, R. N. Misra, R. Riley, H. K. Wu.