45. Morphological and RFLP markers are associated in rice

Z.H. Yu1, T. KINOSHITA2, S. SAT03 and S.D. TANKSLEY1

1) Department of Plant Breeding and Biometry, Cornell University, 252 Emerson Hall, Ithaca, NY 14853, U.S.A.

2) Faculy of Agriculture, Hokkaido University, Sapporo, 060 Japan

3) Faculty of Agriculture, University of Ryukyus, Okinawa, 903 Japan

We have recently associated several morphological and RFLP (restriction fragment length polymorphism) markers in rice. The purpose of this report is to provide rice geneticists and breeders with brief information on this research.

The objective of the project was to investigate linkage relationships between morphological and RFLP markers. The materials used in the research were four F2 populations, derived from crosses between morphological marker stocks, and a set of nearly isogenic lines (NILS) involving individual marker genes. Phenotypic segregation of the observable traits in F2 populations was monitored under the greenhouse conditions during different growth stages. RFLP analysis of all rice materials was performed as described in the paper. As results from the research, chromosomes 1, 2, 3, 4, 5, 6, 7, 9, 10, and 11 were either confirmed by F2 linkag e analysis or tested by NIL positive analysis. Seven morphological marker genes are linked to the RFLP markers using F2 cosegregation analysis (Fig. 1). Among five genes located on the rice chromosomes are: Purple hull (Pr) (16.8+/-7.9 cM away from RG163 on chromosome 4); Phenol staining (Ph) (20.8+/- 8.4 cM apart from RG163 on chromosome 4); glabrous leaf and hull (gl- 1) (14.3+/-7.4 cM from RG182, and 20.9+/-8.3 cM from RG403 on chromosome 5); Brown pericarp (Rc) (12.5+/- 7.2 cM from RG30 on chromosome 7); and lazy growth habit (la) (28.8+/- 9.4 cM from RG118 on chromosome 11). Two other genes, Purple node


Fig. 1. Linkage analysis of F2 cosegregation between RFLP markers and morphological genes. This filter was prepared by digesting with HindIII DNA from 37 F2 individuals of the second cross (83N1059xA-5) segregating for Brown pericarp (Rc) and other genes. Since Rc is a dominant gene, it is not possible to distiguish the homozygous and heterozygous dominants. These two types of individuals were thus combined as '5'. Three individuals with 'O' were dead after heading when phenotypic observations were performed. The distance between Rc and RG30 was estimated to be 12.5+/-7.2cM. Genotype: 1= dominant/dominant; 2=dominant/recessive; 3=recessive/recessive; 5=either 1 or 2. 

Table 1.  RFLP markers putatively associated with morphological genes,
detected via NIL analysis
==============================================================================
Gene       Donor   RFLP marker putatively  Restriction
(chrm)a    parent  positive (chrm)b        enzyme
==============================================================================
sd-1(1)     TN1     RG780(1)                EcoRi
                    RG220(1)                XbaI
                    CDO962(1)               EcoRV
                    CDO251(1)               EcoRI
                    RZ382(1)                ScaI
                    RZ276(1)                HindIII
d-10(1)     N-70    RG462(1)                EcoRI
                    RG350(1)                EcoRI
lax(1)      Fl-7    CDO251(1)               EcoRI
d-5(2)      H-2     RG256(2)                EcoRI
d-30(2)     Fl-3    RG256(2)                EcoRI
Hg(3)       H-126   RG348(3)                EcoRV
d-11(4)     M-17    CDO456                  EcoRV
Cl(6)       H-339   RG172(6)                EcoRV
Dn-1(9)     H-137   RG553(9)                EcoRI
pgl(10)     H0775   RG257(10)               ScaI
                    RG134(10)               XbaI
Rf-1(10)    I-129   RG134(10)               TagI
                    RG561(10)               EcoRI
                    CDO94(10)               ScaI
                    CDO250(10)              ScaI
                    RZ17(10)                PstI
d-27(11)    FI-86   RZ141(11)               DraI
===============================================================================
Note: Chromosome number assigned on the classical map (a), and the RFLP map
(b), of rice, respectively.
(Pn) on chromosome 1 and Aiviied panicle (An-4) on chromosome 8 classically, are loosely linked (over 30 cM) to the RFLP markers on chromosome 5. These loose linkages await further testing with more markers on both chromosomes. In addition, DNA clones, putatively associated with a dozen other different morphological markers, including the agronomically important genes, semi-dwarf (sd-1) and Pollen restoring gene (Rf-1), were identified through screening pairs of rice nearly isogenic lines (NILS) (Table 1).

The research reported here represents a first attempt to associate and eventually integrate two genetic linkage maps of rice. The current classical map of rice consists of 164 morphological markers, including isozyme markers and a number of agronomically important genes (Kinoshita 1990). The current molecular map of rice consists of about 600 RFLP markers, also including isozyme markers and a few agronomically important genes. Further studies should provide additional data required to allow the ultimate fusion of the two maps.

References

Kinoshita, T. 1990. Report of the committee on gene symbolization, nomenclature and linkage groups. RGN 7: 16-57.