42. A molecular genetic map of Japonica rice
        Edilberto D. RedoNa and David J. Mackill
        Dept. of Agronomy and Range Science and USDA-ARS, University of California, Davis, CA95616, U.S.A.

    Molecular maps developed from intrasubspecific crosses are useful in plant breeding since genetic recombination is less influenced by distorted segregation and recombination shrinkage that are associated with the use of wider crosses. Although japonica varieties occupy large areas in temperate and tropical countries, crosses within the japonica subspecies have not been used to construct genetic maps due to limited intrasubspecific genetic diversity and the lack of markers that can assay a large number of loci. The development of other marker technologies such as random amplified polymorphic DNAs (RAPDs; Williams et al., 1990), has increased the number of markers suitable for genetic mapping. RAPDs have been used to clalssify japonica cultivars into temperate and tropical groups (Mackill, 1995), indicating their potential utility for map development in japonica rice. This study reports the construction of a molecular linkage map based on a japonica x japonica rice cross. A molecular map was constructed based on 118 F2 plants derived from a cross between Labelle and Italica Livorno, a southern U.S. and Italian cultivar, respectively. Labelle and Italica Livorno are tropical and temperate japonica types, respectively (Mackill, 1995). Of 800 10-mer RAPD primers surveyed, 105 producing dominant RAPDs were assayed on F2 plants. Linkage analysis used Mapmaker (Lander et al., 1987). Eighteen RFLPs were used to anchor and assign RAPDs to chromosomes. Some linkage groups were located in an RFLP map used for QTL analysis (Redoa and Mackill, 1994).
    The japonica map consisted of 143 markers (125 RAPDs and 18 RFLPs) and 16 linkage groups that were all assigned to the 12 rice chromosomes (Table 1). Distorted marker segregation was low (9%) and was not specific to any particular chromosome. The map spanned 970.9 cM (Kosambi function) with average marker spacing of 7.6 cM. Majority of intervals (71%) were flanked by markers linked in coupling phase (Table 2). Inclusion of RAPDs linked in repulsion phase improved map saturation and would allow determination of heterozygosity of regions mapping these markers. At least seven primers produced pairs of RAPDs closely-linked in repulsion phase that could represent alleles of a single locus exhibiting codominant segregation.
    In terms of percentage of markers mapped to each chromosome, the japonica map had a relatively lower percentage for chromosomes 1 and 2 compared to four other rice molecular maps (Table 3). However, in the japonica map, 18% of all markers mapped to chromosome 10, the least marked chromosome in rice, compared to less than 50% in other maps. Similar results were obtained for chromosome 11 which mapped 15% of the markers used compared to less than 9% in other maps. These results suggest that chromosomes 1 and 2 may not be highly polymorphic, and chromosome 10 may be highly polymorphic, among temperate and tropical japonicas.The japonica map coverage was incomplete as may be expected since the map used a much narrower genetic base. However, the map provides a potential framework for

Table 1. Parameters for the japonica map.
Chrom. number No. of markers Percentage of total Linkage groups(no.) Map lengh (cM) Distance between markers (cM)
1 5 3.4 1 69.0 17.2
2 6 4.2 1 65.7 13.1
3 9 6.3 2 98.1 14.0
4 16 11.2 1 121.0 8.1
5 9 6.3 3 68.2 11.4
6 11 7.7 l 80.7 8.1
7 15 10.5 1 76.5 5.5
8 11 7.7 1 52.0 5.2
9 8 5.6 2 36.2 6.0
10 26 18.2 1 94.7 3.8
11 22 15.4 1 174.2 8.3
12 5 3.4 1 34.6 8.6
Total 143 100.0 16 970.9 7.6(mean)

  Table 2. Comparison of map parameters for markers in coupling-and repulsion-phase linkage
No. of intervals Map length (cM)
Trans Cis Total Cis Total Cis Overall
0 4 0.0 69.0 0.0 17.3
1 4 12.4 53.3 12.4 13.3
1 6 21.3 76.8 21.3 12.8
6 9 34.0 87.0 5.7 9.7
1 5 6.1 62.1 6.1 12.4
2 8 14.8 65.9 7.4 8.2
4 10 14.2 62.3 3.6 6.2
4 6 20.2 31.8 5.1 5.3
2 4 19.6 16.6 9.8 4.2
10 15 21.8 72.9 2.2 4.9
5 16 36.3 137.9 7.3 8.6
1 3 1.3 33.3 1.3 11.1
37 90 202.2 768.9 5.5 8.5
Chrom. Kurata et al. Causse 
et al.		 Saito et al McCouch 
et al.		 Japonica
No. (1994) (1994) (1991) (1988) map
1 14 16 15 17 3
2 10 12 11 13 4
3 11 15 14 7 6
4 8 10 10 11 11
5 9 8 8 7 6
6 11 8 9 10 8
7 8 7 5 8 10
8 6 5 5 4 8
9 6 5 6 6 6
10 5 3 3 1 18
11 7 6 9 7 15
12 5 6 7 7 3
Total Markers 1381 717 351 135 143

mapping important genes in japonica rice and also provides some insights on molecular polymorphisms within japonicas. Since recombination distances are more accurate, the japonica map could be useful for genetic mapping studies as well as in studies aiming to better understand the genetic divergence of tropical and temperate japonica cultivars.

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