TABLE 2.
Calculation of local recombination frequencies (R-local) in chromosome intervals containing target loci
|
R(Local) as defined by positional cloning studies
|
Regional R(map) as determined by anchoring locus to the rice RGP 1391-marker mapa
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|---|---|---|---|---|---|---|---|---|---|---|
| Target allele | Proximal (λ1) crossovers | Distal (λ2) crossovers | R(local)b (kb/cM) | R(local)b (genes/cM) | Chromosome | Physical interval (bp)c | Proximal marker | Distal marker | R(map)d (kb/cM) | R(map)d (genes/cM) |
| bc1 | 5 | 2 | 66.6 | 20.2 | 3 | 17215334–17217366 | C12819 | E61171 | 403.6 | 46.8 |
| bel | 1 | 2 | 169.4 | 27.7 | 3 | 31379697–31385021 | C0012 | S2722 | 140.2 | 21.4 |
| Bph15 | 2 | 3 | 1,780.7 | 416.8 | 4 | 6882835–7231621 | C0708 | R0288 | 1460.4 | 125.4 |
| chl1 | 1 | 2 | 227.7 | 28.6 | 3 | 33894227–33900896 | E50580 | C1484 | 369.9 | 53.8 |
| chl9 | 2 | 3 | 14,718.0 | 1344.2 | 3 | 20204631–20202305 | E61340 | S2992 | 6028.8 | 512.0 |
| cpt1 | 3 | 10 | 700.0 | 49.5 | 2 | 21602296–1927256 | E3634 | E50850 | 175.3 | 20.7 |
| d11 | 5 | 7 | 493.3 | 95.6 | 4 | 23252491–23248070 | S10702 | R0278 | 272.7 | 36.3 |
| d2 | 1 | 1 | 1,800.0 | 300.0 | 1 | 5233425–5241321 | E60110 | C12072 | 250.7 | 31.3 |
| dbs | 2 | 5 | 761.7 | 132.9 | 1 | 18477785–18484690 | C0585 | E60808A | 2944.1 | 316.7 |
| dgl1 | 1 | 3 | 255.9 | 28.8 | 1 | 28463215–28470187 | R1012 | C0922 | 169.3 | 21.3 |
| eui | 1 | 2 | 224.0 | 9.3 | 5 | 23645362–23655166 | S14889 | E30003 | 127.0 | 18.7 |
| eui1 | 1 | 2 | 524.6 | 52.5 | 5 | 23645362–23655166 | S14889 | E30003 | 127.0 | 18.7 |
| f5-DU | 13 | 2 | 93.0 | 12.0 | 5 | 1278649–1379421 | R0830 | S16113 | 106.7 | 11.9 |
| fon1 | 3 | 2 | 725.7 | 48.4 | 6 | 30473475–30469084 | R1479 | E10139 | 185.5 | 26.3 |
| fon4 | 1 | 10 | 1,718.2 | 316.9 | 11 | 22163672–22162134 | E4336 | C0050 | 2171.6 | 236.7 |
| gh2 | 1e | 1e | 976.7 | 97.7 | 2 | 4874079–4870146 | S1511 | S13446 | 177.5 | 23.9 |
| gid1 | 1 | 1 | 684.0 | 72.0 | 5 | 19785334–19788132 | S2689 | C1268 | 252.2 | 28.3 |
| gl-3 | 3 | 3 | 145.5 | 16.6 | 3 | 16469400–16556900 | E0323 | C60318A | 128.5 | 12.5 |
| Gn1a | 1 | 1 | 819.0 | 130.0 | 1 | 5272324–5267274 | E60110 | C12072 | 250.7 | 31.3 |
| hd1 | 1 | 2 | 120.4 | 20.1 | 6 | 9335377–9337570 | C0235 | R10069 | 257.9 | 22.4 |
| Hd6 | 4 | 3 | 211.7 | 8.0 | 3 | 31453402–31447755 | C0012 | S2722 | 140.2 | 21.4 |
| htd1 | 1 | 1 | 1,380.0 | 276.0 | 4 | 27348729–27351393 | C11378 | E51196 | 283.7 | 40.7 |
| moc1 | 2 | 2 | 201.0 | 20.1 | 6 | 24310311–24315385 | S10324 | R1559 | 151.8 | 18.7 |
| Pi36(t) | 2 | 5 | 28.2 | 3.3 | 8 | 2762977–2888909 | S4144B | C60293 | 139.4 | 12.5 |
| Pib | 1 | 3 | 1,322.0 | 198.3 | 2 | 35112900–35107768 | C0379 | S10020 | 98.3 | 12.9 |
| Pi-d2 | 1 | 3 | 3,600.0 | 660.0 | 6 | 17159337–17163823 | C0058 | S20510 | 9503.8 | 840.0 |
| Pi-kh | 6 | 4 | 59.7 | 7.5 | 11 | 24761902–24762922 | R10829 | S5730 | 198.6 | 22.3 |
| pla1 | 1e | 1e | 427.7 | 17.3 | 10 | 13329113–13327360 | C0961 | R1738A | 135.1 | 13.7 |
| Psr1 | 2 | 1 | 321.7 | 25.3 | 1 | 14429394–14435943 | R2501 | C0045 | 428.0 | 39.1 |
| qSh1 | 1 | 2 | 42.4 | 69.2 | 1 | 36776800–36772211 | R0578 | E20351 | 1145.6 | 131.3 |
| qUvr10 | 2 | 1 | 333.0 | 74.0 | 10 | 4433064–4429249 | E30589B | E1064 | 291.7 | 28.2 |
| Rf-1 | 2 | 1 | 1,303.4 | 68.6 | 10 | 18606065–18624126 | S11841 | S21174 | 318.5 | 48.2 |
| S32(t) | 4 | 2 | 224.0 | 24.5 | 2 | 2109653–2227836 | S20351 | R10479 | 201.1 | 22.6 |
| S5n | 1 | 2 | 1,066.7 | 133.3 | 6 | 5606631–5758152 | R1954 | R2349 | 70.7 | 10.0 |
| Skc1 | 1 | 1 | 220.0 | 29.7 | 1 | 11460220–11455734 | E4175 | E10119 | 190.4 | 18.9 |
| spl11 | 2 | 1 | 138.3 | 15.4 | 12 | 23439842–23434652 | E61976 | S5375 | 95.2 | 13.3 |
| spl7 | 1 | 1 | 29.4 | 29.4 | 5 | 26261154–26263625 | C0466 | C11368 | 222.2 | 43.6 |
| Xa1 | 3 | 2 | 96.5 | 27.0 | 4 | 31419036–31425732 | C52068 | S1544 | 298.3 | 45.0 |
| xa13 | 3 | 2 | 439.3 | 59.4 | 8 | 26595951–26593109 | R3961A | R0639 | 109.1 | 16.0 |
| Xa26 | 2 | 14 | 40.1 | 7.2 | 11 | 27688448–27692198 | R1506 | R3342 | 383.4 | 32.5 |
| Xa5 | 1 | 1 | 194.0 | 47.9 | 5 | 323538–325468 | C12015 | C0568 | 111.9 | 13.1 |
For comparison, the genome-wide average R (avg) = 277 kb/cM or 28.0 genes/cM.
Rice Genome Project (RGP) RFLP map based on an F2 population between Nipponbare and Kasalath (http://rgp.dna.affrc.go.jp/) (Harushima et al. 1998).
The local recombination frequency was calculated as follows: R-local = T(local)/m(local), where T(local) is number of kilobases or genes between the closest flanking molecular markers with at least one crossover between each marker and the target locus, and m(local) is genetic distance between these two markers in centimorgans. The value for T(local) is reported in Table 1. The genetic map distance, m(local) = 100 × (λ1 + λ2)/N, where λ1 is number of proximal crossovers (Table 2), λ2 is number of distal crossovers (Table 2), and N is total number of informative chromosomes genotyped (Table 1). In a testcross, m = 100 × λ/progeny (hence m = 100 × recombinants/progeny), whereas in a selfed cross with progeny testing, m = 100 × (λ/2 × progeny) since genotyping permits both chromosomes to contribute to the mapping population.
This is the precise chromosome physical location of the target locus or candidate region on the rice physical map (Version 4.0 TIGR rice pseudomolecules).
R(map) = T(map)/m(map), where T(map) is number of kilobases or genes between the RGP proximal and distal markers containing the target locus as listed in Table 2, and m(map) is genetic map distance between these two RGP markers in centimorgans. These values can be found in supplemental Table 1 at http://www.genetics.org/supplemental/.
Number of recombinants not reported, so set at λ1 = 1 and λ2 = 1.