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© The Korean Society of Breeding Science
This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
| Linesz |
Rice blast isolate (race)y |
|||||
|---|---|---|---|---|---|---|
| 90-008 | 93-072 | 93-093 | 93-456 | 02-319 | 03-177 | |
| (KI1113) | (KJ103) | (KI197) | (KI409) | (KJ105) | (KJ105) | |
|
|
||||||
| ‘Suweon506’ | 4 | 0 | 3 | 0 | 5 | 0 |
| ‘Hwaseong’ | 5 | 5 | 5 | 5 | 5 | 5 |
| ‘Jinbu’ | 2 | 5 | 4 | 0 | 0 | 4 |
| ‘Namil’ | 4 | 4 | 4 | 1 | 5 | 5 |
| ‘Ilpum’ | 5 | 5 | 5 | 4 | 5 | 5 |
| ‘Junam’ | 5 | 0 | 5 | 1 | 5 | 5 |
| ‘Milyang23’ | 3 | 4 | 3 | 2 | 3 | 2 |
z‘Suweon506’ is an introgression line of a wild rice O. minuta (BBCC genome, Acc. 101141) into a Korean Japonica rice cultivar, ‘Hwaseong’
yRice blast isolates were collected from Korean farmers’ fields, and tested on rice lines due to their high compatibility to ‘Hwaseong’, the recurrent parent of ‘Suweon506’
| Markerz |
Physical informationy |
Mirror mapx |
Segregation testw |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ch | Start | Stop | e-PCR | e % | BAC/PAC | cM | cM% | A | H | B | M | χ2 | |
|
|
|||||||||||||
| RM3252 | 1 | 299,681 | 299,852 | 172 | 0.7 | AP002818 | 0.3 | 0.7 | 34 | 66 | 40 | 0 | 0.76 |
| RM600 | 1 | 9,461,346 | 9,461,566 | 221 | 21.7 | AP001081 | 49.6 | 21.7 | 36 | 56 | 48 | 0 | 7.08* |
| RM449 | 1 | 15,305,619 | 15,305,758 | 140 | 35.1 | AP008247 | 72.8 | 35.1 | 35 | 61 | 44 | 0 | 3.10 |
| RM1349 | 1 | 25,398,082 | 25,398,300 | 219 | 58.3 | AP002744 | 103.1 | 57.9 | 30 | 59 | 51 | 0 | 9.02* |
| RM1003 | 1 | 33,803,800 | 33,803,927 | 128 | 77.5 | AP003345 | 136.6 | 77.5 | 29 | 75 | 36 | 0 | 1.16 |
| RM6321 | 1 | 43,251,019 | 43,251,186 | 168 | 99.2 | AP003277 | 181.8 | 99.2 | 37 | 72 | 31 | 0 | 0.45 |
|
|
|||||||||||||
| RM7 | 3 | 9,808,540 | 9,808,710 | 171 | 27.0 | AC134232 | 44.4 | 27.0 | 15 | 59 | 66 | 0 | 39.02*** |
| RM1164 | 3 | 14,840,558 | 14,840,757 | 200 | 40.8 | AC084766 | 68.7 | 40.8 | 19 | 77 | 44 | 0 | 9.53** |
| RM1350 | 3 | 28,632,514 | 28,632,682 | 169 | 78.8 | AC087181 | 126.8 | 78.8 | 28 | 74 | 38 | 0 | 1.56 |
| RM3585 | 3 | 36,080,616 | 36,080,784 | 169 | 99.3 | AC128647 | 161.7 | 99.3 | 21 | 82 | 37 | 0 | 7.16* |
|
|
|||||||||||||
| RM551 | 4 | 168,620 | 168,811 | 192 | 0.5 | AL606442 | 3.1 | 0.5 | 38 | 73 | 29 | 0 | 1.13 |
| RM5633 | 4 | 13,059,370 | 13,059,580 | 211 | 37.1 | AL731595 | 19.9 | 37.1 | 34 | 73 | 33 | 0 | 0.16 |
| RM3524 | 4 | 22,674,720 | 22,674,847 | 128 | 64.3 | AL606636 | 68.3 | 64.3 | 30 | 73 | 37 | 0 | 0.73 |
| RM349 | 4 | 32,465,508 | 32,465,652 | 145 | 92.1 | AL606455 | 111.3 | 92.1 | 24 | 70 | 44 | 2 | 5.25 |
| RM559 | 4 | 35,117,645 | 35,117,804 | 160 | 99.6 | AL606637 | 129.6 | 99.6 | 32 | 76 | 32 | 0 | 0.79 |
|
|
|||||||||||||
| RM5693 | 5 | 441,872 | 442,071 | 200 | 1.5 | AC129716 | 4.6 | 1.5 | 37 | 67 | 36 | 0 | 0.16 |
| RM5558 | 5 | 21,168,727 | 21,168,899 | 173 | 70.9 | AC105769 | 86.0 | 70.9 | 46 | 64 | 30 | 0 | 4.16 |
| RM1054 | 5 | 29,144,035 | 29,144,184 | 150 | 97.6 | AC098598 | 122.0 | 97.6 | 31 | 77 | 32 | 0 | 1.13 |
|
|
|||||||||||||
| RM3353 | 6 | 435,582 | 435,697 | 116 | 1.4 | AP001129 | 1.4 | 1.4 | 21 | 77 | 42 | 0 | 7.02* |
| RM276 | 6 | 6,230,046 | 6,230,169 | 124 | 19.9 | AP003488 | 33.5 | 19.9 | 17 | 83 | 40 | 0 | 11.56*** |
| RM6818 | 6 | 16,581,413 | 16,581,542 | 130 | 53.1 | AP004012 | 65.8 | 53.1 | 30 | 76 | 34 | 0 | 1.02 |
| RM3628 | 6 | 23,737,032 | 23,737,157 | 126 | 76.0 | AP003612 | 85.4 | 76.0 | 25 | 88 | 27 | 0 | 8.56* |
| RM5753 | 6 | 30,966,850 | 30,967,050 | 201 | 99.1 | AP004685 | 124.4 | 99.1 | 34 | 78 | 28 | 0 | 2.02 |
|
|
|||||||||||||
| RM1093 | 7 | 668,161 | 668,310 | 150 | 2.0 | AP003746 | 2.5 | 2.3 | 36 | 72 | 32 | 0 | 0.22 |
| RM1377 | 7 | 12,782,829 | 12,783,009 | 181 | 43.1 | AP004305 | 49.7 | 43.1 | 35 | 71 | 34 | 0 | 0.02 |
| RM3743 | 7 | 19,342,334 | 19,342,513 | 180 | 65.2 | AP003815 | 67.0 | 65.2 | 37 | 74 | 29 | 0 | 1.10 |
| RM172 | 7 | 29,560,592 | 29,560,750 | 159 | 99.6 | AP005199 | 118.6 | 99.6 | 45 | 70 | 25 | 0 | 5.16 |
|
|
|||||||||||||
| RM408 | 8 | 119,935 | 120,063 | 129 | 0.4 | AP005406 | 0.5 | 0.4 | 33 | 64 | 43 | 0 | 2.10 |
| RM547 | 8 | 5,586,058 | 5,586,291 | 234 | 19.7 | AP004746 | 40.2 | 19.7 | 37 | 73 | 25 | 5 | 2.61 |
| RM3262 | 8 | 22,248,334 | 22,248,500 | 167 | 78.6 | AP005483 | 86.7 | 78.6 | 34 | 76 | 29 | 1 | 1.31 |
| RM5545 | 8 | 28,141,927 | 28,142,083 | 157 | 99.4 | AP004623 | 121.2 | 99.4 | 35 | 68 | 37 | 0 | 0.10 |
|
|
|||||||||||||
| RM316 | 9 | 1,074,933 | 1,075,126 | 194 | 4.7 | AP005860 | 0.8 | 4.5 | 44 | 58 | 38 | 0 | 4.13 |
| RM219 | 9 | 7,887,585 | NA | 34.3 | AP005912 | 20.7 | 34.5 | 44 | 60 | 36 | 0 | 3.36 | |
| RM566 | 9 | 14,704,798 | 14,705,036 | 239 | 63.9 | AP005397 | 50.7 | 63.9 | 35 | 78 | 27 | 0 | 2.42 |
| RM205 | 9 | 22,720,646 | 22,720,801 | 156 | 98.7 | AP005546 | 93.5 | 98.7 | 29 | 76 | 35 | 0 | 1.30 |
|
|
|||||||||||||
| RM1375 | 10 | 16,386,764 | 16,386,943 | 180 | 71.6 | AC025905 | 42.7 | 71.6 | 39 | 74 | 27 | 0 | 2.13 |
| RM590 | 10 | 22,784,993 | 22,785,130 | 138 | 99.6 | AC018727 | 83.8 | 99.6 | 35 | 68 | 37 | 0 | 0.10 |
|
|
|||||||||||||
| RM332 | 11 | 2,840,211 | 2,840,381 | 171 | 10.0 | AC133217 | 10.3 | 10.0 | 26 | 77 | 37 | 0 | 2.73 |
| RM536 | 11 | 8,968,470 | 8,968,712 | 243 | 31.5 | AC138197 | 49.1 | 31.5 | 32 | 63 | 45 | 0 | 3.36 |
| RM5961 | 11 | 19,425,385 | 19,425,513 | 129 | 68.2 | AC108223 | 79.9 | 68.2 | 30 | 75 | 35 | 0 | 0.88 |
| RM144 | 11 | 28,246,930 | 28,247,154 | 225 | 99.2 | AC134045 | 116.2 | 99.2 | 38 | 64 | 38 | 0 | 0.79 |
|
|
|||||||||||||
| RM8215 | 12 | 1,585,781 | 1,586,001 | 221 | 5.8 | BX000498 | 10.8 | 9.9 | 8 | 65 | 66 | 1 | 47.27*** |
| RM3747 | 12 | 2,304,368 | 2,304,510 | 143 | 8.4 | AL954364 | 19.1 | 17.5 | 11 | 61 | 68 | 0 | 46.99*** |
| RM6296 | 12 | 3,200,576 | 3,200,730 | 155 | 11.6 | AL713906 | 26.7 | 24.5 | 13 | 79 | 47 | 1 | 18.13*** |
| RM3472 | 12 | 3,520,117 | 3,520,331 | 215 | 12.8 | AL713902 | 27.1 | 24.8 | 11 | 63 | 66 | 0 | 42.96*** |
| RM101 | 12 | 8,826,829 | NA | 32.1 | AL928776 | 48.2 | 44.1 | 22 | 65 | 53 | 0 | 13.50*** | |
| S10704 | 12 | 10,081,374 | NA | AL731739 | 49.3 | 45.1 | 23 | 65 | 52 | 0 | 13.82*** | ||
| RM1337 | 12 | 11,933,319 | 11,933,500 | 182 | 43.4 | BX000556 | 50.5 | 47.2 | 22 | 66 | 52 | 0 | 12.42*** |
| RM277 | 12 | 18,290,458 | NA | 66.5 | AL831799 | 63.3 | 58.0 | 15 | 70 | 54 | 1 | 20.78*** | |
| RM1300 | 12 | 25,965,369 | 25,965,533 | 165 | 94.4 | AL713940 | 100.2 | 93.4 | 10 | 66 | 64 | 0 | 40.53*** |
| RM17 | 12 | 26,954,668 | 26,954,835 | 168 | 98.0 | AC027133 | 107.4 | 98.4 | 13 | 63 | 64 | 0 | 37.02*** |
zA total of 55 DNA markers are listed, in which 51 SSR anchor markers were used to construct ‘linkage map skeleton’, and 4 DNA markers (underlined; RM3747, RM3472, S10704, and RM1337) were included, after conducting initial association analysis, to increase marker density nearby the chromosomal region harboring the blast resistance gene on chromosome 12
yThe primer sequences were used as queries to localize on the ‘Rice Pseudomolecules Release 6’ (http://rice. plantbiology. msu.edu/analyses_search_blast.shtml). When both primer sequences were successfully recognized for their physical locations to be annealed, the expected PCR product size (e-PCR: ‘Stop’-‘Start’+1bp, NA=not available) was used to judge PCR products. If any primer failed for e-Landing, the other primer's location was used to estimate the corresponding point. The determined physical regions followed by e-Landing were used to match corresponding BAC/PAC clones according to the ‘Rice Pseudomolecule Information and Gene Search’(http://rice.plantbiology.msu.edu/)
xThe determined cM position for each BAC/PAC clones was directly adopted from the ‘IRGSP Build5 Pseudomolecules’ (http://rgp.dna.affrc.go.jp/E/IRGSP/Build5/build5.html). To compare the cM positions from various mapping populations with different total lengths, the percentage relative genetic positions, ‘cM%’, was also calculated
wA and B are homozygous for ‘Suweon506’ and ‘Milyang 23’ allele types, respectively, H is for heterozygous progenies at the tested locus, and M indicates the number of plants with missing genotype. Segregation distorted loci are indicated with asterisk; ***P<0.0001, **P<0.01, and *P<0.05
| Locusz | Mirror-mapy |
Individuals used for association analysisx |
Single-locus ANOVAw | Genetic effectv | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| No. of genotypes | Resistance mean | ||||||||||||||||
| (F2) | (F2:3) | ||||||||||||||||
|
|
|
|
|
|
|
||||||||||||
| Marker | Ap | Ch | cM | cM(%) | A | H | B | A | H | B | SSM | SSE | F | R2 | Add | Dom | DeD |
|
|
|||||||||||||||||
| RM3524 | 1 | 4 | 68.3 | 64.3 | 27 | 66 | 32 | 1.28 | 1.54 | 2.26 | 16.3 | 177.1 | 5.6** | 0.084 | 0.49 | -0.23 | -0.47 |
|
|
|||||||||||||||||
| RM6818 | 1 | 6 | 65.8 | 53.1 | 19 | 73 | 33 | 2.37 | 1.68 | 1.25 | 15.3 | 178.1 | 5.2** | 0.079 | -0.56 | -0.13 | 0.24 |
| RM3628 | 1 | 6 | 85.4 | 76 | 19 | 81 | 25 | 2.07 | 1.73 | 1.16 | 9.9 | 183.5 | 3.3* | 0.051 | -0.46 | 0.12 | -0.25 |
|
|
|||||||||||||||||
| RM3747 | 2 | 12 | 19.1 | 17.5 | 11 | 53 | 61 | 0.72 | 1.51 | 1.98 | 17.1 | 176.3 | 5.9** | 0.088 | 0.63 | 0.16 | 0.26 |
| RM6296 | 1 | 12 | 26.7 | 24.5 | 12 | 71 | 41 | 0.63 | 1.58 | 2.16 | 23.1 | 168.1 | 8.3*** | 0.121 | 0.76 | 0.19 | 0.25 |
| RM3472 | 2 | 12 | 27.1 | 24.8 | 11 | 55 | 59 | 0.45 | 1.56 | 2.00 | 23.8 | 169.6 | 8.5*** | 0.123 | 0.78 | 0.33 | 0.43 |
| RM101 | 1 | 12 | 48.2 | 44.1 | 20 | 58 | 47 | 0.55 | 1.38 | 2.51 | 63.2 | 130.2 | 29.6*** | 0.327 | 0.98 | -0.15 | -0.16 |
| S10704 | 2 | 12 | 49.3 | 45.1 | 18 | 61 | 46 | 0.57 | 1.41 | 2.45 | 53.7 | 139.3 | 23.5*** | 0.278 | 0.94 | -0.10 | -0.10 |
| RM1337 | 2 | 12 | 50.5 | 47.2 | 20 | 59 | 46 | 0.53 | 1.38 | 2.54 | 66.0 | 127.4 | 31.6*** | 0.341 | 1.01 | -0.16 | -0.16 |
| RM277 | 1 | 12 | 63.3 | 58.0 | 15 | 62 | 48 | 0.70 | 1.44 | 2.26 | 34.3 | 159.1 | 13.1*** | 0.177 | 0.78 | -0.04 | -0.05 |
zDNA markers were tested on 140 F2 progenies of ‘Suewon506’ × ‘Milyang 23’. After the first round of association analyses with well defined 51 anchor markers (application: Ap=1), additional 4 markers were applied to narrow down the putative location of rice blast resistance gene on chromosome 12 (Ap=2). Markers with significant F value were presented on rice chromosomes 4, 6, and 12
yBoth cM positions and percentage-expressed (cM%) are indicated (see Table 2)
xAssociation analysis was conducted on 125 fertile F2 individuals. By using the corresponding F2:3 seedlings, mean resistance level, against the blast isolate, ‘93-072’, for each genotype categories revealed by DNA markers. A and B are homozygous for ‘Suweon506’ and ‘Milyang 23’ allele types, respectively, and H indicates heterozygous progenies at the tested locus
wThe significance levels corresponding to each F-value are indicated with asterisk; ***P<0.0001, **P<0.01, and *P<0.05
vAdditive effect (Add), and degree of dominance (DeD) were then estimated at the declared loci: Add=(Bmean-Amean)/2 and DeD=Do/Add, where A and B are homozygous F2 individuals for ‘Suweon506’ and ‘Milyang 23’, H is heterozygous individuals at the tested locus, and Do(dominant effect) = Hmean-(Bmean+Amean)/2
반복친인 ‘화성’에 높은 친화성을 발현하는 6개 도열병 균 주 검정에서 ‘수원506호’는 반복친 ‘화성’과 5개 비교품종 들과 다른 저항성 반응을 보여 이들과 다른 야생벼 유래 도열병 저항성 유전자를 보유하는 것으로 판단되었다.
분자마커의 유전자형과 도열병 저항성 간의 연관성평가를 수행한 결과, ‘수원506호’의 도열병 저항성에 관여하는 주 동유전자위는 12번염색체 중단의 RM101-S10704-RM1337 좌위에 위치하는 것으로 추정되었다.
STS 마커 S10704에서 확인된 ‘화성’과 ‘수원506호’의 이 질적인 유전자형은 해당부위에 야생벼 O. minuta의 염색 체 단편이 이입되었다는 것을 증명하였다.
이 좌위는 적어도 9개의 도열병 저항성 유전자들이 위치하 는 것으로 보고된 바 있는데, 추후 정밀분석을 통해 ‘수원 506호’의 도열병 저항성 유전자위와 기 보고된 유전자들 과의 관계를 분석할 계획이다.
Reactions of rice lines to selected Korean virulent blast isolates
| Lines |
Rice blast isolate (race) |
|||||
|---|---|---|---|---|---|---|
| 90-008 | 93-072 | 93-093 | 93-456 | 02-319 | 03-177 | |
| (KI1113) | (KJ103) | (KI197) | (KI409) | (KJ105) | (KJ105) | |
| ‘Suweon506’ | 4 | 0 | 3 | 0 | 5 | 0 |
| ‘Hwaseong’ | 5 | 5 | 5 | 5 | 5 | 5 |
| ‘Jinbu’ | 2 | 5 | 4 | 0 | 0 | 4 |
| ‘Namil’ | 4 | 4 | 4 | 1 | 5 | 5 |
| ‘Ilpum’ | 5 | 5 | 5 | 4 | 5 | 5 |
| ‘Junam’ | 5 | 0 | 5 | 1 | 5 | 5 |
| ‘Milyang23’ | 3 | 4 | 3 | 2 | 3 | 2 |
‘Suweon506’ is an introgression line of a wild rice O. minuta (BBCC genome, Acc. 101141) into a Korean Japonica rice cultivar, ‘Hwaseong’
Rice blast isolates were collected from Korean farmers’ fields, and tested on rice lines due to their high compatibility to ‘Hwaseong’, the recurrent parent of ‘Suweon506’
List of DNA markers, their e-Landing mediated physical positions on rice Pseudomolecule6, corresponding BCA/PAC clones with their determined cM positions, and the segregation test (χ2 test) results on the F2 progenies derived from the cross between ‘Suweon506’ and ‘Milyang23’
| Marker |
Physical information |
Mirror map |
Segregation test |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ch | Start | Stop | e-PCR | e % | BAC/PAC | cM | cM% | A | H | B | M | χ2 | |
| RM3252 | 1 | 299,681 | 299,852 | 172 | 0.7 | AP002818 | 0.3 | 0.7 | 34 | 66 | 40 | 0 | 0.76 |
| RM600 | 1 | 9,461,346 | 9,461,566 | 221 | 21.7 | AP001081 | 49.6 | 21.7 | 36 | 56 | 48 | 0 | 7.08* |
| RM449 | 1 | 15,305,619 | 15,305,758 | 140 | 35.1 | AP008247 | 72.8 | 35.1 | 35 | 61 | 44 | 0 | 3.10 |
| RM1349 | 1 | 25,398,082 | 25,398,300 | 219 | 58.3 | AP002744 | 103.1 | 57.9 | 30 | 59 | 51 | 0 | 9.02* |
| RM1003 | 1 | 33,803,800 | 33,803,927 | 128 | 77.5 | AP003345 | 136.6 | 77.5 | 29 | 75 | 36 | 0 | 1.16 |
| RM6321 | 1 | 43,251,019 | 43,251,186 | 168 | 99.2 | AP003277 | 181.8 | 99.2 | 37 | 72 | 31 | 0 | 0.45 |
| RM7 | 3 | 9,808,540 | 9,808,710 | 171 | 27.0 | AC134232 | 44.4 | 27.0 | 15 | 59 | 66 | 0 | 39.02*** |
| RM1164 | 3 | 14,840,558 | 14,840,757 | 200 | 40.8 | AC084766 | 68.7 | 40.8 | 19 | 77 | 44 | 0 | 9.53** |
| RM1350 | 3 | 28,632,514 | 28,632,682 | 169 | 78.8 | AC087181 | 126.8 | 78.8 | 28 | 74 | 38 | 0 | 1.56 |
| RM3585 | 3 | 36,080,616 | 36,080,784 | 169 | 99.3 | AC128647 | 161.7 | 99.3 | 21 | 82 | 37 | 0 | 7.16* |
| RM551 | 4 | 168,620 | 168,811 | 192 | 0.5 | AL606442 | 3.1 | 0.5 | 38 | 73 | 29 | 0 | 1.13 |
| RM5633 | 4 | 13,059,370 | 13,059,580 | 211 | 37.1 | AL731595 | 19.9 | 37.1 | 34 | 73 | 33 | 0 | 0.16 |
| RM3524 | 4 | 22,674,720 | 22,674,847 | 128 | 64.3 | AL606636 | 68.3 | 64.3 | 30 | 73 | 37 | 0 | 0.73 |
| RM349 | 4 | 32,465,508 | 32,465,652 | 145 | 92.1 | AL606455 | 111.3 | 92.1 | 24 | 70 | 44 | 2 | 5.25 |
| RM559 | 4 | 35,117,645 | 35,117,804 | 160 | 99.6 | AL606637 | 129.6 | 99.6 | 32 | 76 | 32 | 0 | 0.79 |
| RM5693 | 5 | 441,872 | 442,071 | 200 | 1.5 | AC129716 | 4.6 | 1.5 | 37 | 67 | 36 | 0 | 0.16 |
| RM5558 | 5 | 21,168,727 | 21,168,899 | 173 | 70.9 | AC105769 | 86.0 | 70.9 | 46 | 64 | 30 | 0 | 4.16 |
| RM1054 | 5 | 29,144,035 | 29,144,184 | 150 | 97.6 | AC098598 | 122.0 | 97.6 | 31 | 77 | 32 | 0 | 1.13 |
| RM3353 | 6 | 435,582 | 435,697 | 116 | 1.4 | AP001129 | 1.4 | 1.4 | 21 | 77 | 42 | 0 | 7.02* |
| RM276 | 6 | 6,230,046 | 6,230,169 | 124 | 19.9 | AP003488 | 33.5 | 19.9 | 17 | 83 | 40 | 0 | 11.56*** |
| RM6818 | 6 | 16,581,413 | 16,581,542 | 130 | 53.1 | AP004012 | 65.8 | 53.1 | 30 | 76 | 34 | 0 | 1.02 |
| RM3628 | 6 | 23,737,032 | 23,737,157 | 126 | 76.0 | AP003612 | 85.4 | 76.0 | 25 | 88 | 27 | 0 | 8.56* |
| RM5753 | 6 | 30,966,850 | 30,967,050 | 201 | 99.1 | AP004685 | 124.4 | 99.1 | 34 | 78 | 28 | 0 | 2.02 |
| RM1093 | 7 | 668,161 | 668,310 | 150 | 2.0 | AP003746 | 2.5 | 2.3 | 36 | 72 | 32 | 0 | 0.22 |
| RM1377 | 7 | 12,782,829 | 12,783,009 | 181 | 43.1 | AP004305 | 49.7 | 43.1 | 35 | 71 | 34 | 0 | 0.02 |
| RM3743 | 7 | 19,342,334 | 19,342,513 | 180 | 65.2 | AP003815 | 67.0 | 65.2 | 37 | 74 | 29 | 0 | 1.10 |
| RM172 | 7 | 29,560,592 | 29,560,750 | 159 | 99.6 | AP005199 | 118.6 | 99.6 | 45 | 70 | 25 | 0 | 5.16 |
| RM408 | 8 | 119,935 | 120,063 | 129 | 0.4 | AP005406 | 0.5 | 0.4 | 33 | 64 | 43 | 0 | 2.10 |
| RM547 | 8 | 5,586,058 | 5,586,291 | 234 | 19.7 | AP004746 | 40.2 | 19.7 | 37 | 73 | 25 | 5 | 2.61 |
| RM3262 | 8 | 22,248,334 | 22,248,500 | 167 | 78.6 | AP005483 | 86.7 | 78.6 | 34 | 76 | 29 | 1 | 1.31 |
| RM5545 | 8 | 28,141,927 | 28,142,083 | 157 | 99.4 | AP004623 | 121.2 | 99.4 | 35 | 68 | 37 | 0 | 0.10 |
| RM316 | 9 | 1,074,933 | 1,075,126 | 194 | 4.7 | AP005860 | 0.8 | 4.5 | 44 | 58 | 38 | 0 | 4.13 |
| RM219 | 9 | 7,887,585 | NA | 34.3 | AP005912 | 20.7 | 34.5 | 44 | 60 | 36 | 0 | 3.36 | |
| RM566 | 9 | 14,704,798 | 14,705,036 | 239 | 63.9 | AP005397 | 50.7 | 63.9 | 35 | 78 | 27 | 0 | 2.42 |
| RM205 | 9 | 22,720,646 | 22,720,801 | 156 | 98.7 | AP005546 | 93.5 | 98.7 | 29 | 76 | 35 | 0 | 1.30 |
| RM1375 | 10 | 16,386,764 | 16,386,943 | 180 | 71.6 | AC025905 | 42.7 | 71.6 | 39 | 74 | 27 | 0 | 2.13 |
| RM590 | 10 | 22,784,993 | 22,785,130 | 138 | 99.6 | AC018727 | 83.8 | 99.6 | 35 | 68 | 37 | 0 | 0.10 |
| RM332 | 11 | 2,840,211 | 2,840,381 | 171 | 10.0 | AC133217 | 10.3 | 10.0 | 26 | 77 | 37 | 0 | 2.73 |
| RM536 | 11 | 8,968,470 | 8,968,712 | 243 | 31.5 | AC138197 | 49.1 | 31.5 | 32 | 63 | 45 | 0 | 3.36 |
| RM5961 | 11 | 19,425,385 | 19,425,513 | 129 | 68.2 | AC108223 | 79.9 | 68.2 | 30 | 75 | 35 | 0 | 0.88 |
| RM144 | 11 | 28,246,930 | 28,247,154 | 225 | 99.2 | AC134045 | 116.2 | 99.2 | 38 | 64 | 38 | 0 | 0.79 |
| RM8215 | 12 | 1,585,781 | 1,586,001 | 221 | 5.8 | BX000498 | 10.8 | 9.9 | 8 | 65 | 66 | 1 | 47.27*** |
| RM3747 | 12 | 2,304,368 | 2,304,510 | 143 | 8.4 | AL954364 | 19.1 | 17.5 | 11 | 61 | 68 | 0 | 46.99*** |
| RM6296 | 12 | 3,200,576 | 3,200,730 | 155 | 11.6 | AL713906 | 26.7 | 24.5 | 13 | 79 | 47 | 1 | 18.13*** |
| RM3472 | 12 | 3,520,117 | 3,520,331 | 215 | 12.8 | AL713902 | 27.1 | 24.8 | 11 | 63 | 66 | 0 | 42.96*** |
| RM101 | 12 | 8,826,829 | NA | 32.1 | AL928776 | 48.2 | 44.1 | 22 | 65 | 53 | 0 | 13.50*** | |
| S10704 | 12 | 10,081,374 | NA | AL731739 | 49.3 | 45.1 | 23 | 65 | 52 | 0 | 13.82*** | ||
| RM1337 | 12 | 11,933,319 | 11,933,500 | 182 | 43.4 | BX000556 | 50.5 | 47.2 | 22 | 66 | 52 | 0 | 12.42*** |
| RM277 | 12 | 18,290,458 | NA | 66.5 | AL831799 | 63.3 | 58.0 | 15 | 70 | 54 | 1 | 20.78*** | |
| RM1300 | 12 | 25,965,369 | 25,965,533 | 165 | 94.4 | AL713940 | 100.2 | 93.4 | 10 | 66 | 64 | 0 | 40.53*** |
| RM17 | 12 | 26,954,668 | 26,954,835 | 168 | 98.0 | AC027133 | 107.4 | 98.4 | 13 | 63 | 64 | 0 | 37.02*** |
A total of 55 DNA markers are listed, in which 51 SSR anchor markers were used to construct ‘linkage map skeleton’, and 4 DNA markers (underlined; RM3747, RM3472, S10704, and RM1337) were included, after conducting initial association analysis, to increase marker density nearby the chromosomal region harboring the blast resistance gene on chromosome 12
The primer sequences were used as queries to localize on the ‘Rice Pseudomolecules Release 6’ (
The determined cM position for each BAC/PAC clones was directly adopted from the ‘IRGSP Build5 Pseudomolecules’ (
A and B are homozygous for ‘Suweon506’ and ‘Milyang 23’ allele types, respectively, H is for heterozygous progenies at the tested locus, and M indicates the number of plants with missing genotype. Segregation distorted loci are indicated with asterisk; ***P<0.0001, **P<0.01, and *P<0.05
Summary of association analysis between the SSR marker genotypes of F2 progenies and rice blast resistance level of F2:3 seedlings derived from ‘Suwon506’ × ‘Milyang 23’
| Locus |
Mirror-map |
Individuals used for association analysis |
Single-locus ANOVA |
Genetic effect |
|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| No. of genotypes | Resistance mean | ||||||||||||||||
| (F2) | (F2:3) | ||||||||||||||||
| Marker | Ap | Ch | cM | cM(%) | A | H | B | A | H | B | SSM | SSE | F | R2 | Add | Dom | DeD |
| RM3524 | 1 | 4 | 68.3 | 64.3 | 27 | 66 | 32 | 1.28 | 1.54 | 2.26 | 16.3 | 177.1 | 5.6** | 0.084 | 0.49 | -0.23 | -0.47 |
| RM6818 | 1 | 6 | 65.8 | 53.1 | 19 | 73 | 33 | 2.37 | 1.68 | 1.25 | 15.3 | 178.1 | 5.2** | 0.079 | -0.56 | -0.13 | 0.24 |
| RM3628 | 1 | 6 | 85.4 | 76 | 19 | 81 | 25 | 2.07 | 1.73 | 1.16 | 9.9 | 183.5 | 3.3* | 0.051 | -0.46 | 0.12 | -0.25 |
| RM3747 | 2 | 12 | 19.1 | 17.5 | 11 | 53 | 61 | 0.72 | 1.51 | 1.98 | 17.1 | 176.3 | 5.9** | 0.088 | 0.63 | 0.16 | 0.26 |
| RM6296 | 1 | 12 | 26.7 | 24.5 | 12 | 71 | 41 | 0.63 | 1.58 | 2.16 | 23.1 | 168.1 | 8.3*** | 0.121 | 0.76 | 0.19 | 0.25 |
| RM3472 | 2 | 12 | 27.1 | 24.8 | 11 | 55 | 59 | 0.45 | 1.56 | 2.00 | 23.8 | 169.6 | 8.5*** | 0.123 | 0.78 | 0.33 | 0.43 |
| RM101 | 1 | 12 | 48.2 | 44.1 | 20 | 58 | 47 | 0.55 | 1.38 | 2.51 | 63.2 | 130.2 | 29.6*** | 0.327 | 0.98 | -0.15 | -0.16 |
| S10704 | 2 | 12 | 49.3 | 45.1 | 18 | 61 | 46 | 0.57 | 1.41 | 2.45 | 53.7 | 139.3 | 23.5*** | 0.278 | 0.94 | -0.10 | -0.10 |
| RM1337 | 2 | 12 | 50.5 | 47.2 | 20 | 59 | 46 | 0.53 | 1.38 | 2.54 | 66.0 | 127.4 | 31.6*** | 0.341 | 1.01 | -0.16 | -0.16 |
| RM277 | 1 | 12 | 63.3 | 58.0 | 15 | 62 | 48 | 0.70 | 1.44 | 2.26 | 34.3 | 159.1 | 13.1*** | 0.177 | 0.78 | -0.04 | -0.05 |
DNA markers were tested on 140 F2 progenies of ‘Suewon506’ × ‘Milyang 23’. After the first round of association analyses with well defined 51 anchor markers (application: Ap=1), additional 4 markers were applied to narrow down the putative location of rice blast resistance gene on chromosome 12 (Ap=2). Markers with significant F value were presented on rice chromosomes 4, 6, and 12
Both cM positions and percentage-expressed (cM%) are indicated (see Table
Association analysis was conducted on 125 fertile F2 individuals. By using the corresponding F2:3 seedlings, mean resistance level, against the blast isolate, ‘93-072’, for each genotype categories revealed by DNA markers. A and B are homozygous for ‘Suweon506’ and ‘Milyang 23’ allele types, respectively, and H indicates heterozygous progenies at the tested locus
The significance levels corresponding to each F-value are indicated with asterisk; ***P<0.0001, **P<0.01, and *P<0.05
Additive effect (Add), and degree of dominance (DeD) were then estimated at the declared loci: Add=(Bmean-Amean)/2 and DeD=Do/Add, where A and B are homozygous F2 individuals for ‘Suweon506’ and ‘Milyang 23’, H is heterozygous individuals at the tested locus, and Do(dominant effect) = Hmean-(Bmean+Amean)/2
‘Suweon506’ is an introgression line of a wild rice O. minuta (BBCC genome, Acc. 101141) into a Korean Japonica rice cultivar, ‘Hwaseong’
Rice blast isolates were collected from Korean farmers’ fields, and tested on rice lines due to their high compatibility to ‘Hwaseong’, the recurrent parent of ‘Suweon506’
A total of 55 DNA markers are listed, in which 51 SSR anchor markers were used to construct ‘linkage map skeleton’, and 4 DNA markers (underlined; RM3747, RM3472, S10704, and RM1337) were included, after conducting initial association analysis, to increase marker density nearby the chromosomal region harboring the blast resistance gene on chromosome 12
The primer sequences were used as queries to localize on the ‘Rice Pseudomolecules Release 6’ (
The determined cM position for each BAC/PAC clones was directly adopted from the ‘IRGSP Build5 Pseudomolecules’ (
A and B are homozygous for ‘Suweon506’ and ‘Milyang 23’ allele types, respectively, H is for heterozygous progenies at the tested locus, and M indicates the number of plants with missing genotype. Segregation distorted loci are indicated with asterisk; ***P<0.0001, **P<0.01, and *P<0.05
DNA markers were tested on 140 F2 progenies of ‘Suewon506’ × ‘Milyang 23’. After the first round of association analyses with well defined 51 anchor markers (application: Ap=1), additional 4 markers were applied to narrow down the putative location of rice blast resistance gene on chromosome 12 (Ap=2). Markers with significant F value were presented on rice chromosomes 4, 6, and 12
Both cM positions and percentage-expressed (cM%) are indicated (see Table
Association analysis was conducted on 125 fertile F2 individuals. By using the corresponding F2:3 seedlings, mean resistance level, against the blast isolate, ‘93-072’, for each genotype categories revealed by DNA markers. A and B are homozygous for ‘Suweon506’ and ‘Milyang 23’ allele types, respectively, and H indicates heterozygous progenies at the tested locus
The significance levels corresponding to each F-value are indicated with asterisk; ***P<0.0001, **P<0.01, and *P<0.05
Additive effect (Add), and degree of dominance (DeD) were then estimated at the declared loci: Add=(Bmean-Amean)/2 and DeD=Do/Add, where A and B are homozygous F2 individuals for ‘Suweon506’ and ‘Milyang 23’, H is heterozygous individuals at the tested locus, and Do(dominant effect) = Hmean-(Bmean+Amean)/2
