Table 2 PCR validation of PAV polymorphisms
From: High presence/absence gene variability in defense-related gene clusters of Cucumis melo
PAV gene | Coordinates (v3.5)a | Partially or fully absent (p/f) | Varietiesb | PAV gapsc | ||
|---|---|---|---|---|---|---|
Size (bp) | Coordinates (v3.5)a | Commentsd | ||||
4241 | 5,250,561-5,252,741 | f | IQ | 6,225 | 5,246,795-5,253,019 | C |
CV | ||||||
4260 | 5,508,406-5,509,772 | p | CV | 498 | 5,508,275-5,508,772 | C, SI (37 nt), E |
4262 | 5,533,446-5,539,663 | p | IQ | - | - | False PAV |
CV | ||||||
4278 | 5,683,128-5,692,676 | p | CV | 1,308 | 5,684,308-5,686,215 | C, I (partial) |
4288 | 5,779,041-5,786,300 | p | IQ | - | - | False PAV |
CV | ||||||
4289 | 5,801,121-5,806,330 | f | IQ | 86,393 | 5,790,312-5,876,704 | C, SI (3 kb) |
p | CV | 739 | 5,802,779-5,803,517 | C, I | ||
4290 | 5,810,121-5,812,410 | f | IQ | 86,393 | 5,790,312-5,876,704 | C, SI (3 kb) |
4291 | 5,840,867-5,843,162 | f | IQ | 86,393 | 5,790,312-5,876,704 | C, SI (3 kb) |
p | PI | 57,737 | 5,843,353-5,901,089 | SI (744 nt) | ||
4292 | 5,855,171-5,860,831 | f | IQ | 86,393 | 5,790,312-5,876,704 | C, SI (3 kb) |
p | CV | 532 | 5,857,419-5,857,950 | C, E (partial), I (partial) | ||
f | PI | 57,737 | 5,843,353-5,901,089 | C, SI (744 nt) | ||
4293 | 5,868,071-5,868,244 | f | IQ | 86,393 | 5,790,312-5,876,704 | C, SI (3 kb) |
f | PI | 57,737 | 5,843,353-5,901,089 | C, SI (744 nt) | ||
4294 | 5,884,952-5,889,556 | f | CV | 40,204 | 5,878,047-5,918,250 | C, SI (3 kb) |
f | PI | 57,737 | 5,843,353-5,901,089 | C, SI (744 nt) | ||
4295 | 5,893,422-5,893,773 | f | CV | 40,204 | 5,878,047-5,918,250 | C, SI (3 kb) |
f | PI | 57,737 | 5,843,353-5,901,089 | C, SI (744 nt) | ||
4299 | 5,951,143-5,955,050 | p | IQ | 525 | 5,953,236-5,953,760 | I |
p | CV | 525 | 5,953,236-5,953,760 | I | ||
p | PI | 524 | 5,953,237-5,953,760 | I | ||
4317 | 6,085,745-6,087,399 | p | PI | - | - | False PAV |
4318 | 6,111,948-6,113,580 | f | CV | 149,716 | 6,088,767-6,238,482 | C |
4319 | 6,144,630-6,145,072 | f | CV | 149,716 | 6,088,767-6,238,482 | C |
f | PI | 87,210 | 6,130,422-6,217,631 | C | ||
4320 | 6,158,620-6,160,417 | f | CV | 149,716 | 6,088,767-6,238,482 | CC |
f | PI | 87,210 | 6,130,422-6,217,631 | C | ||
4321 | 6,180,382-6,182,596 | f | CV | 149,716 | 6,088,767-6,238,482 | C |
f | PI | 87,210 | 6,130,422-6,217,631 | C | ||
4322 | 6,212,481-6,214,658 | f | CV | 149,716 | 6,088,767-6,238,482 | C |
f | PI | 87,210 | 6,130,422-6,217,631 | C | ||
f | IQ | - | - | Not yet confirmed | ||
4323 | 6,219,959-6,220,884 | f | CV | 149,716 | 6,088,767-6,238,482 | C |
4324 | 6,232,683-6,236,414 | p | IQ | 1,637 | 6,234,788-6,236,424 | C, E (partial) |
f | CV | 149,716 | 6,088,767-6,238,482 | C | ||
f | PI | 5,714 | 6,232-627-6,238,340 | C | ||
4326 | 6,251,955-6,252,158 | f | IQ | 3005 | 6,250,865-6,253,869 | C, SI (5.8 kb) |
f | CV | 3588 | 6,250,865-6,254,452 | C, SI (6 kb) | ||
4331 | 6,306,224-6,307,985 | f | PI | 6,370 | 6,306,115-6,312,484 | C |
5453 | 5,239,146-5,239,370 | p | IQ | 0 | 5,239,342-5,239,343 | C, SI (225 bp) |
p | CV | 0 | 5,239,290-5,239,343 | |||
14632 | 4,629,508-4,646,365 | p | CV | 7,278 | 4,628,501-4,635,778 | C, E, I, SI (39 bp) |
14633 | 4,655,610-4,656,362 | f | IQ | 33,861 | 4,646,955-4,680,815 | C, SI (7.5 kb) |
f | PI | 33,861 | 4,646,955-4,680,815 | C, SI (7.5 kb) | ||
14634 | 4,658,485-4,659,820 | f | IQ | 33,861 | 4,646,955-4,680,815 | C, SI (7.5 kb) |
f | PI | 33,861 | 4,646,955-4,680,815 | C, SI (7,5 kb) | ||
14635 | 4,676,224-4,677,197 | f | IQ | 33,861 | 4,646,955-4,680,815 | C, SI (7.5 kb) |
f | PI | 33,861 | 4,646,955-4,680,815 | C, SI (7,5 kb) | ||
15015 | 1,061,280-1,061,542 | f | CV | 28,011 | 1,038,039-1,066,049 | C, SI (2,6 kb, transposon) |
22141 | 1,707,299-1,710,539 | p | IQ | - | - | False PAV |
p | PI | |||||
22145 | 1,728,890-1,744,072 | p | IQ | 9,736 | 1,733,997-1,743,732 | C, E, I, SI (6.5 kb) |
p | CV | 9,736 | 1,733,997-1,743,732 | C, E, I, SI (6.5 kb) | ||
p | PI | 9,736 | 1,733,997- 1,743,732 | C, E, I, SI (6.5 kb) | ||
22153 | 1,815,300-1,819,596 | p | PI | - | - | False PAV |
22154 | 1,823,379-1,831,379 | p | CV | - | - | False PAV |
p | PI | |||||
23276 | 756,768-760,353 | f | IQ | 19,558 | 755,353-774,910 | C, SI (445 bp) |
f | PS | 19,558 | 755,353-774,910 | C, SI (310 bp) | ||
23277 | 765,000-765,855 | f | IQ | 19,558 | 755,353-774,910 | C, SI (445 bp) |
f | PS | 19,558 | 755,353-774,910 | C, SI (310 bp) | ||
23278 | 766,024-767,842 | f | IQ | 19,558 | 755,353-774,910 | C, SI (445 bp) |
f | PS | 19,558 | 755,353-774,910 | C, SI (310 bp) | ||
23577 | 1,518,347-1,521,271 | p | CV | 2,191 | 1,519,298-1,521,488 | C, E, I |
24733 | 294,304-297,983 | p | CV | 193 | 295,122-295,314 | C,I,SI (234 bp, transposon) |
24737 | 344,775-345,020 | f | CV | 4,959 | 344,525-349,483 | C |
24743 | 468,195-469,071 | p | CV | 726 | 468,516-469,241 | C, E, I |