A rapid method to map mutations in Drosophila

Martin, Sophie G; Dobi, Krista C; St Johnston, Daniel

doi:10.1186/gb-2001-2-9-research0036

Table 1 Molecular data of polymorphisms on 3R

From: A rapid method to map mutations in Drosophila

Predicted	Genomic	Base-pair	Polymorphism sequence (FRT chromosome/marker chromosome)	RFLP	TM3
cytological	fragment	position within		enzyme	pattern
region		genomic fragment
82D	AE003605	6135	GCGGTACCTAGAAAC [A/G]GAAATGCTGAAACAG	BslI	M
		17727	TTCAGATTGCACGCA [G/T]GCGCCACATAGGGTG	SphI	FRT
83D	AE003600	130884	AAAACTATTACAGAA [T/C]TGAGTTTGTGGCTCT	-	M
84A	AE003674	3526	CGGTTAAAATGCCCA [TG/AC]GAGCTCGGAATCCTT	StyI	FRT
		3559	CCCACTTCTTCCCGG [C/T]CCTCATATTTCTTTC
84B	AE003673	38157	CTGATTTTTATTGTG [C/G]TGCACCCAAGTTTTT	ApaLI	M
84D	AE003671	10767	ATAGAGCCATATTTT [A/C]CACATTTTCGTACGG
		10834	GTTTGTGTTTTTTGT [A/G]CCACGTTATGCATTT	RsaI	M
84E	AE003676	2498	TTCTAGAGGAGGGTG [G/A]GACCTTTCGGAGACG	AvaII	FRT
	AE003677	15615	TCTGTGCTGGCAAGC [C/G]TCCCGAGCATTTGCT	-	FRT
84F	AE003679	34211	TGAGCAACGCAAACA [A/C]TTTAATTCAAAAACA	-	Other
85D	AE003683	140539	CTATGAGAATTTGAT [A/T]TCATATAATCGAATT	EcoRV	M
85E	AE003684	114149	AAGTAACCATGAAAA [C/T]TGATTCCCCTTGGCT	-	FRT
85F	AE003686	22154	CTGAGTTGAAAATTA [/CCCAAAAAGCCCTGGGCTT]	MvaI	FRT
			CAATGACAGTCGGCC
86C	AE003688	7272	CTTATCTCAAAATTT [/T]GGAAATTTCCCGGGA	-	FRT
		7290	AAATTTCCCGGGAAG [CA/AT]TGCCCGCATGCGCTG	-
86D	AE003690	3998	CTCTTACATTTTTGG [C/T]CATTTTGGCGGCCCC	BglI	FRT
		33879	TGTTATTTATAAATA [C/T]GAGGCACATGAATTT	-	FRT
		33960	TCACATACAACTCCG [C/A]CATTTGAGCCCGGAC	-
86E	AE003692	1660	TGCTGCCTTGAACAC [C/G]TACACGTACAATCGT	RsaI	M
86F	AE003693	19685/19695	TTTTTGCCTTTTGCA [/T]	-	M
			ACGGTCGTA [G/A]TCAGGATGAGAAAAG
87A	AE003694	44195/44208	GCGAAAGTATTTTTT [T/C]CTTTTTTTTTTT [/T]	-	FRT
			ATCATTCACAATGGC
		44267	CTAGGGTTGAGTGGG [C/T]GGGTGTAGGATTACC	-
87C	AE003697	34839	ACATACAAGCGTACA [T/A]AAATTTATTCATATT	-	M
87E	AE003699	18398	TCGATTCAATTCAAT [G/A]ATCAGAACCAACTGT	BclI	FRT
		18419/18428	AACCAACTGTCTGTG [C/T]TGCTTCCG [C/T]
			TTCTGGTTGCAACGG
		18446/18449	CTGGTTGCAACGGGG [C/T]GT [A/C]TGCGTGATGTCTCAC
		18501	GTGCATAAATTTAAG [C/T]GGGCTGCGAAAAATC
		24855/24858	TGCAGCCCCCTTATC [C/G]AG [T/C]TGCTGACTGGATTTT	TaqI	FRT
		24879	ACTGGATTTTTTTTT [/TTT]GTATTCCGAATCCCC
		24992/24998	TGGCGGTCTGCGGCG [A/C]AGTCT [C/A]TGCAAACAGGCCGAG
	AE003700	42096	GCACCTCGTTGCTCG [T/G]CGAATTCTCACGCGT	TaqI	M
87F	AE003702	4931/4937	CTGGCACCTACTAAG [A/G]TTCTA [C/T]CGCAAGAACTCCACT	HinfI	FRT
88C	AE003705	2531	TGCTCGGGTTCTCTT [A/G]CCGGCTTTGAAATCG	-	Other
88D	AE003707	14391	TCATCAGGATTCTTT [C/T]GATTTCTTTGCCACA	TaqI	M
88F	AE003709	2931/2963	GGCGGTACTAGTACT [GGTACTGGTACTGGTACTGGTACTG/A]	ND^*	M
			GTACTGG [G/T]ACT
89A	AE003711	3499	GCATATAAATTTCCC [G/A]TTCACAACGAACCGC	-	FRT
		3555	GATGGCTTTGTAGTC [T/C]TAAAGTCTCTGAGCA	-
89B	AE003712	2764	AAGGTGGCTAGGGTG [G/T]TGGATGCAGCTAGAT
		2809/2820	ACAGGAAGTTCAAAC [C/T]GATAGTGTTA [G/C]	AluI	FRT
			CTGTCCATTGATGGA
		2836	CTGTCCATTGATGGA [T/G]GATTTTATATACGAT
		2895	CTTTGCGGTAGGAAA [C/T]CAAGATGAAAATGTC
89C	AE003713	20964	TTCCCATTCACATTC [A/G]CACATGCTGGGCACG
		20984	TGCTGGGCACGAGTA [C/T]TCGCCGATATCGATC	ScaI	M
89E	AE003715	299	CTAATGGCTCCTACG [A/G]CATTTTGCTTTCTTC
		320	TGCTTTCTTCGAATG [T/A]TTCTGTTACCAAACT	HinfI	FRT
		356	GCTCCGCTCCCTCCA [T/C]TTGTATCTGTCGGAT
90A	AE003716	214757	AAAATATGTTGTACT [AG/GTTGTT]GAATGAAAAGTAAAA	-	FRT
		214807	ATTTTATCTATCGGG [C/A]TACTAATGGAATCTG	-
		214862	CTAATATCTAATGCT [T/A]AGCTACAATATGATG	-
90C	AE003719	15267	ATCGCCTACTAAATG	ND^*	FRT
			[GACCCAATGCCGATCCGTTTCGAGCACTTGCAGTTG/ ]AT...
		15306	G [G/A]AGCT [A/G]TTGGCTGTT [GAC/AAT]TGCGA
			[A/G]GATAACACACAGGAG
90D	AE003720	2929	AGTTCGATTCAGTCG [C/T]TTTGGATAGAGCTCA	-	FRT
		3053	ATTTCAGATGGGAAA [G/C]GCATTAGATCTTGCT	-
91B	AE003723	6105	AAGTGTGCTCTGTTT [C/T]TCGTTTAAGTTACGC
		6202/6208	GTTAAAGCTACAGTT [T/G]CAGTT	ND^*	M
			[ACAGTTTCAGTTACAGTGA/T]CAGTTACAGTT
		6340	AGTTATACCCCACTT [CACTT/ ]GCTCGTTTTAATAAT
91D	AE003724	200	GCACACACACACACA [CAGTT/GGT]ACTGCCCCGCCCACT	RsaI	FRT
91F	AE003725	11172	TTATTATGACAACAT [G/C]CATCCATTAGACCCA	NsiI	FRT
92A	AE003726	519	CTCGTCTCCCTGATC [G/A]CAATGGTAGTGGAAA	BclI	M
		565	TAATAATGGTAATGG [CAATGG/ ]TAATGGTAATGGTGA
		608	CCGCCCCAACACAAC [C/T]GAGTTCGTGAGTGCG
92D	AE003729	7430	CATTCAATTGGTGGG [/G]ACCGCTTTTGCCCAA	-	ND
92E	AE003730	9025	GGCTAATCCGTAATC [/CGTGCCCGTACCCGTACCCCTACC]	ND^*	FRT
			CGTACCCCTACCCGT
93B	AE003733	759	GTCCTTCAAGGCAGA [/TATGGA]TATGGAAGTGCATAA	-	Other
93D	AE003734	25325	AAAGCTAATTGATTT [C/G]CATGAAAGTGAGCCA
		25391	TGAACTCGCTGCTCT [C/T]CCACTTATATACATC	EarI	FRT
93F	AE003736	2695	AAACTTCAGCAACTT [C/A]AGCCGCCAACAACAA	MseI	FRT
	AE003737	587	TTTGCCGTTGAAGCT [GCAGCAGCAGCAGCA/ ]	-	Other
			GCAGCAGCAGCAGCA
		722	ACTTTGCCAACTTCT [T/ ]GTGCCTTTTTGTGCC	-
		144616/144630	GATGCCCTACCCCCT [T/C]CTTCACTTTCGCT [AGA/TGC]	-	M
			AAGGGGAATGTAAAA
94A	AE003738	687	GTGGATGATGATGCC [/C]GGTTGGTGCGTTGTT	ScrFI	M
95A	AE003743	66247	TGCAAAAAAAAAAAA [T/ ]ATATAGCTTGGCTAC	-	M
95B	AE003744	73639	ACCGAACCGCCCAGC [/AC]CACCCACTCAACCG	-	Other
		98594/98607	GGACAACAATTGTAC [T/ ]CCCCCCAAGTAC [A/C]
			CCACGAAAATTTCAT
		98678	AATCTTGAACTCTAA [A/G]CTGGCACGTTAAGTT	AluI	FRT
		98714/98729	AAATAATTGTATTTT [T/G]TGTTTTATCCGTTT [CT/TTC]
95D	AE003746	239	ACAACTAGTTAAATC [C/A]AATTTCGAGCAGAGA
			GTGAAGAAACTGGTT
		313/323/329	TGCATTTTATCGCAT [C/T]CCCCCTCCC [C/T]CCCTT [G/A]	MseI	FRT
			AGGCTAACAACTTTG
		351	ACAACTTTGGACAAC [A/G]TCCGATCATACGCAT
96A	AE003748	492	GATGTTGCTGCTGCC [T/G]TTGCTGCTGTTGCCG	-	M
		631	TCCATCAGACAGCAG [/CACACCAC]CACACCACCACCAAA	-
96B	AE003750	11903	AACCAATCGCAACAA [CTT/GTC]GAATTATTATTTATT	-	Other
		12039	GACGCGTCATCACTC [C/G]GCCGGCCACCTGTGG	-
		13160	TTTTCGCTGCCCCCC [/C]ATCCCAATTCTTCTG	-	ND
		13198	CGCAGTTCTTCGGAC [A/T]TCTCGCTCCCTACGC	-
		13259	CGATCTATCGATCGG [G/A]CGATCGAACTGTAAC	-
96F	AE003753	8873	TTGTCAACGTGGTTG [A/C]ACTCACTTGGCGACC	-	Other
97B	AE003756	204	TAAAAATGGCAGAGG [A/G]CAATCCGCAGTTCCC	-	ND
		300	TTGCCTTCGTCTAAG [A/G]ACACAAGGGGTTCTC	-
		1673	CTCCGTCCTTCAGTC [/CTTCAGGC]AGTCAGTCAGTCAGT	-	M
97C	AE003757	8170/8177	CTCTTCCTAAAGATG [C/A]TAGTTT [/T]	-	M
			AAGGATAGTTTGCGC
		8245	TTTATGATTGCGTTG [G/A]GCATAAAAATGTGAA	-
		8269	ATGTGAAATATTGTT [A/G]AAGCCGAGACATTAA	-
		8883	TCACGCTCTCCTGGC [C/T]AGGATGCACATTTGC	HaeIII	FRT
97F	AE003760	104426	TCGGTTTCGGTTTTG [C/T]CCCACTGAAAAACAT
		104483	CGAAAAATTGGTATT [C/T]AACTAATGGGCAACG	MseI	M
98A	AE003761	1047	CACACGAAACGTAAA [C/G]GATGCGCAGCACTTA	FokI	M
98B	AE003762	1805	CACAATCCCAGCTCG [G/A]GTTATATAAGTCTGT	XhoI	FRT
	AE003763	1291	GCTTAACAAGTTGTG [G/T]CAATTGGTCGGCAAA	-	Other
		3570	ATAATAAAATAAAAC [T/C]CAATATCCTGGCGAG
		3628	GCATGTGAACTATTC [G/A]ATTCGCTCATTTCAT	HinfI	M
98C	AE003764	1318	GATAACTATATGGAT [G/T]GGATATATGGCAGGC	FokI	M
98D	AE003767	38575	GGGGAGGAAAAGCGA [T/C]TTTTCTACTTATTTT	-	M
98E	AE003768	13811	ATTGTCGAAACTGCT [G/A]GCTTCAAATTGAATT	-	ND
		13877	TCAAGCTCCACGCCT [G/A]TTGGAATTCATTTAT	-
99A	AE003769	3234	AACACATTCCCTGTG [A/G]CCACCCAAGCATCCC	HaeIII	M
		3333	AAACTTGAACTCGAA [C/A]TGGTACGGCGAAGTG
99C	AE003771	43332	AACTATCGAGCTGGT [AAAAC/ ]A(13)
		43486	ATACGTTTATCAGGA [G/C]CGC...
		43492	TG[TTTATAGCGAAAATGGGGGAGGGGGGGGGTT/	ND^*	FRT
			AGAGGGGGGTG]GGGGTTAGAT
99E	AE003773	228	GTGAACTTGGCACTG [C/A]GGCGTGACTCAGAAA	-	M
100B	AE003776	497	TTCCTCCCCTAAAAG [A/C]ACCGACAAATGCAGT
		519	AAATGCAGTAGTTAG [C/G]CCAAGACATCATCTC	HaeIII	M
	AE003777	451	AATGTTGGCAGGACC [T/A]CTCGATGAGTTGGCT	DraII	FRT
100C	AE003778	1549	AGAAAACCGCAGGGC [G/T]TGTGGCGCATTTCGA	-	FRT
100F	AE003780	60202	TTACAAATTTTTTTT [/TT]ACCTAGCTTACAATT	-	FRT
		85827	ACATAATGAAGAGAC [T/C]ATTTGAAATATTCAT	-	Other

All the polymorphisms analyzed between the FRT 82B chromosome and the marker chromosome are shown. The table lists the approximate cytological location, the accession number of the genomic scaffold sections, the base-pair position within the section and the sequence of the polymorphisms. In 75% of the cases, the polymorphisms are real SNPs, where one nucleotide is replaced by another. In the other 25%, the nature of the polymorphisms is more complex, and involves multiple base changes or small deletions/insertions. When the polymorphism creates an RFLP (in about 50% of the cases), the experimentally tested enzyme is shown on the right. In four cases, a 2% agarose gel could resolve the migration difference of the two PCR products (when the polymorphisms were deletions of at least 20 bp). In these cases, RFLP patterns were not tested (indicated by ND^*). The last column indicates the pattern of the TM3 balancer chromosome on either RFLP or SSCP gels. M indicates that the TM3 band co-migrates with the marker chromosome and FRT, that it co-migrates with the FRT chromosome. In a few cases, the TM3 migration pattern was different from both of these chromosomes, sindicating the presence of another allele on the balancer.

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