DNA Marker Primer Information
Primer Information
Primer. | f/r | sequence | Taget | Type of markers | Reference | |||||
---|---|---|---|---|---|---|---|---|---|---|
5P2 | f | GTAGCCGTTGTTAAACCAGG TCGAATACTTTATGAAATG |
PS-ID (rpl116-rpl14 linker sequence) | sub-species unique sequence | Nakamura et al. 1997 | |||||
This primer was used to sequence nucleotide from a stop codon of rpl16. SNPs at three sites were recorded as (4-16nt)-(31-36nt)-(61-64t) known as SNP-composition for PS-ID. | ||||||||||
3P | r | ATCTGCAGCATTTAAAA GGGTCTGAGGTTGAATCAT |
PS-ID (rpl116-rpl14 linker sequence) | sub-species unique sequence | ||||||
This primer was used to sequence nucleotide from a stop codon of rpl16. SNPs at three sites were recorded as (4-16nt)-(31-36nt)-(61-64t) known as SNP-composition for PS-ID. | ||||||||||
RCt1 | f | catccttttcaatccaaaatca | Rct1, Nipponbare=A10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt1 | r | tgcctgatgtagggaaaagc | Rct1, Nipponbare=A10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt2 | f | ctgggggggattatacctgt | Rct2, Nipponbare=A11 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt2 | r | atatctctcatttccgacgca | Rct2, Nipponbare=A11 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt3 | f | taggcataattcccaaccca | Rct3, Nipponbare=A10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt3 | r | cttatccatttggagcataggg | Rct3, Nipponbare=A10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt4 | f | acggaattggaacttctttgg | Rct4, Nipponbare=T12 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt4 | r | aaaaggagccttggaatggt | Rct4, Nipponbare=T12 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt5 | f | atttggaatttggacattttcg | Rct5, Nipponbare=T10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt5 | r | actgattcgtaggcgtggac | Rct5, Nipponbare=T10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt6 | f | gaattttagaactttgaattttttaccc | Rct6, Nipponbare=A10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt6 | r | aagcgtaccgaagactcgaa | Rct6, Nipponbare=A10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt7 | f | gtgtcattctctaggcgaac | Rct7, Nipponbare=T10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt7 | r | aaatatgacagaaaagaaaaatagg | Rct7, Nipponbare=T10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt8 | f | atagtcaagaaagaggatctagaat | Rct8, Nipponbare=T17 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt8 | r | accgcgattcaataagagta | Rct8, Nipponbare=T17 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt9 | f | ataaggttattccccgcttacc | Rct9, Nipponbare=T10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt9 | r | aaattgggggaattcgtacc | Rct9, Nipponbare=T10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt10 | f | tcttcatttggaatctgggc | Rct10, Nipponbare=T10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
RCt10 | r | ctattgatgcaaacgctgtacc | Rct10, Nipponbare=T10 | Simple nucleoide repeats | Ishii and McCouch 2000 | |||||
Simple sequence was recorded by 6% sequencing gel | ||||||||||
Reference | Ishi, T. and S.R. McCouch Theor. Appl. Genet. (2000) 100:1257-1266 Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight Gramineas spesies Nakamura, I., N. Kameya, Y. Kato, S. Yamanaka, H. Jomori and Y-I. Sato (1997)Breeding Science 47:385-388. A proposal for the short ID sequence which addressed the plastid subtype of higher plants. |