CAPS analysis of RLD ecotype

[Hiroaki Ichikawa]

Dear netters,

I have performed PCR-amplification/restriction digestion (CAPS 
analysis) in DNAs from RLD, Columbia ecotype (Col) and Landsberg-
erecta (Ler). The result of the CAPS analysis is as follows. I found 
that the restriction pattern of RLD DNA at a particular marker can 
be the same as either that of Col or that of Ler except for the GL1 
marker which confers the novel fragment pattern on RLD. 

I would greatly appreciate that you could kindly confirm the BGL1 
marker/Sau3AI-restriction patterns of Col and Ler. My experiment 
has reproducibly shown that there is no Sau3AI site in a PCR 
product from Col, but a single site in products from both Ler and 
RLD.

In the BGL1 marker, the Sau3AI-restriction pattern of
RLD (0.9 kb + 0.4 kb) was identical to that of Ler. However,
the Sau3AI patterns of Col and Ler in my experiment were opposite
to those reported by Konieczny and Ausubel (1993). There was no 
Sau3AI site in a PCR product from Col, but a single site in products 
from both Ler and RLD.

In response to my inquiry, Dr. Eliana Drenkard in Professor Ausubel 
Lab. has kindly performed the CAPS analysis on the BGL1 marker, 
and has confirmed  that my BGL1 results are reproducible.

Thank you for your kind attention.
With best regards,

Hiroaki Ichikawa


Table .  CAPS analysis of RLD ecotype

Chromosome     Marker        Enzyme      Genotype

I                       PVV4           BsaAI              C
I                       NCC1           RsaI                 L
I                       UFO             TaqI                 C
I                       GAPB           DdeI                C
I                       ADH             XbaI                 L
II                      m246          MaeIII              L
II                      GPA1          AflIII               L
II                      m429         ScrFI                L
III                    GAPC          EcoRV               C
III                    GAPA          DdeI                 L
III                    GL1             TaqI                 R
III                    BGL1           RsaI                 L
                                          Sau3AI             L
                                          AflIII               L
IV                    GA1            BsaBI               C
IV                    g4539         HindIII             C
IV                    AG              XbaI                  L
IV                    PRHA          DdeI                  L
IV                    DHS1          DdeI                  L
                                         BsaBI                L
V                     CTR1          BclI                  C
V                     ASA1          BclI                  L
V                     NIT4           MboII                L
V                     PHYC          ScrFI                 C
V                     DFR            BsaAI                L
V                     LFY3           RsaI                  L

C denotes a Col genotype; L: a Ler genotype; R: a genotype
unique to RLD (0.4 kb + ~0.12 kb).