Plant Molecular Biology 39: 171–176, 1999.
© 1999 Kluwer Academic Publishers. Printed in the Netherlands.
Genetic and physical characterization of a region of Arabidopsis
chromosome 1 containing the CLAVATA1 gene
Robert W. Williams
and Elliot M. Meyerowitz
Division of Biology, 156–29, California Institute of Technology, Pasadena, CA 91125, USA (
author for corre-
Department of Biology, University of Michigan, Ann Arbor, MI 48109–1048, USA;
authors contributed equally to this work
Received 24 March 1998; accepted in revised form 6 July 1998
Key words: Arabidopsis, CLAVATA1, genome sequencing, RFLP, YAC contig
With the advance of Arabidopsis as a model system for understanding plant genetics, development and biochem-
istry, a detailed description of the genome is necessary. As such, focused projects are underway to map and
sequence the Arabidopsis nuclear genome. We have characterized a region of chromosome 1, surrounding the
CLAVATA1 (CLV1) locus. Three (RFLP) clones were mapped relative to clv1-1, and were used to construct an ca.
700 kb yeast artiﬁcial chromosome (YAC) contig. Three cosmids spanning the CLV1 locus were analyzed and ca.
24 kb of genomic DNA was sequenced, including a continuous stretch of 18 kb. In addition to generating clones in
this region of chromosome 1, we have analyzed the size, spacing and organization of several contiguous genes.
Mapping RFLP clones near CLV1
The CLV1 gene, which encodes a receptor-like kinase,
was previously mapped to the bottom of chromosome
1 [1, 2]. This included generating meiotic recombi-
nation breakpoints between clv1-1 and the ﬂanking
visible markers ap1-1 and ga2 and using these recom-
binants to map the m532 RFLP clone [1, 3]. Using
the same recombinants, we mapped three additional
RFLP clones relative to clv1-1. N7-24 mapped 19/124
recombinants proximal to clv1-1. m237  and g6838
 both mapped 9/82 recombinants distal to CLV1
(Figure 1). This ﬁne-scale mapping revealed that the
order of the RFLP clones and their positions relative
to CLV1 are different than previously reported .
Construction of the YAC contig
To construct a physical map of the CLV1 region, three
different RFLP clones were hybridized to the yUP,
The nucleotide sequence data reported will appear in the
EMBL, GenBank and DDBJ Nucleotide Sequence Databases under
the accession number AF049870.
EW and EG YAC libraries [6–8]. The N7-24 clone
hybridized to yUP3G5, yUP7C8, yUP17F5, EW4E10
and EW6G11(Figure 1). The restriction pattern of N7-
24 hybridizing fragments was altered in the yUP7C8
clone so it was determined that N7-24 lies at one
end of the YAC insert. yUP7C8 did not hybridize
to a nearby proximal marker, KG-24, so yUP7C8
probably extends towards the CLV1 gene (data not
shown). Clone m532 hybridizedto yUP4B3,yUP7C7,
yUP13C10, and EG8D6. Clone g6838 also hybridized
to yUP4B3 and EG8D6 as well as to EW1G5. yUP7C7
hybridized to m532 and m237 but not to g6838. This
indicates that even though m237 and g6838 mapped
the same distance from CLV1 based on recombinants,
g6838 is distal to m237.
The left and/or right ends of some of the YACs
were isolated by either inverse PCR or plasmid rescue
[9, 10] (Table 1). The left end of yUP13C10 hy-
bridized to both yUP7C8 and yUP3G5, indicating that
the region from markers N7-24 to m532 was contigu-
ous (Figure 1). The left end of yUP4B3 was used to
isolate a lambda genomic clone calledB2. A polymor-
phism between L-er and Col-0 was identiﬁed and B2