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Keywords type of F. vesca. Our study can serve as a basis for future
FISH · Fragaria vesca · Karyotype · Oligonucleotide probes · comparative cytogenetic research through cross-species
rDNA chromosome painting using bulked oligo probes and will
facilitate the application of breeding technologies that rely
on the identification of chromosomes in the genus Fragaria.
Abstract © 2017 S. Karger AG, Basel
Chromosome identification is critical for many aspects of
cytogenetic research. However, for Fragaria vesca, definite
identification of individual chromosomes is almost impos- The strawberry genus Fragaria includes about 25 spe-
sible because of their small size and high similarity. Here, we cies, the majority being diploid with 2n = 2x = 14; the
demonstrate that bulked oligonucleotide (oligo) probes can polyploids range from tetraploid, hexaploid, and octa-
be used as chromosome-specific DNA markers for chromo- ploid to decaploid [Liu and Davis, 2011]. Many Fragaria
some identification in F. vesca. Oligos specific to entire pseu- species are valued for their edible fruits. The economi-
dochromosomes in the draft genome of F. vesca were identi- cally most important of these is the cultivated strawberry
fied and synthesized as libraries. In all, we synthesized 6 oligo (Fragaria × ananassa) that is grown in over 60 countries.
libraries corresponding to 6 pseudochromosomes of F. ves- The knowledge of phylogenetic relationships and the ge-
ca. These libraries were amplified and labeled as probes for netic affinities among Fragaria species can help to choose
fluorescence in situ hybridization (FISH). Two rounds of mul- parents from various species for introgression of wild
ticolor FISH analysis were sequentially conducted on the genes into cultivars. However, our current understanding
same metaphase cells with each round including 3 probe of the relationships between the diploid Fragaria species
libraries, which permitted simultaneous identification of all and the origin of the polyploid species is limited although
chromosomes of F. vesca. Moreover, 45S and 5S rDNA were various analyses have been carried out [Rousseau-Gueu-
mapped to chromosomes 1, 2, and 7, respectively. A karyo- tin et al., 2009; Njuguna et al., 2013; DiMeglio et al., 2014;
type of metaphase chromosomes was constructed, repre- Hirakawa et al., 2014; Liston et al., 2014; Sargent et al.,
senting the first FISH-based molecular cytogenetic karyo- 2016].
130.241.16.16 - 12/21/2017 10:12:27 AM
E-Mail karger@karger.com
Xuzhou 221116 (China)
www.karger.com/cgr
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which have been used for chromosome identification in in distilled water prior to enzyme treatment (2% cellulose and 1%
many plant species. In the genus Fragaria, the application pectolyase) at 37 ° C for 4 h. The digested root tips were macerated
probes for chromosome identification in F. vesca. in a second ethanol series, and reprobed with different probes. Bi-
In the present study, oligos specific to entire pseudo- otin-labeled probes were detected by Alexa Fluor 488 streptavidin;
digoxigenin-labeled probes were detected by rhodamine anti-di-
chromosomes in the draft genome of F. vesca “Hawaii 4”
goxigenin. When 3 probes were used in a FISH experiment, the first
were identified and synthesized as libraries. In all, we syn- and the second probe were labeled by biotin and digoxigenin, re-
thesized 6 oligo libraries corresponding to 6 pseudochro- spectively; the third probe was labeled by biotin and digoxigenin
mosomes of F. vesca. These libraries were amplified and (1: 1), which resulted in a yellow detection color. Chromosomes
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Measurements a b c
For each F. vesca accession, 3 of the best images were selected
for measuring the long and short arm lengths. The images of
DAPI-stained chromosomes were converted into black-white im-
ages to clearly show the centromere position. The “measurement”
tool of Adobe Photoshop was used for all size estimations. Relative
chromosome length and arm ratio were calculated based on mea-
suring 3 metaphase cells. Chromosomes were classified according
to Levan et al. [1964]. d e f
Results g
a b d
a b g
c e f h
Fig. 2. Karyotyping of Fragaria vesca from Shenyang Agricultural Fig. 3. FISH of oligo probes and 5S and 45S rDNA in Fragaria
University using oligo libraries. a Simultaneous hybridization of vesca subsp. vesca (a–d) and F. vesca from Shenyang Agricultural
libraries 1 (red), 2 (green), and 3 (yellow). b The same cell as in a University (e–h). a, e Simultaneous hybridization of libraries 1
reprobed with libraries 4 (yellow), 5 (red), and 6 (green). c The (green) and 2 (red). b, f The same cells as in a and e were reprobed
DAPI-stained chromosomes in a were converted into black-white with 5S rDNA (red) and 45S rDNA (green). c, g The chromosomes
images to clearly show the centromere position, cut out, and ar- with the 5S rDNA (red) and 45S rDNA (green) signals in b and f,
ranged. The results of the karyotype analysis are given in Table 1. respectively. DAPI-stained chromosomes were converted into
Scale bar, 5 μm. black-white images to clearly show satellites and secondary con-
strictions. d The chromosomes with 5S (red) and 45S rDNA
(green) signals from Figure 1f. h The chromosomes with 5S (red)
and 45S rDNA (green) signals from another metaphase cell of F.
vesca from Shenyang Agricultural University. Scale bars, 5 μm.
Table 1. Relative lengths and arm ratios of mitotic metaphase chro- and Figure 1h, with chromosome nomenclature follow-
mosomes of 2 Fragaria vesca accessions ing the pseudochromosomes in the draft genome of F.
vesca “Hawaii 4” [Shulaev et al., 2011].
Accession Chromosome Relative Arm ratiob Chromosome
number lengtha, % morphologyc We also analyzed the karyotype of the F. vesca acces-
sion obtained from Shenyang Agricultural University
F. vesca subsp. 1 12.88 ± 1.10 1.99 ± 0.13 sm
vesca 2 14.89 ± 0.06 1.32 ± 0.13 m
with this set of oligo probes. This accession exhibited sim-
3 16.12 ± 0.66 1.23 ± 0.06 m ilar karyotype results to F. vesca subsp. vesca, although the
4 14.62 ± 0.33 1.29 ± 0.21 m descending orders of chromosome lengths were different
5 13.55 ± 0.59 1.58 ± 0.21 m for both F. vesca accessions (Fig. 2; Table 1). Both acces-
6 16.99 ± 0.74 1.17 ± 0.15 m sions had 5 pairs of metacentric chromosomes (chromo-
7 10.95 ± 0.86 2.39 ± 0.19 sm
somes 2 to 6) and 2 pairs of submetacentric chromosomes
F. vesca from 1 12.09 ± 1.08 1.77 ± 0.17 sm (chromosomes 1 and 7). The longest chromosome was
Shenyang 2 14.12 ± 0.52 1.48 ± 0.20 m
3 15.79 ± 0.08 1.19 ± 0.04 m
chromosome 6, and the shortest one was chromosome 7.
4 13.78 ± 0.95 1.42 ± 0.11 m However, the 2 accessions differed from each other in the
5 15.27 ± 1.36 1.65 ± 0.15 m number of 45S rDNA sites. In F. vesca subsp. vesca, only
6 17.95 ± 1.01 1.05 ± 0.02 m one chromosome 7 had 45S rDNA signals at the satellite
7 11.00 ± 0.91 2.07 ± 0.01 sm and secondary constriction (Fig. 3c, d, indicated by ar-
a
Relative length = 100 × chromosome length/total complement length. rows). The other chromosome 7 displayed no 45S rDNA
b
Arm ratio = length of the long arm/length of the short arm. signals and did not have the satellite and secondary con-
c
m, metacentric; sm, submetacentric. striction. In contrast, in the F. vesca accession from
Shenyang Agricultural University, both chromosomes 7
had 45S rDNA sites (Fig. 3f–h). Furthermore, differences
in signal size and intensity were observed among the three
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