Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber.
Cucumber is an important model crop and the first species sequenced in Cucurbitaceae family. Compared to the fast increasing genetic and genomics resources, the molecular cytogenetic researches in cucumber are still very limited, which results in directly the shortage of relation between plenty of p...
Main Authors: | , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Public Library of Science (PLoS)
2013-01-01
|
Series: | PLoS ONE |
Online Access: | http://europepmc.org/articles/PMC3646037?pdf=render |
id |
doaj-4bc9ec0736aa46b9a9b369f37ee192da |
---|---|
record_format |
Article |
spelling |
doaj-4bc9ec0736aa46b9a9b369f37ee192da2020-11-25T02:23:38ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0185e6267610.1371/journal.pone.0062676Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber.Qunfeng LouYuhua HeChunyan ChengZhonghua ZhangJi LiSanwen HuangJinfeng ChenCucumber is an important model crop and the first species sequenced in Cucurbitaceae family. Compared to the fast increasing genetic and genomics resources, the molecular cytogenetic researches in cucumber are still very limited, which results in directly the shortage of relation between plenty of physical sequences or genetic data and chromosome structure. We mapped twenty-three fosmids anchored by SSR markers from LG-3, the longest linkage group, and LG-4, the shortest linkage group on pachytene chromosomes 3 and 4, using uorescence in situ hybridization (FISH). Integrated molecular cytogenetic maps of chromosomes 3 and 4 were constructed. Except for three SSR markers located on heterochromatin region, the cytological order of markers was concordant with those on the linkage maps. Distinct structural differences between chromosomes 3 and 4 were revealed by the high resolution pachytene chromosomes. The extreme difference of genetic length between LG-3 and LG-4 was mainly attributed to the difference of overall recombination frequency. The significant differentiation of heterochromatin contents in chromosomes 3 and 4 might have a direct correlation with recombination frequency. Meanwhile, the uneven distribution of recombination frequency along chromosome 4 was observed, and recombination frequency of the long arm was nearly 3.5 times higher than that of the short arm. The severe suppression of recombination was exhibited in centromeric and heterochromatin domains of chromosome 4. Whereas a close correlation between the gene density and recombination frequency was observed in chromosome 4, no significant correlation was observed between them along chromosome 3. The comparison between cytogenetic and sequence maps revealed a large gap on the pericentromeric heterochromatin region of sequence map of chromosome 4. These results showed that integrated molecular cytogenetic maps can provide important information for the study of genetic and genomics in cucumber.http://europepmc.org/articles/PMC3646037?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Qunfeng Lou Yuhua He Chunyan Cheng Zhonghua Zhang Ji Li Sanwen Huang Jinfeng Chen |
spellingShingle |
Qunfeng Lou Yuhua He Chunyan Cheng Zhonghua Zhang Ji Li Sanwen Huang Jinfeng Chen Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber. PLoS ONE |
author_facet |
Qunfeng Lou Yuhua He Chunyan Cheng Zhonghua Zhang Ji Li Sanwen Huang Jinfeng Chen |
author_sort |
Qunfeng Lou |
title |
Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber. |
title_short |
Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber. |
title_full |
Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber. |
title_fullStr |
Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber. |
title_full_unstemmed |
Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber. |
title_sort |
integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2013-01-01 |
description |
Cucumber is an important model crop and the first species sequenced in Cucurbitaceae family. Compared to the fast increasing genetic and genomics resources, the molecular cytogenetic researches in cucumber are still very limited, which results in directly the shortage of relation between plenty of physical sequences or genetic data and chromosome structure. We mapped twenty-three fosmids anchored by SSR markers from LG-3, the longest linkage group, and LG-4, the shortest linkage group on pachytene chromosomes 3 and 4, using uorescence in situ hybridization (FISH). Integrated molecular cytogenetic maps of chromosomes 3 and 4 were constructed. Except for three SSR markers located on heterochromatin region, the cytological order of markers was concordant with those on the linkage maps. Distinct structural differences between chromosomes 3 and 4 were revealed by the high resolution pachytene chromosomes. The extreme difference of genetic length between LG-3 and LG-4 was mainly attributed to the difference of overall recombination frequency. The significant differentiation of heterochromatin contents in chromosomes 3 and 4 might have a direct correlation with recombination frequency. Meanwhile, the uneven distribution of recombination frequency along chromosome 4 was observed, and recombination frequency of the long arm was nearly 3.5 times higher than that of the short arm. The severe suppression of recombination was exhibited in centromeric and heterochromatin domains of chromosome 4. Whereas a close correlation between the gene density and recombination frequency was observed in chromosome 4, no significant correlation was observed between them along chromosome 3. The comparison between cytogenetic and sequence maps revealed a large gap on the pericentromeric heterochromatin region of sequence map of chromosome 4. These results showed that integrated molecular cytogenetic maps can provide important information for the study of genetic and genomics in cucumber. |
url |
http://europepmc.org/articles/PMC3646037?pdf=render |
work_keys_str_mv |
AT qunfenglou integrationofhighresolutionphysicalandgeneticmaprevealsdifferentialrecombinationfrequencybetweenchromosomesandthegenomeassemblingqualityincucumber AT yuhuahe integrationofhighresolutionphysicalandgeneticmaprevealsdifferentialrecombinationfrequencybetweenchromosomesandthegenomeassemblingqualityincucumber AT chunyancheng integrationofhighresolutionphysicalandgeneticmaprevealsdifferentialrecombinationfrequencybetweenchromosomesandthegenomeassemblingqualityincucumber AT zhonghuazhang integrationofhighresolutionphysicalandgeneticmaprevealsdifferentialrecombinationfrequencybetweenchromosomesandthegenomeassemblingqualityincucumber AT jili integrationofhighresolutionphysicalandgeneticmaprevealsdifferentialrecombinationfrequencybetweenchromosomesandthegenomeassemblingqualityincucumber AT sanwenhuang integrationofhighresolutionphysicalandgeneticmaprevealsdifferentialrecombinationfrequencybetweenchromosomesandthegenomeassemblingqualityincucumber AT jinfengchen integrationofhighresolutionphysicalandgeneticmaprevealsdifferentialrecombinationfrequencybetweenchromosomesandthegenomeassemblingqualityincucumber |
_version_ |
1724858204996763648 |