Integration of High-Resolution Physical and Genetic Map Reveals Differential Recombination Frequency between Chromosomes and the Genome Assembling Quality in Cucumber

Qunfeng Lou,Zhonghua Zhang,Sanwen Huang,Ji Li,Jinfeng Chen,Chunyan Cheng,Yuhua He,Tongming Yin

doi:10.1371/journal.pone.0062676

Abstract

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.

Highlights

Cucurbitaceae is a moderately family composed of about 130 genera and 900 species [1]
The difference of recombination frequency along chromosome had been reported in many species [18,20,26]
The severe recombination repression has been frequently found on the pericentromeric heterochromatin domains in higher plants, which leads to gathering distribution of multiple molecular markers in closely spaced positions of linkage map [17,18,20,27]

Summary

Introduction

Cucurbitaceae is a moderately family composed of about 130 genera and 900 species [1]. Substantial genetic and genomics researches have been conducted in cucumber, including high density genetic maps [6,7], large insert DNA library such as fosmid [6], and three drafts of genome sequence from Chinese type cucumber [3], American type cucumber [8], and European type cucumber [9]. The molecular cytogenetic map of chromosome 2 of cucumber inbred line 9930 was recently constructed based on the fosmid-FISH on pachytene chromosome [23]. FISH based on high resolution pachytene chromosomes will be able to provide a powerful tool to construct the molecular cytogenetic map, and produce substantial information to polish sequence assembly

Methods

Results

Conclusion