Articles
LATEST ADVANCES IN WATERMELON GENOMICS
Article number
871_82
Pages
599 – 606
Language
English
Abstract
Watermelon is an important vegetable crop throughout the world and its worldwide harvested area is 21.7% of that of all vegetables.
The genetic diversity of cultivated watermelon is very narrow, which is a major limiting factor of its breeding.
Therefore it is necessary to develop new resources that can be used to widen watermelon genetic basis.
We have initiated the Watermelon Whole Genome Sequencing project and currently have generated Solexa sequences which represent more than 89.9X coverage of the genome of watermelon cv. 97103 and covered 95% of the whole genome and 98% of the genic region.
Further genome sequencing of 97103 using the traditional Sanger technology, comparative genome sequencing of watermelon cv. 90-4304 (10X coverage Solexa sequences), genome annotation is currently underway.
In addition, using Roche 454 GS-FLX massively parallel pyrosequencing technology, we have generated 715,059 ESTs with an average length of 250 bp from fruits of 97103 during different developmental stages.
These sequences are being assembled and functionally annotated.
SSR markers and pathway prediction have been analyzed preliminarily.
A comprehensive digital expression map during watermelon fruit development is being created.
Furthermore, we have constructed a SSH library from root tissues of watermelon cv. PI296341-FR infected by Fusarium wilt race1 and randomly sequenced approximately 3,895 SSH clones.
Sequence analysis indicated that 28.3% of the unique ESTs were related to defense response, signal transduction and interaction with the environment.
GFP gene is used as the marker to detect the infection process of Fusarium wilt in root tissue.
Three hundred twenty-four SSR and EST-SSR markers consist of the watermelon RIL SSR genetic map.
The relationships between four Chromosomes and the genome are identified by FISH.
The genetic diversity of cultivated watermelon is very narrow, which is a major limiting factor of its breeding.
Therefore it is necessary to develop new resources that can be used to widen watermelon genetic basis.
We have initiated the Watermelon Whole Genome Sequencing project and currently have generated Solexa sequences which represent more than 89.9X coverage of the genome of watermelon cv. 97103 and covered 95% of the whole genome and 98% of the genic region.
Further genome sequencing of 97103 using the traditional Sanger technology, comparative genome sequencing of watermelon cv. 90-4304 (10X coverage Solexa sequences), genome annotation is currently underway.
In addition, using Roche 454 GS-FLX massively parallel pyrosequencing technology, we have generated 715,059 ESTs with an average length of 250 bp from fruits of 97103 during different developmental stages.
These sequences are being assembled and functionally annotated.
SSR markers and pathway prediction have been analyzed preliminarily.
A comprehensive digital expression map during watermelon fruit development is being created.
Furthermore, we have constructed a SSH library from root tissues of watermelon cv. PI296341-FR infected by Fusarium wilt race1 and randomly sequenced approximately 3,895 SSH clones.
Sequence analysis indicated that 28.3% of the unique ESTs were related to defense response, signal transduction and interaction with the environment.
GFP gene is used as the marker to detect the infection process of Fusarium wilt in root tissue.
Three hundred twenty-four SSR and EST-SSR markers consist of the watermelon RIL SSR genetic map.
The relationships between four Chromosomes and the genome are identified by FISH.
Publication
Authors
Shaogui Guo, Yong Xu, Haiying Zhang, Guoyi Gong, Sanwen Huang, Hongping Yi, Mingzhu Wu, Yi Zheng, Zhangjun Fei
Keywords
whole genome sequencing, EST, fruit development, digital expression, SSR, SSH, genetic map
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