Cucumber Genome Resequenced Revealing An Evolutionary Enigma
October 21, 2013

Re-Sequencing Project Could Aid Genetic Enhancement Of Cucumbers

redOrbit Staff & Wire Reports - Your Universe Online

Large-scale, deep re-sequencing of 115 cucumbers worldwide has led to the creation of a genomic variation map for the vegetable that includes 3.6 million variants, an international team of scientists report in a new study.

The authors, who hail from the Genome Centre of the Chinese Academy of Agricultural Sciences (CAAS), the Beijing Genomics Institute (BGI) and other institutions, have published their work in the online edition of the journal Nature Genetics.

Their research sheds new light on the genetic basis of the domestication and diversity of this essential vegetable, and provides new insight for those trying to improve cucumber crops through genetic variation. In 2009, cucumbers became the seventh plant to have its genome sequence published, and in addition to being a widely-consumed agricultural product, it also serves as a model system for both sex determination and plant vascular biology.

In the new study, CAAS and BGI researchers re-sequenced 115 cucumber lines sampled from over 3,300 accessions throughout the world. They also performed de novo sequencing (sequencing involving the assembly of short reads to create full-length, sometimes novel sequences) on a wild cucumber.

The study authors said that they were able to detect a total of more than 3.3 million single-nucleotide polymorphisms (SNPs), or DNA sequence variations occurring when a lone nucleotide in the genome differs between members, over 330,000 small insertions and deletions (indels) and nearly 600 presence-absence variations (PAVs). They used this information to craft a comprehensive variation map of the cucumber.

In addition, they performed a series of model-based analyses of population structure and phylogenetic reconstruction, and found that the Eurasian, East Asian, and Xishuangbanna cultivated groups of cucumber are each monophyletic and genetically somewhat homogeneous. However, they uncovered evidence of substructure and genetic heterogeneity in the Indian group, and additional research found that this subset “holds great potential for introducing new alleles into the cultivated gene pool,” researchers from BGI Shenzen said in a statement Sunday.

“To understand the population bottlenecks during domestication, researchers made a comparison analysis between vegetable and grain food crops,” the institute added. “The comparison result indicated that the three vegetable crops (cucumber, watermelon, and tomato) probably underwent narrower bottleneck events during domestication than the grain food crops (rice, maize, and soybean).”

The BGI and CAAS-led scientists were also able to identify 112 putative domestication sweeps in the cucumber genome – a discovery which they claim could inspire the use of wild germplasm in future vegetable breeding. The genetic variations include the loss of the bitter taste found in wild cucumbers,  a change that occured during the domestication process, as well as the β-carotene hydroxylase gene found only in the Xishuangbanna group. By adding that gene during cucumber breeding, the researchers said that they could enhance the crop’s nutritional value.

“This study not only generates valuable genomic resource including additional wild reference genome, genome-wide variations for further studies and breeding applications on cucumber, but also gave us a better picture about how the cucumber genome evolved during domestication,” explained Xin Liu, Project Manager from BGI. “It is also a good example for studies on vegetable or other economic crops. Large scale sequencing approach and genome wide analysis can be applied on different economic crops for better understanding their evolutionary process and specific traits, providing unique opportunities for further applications.”