Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Large-scale deep re-sequencing reveals cucumber's evolutionary enigma

21.10.2013
The latest study was published online in Nature Genetics

In a collaborative study published online today in Nature Genetics, researchers from the Genome Centre of Chinese Academy of Agricultural Sciences (CAAS), BGI, and other institutes present a cucumber genomic variation map that includes about 3.6 million variants revealed by deep resequencing of 115 cucumbers worldwide.

This work provides new insights for understanding the genetic basis of domestication and diversity of this important crop, and provides guidance for breeders to harness genetic variation for crop improvement.

Cucumber is a major vegetable crop consumed worldwide as well as a model system for sex determination and plant vascular biology. In 2009, cucumber became the seventh plant to have its genome sequence published, following the well-studied model plant Arabidopsis thaliana, the poplar tree, grapevine, papaya, and the crops rice and sorghum. More efforts have been put into cucumber genomics research since then.

As a part of these efforts, researchers from CAAS and BGI re-sequenced 115 cucumber lines sampled from 3,342 accessions worldwide, and also conducted de novo sequencing on a wild cucumber. In total, they detected more than 3.3 million SNPs, over 0.33 million small insertion and deletions (indels), and 594 presence-absence variations (PAVs), and then constructed a comprehensive variation map of cucumber.

Furthermore, researchers did a suite of model-based analyses of population structure and phylogenetic reconstruction. The results indicated that the three cultivated groups (Eurasian, East Asian, and Xishuangbanna) each are monophyletic and genetically quite homogeneous, but the Indian group shows clear evidence of substructure and genetic heterogeneity. Their further analysis also provide evidence on the ancestral status of the Indian group, which holds great potential for introducing new alleles into the cultivated gene pool.

To understand the population bottlenecks during domestication, researchers made a comparison analysis between vegetable and grain food crops. 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). In addition, they also identified 112 putative domestication sweeps in the cucumber genome. These findings provide additional impetus for the use of wild germplasm in future vegetable breeding.

Wild cucumber is an extremely bitter fruit. An essential step in the domestication of the wild cucumber into a eatable vegetable must have degenerated its bitter taste. Two genetic loci, Bi and Bt, are known to confer bitterness in cucumber. In this study, researchers found that the Bt locus was delimited to a 442-kb region on chromosome 5 that harbors 67 predicted genes.

They further investigated the genomic basis of divergence among the cultivated populations for identifying genes controlling important traits. The most obvious trait is the orange endocarp, which distinguishes the Xishuangbanna group from the other groups. This trait is caused by the accumulation of large amounts of â-carotene that was reported to be controlled by a single recessive gene ore. In this study, researchers discovered a key natural variation in a â-carotene hydroxylase gene that could be used to breed cucumber with enhanced nutritional value.

Xin Liu, Project Manager from BGI, said "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. 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."

About BGI

BGI was founded in 1999 with the mission of being a premier scientific partner to the global research community. The goal of BGI is to make leading-edge genomic science highly accessible through its investment in infrastructure that leverages the best available technology, economies of scale, and expert bioinformatics resources. BGI, which includes both private non-profit genomic research institutes and sequencing application commercial units, and its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications.

BGI has established a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research which has generated over 250 publications in top-tier journals such as Nature and Science. These accomplishments include sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and German deadly E. coli, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, most recently, have sequenced the human Gut metagenome, and a significant proportion of the genomes for 1,000 genomes. For more information about BGI please visit http://www.genomics.cn.

Contact Information:

Bicheng Yang, Ph.D.Public Communication Officer
BGI+86-755-82639701yangbicheng@genomics.cnhttp://www.genomics.cn

Jia Liu | EurekAlert!
Further information:
http://www.genomics.cn

More articles from Studies and Analyses:

nachricht Smart Data Transformation – Surfing the Big Wave
02.12.2016 | Fraunhofer-Institut für Angewandte Informationstechnik FIT

nachricht Climate change could outpace EPA Lake Champlain protections
18.11.2016 | University of Vermont

All articles from Studies and Analyses >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

Im Focus: Molecules change shape when wet

Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water

In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...

Im Focus: Fraunhofer ISE Develops Highly Compact, High Frequency DC/DC Converter for Aviation

The efficiency of power electronic systems is not solely dependent on electrical efficiency but also on weight, for example, in mobile systems. When the weight of relevant components and devices in airplanes, for instance, is reduced, fuel savings can be achieved and correspondingly greenhouse gas emissions decreased. New materials and components based on gallium nitride (GaN) can help to reduce weight and increase the efficiency. With these new materials, power electronic switches can be operated at higher switching frequency, resulting in higher power density and lower material costs.

Researchers at the Fraunhofer Institute for Solar Energy Systems ISE together with partners have investigated how these materials can be used to make power...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

UTSA study describes new minimally invasive device to treat cancer and other illnesses

02.12.2016 | Medical Engineering

Plasma-zapping process could yield trans fat-free soybean oil product

02.12.2016 | Agricultural and Forestry Science

What do Netflix, Google and planetary systems have in common?

02.12.2016 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>