home news forum careers events suppliers solutions markets expos directories catalogs resources advertise contacts
 
News Page

The news
and
beyond the news
Index of news sources
All Africa Asia/Pacific Europe Latin America Middle East North America
  Topics
  Species
Archives
News archive 1997-2008
 

New achievements made in cucumber genomic study


China
October 25, 2013

In a collaborative study published online in Nature Genetics on October 21, the research team led by Pro. Huang Sanwen from the Institute of Vegetables and Flower of Chinese Academy of Agricultural Sciences (CAAS) presented a genomic variation map demonstrating cucumber's evolutionary enigma. As the latest progress in this research area, the map 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 also delivers guidance for breeders to harness genetic variation for crop improvement.

 

 

 

Traditionally, 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, the above-mentioned research team re-sequenced 115 cucumber lines sampled from 3,342 accessions worldwide, and conducted de novo sequencing on a wild cucumber. In total, the researchers 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, the 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 provides 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, the 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 an eatable vegetable is to degenerate its bitter taste. Two genetic loci, Bi and Bt, are known to confer bitterness in cucumber. In this study, the 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 β-carotene that was reported to be controlled by a single recessive gene ore. Accordingly, the researchers concluded that it is a key natural variation in a β-carotene hydroxylase gene that could be used to breed cucumber with enhanced nutritional value.

 

In summary, 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 provides a better picture about how the cucumber genome evolved during domestication. It sets a good example that large scale sequencing approach can be applied widely in genome analysis, particularly in studying the evolutionary process and specific traits of various economic crops. 

 

Adapted from Large-scale deep re-sequencing reveals cucumber's evolutionary enigma (http://phys.org/news/2013-10-large-scale-deep-re-sequencing-reveals-cucumber.html)

 



More news from: China, Ministry of Agriculture


Website: http://www.agri.gov.cn

Published: October 25, 2013

The news item on this page is copyright by the organization where it originated
Fair use notice

 

 

 

 

 

 

 

 

 

 

 


Copyright @ 1992-2024 SeedQuest - All rights reserved