Presenting the first fully annotated reference genome of bread wheat

An international team of researchers has presented a fully annotated reference genome for bread wheat, one of the world's most important and widely cultivated crops. This landmark genomic sequence offers scientists a powerful new tool for accelerating the development of new wheat varieties designed to address human nutrition and crop resiliency needs. The advancement is highlighted in two Science reports, as well as one in Science Advances, all of which underscore the impact of this high-quality genome on understanding wheat biology and its potential for innovation in genomics-assisted breeding.

Wheat is a major source of nutrition worldwide, and with rapidly growing human populations and changing environments there is a strong demand for new varieties capable of improved yields, high nutrition, pest resistance and tolerance to changes in growing conditions. Detailed genome sequences of crops can lead to significant advances in creating hardier varieties by providing a guide to the underlying crops' most helpful traits; however, modern bread wheat is a complicated mix of three separate ancestral genomes, and as a result, fully decoding the plant's genome has been challenging.

In a Science report, the International Wheat Genome Sequencing Consortium (IWGSC) presents the first high-quality fully annotated reference genome sequence of the bread wheat variety Chinese Spring. Like an atlas the IWGSC Reference Sequence (RefSeqv1.0), provides the location and organization of over 107,000 genes and more than 4 million markers across all of this wheat variety's 21 chromosomes – some related to traits important to agriculture. According to the authors, the sequence can be leveraged for research in a variety of ways, including CRISPR- based genome modification.

A second study in Science uses the new reference genome to perform a genome-wide analysis of the expression of homoelogs, or gene copies that are similar but originate in different ancestral genomes. Pinpointing these in bread wheat will help scientists better understand the fundamental biology of polyploid wheat. By combining gene expression datasets with the IWGSC RefSeqv1 wheat genome sequence, Ricardo Ramirez-Gonzalez et al. revealed the balance of gene expression among homeologs across the various tissues, developmental stages and cultivars of wheat. Ramirez-Gonzalez et al. identified tissue-specific biases in gene expression and co-expression networks during development and exposure to stress. According to the authors, their work provides a framework to target key genes that underpin valuable agricultural traits in wheat.

Finally, in a Science Advances study leveraging the new IWGSC reference sequence, researchers closely examined the proteins contributing to various wheat-immune diseases and allergies, like celiac, baker's asthma and wheat-dependent exercise-induced anaphylaxis (WDEIA). Exposure to specific proteins in wheat can cause severe allergic reactions in some people. Celiac disease, for example – a globally prevalent chronic inflammatory disorder – is triggered by prolamin proteins gliadin and glutenin, both common in wheat. In addition, respiratory or skin exposure to other types of proteins have also been implicated in adverse immune responses. However, due to the complexity of the wheat genome and the lack of complete genome information for this crop, a detailed understanding of the nature of these proteins has remained elusive. Angela Juhász et al. used the IWGSC RefSeqv1.0 wheat genome to search for the genes that encode known allergy-inducing wheat proteins and mapped each across the entire sequence. Juhász et al.'s analysis identified 828 known and previously unknown genes potentially related to immune-responsive proteins. The results show that the genes related to celiac and WDEIA are expressed in the starchy endosperm (the source of baking flour), while various lipid transfer proteins and alpha-amylase trypsin inhibitor gene families are involved in baker's asthma. Furthermore, the study revealed that temperature stress during flowering can increase the levels of major celiac and WDEIA proteins. The researchers' detailed analysis offers important insights into the role of environment and growing conditions on the levels of proteins problematic for human consumers, they say. Their work will also inform production of low allergy wheat varieties, among others useful to the food industry.

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       http://dx.doi.org/10.1126/science.aar7191 
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