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Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat

Counts:1326DateTime:2016-11-10 12:01:26 Source: Wheat Research Institute

Miao Liu1,2, Jiri Stiller1, Kateřina Holušová3, Jan Vrána3, Dengcai Liu2, Jaroslav Doleže&Chunji Liu1,4

1 CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD 4067, Australia. 

2 Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China. 
3 Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.
4 School of Plant Biology, The University of Western Australia, Perth, WA 6009, Australia. 
Correspondence and requests for materials should be addressed to C.L. (email: chunji.liu@csiro.au)


Scientific Reports | 6:36398 | DOI: 10.1038/srep36398


The hexaploid wheat genotype Chinese Spring (CS) has been used worldwide as the reference base for wheat genetics and genomics, and significant resources have been used by the international community to generate a reference wheat genome based on this genotype. By sequencing flow-sorted 3B chromosome from a hexaploid wheat genotype CRNIL1A and comparing the obtained sequences with those available for CS, we detected that a large number of sequences in the former were missing in the latter. If the distribution of such sequences in the hexaploid wheat genome is random, CRNILA sequences missing in CS could be as much as 159.3 Mb even if only fragments of 50 bp or longer were considered. Analysing RNA sequences available in the public domains also revealed that dispensable genes are common in hexaploid wheat. Together with those extensive intra- and interchromosomal rearrangements in CS, the existence of such dispensable genes is another factor highlighting potential issues with the use of reference genomes in various studies. Strong deviation in distributions of these dispensable sequences among genotypes with different geographical origins provided the first evidence
indicating that they could be associated with adaptation in wheat.