Resequencing Of Wheat Chromosome 3B And Analyzing On Stripe Rust Resistance In Aegilops Tauschii

The hexaploid wheat genotype Chinese Spring(CS)has been widely used in genetics and genomics studies.The International Wheat Genome Sequencing Consortium(IWGSC)has obtained its genome draft/reference sequence by adopting a strategy of physical mapping and sequencing individual chromosomes/arms.This work is a foundation to further compare and analyze the genetic variation of different wheat lines at the genomic level.Here,the CS sequence is used to compare with those from the hexaploid wheat genotype "CRNIL1A" that was obtained by sequencing flow-sorted 3B chromosome.We revealed the genomic variants between the two genotypes and further investigated the distribution of CRNIL1A-specific sequences among wheat genotypes with a diversely geographical origin and the dispensable genes on wheat genome based on wheat RNA sequences.The main results include:We obtained?36.6Gb raw sequences after sequencing flow-sorted 3B chromosome of the wheat genotype "CRNIL1A".About 87.9%of filtered reads with high quality were successfully mapped to "CS" 3B pseudomolecule.However,we identified about 8.3 Mb CRNIL1A-specific sequences absent in "CS" genome.We confirmed this by PCR amplification of randomly selected specific sequences.Further Linkage analyses also confirmed this since the specific fragments generated by 11 pairs of primers were all from chromosome 3B.Functional analysis showed that CRNIL1A-specific sequences are not randomly distributed among the GO function groups and most of them were involved in metabolic process,cell-associated,and nucleotide binding domains.We speculated that a large proportion of the non-CS sequences were not randomly distributed across genotypes.We confirmed this speculation by analyzing on wheat lines from different geographical origins since the distributions of some of these sequences were so extreme that they could only be detected from genotypes belonging to a certain geographical region,thus indicating that they may be associated with adaptation in wheat.Analyzing the RNA sequences available from 26 hexaploid wheat found 9,573 novel transcripts absent in "CS" genome,again suggesting that dispensable genes are probably common in wheat.Th comparison of sequences between "CRNILIA" 3B chromosome and "CS" 3B pseudomolecule detected a large number of variants including 2,125,304 SNPs(single nucleotide polymorphisms),47,428 MNVs(multinucleotide variants),43,870 insertions,45,007 deletions,and 3,343 replacements.Meanwhile,we identified 21,542 SSRs from the CRNIL1A sequences.These variants are useful for the development of diagnostic markers targeting locus on this chromosome.Contrast to the usually expected 'V-shaped' pattern,the levels of sequence variation around the centromeric regions detected between "CS" and "CRNIL1A" were not lower than other regions along this chromosome.Aegilops tauschii Coss.,the D-genome progenitor of hexaploid wheat,contains abundant genetic variations valuable for wheat improvement.Wheat stripe rust is one of the most devastating diseases worldwide.It is still necessary to evaluate the stripe rust resistance of Ae.tauschii and to investigate the genetic relationship between resistance Ae.tauschii accessions.We here characterized the adult-plant resistance of a germplasm collection with 149 Ae.tauschii accessions using prevalent Puccinia striiformis f.sp.tritici(Pst)races in the current wheat production in China.Out of the 149 accessions,39 belonged subsp.strangulata and 110 belonged subsp.tauschii.All the 39 S accessions were resistant,while only 19 out of 110 ssp.tauschii accessions were resistant.These resistant accessions are mainly distributed in the Caspian Sea region.Our results showed that the stripe rust resistance in Ae.tauschii was related to their geographical origins and taxon.We further analyzed the inheritance of stripe rust resistance by inoculating F2 plants of 39 populations with a mixture of Chinese Pst races.These allelic tests involving in 15 highly resistant accessions indicated the common presence of YrAS2388,previously mapped on chromosome arm 4DS,in all the analyzed accessions.