Wheat is one of the major staple crops in the world. Ever since the early 20th century with the beginning from landraces, modern breeding has improved wheat yield for more than 10 folds to meet requirements of increasing population. However, the genomic change involved in wheat breeding is still unclear. The availability of high-quality genomes of landrace CS and commercial variety AK58 provides a precious opportunity for extensive comparison of intraspecific genome variations incurred by modern breeding.

The plant statures are extremely different between CS and AK58. The plant height of CS is about twice as that of AK58 (124cm vs. 62cm), the grain size of CS is smaller than that of AK58 (TGW 28g vs 43g), and AK58 heads one week earlier than CS. When each pair of pseudochromosomes was aligned, approximately 86.0% of the AK58 genome sequences matched in one-to-one syntenic blocks with 87.5% of CS genome sequences. The largest nonsyntenic sequences between the two genomes were on the short arm of Chr1B because of the 1B/1R translocation in AK58. On average, more than 10% genomic difference (including regions not been sequenced) existed between modern variety AK58 and landrace CS. 7,020 CS genes and 8,823 AK58 genes were nonsyntenic, accounting for 6.49% and 7.52% of the total analyzed genes in the CS and AK58 genomes. Gene ontology (GO) enrichment showed those genotype-specific genes rich in secondary and energy metabolism. We found 30,504,165 SNPs and 3,108,702 Insertion/Deletions (InDels, length shorter than 200bp) between the two hexaploid wheat genomes. The density of SNPs and InDels was much higher in the distal region of long/short arm(s) of chromosomes than in the pericentromeric regions. Of the total SNPs and InDels, 677,770 SNPs and 127,866 InDels were identified from 24,291 and 3,845 genes, averaged 28 SNPs and two InDels per gene, respectively (not excluded redundancy).

Functional divergence of orthologous genes can be inferred by selection pressures based on nonsynonymous substitutions rate (Ka) versus the synonymous substitutions rate (Ks). Totally, 22860 orthologous pairs between CS and AK58 had both types of substitutions. We found 1697 orthologous gene pairs (7.4%) were under positive selection (Ka/Ks > 1), of which, 23 genes expressed differently between CS and AK58. Detailed structural variations and functional differentiation were identified for genes or genomic regions conferring agronomically important traits. The potential applications in wheat improvement in the future were discussed.