Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly

Abstract

Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high-confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.

The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat (Triticum turgidum L.) Population: Chinese Landrace “Ailanmai” × Wild Emmer

“…Sequences of the markers were blasted against the durum wheat (Svevo) (Maccaferri et al, 2019 ), wild emmer (Zavitan; v2.0) (Zhu et al, 2019 ), and common wheat genotype “Chinese Spring” (CS; v2.1) (Zhu et al, 2021 ) genome to identify their physical positions. Svevo and Zavitan genomes were used when considering the physical positions of QTLs detected from AL and LM001, respectively.…”

The 55K SNP-Based Exploration of QTL for Spikelet Number Per Spike in a Tetraploid Wheat (Triticum turgidum L.) Population: Chinese Landrace ‘Ailanmai’ × Wild Emmer

“…Sequences of the markers were blasted against the durum wheat (Svevo) (Maccaferri et al, 2019), wild emmer (Zavitan; v2.0) (Zhu et al, 2019), and common wheat genotype ‘Chinese Spring’ (CS; v2.1) (Zhu et al, 2021) genomes to identify their physical positions. The Svevo and Zavitan genomes were used when considering the physical positions of QTL detected from AL and LM001, respectively.…”

Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects

“…Therefore, these optical maps span genomic regions that are challenging to resolve by other DNA sequencing technologies and are used for genome assembly improvement, to identify large SVs, and in haplotype phasing [16]. Most recently, optical mapping was used to refine the assembly of the wheat genome by producing RefSeq v2.1 [17].…”