BacPhase: Long-insert paired-end sequencing for bin marker construction and genome phasing

This study is led by Professor Guangcun Li (State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China). The authors evaluated 14 restriction enzymes to select optimal restriction enzymes in multiple crop species, as the restriction enzyme used affects the evenness and spacing of markers.

Then they present BacPhase, an innovative sequence-based approach in which constructed BACs are digested with a restriction enzyme and self-ligated to produce small inserts that can be amplified by PCR and sequenced, thus removing the need for selecting single colonies.

Using PacBio HiFi long-read sequencing to span repetitive regions, we generated 39,484 high-confidence, high-resolution bin markers in potato. Unlike Hi-C, which relies on chromatin interactions, BacPhase uses sequence polymorphisms directly, enabling precise haplotype resolution. Indeed, BacPhase anchored 59.58% of scaffolds to the chromosomes in the autotetraploid potato cultivar C88, substantially improving contiguity without requiring physical maps or Hi-C data.

The BacPhase method could facilitate trait mapping, genomic selection, and accelerated breeding in polyploid crops such as potato, sugarcane (Saccharum officinarum), and alfalfa (Medicago sativa).

See the article:

BacPhase: Long-insert paired-end sequencing for bin marker construction and genome phasing

https://www.sciencedirect.com/science/article/pii/S266217382500219X