|
Linkage Disequilibrium in Plant U-box Gene in Sugarcane (Saccharum spp.) |
|---|---|
| รหัสดีโอไอ | |
| Creator | Krittiya Ninkaeo |
| Title | Linkage Disequilibrium in Plant U-box Gene in Sugarcane (Saccharum spp.) |
| Contributor | Sithichoke Tangphatsornruang, Chutima Sonthirod, Kittipat Ukoskit |
| Publisher | Thammasat University |
| Publication Year | 2564 |
| Journal Title | Thai Journal of Science and Technology |
| Journal Vol. | 10 |
| Journal No. | 3 |
| Page no. | 251-263 |
| Keyword | sugarcane, single nucleotide polymorphism (SNP), linkage disequilibrium (LD), PacBio single olecule, real-time (SMRT) sequencing technology |
| URL Website | https://www.tci-thaijo.org/ |
| Website title | THAIJO |
| ISSN | 2286-7333 |
| Abstract | Understanding linkage disequilibrium (LD) is important for planning breeding strategies to target beneficial alleles for agronomic traits. In the present study, we analyzed the LD pattern of U-box domain-containing protein35 gene (SaPUB35) in 68 exotic sugarcane collections and 73 sugarcane breeding lines. PacBio single molecule, real-time (SMRT) sequencing was performed to identify 126 single nucleotide polymorphisms (SNPs) and 50 Insertion/deletions (InDels) in 5731 bp of SaPUB35. The exotic sugarcane population has more variants than the breeding line population. Pairwise LD analysis revealed that mean LD, at a threshold of squared allele frequency correlations (r2 ) =?0.1, extends to at least 1500 bp in the breeding line population but is eroded to 1400 bp in exotic sugarcane population. This implies a signature of a selective sweep for a beneficial mutation during the selection processes of sugarcane breeding. Uncovering allelic erosion and a diversity bottleneck due to modern sugarcane breeding will be useful for understanding sugarcane breeding targets and in devising future breeding strategies to target beneficial alleles currently not pursued. |
