การวิเคราะห์ความไม่สมดุลของลิงเกจภายในยีน Plant U-box ในอ้อย

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กฤติยา นิลแก้ว
กิตติพัฒน์ อุโฆษกิจ
สิทธิโชค ตั้งภัสสรเรือง
ชุติมา สนธิรอต

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.

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