Linkage Group Assembly and Ordering as a Source of Spurious Qtl Estimates in Mango

Objective: This study aimed to align genetic linkage groups (LGs) with the mango physical map by comparing single nucleotide polymorphism (SNP) sequences in the 'Alphonso' mango genome. Theoretical Framework: Few studies have evaluated the impact of linkage group (LG) formation and marker ordering on quantitative trait loci (QTL) estimates for marker-assisted selection (MAS). Method: SNPs from the mango linkage groups (n=20) were aligned on the chromosomes of the genome sequence of the 'Alphonso' mango (n=20), evaluating the correspondence between the genetic linkage map and the physical map. Results and Discussion: Four major aberrations were identified: (a) chromosome 1 was divided into LGs 9 and 14; (b) chromosome 4 was split between LGs 1 and 3; (c) LG 8 was formed by combining SNPs from chromosomes 9 and 17 of 'Alphonso'; and (d) chromosome 18 was not represented in any of the 20 LGs. All remaining LGs, except LGs 11, 14 and 20, contained at least one SNP from non-corresponding reference chromosomes. Significant discrepancies in SNP ordering were observed across the 20 LGs, particularly in 12 LGs. Research Implications: For species with available genome sequences, physical maps, created through SNP sequence Blast alignment, yield better results for quantitative trait mapping aimed at marker-assisted selection. Originality/Value: QTLs utilization in MAS remains limited. Insufficient attention has been given to limitations in linkage group formation and marker ordering compared to physical mapping as sources of spurious QTL estimates.