A novel QTL linked to asparagine synthetase gene for stem height increment in oil palm ( E. guineensis Jacq.) identified and validated through integrated genomic approaches

The tallness of the oil palm is a major hurdle for harvesting of ripened bunches after attaining the age of 25 years. Hence, the study conducted with an objective to identify and validate the major loci for dwarf trait using integrated genomic approaches viz ., bulk segregant analysis (BSA), genome wide association mapping (GWAS), and bioinformatics. The average height increment of the germplasm was found to be 28.6 cm which ranges from 10.12 to 58.21 cm. The principal component analysis results showed that Zambian and Cameroon genotypes are having less height increment nature. The GWAS resulted in identification of six QTLs on chromosomes 4, 8, and 14. Out of the six QTLs, two SSRs (mEgCIR3350andmEgCIR0059) linked to two QTLs (qtlH1 and qtlH2 respectively) were significant. The BSA analysis also showed that the marker mEgCIR0059 is tightly linked to less height increment. Interestingly, the qtlH2 (mEgCIR0059) is found to be linked by both the BSA and GWAS analysis. The bioinformatics analysis of qtlH2 (mEgCIR0059) also confirmed that it is linked to the asparagine synthetase candidate gene. The marker was validated on large number of populations consisting of African germplasm, progeny derived from the cross between dwarf and tall germplasm, and dwarf palm which is available at our experimental farm. This marker can be effectively used in molecular breeding programmes to select dwarf germplasm at an early stage.