Genome-wide association study (GWAS) for stem height increment in oil palm (Elaeis guineensis) germplasm using SNP markers

Abstract

Oil palm germplasms belonging to four African countries were used in GWAS for stem height increment. Till now, there has been no report available on GWAS study of African oil palm germplasm using single-nucleotide polymorphisms (SNPs) by genotyping by sequencing (GBS) method for height increment. GBS generated a total of 325 million reads covering 50.78 Gb of sequence data, with an average of 3.4 million reads per sample. For the final dataset, we were able to retain 4031 SNPs across the 96 genotypes. The range of height increment varied from 11.43 to 58.21 cm at an average of 29.19 cm. Association mapping resulted in identification of five significant quantitative trait loci (QTLs) on chromosome 6, 7, and 9. Interestingly, three QTLs located on chromosome 7 itself, while one each on chromosome 6 and 9 at a P value of < 0.00001. Out of the five QTLs, qtlH7.1 on chromosome 7 was found to be highly significant which explained a phenotypic variance of 15% at a P of 2 × 10−5. The blast results of qtlH7.1 showed that it was found to be more similar to oil palm B3 domain containing protein (LOC 105043719) transcript variant X3, mRNA. The B3 domain containing proteins consisted of families like auxin response factors (ARFs) and abscisic acid insensitive 3 (ABI3). These results showed that qtlH7.1 might be playing an important role in stem height increment. The QTLs identified in the present study could be used in selection of oil palm germplasm for low height increment.