Genome wide association study (GWAS) and identification of candidate genes for yield and oil yield related traits in oil palm (Eleaeis guineensis) using SNPs by genotyping-based sequencing.

The genotyping-based sequencing (GBS) method used for GWAS of four yield and seven oil yield related traits on highly diverse African oil palm germplasm. GBS generated 325 million-reads covering 50.78Gb of sequence data, with an average of 3.4 million-reads per sample. Finally, 4031 fully informative SNPs with a range between 157 on chromosome 15 to 455 on chromosome 1 were used for GWAS. Association mapping resulted in identification of 40 highly significant loci, where more genetic loci were found to be associated with oil to bunch (OB), followed by average bunch weight (ABW). The loci, SGI|593,593|linked to QTNOB3 explained high amount of phenotypic variance (25.3%). The nucleotide sequences of linked genetic loci for OB were found to be similar to mitogen activated protein kinase-5 (MAPK-5) protein which is an early flowering protein. The significant loci identified can be used to select desirable palms at early stage through marker assisted selection.

Genome-wide association study for leaf area, rachis length and total dry weight in oil palm (Eleaeisguineensis) using genotyping by sequencing.

The marker-trait association for complex traits using genotyping by sequencing (GBS) method is being widely spread in plants. The study aimed to identify significant single nucleotide polymorphism (SNP) associations for rachis length (RL), leaf area (LA) and total dry weight (TrDW) in oil palm among diverse African germplasm. The Illumina NextSeq platform has been used for SNP genotyping and retained 4031 fully informative SNPs after applying the filter criterion. These 4031 SNPs were used for genome wide association study for the above three traits. The LD decay rates of the African germplasm using GBS data of SNP is observed to be 25 Kb at 0.45 of average pair wise correlation coefficient (r2). Association mapping led to the identification of seven significant associations for three traits using MLM approach at a P value of ≤ 0.001. Three associations were identified for total dry weight, two each for leaf area index and rachis length. The qtlLA1 was found to be highly significant at a P value of 7.39E-05 (18.4% phenotypic variance) which is located on chromosome 4. Two QTLs (qtlLA2 and qtlRL1) were located on chromosome 1, which explained 11.9% and 12.4% of phenotypic variance respectively. Three QTLs for total dry weight were located on chromosome 2, 14 and 16, all-together explained 40% phenotypic variance. The results showed that the SNP-trait associations identified in the present study could be used in selection of elite oil palm germplasm for higher yields.

Development, identification and validation of CAPS marker for SHELL trait which governs dura, pisifera and tenera fruit forms in oil palm (Elaeis guineensis Jacq.).

The oil palm fruit forms (dura, pisifera and tenera) governed by the shell thickness gene (Sh) plays a major role in identification of fruit type and also influences palm oil yield. Identification of desired fruit type is a major asset to the breeders and oil palm workers for applications in breeding, seed certification and to reduce time, space and money spent on identification of fruit form. In the present study, we developed Sh gene specific primer pairs and bulk segregant analysis was done using 300 genomic and 8 genic SSR markers. We identified one cleaved amplified polymorphic site (CAPS) marker for differentiation of oil palm fruit type which produced two alleles (280 and 250bp) in dura genotypes, three alleles in tenera genotypes (550, 280, and 250bp) and one allele in pisifera genotypes (550bp). The shell allele sequencing results showed that two SNPs were present, of which SNP2 contributed for variation of fruit forms. The nucleotide 'A' was present in only dura genotypes, where as 'T' was present only in pisifera genotypes, which in turn led to the change of amino acid lysine to aspargine. The identified CAPS marker was validated on 300 dura, 25 pisifera and 80 tenera genotypes, 80 dura/ pisifera cross progenies and 60 lines of tenera/ tenera cross progeny. Association mapping of marker data with phenotypic data of eight oil yield related traits resulted in identification of seven significant QTLs by GLM approach, four by MLM approach at a significant threshold (P) level of 0.001. Significant QTLs were identified for fruit to bunch and oil to bunch traits, which explained R2 of 12.9% and 11.5% respectively. The CAPS marker used in the present study facilitate selection and timely distribution of desirable high yielding tenera sprouts to the farmers instead of waiting for 4-5 years. This saves a lot of land, time and money which will be a major breakthrough to the oil palm community.