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

• Published in: PloS one Vol. 14; no. 8; p. e0220626
• Main Authors: Babu, B Kalyana, Mathur, R K, Ravichandran, G, Anitha, P, Venu, M V B
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 07-08-2019; Public Library of Science (PLoS)
• Subjects: Agricultural production; Arecaceae - anatomy & histology; Arecaceae - genetics; Bioinformatics; Biology and Life Sciences; Biomass; Chromosome 1; Chromosome 2; Chromosome 4; Chromosomes; Correlation coefficient; Correlation coefficients; Crops; Decay rate; Deoxyribonucleic acid; DNA; DNA sequencing; Drying oils; Gene mapping; Genetic aspects; Genetic polymorphisms; Genetic testing; Genome, Plant - genetics; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomics; Genotyping; Genotyping Techniques; Germplasm; Identification; Identification and classification; Leaf area; Leaf area index; Mapping; Methods; Morphology; Nucleotides; Oil palm; Palm Oil; Phenotype; Phenotypic variations; Physiological aspects; Plant Leaves - anatomy & histology; Plant Leaves - genetics; Plant Stems - anatomy & histology; Plant Stems - genetics; Polymorphism; Polymorphism, Single Nucleotide; Principal components analysis; Quantitative Trait Loci; Research and Analysis Methods; Rice; Seeds; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Studies; Vegetable oils; Weight; India
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0220626

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.