Association Mapping between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids

Abstract

Oil palm production is gaining importance in Central and South America. However, the main species Elaeis guineensis (Eg) is suffering severely from bud rod disease, restricting the potential cultivation areas. Therefore, breeding companies have started to work with interspecific Elaeis oleifera × Eg (Eo × Eg) hybrids which are tolerant to this disease. We performed association studies between candidate gene (CG) single nucleotide polymorphisms (SNP) and six production and 19 oil quality traits in 198 accessions of interspecific oil palm hybrids from five different origins. For this purpose, barcoded amplicons of initially 167 CG were produced from each genotype and sequenced with Ion Torrent. After sequence cleaning 115 SNP remained targeting 62 CG. The influence of the origins on the different traits was analyzed and a genetic diversity study was performed. Two generalized linear models (GLM) with principle component analysis (PCA) or structure (Q) matrixes as covariates and two mixed linear models (MLM) which included in addition a Kinship (K) matrix were applied for association mapping using GAPIT. False discovery rate (FDR) multiple testing corrections were applied in order to avoid Type I errors. However, with FDR adjusted p values no significant associations between SNP and traits were detected. If using unadjusted p values below 0.05, seven of the studied CG showed potential associations with production traits, while 23 CG may influence different quality traits. Under these conditions the current approach and the detected candidate genes could be exploited for selecting genotypes with superior CG alleles in Marker Assisted Selection systems.

Genome-Wide Association Study for Ultraviolet-B Resistance in Soybean (Glycine max L.)

“…A mixed linear model (MLM), which generally outperforms a general linear model (GLM) by adding random effects of SNPs, was used to analyze associations between SNP genotypes and UV-B responses. The false discovery rate (FDR) adjusted p -values from GAPIT were found to be very stringent because the marker effects could have been overcorrecting based on both population structure Q and kinship K [ 57 , 58 ]. Therefore, an FDR-unadjusted p -value of 0.0001 was used as the threshold to identify significant SNPs for UV-B resistance.…”

Meta-Analysis of Influence of Diversity of Parental Forms on Heterosis and Specific Combining Ability of Their Hybrids

“…Association mapping is also conducted for hybrids of many plant species [94][95][96][97]. Recently, an attempt has been made to study the relationship between molecular markers and heterosis effects in maize [33].…”

Construction of a high density linkage map in Oil Palm using SPET markers

“…A missing data threshold of 20% was used in our study, but the values were imputed using Beagle 5.0 Software which has a very low error rate <1% 21 . Obviously the quality of a map will be better with less missing values, but also Astorkia et al 22,23 published association mapping studies in oil palm using a missing value rate of 20%.…”