Mixed model approach for IBD-based QTL mapping in a complex oil palm pedigree

Abstract

BackgroundElaeis guineensis is the world’s leading source of vegetable oil, and the demand is still increasing. Oil palm breeding would benefit from marker-assisted selection but genetic studies are scarce and inconclusive. This study aims to identify genetic bases of oil palm production using a pedigree-based approach that is innovative in plant genetics.ResultsA quantitative trait locus (QTL) mapping approach involving two-step variance component analysis was employed using phenotypic data on 30852 palms from crosses between more than 300 genotyped parents of two heterotic groups. Genome scans were performed at parental level by modeling QTL effects as random terms in linear mixed models with identity-by-descent (IBD) kinship matrices. Eighteen QTL regions controlling production traits were identified among a large genetically diversified sample from breeding program. QTL patterns depended on the genetic origin, with only one region shared between heterotic groups. Contrasting effects of QTLs on bunch number and weights reflected the close negative correlation between the two traits.ConclusionsThe pedigree-based approach using data from ongoing breeding programs is a powerful, relevant and economic approach to map QTLs. Genetic determinisms contributing to heterotic effects have been identified and provide valuable information for orienting oil palm breeding strategies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1985-3) contains supplementary material, which is available to authorized users.

Breeding the oil palm (Elaeis guineensisJacq.) for climate change

“…The genetic determinism of several characters of agronomic interest has been elucidated, such as oil quality (Morcillo et al, 2013), shell thickness (Singh et al, 2013b), fruit colour (Singh et al, 2014) or the mantled somaclonal variation (Jaligot et al, 2014;Ong-Abdullah et al, 2015) together with gene networks at work for oil biosynthesis (Guerin et al, 2016). Furthermore, Tisné et al (2015) developed a pedigree-based approach using data from ongoing breeding programs to map QTLs. Genetic determinisms contributing to heterotic effects were identified and they provided valuable information for orienting oil palm breeding strategies.…”

Identification and Validation of Candidate Genes Involved in Fatty Acid Content in Oil Palm by Genome-Wide Association Analysis

“…Compared with QTL (quantitative trait loci) mapping in biparental cross populations, association analysis using natural populations is more time- and cost-effective, especially for woody perennial crops that have long life cycles and/or that require large planting areas. In oil palm, QTL mapping has been used to resolve the genetic bases of several complex traits, including yield components (Rance et al, 2001; Billotte et al, 2010; Jeennor and Volkaert, 2014; Tisne et al, 2015), fatty acid composition (Singh et al, 2009; Montoya et al, 2013), sex ratio (Ukoskit et al, 2014), and embryogenesis (Ting et al, 2013). Unfortunately, the contribution of QTL mapping studies to marker-assisted breeding outcomes has been less than expected.…”

Linkage Analysis and Association Mapping QTL Detection Models for Hybrids Between Multiparental Populations from Two Heterotic Groups: Application to Biomass Production in Maize (Zea mays L.)

“…It would be interesting to adapt this strategy to factorial designs. Another possibility for more complex pedigree could be to consider QTL effects as random and use markers to compute local similarity, as done by Crepieux et al (2004) on wheat inbred line data and recently by Tisné et al (2015) in oil palm hybrids. van Eeuwijk et al (2010) performed QTL detection in a factorial design issued from a private breeding program that was derived by crossing a large number of parental lines (but not structured in balanced families as in our design).…”