Abstract
BackgroundOil palm (Elaeis guineensis, Jacq.) is the most important source of edible oil. The improvement of oil yield is currently slow in conventional breeding programs due to long generation intervals. Marker-assisted selection (MAS) has the potential to accelerate genetic improvement. To identify DNA markers associated with oil content traits for MAS, we performed quantitative trait loci (QTL) mapping using genotyping by sequencing (GBS) in a breeding population derived from a cross between Deli Dura and Ghana Pisifera, containing 153 F1 trees.ResultsWe constructed a high-density linkage map containing 1357 SNPs and 123 microsatellites. The 16 linkage groups (LGs) spanned 1527 cM, with an average marker space of 1.03 cM. One significant and three suggestive QTL for oil to bunch (O/B) and oil to dry mesocarp (O/DM) were mapped on LG1, LG8, and LG10 in a F1 breeding population, respectively. These QTL explained 7.6–13.3% of phenotypic variance. DNA markers associated with oil content in these QTL were identified. Trees with beneficial genotypes at two QTL for O/B showed an average O/B of 30.97%, significantly (P < 0.01) higher than that of trees without any beneficial QTL genotypes (average O/B of 28.24%). QTL combinations showed that the higher the number of QTL with beneficial genotypes, the higher the resulting average O/B in the breeding population.ConclusionsA linkage map with 1480 DNA markers was constructed and used to identify QTL for oil content traits. Pyramiding the identified QTL with beneficial genotypes associated with oil content traits using DNA markers has the potential to accelerate genetic improvement for oil yield in the breeding population of oil palm.
Highlights
Oil palm (Elaeis guineensis, Jacq.) is the most important source of edible oil
Genotyping Single nucleotide polymorphisms (SNP) and Simple sequence repeats (SSR) in a breeding population Five sequencing libraries containing 177 F1 trees from the population and two parents were constructed by double-digest Restriction-site-associated DNA sequencing (RAD-seq) approaches, and a total of 693.3 million clean reads were produced by the Illumina NextSeq 500 platform
After sequential quality filtering and sequence trimming, 20.7 and 17.7 million reads were produced for the two parents, and an average of 3.7 million clean reads were produced in each progeny
Summary
Oil palm (Elaeis guineensis, Jacq.) is the most important source of edible oil. The improvement of oil yield is currently slow in conventional breeding programs due to long generation intervals. To identify DNA markers associated with oil content traits for MAS, we performed quantitative trait loci (QTL) mapping using genotyping by sequencing (GBS) in a breeding population derived from a cross between Deli Dura and Ghana Pisifera, containing 153 F1 trees. Restriction-site-associated DNA sequencing (RAD-seq) using NGS is an efficient approach to discover and genotype a large number of SNP markers [8, 9]. It has resulted in rapid and cost-effective massive marker discovery and has been successfully used to construct high-density linkage maps and fine QTL mapping in several plant species [10, 11]. To facilitate MAS in oil palm, it is necessary to further identify and verify QTL for important traits in different genetic backgrounds
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