Pedigree-based linkage map in two genetic groups of oil palm

Abstract

A microsatellite genetic linkage map was constructed for oil palm (Elaeis guineensis Jacq.) using segregation data from two three/four-generation outbred pedigrees. The first was mainly a Deli population and the second consisted of La Mé and Yangambi populations. A total of 363 microsatellite markers (SSR) were genotyped and analyzed with CRI-MAP software. On the initial 363 SSR, 252 and 277 SSR markers for the first and second groups, respectively, were mapped in 16 linkage groups. The maps covered 2078 and 1845 cM, with an average density of one marker every 9 and 7 cM. An integrated map was built, grouping 281 markers on 1935 cM, with an average density of one marker every 7.4 cM. The linear orders of markers among the three genetic maps and with the physical map were highly consistent. These results showed the ability to override the existing experimental limits for linkage mapping in oil palm, namely a limited number of palms per cross. This represents the first step towards efficient pedigree-based quantitative trait locus (QTL) mapping using the first intercrossed generations in current breeding programs. (Résumé d'auteur

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

“…The latter would be interesting for QTLs identified in less well covered regions (e.g. top of linkage group 14) caused by difficulties in genetic map construction [ 33 ].…”

“…A consensus linkage map (Additional file 1 : Figure S2) based on the pedigree of both groups A and B was constructed with CRIMAP version 2.4 [ 32 ], as described in [ 33 ]. The genetic map was drawn using MapChart software [ 34 ].…”

Identification ofGanodermaDisease Resistance Loci Using Natural Field Infection of an Oil Palm Multiparental Population

“…In a previous study, 116 individuals from the reference family D2L1 were genotyped with 390 single sequence repeat (SSR) markers, and a first reference high density linkage map grouping 255 SSRs and 688 amplified fragments length polymorphisms (AFLP) markers was published ( Billotte et al 2005 ). The SSR markers, plus 26 SSR additional markers previously mapped in a pedigree-based linkage analysis that was recently published ( Cochard et al 2015 ), were used to genotype 604 individuals from nine Eg 9PP families, including D2L1, which constituted the mapping population ( Figure 1 ). Based on genotyping of the Eg 9PP parents, and the genetic position of SSR markers, different SSR marker subsets were used depending on the family, to optimize the genome coverage and marker information level (see Table S4 and Table S5 for individual genotypes).…”

“…A QTL region identified in the linkage analysis of the mapping population ( n = 604) was investigated in further detail by genotyping all of the 757 sampled individuals from the 14 Eg 9PP families with all of the SSR markers mapped in the region plus two markers (see Table S4 ). DNA extraction, microsatellite amplification, and analyses were performed according to the protocol described in Cochard et al (2015) , and raw genotype data are available in Table S5 .…”

GENETIC MAP CONSTRUCTION OF IOPRI'S OIL PALM (Elaeis guineensis JACQ.) MAPPING POPULATION DERIVED FROM SP540T BY USING RESTRICTION SITE ASSOCIATED DNA (RAD) MARKERS

“…Retno Diah Setiowati ( ) perbaikan genetik telah berkontribusi dalam meningkatkan produksi kelapa sawit sebesar 60% (Durand-Gasselin et al, 2010, Cochard et al, 2015. Namun diperlukan strategi baru untuk percepatan perbaikan genetik dan memotong siklus seleksi kelapa sawit seperti aplikasi perangkat teknologi genomik (Barcelos et al, 2015) maupun (Marker Assisted Selection, MAS) (Ihase et al, 2014).…”