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. 2010 May;120(8):1673-87.
doi: 10.1007/s00122-010-1284-y. Epub 2010 Feb 25.

QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.)

N Billotte  1 , M F Jourjon, N Marseillac, A Berger, A Flori, H Asmady, B Adon, R Singh, B Nouy, F Potier, S C Cheah, W Rohde, E Ritter, B Courtois, A Charrier, B Mangin
Affiliations

QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.)

N Billotte et al. Theor Appl Genet. 2010 May.

Abstract

A quantitative trait locus (QTL) analysis designed for a multi-parent population was carried out and tested in oil palm (Elaeis guineensis Jacq.), which is a diploid cross-fertilising perennial species. A new extension of the MCQTL package was especially designed for crosses between heterozygous parents. The algorithm, which is now available for any allogamous species, was used to perform and compare two types of QTL search for small size families, within-family analysis and across-family analysis, using data from a 2 x 2 complete factorial mating experiment involving four parents from three selected gene pools. A consensus genetic map of the factorial design was produced using 251 microsatellite loci, the locus of the Sh major gene controlling fruit shell presence, and an AFLP marker of that gene. A set of 76 QTLs involved in 24 quantitative phenotypic traits was identified. A comparison of the QTL detection results showed that the across-family analysis proved to be efficient due to the interconnected families, but the family size issue is just partially solved. The identification of QTL markers for small progeny numbers and for marker-assisted selection strategies is discussed.

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Figures

Fig. 1
Fig. 1
Multi-parent mating design of four connected full-sibs families, with eight potential alleles segregating from parent genotypes ij
Fig. 2
Fig. 2
Seventy-six QTLs of vegetative and production traits identified in four connected crosses on a 2 × 2 factorial mating design, at an α genome-wide risk of 4% per population by the iQTLm scan method using a within-family or an across-family model, under MCQTL Outbred (INRA, Toulouse, France). The QTLs are located on the Haldane’s consensus SSR linkage map of the 2 × 2 complete factorial design, constructed at LOD 3.0 and Recmax = 0.5. The linkage map encompasses 253 markers (251 SSRs, the Sh locus and its AFLP marker E-Agg/M-CAA132). The names and the positions (cM) of the markers are given on the right side of the linkage groups. mEgCIR: E. guineensis SSR marker, mCnCIR: Cocos nucifera SSR marker. The names, positions and confidence regions of the QTLs are given on the left side of the linkage groups. In red: are figured the QTLs of production traits; in blue: the QTLs of bunch quality traits, in green: the QTLs of vegetative traits
Fig. 2
Fig. 2
Seventy-six QTLs of vegetative and production traits identified in four connected crosses on a 2 × 2 factorial mating design, at an α genome-wide risk of 4% per population by the iQTLm scan method using a within-family or an across-family model, under MCQTL Outbred (INRA, Toulouse, France). The QTLs are located on the Haldane’s consensus SSR linkage map of the 2 × 2 complete factorial design, constructed at LOD 3.0 and Recmax = 0.5. The linkage map encompasses 253 markers (251 SSRs, the Sh locus and its AFLP marker E-Agg/M-CAA132). The names and the positions (cM) of the markers are given on the right side of the linkage groups. mEgCIR: E. guineensis SSR marker, mCnCIR: Cocos nucifera SSR marker. The names, positions and confidence regions of the QTLs are given on the left side of the linkage groups. In red: are figured the QTLs of production traits; in blue: the QTLs of bunch quality traits, in green: the QTLs of vegetative traits
Fig. 2
Fig. 2
Seventy-six QTLs of vegetative and production traits identified in four connected crosses on a 2 × 2 factorial mating design, at an α genome-wide risk of 4% per population by the iQTLm scan method using a within-family or an across-family model, under MCQTL Outbred (INRA, Toulouse, France). The QTLs are located on the Haldane’s consensus SSR linkage map of the 2 × 2 complete factorial design, constructed at LOD 3.0 and Recmax = 0.5. The linkage map encompasses 253 markers (251 SSRs, the Sh locus and its AFLP marker E-Agg/M-CAA132). The names and the positions (cM) of the markers are given on the right side of the linkage groups. mEgCIR: E. guineensis SSR marker, mCnCIR: Cocos nucifera SSR marker. The names, positions and confidence regions of the QTLs are given on the left side of the linkage groups. In red: are figured the QTLs of production traits; in blue: the QTLs of bunch quality traits, in green: the QTLs of vegetative traits
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