An AFLP linkage map for Douglas-fir based upon multiple full-sib families

Abstract

An amplified fragment length polymorphism (AFLP) linkage map for coastal Douglas-fir (Pseudotsuga menziesii) was constructed from eight full-sib families each consisting of 40 progeny. These families were part of the British Columbia Ministry of Forests second-generation progeny test program and represent typical family sizes used in progeny trials. For map construction, ten primer pairs using EcoRI+3 and MseI+4 were employed to identify and assay AFLP loci that segregated in backcross configurations. A new technique was used to obtain a single recombination rate for each pair of marker loci: for each locus pair, a recombination rate and log-odd value were estimated across all segregating families using a joint maximum likelihood function that considered the full dataset of segregating genotypes. The resulting matrix of recombination rates between all pairs of loci was used to construct an integrated linkage map using JoinMap. The final map consisted of 19 linkage groups spanning 938.6 cM at an average distance of 9.3 cM between markers. The simultaneous integration of data from multiple families may provide an effective way to construct a linkage map, using the genetic resources inherent in most tree improvement programs, where progeny tests of small size are conducted. The statistical property of number of families used is briefly discussed. For our data, at least three to four families greatly increased the chance of obtaining an informative locus in at least one family. Families as small as ten are adequate for closely linked loci (<10 cM), while the size used in our study (40) is adequate for loci within 30 cM.

Genetic Linkage Maps of Betula platyphylla Suk Based on ISSR and AFLP Markers

“…It has been shown that the AFLP technique is one of the most powerful technologies for linkage map studies of plant species (Marques et al 1998;Costa et al 2000). Although AFLPs require more inputs in parameters (Wang et al 2004), AFLP markers have the potential to efficiently and rapidly construct high-resolution maps and to identify and isolate those markers that are tightly linked without the requirement for a priori sequence information (Hanley et al 2002;Beedanagari et al 2005;Ukrainetz et al 2008). In our experience, this method allowed us to generate a Marker names are shown on the right of each linkage group with map distances (in cM) on the left.…”

“…DNA-based markers such as restriction fragment-length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), inter-simple sequence repeat (ISSR), and amplified fragment length polymorphism (AFLP) have been widely used for map construction in various species, either in combination (Melauku et al 2001;La Rosa et al 2003;Scalfi et al 2004;Lanteri et al 2006) or individually (Remington et al 1999;Chagne et al 2002;Billotte et al 2005;Okogbenin et al 2006;Nicholas et al 2008). Genetic maps have become milestones in both basic genetic research and plant breeding.…”

Identification of quantitative trait loci for wood quality and growth across eight full-sib coastal Douglas-fir families

“…Genotypic data and map construction Ten amplified fragment length polymorphisms (AFLP) marker combinations were used to develop a comprehensive linkage map for the eight full-sib families used in this study (Ukrainetz et al 2007). The map was generated by calculating average LOD and recombination rates across families using a joint likelihood function (Hu et al 2004).…”

Population genetic structure, gene flow and recombination of Cochliobolus miyabeanus on cultivated wildrice (Zizania palustris)

“…Today, the main production areas are located in the northern part of the state (Oelke, 2007). The combined grain production of wildrice in Minnesota reached more than 9500 t during 2008 and2009 (B. Nelson, Minnesota Cultivated Wildrice Council, personal communication).…”

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A collection of 168 Cochliobolus miyabeanus isolates was made from cultivated wildrice (Zizania palustris) paddies in Minnesota, USA, during 2007 and2008. Analysis of 26 polymorphic amplified fragment length polymorphism (AFLP) markers generated with three primer-pair combinations indicated a moderate average gene diversity (Ĥ) of 0AE283.

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