APPLICATIONS OF FINGERPRINTING IN FOREST TREE BREEDING

INTRODUCTION

1.4 APPLICATIONS OF FINGERPRINTING IN FOREST TREE BREEDING

Boolean vectors of one entity from another. A matrix consisting of all pair-wise squared Euclidean distances between all entities is constructed and used in the analysis (Excoffier et al., 1992).

Squared Euclidean distances are calculated according to the following formula:

~

e

^2jk

=

(Pi - Pk)' W (pj - Pk), (Excoffier et aI., 1992)

Where W is a matrix of differential weights for the various sites.

Using the constructed matrix, a hierarchical analysis of variance is performed to determine the subdivision. Usually, in the simple cases, the total variance is partitioned into between populations and within populations to give an idea as to how much of the genetic diversity can be attributed to each of these components. Variance can however be further subdivided into within individual differences, between individuals within populations, between populations within groups and between groups.

Table 1.3 Selected examples of association of molecular markers with the desired traits in different crops.

Characteristics

Wheat

Powdery mildew resistance genes Pm-1 and Pm-2

Maize

Examples

RFLP markers 3cM from Pm-1 and 3cM from Pm-2

References

Hartl et al., 1995

Leaf blight resistancerhmgene

Northem corn blight resistance gene Htn-1

Sorghum

Head smut resistance Shs

Barley

Tight linkage ofrhmwith RFLP Zaitlin et aI., 1993 loci UMC85 and p144

Htn-1gene O.8cM distal to RFLP Simcox and Bennetzen, 1993 UMC117

Linkage with RFLP loci detected Oh et aI., 1994 by probes pFBT^IxS560 and

xS1294. One RAPD locus from primer OPG5

Stem rust resistance gene Rpg 1

Stem rust resistance gene rpg4

Resistance to Rhynchosporium secalis

Soybean

Cyst nematode resistance

RFLP marker ABG704 on chromosome 1

3 RAPD markers on chromosome 7M

Cosegregation with RFLP markers on chromosome 3

Two RFLP markers associated resistance

Killian et al.^I 1994 Penner et al.. 1995

Borovkova et aI., 1995

Graner and Tekauz, 1996

Skorupska et aI., 1994

Resistance to soybean mosaic virus Rsv gene

Pea

Marker at 0.5, 1.5 and 2.1 cM Yu et aI., 1994

Powdery mildew resistance

Alfalfa

Somatic embryogenesis

Tomato

Insect resistance mediated by 2- tridecanone (2-TD)

Nematode resistanceMi gene

Resistance to powdery mildew caused by Oidium Iycopersicum 01-1 gene

Soluble solid content (SS)

Potato

Cyst nematode resistance H1 gene

Cyst nematode GroV110cus in solanum vemei

RFLP markers at 11 cM Dirlewanger et aI., 1994

RAPD markers Yu and Pauls, 1993

Direct selection for RFLP loci Nienhuis et al., 1987 increased the frequency of 2-TD-

mediated resistance

RFLP markers tightly linked Klein-Lankhorst et al., 1991

NearAps-1 region on Van de Seek, 1994 chromosome 6 close toMi and

Cf-21Cf-5genes

RFLPs linked to SS Osbom et al., 1987

RFLP marker at 2.7 cM from H1 Pineda et al., 1993

RFLP markers on chromosome 5 Jacobs et al., 1996

The main area where microsatellite markers are being applied in forestry trees include studies of genetic variation in natural and breeding populations, particularly in species with low levels of gene flow, pollen and/or seed dispersal and mating systems (Kostia et al., 1995). As these parameters are relevant to the conservation of forest genetic resources, microsatellites are being used to monitor genetic impacts of forest management practices and of fragmentation. The first microsatellites developed in forestry trees were for Pinus radiata (Smith and Devey, 1994), in which 24 loci were

characterised. They have since been developed from a range of temperate and tropical forestry trees, including Eucalyptus sieberi (Glaubitz et aI., 1999), Eucalyptus grandis (Brondani et al., 1998), Eucalyptus nitens (Byrne et al., 1997), and in several pine species (Kostia et al., 1995; Echt et al., 1996; Hicks et al., 1998) to name a few.

Bundock et al. (2000), constructed linkage maps using microsatellite markers in Eucalyptus globulus. They found that the male parent had 13 linkage groups covering 1013 cM, while the female parent had 11 linkage groups covering 701 cM.

Restriction fragment length polymorphism (RFLP) mapping in tree improvement has many useful applications. It adds to the number of genetic markers known in trees, facilitates the assessment of genomic organisation, is used to determine population genetic variation, and is employed to evaluate evolutionary relationships. One of the greatest limitations of this technology is the amount of prior research required before the technology can be employed. Specific probes or primers have to be developed which is a lengthy and expensive process (Neale and Williams, 1990).

The applications of RAPD markers in forestry have been very successful. The application of RAPDs to forest trees includes identification of genotypes and genetic relatedness within and between populations. RAPD markers have been used for identity studies in Populus (Sanchez et al., 1998) where 25 poplar clones were screened for RAPD markers in order to evaluate the use of RAPD analysis to distinguish between species. The marker produced characteristic bands for every species. De Laia et al.

(2000) also used RAPD markers to analyse the genotypes of Eucalyptus clones hybrids obtained by vegetative micropropagation. Various diversity studies have also employed RAPD technology. Mosseler et al. (1992) used RAPD markers to confirm the low levels of genetic diversity in red pine which demonstrated the long time periods required for recovery following a loss of genetic diversity in long-lived, long-generation organisms like trees. In 1995, Bucci and Menozzi investigated the genetic variation of RAPD markers in an Italian population of Norway spruce. Here they found that the expected genetic diversity ranged from 0.119 to 0.508 and the single-locus inbreeding estimates were calculated at -0.136 indicating an excess of heterozygotes.

Research achievements that relate to the employment of molecular technologies in black wattle are limited. Studies include the examination of genetic variation in natural populations ofAcacia mearnsii(Searle and Bell, 1998). Twenty-three isozyme loci were examined within and between 19 natural populations of Acacia mearnsii. Acacia mearnsii was found to have moderate genetic variation (0.201) with the majority (89.2 %) of variation occurring within populations. Another study conducted by Butcher et al. (1998) estimated the genetic variation in Acacia mangium using 57 anonymous RFLP loci for ten individuals from each of ten natural populations. The level of genetic variation varied significantly among the populations, ranging from 0.01 on the island of Ceram in Indonesia to 0.21 in Muting, New Guinea. The small, geographically isolated populations of Daintree, Townsville, Ceram and Sidei had low levels of diversity (0.01 to 0.09) whereas the large New Guinea and the Cape York Peninsula populations had higher levels of variation (0.16 to 0.21).