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Mapping Populations






The fi rst step in developing a genetic link- age map is to choose a population in which to make the map. Since the map is based on segregation of heterozygous markers in one or both parents, at least one parent should be heterozygous. If trait genes are to be mapped in the same population, then these also must be heterozygous in the same parent(s). Generally, mapping populations are formed by crossing a specifi c female with a specifi c male and using the progeny as the mapping population. The population should be large enough to allow mapping to the desired marker density. If the breeder wishes to develop a dense map, with very closely spaced markers, then the popula-


 

© CAB International 2007. Citrus Genetics, Breeding and Biotechnology (ed. I.A. Khan) 275


tion size must be large in order for there to be an adequate number of progeny with crossovers between closely spaced markers. For example, with a population size of 100, if one parent is heterozygous for markers having 2% recombination, then we expect only about two recombinant progeny, and there is a fair chance that we will observe none, in which case the two markers cannot be ordered. In the early days of mapping, citrus geneticists often used relatively small mapping populations (50–60 progeny) because resources were limited and devel- opment of dense maps seemed unlikely. The development of new high-throughput methods for marker analysis makes it possi- ble to develop much denser maps and, if this is anticipated, then the mapping popu- lation should be larger (100–300 progeny). A discussion of mapping population sizes is given by Maliepaard et al. (1997).

A second choice that the mapper must face is the type of population. In annual crops where homozygous lines are avail- able, mapping is much simpler because seg- regation of markers and traits is predictable. In citrus, virtually all genotypes are het- erozygous. An advantage of this situation is that elite cultivars can be used as parents, but a disadvantage is that markers will show various types of segregation which complicates mapping. This can be illus- trated by considering the mapping popula- tion used by Jarrell et al. (1992). This population is a cross of two citrus root-


 

stocks, Sacaton citrumelo ´ Troyer citrange ((Citrus paradisi ´ Poncirus trifoliata) ´ (C. sinensis ´ P. trifoliata)). For each linkage group, each parent contains one chromo- some derived from a Citrus parent and one derived from a Poncirus parent. Depending on the specifi c allele carried by each chro- mosome, three types of segregation can be observed for each marker locus (see Table 12.1). These different segregation types lead to different mapping strategies and several different maps. The different map types are listed in the last column of Table 12.1. Markers that segregate in only one parent, say Sacaton, can be used to construct a map of that parent that refl ects the frequency of crossovers between homologous chromo- somes in that genotype. A parallel map can be prepared for those markers that segregate only in the other parent. Markers showing the 1: 1: 1: 1 segregation can also be com- bined with those segregating 1: 1 by ‘renam- ing’ the two alleles in the homozygous parent. For example, segregation type ab1 ´

ab2 can be combined with ab ´ aa by renam-

ing all b2 alleles as a alleles. Markers segre- gating in 3: 1 and 1: 2: 1 ratios can be

combined with each other, but cannot be accurately mapped with 1: 1 markers (Maliepaard et al., 1997), essentially because recombinant gametes from one parent are identical to non-recombinant gametes from the other parent. Similarly, for dominant markers in an F2 confi gura- tion, only markers in coupling phase (dom-


 

Table 12.1. Types of marker segregation that can be expected in a cross between two heterozygous parents (Sacaton and Troyer).

 

  Sacaton   Troyer   Progeny Expected segregation ratio   Map
aa ab aa, ab 1: 1 Troyer
bb ab bb, ab 1: 1 Troyer
ab aa aa, ab 1: 1 Sacaton
ab bb aa, ab 1: 1 Sacaton
ab ab aa, ab, bb 1: 2: 1 Sacaton*, Troyer*, F2
Aa Aa A_, aa 3: 1 F2
a1b a2b a1a2, a1b, ba2, bb 1: 1: 1: 1 Sacaton, Troyer, F2
a b1 ab2 aa, ab2, b1a, b1b2 1: 1: 1: 1 Sacaton, Troyer, F2
a1b1 a2b2 a1a2, a1b2, b1a2, b1b2 1: 1: 1: 1 Sacaton, Troyer, F2

 


inant alleles on one chromosome and reces- sive alleles on the homologue) can be accu- rately mapped (Knapp et al., 1995).

One mapping strategy is the ‘pseudo- testcross’ in which two maps are prepared, one for each parent, using only those loci that segregate 1: 1 or 1: 1: 1: 1. An ‘F2-type’

map can also be prepared using loci that

segregate 1: 2: 1, 3: 1 or 1: 1: 1: 1. The F2 map can then be merged with the single parent maps, using the 1: 1: 1: 1 loci that occur on all maps as anchors. The F2 population type is more effi cient because recombination fre- quency from two meioses (one in each parent) per progeny plant is determined. However, if recombination frequencies are quite different in the two parents, then this map is a compromise that does not refl ect the biology of either parent.

Another issue that must be considered in choosing a mapping population is inbreeding in the parents. Whether the cross considered is a backcross type, or F2, if the heterozygous parent(s) are somewhat inbred, then there may be regions of the genome that are homozygous (identical-by- descent) in that parent. Such regions cannot be mapped because there will be no het- erozygous markers. It should be noted that such regions may occur in parents not known to be inbred. For example, P. trifoli- ata genotypes are capable of self-pollina- tion, and many zygotic seedlings apparently originate by selfi ng (Khan and Roose, 1988). It is possible that standard cultivars originated through selfing or mating between relatives and, if so, then we would expect to fi nd such homozygous regions. Comparison between maps of Poncirus and Poncirus ´ Citrus hybrids, which should not contain homozygous seg- ments, should reveal homozygous segments provided that the maps share a suffi cient density of common markers.

 

 






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