Published online 1 September 2007
Published in Crop Sci 47:1878-1886 (2007)
© 2007 Crop Science Society of America
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CROP BREEDING & GENETICS
Optimization of the Marker-Based Procedures for Pyramiding Genes from Multiple Donor Lines: II. Strategies for Selecting the Objective Homozygous Plant
T. Ishiia and
K. Yonezawab,*
a Marker-Assisted Rice Breeding Research Team, National Institute of Crop Science, Tsukuba 305-8518, Japan
b Dep. of Biotechnology, Kyoto Sangyo Univ., Kyoto 603-8555, Japan
* Corresponding author (yonezaw{at}cc.kyoto-su.ac.jp).
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ABSTRACT
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For extended application of marker-based plant breeding, strategies are discussed for selecting a high-degree gene-pyramided line from among progeny of a multiparentally produced heterozygous plant (root genotype). A strategy with combined use of haplo-diploidization and crossing between selected plants will be highly efficient; selection starts with haplo-diploidized plants raised from the root genotype, and in the absence of a plant with the objective marker genotype, two plants with the best complementary genotypes are crossed to produce a hybrid, which in turn is haplo-diploidized for the next round of selection. In this strategy, even a plant having as many as 20 target markers can be obtained at an almost perfect certainty in about three rounds of selection with a maximum of 200 tested plants per round. When haplo-diploidized plants are unavailable, a plant with the most promising marker genotype should be selected and self-fertilized in each generation, or in the absence of any promising plant, two plants with the best complementary genotypes are crossed for the next round of selection. In this strategy, the number of tested plants in the first two generations counts when the markers are codominant, whereas the rounds of selection counts when the markers are dominant. Of various supplementary measures for this strategy, backcrossing the root genotype with one of the donors could be useful when the donor has more than 70% of all targeted markers.
Abbreviations: CGP, a pair of plants with complementary marker genotypes CPP, a pair of plants with complementary marker phenotypes CRO, expected number of crossings performed in a selection strategy GEN, expected rounds of selection performed in a selection strategy GNP, expected number of plants tested per selection round HF2, a selection strategy with combined use of F2 enrichment and haplo-diploidization IG, a plant with the objective homozygous marker genotype PG, a plant with promising marker genotype PP, a plant with promising marker phenotype PRO, the probability of success; RHC, a selection strategy with recurrent use of haplo-diploidization and crossing between the best complementary genotypes RSC, a recurrent selection strategy with selfing or crossing of selected plants SH, a selection strategy with a single round of haplo-diploidization and selection TPN, expected total number of tested plants in a selection strategy
Optimization of the Marker-Based Procedures for Pyramiding Genes from Multiple Donor Lines: II. Strategies for Selecting the Objective Homozygous Plant
T. Ishiia and
K. Yonezawab,*
a Marker-Assisted Rice Breeding Research Team, National Institute of Crop Science, Tsukuba 305-8518, Japan
b Dep. of Biotechnology, Kyoto Sangyo Univ., Kyoto 603-8555, Japan
* Corresponding author (yonezaw{at}cc.kyoto-su.ac.jp).
For extended application of marker-based plant breeding, strategies are discussed for selecting a high-degree gene-pyramided line from among progeny of a multiparentally produced heterozygous plant (root genotype). A strategy with combined use of haplo-diploidization and crossing between selected plants will be highly efficient; selection starts with haplo-diploidized plants raised from the root genotype, and in the absence of a plant with the objective marker genotype, two plants with the best complementary genotypes are crossed to produce a hybrid, which in turn is haplo-diploidized for the next round of selection. In this strategy, even a plant having as many as 20 target markers can be obtained at an almost perfect certainty in about three rounds of selection with a maximum of 200 tested plants per round. When haplo-diploidized plants are unavailable, a plant with the most promising marker genotype should be selected and self-fertilized in each generation, or in the absence of any promising plant, two plants with the best complementary genotypes are crossed for the next round of selection. In this strategy, the number of tested plants in the first two generations counts when the markers are codominant, whereas the rounds of selection counts when the markers are dominant. Of various supplementary measures for this strategy, backcrossing the root genotype with one of the donors could be useful when the donor has more than 70% of all targeted markers.
Abbreviations: CGP, a pair of plants with complementary marker genotypes CPP, a pair of plants with complementary marker phenotypes CRO, expected number of crossings performed in a selection strategy GEN, expected rounds of selection performed in a selection strategy GNP, expected number of plants tested per selection round HF2, a selection strategy with combined use of F2 enrichment and haplo-diploidization IG, a plant with the objective homozygous marker genotype PG, a plant with promising marker genotype PP, a plant with promising marker phenotype PRO, the probability of success; RHC, a selection strategy with recurrent use of haplo-diploidization and crossing between the best complementary genotypes RSC, a recurrent selection strategy with selfing or crossing of selected plants SH, a selection strategy with a single round of haplo-diploidization and selection TPN, expected total number of tested plants in a selection strategy
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INTRODUCTION
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INCREASING NUMBERS of DNA markers that are closely linked with desirable trait genes have been detected and validated in various crop plants in recent years (Charlson et al., 2005; Landi et al., 2005; Gordon et al., 2006; Jena et al., 2006; Liu et al., 2006). The practical application of these markers will be extended if they are accumulated into single plant genomes to construct high-degree gene-pyramided lines.
When obtaining a gene-pyramided homozygous line via assembling markers from multiple donor lines, a plant that has all the markers in a heterozygous state must be produced in any stage within the program. Any gene accumulation program, therefore, can be separated in two parts: the process (named step I in Ishii and Yonezawa, 2007) for producing such a heterozygous genotype, and the process (named step II) in which a plant that has all the targeted markers in a homozygous state is selected from among the progeny of the heterozygous genotype produced via step I. Because the efficiency of steps I and II depends on different parameters, optimization of these steps can be discussed separately. The efficiency of step I depends on the schedule of crossing between donor lines, the optimization of which was discussed in Ishii and Yonezawa (2007). The efficiency of step II, on the other hand, depends on the selection procedures for the progeny plants of the heterozygous genotype obtained in step I. Optimum procedures for step II are discussed in this paper.
Marker-assisted selection strategies have been discussed in various contexts, such as introgressing useful genes via backcrossing (Hospital et al., 1992; Tanksley and Nelson, 1996), improving population mean (Lande and Thompson, 1990; Whittaker et al., 1995; Bernardo, 1999; Liu et al., 2003), heightening the frequency of a favorable allele at each locus concerned (Luo et al., 1997; Hospital et al., 2000), selecting lines with a desired trait in early generations (Monforte et al., 1996; Igartua et al., 2000), and identifying pairs of recombinant inbred lines or haplo-diploidized lines with desirable crossing potentials (van Berloo and Stam, 1998; Charmet et al., 1999). It was assumed in these studies that the target population is initiated biparentally and both detection of useful markers and selection assisted by the detected makers are performed, in either parallel or tandem, within the breeding program concerned. In the context of our discussion, the selection is based on markers that have already been validated in each donor line, and the objective of selection is to obtain a plant with a particular marker genotype that carries all the markers in a homozygous state.
Selection strategies in such a context have been discussed by a number of research teams. Howes et al. (1998) compared the effectiveness of a number of different strategies using the haplo-diploidization method, having proposed two strategies named RF2Sel and RDHS (explained later) in which haplo-diploidization, combined with random intercrossing between selected plants, is used. The recurrent selection strategy employed in the discussion of Charmet et al. (1999) could also be used in the present context of selection. When assembling a group of markers that are located on the same linkage block, Servin et al. (2004) suggested crossing the initial heterozygous genotype with a "blank parent" (a line carrying no target marker) or a "founding parent" (a donor line carrying a single marker). Meanwhile, Bonnett et al. (2005) proposed combined use of F2 enrichment (elimination of genotypes that are homozygous for untargeted or null markers at one or more loci concerned) and generation advancement after F2 to increase the homozygosity of plants. The purpose of our discussion is to provide some additional guidelines for practitioners via comparing the effectiveness of various strategies and supplementary measures suggested hitherto. Our discussion is based on the stochastic calculations using more realistic selection models and a wider range of conditions of related parameters than those employed previously.
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MATERIALS AND METHODS
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Selection Strategies
Four strategies of marker-based selection, recurrent selection with crossing between selected plants (RSC), recurrent haplo-diploidization and crossing (RHC), haplo-diploidization of F2 plants (HF2), and a single round of haplo-diploidization and selection (SH) are discussed; workflows in the former three strategies are described in Fig. 1
. Each of these strategies starts with a population generated via self-fertilization or haplo-diploidization of a plant (denoted I0 in Fig. 1), which has been produced via a schedule of crossing in step I mentioned before and carries all target markers in a heterozygous state. In what follows, the individual I0 will be referred to as "root genotype," and the homozygous genotype to be obtained via step II, as "ideal genotype" or "ideotype," following the terminology of Servin et al. (2004). Unless otherwise stated, the target markers are assumed to be either codominant or dominant and independently inherited, each of which is perfectly linked with a desirable trait gene.

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Figure 1. Diagrammatical definition of the selection strategies to be compared. I0 represents an initial heterozygous plant (root genotype) that has been produced via a schedule of crossing between multiple donor lines (Ishii and Yonezawa, 2007). For simplicity, generations in all strategies were designated by the same symbol Gi (i = 1,..., T). Selection procedures with codominant and dominant markers were written in roman and italic letters, respectively. No difference exists between codominance and dominance in strategy recurrent haplo-diploidization and crossing (RHC). Marker genotyping may be performed for haploids, only ones with a desirable genotype being haplo-diploidized. Symbols are defined as follows: Ni = a maximum permissible number of plants genotyped in generation Gi, IG = a plant with objective homozygous marker genotype, PG = a plant with a promising genotype that has a potential to leave IG in its progeny, CGP = a pair of plants with the best complementary genotypes to leave IG, PP = a plant with a promising marker phenotype (defined when the markers are dominant), and CPP = a pair of plants with complementary marker phenotypes.
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In strategy RSC, the haplo-diploidization method is not used; a plant with the most promising marker genotype that has the highest potential to leave an ideotype (denoted IG in short) in its progeny is selected in each generation, being self-fertilized to give rise to a population for the next round of selection. In the absence of any promising genotype (denoted PG), two plants with the best complementary genotypes (denoted CGP) are crossed for the next round of selection. The selection is performed in T generations at the maximum, ending in any generation before the Tth when an IG is found (counted as a success), or, neither IG, PG, nor CGP is found (counted as a failure). A maximum of Ni plants is allowed in generation Gi (i = 1, 2, ..., T). When the markers are dominant, IG and PG cannot be distinguished from each other, and plants with all kinds of PG exhibit the same promising marker phenotype (denoted PP). In this case, a plant with PP found first is selected and self-fertilized in each generation, or, in the absence of such a plant, two plants with the best complementary marker phenotypes (denoted CPP) are crossed. The selection ends at a generation (excluding the first generation G1 in Fig. 1) when all tested plants exhibit PP (counted as a success because the plants can be regarded as having been fixed to IG), or no plants with PP or CPP are found (a failure).
Selection in RHC starts with a population of haplo-diploidized plants produced from the root genotype I0, and ends at a generation when an IG is found (success), or neither IG nor CGP is found (failure). Otherwise, two plants with the best CGP are crossed to produce a hybrid, which is haplo-diploidized for the next round of selection. In strategy RHC, selection is performed in T rounds at the maximum, and the type of dominance, codominance versus dominance, makes no difference because all tested plants are homozygous. Strategy RHC is of the same type as RDHS of Howes et al. (1998) and the recurrent selection strategy adopted in Charmet et al. (1999); in all of these strategies, selection is performed recurrently with haplo-diploidized plants. These strategies differ in some procedural parameters, most importantly, in the number of plants selected per round; in RHC, only two plants with the best complementary marker genotypes are selected and crossed for the next round of selection, whereas, in the strategies of Howes et al. (1998) and Charmet et al. (1999), multiple plants are selected and crossed in multiple pairs. Not only haplo-diploidized plants selected but also one of the two parents used for the initiation of the population are incorporated in the crossing in the strategy of Charmet et al. (1999). Strategy RHC is more practicable (resource-saving) than the previously discussed ones. The idea of recurrent selection with haplo-diploidized plants traces back to the theory of Fouilloux (1980).
In strategy HF2 of Fig. 1, selection starts with a population (G1) produced via self-fertilization of I0. The selection ends at generation G1 when an IG (success) or none of IG, PG, and CGP (failure) is detected. Otherwise, a plant with the best PG is haplo-diploidized to raise a population for the second (final) round of selection, or in the absence of PG, two plants with the best CGP are crossed to produce a hybrid plant, which in turn is haplo-diploidized to raise plants for the final round of selection. When the markers are dominant, the selection ends at G1 when neither PP nor CPP is found (a failure). Otherwise, PP found first or a hybrid plant of the best CPP is haplo-diploidized for the final selection.
Strategy HF2 resembles RF2Sel of Howes et al. (1998) and DH of Bonnett et al. (2005) that was defined under item "with F2 enrichment for all marker loci" (cf., items 4.2 and 6.2 in their Tables 4 and 6, respectively). In all of these strategies, selection starts with F2 population. In RF2Sel, all F2 plants with desirable marker genotypes (having all target markers in either homozygous or heterozygous state) are selected and randomly intercrossed to give rise to a population, from which plants with desirable genotypes are again selected and haplo-diploidized for the final round of selection. In the DH with F2 enrichment of Bonnett et al. (2005), all F2 plants with desirable marker genotypes are haplo-diploidized for the final selection. Both of these strategies will be impracticably resource-consuming because many plants are treated for crossing and/or chromosome doubling. Our HF2 is practicable and used here as a check for examining the efficiency of combined use of F2 enrichment and haplo-diploidization.
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Table 4. Efficiency of strategy RSC with different permissible population sizes per generation (N) calculated under five permissible selection rounds (T).
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Table 6. Efficiency of strategy RSC with different permissible rounds of selection (T) under 100 permissible tested plants (N).
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Strategy SH is the simplest one using haplo-diploidization method, in which selection is performed only once for haplo-diploidized plants raised from the root genotype. Strategy SH is the same as DH of Bonnett et al. (2005) that was defined under item "without selection in F2 generation" (cf., item 4.1 in their Table 4 and item 6.1 in their Table 6). There will be no difference between SH and RHC when only a few markers are targeted with a large population size (Ni) because in both strategies the selection ends in a success with only one round of selection. In any strategy employing haplo-diploidization method, much of the resources could be saved if plants are genotyped at the haploid stage, with only those with a desirable marker genotype being subject to chromosome doubling.
Efficiency Indicators
The efficiency of our selection strategies is evaluated based on the following five efficiency indicators:
- PRO: the probability that a selection program ends with a successful result, that is, an IG is obtained within permissible numbers of generations (T) and genotyped plants per generation (Ni; symbol N is used when Ni is the same across generations),
- GEN: the expected number of generations in which selection is performed, being calculated across all possible results of selection, whether ending with a successful or unsuccessful result under the pre-assigned conditions for T and N,
- CRO: the expected number of crossings between selected plants (CGP) performed in the selection program,
- TNP: the expected total number of plants genotyped in the selection program, and
- GNP: the average number of plants genotyped per generation, being calculated by TNP/GEN.
With given conditions for Ni and T, a selection strategy with a higher value of PRO and smaller values of GEN, CRO, TNP, and GNP will be more efficient. Of these five indicators, PRO should be the most important because the expense is wasted when the selection fails. Our discussion therefore will be based mainly on PRO.
Discussion in the previous studies for step II was based on the expected segregation proportion of IG, the expected number (average of all possible numbers) of plants required to be genotyped for finding an IG, or the number of plants required for obtaining IG with a 0.95 or higher probability (Howes et al., 1998; Charmet et al., 1999; Servin et al., 2004; Bonnett et al., 2005). Either of these indicators will be good to rank the superiority of different strategies, but each of them has a weakness of its own; the expected segregation proportion does not directly indicate what the breeder wants to know; the expected plant number is rather small, which may bring about an undeserved optimism for the success; and the plant number for such a high probability of success is impractically large when many markers are involved, bringing about an unproductive reluctance to use marker-based breeding. Such weaknesses can be avoided if an indicator is used in which econo-technical limitations imposed on the program are considered. There should be maximum permissible sizes of N and T in any actual selection programs, and because of random drift, the selection is not always performed in scheduled rounds, ending at any round before the scheduled final round, when IG is found (a success) or no plant with a desirable genotype is found (a failure). Our indicators were introduced to conform to this reality.
Stochastic simulations are used to calculate our indicators. Ten thousand repeated runs are made for each set of conditions of the genetic and procedural variables concerned. The PRO is obtained as the proportion of runs that ended with a successful result. The values of the other indicators are obtained as the average across all repeated runs, whether ending in a success or failure. With 10,000 runs, calculations of the indicators are not completely immune from chance error, but exact enough to capture major points. The computer programs for the calculations are written in Fortran90, and SGI Altix3700 is used to generate random digits in each necessary step in the simulation. The programs are available on request.
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NUMERICAL CALCULATIONS
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Comparison of the Strategies
Our discussion is directed first to the cases where all of the target markers are codominant and independently inherited. Calculations for N = 200 and T = 5 (Table 1
) show that the superiority of the strategies changes, more or less, with the number of markers concerned (m). When m = 5, all strategies, RSC, HF2, SH, and RHC, give almost a perfect probability of success (PRO = 1). Of these four, SH and RHC could be preferred because they require much fewer GEN and TNP than the other strategies. Usefulness of SH is lost when m = 10; PRO of SH is as low as 0.183, whereas those of the other three strategies are still almost perfect. Of the three strategies, HF2 and RHC are superior to RSC because of much fewer GEN and TNP.
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Table 1. Calculations of the efficiency indicators under the four selection strategies with m independently inherited markers. The target markers were assumed to be either codominant or dominant exclusively. Calculated under 200 permissible tested plants (N) and five permissible rounds of selection (T).
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The superiority of the strategies gets much more pronounced when m is as large as 15. The PRO of SH becomes practically zero, and that of HF2, lower than 0.5. The PRO of RSC also decreases significantly, although it remains higher than 0.9. By contrast, in RHC, PRO is still perfect and GEN and TPN are much fewer than those in RSC. When m = 20, PRO of RSC declines to 0.524, but that of RHC is still nearly perfect (0.998). The PRO of RHC is as high as 0.916 (GEN = 2.866, TPN = 419.1, and GNP = 145.2) even with m = 25 (not presented in Table 1). Therefore, RHC is by far most efficient when as many as or more than 15 markers are involved.
When the markers are dominant, PRO of RSC and HF2 decrease markedly compared with those with codominant markers; PRO of RSC is as low as 0.340 even when m = 5, and that of HF2 is 0.774 when m = 10 (Table 1). Of course, the effectiveness of RHC is unchanged whether the target markers are codominant or dominant.
Our calculations, therefore, confirm the superiority of RHC. Breeders may be rather reluctant to use RHC because it requires an extra expense of producing haplo-diploidized plants. This expense, however, could be readily recovered; as the calculations of Table 2
show, RHC gives a sufficiently high probability of success even when N = 50 and 100, unless m exceeds 15. Strategies HF2 and SH will not be useful, and much less efficient than RSC when as many as 15 codominant markers are involved (Table 1). The CRO of strategy RSC is negligibly small unless m exceeds 10, indicating that crossing between selected plants is rarely needed.
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Table 2. Efficiency of strategy RHC under different permissible population sizes per generation (N). Calculated under five permissible rounds of selection (T).
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Comparison with Linked Markers
To know modifications due to linkage between markers, calculations were made under four typical configurations of linkage (including a case of independent markers), that is, cases (a) to (d) in Table 3
. By the calculations, the superiority rank of the four selection strategies is the same whether or not linkages are involved, although TNP and GEN change depending on the configurations of linkages; more plants and generations will be needed when repulsion linkage dominates [cf., cases (a) and (b)], whereas fewer plants and generations will be sufficient when coupling linkage dominates [cf., cases (a) and (d)]. In strategy RSC with codominant markers, the disadvantage due to repulsion linkages is largely cancelled when coexisting with coupling linkages; PRO declines rather slightly from 0.999 to 0.915 [cf., cases (a) and (c)].
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Table 3. Efficiency of the four selection strategies in the presence of linkage between markers. Calculated under 200 permissible tested plants (N), five permissible selection rounds (T), and 12 target markers (m). The map distance between two linked markers in each pair was assumed to be 5 cM.
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When the root genotype has been produced via crossing of multiple donor lines, coupling linkage should dominate because only markers that were incorporated in the latest stage can be linked in repulsion phase. As predicted from the trends in Table 3, the disadvantage of repulsion linkage will not be serious in such a case. Repulsion linkages may dominate when the root genotype is a hybrid of two inbred donor lines, as assumed in the discussion of Bonnett et al. (2005). In such a case, only strategy RHC will be effective enough; in case (b) of Table 3, only RHC gives a sufficiently high probability (0.996). In conclusion, the superiority of RHC is even more pronounced when linkages are involved.
Supplementary Measures for Increasing the Efficiency of RSC Strategy
Strategy RSC is the only choice when haplo-diploidization method is not available. There are a number of possible measures for improving the efficiency of RSC. Increasing either N or T or incorporating some rounds of generation advancement is the simplest and most practicable measure. Some more refined measures, such as backcrossing the root genotype I0 with one of the donor lines (Servin et al., 2004; Bonnett et al., 2005) and crossing I0 with a blank parent (Servin et al., 2004), have been suggested previously. The effectiveness of these measures is examined here.
Calculations in Table 4
show that, with codominant markers, increase in the population size N causes a marked increase in PRO when m = 15. With fewer markers (m
10), the contribution of increased N occurs as a decrease in GEN because PRO is almost perfect even when N is as small as 50. Increase in N provides no noticeable advantage when the markers are dominant.
A weighted rather than uniform allocation of population sizes across generations is expected to be useful when many codominant markers are involved. Comparison of uniform versus weighted allocations, under the same total tested plant number N1 + N2 + ... + N5 = 500 (Table 5
), reveals that PRO is significantly improved with weighting for earlier generations, that is, from 0.795 to 0.982 (under VN-2) when m = 15 and from 0.524 to 0.851 (under VN-2) when m = 20, although TNP and GNP increase to some extent. Our calculations, therefore, substantiate the importance of population sizes of the first and second generations, N1 and N2. It is also known from Table 5 that PRO is maximized with VN-2, not with VN-1 and VN-3, indicating existence of an optimum allocation of N1 relative to N2.
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Table 5. Efficiency of strategy recurrent selection with crossing (RSC) with codominant markers under some weighted allocations of population sizes (Ni) across generations.
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Increase in generations (T) produces no advantage with codominant markers (Table 6
); all indicators take practically the same values under any values of T assumed, reflecting the fact that the result of selection, i.e., success or failure, is determined in early generations. With dominant markers, on the other hand, PRO increases significantly with increase in T, although being accompanied by increase in GEN, TNP, and GNP.
Advantage of generation advancement was not recognized in our calculations. With codominant markers, PRO decreased when RSC was started after any rounds of generation advancement (data not presented), indicating that advancing generations without selection is of no practical use. Generation advancement had some advantage when the markers are dominant (Table 7
); when m equaled 5 and RSC was performed after two rounds of generation advancement, PRO increased from 0.331 (Table 4) to 0.446 (Table 7) under N = 100 and from 0.340 (Table 4) to 0.447 (Table 7) under N = 200. These increases would not be cost-effective. With m
10, PRO rather decreases when generation advancement is used, reflecting the fact that, because of random drift, desirable genotypes are subject to a high risk of failure during generation advancement.
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Table 7. Efficiency of selection based on dominant markers when performed in strategy recurrent selection with crossing (RSC) after two rounds of generation advancement (F2 and F3 generations) with single seed descent method. Calculated under 100 and 200 permissible tested plants (N) and three permissible selection rounds (T). Generations F2 and F3 were not included in T and GEN.
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When assembling markers from two wheat (Triticum aestivum L.) donor lines, Bonnett et al. (2005) proposed backcrossing F1 plant (I0 in our terminology) with one of the two donors carrying more target markers (cf., example 2 in Bonnett et al., 2005). This backcross is applied to increase desirable marker genotypes, not for the recovery of the genetic background of the donor. Such a backcross could also be used when three or more donors are involved as assumed in our study (Ishii and Yonezawa, 2007); the root genotype (I0 in Fig. 1) could be backcrossed with a donor having the largest number of targeted markers.
The backcross should be advantageous for a locus where both of the heterozygous plant and the chosen donor have the targeted marker, but disadvantageous for a locus where the donor does not carry the targeted marker. For efficient backcrossing, therefore, the donor should have a sufficiently high proportion of the targeted markers. Calculations of Table 8
demonstrate that the proportion (f) must be higher than 0.7. When this condition is satisfied, the advantage of the backcross occurs in different modes depending on the kinds of dominance (codominance versus dominance) as well as the number of markers (m) involved. With codominant markers, the advantage occurs as a reduction in TNP and GNP when m = 6 (at a proportion of 0.83), as a reduction in GEN, TNP, and GNP when m = 10, and as a large improvement in PRO and a reduction in CRO when m = 15. No noticeable increase in PRO occurs with m = 6 and 10 because it is almost unity even without the backcross. With dominant markers, PRO is improved with all the three magnitudes of m, being accompanied by a substantial decrease in TNP and GNP when m = 10 and 15.
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Table 8. Efficiency of strategy recurrent selection with crossing (RSC) when the initial population is produced via backcrossing the root genotype with one of the donors involved. The donor is assumed to have a proportion (f) of all targeted markers (m). Calculated under 100 permissible tested plants (N) and five permissible selection rounds (T).
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No simple guideline, such as f > 0.7, could be derived when linked markers were considered. The effectiveness of crossing with a donor or blank parent (Servin et al., 2004; Bonnett et al., 2005) varied depending on the number, linkage configuration, as well as the type of dominance of target markers (data not presented).
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RESULTS AND DISCUSSION
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Our calculations showed that a selection strategy with combined use of haplo-diploidization and crossing between selected plants, that is, RHC, is highly efficient when producing a high-degree gene-pyramided line (m > 10); this strategy is efficient whether the markers are codominant or dominant, giving a sufficiently high probability of success under a quite affordable resource expense (GEN, CRO, TNP, and GNP) even when more than 20 markers are targeted. Strategies using haplo-diploidization of F2 plants, such as our HF2, RF2Sel of Howes et al. (1998), and DH of Bonnett et al. (2005), are not useful. When haplo-diploidized plants are not available, strategy RSC should be used such that a maximum permissible number of plants is tested in the first two generations when most markers are codominant, or, the largest possible number of generations is used with relatively few plants (fewer than 100 when m < 20) being tested per generation when the markers are dominant. Incorporating generation advancement for a higher homozygosity is not advantageous. Backcrossing the root genotype with one of the donors will be useful when the donor has a sufficiently high proportion of the objective markers, i.e., higher than 70% with independently inherited markers (Table 8).
Howes et al. (1998) predicted that combining more than 12 target markers might not be feasible whether RDHS or RF2Sel is used, because these strategies require a prohibitively large number of tested plants. The number 12 seems to have been adopted as a guideline in many practical breeding projects. Strategy RDHS is similar to our RHC under T = 2. Calculations of RHC under T = 2 and N = 200 showed that combining 12 target markers was never difficult but achievable with an almost perfect certainty (PRO = 0.998) and at quite an affordable resource expense (GEN = 1.952, CRO = 0.952, TNP = 209.1, and GNP = 107.4). The gap between the prediction of Howes et al. (1998) and ours could be ascribed to the difference in the procedures for raising a population for the second (final) round of selection. In RDHS, plants having "most of the target markers" are selected and randomly intercrossed (from the context of their discussion, a fairly large number of plants seem to be selected though not explicitly described), whereas only two plants with the best complementary marker genotypes are crossed in our RHC. Our calculations, therefore, show that intercrossing between many selected plants is not advantageous, emphasizing that efforts should be concentrated on a single best or two best complementary plants. Strategy RHC is highly effective, enabling one to obtain a plant even carrying 25 target markers, with PRO = 0.916, GEN = 3.037, CRO = 2.037, TNP = 439.1, and GNP = 174.6, when performed under N = 200 and T = 5.
The guideline condition f > 0.7 mentioned before, the reality of which was also confirmed with analytical calculations (not presented), indicates that the supplementary backcrossing is of rather limited application. This condition would not often be satisfied when the root genotype is produced with multiple donor lines; no single donor would have such a high proportion of targeted markers when three or more donors are involved. The application of the backcross may be even more restricted when linked markers are involved; in the genome of a multiparentally produced root genotype, coupling rather than repulsion linkages will dominate, which may be broken by backcrossing. Crossing the root parent with a blank parent or a parent that carries a single marker (Servin et al., 2004) would not be of general use either; such a crossing will be advantageous for assembling markers that are strongly linked in repulsion phase, but not for markers that are independent or linked in coupling phase. As suggested by Servin et al. (2004), a blank parent may effectively be employed in some stage in step I rather than in step II. The major concern of the discussion of Servin et al. (2004) was for the procedures of step I. We must confess that that we did not notice their work at the writing of our previous paper, Ishii and Yonezawa (2007).
Throughout this paper, the effectiveness of strategy RSC has been discussed only for the cases where all target markers are codominant or dominant. Both codominant and dominant markers may be targeted in the same selection program. Our calculations (not presented) showed that the effectiveness of selection decreased largely when only a few among many markers are dominant; PRO under N = 200 and T = 5 decreases from 1 to 0.640 when only two out of 10 independent target markers are dominant, and from 0.524 to 0.211 when four out of 20 markers are dominant, emphasizing the importance of developing codominant markers or technologies of haplo-diploidization. The problem of dominant markers does not occur when RHC is used.
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ACKNOWLEDGMENTS
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The authors would like to thank an anonymous reviewer for valuable comments and suggestions. His or her suggestions, especially the reminder of some important papers, were highly helpful for widening the scope of our discussion.
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NOTES
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All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.
Received for publication November 28, 2006.
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