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Published online 1 January 2005
Published in Crop Sci 45:147-156 (2005)
© 2005 Crop Science Society of America
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Linkage Analysis between Gametophytic Restorer Rf2 Gene and Genetic Markers in Cotton

Jinfa Zhanga,*, J. M. Stewartb and Tonghui Wanga

a Dep. of Mathematical Sciences, Box 30001, New Mexico State Univ., Las Cruces, NM 88003
b Dep. of Crop, Soil and Environmental Sciences, 115 Plant Science Building, Univ. of Arkansas, Fayetteville, AR72701

* Corresponding author (jinzhang{at}nmsu.edu).


    ABSTRACT
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 APPENDIX
 REFERENCES
 
In heterozygous fertility restored F1 plants of the CMS-D8-Rf2 gametophytic restoration system of cotton (Gossypium hirsutum L.), only the pollen grains with the Rf2 allele are functional; consequently, all F2 plants are fertile. Our objective was to develop a statistical method to estimate the recombination fraction (r) between Rf2 and genetic markers linked in repulsion or coupling phases in fertile F2 populations. Alleles linked to Rf2 are preferentially transmitted through pollen, whereas the transmission of alleles linked to rf2 is reduced. Thus, linked genes give distorted segregation ratios depending on the linkage strength. Genes independent of Rf show normal segregation. The traditional 3:1 or other appropriate ratios can be used to test the linkage between a marker and the Rf locus in an F2 population. Examples are given for two crosses: (D8R x T586) F2 for repulsion linkage and (D8R x T582) F2 for coupling phase linkage. The morphological data confirmed that Rf2 is not linked to nine dominant genes in T586 or to five recessive genes in T582. However, a RAPD marker, UBC188500, present in D8R and absent in nonrestoring lines, exhibited extremely skewed segregation in the D8R x T586 F2 population with only two plants without UBC188500 in a population of 76 plants. The recombination frequency between Rf2 and this marker is 5.26%, which agrees with our previous estimate from a testcross, (D8R x T586) x H1330. This indicates that the proposed method is a valid alternative for mapping gametophytic Rf2. Its advantages and limitations are discussed.

Abbreviations: CMS, cytoplasmic male sterility • ML, maximum likelihood • PCR, polymerase chain reaction • RAPD, random amplified polymorphic DNA • SD, segregation distorter


    INTRODUCTION
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 APPENDIX
 REFERENCES
 
LINKAGE TESTS require normal segregation of alleles at the target loci. Many different statistical methods can be employed to test whether two or more loci are linked (Liu, 1998). For example, the Chi-square test is a traditional method that determines if an observed segregation ratio fits an expected ratio such as 9:3:3:1 for F2 populations and 1:1:1:1 for a testcross. The test will fail if strong gametophytic or sporophytic selection occurs. Distorted segregation of genetic markers is often encountered in progenies of interspecific or intraspecific hybrids when molecular linkage maps are constructed (Wendel and Parks, 1984; Altaf et al., 1998; Faris et al., 1998; Virk et al., 1998). The differential transmission of markers is attributed to competition among gametes or to the abortion of the gametes or zygotes. Genetic studies have revealed that the differential transmission of genes is controlled by nuclear genes (Wendel et al., 1987). For example, in Drosophila melanogaster, segregation distorter (SD), a meiotic drive system, results in transmission of the SD chromosome in vast excess over the normal SD+ homolog in heterozygous SD/SD+ males (Powers and Ganetzky, 1991). Some evidence indicates that nucleocytoplasmic interactions can also affect gametophyte competition (Faris et al., 1998). An extreme example is the gametophytic sterility found in some cytoplasmic male sterility (CMS) systems in plants. When a CMS plant is crossed with its restorer (RfRf), the F1 heterozygote Rfrf (for one-locus model) produces one-half normal and one-half aborted pollen grains. Subsequent F2 plants are all fertile since only the Rf pollen participates in fertilization. This type of gametophytic restoration has been found in CMS-S of maize, Zea mays L. (Laughnan and Gabay-Laughnan, 1983), CMS-boro of rice, Oryza sativa L. (Varmani, 1996), IS1112C of sorghum, Sorghum bicolor (L.) Moench (Tang et al., 1998), and CMS-D8 of cotton (Stewart, 1992; Stewart et al., 1996). In such cases, the F2 population cannot be used to determine the genetics of restoration because there is no segregation in male fertility. The fertile F2 population also complicates linkage tests between Rf and other genetic markers. Usually for these tests, the heterozygous restored plants with CMS cytoplasm are used as females to cross with normal cultivars without Rf gene(s).

Self-pollination is much easier than crossing to generate large segregating populations, and in working with CMS-D8, an F2 population is more convenient for conducting linkage tests. Previously, we demonstrated that restoration of male fertility in CMS-D8 was controlled by a single dominant gene, Rf2, from the D8 restorer (Stewart et al., 1996; Zhang and Stewart, 2001a). Despite the lack of fertility segregation in the F2, the random transmission of other genes or DNA sequences through pollen is expected to be unaffected unless they are linked to the restorer allele (Rf2). Therefore, it is feasible to use a fertile F2 population to conduct linkage tests; genes independent of Rf2 will transmit normally and show normal segregation ratios. Conversely, alleles linked to Rf2 will be preferentially transmitted through pollen, whereas pollen transmission of rf2–linked alleles will be reduced depending on their genetic distance. Thus, Rf2–linked genes or markers will give distorted segregation ratios. This situation has not been taken into consideration in most statistical packages for linkage analysis, and no methods are available for estimating recombination fraction (r) between a gametophytic Rf gene and its linked genetic markers when a fertile F2 population is used. Our objective was to develop a statistical method with which F2 progeny can be used to estimate the linkage between genetic markers and gametophytic restorer genes.


    MATERIALS AND METHODS
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 APPENDIX
 REFERENCES
 
Plant Materials and Segregating Populations
The homozygous D8 restorer selection G7-5 with CMS-D8 cytoplasm and restorer gene (Rf2) was crossed as female to T586 and T582, respectively. G7-5 was developed by repeatedly backcrossing fertile plants of a hexaploid (D8AD) derived lineage as female to Upland cotton. G7-5 has a normal Upland cotton type in that it has green leaves, normal leaf and branch types, glanded plant body, normal bracts, cream colored flowers and pollen, pubescent plant parts, seed fuzz, and white fiber. T586 is a multiple dominant marker line carrying nine dominant mutations, while T582 is a multiple recessive marker line carrying five recessive mutations (Table 1; Endrizzi et al., 1984). In total, these markers are located on at least nine chromosomes. In the greenhouse, the two fertile F1s were self-pollinated to generate F2 populations. The F1 from G7-5 x T586 was testcrossed as female with a normal nonrestoring genotype, H1330 (Bourland, 1996), while the F1 from G7-5 x T582 was used as female in a backcross with T582. The F2 and testcross populations were grown in the field at the University of Arkansas Main Experiment Station at Fayetteville in 1998.


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Table 1. Morphological markers in the two multiple marker stocks, T586 and T582, used for linkage analysis.

 
Male Fertility and Morphological Markers
At flowering, male fertility and morphological characteristics were recorded on individual plants. Compared with the normal fertile plants, male-sterile plants have smaller flowers and anthers, which fail to shed pollen. The sterile plants could be identified when no pollen could be seen after the anthers were squeezed between fingers.

DNA Extraction and RAPD Analysis
To investigate the linkage between Rf2 and genetic markers, polymerase chain reaction (PCR)-based RAPD (random amplified polymorphic DNA) markers were employed to screen the F2 population of G7-5 x T586. The DNA from individual F2 plants was extracted according to the rapid DNA isolation method described by Zhang and Stewart (2000). The PCR reaction conditions were as reported by Zhang and Stewart (2000). A specific primer, UBC188 (5'-GCTGGACATC-3'), was used since it amplifies a genomic sequence closely linked to Rf2 (Zhang and Stewart, 2004).

Statistical Method—Repulsion Linkage
Consider a restorer line (R) with the CMS cytoplasm and a dominant restorer gene (Rf), such as the D8 restorer line G7-5. To test if Rf is linked to a recessive gene (m), the restorer (RfRfmm) is used as female in a cross with a maintainer line (B) having the nonrestorer gene allele (rf) and a dominant allele (M), for example, marker gene alleles in T586. The heterozygous F1 produces four types of gametes: RfM, Rfm, rfM, and rfm. The two male gametes, rfM and rfm, can be ignored because the nonrestorer allele (rf) cannot be transmitted via the male gamete. Gamete frequencies are listed in Table 2, together with the F2 progenies and their genotype frequencies. Under complete dominance, only six genotypes and two phenotypes (Rf_M_ and Rf_mm) are produced, compared with nine genotypes and four phenotypes in the normal situation (Table 3).


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Table 2. Genotypes of F1 gametes and F2 progeny in repulsion linkage between Rf and recessive allele when rf pollen is nonviable.

 

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Table 3. Comparison of genotypes, phenotypes, and their predicted frequencies in an F2 population with independent segregation and repulsion linkage without or with selection against rf male gametes.

 
In regard to each locus, the probabilities of the respective genotypes when rf pollen is discounted, are

Homozygous dominant

Formula

Formula

Heterozygous dominant

Formula

Formula

Formula

Recessive

Formula

Formula

Normally, whether the Rf locus is linked to a marker or not, the three genotypes, RfRf, Rfrf, and rfrf, follow a normal 1/4:1/2:1/4 segregation ratio. In the case of gametophytic restoration, the genotype rfrf does not exist since the male gamete carrying rf allele is nonviable. The frequencies for RfRf and Rfrf in the locus Rf are 1/2:1/2, that is, the frequency of RfRf increases to 1/2 from the normal 1/4. The frequencies for MM, Mm, and mm in the marker locus are 1/2r:1/2:1/2(1 – r). Although the frequency of the heterozygous genotype (Mm) remains unchanged (i.e., 1/2, same as for Rfrf), the frequencies for the two homozygous genotypes depend on the recombination fraction [1/2 r for MM and 1/2(1 – r) for mm]. The frequency for Rf_M_ and Rf_mm has a linear relationship with the recombination fraction. The frequency of Rf_mm decreases linearly from 1/2 (when r = 0) to 1/4 (when r = 1/2); the frequency for Rf_M_ increases linearly from 1/2 (when r = 0) to 3/4 (when r = 1/2). That is, when Rf and m are cosegregating (r = 0), genotype MM will not be produced, while genotype mm will be 1/2. On the other hand, when the two loci are independent (r = 1/2), the segregation in locus M will be normal (3:1). In normal repulsion linkage the relationships between the frequencies for the normal four phenotypes and the recombination fractions are all nonlinear (Table 3).

To estimate the recombination fraction r, three different estimators can be simply derived from Table 3,

Formula
and

Formula

The estimators for the recombination fraction r can also be obtained by using the maximum likelihood (ML) method (see the Appendix for details). The ML estimator for r is

Formula

Because f(mm) = 1 – f(M_), the rML given above can be also rewritten as

Formula
or

Formula

The significance of linkage can be tested by the goodness of fit {chi}2 test against 3:1 (or 1:2:1) ratio. If a significant deviation from 3:1 is encountered, the estimated recombination fraction rML and its variance can be estimated.

From the Appendix, we know that the information content per observation for r is

Formula
The variance for rML is

Formula

Statistical Method—Coupling Linkage
Assume a restorer R line with the CMS cytoplasm and a dominant restorer gene (Rf), such as the D8 restorer line G7-5. To test the linkage between Rf and any dominant genetic marker (MM), the restorer (RfRfMM) is used as female in a cross with a tester (rfrfmm), such as marker gene alleles in T582. Tables 4 and 5 summarize the expected genotypes and their frequencies for F2 progeny in coupling linkage phase. As in Table 2, the male gametes rfM and rfm cannot participate in fertilization.


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Table 4. Genotypes of F1 gametes and F2 progeny in coupling linkage between Rf and a dominant marker when rf pollen is nonviable.

 

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Table 5. Comparison of genotypes, phenotypes, and their predicted frequencies in an F2 population with independent segregation and coupling linkage without and with selection against rf male gametes.

 
Again, the phenotypic frequencies of Rf_M_ and Rf_mm are linear functions of the recombination fraction. The frequency of Rf_M_ decreases from 1 (when r = 0) to 3/4 (when r = 1/2), while P(Rf_mm) increases from 0 (when r = 0) to 1/4 (when r = 1/2). However, the frequencies for the two phenotypes have a quadratic relationship with r in the normal linkage situation (see Table 5).

Since P(M_) = 1/2 (2 – r) and P(mm) = 1/2 r (see Table 5), r can be estimated by solving the equations

Formula
From the Appendix, the ML estimator of r is

Formula
Since n = nM_ + nmm, the other estimator for r is

Formula
The information content per observation for r is

Formula
and the variance of rML is

Formula


    RESULTS AND DISCUSSION
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 APPENDIX
 REFERENCES
 
Morphological Markers
In the triploid interspecific hybrid (AD1 x D8) between G. trilobum L. containing the D8 cytoplasm and Upland cotton (AD1), an average of 12 bivalents involving D8–Dh combinations forms during meiosis (Phillips, 1975; Umbeck and Stewart, 1985). Therefore, when the original hexaploid 2(AD1 x D8) was crossed with tetraploid cotton, genetic recombination involving D8 chromosomes would mostly occur with D-subgenome chromosomes. We assume that the D8 restorer gene Rf2 and its tightly linked or cosegregated DNA fragments should be introgressed into the D-subgenome in the D8 restorer line during several generations of repeated backcrossing with Upland cotton. T586 and T582 have a total of 14 morphological markers, among which the loci H2, P1, Y1, R2, Lc1, N1, and fg are located on A subgenome chromosomes, and the loci Lo, R1, Lg, v1, and cl1 are on D-subgenome chromosomes. As shown in Table 6, except for the locus N1, all loci had a 3:1 segregation ratio with a recombination fraction (r) between 0.4 and 0.64 in the F2 population between D8R as female and T586. This indicates that these eight morphological markers segregate normally in CMS-D8 cytoplasm and are not linked to the restorer gene Rf2. Surprisingly, more plants with fuzzy seed (n1n1) than expected were observed, which would indicate linkage between Rf2 and N1, with a recombination fraction of 0.32. However, since N1 is located on chromosome 12 of the A subgenome (Endrizzi et al., 1984), it is unlikely that it is linked to Rf2 unless Rf2 was introgressed into the A subgenome from D8 chromosomes during the development of the D8 restorer. Even though genetic recombination between nonhomologous chromosomes can occur, the possibility that Rf2 exists in the A subgenome is very low.


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Table 6. Segregation of morphological traits in a (D8R x T586) F2 population: Repulsion phase.

 
Additional evidence on the linkages was obtained from the cross of the F1 of D8R/T586 as female with the double recessive genotype, H1330, which carries the nonrestoring allele (rf2) and recessive alleles at nine loci for morphological traits. As expected, four different genotypes were observed in the testcross for male fertility and each of the markers except for pollen color which could not be scored in sterile anthers (Table 7). For example, considering male fertility and leaf type, the four categories of the segregants are: okra leaf-fertile (LolRf2rf2), normal leaf-sterile (llrf2rf2), okra leaf-sterile (Lolrf2rf2), and normal leaf-fertile (llRf2rf2). The first two are recombinants, and the last two are the parental types. Although significant {chi}2 values suggested that the locus for leaf type was linked to Rf2, the estimate of the recombination fraction was 0.638, indicating independent inheritance. The higher frequency of the two recombinants than the parental types led us to look at segregation for leaf type. Male fertility in the testcross segregated in a 1:1 ratio, while the segregation for leaf type did not follow the 1:1 rule. More recessive plants than expected accounted for the Lo locus. The same is true for R1 and N1 loci, while more dominant brown lint plants were obtained for the Lc1 locus. The estimators for r between these genes and Rf2 were all higher than 0.50, indicating no linkage.


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Table 7. Linkage test between Rf2 and morphological markers in the testcross population (D8R x T586)F1 x H1330: Repulsion phase.

 
There are a few explanations for the distorted segregation of these loci. One possibility is that the T586 used as the male parent to make crosses might not have been homozygous. Any heterozygosity at loci controlling the morphological markers would result in more recessive types when the F1 was crossed with the double recessive parent, H1330. However, this was not the case in these results. Only five F1 plants were grown in the greenhouse and scored individually for male fertility and the morphological traits. The F1 plants were all fertile and showed heterozygous dominant performance in all nine markers, indicating that one of the parents, T-586, was a true breeding line homozygous in these nine morphological traits. Also, if the traits with atypical segregation were not homozygous, it should have been the same for all the markers, based on the assumption that T-586 was contaminated. But, the segregation at loci H2, P1, R2, and Lg was normal. Zygote selection could play a role in survival of some genotypes; however, the normal segregation in the F2 population for these markers rules out this possibility. The most reasonable conclusion concerning the distorted ratio is that a larger plant population size is necessary to make an accurate evaluation. Furthermore, misclassification could be a factor because difficulty was encountered in accurately making distinctions between brown lint and green lint. Also, homozygous naked seed was very easy to separate from fuzzy seed, while the distinction of heterozygous naked seed from fuzzy seed was difficult. So, the latter category would be inflated by misclassification of heterozygous seeds. A higher number of recessive plants with seed fuzz would result in a lower estimate of r in the F2 and higher estimate of r in the testcross.

With regard to the pollen color locus (P1), only two classes were observed in the testcross: cream pollen-fertile (a parental type) and yellow pollen-fertile (a recombinant type). Pollen color could not be scored in sterile anthers because of the absence of pollen, so that yellow pollen-sterile plants were indistinguishable from cream pollen-sterile plants. It seemed that r could not be calculated. However, statistically, since fertile plants make up 1/2 of the population, and the yellow pollen-fertile plant recombinant type accounts for 1/2 r, the recombination fraction (r) can be easily computed according to the proportion of the new type in the population, r = 2 P(P1P1). Out of 39 fertile plants, 21 had yellow pollen, while 18 had cream pollen. The segregation agreed with a 1:1 ratio Formula. The yellow-pollen plants accounted for 26.6% of the population (39 fertile and 40 sterile plants), giving 0.532 as the estimator for r. The results confirmed no linkage between Rf2 and P1.

In coupling phase, the F2 population from D8R x T582 gave a normal 3:1 segregation ratio for all five characteristics tested (Table 8), indicating that the Rf2 gene is not linked to any of the five loci (v1, cl1, cu, fg, and gl1). The results were confirmed by the testcross that was derived from the backcross of D8R/T582 as female with T582. It produced four phenotypes and genotypes: two parental types (FgfgRf2rf2 and fgfgrf2rf2) and two recombinants (e.g., Fgfgrf2rf2 and fgfgRf2rf2). The Chi-square test showed that the two new types were equal in number to the parental types with the estimator of recombination fraction ranging from 0.468 to 0.574, indicating no linkage between Rf2 and the morphological markers scored (Table 9).


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Table 8. Segregation of morphological traits in D8R x T582 F2 population: Coupling phase.

 

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Table 9. Linkage test between Rf2 and morphological markers in testcross D8R x T582 F1 x T582: Coupling phase.

 
Kohel et al. (1984) did not detect any linkage between the D2 restorer gene, Rf1, and 14 morphological markers (excluding pollen color) included in their study. Our data indicates that Rf2 also is not linked to any of the 14 markers, which is consistent with the previous report. The restorer gene Rf1 for CMS-D2 and Rf2 are tightly linked (Zhang and Stewart, 2001b).

RAPD Marker
A RAPD marker, UBC188500, is tightly linked to the restorer gene, Rf2, with recombination fractions ranging from 2.7 to 4.9% in three testcross populations (Zhang and Stewart, 2004). This marker segregated normally (1:1), as expected. The RAPD marker is only present in the D8 restorer and absent in nonrestoring cottons including T586. In the present study, this marker was used to screen an F2 population of G7-5 x T586 grown in the field. All the F2 plants were fertile, and among 76 plants that produced the PCR product, UBC188500 was present in 74 plants and absent in two. The segregation of UBC188500 deviated significantly from an expected 3:1 ratio Formula, indicating linkage between the Rf2 allele and UBC188500. According to the statistical method for computing recombination frequency (r) proposed previously for coupling linkage, r equals twice the frequency of the number of the plants without the UBC188500 fragment. Thus, the observed r between Rf2 and UBC188500 is 5.26% with a standard error of 2.56%. This value is close to that (4.9%) obtained for the testcross when (D8R x T586)F1 was crossed as female to H1330, that is, ARK8518 (Zhang and Stewart, 2004).

Advantages and Limitations in Using an F2 Population
One of the advantages of using an F2 population in the linkage test is that the linkage between Rf2 and pollen color can be evaluated by testing its segregation ratio against the expected 3:1. A distorted segregation ratio in a pollen trait could be an indication of linkage with the gametophytic fertility restorer gene. However, in the testcross situation, pollen color in sterile plants could not be scored because pollen in dominant P1_ and recessive p1p1 plants was absent. No viable pollen grains were produced in sterile plants, and the sterile anthers did not accumulate the yellow carotenoid pigments. Consequently, any pollen traits could not be evaluated for linkage analysis using a traditional testcross population.

Another advantage of the F2 system is that it requires a similar number of plants to conduct the linkage analysis, compared with a backcross population. To obtain a significant level for a linkage test, the minimum plant number (n) can be computed according to the following formula

Formula
or

Formula
where z{alpha} and {chi}2{alpha} are {alpha}-level critical values of normal and Chi-square distributions, respectively, at a significance level of {alpha} = 0.10, 0.05, or 0.01.

Statistically, the two formulas give the same results. The minimum number of plants can be computed, given certain recombination fractions at 0.05 and 0.01 significance levels. At the significance level {alpha} = 0.05, when r < 0.1, no more than 20 F2 plants are required; when r is between 0.2 to 0.3, 35 to 72 F2 plants will be sufficient for linkage tests. The number of plants scored in the present study was 76 to 153 for the cross involving T586, and 35 for the cross involving T582. Thus, the populations used were sufficiently large to detect linkage between Rf2 and the markers within a genetic distance of 20 to 30 cM.

In a backcross (BC) population, the variance of rML (see Appendix) for the case where {theta} = r, is

Formula
Comparing the standard error, S(r), of r for F2 and BC populations, when n = 100, if r < 0.2, S(r) for F2 in coupling phase and BC are close to each other, ranging from 0.022 (when r = 0.05) to 0.040 (when r = 0.20) for BC, and from 0.031 (when r = 0.05) to 0.060 (when r = 0.20) for F2. Therefore, both populations will give narrow confidence interval estimators for r. When the linkage in coupling phase is not tight, the difference in S(r) becomes obvious: for example, 0.046 for BC and 0.071 for F2 at r = 0.30, and 0.049 and 0.080, respectively, at r = 0.40. The interval estimates for r will be slightly wider only when the genetic distance is >30 cM if the F2 population is used. Thus, statistically, F2 and BC populations are almost equally reliable with similar accuracy in estimating r when the Rf gene is close to a marker. However, the standard error of r for F2 in repulsion phase will be higher, ranging from 0.099 (when r = 0.10) to 0.092 (when r = 0.40) when n is 100.

Another advantage in using an F2 population for gametophytic Rf gene mapping is that any markers that are polymorphic between two closely related parents and segregate favorably with the R line genotype in a small sample of the F2 mapping population, potentially could be useful markers for the Rf gene. The extreme example would be the absence of recombination in all fertile progeny (cosegregation with the R line restorer allele). This would be an indication of complete linkage between Rf and the marker.

One note of caution should be made concerning the proposed method: distorted segregation of DNA markers is commonly encountered, especially in interspecific crosses, and most of them are not associated with a fertility restorer gene such as Rf2. To control for this possibility, marker segregation could be tested in a control F2 population carrying the Rf gene in the absence of CMS. In such a control population, the candidate-linked markers should display a normal nondistorted Mendelian segregation. The proposed method may not be convincingly used to replace testcrosses. We suggest that for high resolution mapping using a large F2 population, a small testcross population should be tested for normal segregation of the candidate-linked markers. In our case, even though the D8 restorer line was developed by many generations of backcrossing with Upland cotton as the recurrent parent, one could argue that its complex genetic background with substantial genetic contribution, including Rf2 gene, from the wild and distant G. trilobum species could cause distorted segregations of other genes or DNA markers not related to preferential transmission of the Rf2 allele. However, of 14 polymorphic RAPD markers that were not linked to Rf2, all but one exhibited dominant inheritance and had an expected 1:1 segregation ratio in the testcross population, (D8R x T586)F1 x ARK8518 (Zhang and Stewart, 2004).

In conclusion, whether a marker is linked to a gametophytic restorer gene (Rf) or not can be tested according to whether segregation of the marker is skewed or not in an F2 population. In repulsion linkage, the frequency for the recessive genotype of the marker will be significantly increased if Rf is linked to the recessive allele of the genetic marker. On the contrary, the recessive genotype of the marker will be significantly reduced if Rf is linked to the dominant allele of the marker. The magnitude of the deviation from 1/4 (the expected frequency for the recessive genotype) reflects the degree of linkage. Therefore, a binomial distribution or {chi}2 test could be used to determine if the segregation of a marker fits a simple 3:1 ratio. After incorporation of theoretical considerations in the present study, estimators for recombination fraction between Rf and a marker have been proposed. Empirical data on fertility restoration to CMS-D8 by the gametophytic restorer gene Rf2 were collected and served as an example to demonstrate the usefulness of the methods. Fourteen morphological markers controlled by nine dominant genes and five recessive genes were tested for linkage with Rf2 and found to have no association. A RAPD marker with distorted segregation in the F2 population was calculated to be linked to Rf2 with a recombination frequency of 5.26%. The results were confirmed by segregation analysis from two testcrosses, and were also consistent with the report published for the D2 restorer gene, Rf1, located on the same chromosome as Rf2 with a genetic distance of <1 cM between them (Zhang and Stewart, 2001b).


    APPENDIX
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 APPENDIX
 REFERENCES
 
The Maximum Likelihood Estimator of r
Let

Formula
Consider the experiment of total plant count n = nM_ + nmm, where nM_ and nmm are plant counts for phenotypes M_ and mm, respectively. Assume that P(M_) and P(mm) are the same for each plant and all plants are independent. Then, the random valuable of nmm is binomially distributed with parameters n and {theta}, and the likelihood function for {theta} is

Formula
where

Formula

The likelihood function for {theta} is equivalent to the likelihood function for r,

Formula
Thus, the log-likelihood function of r is

Formula
where

Formula

By setting the first derivative of l(r) with respect to r, to zero,

Formula
the maximum likelihood (ML) estimate for r is

Formula
Note that

Formula
thus, the rML obtained above is indeed the ML estimate of r. The variance of rML is

Formula

Similarly, in the coupling linkage situation where

Formula
the ML estimator of {theta} is {theta}ML = nmm/n, which is equivalent to

Formula
The variance of rML is

Formula

The Fisher Information for r
The information content per observation for r is the Fisher information of the parameter nmm per observation and is obtained by the distribution of nmm as follows. The probability mass function of nmm, when n = 1, is

Formula
where nmm = 0 or 1. Then the logarithm of g(nmm) is

Formula

The Fisher information of r is given by the negative expected value of the second derivative of log [g(nmm)] with respect to r:

Formula
Since E(nmm) = 1/2(1 – r),

Formula
Thus,

Formula
that is, the ML estimator of r is also the efficient estimator.

Similarly, in coupling linkage situation where {theta} = P(mm) = r/2, the probability mass function of nmm, when n = 1, is

Formula
where nmm = 0 or 1.

The Fisher information for r can be obtained as

Formula
and the variance of rML is

Formula

Three-Point Linkage Test
This study considers a simplified situation where Rf is linked to a single genetic marker. However, similar deductions can be extended to include three-point linkage analysis. For example, assume that Rf is linked to genetic markers M and N in the order of RfMN (with r1 between Rf and M, and r2 between M and N). For the heterozygous trihybrid RfrfMmNn in coupling phase, eight types of female gametes will be produced, including RfMN and rfmn [parental types, each with frequency of 1/2(1 – r1 – r2 + r1r2), assuming no interference], RfMn and rfmN [single crossover between M and N, each with frequency of 1/2(r2 – r1r2)], Rfmn and rfMN [single crossover between Rf and M, each with frequency of 1/2(r1 – r1r2)], and RfmN and rfMn (double crossover, each with frequency of 1/2 r1r2). However, male gametes with the recessive rf allele are sterile and unable to participate in fertilization. Even though this will result in only 19 genotypes in the F2 instead of 27 genotypes under a normal linkage situation, the recombination fraction between Rf and the two markers can be easily determined. For example, if r1 between Rf and M is 0.05, r between Rf and N is 0.15, and r2 between M and N is 0.10, then the three two-point linkage analyses place M between Rf and N. As such, the linear relationship between Rf and linked markers can be resolved. Therefore, the models presented here can be extended for high-resolution mapping of gametophytic Rf gene(s). Statistical packages for genome-wide mapping can be modified to take this situation into consideration. If male fertility is controlled by two gametophytic restorer genes (e.g., A3 in sorghum), or by one gametophytic Rf gene and one sporophytic Rf gene (as in cotton), an extension can be easily made based on the models presented here. However, the question as to whether or not male gamete selection related to the gametophytic Rf affects the results of genome-wide mapping remains an unanswered question.

Received for publication April 7, 2004.


    REFERENCES
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 APPENDIX
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