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Genetic diversity among CIMMYT maize inbred lines investigated with SSR markers: I. lowland tropical maize.

FEW AGRONOMIC IMPROVEMENTS during the 20th century rival the development of hybrid maize (Brummer, 1999). Yields in maize increased dramatically as breeders moved away from open-pollinated cultivars and began developing double-cross and later single-cross hybrids (Duvick, 2001). This yield advance can be attributed to the successful harnessing of heterosis. Clearly defined heterotic groups and patterns improved by RRS programs are of fundamental importance for a systematic exploitation of heterosis. In temperate maize, heterotic patterns were established empirically by relating the heterosis observed in crosses with the origin of the parents included in the crosses (Hallauer et al., 1988).

Breeding efforts at CIMMYT in the early 1960s and 1970s were focused on intrapopulation improvement via recurrent selection based on the formation of 100 populations and 30 genetically broad-based backup pools. The formation of these populations disregarded known racial complexes (Vasal et al., 1999). With the decision to embark on a hybrid breeding program, several diallel studies were performed to identify suitable germplasm for hybrid breeding (Crossa et al., 1990; Vasal et al., 1992a). However, the mixed genetic constitution of the populations and pools made the task of assigning them to genetically diverse and complementary heterotic groups difficult. Nevertheless, the germplasm was categorized based on their yield performance into different heterotic groups, and some promising heterotic patterns are under development in RRS programs (Vasal et al., 1999).

Since its inception in 1984, the hybrid maize program of CIMMYT has developed and released 497 CIMMYT maize inbred lines (CMLs) derived from the above mentioned broad-based pools and populations. These CMLs, and CIMMYT germplasm in general, have played an important role in hybrid maize production in developing countries (Morris, 2001). The lowland tropical CMLs were selected from approximately 60 populations or pools based on their per se performance and combining ability when crossed to testers. Little information is available on the relationships among these populations and pools, and consequently on the CMLs derived from them.

Detailed knowledge regarding genetic diversity and the relationship among breeding materials is indispensable for the development of new maize inbred lines, the assignment of maize inbred lines to heterotic groups, and the choice of testers for trials of hybrid combinations in maize breeding. Molecular genetic markers are a powerful tool to delimit heterotic groups and to assign inbred lines into existing heterotic groups (Melchinger, 1999). The SSR markers offer advantages in reliability, reproducibility, discrimination, standardization, and cost effectiveness over other marker types (Smith et al., 1997).

The objectives of our study were to (i) investigate the genetic diversity among 155 CIMMYT tropical lowland inbred lines with 79 SSR markers and (ii) delimit heterotic groups in this germplasm.


Plant Materials

In the present study, 86 white and 69 yellow CMLs representing the lowland tropical gene pool were analyzed with 79 SSR markers (Table 1). The lines included represent nearly all the lowland tropical maize inbreds created by CIMMYT breeders, excluding many of the very closely related sister lines. These lines were extracted from populations, which were established mostly by intermixing germplasm from different racial complexes resulting in a huge number of lines with miscellaneous origin but a small proportion of flint lines. Detailed information about the populations has been published as supporting information at webp/support/publications/support_materials/ssr mw1 .htm (verified 21 July 2004).

SSR Analyses

The DNA was extracted employing a CTAB procedure (Saghai-Maroof et al., 1984) and modified based on the CIMMYT Applied Biotechnology Center's 2001 manual of laboratory protocols ( manualABC.html; verified 15 July 2004). The 79 SSR markers were chosen from the MaizeGDB database (http://nucleus.; verified 15 July 2004) based on repeat unit and bin location to provide a uniform coverage of the entire maize genome. Primers (excluding phi014, phi041, phi073, and phi078, which were not used in the current study) and PCR conditions were described in detail by Warburton et al. (2002). Briefly, SSR primers were multiplexed for maximum efficiency. Fragments were separated using acrylamide gels run on an AB1 377 automatic DNA sequencer. Fragment sizes were calculated with GeneScan 3.1 (Perkin-Ehner/Applied Biosystems) using the GeneScan 350 or 500 molecular weight standard and the Local Southern sizing method (Elder and Souther, 1987); allele identity was assigned using Genotyper 2.1 (PerkinElmer/Applied Biosystems), and the two inbred lines CML51 and CML292 were included in every gel as controls. All data were stored in the MaizeGDB database (; verified 15 July 2004).

Statistical Analysis

We calculated the modified Roger's distance (MRD) between two inbred lines (Wright, 1978, p. 91; Goodman and Stuber, 1983) as:


Here, [p.sub.ij] and [q.sub.ij] are the allele frequencies of the jth allele at the ith marker in the two lines under consideration, [a.sub.i] is the number of alleles at the ith marker, and m refers to the number of markers. Standard errors were calculated using the jackknife estimator (Melchinger et al., 1991; Messmer et al., 1992). The PIC for each marker was determined as described by Smith et al. (1997). Average linkage (UPGMA, Unweighted Paired Group Method using Arithmetic Averages) clustering was calculated based on MRD estimates between pairs of inbred lines for the yellow and white lines separately. To evaluate the robustness of the UPGMA dendrogram, the cophenetic correlation was calculated (Sneath and Sokal, 1973). The breeding strategy of CIMMYT resulted in a small proportion of flint lines, and thus the data set contains a low number of flint lines. Therefore, we took an already published but balanced data set (Reif et al., 2003) with individuals from Pop21, 22, 25, 29, 32, 43, and Pool24 based on the same marker set and performed a principal component analysis (PCA). The obtained transformation matrix of the analysis of the seven tropical populations was then used for plotting a scatterplot of the lines extracted from Pop21, 22, 25, 29, 32, 43, 49, and Pool24 and the percentage of variance explained by the principal components was calculated with the data set of Reif et al. (2003). All analyses were performed with Version 2 of the Plabsim software (Frisch et al., 2000), which is implemented as an extension to the statistical software R (Ihaka and Gentleman, 1996).


Genetic Diversity among the Inbred Lines

The 79 SSRs produced a total of 584 alleles, with a range of 2 to 18 alleles per marker. An average residual heterozygosity of 4.8% was found, which is in accordance with results reported by Heckenberger et al. (2002). The SSR haplotypes for each inbred line are listed in the MaizeGDB database and can be accessed via the World Wide Web at (verified 15 July 2004). We found, on average, a higher number of alleles per marker (7.4) than reported by Warburton et al. (2002) analyzing 57 CML lines with 85 SSR markers (4.9), Lu and Bernardo (2001) evaluating 40 U.S. inbred lines with 83 SSR markers (4.9), Senior et al. (1998) investigating 94 elite U.S. maize inbreds with 70 SSR markers (5.0), and Pejic et al. (1998) examining 33 U.S. maize lines with 27 SSR markers (6.8). It is important to remember that the total number of alleles reported in diversity studies is usually proportional to sample size, and some differences seen here may be attributable to sampling differences. However, another factor which influences number of alleles reported is the use of dinucleotide repeat SSRs, which can greatly increase the number of alleles. Therefore, an even higher number of alleles would have been expected in some of the previously reported studies, which employed either exclusively dinucleotide repeat SSRs (Pejic et al., 1998) or a considerable proportion (Senior et al., 1998) of them. In the current study, only tri-, tetra-, penta-or hexanucleotide repeat unit SSRs were employed, except for bnlg118 and phi112. Despite this confounding effect, we still found a higher number of alleles per marker than reported in the literature, which (within the limitations of comparing data sets of different sizes) suggests a broad genetic base of the CMLs analyzed here.

The PIC values for the 79 SSR loci ranged from 0.13 to 0.87, with an average of 0.60. This is consistent with the results of Smith et al. (1997) and Senior et al. (1998), who found average PIC values of 0.62 and 0.59 in their SSR studies with 58 and 94 U.S. maize inbreds, respectively. The average PIC value in combination with the high number of alleles in the CIMMYT germplasm indicates presence of a higher number of rare alleles than in temperate maize inbred lines. This can be explained by the large number of populations used to extract the CMLs, the mixed origin and broad genetic base of the CIMMYT germplasm, the large effective population size in recurrent selection programs, fewer generations of selection, or a lower selection intensity applied in the CIMMYT maize breeding program.

Under the assumptions that (i) the genotypes investigated are homozygous (which has proven true in previous studies of CIMMYT inbreds, such as Warburton et al., 2002), (ii) each marker maps to one locus, and (iii) each band is an allele of a marker, distance and similarity measures are related as follows:

MRD = [square root of [D.sub.Nei-Li]] = [square root of 1 - [S.sub.Dice]],

where [D.sub.Nei-Li] is the Nei-Li distance (Nei and Li, 1979) and [S.sub.Dice] is the Dice similarity coefficient (Dice, 1945). Thus, we converted the distances reported in the literature and found a slightly lower average MRD among pairs of the 155 inbred lines (0.76) (average standard error of 0.04 with a range from 0.03-0.06) than reported for temperature-adapted maize in Enoki et al. (2002; 0.83) and Pejic et al. (1998, 0.86). The lower average MRD in the current survey studies suggests a higher average degree of relatedness among the tropical than among temperate adapted inbred lines. This can be related to various causes: (i) the mixed genetic constitution of the germplasm used to extract the lines and the resulting loss of diversity between the populations and pools, (ii) different breeding strategies, (iii) the small number of testers used to evaluate the lines, and (iv) sampling effects caused by different criteria used to choose the plant material for a study. The mixed constitution of the CIMMYT germplasm and the low variance between the populations were clearly demonstrated in a study by Reif et al. (2003), investigating the diversity among seven of CIMMYT's tropical maize populations with molecular markers. Furthermore, only a fraction of the populations and pools used to extract the inbred lines has been improved by RRS improvement programs. The existing RRS programs have been initialized in 1990 and could not diverge the groups as far as in the temperate adapted germplasm. For example, Labate et al. (1999) observed a considerable increase in the genetic distance between the two heterotic populations Iowa Stiff Stalk Synthetic and Iowa Corn Borer Synthetic #1 after 12 cycles of RRS. In addition to the small number of selection cycles via RRS, the small number of testers used in CIMMYT's hybrid breeding program to evaluate the combining ability could be related to a higher degree of relatedness among the inbred lines. Unlike lines included in the studies of Enoki et al. (2002), Lu and Bernardo (2001), and Pejic et al. (1998), our germplasm was not chosen based on pedigree information. Hence, sampling effects are probably a further minor cause for the decrease in average MRD in our study compared with results reported in the literature.

Wellhausen (1978) suggested breeding white and yellow populations in a joint breeding program, and then extracting either white or yellow lines. However, this proved to be practically difficult and thus prompted the separation of yellow and white CIMMYT breeding populations. The MRDs for line combinations white x white and yellow x yellow ranged from 0.37 to 0.89 and 0.44 to 0.88, respectively (both averaging 0.76) (Fig. 1). The wide range of MRDs observed for line combinations white x white and yellow x yellow indicates that CMLs vary considerably in their genetic distance at the molecular level. This result was expected because the lines were extracted from germplasm with a broad genetic base. The MRDs for white x yellow type line combinations had an average MRD of 0.77, which is similar to the average MRD for white x white and yellow x yellow line combinations. This is in accordance with results from Coe et al. (1988), who reported only minor differences (such as a major gene conditioning pigmentation plus a few regulatory factors) between white and yellow germplasm. Although the molecular results do not support the separation into yellow and white germplasm, we investigated both materials separately because of practical breeding considerations owing to consumer demands.

Grouping of Germplasm

Wellhausen (1978) described several heterotic patterns and proposed to establish two broad-based heterotic groups for the tropical maize germplasm: (i) a dent composite, consisting of Tuxpefio and related dents, and (ii) a flint composite, consisting mainly of the Cuban, Coastal Tropical, and Cateto flints. However, instead of establishing two heterotic groups, CIMMYT devoted its major efforts to the formation, development, and improvement of broad-based populations and pools, mostly disregarding the natural heterotic patterns which exist between the flint and dent germplasm complexes (Vasal et al., 1999). This strategy seemed promising for breeding open-pollinated varieties. Before starting a hybrid breeding program in the 1980s, CIMMYT conducted several diallel studies with different germplasm sources to detect heterotic patterns in the germplasm with mixed origin (Crossa et al., 1990; Vasal et al., 1992a). Some heterotic patterns were suggested, and the following five pairs of heterotic populations have been improved by RRS in the lowland tropical program of CIMMYT: Pop21 x Pop32, Pop22 x Pop43, Pop28 x Pop36, Pop27 x Pop24, and Pop23 x P49. The first testers used in RRS were 12-line, inbreeding-tolerant synthetics. Vasal et al. (1992b) investigated the use of inbred lines as testers, and two lines were chosen to represent yellow germplasm and two lines were chosen to represent white germplasm. These lines were defined as testers based on field trials. The two white lines were CML247, derived from Pool24, and CML254, which was extracted from Pop21. Yellow lines identified as testers were CME287 and CML413, extracted from Pop24 and SATSR, respectively (Vasal and McLean, 1994). From the 155 inbred lines investigated, 66 originated from the populations improved via RRS and 25 were grouped into Heterotic Group A or B according to their combining ability with the testers mentioned above.

The correlations between cophenetic values and MRDs was for the white germplasm 0.63 and for the yellow germplasm 0.67. Most of the white lines from the Tuxpeno synthetic Pop43 formed one group (CML043, CML047, CML273, CML274, CML275, CML277, CML279, CML281, CML310, CML339, CML341, CML342, CML343) (Fig. 2). CML141, CML142, CMLI47, CML151, CML153, CML155, CML157, and CML159, originating from the two quality protein maize populations Pop62 and Pop63, clustered together with CML237, CML261, CML346, and CML446. The majority of the CMLs extracted from the Tuxpefio-based Pop21 (CML001, CML007, CML009, CML011, CML013, CML061, CML063, CML253, CML 254, CML255, CML257, CML258, CML259, CML263, CML264, CML397, CML399, CML401, and CML448) clustered together with lines also extracted from populations containing Tuxpeno germplasm (Pool24, Pop43, Pop29, Pop49, TS6, and Pop62) and the two flint lines CML037 and CML053. The grouping of the lines extracted from Tuxpeno germplasm and from miscellaneous origin was expected based on the pedigree information. However, the wide dispersion of the flint lines was surprising.


In a combined analysis of SSR and field data with the seven tropical populations Pop21, Pop22, Pop25, Pop29, Pop32, Pop43, and Pool24, the flint germplasm (Pop25 and Pop32) was clearly separated from the Tuxpeno-based populations, and four heterotic groups were proposed (Reif et al., 2003): Heterotic Group A (Pop21, Pop22, Pop29, and Pool24), B (Pop32), C (Pop25), and D (Pop43). The clear separation of the flint germplasm (P32 and P25) from the Tuxpeno-based germplasm (Pop21, Pop22, Pop29, Pop43, and Pool24) reported by Reif et al. (2003) cannot be found anymore in the PCA of the inbred lines extracted from these populations (Fig. 2). Furthermore, only a few lines were extracted from the flint populations via the use of inbred testers. This underlines the importance of an appropriate choice of testers used for interpopulation improvement. Both white testers CML247 and CML254 were chosen from populations from heterotic group A. Considering the heterotic patterns, we expect that lines extracted from heterotic groups B, C, or D would combine well with the testers. Thus, selection of inbred lines based on their combining ability should lead to a high number of lines originating from the two flint populations Pop25 and Pop32, which is not the case. This can be explained by the relatedness of the two testers both to each other and to lines extracted from heterotic groups B and C (Fig. 3). Thus, marker-based analysis of the relationships among inbred lines can support the choice of a representative tester in interpopulation improvement programs.


The UPGMA cluster analysis of the tropical yellow CMLs revealed few clear groups: however, the following lines did cluster together: (i) CML295, CML297, CML299, CML301, CML303, CML305, CML307, and CML413 extracted from SATSR; (ii) the Antigua-based lines CML059, CML067, CML071, and CML073; and (iii) CML359, CML434, CML435, CML436, and CML439 from the acid tolerant populations SA3 and SA5 (Fig. 4). Furthermore, the following pairs of lines clustered together: (i) CML289 and CML453 (Pop24), (ii) CML425 and CML426 (Pop31), and (iii) CML019 and CML287 (Pop24). However, no clearly defined groups could be observed. The absence of a clear structure among the lowland tropical yellow lines can again be explained by the high proportion of CMLs extracted from populations and pools with a mixed origin.


On the basis of theoretical and experimental results, Melchinger (1999) demonstrated that organization of germplasm in genetically divergent heterotic groups is beneficial for a systematic and optimum exploitation of heterosis. Among the lowland tropical yellow material, almost all germplasm sources used to extract the lines were established based on a mixture of different racial complexes. This mixing of CIMMYT germplasm has resulted in populations and pools that cannot easily be assigned into distinct heterotic groups. If a preexisting structure was formed during a long-term separate evolution and breeding history that separates different racial complexes, this structure is destroyed by crossing these racial complexes, and it is extremely difficult to restore it or to build up well-structured germplasm pools. One option would be to go back to the original germplasm sources with pure racial complexes, select promising germplasm from them, and start a hybrid breeding program from the bottom up. However, this would disregard all the progress that has been made by intrapopulation improvement during the past 30 yr at CIMMYT. Furthermore, there is evidence that the races are not completely separated at the molecular level, suggesting that finding pure races may be more difficult than once imagined (Pressoir and Berthaud, 2004). Another possibility is to identify those that are most suitable for hybrid breeding from the large number of populations of the CIMMYT maize program. This can be accomplished by a joint analysis of SSR-based genetic distances and field data for per se and hybrid performance of the available populations, as demonstrated by Reif et al. (2003). For the lowland tropical white lines, where germplasm with pure origin is still available, CMLs based on pure Tuxpeno germplasm clustered together; these could form good heterotic partners to CMLs based on flint germplasm. Only a few lines from pure flint populations are available. However, they lack a clear structure among them because of the choice of testers employed in selecting the CMLs that were unrepresentative of the heterotic groups to which they were assigned. We recommend a combined approach based on SSR and field data to identify representative testers for evaluating inbred lines in such broad-based populations. Thus, the outstanding flint-dent heterotic patterns can be exploited to the highest extent possible. Furthermore, breeding lines in alternative heterotic groups can be more quickly diverged via RRS using molecular markers to choose the most genetically distant lines from a set of lines chosen as acceptable based on field performance.
Table 1. Description of the 155 tropical CIMMYT maize lines (CMLs)
used in this study.

Germplasm source                          CML No.

                                   Tuxpeno and related dents

Tropical white CMLs
  Pop21                       001, 003, 007, 009, 011, 013, 061, 063,
                                253, 254, 255, 257, 258, 259, 261, 263,
                                264, 265, 397, 399, 401, 448
  Pop43                       043, 045, 047, 273, 274, 275, 277, 279,
                                281, 309, 310, 339, 341, 342, 343, 405,
  Pool24                      055, 149, 247, 249, 407
  Pop63                       145, 147, 159
  Tuxpeno                     344
  Pop49                       417
Tropical yellow CMLs
  Pop24                       019, 021, 285, 287, 289, 409, 453

                              Cuban, Coastal Tropical, and Cateto

Tropical white CMLs
  Pop25                       023, 066, 269
  Pop32                       037, 039, 449
  others                      053, 419
Tropical yellow CMLs
  Pool25                      161, 167, 451

                              Miscellaneous origin

Tropical white CMLs
  Pop22                       015, 017, 065, 267, 403
  Pop29                       035, 273
  Pop62                       141, 142, 143, 151, 153, 155, 157
  Others                      049, 219, 221, 231, 233, 235, 237, 238,
                                268, 345, 346, 365, 366, 446, 450
Tropical yellow CMLs
  Pop27                       027, 029, 031, 454
  Pop28                       033, 291, 293, 411, 452
  Pop36                       041, 069
  Pool26                      057, 163, 169, 347, 348
  Antigua                     059, 067, 071, 073
  SA3, SA4, SA5, SA8, SATSR   295, 297, 299, 301, 303, 305, 307, 357,
                                359, 361, 363, 413, 434, 435, 436, 437,
                                438, 439
  Others                      026, 051, 165, 217, 227, 229, 282, 283,
                                415, 421, 423, 424, 425, 426, 429, 430,
                                431, 432, 433


The molecular marker analysis of this research was supported by funds from the German "Bundesministerium fur wirtschaftliche Zusammenarbeit und Entwicklung" Projekt No. 98.7860.4-001-01.

Abbreviations: CIMMYT, International Maize and Wheat Improvement Center; CML, CIMMYT maize inbred line; MRD, modified Roger's distance; PCA, principal component analysis; PIC, polymorphic information content: RRS, reciprocal recurrent selection; SSR, simple sequence repeat; UPGMA, Unweighted Paired Group Method using Arithmetic Averages.


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X.C. Xia, Inst. of Crop Breeding and Cultivation, Chinese Academy of Agricultural Sciences, Zhongguancun South Street No. 12, 100081, Beijing, China; D.A. Hoisington and M.L. Warburton, CIMMYT, Int. Applied Biotechnology Center, Apdo Postal 6-641 06600 Mexico D.F., Mexico; J.C. Reif, A.E. Melchinger, and M. Frisch, Inst. of Plant Breeding, Seed Science, and Population Genetics, Univ. of Hohenheim, 70593 Stuttgart, Germany. Received 28 Apr. 2003. * Corresponding author (
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Title Annotation:Plant Genetic Resources
Author:Xia, X.C.; Reif, J.C.; Hoisington, D.A.; Melchinger, A.E.; Frisch, M.; Warburton, M.L.
Publication:Crop Science
Date:Nov 1, 2004
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