Roger's Distance Research Articles

Molecular Genetic Diversity among Progenitors and Derived Elite Lines of BSSS and BSCB1 Maize Populations

The maize (Zea mays L.) populations Iowa Stiff Stalk Synthetic (BSSS) and Iowa Corn Borer Synthetic No. 1 (BSCB1) have undergone reciprocal recurrent selection (RRS) since their establishment in 1949. This study focused on molecular genetic variation of the progenitor inbred lines used to synthesize BSSS and BSCB1 as well as elite inbred lines derived from different cycles of selection. Our objectives were to investigate changes in allele frequencies and genetic diversity from progenitors to derived lines and evaluate trends in genetic diversity among elite lines derived from early and advanced selection cycles. Genotypic data for 105 restriction fragment length polymorphism (RFLP) loci were collected from four groups: 16 progenitors and 18 elite lines derived from BSSS, 12 progenitors and 7 elite lines derived from BSCB1. Each progenitor group had a broad genetic base but both were genetically similar. The groups of derived lines diverged substantially from each other. A larger Roger's distance was found between the groups of lines derived from advanced cycles than between the groups of lines derived from Cycle 0. Allelic variation within each group of lines, however, decreased just slightly with the elite lines capturing almost 75 and 67% of the allelic variation present in the progenitor lines of BSSS and BSCB1, respectively. The results of this study confirm the long-term potential of this RRS program and the importance of the choice of broadly based progenitor materials.

Prediction of hybrid performance in grain sorghum using RFLP markers.

Heterosis is an important component of hybrid yield performance. Identifying high yielding hybrids is expensive and involves testing large numbers of hybrid combinations in multi-environment trials. Molecular marker diversity has been proposed as a more efficient method of selecting superior combinations. The aim of this study was to investigate the value of molecular marker-based distance information to identify high yielding grain sorghum hybrids in Australia. Data from 48 trials were used to produce hybrid performance-estimates for four traits (yield, height, maturity and stay green) for 162 hybrid combinations derived from 70 inbred parent lines. Each line was screened with 113 mapped RFLP markers. The Rogers distances between the parents of each hybrid were calculated from the marker information on a genome basis and individually for each of the ten linkage groups of sorghum. Some of the inbred parents were related so the hybrids were classified into 75 groups with each group containing individual hybrids that showed similar patterns of Rogers distances across linkage groups. Correlations between hybrid-group performance and hybrid-group Rogers distances were calculated. A significant correlation was observed between whole genome-based Rogers distance and yield ( r = 0.42). This association is too weak to be of value for identifying superior hybrid combinations. One reason for the generally poor association between parental genetic diversity and yield may be that important QTLs influencing heterosis are located in particular chromosome regions and not distributed evenly over the genome. Variation in the sign and magnitude of correlations between Rogers distance and hybrid-group performance for particular linkage groups observed in this study support this hypothesis. The concept of using diversity on individual linkage groups to predict performance was explored. Using data from just two linkage groups 38% of the variation in hybrid performance for grain yield could be explained. A model combining phenotypic trait data and parental diversity on particular linkage groups explained 71% of the variation in grain yield and has potential for use in the selection of heterotic hybrids.

Analysis of genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm using microsatellite DNA, with special emphasis on the Fiji Dwarf cultivar.

Using 15 simple sequence repeat (SSR) microsatellite DNA loci, we analyzed genetic variation within Cocos nucifera germplasm collections at two locations in south Florida, representing eight cultivars. The loci were also used in a parentage analysis of progeny of the 'Fiji Dwarf' variety at both locations. A total of 67 alleles were detected, with eight the highest number at any one locus. These loci identified 83 of the 110 individual palms. Gene diversity of the 15 loci ranged from 0.778 to 0.223, with a mean of 0.574. 'Fiji Dwarf', 'Malayan Dwarf', 'Green Niño' and 'Red Spicata' cultivars resolve as distinct clusters in a neighbor joining tree using modified Rogers distance, while the tall varieties form two aggregates. The highest gene diversity was found in the tall cultivars (H = 0.583 cumulatively), and the lowest in the 'Malayan Dwarf' (H = 0.202). After the tall coconuts, the 'Fiji Dwarf' was most genetically diverse (H = 0.436), and had the largest number of unique alleles. Genetic identity is highest among the 'Malayan Dwarf' phenotypes, and between the tall varieties. The 'Red Malayan Dwarf' is genetically distinct from the 'Green' and 'Yellow Malayan Dwarf' phenotypes, which cannot be distinguished with the SSR loci used. Off-type 'Malayan Dwarf' phenotypes (putative hybrids with talls) can be identified genotypically. Parentage analyses of 30 'Fiji Dwarf' progeny propagated from five adults surrounded by other cultivars estimate that only 20% of the progeny were out-crossed to the other varieties, while 40-46% were possible selfs. This suggests that a seed-production orchard of the variety maintained at reasonable distance from other varieties, will likely yield only 'Fiji Dwarf' genotypes. Our data are discussed in the context of hypotheses of coconut dissemination around the world.

A new aspect of genetic diversity of Indonesian oil palm (Elaeis guineensis Jacq.) revealed by isoenzyme and AFLP markers and its consequences for breeding

Oil palm (Elaeis guineensis Jacq.) plays an important economic role in some countries of Southeast Asia like Indonesia, which is the world’s second producer of palm and palm kernel oil. The quality improvement of planting material needs a better understanding of the genetic relationships between genotypes from different populations used in the breeding programmes. In this study, 48 parents, representative of four populations used in Indonesian Oil Palm Research Institute (IOPRI) breeding programmes, were analysed with five selected AFLP primer pairs and four isoenzymatic systems. One hundred and fifty eight scorable band levels were generated of which 96 (61%) were polymorphic. AFLP allowed us to identify off–type descendants which were excluded from analysis. The use of unbiased Rogers distance clearly separated the four studied populations. The Neighbor-Joining method re-groups two African populations which are known as originating from different regions. Nevertheless, the variability revealed is in accordance with oil palm breeders’ knowledge. The results obtained with AFLP showed that the crosses among the African sub-population, which is excluded in oil palm reciprocal recurrent selection (RRS) breeding programmes, may be more interesting than the crosses between the African and the Deli populations.

Estimates of relatedness and inbreeding in goose strains from DNA fingerprints

The purpose of this study was to determine if DNA fingerprints (DFPs) could be used to estimate relatedness and inbreeding of strains of geese and to compare three methods of calculating relatedness indices. Strains included a control and selected strain from each of the Chinese and Synthetic (Chinese, Hungarian and Pilgrim) breeds. DFP patterns for each strain were based on individual DNA samples from six females, or on pooled DNA from 15 females different from those used for individual samples. Three relatedness indices were used, namely, genetic distance, modified Rogers distance and band sharing. All relatedness indices showed a closer relationship of strains within than between breeds. Correlation coefficients among relatedness indices were higher based on pooled DNA (r > or = magnitude of 0.97) than those based on individual DNA (r > or = magnitude of 0.741). Inbreeding estimates were higher for selected compared with control strains. It appears that the use of DFPs to estimate relatedness, regardless of index used, and inbreeding can be valuable for studying geese where there is a limited breeding history.

Genetic diversity among progenitors and elite lines from the Iowa Stiff Stalk Synthetic (BSSS) maize population: comparison of allozyme and RFLP data

Data for restriction fragment length polymorphisms (RFLPs) of 144 clone-enzyme combinations and for 22 allozyme loci from 21 U.S. Corn Belt maize (Zea mays L.) inbreds were analyzed. The genetic materials included 14 progenitors of the Iowa Stiff Stalk Synthetic (BSSS) maize population, both parents of one missing BSSS progenitor, four elite inbreds derived from BSSS, and inbred Mo17. Objectives were to characterize the genetic variation among these 21 inbreds for both allozymes and RFLPs, to compare the results from both types of molecular markers, and to estimate the proportion of unique alleles in the BSSS progenitors. Genetic diversity among the 21 inbreds was substantially greater for RFLPs than for allozymes, but the percentages of unique RFLP variants (27%) and unique allozyme alleles (25%) in the BSSS progenitors were similar. Genetic distances between inbreds, estimated as Rogers' distance (RD), were, on average, twice as large for RFLP (0.51) as for allozyme data (0.24). RDs obtained from allozyme and RFLP data for individual line combinations were only poorly correlated (r = 0.23); possible reasons for discrepancies are discussed. Principal component analysis of RFLP data, in contrast to allozyme data, resulted in separate groupings of the ten BSSS progenitors derived from the 'Reid Yellow Dent' population, the four BSSS elite lines, and Mo17. The remaining six BSSS progenitors were genetically rather diverse and contributed a large number of rare alleles to BSSS. The results of this study corroborate the fact that RFLPs are superior to allozymes for characterizing the genetic diversity of maize breeding materials, because of (1) the almost unlimited number of markers available and (2) the greater amount of polymorphisms found. In particular, RFLPs allow related lines and inbreds with common genetic background to be identified, but a large number of probe-enzyme combinations is needed to estimate genetic distances with the precision required.

Diversity and Relationships among U.S. Maize Inbreds Revealed by Restriction Fragment Length Polymorphisms

Restriction fragment length polymorphisms (RFLPs) have been proposed as molecular markers for characterizing the genetic diversity in maize (Zea mays L.). The objectives of this study were to evaluate the usefulness of RFLP data for (i) elucidating heterotic patterns among maize inbreds and (ii) assessing genetic similarity among related and unrelated lines. Thirty‐two maize inbreds from the U.S. Corn Belt were analyzed for RFLPs with two restriction enzymes and 83 DNA probes distributed over the maize genome. Eighty‐two probes detected polymorphisms with at least one enzyme. On average, 4.3 variants were found per probe‐enzyme combination across all 32 inbreds. Genetic distances among lines, estimated from RFLP data as Rogers' distance (RD), revealed considerable diversity among lines from Iowa Stiff Stalk Synthetic (BSSS), Reid Yellow Dent (RYD), and Lancaster Sure Crop (LSC). Lines from different heterotic groups had a slightly greater RD mean than unrelated lines from the same heterotic group, yet differences were small when compared with the wide range of RDs for individual lines combinations within each group. RDs between related lines agreed well with expectations based on coancestry coefficients determined from pedigree data with few exceptions. Principal component analyses of RFLP data resulted in a separate grouping of lines from BSSS/RYD and LSC. Dispersion of lines of miscellaneous origins was generally consistent with expectations based on known breeding behavior and pedigrees. Results from this study suggest that RFLP data can be used for assigning inbreds into heterotic groups and quantifying genetic similarity between related lines, but it seems that a large number of probe‐enzyme combinations are required to obtain reliable estimates of genetic distance.

Molecular Markers and Grouping of Parents in Maize Breeding Programs

In maize (Zea mays L.) breeding programs identifying potentially high yielding hybrids, assigning new inbreds to heterotic groups, and determining the parental line in a hybrid to which a potential donor line is most closely related, are significant problems. Data from a diallel cross among 14 maize inbreds were analyzed to evaluate use of molecular marker date to (i) predict yield potential of hybrids, (ii) assign inbreds to heterotic groups, and (iii) determine to which of the two inbred parents of a single cross a donor line is most closely related. Four of the inbreds were from Iowa Stiff Stalk Synthetic background, five were from a Lancaster Sure Crop background and five were unrelated to either Stiff Stalk Synthetic or Lancaster Sure Crop. Allozyme genotypes at 14 loci and restriction fragment length polymorphism (RFLP) variant types for 52 cDNA clones were obtained for the 14 inbreds. Modified Roger's distance (MRD) values (a measure of genetic distance between inbreds based on marker data) were not significantly correlated with hybrid yields; however, a hybrid value based on the number of marker loci having the highest yielding genotype was significantly correlated with hybrid yield. Cluster analysis based on MRD values agreed well with pedigree information, but did not always agree with groupings based on yield. Where parents of hybrids were distantly related, a measure of relative relationship based on proportion of homomorphic marker loci was significantly correlated with a measure of relationship based on yield. Where parents of a hybrid were more closely related, however, such correlations were low.

A Comparison of the Suitability of the Rogers, Modified Rogers, Manhattan, and Cavalli-sforza and Edwards Distances for Inferring Phylogenetic Trees from Allele Frequencies

Theoretical considerations and the results of computer simulations demonstrate that Swofford and Berlocher's (1987, Syst. Zool. 36:293-325) reason for preferring the Manhattan metric over Rogers's distance for inferring phylogenetic trees from allele frequencies under the principle of maximum parsimony is not necessarily valid. The theoretical considerations lead to the proposal of a new general criterion for choosing between cladograms or trees of equal length for qualitative characters as well―when two trees are of equal length, the one that is consistent with more possible transformation series of the characters under consideration is preferable

Genetic diversity for restriction fragment length polymorphisms and heterosis for two diallel sets of maize inbreds

Changes that may have occurred over the past 50 years of hybrid breeding in maize (Zea maize L.) with respect to heterosis for yield and heterozygosity at the molecular level are of interest to both maize breeders and quantitative geneticists. The objectives of this study were twofold: The first, to compare two diallels produced from six older maize inbreds released in the 1950's and earlier and six newer inbreds released during the 1970's with respect to (a) genetic variation for restriction fragment length polymorphisms (RFLPs) and (b) the size of heterosis and epistatic effects, and the second, to evaluate the usefulness of RFLP-based genetic distance measures in predicting heterosis and performance of single-cross hybrids. Five generations (parents, F1; F2, and backcrosses) from the 15 crosses in each diallel were evaluated for grain yield and yield components in four Iowa environments. Genetic effects were estimated from generation means by ordinary diallel analyses and by the Eberhart-Gardner model. Newer lines showed significantly greater yield for inbred generations than did older lines but smaller heterosis estimates. In most cases, estimates of additive x additive epistatic effects for yield and yield components were significantly positive for both groups of lines. RFLP analyses of inbred lines included two restriction enzymes and 82 genomic DNA clones distributed over the maize genome. Eighty-one clones revealed polymorphisms with at least one enzyme. In each set, about three different RFLP variants were typically found per RFLP locus. Genetic distances between inbred lines were estimated from RFLP data as Rogers' distance (RD), which was subdivided into general (GRD) and specific (SRD) Rogers' distances within each diallel. The mean and range of RDs were similar for the older and newer lines, suggesting that the level of heterozygosity at the molecular level had not changed. GRD explained about 50% of the variation among RD values in both sets. Cluster analyses, based on modified Rogers' distances, revealed associations among lines that were generally consistent with expectations based on known pedigree and on previous research. Correlations of RD and SRD with f1 performance, specific combining ability, and heterosis for yield and yield components, were generally positive, but too small to be of predictive value. In agreement with previous studies, our results suggest that RFLPs can be used to investigate relationships among maize inbreds, but that they are of limited usefulness for predicting the heterotic performance of single crosses between unrelated lines.

Relationship of restriction fragment length polymorphisms to single-cross hybrid performance of maize

Isozymes and restriction fragment length polymorphisms (RFLPs) have been proposed for use in varietal identification and selection for agronomic traits. Although the use of isozymes for these purposes has been well documented, evaluation of the efficacy of RFLP technology as applied to crop improvement is far from complete. This investigation was conducted to study the relationship between RFLP-derived genotypes and heterotic patterns of a group of maize (Zea mays L.) inbred lines. A total of 22 inbreds was crossed to four testers (B73, B76, Mo17, and Va26) in combinations that minimized crossing within heterotic groups. Forty-seven single-cross progeny were subsequently evaluated for several agronomic traits (including grain yield and moisture, ear height, and root lodging) over 2-4 consecutive years at two to four Iowa locations in a randomized complete-block design. The inbred lines were subjected to RFLP analysis, which involved 47 genomic clones and the restriction enzymes EcoRI and HindIII. Hybrid RFLP patterns were predicted from their inbred parents. Modified Roger's distances were computed to estimate genetic distance among the inbred lines. Principal component analysis facilitated ascertainment of relative dispersion of the inbreds based on the frequency of variants at specific RFLP loci. Evident associations of variants with genes affecting agronomic traits were identified by principal component regression analysis, in which adjusted hybrid means were regressed on the matrix of hybrid variants frequencies. The hybrid means were adjusted by removing environmental effects, using residuals as dependent variables in the regression analysis. Results from this study suggest that RFLP analysis may be of value in allocating maize inbreds to heterotic groups, but no relationship between RFLP-based genetic distance and hybrid performance was apparent. Principal component regression identified variants potentially linked to genes that control specific agronomic traits.