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

Summary 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.Joint contribution from Cereal and Soybean Research Unit, USDA, Agricultural Research Service and Journal Paper no. J-13929 of the Iowa Agric and Home Economics Exp Stn, Ames, IA 50011. Projects no. 2818 and 2778A.E.M. is presently at the Iowa State University on leave from University of Hohenheim, D-7000 Stuttgart 70, Federal Republic of Germany     

Comparison of phenotypic and molecular distances to predict heterosis and F1 performance in Ethiopian mustard (Brassica carinata A. Braun)

Predicting heterosis and F₁ performance from the parental generation could largely enhance the efficiency of breeding hybrid or synthetic cultivars. This study was undertaken to determine the relationship between parental distances estimated from phenotypic traits or molecular markers with heterosis, F₁ performance and general combining ability (GCA) in Ethiopian mustard (Brassica carinata). Nine inbred lines representing seven different geographic regions of Ethiopia were crossed in half-diallel. The nine parents along with their 36 F₁s were evaluated in a replicated field trail at three locations in Ethiopia. Distances among the parents were calculated from 14 phenotypic traits (Euclidean distance, ED) and 182 random amplified polymorphic DNA (RAPD) markers (Jaccard’s distances, JD), and correlated with heterosis, F₁ performance and GCA sum of parents (GCA_sum). The correlation between phenotypic and molecular distances was low (r=0.34, P≤0.05). Parents with low molecular distance also had low phenotypic distance, but parents with high molecular distance had either high, intermediate or low phenotypic distance. Phenotypic distance was highly significantly correlated with mid-parent heterosis (r=0.53), F₁ performance (r=0.61) and GCA (r=0.79) for seed yield. Phenotypic distance was also positively correlated with (1) heterosis, F₁ performance and GCA for plant height and seeds plant⁻¹, (2) heterosis for number of pods plant⁻¹, and (3) F₁ performance for 1,000 seed weight. Molecular distance was correlated with GCA_sum (r=0.36, P≤0.05) but not significantly with heterosis and F₁ performance for seed yield. For each parent a mean distance was calculated by averaging the distances to the eight other parents. Likewise, mean heterosis was estimated by averaging the heterosis obtained when each parent is crossed with the other eight. For seed yield, both mean ED and JD were significantly correlated with GCA (r=0.90, P≤0.01 for ED and r=0.68, P≤0.05 for JD) and mean heterosis (r=0.79, P≤0.05 for ED and r=0.77, P≤0.05 for JD). In conclusion, parental distances estimated from phenotypic traits better predicted heterosis, F₁ performance and GCA than distances estimated from RAPD markers. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Analysis of inbreeding in a colonizing population of Drosophila subobscura

An analysis of the effects of inbreeding on the genetic structure of a colonizing population of Drosophila subobscura has been carried out. Species of Drosophila, particularly D. subobscura, may have lethal alleles associated with chromosomal inversions and our aim was to assess the extent to which the genome is balanced in this way. The frequencies of chromosomal inversions were compared between a large population and a set of 72 lines that were maintained by brother-sister mating for 10 generations. Fisher's matrix method was used to calculate the expected homozygosity in these inbred lines for 5 allozyme loci (Aph, Hk-1, Lap, Odh, and Pept-1) used as markers of large chromosomal segments. Furthermore, the expected rates of fixation corresponding to these allozyme loci were also calculated. The results show that the amount of homozygosis observed did not differ significantly from expectations (with the corresponding loss of lines as a consequence of the reduction in viability). However, two deviations from strict neutrality were observed: there was a heterozygote excess at the Lap locus, and the frequency of the O ₅ inversion (always associated with a lethal gene in colonizing populations) was higher than expected.     

Effect of rate of inbreeding on inbreeding depression in Drosophila melanogaster

Summary This experiment was designed to study the relationship between rate of inbreeding and observed inbreeding depression of larval viability, adult fecundity and cold shock mortality in Drosophila melanogaster. Rates of inbreeding used were full-sib mating and closed lines of N=4 and N=20. Eight generations of mating in the N=20 lines, three generations in the N=4 lines and one generation of full-sib mating were synchronised to simultaneously produce individuals with an expected level of inbreeding coefficient (F) of approximately 0.25. Inbreeding depression for the three traits was significant at F=0.25. N=20 lines showed significantly less inbreeding depression than full-sib mated lines for larval viability at approximately the same level of F. A similar trend was observed for fecundity. No effect of rate of inbreeding depression was found for cold shock mortality, but this trait was measured with less precision than the other two. Natural selection acting on loci influencing larval viability and fecundity during the process of inbreeding could explain these results. Selection is expected to be more effective with slow rates of inbreeding because there are more generations and greater opportunity for selection to act before F=0.25 is reached. Selection intensities seem to have been different in the three traits measured. Selection was most intense for larval viability, less intense for fecundity and, perhaps, negligible at loci influencing cold shock mortality.     

RFLP variation and genealogical distance,multivariate distance,heterosis, and genetic variance in oats

Patterns of restriction fragment length polymorphisms (RFLPs) have been proposed as estimators of genetic diversity among breeding lines and as predictors of heterosis and genetic variance. We evaluated these proposals by using a set of nine elite oat lines crossed in a diallel mating design without reciprocals. RFLP analysis was conducted using HindIII-digested DNA and a total of 107 probes from three different sources: 14 heterologous wheat cDNA clones, 17 oat genomic clones, and 76 oat cDNA clones. Of the 77 probes that produced high-quality autoradiographs, 26 detected polymorphisms among this set of lines, with an average of 2.6 variants per probe. RFLP-based genetic distance (FD) was calculated from these data by using Nei and Li's measure of genetic similarity, and was compared with two other measures of genetic divergence. Genealogical distance (GD ^*) was obtained from the coefficients of parentage based on known parental pedigrees, and multivariate distance (DI) was calculated by using the first five principal components of the parental correlation matrix for 12 agronomic traits. FD was significantly correlated with GD ^* (r=0.63, P<0.01), but not with DI (r=-0.05). Cluster analysis based on these three distance estimates did not produce equivalent groupings, but the FD and GD ^* clusters were more similar to each other than to the DI clusters. These results indicate that: (1) sufficient variation exists for further application of RFLP technologyto oats, (2) RFLPs could provide accurate estimates of genetic divergence among elite oat lines, and (3) it is unlikely that dispersed markers can predict heterosis or population genetic variance in oats. Further investigations will require more parental lines, a larger set of markers, and more information on the linkage relationships between RFLP markers and loci controlling the trait of interest.Journal paper No. J-15302 of the Iowa Agriculture and Home Economics Experiment Station, Ames, IA 50011, USA. Project No. 2818 and 2447. Supported by Quaker Oats grant to M. Lee     

Heterosis in crosses between geographically separated populations of Drosophila melanogaster

Summary An experiment was performed to test the hypothesis that the genetic distance between populations estimated from enzyme loci could be used to predict the amount of heterosis that would occur in crosses between these populations. A partial diallel cross using 11 populations of Drosophila melanogaster from the AustralianPacific region and from England was carried out. Heterosis for larval viability, fecundity, cold shock mortality, and an index of these three traits was recorded. When two populations originating from the same location were crossed, no heterosis occurred, but otherwise heterosis was significant for all traits. For larval viability, a similar low level of heterosis occurred in all crosses. For cold shock mortality, the level of heterosis varied widely and fecundity showed a pattern intermediate between these two. The geographic distance between the sites from which populations originated was not correlated with the amount of heterosis in their crosses. There was a tendency for populations from ecologically different environments to show heterosis in crosses. Genetic distance based on ten enzyme loci was correlated with heterosis for cold shock mortality and the combined trait index. These results can be explained by the hypothesis that genes affecting larval viability are subject to strong, uniform selection in all populations, which limits the extent to which gene frequencies can drift apart. However, genes affecting cold shock mortality and the enzyme loci are subject to different selection pressures in different environments. This divergent selection combined with genetic drift causes divergence in gene frequency and heterosis.     

Segregation of Microsatellite Alleles in Gynogenetic Diploid Pacific Abalone (Haliotis discus hannai)

Inheritance of 9 microsatellite loci was examined in 3 families of gynogenetic Pacific abalone Haliotis discus hannai produced by fertilizing eggs with UV-irradiated sperm followed by inhibition of the second meiotic division. The proportion of heterozygous progeny was used to estimate marker-centromere (M-C) distances. All loci conformed to Mendelian segregation in the control crosses when null alleles were accounted for. The absence of paternal alleles confirmed the gynogenetic origin of the offspring and indicated 100% success for 3 families. Estimated recombinant frequencies ranged from 0.10 to 0.60, which is lower than those observed in other gynogenetic diploid animals. The mean recombination frequency was 0.22, corresponding to a fixation index of 0.78 in one generation. This is 3.12 times the increase in homozygosity expected after one generation of sib mating (0.25), suggesting meiotic gynogenesis may be an effective means of rapid inbreeding in the abalone. M-C map distances for the 9 loci varied between 5 and 30 cM under the assumption of complete interference. The information about M-C distances will be useful for future gene mapping in H. discus hannai.     

FITNESS CONSEQUENCES OF OUTCROSSING IN A SOCIAL SPIDER WITH AN INBREEDING MATING SYSTEM

Inbreeding mating systems are uncommon because of inbreeding depression. Mating among close relatives can evolve, however, when outcrossing is constrained. Social spiders show obligatory mating among siblings. In combination with a female‐biased sex ratio, sib‐mating results in small effective populations. In such a system, high genetic homozygosity is expected, and drift may cause population divergence. We tested the effect of outcrossing in the social spider Stegodyphus dumicola. Females were mated to sib‐males, to a non‐nestmate within the population, or to a male from a distant population, and fitness traits of F1s were compared. We found reduced hatching success of broods from between‐population crosses, suggesting the presence of population divergence at a large geographical scale that may result in population incompatibility. However, a lack of a difference in offspring performance between inbred and outbred crosses indicates little genetic variation between populations, and could suggest recent colonization by a common ancestor. This is consistent with population dynamics of frequent colonizations by single sib‐mated females of common origin, and extinctions of populations after few generations. Although drift or single mutations can lead to population divergence at a relatively short time scale, it is possible that dynamic population processes homogenize these effects at longer time scales.     

Pedigree and marker information requirements to monitor genetic variability

There are several measures available to describe the genetic variability of populations. The average inbreeding coefficient of a population based on pedigree information is a frequently chosen option. Due to the developments in molecular genetics it is also possible to calculate inbreeding coefficients based on genetic marker information. A simulation study was carried out involving ten sires and 50 dams. The animals were mated over a period of 20 discrete generations. The population size was kept constant. Different situations with regard to the level of polymorphism and initial allele frequencies and mating scheme (random mating, avoidance of full sib mating, avoidance of full sib and half sib mating) were considered. Pedigree inbreeding coefficients of the last generation using full pedigree or 10, 5 and 2 generations of the pedigree were calculated. Marker inbreeding coefficients based on different sets of microsatellite loci were also investigated. Under random mating, pedigree-inbreeding coefficients are clearly more closely related to true autozygosity (i.e., the actual proportion of loci with alleles identical by descent) than marker-inbreeding coefficients. If mating is not random, the demands on the quality and quantity of pedigree records increase. Greater attention must be paid to the correct parentage of the animals.     

Long‐distance dispersal in a fire‐ and livestock‐protected savanna

Savannas are highly diverse and dynamic environments that can shift to forest formations due to protection policies. Long‐distance dispersal may shape the genetic structure of these new closed forest formations. We analyzed eight microsatellite loci using a single‐time approach to understand contemporary pollen and effective seed dispersal of the tropical tree, Copaifera langsdorffii Desf. (Fabaceae), occurring in a Brazilian fire‐ and livestock‐protected savanna. We sampled all adult trees found within a 10.24 ha permanent plot, young trees within a subplot of 1.44 ha and open‐pollinated seeds. We detected a very high level of genetic diversity among the three generations in the studied plot. Parentage analysis revealed high pollen immigration rate (0.64) and a mean contemporary pollen dispersal distance of 74 m. In addition, half‐sib production was 1.8 times higher than full‐sibs in significant higher distances, indicating foraging activity preference for different trees at long distances. There was a significant and negative correlation between diameter at breast height (DBH) of the pollen donor with the number of seeds (r = ?0.640, P‐value = 0.032), suggesting that pollen donor trees with a higher DBH produce less seeds. The mean distance of realized seed dispersal (recruitment kernel) was 135 m due to the large home range dispersers (birds and mammals) in the area. The small magnitude of spatial genetic structure found in young trees may be a consequence of overlapping seed shadows and increased tree density. Our results show the positive side of closed canopy expansion, where animal activities regarding pollination and seed dispersal are extremely high.     

Predictive potential of DNA markers in heterosis breeding of maize

PCR-analysis of maize inbred lines has been carried out. Genetic distances between the lines have been calculated, allelic composition and heterosis level of F-hybrids have been determined. Heterosis level of hybrid seed yield rised according to increasing of genetic distances between initial lines. Correlation of allelic composition of inbred line microsatellite loci and heterosis level of the respective hybrids has been revealed.     

Efficiency of the use of pedigree and molecular marker information in conservation programs

The value of molecular markers and pedigree records, separately or in combination, to assist in the management of conserved populations has been tested. The general strategy for managing the population was to optimize contributions of parents to the next generation for minimizing the global weighted coancestry. Strategies differed in the type of information used to compute global coancestries, the number and type of evaluated individuals, and the system of mating. Genealogical information proved to be very useful (at least for 10 generations of management) to arrange individuals' contributions via the minimization of global coancestry. In fact, the level of expected heterozygosity after 10 generations yielded by this strategy was 88-100% of the maximum possible improvement obtained if the genotype for all loci was known. Marker information was of very limited value if used alone. The amount and degree of polymorphism of markers to be used to compute molecular coancestry had to be high to mimic the performance of the strategy relying on pedigree, especially in the short term (for example, >10 markers per chromosome with 10 alleles each were needed if only the parents' genotype was available). When both sources of information are combined to calculate the coancestry conditional on markers, clear increases in effective population size (Ne) were found, but observed diversity levels (either gene or allelic diversity) in the early generations were quite similar to the ones obtained with pedigree alone. The advantage of including molecular information is greater when information is available on a greater number of individuals (offspring and parents vs. parents only). However, for realistic situations (i.e., large genomes) the benefits of using information on offspring are small. The same conclusions were reached when comparing the use of the different types of information (genealogical or/and molecular) to perform minimum coancestry matings.     

Evaluation of soybean RFLP marker diversity in adapted germ plasm

Summary Soybean RFLP markers have been primarily developed and genetically mapped using wide crosses between exotic and adapted genotypes. We have screened 38 soybean lines at 128 RFLP marker loci primarily to characterize germ plasm structure but also to evaluate the utility of RFLP markers identified in unadapted populations. Of these DNA probes 70% detected RFLPs in this set of soybean lines with an average polymorphism index of 0.30. This means that only 1 out of 5 marker loci was informative between any particular pair of adapted soybean lines. The variance associated with the estimation of RFLP genetic distance (GD_R) was determined, and the value obtained suggested that the use of more than 65–90 marker loci for germ plasm surveys will add little precision. Cluster analysis and principal coordinate analysis of the GD_R matrix revealed the relative lack of diversity in adapted germ plasm. Within the cultivated lines, several lines adapted to Southern US maturity zones also appeared as a separate group. GD_R data was compared to the genetic distance estimates obtained from pedigree analysis (GD_P). These two measures were correlated with r = 0.54 for all 38 lines, but the correlation increased to r = 0.73 when only adapted lines were analyzed.     

Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population

The effects of intermating on recombination and the development of linkage maps were assessed in maize. Progeny derived from a common population (B73 × Mo17) before and after five generations of intermating were genotyped at the same set of 190 RFLP loci. Intermating resulted in nearly a four-fold increase in the genetic map distance and increased the potential for improved genetic resolution in 91% of the intervals evaluated. This mapping population and related information should connect research involving dense genetic maps, physical mapping, gene isolation, comparative genomics, analysis of quantitative trait loci and investigations of heterosis.     

新铁炮百合自交初代遗传分化的等位酶分析

采用等位酶分析技术,检测了新铁炮百合自交初代各株系的遗传多样性与遗传分化。结果表明,在人工辅助自交和选择作用下,随着世代的增加,多态位点的比率下降,每个位点平均等位基因数降低,观测杂合度和期望杂合度下降。由于选择作用,株系间纯合的位点和速度不同,固定的等位基因不同。F4代株系间平均遗传距离较F3、代株系有一定增大,加强了株系间的分化。     

Extending the rapeseed gene pool with resynthesized <Emphasis Type="Italic">Brassica napus</Emphasis> II: Heterosis

Hybrid breeding relies on the combination of parents from two differing heterotic groups. However, the genetic diversity in adapted oilseed rape breeding material is rather limited. Therefore, the use of resynthesized Brassica napus as a distant gene pool was investigated. Hybrids were derived from crosses between 44 resynthesized lines with a diverse genetic background and two male sterile winter oilseed rape tester lines. The hybrids were evaluated together with their parents and check cultivars in 2 years and five locations in Germany. Yield, plant height, seed oil, and protein content were monitored, and genetic distances were estimated with molecular markers (127 polymorphic RFLP fragments). Resynthesized lines varied in yield between 40.9 dt/ha and 21.5 dt/ha, or between 85.1 and 44.6% of check cultivar yields. Relative to check cultivars, hybrids varied from 91.6 to 116.6% in yield and from 94.5 to 103.3% in seed oil content. Mid-parent heterosis varied from −3.5 to 47.2% for yield. The genetic distance of parental lines was not significantly correlated with heterosis or hybrid yield. Although resynthesized lines do not meet the elite rapeseed standards, they are a valuable source for hybrid breeding due to their large distance from present breeding material and their high heterosis when combined with European winter oilseed rape.     

Effect of non-random mating on genomic and BLUP selection schemes

Background

The risk of long-term unequal contribution of mating pairs to the gene pool is that deleterious recessive genes can be expressed. Such consequences could be alleviated by appropriately designing and optimizing breeding schemes i.e. by improving selection and mating procedures.

Methods

We studied the effect of mating designs, random, minimum coancestry and minimum covariance of ancestral contributions on rate of inbreeding and genetic gain for schemes with different information sources, i.e. sib test or own performance records, different genetic evaluation methods, i.e. BLUP or genomic selection, and different family structures, i.e. factorial or pair-wise.

Results

Results showed that substantial differences in rates of inbreeding due to mating design were present under schemes with a pair-wise family structure, for which minimum coancestry turned out to be more effective to generate lower rates of inbreeding. Specifically, substantial reductions in rates of inbreeding were observed in schemes using sib test records and BLUP evaluation. However, with a factorial family structure, differences in rates of inbreeding due mating designs were minor. Moreover, non-random mating had only a small effect in breeding schemes that used genomic evaluation, regardless of the information source.

Conclusions

It was concluded that minimum coancestry remains an efficient mating design when BLUP is used for genetic evaluation or when the size of the population is small, whereas the effect of non-random mating is smaller in schemes using genomic evaluation.     

Population genetics and gene variation in screwworms (Diptera: Calliphoridae) from Brazil

Allozyme variation in New World screwworm,Cochliomyia hominivorax (Coquerel), populations from Brazil was examined. Variability was observed in 8 of 13 enzyme loci and the frequency of the most common allele was <0.95 for seven loci. Observed and expected heterozygosities were 0.159 and 0.165, respectively. Comparisons of the Brazilian populations with previously studied populations from Costa Rica resulted in Nei's genetic distances of between 0.000 and 0.006, with the greatest distance being between populations within Brazil. Comparisons with Mexican populations using only three loci resulted in genetic distances ≤0.031. Goodness-of-fit statistics for Hardy-Weinberg equilibrium and Wright'sF statistics indicated small deviations from expected equilibrium genotype frequencies and low levels of differentiation between populations within Brazil. Differentiation among screwworm populations from Brazil, Costa Rica, and Mexico was minimal.     

Associations between quantitative traits and enzyme loci in the F2 population of a maize hybrid

Summary Univariate and multivariate analyses were used to identify associations between eight enzyme marker loci and 11 quantitative traits of maize (Zea mays L.). The material analyzed included inbred lines Wf9 and Pa405, single-cross hybrid Wf9 X Pa405, and the F2 generation of the selfed single-cross hybrid. Each enzyme locus assayed was associated with at least one quantitative trait, and all quantitative traits were associated with genotypes at particular enzyme loci. Significant associations also were found between the level of heterozygosity per individual and nine of 11 quantitative traits. The total contribution to heterosis, for seed yield per plant, of genes linked with the eight enzyme loci, was 27% of the F2 mean and 18% of the difference in mean between the F1 hybrid and the inbred parents. Genes linked with Glu1 accounted for nearly one third of the total dominance effect detected by the eight enzyme loci. The chromosome segments marked by loci with significant effects on seed yield were markedly overdominant. The large heterotic effects of chromosome segments marked by particular loci suggest that enzyme loci could be used to help transfer genes responsible for heterosis to inbred lines. We conclude that analyses of additional inbred lines, F1 hybrids, and F2 populations in more environments will halp identify specific associations between enzyme loci, or chromosome segments which they mark, and important agronomic traits.Cooperative investigations of the USDA, ARS and Dept. of Plant Sciences, South Dakota State Univ. (SDSU), Brookings, Journal Series No. 2039; and the Institute of Animal Resource Ecology, Univ. of British Columbia, Vancouver, B.C. V6T 1W5, Canada     

Genetic drift in an outbred stock of mice.

Survey in protein polymorphism in the nucleus colony of the Him: OF 1-mouse outbred stock showed that 8 of 53 loci were variable in the stock. Allele frequencies of these eight loci (Idh-1, Mup-1, Pgm-1; Ldr-1, Gpi-1s, Hbb, Mod-1, Ce-2) changed between generations investigated. The average percentage of heterozygote animals for these loci decreased with generation. These suggested that genetic drift occurred in the breeding stock. Examination in the breeding record sheets showed that genetic drift was caused by mistakes in mating probably due to repeated personnel changes and insufficient training of the animal technicians. Mice had not been paired according to the schemes prescribed, pairing among relatives and reduction of the number of litters used for mating occurred. The increase in homozygosity showed only little effect on breeding parameters: The interval between pairing and first and second litter increased significantly.