Effect of gametic disequilibrium on means and on genetic variances of autotetraploid synthetic varieties

Summary The occurrence and effects of a gametic disequilibrium (DSE) in the first generation of a theoretical two-population synthetic variety were investigated. Theoretical development was limited to the genetics at a single locus with two alleles in an autotetraploid species with random chromosome inheritance. Algebraic expressions were developed for the differences between the mean genotypic values of the two-population synthetic variety at generation one and in random mating equilibrium (RME). For the situation where both parents of the synthetic were in RME, a numerical analysis was performed for all possible allele frequencies assuming the following types of genic action: monoplex dominance, partial monoplex dominance, duplex dominance, partial duplex dominance, and additive. The result indicated that with non-additive genic action the DSE could, in some cases, greatly depress or inflate the mean genotypic value of the first generation (Syn-1_(RME)). Thus, any change of means over advancing generations with loss of DSE could be positive or negative. When additive genic action was assumed, there was no effect associated with DSE and when both parents had the same allele frequencies there was no DSE. The DSE, with only a minor exception, decreased the genetic variance and in numerous cases forced it near zero. Expressions were developed for mean genotypic values of a first generation synthetic with DSE in one parent (Syn-1_(DSE/RME)) or both parents (Syn-1_(DSE)). The deviation of these means from those of Syn-1_(RME) was a function of digenic and quadragenic population effects. An inspection of the response equations for Syn-1_(RME) indicated that in a series of crosses with one common parent the rankings of first generation means would be the same as the ranking of populations at equilibrium though the individual means would be biased. More importantly with DSE of one or both parents there are situations when a ranking of first generation mean genotypic values would not reflect relative frequency of desirable alleles in the populations. These results indicate that statistical analyses and selections based on means of the Syn-1 generation can have an error which is not avoidable by improvement in precision of evaluation.Cooperative investigations of the Alfalfa Production Research Unit, United States Department of Agriculture, Agricultural Research Service, and the Nevada Agricultural Experiment Station, Reno, Nevada, USAPaper No. 590 Scientific Journal Series, Nevada Agricultural Experiment Station     

Theoretical value of estimates of general combining ability in the autotetraploid crop

Summary The means of half-sib progenies have been indicated as selection criteria for intra-population improvement while the average of the means of full-sib progenies in diallel analyses have been proposed as predictors, in part, of the means of untested synthetic varieties. When these measures based on progeny means are expressed as deviations from a defined greater population of crosses, they are often termed the general combining ability (GCA). In this study the GCA estimates or a facsimile were theoretically investigated for the one locus, digene, autotetraploid model to verify the genetic basis and its value for selection and prediction in the presence of a naturally occurring phenomena of autopolyploids called gametic disequilibrium with three types of non-additive inheritance. Two breeding objectives were envisioned, the selection of best parents with recurrent selection based on GCA in the continued development of elite populations and the prediction of advanced generation synthetic variety performance. The first generation means of progenies with a potential bias due to gametic disequilibrium were compared to GCA estimation of same progenies in the absence of gametic disequilibrium. The results indicated that testcrossing plants to a population without gametic disequilibrium could be used for selection of best parents. The gametic disequilibrium in the cross may increase or depress selection response dependent on the array of genotypes which happen to be evaluated, on the type of genic action at the locus, and on the frequency of the desirable allele in the testor population. The GCA estimates for prediction of synthetic performance were potentially biased by gametic disequilibrium. An assumption of pollination by the same array of gametes was made for all plants, but obviously was unrealistic for GCA estimation with partial diallels, or with no selfing, and in other situations. The GCA estimate was shown to be an unreliable predictor of synthetic variety performance. When it was assumed that different plants were pollinated by different arrays of gametes, a more realistic situation, no genetic interpretation of GCA values was possible even with purely additive gene action at the locus.Cooperative investigation of the Alfalfa Production Research Unit, United States Department of Agriculture, Agricultural Research Service, and the Nevada Agricultural Experiment Station, Reno, Nevada     

Combined S2 and crossbred family selection in full-sib reciprocal recurrent selection

Summary A method (CRRS) that combines S₂ and crossbred family selection in full-sib reciprocal recurrent selection (FSRRS) is proposed. The method requires four generations per cycle in single-eared maize populations. Selection is based on performance of S₂ and full-sib families by applying selection index theory. Equations to estimate the coefficients included in the index are given. These estimates are functions of the genetic and phenotypic variances and covariances among and between the two kinds of families. Comparisons of FSRRS and CRRS under equivalent amount of effort show that CRRS has some advantage over FSRRS for low heritability of the trait being selected (e.g., maize yield) and when only one or two locations with two replications are involved in the selection experiment.Joint contribution: Institute Nacional de Investigaciones Agrarias, La Coruna, Spain; and Agricultural Research, Science and Education Administration, U.S. Department of Agriculture, and Journal Paper No. J-10118 of the Iowa Agriculture and Home Economics Experiment Station, Ames, IA 50011. Project 2194     

Effect on linkage disequilibrium of selection for a quantitative character with epistasis

Summary Selection for a character controlled by additive genes induces linkage disequilibrium which reduces the additive genetic variance usable for further selective gains. Additive x additive epistasis contributes to selection response through development of linkage disequilibrium between interacting loci. To investigate the relative importance of the two effects of linkage disequilibrium, formulae are presented and results are reported of simulations using models involving additive, additive x additive and dominance components. The results suggest that so long as epistatic effects are not large relative to additive effects, and the proportion of pairs of loci which show epistasis is not very high, the predominant effect of linkage disequilibrium will be to reduce the rate of selection response.     

Nodulation of lucerne (Medicago sativa L.) in an acid soil: pH dynamics in the rhizosphere of seedlings growing in rhizotrons

A lime-pellet around seeds of lucerne significantly increased crown nodulation in an acid soil. To investigate whether neutralization or calcium were of importance when lime was supplied, experiments with plants were done either in pots or in rhizotrons. Crown nodulation was used to quantify the effect of these two parameters.For the neutralization of the soil, KOH (in pots) or K₂CO₃ (in rhizotrons) was added. The crown nodulation of pot-grown plants increased from 31% to 53%. In rhizotrons, the number of crown-nodulated seedlings increased from 9% to 53%. If calcium was supplied additionally (as CaCl₂ or CaSO₄), 63% crown nodulation was found in pots, and 68% in rhizotrons. These numbers are close to the crown nodulation with lime (CaCO₃) alone: 70% in pots and 71% in rhizotrons. In the soil studied, the beneficial effect of lime is largely due to neutralization (80%), and only a minor part (20%) is due to the input of calcium.Using rhizotrons, the dynamics of the pH in the rhizosphere of lime-treated and untreated seedlings was followed during a period of 12 days. It was found that, even in the absence of lime, the pH along the taproot increased from 5.1 to 5.7. However, this did not result in the formation of root nodules. Nodulation was obtained only by adding neutralizing chemicals, which increased the pH during the initial 3 days, the acid sensitive period of the process.     

Choice of environments in reciprocal recurrent selection programs

Summary An alternative method of reciprocal recurrent selection (RRS) in which populations A and B are each evaluated in a different environment is proposed. This method is called dual-environment reciprocal recurrent selection (DERRS). Two genetic models are considered in the theoretical study. A comparison of selection methods shows that genetic gain is larger in DERRS than in RRS for the two models. The difference grows greater as the dominance effects operating in the two environments are more divergent and as the number of selection cycles increases. A greater gain is obtained when the genetic covariances between crosses in the two chosen environments are lower.     

Association of AFLP markers with downy mildew resistance in autotetraploid alfalfa

The amplified fragment length polymorphism (AFLP) assay is an efficient method for the identification of molecular markers useful in the improvement of numerous crop species. The identification of AFLP markers linked to disease resistance genes has been shown in segregating populations from crosses of inbred lines. The development of inbred lines in alfalfa is not possible, but existing breeding programs have produced populations selected for resistance to a single pest. Two such populations, UC-123 and UC-143, differing only in selection for resistance to downy mildew (Peronospora trifoliorum de Bary) isolate I-8, were used in this study. Thirty-six resistant plants from UC-143, and 36 susceptible plants from UC-123 were screened for DNA polymorphisms using fourteen AFLP primer combinations. Four AFLP fragment markers, ACACTC₂₀₈, ACACTC₁₅₀, ACACAT₂₁₆ and ACACTC₄₈₆, were found to be significantly associated with disease susceptibility or resistance. Resistant and susceptible plants were crossed in a diallel scheme and the progeny were screened for resistance to P. trifoliorum isolate I8. Two of the AFLP markers, ACACTC₂₀₈ and ACACTC₄₈₆ were significantly associated with resistance in the F₁ and S₁ progeny. The utilization of two populations, comprised of 36 resistant and 36 susceptible plants, for the identification of DNA fragments associated with disease resistance proved successful. Seventy-two plants is a very manageable number and provides a starting point for further refinement of marker-trait associations.     

Microgametophytic selection in two alfalfa (Medicago sativa L.) clones

Summary Microgametophytic selection was investigated using two ecologically diverse autotetraploid clones of alfalfa. Several selection pressures (drying, aging, freezing, and high and low temperatures) were applied to microgametophytes at three stages of the life cycle, 1) during microsporogenesis, 2) post-anthesis, and 3) pollen tube growth. Pollen aging produced a progeny population with a greater mean plant size and a lower coefficient of variation than the control progeny. High temperature (29.5 °C) applied both during microsporogenesis and pollen tube growth resulted in progeny populations which were significantly taller and, in one case, had a larger leaf number than the control populations. In contrast, air dried pollen resulted in a progeny population which had significantly smaller character means and larger coefficients of variation than the control population. Also, low temperature (15 °C) during pollen tube growth yielded progeny with reduced branch number and a larger coefficient of variation than the control progeny. In cases where progeny derived from selected microgametophytes were found to differ from the control offspring, corresponding shifts in the reciprocal cross were not observed. For the temperature stress treatments, the lack of reciprocal differences may be related to the different temperature adaptations of the two ecotypes. These results suggest that microgametophytic selection can be effective in shifting the mean of the progeny generation; however, the results obtained will vary depending upon the selection pressure, stage of selection, and the parents used.     

Combined genetic analysis of partial blast resistance in an upland rice population and recurrent selection for line and hybrid values

The CNA-IRAT 5 upland rice population has been improved for 4 years by recurrent selection for blast resistance in Brazil. In order to predict the efficiency of recurrent selection in different test systems and to compare the relative advantage of hybrids versus pure line breeding, a combined genetic analysis of partial blast resistance in the CNA-IRAT 5 population was undertaken. A three-level hierarchical design in inbreeding and a factorial design were derived from the base population. Partial blast resistance of lines and hybrids was evaluated in the greenhouse and in the field by inoculation with one virulent blast isolate. The means and genetic variances of the hybrids and lines were estimated. Genetic advance by recurrent selection was predicted from estimates of variance components. The inheritance of partial blast resistance was mainly additive but non-additive effects were detected at both levels of means and variances. Mean heterosis ranged from 4%–8% for lesion size and lesion density to 10–12% for leaf and panicle resistance. High dominance or homozygous dominance variances relative to additive variance and negative covariance between additive and homozygous dominance effects were estimated. A low frequency of favourable alleles for partial resistance would explain the observed organisation of genetic variability in the base population. Recurrent selection will efficiently improve partial blast resistance of the CNA-IRAT 5 population. Genetic advance for line or hybrid values was expected to be higher testing doubled haploid lines than S1 lines, or than general combining ability. Two components of partial resistance assessed in the greenhouse, lesion size and lesion density, could be used as indirect selection criteria to improve field resistance. On the whole, hybrid breeding for partial blast resistance appeared to be slightly more advantageous than pure line breeding.     

Relative efficiency of two mating systems and selection procedures for yield improvement in wheat (Triticum aestivum L.)

Summary The relative efficiences of the biparental mating systems and selfing series in connection with phenotypic and geno-phenotypic selection procedures were evaluated for yield improvement in a cross HP1102 X CPAN 1681 of wheat. Two selection cycles having a 4 per cent selection intensity for grain yield were carried out following both selection procedures under the two mating systems. Following these selection procedures, a greater improvement for grain yield could be achieved with the biparental mating system than with the selfing series. During the first selection cycle, the geno-phenotypic selection procedure had an edge over phenotypic selection procedure. The realized response due to the second cycle of selection and the predicted response for the third selection cycle indicated that the phenotypic selection procedure is more efficient than the geno-phenotypic selection procedure. It is suggested that selection following intermating in early segregating generations is able to overcome several inherent limitations of the simple pedigree method as it is possible to increase genetic variation and to concentrate favourable genes and gene combinations for grain yield. An increase in grain yield was, in general, accompanied by an increase in plant height, peduncle length, 100 grain weight, tiller number and biological yield. Therefore, it is suggested that an index comprised of grain yield, plant height, tiller number, grain weight and biological yield could be used for selecting high yielding genotypes of suitable height.     

Free proline contents in two different groups of rice mutants resistant to hydroxy-L-proline

Summary In four rice (Oryza sativa L.) mutants resistant to hydroxy-L-proline (Hyp), HYP101, HYP203, HYP205 and HYP210, and in their original variety, Nipponbare, free proline and Hyp contents in the seeds and in the 14-day-old seedlings have been determined. The four mutants can be divided into two groups: HYP101 and HYP203 are classified as to recessive gene and the levels of free proline are similar to that of the original variety; the second group includes mutants HYP205 and HYP210 where the Hyp resistance is transmitted heterozygously and, both in the seeds and in the seedlings, a remarkable increase in free proline content is observed. In particular, free proline contents in the seeds of HYP205 and HYP210 are, respectively, 24 and 12 times that of the original variety. Hyp is detected only in the seedlings cultured with Hyp solution. In the Hyp resistant seedlings of HYP205 and HYP210, Hyp contents are twice that of the original variety and less than half in the seedlings of HYP101 and HYP203. Hyp resistance and differential proline levels are also evident in the callus initiated from the mutants. This suggests that the Hyp resistant mutants are good genetic markers both in planta and in vitro. The Hyp mutants are also discussed with regard to stress resistance.     

Non-antibiotic,efficient selection for alfalfa genetic engineering

A selectable marker gene (SMG), usually conferring resistance to an antibiotic or herbicide, is generally introduced into the plant cells with the gene(s) for the trait of interest to allow only the cells that have integrated and express the foreign sequences to regenerate into a plant. The availability of several SMGs for each plant species is useful for both basic and applied research to combine several genes of interest in the same plant. A selection system based on gabaculine (3-amino-2,3-dihydrobenzoic acid) as the selective substance and the bacterial hemL gene [encoding a mutant for of the enzyme glutamate 1-semialdehyde aminotransferase (GSA-AT)] as the SMG was previously used for genetic transformation of tobacco. The hemL gene is a good candidate for a safe SMG, because GSA-AT is present in all plants and is likely involved in one metabolic step only, so that unintended effects of its overexpression in plants are not probable. In this work, we have compared this new selection system with the conventional, kanamycin-based system for alfalfa Agrobacterium-mediated transformation. The hemL and NptII genes were placed together into a T-DNA under the control of identical promoters and terminators. We show that the gabaculine-based system is more efficient than the conventional, kanamycin-based system. The inheritance of hemL was Mendelian, and no obvious phenotypic effect of its expression was observed.     

Pleiotropic effects of purine auxotrophy inRhizobium meliloti on cell surface molecules

Rhizobial purine auxotrophs have earlier been shown to be defective in symbiosis, though the exact reason for this failure is not clear. Using various dyes that specifically bind different cell surface molecules, we show that there are multiple changes in the cell surface molecules associated with different purine auxotrophs. Affected molecules in different purine auxotrophs that were tested include (i) acidic exopolysaccharides, (ii) cellulose fibrils, and (iii) beta (1–3) glucans. Our results show that the symbiotic deficiency of purine auxotrophs is likely to be a result of these associated changes on the cell surface     

Efficient selection intensity in early generation index selection in groundnut (Arachis hypogaea L.)

Summary The F₂ potential of single and three-way crosses was evaluated using a set of physiological and yield components. Results were based on an index of selection using (a) only yield components and (b) both physiological and yield components. The indices were constructed using the percentage improvement of F₂ over the better parent of the corresponding F₁ cross for every character. The performance of F₂ plants assessed by the expected value of the regression index was ranked in descending order to provide a ranked F₂ distribution (FRD). The FRD was divided into four equal parts, T₂₅ (top 25%), T₅₀ (26–50%), T₇₅ (51–75%) and T₁₀₀ (76–100%). F₃ families derived from F₂ plants in T₂₅ were found to provide a higher frequency of selections for pod number than T₅₀, T₇₅ and T₁₀₀. The frequency of selections was higher in three-way than single crosses. Selection index based on physiological and yield components was more efficient in trapping F₂ plants providing selections in F₃ than the index based on yield components only. The results brought out the importance of bunch x bunch crosses as a complement to the usually advocated bunch x runner ones.     

Effect of selection intensity and population size on percent oil in maize,Zea mays L

Summary The effect of selection intensity and population size on the response to selection for percent oil in the grain of maize (Zea mays L.) was evaluated in a replicated experiment over ten cycles of selection. An open-pollinated variety, Armel's Reid Yellow Dent, was divided into subpopulations of 6,10 and 50 plants. Selection proportions of 17% and 5% were imposed upon each subpopulation. Selection was based on the percentage of oil in individual kernels as determined by wide-line nuclear magnetic resonance spectroscopy. As expected, total response to selection increased with larger population sizes and selection intensities. The concave shape of the response curves suggested that an appreciable part of the genetic variance can be attributed to additive genes at high initial frequencies, dominance genes at low initial frequencies, or to the generation of negative linkage disequilibrium due to selection. The consistently greater loss of vigor experienced by the more intensely selected populations reflects the enhancement of inbreeding due to artificial selection, an effect that increases with the intensity of selection. The results indicate that combined selection, based on kernels and using within- and amongfamily information, will be more efficient than other conventional selection procedures, including the normal combined scheme where selection is based on plants.Deceased     

The gametic algebra for polyploidy with several loci

In this paper it is shown that the genetic algebra of an infinitely large random mating population of polyploid individuals which differ at n linked loci, between which recombination may occur, is a genetic algebra.It has been assumed that at every locus there is a finite number of alleles and there is an arbitrary amount of double reduction.     

Effects of population size and linkage on optimal selection intensity

Following Robertson (1970a) it is generally considered that for mass selection the selected proportion that maximises ultimate response is 0.5. This prediction has been partly tested by different authors. Here we explicitly address the question using computer simulations of selection in finite populations with linkage. The results show that the response achieved is always lower than the one predicted by standard methods, and that optimum selection intensity may be much lower than predicted unless population size is small.     

Genetics of tassel branch number in maize and its implications for a selection program for small tassel size

Summary Tassel branch numbers of six crosses of maize (Zea mays L.) were analyzed to determine inheritance of this trait. Generation mean analyses were used to estimate genetic effects, and additive and nonadditive components of variance were calculated and evaluated for bias due to linkage. Both narrow-sense and broad-sense heritabilities were estimated. Additive genetic variance estimates were significant in five of the six crosses, whereas estimates of variance due to nonadditive components were significant in only three crosses. Additionally, estimates of additive variance components usually were larger than corresponding nonadditive components. There was no evidence for linkage bias in these estimates. Estimates of additive genetic effects were significant in four of six crosses, but significant dominance, additive × additive and additive × dominance effects also were detected. Additive, dominance, and epistatic gene action, therefore, all influenced the inheritance of tassel branch number, but additive gene action was most important. Both narrow-sense and broadsense heritability estimates were larger than those reported for other physiological traits of maize and corroborated conclusions concerning the importance of additive gene action inferred from analyses of genetic effects and variances. We concluded that selection for smalltasseled inbreds could be accomplished most easily through a mass-selection and/or pedigree-selection system. Production of a small-tasseled hybrid would require crossing of two small-tasseled inbreds. We proposed two genetic models to explain unexpected results obtained for two crosses. One model involved five interacting loci and the other employed two loci displaying only additive and additive × additive gene action.Journal Paper No. J-9231 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa 50011. Project No. 2152     

Segregation and conditional probability association of molecular markers with traits in autotetraploid alfalfa

The complications introduced by the autotetraploid, outcrossing nature of alfalfa (Medicago sativa L.) as related to detecting associations of marker loci and traits of interest are discussed, and a new method of detecting marker-trait associations is suggested. This method utilizes plant populations that are likely to have been produced through the plant breeding process: populations selected for one trait, and the base, unselected population. Marker allele frequency shifts between the populations are indicative of genomic regions involved in trait expression, and may indicate alleles that have reached the triplex or homozygous state and do not segregate in S₁ or F₁ populations. However, because many, perhaps hundreds, of sequential frequency comparisons are needed to detect fragments in significantly different proportions in the two populations, the type I error rate is very high. A resampling-based analysis method is proposed to address the concern of the type I error rate, and identify marker alleles associated with this trait of interest. The utility of marker-trait associations thus defined for identifying individual plants from heterogeneous populations was investigated through model-building and conditional probability studies. Factors investigated that influenced the utility of the marker associations and (in the base population) the frequencies of the trait and marker, and the frequencies of the markers in plants exhibiting the trait and in the plants not exhibiting the trait. The frequency of occurrence of a marker in undesirable plants profoundly influenced the efficiency with which the marker could be used to select desirable plants, however, under some circumstances, markers or combinations of markers can be highly efficient for selecting rare, desirable plants from a heterogeneous base population.     

Heterogeneous selection in subdivided populations

The dynamics of allele frequencies changing under migration and heterogeneous selection in a subdivided population are investigated. Using perturbation techniques, a stationary state is obtained when migration and selection are both small. Heterogeneous selection leads to a positive correlation between values of F-statistics and heterozygosities when these are compared among sets of subdivided populations. This contrasts with a negative value of the correlation obtained under Wright's classical model of homogeneous selection, and with the absence of correlation in the completely neutral situation.Research supported in part by NIH grants GM 28016 and GM 10452 and a grant from the John D. and Catherine T. MacArthur Foundation