Pooled analysis of data from multiple quantitative trait locus mapping populations.

Quantitative trait locus (QTL) analysis on pooled data from multiple populations (pooled analysis) provides a means for evaluating, as a whole, evidence for existence of a QTL from different studies and examining differences in gene effect of a QTL among different populations. Objectives of this study were to: (1) develop a method for pooled analysis and (2) conduct pooled analysis on data from two soybean mapping populations. Least square interval mapping was extended for pooled analysis by inclusion of populations and cofactor markers as indicator variables and covariate variables separately in the multiple linear models. The general linear test approach was applied for detecting a QTL. Single population-based and pooled analyses were conducted on data from two F(2:3) mapping populations, Hamilton (susceptible) x PI 90763 (resistant) and Magellan (susceptible) x PI 404198A (resistant), for resistance to soybean cyst nematode (SCN) in soybean. It was demonstrated that where a QTL was shared among populations, pooled analysis showed increased LOD values on the QTL candidate region over single population analyses. Where a QTL was not shared among populations, however, the pooled analysis showed decreased LOD values on the QTL candidate region over single population analyses. Pooled analysis on data from genetically similar populations may have higher power of QTL detection than single population-based analyses. QTLs were identified by pooled analysis on linkage groups (LGs) G, B1 and J for resistance to SCN race 2 whereas QTLs on LGs G, B1 and E for resistance to SCN race 5 in soybean PI 90763 and PI 404198A. QTLs on LG G and B1 were identified in both PI 90763 and PI 404198A whereas QTLs on LG E and J were identified in PI 90763 only. QTLs on LGs G and B1 for resistance to race 2 may be the same or closely linked with QTLs on LG G and B1 for resistance to race 5, respectively. It was further demonstrated that QTLs on G and B1 carried by PI 90763 were not significantly different in gene effect from QTLs on LGs G and B1 in PI 404198A, respectively.

Identification of QTLs associated with resistance to soybean cyst nematode races 2, 3 and 5 in soybean PI 90763.

Soybean cyst nematode (SCN) is a major soybean pest throughout the soybean growing regions in the world, including the USA. Soybean PI 90763 is an important SCN resistance source. It is resistant to several SCN populations including races 2, 3 and 5. But its genetics of resistance is not well known. The objectives of this study were to: (1) confirm quantitative trait loci (QTLs) for resistance to SCN race 3 in PI 90763 and (2) identify QTLs for resistance to SCN races 2 and 5. QTLs were searched in Hamilton x PI 90763 F(2:3)populations using 193 polymorphic simple sequence repeats (SSRs) covering 20 linkage groups (LGs). QTLs for resistance to SCN were identified on LGs A2, B1, E, G, J and L. The same QTL was suggested for resistance to different SCN races where their 1-LOD support intervals of QTL positions highly overlapped. The QTL on LG G was associated with resistance to races 2, 3 and 5. The QTL on LG B1 was associated with resistance to races 2 and 5. The QTL on LG J was associated with resistance to races 2 and 3. The QTLs on LGs A2 and L were associated with resistance to race 3. The QTL on LG E was associated with resistance to race 5. We conclude that LGs A2 and B1 may represent an important distinction between resistance to SCN race 3 and resistance to SCN races 2 and 5 in soybean.

Soybean Cultivar and Foliar Fungicide Effects on Phomopsis sp. Seed Infection.

Phomopsis seed decay (PSD) caused by Phomopsis spp. can be severe when soybean seed producers in the southern United States use the early soybean production system (ESPS) to avoid late-July through early-September drought damage to soybean. The usefulness of this production system would be greater if developing seed could be protected from PSD by foliar application of fungicides or by planting Phomopsis spp.-resistant soybean lines. The objective of this research was to determine the affects of the fungicides benomyl and azoxystrobin applied to soybean, at various times, on percent Phomopsis spp. infection of seed in Asgrow 3834, a PSD-susceptible cultivar, and SS93-6012, a PSD-resistant soybean line, planted in mid-April. The percent Phomopsis spp. infection of Asgrow 3834 seed averaged over years was significantly less for the benomyl (0.28 kg a.i. ha-1) applied at R3 + R5 treatment (48.6% seed infection) than the control (52.8% seed infection) and significantly greater for the azoxystrobin (0.17 kg a.i. ha-1) applied at R3 + R5 treatment (61.6% seed infection) than the control (52.8% seed infection). This method of managing PSD will not be acceptable to soybean growers. The percent of Phomopsis spp. infection of Asgrow 3834 seed averaged over years (52.8% seed infection) was significantly greater than for line SS93-6012 (2.8% seed infection). There were no differences in percent Phomopsis spp. infection of SS93-6012 seed between the control (2.8% seed infection) and benomyl treatment (4.0% seed infection). The most effective method for PSD management was to plant a resistant soybean line. Line SS93-6012 will be useful in breeding programs focused on developing high yielding PSD-resistant cultivars.

Planting Date and Cultivar Effects on Soybean Yield, Seed Quality, and Phomopsis sp. Seed Infection.

Incidence of Phomopsis seed decay is frequently high and quality low in seed from early-maturing maturity group III and IV soybean cultivars planted in early to mid-April in the southern United States. Cultivars resistant to this disease have not been available until the recent release of germ plasm lines SS 93-6012 and SS 93-6181. Our objective was to determine the effects of planting dates with these lines and one Phomopsis seed decay-susceptible soybean cultivar, Asgrow 3834, on seed infection by Phomopsis spp. and on yield and the correlation between percentage of Asgrow 3834 infected with Phomopsis spp. and seed quality. Generally, yields averaged over years were significantly greater for mid-April than mid-June plantings, and yields of cultivars were similar within a planting date. Soybean lines SS 93-6012 and SS 93-6181 were highly resistant to Phomopsis seed decay compared with the susceptible cultivar, Asgrow 3834. There was a significant, negative correlation between germination of seed from mid-April plantings of Asgrow 3834 and percentage of these seed infected with Phomopsis spp. Moreover, there were significant correlations between fatty acid composition of Asgrow 3834 seed and the percentage of these seed infected with Phomopsis spp. This altered composition of fatty acids may be responsible for reduced quality of oil derived from seed infected with this fungus. Phomopsis seed decay-resistant soybean lines SS 93-6012 and SS 93-6181 should be useful in breeding programs focused on developing high-yielding cultivars resistant to this disease.

Use of a rat model to evaluate tall fescue seed infected with introduced strains of Neotyphodium coenophialum.

Experimental cultivars of the pasture grass tall fescue are infected with unique strains of the fungal endophyte Neotyphodium coenophialum, which produce low concentrations of ergot alkaloids. A rat model was evaluated as a tool for rapid, initial screening of experimental cultivars considered to be nontoxic. Rats were fed diets that included seed from experimental cultivars of tall fescue with introduced strains of N. coenophialum and a toxic control diet containing seed of the cultivar Kentucky 31 (KY31), with its endemic strain of N. coenophialum. Rats were preconditioned to a nontoxic diet and then fed treatment diets for 13 days with 5 days at thermoneutrality (21 degrees C) followed by 8 days under heat stress (31 degrees C). For most of the 13-day treatment period, rats fed KY31 exhibited depressed daily intake compared to those fed diets of cultivars with introduced endophytes (P < 0.05). In addition, rats fed KY31 exhibited significantly less weight than rats on other diets after heat treatment was imposed. For all initial trials and repeated trials, total intake and total gain calculated at the end of each trial were the most consistent indicators of toxicity.

Genomic in situ hybridization (GISH) reveals high chromosome pairing affinity between Lolium perenne and Festuca mairei.

Intergeneric hybridizations have been made between species of Lolium and Festuca. It has been demonstrated, largely through conventional cytogenetic analysis, that the genomes of the two genera are related, however, much information is lacking on exactly how closely related the genomes are between the two species. We applied genomic in situ hybridization (GISH) techniques to the F1 hybrids of tetraploid Festuca mairei with a genomic constitution of M1M1M2M2 and diploid Lolium perenne with a genomic constitution of LL. It was shown in the triploid hybrids (LM1M2) that the chromosomes of M1 and M2 from F. mairei could pair with each other, and it was further discovered that L chromosomes of L. perenne paired with M1 and M2 chromosomes. Our results showed that meiocytes of Lolium-Festuca are amenable to GISH analysis, and provided direct evidence for the hypothesis that the chromosomes of Lolium and Festuca may be genetically equivalent and that reciprocal mixing of the genomes may be possible.

Genome mapping of polyploid tall fescue (Festuca arundinacea Schreb.) with RFLP markers.

Genetic mapping using molecular markers such as restriction fragment length polymorphisms (RFLPs) has become a powerful tool for plant geneticists and breeders. Like many economically important polyploid plant species, detailed genetic studies of hexaploid tall fescue (Festuca arundinacea Schreb.) are complicated, and no genetic map has been established. We report here the first tall fescue genetic map. This map was generated from an F2 population of HD28-56 by 'Kentucky-31' and contains 108 RFLP markers. Although the two parental plants were heterozygous, the perennial and tillering growth habit, high degree of RFLP, and disomic inheritance of tall fescue enabled us to identify the segregating homologous alleles. The map covers 1274 cM on 19 linkage groups with an average of 5 loci per linkage group (LG) and 17.9 cM between loci. Mapping the homoeologous loci detected by the same probe allowed us to identify five homoeologous groups within which the gene orders were found to be generally conserved among homoeologous chromosomes. An exception was homoeologous group 5, in which only 2 of the 3 homoeologous chromosomes were identified. Using 12 genome-specific probes, we were able to assign several linkage groups to one of the three genomes (PG1G2) in tall fescue. All the loci detected by the 11 probes specific to the G1 and/or G2 genomes, with one exception, identified loci located on 4 chromosomes of two homoeologous groups (LG2a, LG2c, LG3a, and LG3c). A P-genome-specific probe was used to map a locus on LG5c. Comparative genome mapping with maize probes indicated that homoeologous group 3 and 2 chromosomes in tall fescue corresponded to maize chromosome 1. Difficulties and advantages of applying RFLP technology in polyploids with high levels of heterozygosity are discussed.

Phylogeny of tall fescue and related species using RFLPs.

The wild species of tall fescue (Festuca arundinacea var.genuina Schreb.) represent a wide range of genetic variation and constitute potential germplasm for tall fescue improvement. Our objective was to evaluate genome specificity of the previously-identified DNA probes and to examine the phylogenetic relationship of tall fescue with six related species by using RFLP data. A total of 29 DNA probes from aPstI-genomic library of tall fescue were hybridized toEcoRI-orHindIII-digested DNA of 32 plants from sixFestuca species and fromLolium perenne L. Fifteen probes hybridized to all seven species. The remaining 14 probes showed differential hybridization patterns (i.e., ±), especially at the diploid and tetraploid levels. This hybridization pattern reflected genome divergence in these species. The DNA probes will be useful markers in breeding programs involving interspecific and intergeneric hybridization. Cluster analyses were performed using the average genetic distances calculated with the RFLP data from 53 probe-enzyme combinations. Generally, genotypes from the same species were grouped in the same cluster. These data indicated that tall fescue has a close relationship withF. pratensis Huds. (diploid),F. arundinacea var.glaucescens Boiss. (tetraploid), andL. perenne L. (diploid) and thatFestuca pratensis andL. perenne had the closest degree of relationship.

Using plant breeding and genetics to overcome the incidence of grass tetany.

Plant breeders developing cultivars to minimize the hazards of grass tetany are concentrating largely on increasing herbage Mg concentrations in cool-season (C3) grasses. Significant genetic variation has been found for Mg, Ca and K concentrations within C3 grass species studied to date. For most C3 forage grass species, heritability estimates are highest for Mg, slightly lower for Ca and lowest for K concentrations. The largest genotype x environmental interactions are found for K values, whereas small environmental effects have been observed for Mg and Ca values. No C3 forage grass cultivar has been developed to date that would eliminate hypomagnesemia. Grass breeders need to develop more experimental C3 plant populations that have high Mg and Ca concentrations. These experimental synthetics with genetically altered mineral concentrations need to be fed to ruminants susceptible to grass tetany to determine whether grass tetany can be eliminated or reduced. Limited feeding trials using ruminants show that improved animal performance can be expected when feeding forage grasses bred for higher Mg concentrations.

Theory and application of half-sib matings in forage grass breeding.

Half-sib (HS) matings, including polycross, topcross, and open-pollination, are useful in the breeding of cross-pollinated sexual perennial forage grasses to evaluate general combining ability of parental clones for synthetic cultivar development, recombine selected entries in recurrent selection programs, and obtain quantitative genetic information. The objective of this paper is to review uses of HS matings in breeding of these forage grasses with emphasis on theoretical aspects related to quantitative genetic analysis.Polycross mating with adequate replications and sufficient isolation is recommended over topcross and open-pollinated mating schemes in generating HS families for quantitative genetic studies. For the estimates of many genetic parameters to be valid, the parents must be a random sample from a random mating population in linkage equilibrium. Precision of the estimates depends on adequante sampling of the population of genotypes and environments used for evaluation.Analyses of variance on HS families and parental clones, and analysis of covariance between parent and offspring provide useful information on additivity of genetic effects and on genotype × environment interactions. Classical, narrow-sense heritability on an individual plant basis can be estimated and used to predict genetic gain from individual (mass) selection, providing that within family variance is estimable. If the forage breeder uses family selection, heritability should be estimated according to the proposed unit of selection. The selection unit must be specified in terms of numbers of replications, years, and locations. Polycross HS family selection can be readily adapted to a population improvement program in forage grass breeding.Narrow-sense heritability can also be estimated by doubling the linear regression coefficient of HS prog eny means on parental means. When HS families and parents are evaluated together in replicated experiments under similar environments, covariance analysis is recommended to remove the genotype × environment interaction covariance and environmental error covariance between parent and offspring, since these nongenetic covariances may result in inflated heritability estimates and misleading expected genetic gains from selection.

Genetic variability of mineral concentrations in Festuca arundinacea Schreb.

Nine randomly chosen clones of tall fescue (Festuca arundinacea Schreb.) were mated in all possible combinations to determine the nature of genetic variation for Mg, Ca, K, and P concentrations in a broad genetic base population. General combining ability mean squares were significant for most variables, whereas specific combining ability mean squares were not significant in most instances indicating that additive genetic variance was more important. Genotype x year interactions were significant for most variables, suggesting that selection should be evaluated over many environments. Broad-sense heritability estimates based on parental and progeny variance components were generally high for P, K, Ca, and Mg but low for the ratio K/(Ca + Mg). Narrow-sense heritabilities for these minerals were close to the broad sense values since the additive genetic variance was the largest component of the total genetic variation. Correlations between mineral concentrations and herbage dry matter yield were low. It was concluded that adequate genetic variation exists to improve mineral concentration without altering herbage dry matter yields.