Overlapping chromosomal regions for fertility traits and production traits in the Danish Holstein population

Before implementing selection based on quantitative trait loci (QTL) for fertility, it is important to determine the existence of correlated effects between the fertility QTL and QTL with effects on production traits. When a QTL is detected for a trait that is a composite of subtraits, it is of interest to validate which of the subtraits are affected by the QTL. Phenotypic and marker data were collected from 34 grandsire families from the Danish Holstein population. First, the trait data for "fertility treatments" were separated into their underlying subtraits: uterine infections, antibiotics placed in the placenta, and abortions. In addition, retained placenta was selected for analysis because it is related to uterine infections. A genome scan was performed using 416 microsatellite markers for the fertility treatment subtraits and retained placenta, and an additional genome scan for milk production traits conditional on the QTL regions for the subtraits and retained placenta was conducted. Second, we selected 24 genomic regions harboring QTL for fertility traits from a previous study. A QTL scan for milk production traits conditional on the selected regions was conducted. We found that 16 selected genomic regions containing a QTL for fertility (including the fertility treatment subtraits and retained placenta) also harbored QTL for milk yield or milk composition traits. Furthermore, 12 QTL regions corresponding to 9 different fertility traits (including the fertility treatment subtraits) did not harbor a QTL for milk production or milk composition traits; that is, the region was specific for the fertility trait. The genome scan for the fertility treatment subtraits did not correspond to the QTL found for fertility treatments. No QTL were detected for the subtrait abortion, however genome scans for retained placenta revealed 4 different QTL.

Heterogeneity of gene expression in stromal fibroblasts of human breast carcinomas and normal breast

Breast carcinoma invasion is associated with prominent alterations in stromal fibroblasts. Carcinoma-associated fibroblasts (CAF) support and promote tumorigenesis, whereas normal mammary fibroblasts (NF) are thought to suppress tumor progression. Little is known about the difference in gene expression between CAF and NF or the patient-to-patient variability in gene expression. Paired CAF and NF were isolated from six primary human breast carcinoma specimens. RNA was extracted from low-passage cultures of CAF and NF and analyzed with Affymetrix Human Genome U133 Plus 2.0 arrays. The array data were examined with an empirical Bayes model and filtered according to the posterior probability of equivalent expression and fold difference in expression. Twenty-one genes (27 probe sets) were up-regulated in CAF, as compared to NF. Known functions of these genes relate to paracrine or intracellular signaling, transcriptional regulation, extracellular matrix and cell adhesion/migration. Ten genes (14 probe sets) were down-regulated in CAF, including the pluripotency transcription factor KLF4. Quantitative RT-PCR analysis of 10 genes validated the array results. Immunohistochemical staining for three gene products confirmed stromal expression in terms of location and relative quantity. Surprisingly, the variability of gene expression was slightly higher in NF than in CAF, suggesting inter-individual heterogeneity of normal stroma.

Improvement in genetic evaluation of female fertility in dairy cattle using multiple-trait models including milk production traits

This study investigated the improvement in genetic evaluation of fertility traits by using production traits as secondary traits (MILK = 305-d milk yield, FAT = 305-d fat yield, and PROT = 305-d protein yield). Data including 471,742 records from first lactations of Denmark Holstein cows, covering the years of inseminations during first lactations from 1995 to 2004, were analyzed. Six fertility traits (i.e., interval in days from calving to first insemination, calving interval, days open, interval in days from first to last insemination, numbers of inseminations per conception, and nonreturn rate within 56 d after first service) were analyzed using single- and multiple-trait sire models including 1 or 3 production traits. Model stability was evaluated by correlation between EBV from 2 sub-data sets (DATA(A) and DATA(B)). Model predictive ability was assessed by the correlation between EBV from training data (DATA(A) or DATA(B)) and daughter performance (yield deviation, defined as average of daughter-records adjusted for nongenetic effects) from test data (DATA(B) or DATA(A)) in a cross-validation procedure, and correlation between EBV obtained from the whole data set (DATA(T)) and from a reduced data set (DATA(C1), which only contained the first crop daughters) for proven bulls. In addition, the superiority of the models was evaluated by expected reliability of EBV, calculated from the prediction error variance of EBV. Based on these criteria, the models combining milk production traits showed better model stability and predictive ability than single-trait models for all the fertility traits, except for nonreturn rate within 56 d after first service. The stability and predictive ability for the model including MILK or PROT were similar to the model including all 3 milk production traits and better than the model including FAT. In addition, it was found that single-trait models underestimated genetic trend of fertility traits. These results suggested that genetic evaluation of fertility traits would be improved using a multiple-trait model including MILK or PROT.

Comparison between a sire model and an animal model for genetic evaluation of fertility traits in Danish Holstein population

Comparisons between a sire model, a sire-dam model, and an animal model were carried out to evaluate the ability of the models to predict breeding values of fertility traits, based on data including 471,742 records from the first lactation of Danish Holstein cows, covering insemination years from 1995 to 2004. The traits in the analysis were days from calving to first insemination, calving interval, days open, days from first to last insemination, number of inseminations per conception, and nonreturn rate within 56 d after first service. The correlations between sire estimated breeding value (EBV) from the animal model and the sire-dam model were close to 1 for all the traits, and those between the animal model and the sire model ranged from 0.95 to 0.97. Model ability to predict sire breeding value was assessed using 4 criteria: 1) the correlation between sire EBV from 2 data subsets (DATA(A) and DATA(B)); 2) the correlation between sire EBV from training data (DATA(A) or DATA(B)) and yield deviation from test data (DATA(B) or DATA(A)) in a cross-validation procedure; 3) the correlation between the EBV of proven bulls, obtained from the whole data set (DATA(T)) and from a reduced set of data (DATA(C1)) that contained only the first-crop daughters of sires; and 4) the reliability of sire EBV, calculated from the prediction error variance of EBV. All criteria used showed that the animal model was superior to the sire model for all the traits. The sire-dam model performed as well as the animal model and had a slightly smaller computational demand. Averaged over the 6 traits, the correlations between sire EBV from DATA(A) and DATA(B) were 0.61 (sire model) versus 0.64 (animal model), the correlations between EBV from DATA(T) and DATA(C1) for proven bulls were 0.59 versus 0.67, the correlations between EBV and yield deviation in the cross-validation were 0.21 versus 0.24, and the reliabilities of sire EBV were 0.42 versus 0.46. Model ability to predict cow breeding value was measured by the reliability of cow EBV, which increased from 0.21 using the sire model to 0.27 using the animal model. All the results suggest that the animal model, rather than the sire model, should be used for genetic evaluation of fertility traits.

Genome scan detects quantitative trait loci affecting female fertility traits in Danish and Swedish Holstein cattle

Data from the joint Nordic breeding value prediction for Danish and Swedish Holstein grandsire families were used to locate quantitative trait loci (QTL) for female fertility traits in Danish and Swedish Holstein cattle. Up to 36 Holstein grandsires with over 2,000 sons were genotyped for 416 microsatellite markers. Single trait breeding values were used for 12 traits relating to female fertility and female reproductive disorders. Data were analyzed by least squares regression analysis within and across families. Twenty-six QTL were detected on 17 different chromosomes. The best evidence was found for QTL segregating on Bos taurus chromosome (BTA)1, BTA7, BTA10, and BTA26. On each of these chromosomes, several QTL were detected affecting more than one of the fertility traits investigated in this study. Evidence for segregation of additional QTL on BTA2, BTA9, and BTA24 was found.

Genetic analysis of days from calving to first insemination and days open in Danish Holsteins using different models and censoring scenarios

The objectives of this study were to estimate genetic parameters and evaluate models for genetic evaluation of days from calving to first insemination (ICF) and days open (DO). Data including 509,512 first-parity records of Danish Holstein cows were analyzed using 5 alternative sire models that dealt with censored records in different ways: 1) a conventional linear model (LM) in which a penalty of 21 d was added to censored records; 2) a bivariate threshold-linear model (TLM), which included a threshold model for censoring status (0, 1) of the observations, and a linear model for ICF or DO without any penalty on censored records; 3) a right-censored linear model (CLM); 4) a Weibull proportional hazard model (SMW); and 5) a Cox proportional hazard model (SMC) constructed with piecewise constant baseline hazard function. The variance components for ICF and DO estimated from LM and TLM were similar, whereas CLM gave higher estimates of both additive genetic and residual components. Estimates of heritability from models LM, TLM, and CLM were very similar (0.102 to 0.108 for ICF, and 0.066 to 0.069 for DO). Heritabilities estimated using model SMW were 0.213 for ICF and 0.121 for DO in logarithmic scale. Using SMC, the estimates of heritability, defined as the log-hazard proportional factor for ICF and DO, were 0.013 and 0.009, respectively. Correlations between predicted transmitting ability from different models for sires with records from at least 20 daughters were far from unity, indicating that different models could lead to different rankings. The largest reranking was found between SMW and SMC, whereas negligible reranking was found among LM, TLM, and CLM. The 5 models were evaluated by comparing correlations between predicted transmitting ability from different data sets (the whole data set and 2 subsets, each containing half of the whole data set), for sires with records from at least 20 daughters, and chi(2) statistics based on predicted and observed daughter frequencies using a cross validation. The model comparisons showed that SMC had the best performance in predicting breeding values of the 2 traits. No significant difference was found among models LM, TLM, and CLM. The SMW model had a relatively poor performance, probably because the data are far from a Weibull distribution. The results from the present study suggest that SMC could be a good alternative for predicting breeding values of ICF and DO in the Danish Holstein population.

Heterogeneity of gene expression in stromal fibroblasts of breast carcinomas and normal breast

Abstract #105

Background: The cancer microenvironment plays a critical role in tumor development and progression. Cancer associated fibroblasts (CAF) constitute a significant component of the tumor stroma and participate in reciprocal communication with the tumor cells. Information on differential gene expression specifically in stromal fibroblasts is sparse and data describing the variability of gene expression in CAF and normal fibroblasts (NF) is currently lacking. The purpose of this study was to identify genes differentially expressed in CAF and matched NF and to analyze the heterogeneity of gene expression profiles in the two cell types.
 Materials and methods: Fibroblast cell cultures were established from 6 patients with primary invasive breast cancer. Gene expression profiles were generated using oligonucleotide microarrays (Affymetrix HG-U133 Plus 2.0). Differentially expressed genes were ranked using Empirical Bayes modeling. A cut-off value of 0.005 was chosen for the posterior probability of equivalent expression. Lists of overexpressed genes were generated after eliminating genes with less than two-fold overexpression.
 Results: 17 genes were overexpressed in CAF compared to NF with known functions in paracrine and intracellular signaling, transcription regulation and extracellular matrix production. Using the same posterior probability cut-off, we identified 7 genes which were expressed at least two-fold higher in NF than in CAF. These genes have purported roles in steroid hormone metabolism, transcription, migration and cell signaling. Using semiquantitative RT-PCR and immunohistochemistry, we confirmed the over- and underexpression of a subset of 10 differentially expressed genes. The heterogeneity of gene expression in CAF vs. NF was compared with F-tests to determine variances. The estimated probability of NF gene expression variance being higher than CAF gene expression variance was 0.547 with a 95% confidence interval of 0.543 to 0.551 (p<0.0001), indicating that gene expression is more variable in NF than in CAF. By ranking the q-values of individual genes we identified 3 known genes, which show a significant difference in variance between CAF and NF (p<0.05).
 Conclusion: Altered gene expression in fibroblasts likely contributes to tumor growth and progression by enhancing ECM production, promoting stromal-epithelial paracrine signaling and altering steroid hormone metabolism. The inter-individual heterogeneity of gene expression in NF may indicate that the mammary stroma varies between individuals, supporting the hypothesis that the ability of the stroma to act as a barrier to cancer development and tumor progression may also be variable. Conversely, the heterogeneous gene expression in NF may be a reflection of a relative synchronization and uniformity of gene expression in CAF.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 105.

The application of random regression models in the genetic analysis of monthly egg production in turkeys and a comparison with alternative longitudinal models

Random regression models (RR) have become a popular methodology for the genetic study of longitudinal data since the last decade. The first objective of the current study was to investigate the application of RR models for the genetic analysis of egg production in turkeys. Data collected from a heavy dam line were used to estimate genetic parameters with 2 RR models, one having second-order Legendre polynomials as regression over time (RR2) and another with third-order polynomials (RR3). The second objective was to benchmark the performance of RR models with more conventional methods, so genetic parameters were reestimated using a multitrait (MT) and a repeatability model. To assess the model efficiency of predicting missing values, a reduced data set was used, and for each model, the predicted values of the deleted records were compared with the true values. The RR models were further compared against each other by eliminating the last period and estimating the MS error of the predictions for both models. The repeatability model had the poorest performance in predicting missing values. Heritability estimates from RR2 and MT models were close, whereas the RR3 model estimates were different. Both RR models demonstrated better prediction ability than the MT model. However, when RR models were compared solely, the RR2 model resulted in the smallest MS error. The results indicated that the RR3 model overfitted the data, suggesting that the choice of the appropriate polynomial order requires careful consideration. The present study illustrated that the application of RR models for the genetic analysis of egg production in turkeys is not only feasible but also offers a high accuracy of prediction.

Selection for litter size at day five to improve litter size at weaning and piglet survival rate

Selection for total number of piglets born (TNB) since 1992 has led to a significant increase in this trait in Danish Landrace and Danish Yorkshire but has also been accompanied by an increase in piglet mortality. The objective of this study was to estimate the genetic and phenotypic parameters for litter size and survival to find alternative selection criteria to improve litter size at weaning. Data from Landrace (9,300 litters) and Yorkshire (6,861 litters) were analyzed using REML based on a linear model including genetic effects of sow and service-sire. The estimates of heritability (based on the sow component) for TNB, number born alive (NBA), and number alive at d 5 after birth (N5D) and at weaning (about 3 wk, N3W) ranged from 0.066 to 0.090 in Landrace and 0.050 to 0.070 in Yorkshire. Genetic correlations between TNB and N3W were 0.289 in Landrace and 0.561 in Yorkshire, but between N5D and N3W the estimated genetic correlation was 0.995 in both populations. The approximate estimates of heritability for survival rate per litter at birth (SVB = NBA/TNB), from birth to d 5 (SV5 = N5D/NBA), and from d 5 to weaning (SVW = N3W/N5D) were 0.130, 0.131, and 0.023, respectively, in Landrace, and 0.095, 0.043, and 0.009, respectively, in Yorkshire. Genetic correlations between TNB and survival rates at different stages were negative. On the other hand, genetic correlations between N5D and survival rates and between N3W and survival rates were strongly or moderately positive, except for the correlations with SVW in Yorkshire. The results suggest that selection for N5D could be an interesting alternative to improve litter size at weaning and piglet survival for Danish Landrace and Danish Yorkshire.

Bayesian analysis of the linear reaction norm model with unknown covariates

The reaction norm model is becoming a popular approach for the analysis of genotype x environment interactions. In a classical reaction norm model, the expression of a genotype in different environments is described as a linear function (a reaction norm) of an environmental gradient or value. An environmental value is typically defined as the mean performance of all genotypes in the environment, which is usually unknown. One approximation is to estimate the mean phenotypic performance in each environment and then treat these estimates as known covariates in the model. However, a more satisfactory alternative is to infer environmental values simultaneously with the other parameters of the model. This study describes a method and its Bayesian Markov Chain Monte Carlo implementation that makes this possible. Frequentist properties of the proposed method are tested in a simulation study. Estimates of parameters of interest agree well with the true values. Further, inferences about genetic parameters from the proposed method are similar to those derived from a reaction norm model using true environmental values. On the other hand, using phenotypic means as proxies for environmental values results in poor inferences.

Foot Pad Dermatitis and Hock Burn in Broiler Chickens and Degree of Inheritance

A total of 2,118 birds from 2 strains were allocated to 12 groups of 93 to 100 each in 2 time-separated replicates. The development of foot pad dermatitis (FPD) and hock burn (HB) were recorded weekly from d 8 to slaughter on a set sample of live animals (7 per group). In addition, feet and hocks of all birds were investigated at slaughter at either 4, 6 (fast-growing strain), 8, or 10 (slow-growing strain) wk of age. Lesions were scored for both the left and right foot and classified according to a scale from 1 (no lesion) to 9 (very severe lesions) for FPD and from 1 (no lesion) to 3 (very severe lesions) for HB. No FPD lesions and very few low-grade HB lesions were found in chickens from the slow-growing strain. In the fast-growing strain, the first signs of FPD and HB were seen in wk 2. The incidence of both types of lesions increased thereafter. Foot pad dermatitis was more frequent in females (49 vs. 36%, P < 0.05). Body weight did not affect FPD, but more HB were found at higher BW (P < 0.01). Egg weight influenced neither FPD nor HB. Variance and covariance components were analyzed using a multivariate animal model, in which scores for FPD and HB were transformed into logarithmic scale. The analyses were carried out using restricted maximum likelihood algorithm. Heritabilities were estimated to be 0.31 +/- 0.12 (SE) for FPD, 0.08 +/- 0.08 for HB, and 0.38 +/- 0.13 for BW. Genetic correlations among these traits were low and nonsignificant. Phenotypic correlation between BW and FPD was low and nonsignificant and between BW and HB was 0.17 +/- 0.05 (P < 0.01). The relative high heritability of FPD and the low genetic correlation to BW suggested that genetic selection against susceptibility to FPD should be possible without negative effects on BW gain.

Activation of the stress protein response prevents the development of pulmonary edema by inhibiting VEGF cell signaling in a model of lung ischemia-reperfusion injury in rats

Lung endothelial damage is a characteristic morphological feature of ischemia-reperfusion (I/R) injury, although the molecular steps involved in the loss of endothelial integrity are still poorly understood. We tested the hypothesis that the activation of vascular endothelial growth factor (VEGF) cell signaling would be responsible for the increase in lung vascular permeability seen early after the onset of I/R in rats. Furthermore, we hypothesized that the I/R-induced pulmonary edema would be significantly attenuated in rats by the activation of the stress protein response. Pretreatment with Ad Flk-1, an adenovirus encoding for the soluble VEGF receptor type II, prevented I/R-mediated increase in lung vascular permeability in rats. Furthermore, the I/R-induced lung injury was significantly decreased by prior activation of the stress protein response with geldanamycin or pyrrolidine dithiocarbamate. In vitro studies demonstrated that VEGF caused an increase in protein permeability across primary cultures of bovine macro- and microvascular lung endothelial cell monolayers that were associated with a phosphorylation of VE- and E-cadherin and the formation of actin stress fibers. Activation of the stress protein response prevented the VEGF-mediated changes in protein permeability across these cell monolayers and reduced the phosphorylation of VE-and E-cadherins, as well as the formation of actin stress fibers in these cells.

Divergent Selection on Feather Pecking Behavior in Laying Hens Has Caused Differences Between Lines in Egg Production, Egg Quality, and Feed Efficiency

The correlated changes in egg production, egg quality, and feed efficiency (FE) due to selection for feather pecking (FP) were investigated by analyzing the data from an experiment including 2 divergently selected lines and a control line. The experiment was conducted with hens from 42 to 46 wk (hatch 1) and 39 to 43 wk (hatch 2) of age in the fifth generation of selection. The number of FP bouts per hour in the low FP line (LFP) was lower than the high FP line (HFP; 0.38 vs. 2.01), and total plumage score in line LFP was better than in line HFP (16.9 vs. 11.6). During the 4 wk, egg number and egg mass in line LFP were higher than those in HFP (24.4 vs. 18.3 and 1,223 vs. 1,132 g, respectively). On the other hand, line HFP had greater egg weight (60.7 vs. 59.2 g), albumen height (73.0 vs. 64.9 in Haugh units), shell thickness (38.1 vs. 37.0 mm), and yolk percentage (30.6 vs. 29.5%) than the LFP line. The control line was intermediate for those traits. The residual feed consumption (RFC) was highest in line HFP, lowest in line LFP, and intermediate in line C. Partial regressions of feed consumption (FC) on BW gain and egg mass were not significantly different among the 3 lines, whereas a significant difference in regression on metabolic BW (32.6 g/d in line LFP, 38.0 g/d in control line, and 43.4 g/d in line HFP) was observed. In addition, there was a negative regression of FC per day on plumage score (-1.73 g). The adjustment for plumage score accounted for 60% of the difference between regressions on metabolic BW in lines LFP and HFP. These results indicated that selection for FP has led to a change in egg production, egg quality, and FE. The better FE in line LFP resulted from a lower requirement for maintenance energy. The later was partly accounted for by a better plumage cover.

Variance components and selection response for feather-pecking behavior in laying hens

Variance components and selection response for feather pecking behavior were studied by analyzing the data from a divergent selection experiment. An investigation indicated that a Box-Cox transformation with power lambda = -0.2 made the data approximately normally distributed and gave the best fit for the model. Variance components and selection response were estimated using Bayesian analysis with Gibbs sampling technique. The total variation was rather large for the investigated traits in both the low feather-pecking line (LP) and the high feather-pecking line (HP). Based on the mean of marginal posterior distribution, in the Box-Cox transformed scale, heritability for number of feather pecking bouts (FP bouts) was 0.174 in line LP and 0.139 in line HP. For number of feather-pecking pecks (FP pecks), heritability was 0.139 in line LP and 0.105 in line HP. No full-sib group effect and observation pen effect were found in the 2 traits. After 4 generations of selection, the total response for number of FP bouts in the transformed scale was 58 and 74% of the mean of the first generation in line LP and line HP, respectively. The total response for number of FP pecks was 47 and 46% of the mean of the first generation in line LP and line HP, respectively. The variance components and the realized selection response together suggest that genetic selection can be effective in minimizing FP behavior. This would be expected to reduce one of the major welfare problems in laying hens.

Influence of early or late start of first feeding on growth and immune phenotype of broilers

1. The changes in body weight (BW) gain, immune phenotype and viability of commercial broilers, either given feed and water immediately after hatch or food-deprived for 24 or 48 h, were analysed in order to study the effect of early or late start of first feeding. 2. Chickens fed immediately had a 6.1% higher BW at slaughter age than those food-deprived for 48 h, while those chickens food-deprived for 24 h only had a 1.4% higher weight than those deprived for 48 h. 3. Those fed immediately and those food-deprived for 24 h did not differ significantly in BW. 4. Humoral immune status was measured as specific IgG antibody production and concentration of IgM and IgG in serum. Cellular immunological variables were the proportion of circulating leukocyte subpopulations and the relative expression of leukocyte surface markers, including the relative expression of Major Histocompatibility Complex (MHC) antigens. 5. Differences were found between the three feeding treatments in the relative expression of MHC class II molecules, the relative expression of BU-1 molecules, and the ratio of CD4:CD8 single positive cells. 6. For the MHC class II molecules, a lower expression was found on the surface of mainly B-cells in chickens fed immediately compared with the two other feeding regimes. 7. These results suggest that food deprivation for 48 h may be unfavourable to the growth, viability, and the immune performance of broilers, whereas deprivation for 24 h appears to be acceptable for growth and normal immunological performance.

Historical and contemporary multilocus population structure of Ascochyta rabiei (teleomorph: Didymella rabiei) in the Pacific Northwest of the United States

The historical and contemporary population genetic structure of the chickpea Ascochyta blight pathogen, Ascochyta rabiei (teleomorph: Didymella rabiei), was determined in the US Pacific Northwest (PNW) using 17 putative AFLP loci, four genetically characterized, sequence-tagged microsatellite loci (STMS) and the mating type locus (MAT). A single multilocus genotype of A. rabiei (MAT1-1) was detected in 1983, which represented the first recorded appearance of Ascochyta blight of chickpea in the PNW. During the following year many additional alleles, including the other mating type allele (MAT1-2), were detected. By 1987, all alleles currently found in the PNW had been introduced. Highly significant genetic differentiation was detected among contemporary subpopulations from different hosts and geographical locations indicating restricted gene flow and/or genetic drift occurring within and among subpopulations and possible selection by host cultivar. Two distinct populations were inferred with high posterior probability which correlated to host of origin and date of sample using Bayesian model-based population structure analyses of multilocus genotypes. Allele frequencies, genotype distributions and population assignment probabilities were significantly different between the historical and contemporary samples of isolates and between isolates sampled from a resistance screening nursery and those sampled from commercial chickpea fields. A random mating model could not be rejected in any subpopulation, indicating the importance of the sexual stage of the fungus both as a source of primary inoculum for Ascochyta blight epidemics and potentially adaptive genotypic diversity.

Molecular systematics of citrus-associated Alternaria species

The causal agents of Alternaria brown spot of tangerines and tangerine hybrids, Alternaria leaf spot of rough lemon and Alternaria black rot of citrus historically have been referred to as Alternaria citri or A. alternata. Ten species of Alternaria recently were described among a set of isolates from leaf lesions on rough lemon (Citrus jambhiri) and tangelo (C. paradisi × C. reticulata), and none of these isolates was considered representative of A. alternata or A. citri. To test the hypothesis that these newly described morphological species are congruent with phylogenetic species, selected Alternaria brown spot and leaf spot isolates, citrus black rot isolates (post-harvest pathogens), isolates associated with healthy citrus tissue and reference species of Alternaria from noncitrus hosts were scored for sequence variation at five genomic regions and used to estimate phylogenies. These data included 432 bp from the 5' end of the mitochondrial ribosomal large subunit (mtLSU), 365 bp from the 5' end of the beta-tubulin gene, 464 bp of an endopolygalacturonase gene (endoPG) and 559 and 571 bp, respectively, of two anonymous genomic regions (OPA1-3 and OPA2-1). The mtLSU and beta-tubulin phylogenies clearly differentiated A. limicola, a large-spored species causing leaf spot of Mexican lime, from the small-spored isolates associated with citrus but were insufficiently variable to resolve evolutionary relationships among the small-spored isolates from citrus and other hosts. Sequence analysis of translation elongation factor alpha, calmodulin, actin, chitin synthase and 1, 3, 8-trihydroxynaphthalene reductase genes similarly failed to uncover significant variation among the small-spored isolates. Phylogenies estimated independently from endoPG, OPA1-3 and OPA2-1 data were congruent, and analysis of the combined data from these regions revealed nine clades, eight of which contained small-spored, citrus-associated isolates. Lineages inferred from analysis of the combined dataset were in general agreement with described morphospecies, however, three clades contained more than one morphological species and one morphospecies (A. citrimacularis) was polyphyletic. Citrus black rot isolates also were found to be members of more than a single lineage. The number of morphospecies associated with citrus exceeded that which could be supported under a phylogenetic species concept, and isolates in only five of nine phylogenetic lineages consistently were correlated with a specific host, disease or ecological niche on citrus. We advocate collapsing all small-spored, citrus-associated isolates of Alternaria into a single phylogenetic species, A. alternata.