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PubMed1999

History of plant population genetics.

This review of plant population genetics focuses on the genetic foundations of the processes that have led to documentable improvements in cultivated plants since the earliest domestications took place perhaps 13,000 years ago. Nearly all human civilizations have depended heavily on inbreeding plants (particularly wheat, barley, soybeans and other inbreeding legumes), as well as outbreeding vegetatively propagated species (white potatoes, yams) as their dietary standbys. The principal exception is maize (corn), an annual seed-produced outbreeder in nature. It is noteworthy that maize joined wheat, rice, and barley as a truly major crop worldwide only after its conversion to self-pollination combined with hybridization between favorably interacting inbred lines increased yield of maize several-fold in the twentieth century.

Agriculture↗
PubMed2001

Consanguinity and prereproductive mortality in the Utah Mormon population.

To test the effects of parental consanguinity on mortality among offspring, inbreeding coefficients were estimated for 303,675 members of the Utah Mormon population who were born between 1847 and 1945. Although consanguinity has been relatively rare in this population, the large sample size permitted the identification of more than 3,500 inbred offspring. Among the offspring of unrelated parents, 13.2% died before the age of 16. Significant elevations in prereproductive mortality were seen among the offspring of first-cousin marriages (22%) and among the offspring of closer unions (32%). The cor- responding relative risks are 1.70 (95% confidence limits = 1.52, 1.91) and 2.41 (95% confidence limits = 1.59, 3.41), respectively. Other categories of relationship did not produce significant elevations in offspring mortality. Similar results were obtained when a case-control approach was used to remove the effects of socioeconomic variation. Consistent with many other studies of populations with low consanguinity rates, this population experienced a relatively high absolute increase in mortality among the offspring of first-cousin marriages (9%). Preliminary evidence is offered for the hypothesis that mortality differentials are larger in populations with low inbreeding and low mortality because nongenetic causes of death do not obscure the effects of consanguinity.

Christianity↗
PubMed1989

Familial factors in Alzheimer's disease (IMAGE project). A case-control study in the Saguenay-Lac-St-Jean region (Quebec, Canada).

Alzheimer's disease is now recognized as a major public health problem. Many hypotheses have tried to explain the etiology of Alzheimer's disease and, among them, genetic factors are considered one of the most plausible. A case-control study of familial factors, including sex distribution, age at onset, birth order, parental age, fertility, mortality, inbreeding and kindship, was conducted on 130 clinically diagnosed patients born in the Saguenay-Lac-St-Jean region (Quebec, Canada). The cases were screened by the IMAGE project. Our results showed that most factors studied are not associated with Alzheimer's disease. Inbreeding was found to be slightly increased in the Alzheimer group. Kindship was higher in the Alzheimer group than in the control groups, therefore confirming that familial predisposition is a very important risk factor.

Adult↗
PubMed1977

A demographic approach to population structure in Gyoda and Hasuda, Japan.

The mean inbreeding coefficients for Gyoda and Hasuda cities were 0.00295 for 600 couples and 0.00320 for 621 couples, respectively. The mean inbreeding coefficient decreased and the mean marital distance increased with a more recent year of marriage. The mean distances and its standard deviations between birthplaces of mates, father-offspring, mother-offspring, and sibs are 53.95 +/- 159.30 km, 43.38 +/- 174.29 km, 37.61 +/- 131.32 km and 9.42 +/- 66.39 km, respectively for the Gyoda population. These values are 98.49 +/- 270.77 km, 87.60 +/- 249.91 km, 60.05 +/- 193.63 km, and 16.36 +/- 64.64 km, respectively for the Hasuda population. The dimensionality of migration seems to be one.

Consanguinity↗
PubMed1978

Population structure in Kanoya population, Japan.

The mean inbreeding coefficients found for Minami-cho (366 couples) and Shinsei-cho (511 couples) were 0.00307 and 0.00191, respectively. The mean inbreeding coefficient decreased and the mean marital distance increased as the year of marriage becomes more recent. The mean distances and their standard deviations between birthplaces of mates, father-offspring, mother-offspring, and sibs are 69.05 +/- 229.64, 73.09 +/- 246.66, 49.81 +/- 158.43, and 39.53 +/- 159.51 km, respectively, at Minami-cho. These values are 188.45 +/- 387.05, 187.79 +/- 562.59, 148.26 +/- 326.35, and 73.93 +/- 225.92 km, respectively, at Shinsei-cho. The dimensionality of migration is closest to one dimension.

Consanguinity↗
PubMed1985

Variability of genetic load with changing socio-cultural environment.

Variability in genetic load has been studied against their contrasting socioeconomic and cultural backgrounds in two endogamous populations, namely, the well-off Brahmins and the low income Jalaris of Visakhapatnam, India. The A (genetic and environmental damage) and B (hidden genetic damage) estimates are higher in Jalaris. Decreased A estimates indicate the better medical care in Brahmins; the value of B could be low since many of the deaths in consanguineous families due to infectious diseases are now rarer. The genetic load (B/A ratio) indicates that the average gamete carries 0.057 and 2.123 deleterious genes, respectively, in Brahmins and Jalaris, which, if made homozygous, would kill an individual before reproductive age. The load is 35 times higher in Jalaris; this may be due to their higher inbreeding level. Contrasting socioeconomic differences and meagre medical aid might add another bias towards relatively higher B/A in Jalaris. In general the observed genetic load in both populations are lower than in other studies which may be due to gradual elimination of deleterious genes by continued practice of inbreeding.

Consanguinity↗
PubMed1995

Reproductive impairment in the Florida panther: nature or nurture?

Many of the remaining members of the endangered Florida panther (Felis concolor coryi) population suffer from one or more of a variety of physiological, reproductive, endocrine, and immune system defects including congenital heart defects, abnormal sperm, low sperm density, cryptorchidism, thyroid dysfunction, and possible immunosuppression. Mercury contamination, determined to be the cause of death of a female panther in 1989, was presented as the likely cause of thyroid dysfunction. As genetic diversity in the species was less than expected, all of the other abnormalities have been attributed to inbreeding. However, exposure to a variety of chemical compounds, especially those that have been identified as environmental endocrine disrupters (including mercury, p,p'-DDE, and polychlorinated biphenyls), has elicited all of the listed abnormalities in other species. A number of these contaminants are present in South Florida. An exposure pathway has been identified, and evidence presented in this paper, including the fact that there appears to be no significant difference between serum estradiol levels in males and females, suggests that many male panthers may have been demasculinized and feminized as a result of either prenatal or postnatal exposure. Thus, regardless of the effects of inbreeding, current evidence seems to indicate that environmental contaminants may be a major factor contributing to reproductive impairment in the Florida panther population.

Animals↗
PubMed2004

Socioeconomic, demographic, and geographic variables affecting the diverse degrees of consanguineous marriages in Spain.

In a population the inbreeding coefficient alpha is determined by the relative incidence of the various degrees of consanguineous marriages--uncle-niece or aunt-nephew (C12), first cousin (C22), first cousin once removed (C23), second cousin (C33)--which may be related to temporal, geographic, demographic, and economic factors. Using published information from Spain corresponding to urban and rural areas, in this article we seek to establish how each specific relationship behaves with respect to geographic, demographic, and socioeconomic factors, to determine differential urban-rural patterns, and to study whether the diverse types of consanguineous matings relate homogeneously to these factors. For this purpose we performed multiple regressions in which the dependent variables were the different degrees of consanguinity previously selected and the independent variables were geographic, demographic, and economic factors. Our results indicate that the various types of consanguineous marriages in Spain are more conditioned by geographic, demographic, and economic variables than by the inbreeding level alpha (the coefficient of determination was between 0.22 and 0.72; the maximum for alpha was 0.35). A regional pattern exists in Spain and corresponds to close and to remote kinship, which may be mainly related to economic and family factors. Close relationships appear to be more associated with economic variables, whereas second-cousin marriages correspond largely to rural areas of the Spanish Central Plateau.

Catholicism↗
PubMed2004

Population genetics of the wild yeast Saccharomyces paradoxus.

Saccharomyces paradoxus is the closest known relative of the well-known S. cerevisiae and an attractive model organism for population genetic and genomic studies. Here we characterize a set of 28 wild isolates from a 10-km(2) sampling area in southern England. All 28 isolates are homothallic (capable of mating-type switching) and wild type with respect to nutrient requirements. Nine wild isolates and two lab strains of S. paradoxus were surveyed for sequence variation at six loci totaling 7 kb, and all 28 wild isolates were then genotyped at seven polymorphic loci. These data were used to calculate nucleotide diversity and number of segregating sites in S. paradoxus and to investigate geographic differentiation, population structure, and linkage disequilibrium. Synonymous site diversity is approximately 0.3%. Extensive incompatibilities between gene genealogies indicate frequent recombination between unlinked loci, but there is no evidence of recombination within genes. Some localized clonal growth is apparent. The frequency of outcrossing relative to inbreeding is estimated at 1.1% on the basis of heterozygosity. Thus, all three modes of reproduction known in the lab (clonal replication, inbreeding, and outcrossing) have been important in molding genetic variation in this species.

Base Sequence↗
PubMed1997

The nature of selection on the major histocompatibility complex.

Only natural selection can account for the extreme genetic diversity of genes of the major histocompatibility complex (MHC). Although the structure and function of classic MHC genes is well understood at the molecular and cellular levels, there is controversy about how MHC diversity is selectively maintained. The diversifying selection can be driven by pathogen interactions and inbreeding avoidance mechanisms. Pathogen-driven selection can maintain MHC polymorphism based on heterozygote advantage or frequency-dependent selection due to pathogen evasion of MHC-dependent immune recognition. Empirical evidence demonstrates that specific MHC haplotypes are resistant to certain infectious agents, while susceptible to others. These data are consistent with both heterozygote advantage and frequency-dependent models. Additional research is needed to discriminate between these mechanisms. Infectious agents can precipitate autoimmunity and can potentially contribute to MHC diversity through molecular mimicry and by favoring immunodominance. MHC-dependent abortion and mate choice, based on olfaction, can also maintain MHC diversity and probably functions both to avoid genome-wide inbreeding and produce MHC-heterozygous offspring with increased immune responsiveness. Although this diverse set of hypotheses are often treated as competing alternatives, we believe that they all fit into a coherent, internally consistent thesis. It is likely that at least in some species, all of these mechanisms operate, leading to the extreme diversification found in MHC genes.

Animals↗
PubMed2003

Spurious genotypes in female nematodes resulting from contamination with male DNA.

Females of many invertebrates contain stored sperm or fertilized eggs or both, causing potential genotyping errors. We investigated errors caused by male DNA contamination by amplifying 5 microsatellites in DNA isolated from various tissue types in the nematode Ascaris lumbricoides. We observed additional alleles in 30/135 uterus-derived samples when compared with muscle controls, resulting in 20/135 (15%) incorrect genotypes and an underestimation of inbreeding. In contrast, we observed additional alleles in only 5/143 ovary-derived samples, resulting in 4/143 (3%) incorrect genotypes and no significant influence on inbreeding estimates. Because uterus constitutes approximately 17% of a female's organ weight, a substantial proportion of samples isolated from female tissue may contain male-derived DNA. Male contamination is easily avoided when using large nematodes such as A. lumbricoides. However, we urge caution for studies using DNA isolated from small invertebrates that store sperm or fertilized eggs or both.

Animals↗
PubMed2001

The newly inbred cohen diabetic rat: a nonobese normolipidemic genetic model of diet-induced type 2 diabetes expressing sex differences.

The newly inbred Cohen diabetic rat is an exceptional experimental model of diet-induced type 2 diabetes mellitus that is the result of secondary inbreeding nearly 30 years after it originally had been established. Animals from the original colony were selectively inbred by stringent criteria for 10 additional generations, bringing overall inbreeding to >50 generations. The metabolic phenotypes of the resulting contrasting strains, designated as the Cohen diabetic-sensitive (CDs) and -resistant (CDr) rats, were characterized. The phenotype of the CDs strain that was fed a regular diet consisted of fasting normoglycemia, normal glucose tolerance to intraperitoneal glucose loading, normal fasting insulin levels, and a normal insulin response to glucose loading. In contrast, CDs rats that were fed a custom-prepared high-sucrose low-copper diabetogenic diet became overtly diabetic: fasting glucose levels were normal or elevated, and the blood glucose insulin response to glucose loading was markedly abnormal. CDr rats that were fed a regular or diabetogenic diet did not develop diabetes and maintained normal glucose tolerance and insulin secretion. A striking sex difference was observed in CDs rats that were fed a diabetogenic diet: males had a lower growth rate and a more severe glucose intolerance pattern than females. Gonadectomy shortly after weaning did not prevent the development of the diabetic phenotype in its early phase in either sex but markedly attenuated its expression in males at a later phase, abolishing the sex differences. Alternate-day feeding, as opposed to daily feeding, also attenuated the metabolic phenotype in males. The development of the diabetic phenotype in CDs rats that were fed a diabetogenic diet was not accompanied by obesity or hyperlipidemia. The genetic profile of the strains was established using 550 microsatellite markers evenly distributed throughout the rat genome. The rate of homozygosity within strain was > or = 96%. The rate of polymorphism between the contrasting strains was 43%. We conclude that the metabolic phenotypes of the rebred colony of CDs and CDr rats and their genetic makeup render the Cohen diabetic rat a useful experimental model that is highly suitable for studying the interaction between nutritional-metabolic environmental factors and genetic susceptibility (sensitivity and resistance) for the development of type 2 diabetes. The model is also distinctively useful for investigating the effect of sex on the expression of the diabetic phenotype.

Animals↗
PubMed1994

Genetic analysis of calving date in Miles City Line 1 Hereford cattle.

A model for genetic analysis of calving date was proposed and variance components, genetic trends, and fixed effects for calving date were estimated in the Miles City Line 1 Hereford cattle population. There were 951 pedigree records that predated 1935, when data collection began, and 4,692 subsequent recorded calving dates through 1989. The statistical model included fixed linear continuous effects for inbreeding of calf and inbreeding of dam, discrete fixed effects for year, sex of calf, and age and previous parity of dam, and random sources of variation for individual (calf) and maternal additive genetic effects, and environmental effects of dams, mating groups, and residuals. All effects were estimated simultaneously by derivative-free procedures for REML. Male calves were born 1.58 +/- .40 d later than female calves. Cows failing to wean a calf in the previous year calved 2.81 +/- .81 d earlier than cows that had weaned a calf. Other fixed effects were small. Variance components (d2) were 23.0 for individual additive genetic effects, 5.8 for maternal additive genetic effects, 9.2 for maternal permanent environmental effects, 11.8 for contemporary group effects, and 161.3 for residual effects. Environmental trend was +.17 d/yr and individual additive genetic trend was -.07 d/yr. No maternal additive genetic trend was detected. These results do not encourage the use of calving day as a selection criterion for improving fertility of beef cattle.

Animals↗
PubMed1994

Evaluation of cytoplasmic genetic effects in Miles City Line 1 Hereford cattle.

Mixed-model techniques were used to evaluate the importance of cytoplasmic genetic effects on growth traits in beef cattle. The data used were records on birth weight (BWT, n = 4,716), preweaning average daily gain (PREADG, n = 4,428), and postweaning average daily gain (POSTADG, n = 3,476) collected from 1935 through 1989 in a closed line of Hereford cattle (Miles City Line 1). Selection criterion was adjusted yearling weight. Cytoplasmic genetic effects were evaluated as both potential fixed and random genetic effects. Cytoplasmic sources (n = 26) were determined based on the foundation female in the maternal lineage of each animal. All foundation females were at least five generations removed from any descendant that produced a performance record. An animal model was used to account for all nuclear additive genetic variation among animals. Direct additive effects were estimated for all traits. Maternal additive and permanent environmental effects were estimated for BWT and PREADG. Fixed effects included year of birth, age of dam, sex of calf, and regressions on inbreeding of calf, inbreeding of dam, and age off postweaning gain test (POSTADG only). When cytoplasm was fit as a fixed effect, F-tests for cytoplasmic effects were not significant (P = .10 to .99) for any trait. Inclusion of cytoplasmic source (fixed) in the statistical model reduced residual standard deviations less than .1%. Variance components for cytoplasmic genetic effects were estimated simultaneously with variance components for direct, maternal, direct-maternal covariance, and maternal permanent environment using REML techniques. Cytoplasmic source accounted for .40, .00 and .00% of the phenotypic variance for BWT, PREADG, and POSTADG, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1996

Characterization of DNA polymorphisms in three populations of hereford cattle and their associations with growth and maternal EPD in line 1 herefords.

Three populations of Hereford cattle differing in inbreeding levels and genetic potential for growth were genotyped for seven DNA polymorphisms. The populations were compared to determine differences in allele frequency and genetic variation. Significant differences in allele frequency among the populations were found at six of the seven polymorphisms genotyped, and average genetic variation differed as expected when inbreeding levels were considered. Effects of several polymorphisms on growth and maternal EPD were evaluated for one population (Miles City Line 1 Herefords) using regression analysis. Substitution of a B allele for an A allele of the kappa-casein polymorphism accounted for significant decreases in direct birth weight and maternal 180-d gain from birth to weaning EPD explaining 15% and 8%, respectively, of EPD variability. Several other significant effects accounting for small portions of EPD variability were also detected.

Alleles↗
PubMed1997

Influence of dominance relationships on the estimation of dominance variance with sire-dam subclass effects.

Two data sets from the USDA Livestock and Range Research Laboratory were analyzed to study dominance variance and the influence of dominance relationships. The first consisted of 4,155 birth weight (3,884 weaning weight) records of inbred USDA Line 1 Herefords. The second consisted of 8,065 birth weight (7,380 weaning weight) records from a line-cross experiment with five lines. Two models were used. Both included fixed effects of year-sex of calf and age of dam, and covariates for calving date, inbreeding of animal, and inbreeding of dam. For the second set, additional covariates were line composition and heterozygosity coefficients. Random effects were direct and maternal additive genetic, maternal permanent environment, sire-dam subclass, and residual. Model 1 considered sire-dam subclasses unrelated. Model 2 related sire-dam subclasses with a parental dominance relationship matrix. Variance components were estimated using REML. Differences between estimates with Model 1 and 2 were unimportant except for dominance variance. For the first data set, estimates with Model 2 of relative genetic direct and maternal variances, direct-maternal correlation, permanent environment, and dominance variances for birth weight were .35, .13, -.02, .03, and .25, respectively, and they were .39, .11, .04, .06 and .14 for the second data set. For weaning weight, the first data set estimates were .20, .15, -.37, .19, and .11, respectively, and they were .16, .20, -.07, .18, and .18 for the second data set. Changes, decreases and increases, in estimates of dominance variances may be due to increased information from relationships and family types other than full-sibs. The assumption of unrelated sire-dam subclasses might not be appropriate for estimation of dominance variance in populations with many dominance relationships among sire-dam classes.

Animals↗
PubMed1997

Benefit of multiple trait selection to increase reproductive traits: experimental evidence from golden hamsters.

Fifteen generations of selection were conducted to study responses for litter size at birth (LSB), weight at weaning of standardized litter (LWW), and individual body weight at 8 wk of age (BW8) using golden hamsters as an experimental model for pigs. The experiment involved three lines: selection on an aggregate breeding value of LSB, LWW, and BW8 (line W); selection on an aggregate breeding value of LSB and LWW (line R); and a randomly selected control (line C). Selection in W and R was based on breeding values from a multiple trait animal model. Restricted maximum likelihood with an animal model was used to estimate genetic parameters and genetic trends. Heritability estimates for LSB, LWW, and BW8 were .10, .47, and .52, respectively, and genetic correlations between traits were all positive. The mean estimated breeding value (EBV) for LSB in generation 15 was +2.2 pups in W and R. The mean EBV for LWW in generation 15 was +318 g for W and +174 g for R, and for BW8 means were +64 g and +24 g, respectively. Average inbreeding at generation 16 was 13.4, 19.5, and 8.0% for W, R, and C, respectively. Including BW8 in the selection criterion reduced inbreeding and had a beneficial effect on selection responses in LSB, LWW, and BW8.

Animals↗
PubMed1999

Two-stage selection strategies utilizing marker-quantitative trait locus information and individual performance.

Short- and long-term response to marker-assisted selection in two stages was studied using a stochastic simulation of a closed nucleus herd for beef production. First-stage selection was carried out within families based on information at a fully additive quantitative trait locus (QTL). Second-stage selection strategies were based on 1) individual phenotype, 2) individual phenotype precorrected for QTL, 3) a selection index incorporating phenotype and QTL information, 4) a standard animal model BLUP, and 5) a selection index incorporating marker-QTL information and standard animal model BLUP on records precorrected for QTL. All strategies were efficient in moving the favorable allele at the QTL to fixation, but they differed in the time to reach fixation. Mass selection was less efficient in changing allele frequencies than BLUP. Discounted accumulated response, accounting for the time response was realized and inflation rate, was proposed to rank strategies and to elude the conflict between short- and long-term response in marker-assisted selection. Discounted accumulated response at a time horizon of 20 yr for alternative two-stage selection strategies was compared with conventional BLUP carried out in second stage only. Within-family selection increased discounted accumulated response by more than 11% using Strategy 4 and by up to 12% using Strategy 5 at an inflation rate of 2%. The percentage increase in response was less for highly heritable traits and when the proportion of additive variance explained by the QTL was small. Strategy 5 gave larger response with reduced inbreeding. This strategy also resulted in the lowest cost-benefit ratio, requiring less genotyping per unit of response. Cost-benefit ratio for discounted genotyping and for discounted in vitro production of embryos for traits with low heritability was two to four times that for traits with high heritability. The use of first-stage selection slightly increased the level of inbreeding for both mass (Strategy 1) and BLUP selection (Strategies 4 and 5).

Animals↗