Homozygosity and Heterozygosity in three Populations of Rivulus marmoratus

Rivulus marmoratus is a self-fertilizing hermaphroditic fish found in the tropical Atlantic as populations of homozygous clones, with the exception of a single site in Belize where male fish are abundant and heterozygosity is the norm. The presence of male fish apparently leads to outcrossing and heterozygosity, but males have been found in limited numbers in other populations which are homozygous. DNA fingerprinting now reveals that the Belize population has remained heterozygous, with a high proportion of males (20–25%), for several years. In addition, two newly discovered populations with a lower percentage of males (1–2%) are reported from the Bahamas and Honduras. One of these populations (Bahamas) consists of homozygous clones, while the other (Honduras) displays a limited proportion of heterozygosity. The Honduras population is only the second outcrossing population known in this species, and the limited heterozygosity seen here may reflect the lower proportion of males.     

A reciprocal relationship between heterozygosities of the phosphogiucomutase and glucose phosphate isomerase loci

Examination of the published literature shows that generally there is an association between heterozygosities of the phosphoglucomutase and glucose phosphate isomerase loci such that either heterozygosity of one locus is low when heterozygosity of the other is high; or both loci have low heterozygosities. There appears to be a general constraint that prevents both loci from being highly heterozygous together. An exception to this general rule is reported and the significance of this discovery is discussed.     

Extensive heterozygosity at three enzyme loci in hybrid sunfish populations

Hybrid populations of sunfishes were produced in two different ponds, and the frequencies of allelic isozyme phenotypes were determined for three enzyme systems—malate dehydrogenase (NAD), esterases, and tetrazolium oxidase—in order to estimate the extent of heterozygosity at four different genetic loci. Interspecific F₁ hybrid fry (red-ear male × bluegill female) were produced in vitro. These fry were stocked in ponds at the free-swimming stage. When 1 year old, the F₁ hybrids produced a large F₂ hybrid population. Successful hybrid reproduction occurred each year thereafter. In one pond, a 1-year-old F₂ population exhibited all three isozyme phenotypes (red-ear, F₁, bluegill) at most loci in the approximate ratio of the 1:2:1 expected. In a second pond, 5-year-old individuals of the F₂ generation were morphologically like the F₁ and were all heterozygous for the enzyme loci studied. This unusual degree of heterozygosity in the older F₂ population appeared to be the result of differential survival of mature heterozygous individuals and not the result of early embryonic lethality. The increased heterozygosity at these unlinked loci was assumed to reflect the condition at other genetic loci in the F₂ hybrids. Several possible mechanisms are advanced to explain this apparent heterosis.This research was supported by NSF grant GB-16425 (G.S.W.) and by funds from the Illinois Natural History Survey (W.F.C.).     

The direct assessment of genetic heterozygosity through scent in the mouse

The role of individual genetic heterozygosity in mate choice is the subject of much current debate. Several recent studies have reported female preference for more heterozygous males, but the mechanisms underlying heterozygote preference remain largely unknown. Females could favor males that are more successful in intrasexual competition, but they could also assess male heterozygosity directly at specific polymorphic genetic markers. Here, we use a breeding program to remove the intrinsic correlation between genome-wide heterozygosity and two highly polymorphic gene clusters that could allow direct assessment of heterozygosity through scent in mice: the major histocompatibility complex (MHC) and the major urinary proteins (MUPs). When other sources of variation are controlled and intrasexual competition is minimized, female mice prefer to associate with MUP heterozygous over MUP homozygous males. MHC heterozygosity does not influence preference, and neither does heterozygosity across the rest of the genome when intrasexual competition between males is restricted. Female mice thus assess male heterozygosity directly through multiple MUP isoforms expressed in scent signals, independently of the effects of genome-wide heterozygosity on male competitiveness. This is the first evidence that animals may use signals of genetic heterozygosity that have no direct association with individual vigour.     

HL-A antigens in North American black families

The polymorphic HL-A histocompatibility system has been studied in North American black families. The family studies show that haplotype frequencies differ between black and white populations. Seven haplotypes (W28,W5; W28,W17; W28, undefined four; W23,W5; W19,W5; undefined LA,W5; and undefined LA, undefined four) were significantly more frequent in blacks than whites, while haplotypes 1,8 and 3,7 were significantly less frequent. Some of these differences may be accounted for by differences in gene frequencies between the two groups; other differences may be explained by linkage disequilibrium in the white population. No significant linkage disequilibrium between the LA and FOUR loci was found in the black population.     

Variation of Loci Encoding Homologous Enzymes in the Evolutionary Series of Vertebrates

A study of variability of 11 allozyme loci (sAat, G3pdh, Gpi, sIdh, Ldh-A, Ldh-B, sMdh, sMe, sSod, Pgdh, and Sdh) in the evolutionary series of vertebrates from Cyclostomat to Mammalia revealed that (1) in vertebrates, these loci encoding multimeric enzymes are characterized by different heterozygosity levels, the extremes of which (represented by loci Ldh-A and Pgdh) differ from each other more than by a factor of 4; (2) classes of vertebrates markedly differed from one another in genetic variation; lower Tetrapoda are characterized by the highest level of genetic polymorphism, the classes representing the margins of the phyletic line—primitive (Cyclostomata and Chondrchthyes) and advanced (Aves and Mammalia)—have minimum heterozygosity levels, whereas Osteichthyes are characterized by intermediate heterozygosity level; (3) in the evolutionary series of vertebrates, heterozygosity varies rather independently in the groups of loci characterized by low, medium, and high variability. These patterns are explained in the context of intraorganismic factors: integration of mono- and polygenic traits (primarily, body size and ontogeny rate) and evolutionary specialization.     

CCR5Δ32 Genotypes in a German HIV-1 Seroconverter Cohort and Report of HIV-1 Infection in a CCR5Δ32 Homozygous Individual

Background

Homozygosity (Δ32/Δ32) for the 32 bp deletion in the chemokine receptor 5 (CCR5) gene is associated with strong resistance against HIV infection. Heterozygosity is associated with protection of HIV-1 disease progression.

Methodology/Principal Findings

We genotyped a population of 737 HIV-positive adults and 463 healthy controls for the CCR5Δ32 deletion and found heterozygous frequencies of 16.2% (HIV-negative) and 17.5% (HIV-positive) among Caucasian individuals. Analysis of CCR5Δ32 influence on disease progression showed notably lower viral setpoints and a longer time to a CD4 count of <200 µl⁻¹ in seroconverters heterozygous for the deletion. Furthermore, we identified one HIV-positive man homozygous for the Δ32 deletion.

Conclusions/Significance

The protective effect of CCR5 Δ32 heterozygosity is confimed in a large cohort of German seroconverters. The HIV-infected CCR5 Δ32 homozygous individual, however, displays extremely rapid disease progression. This is the 12th case of HIV-infection in this genotype described worldwide.     

The joint variability of the growth-weight characteristics and biochemical gene markers in newborn infants

A relationship between heterozygosity of 6 biochemical loci and variability of 4 anthropometric traits at birth has been studied in 304 boys and girls from Moscow population. All 4 traits in boys are positively correlated with the number of loci for which they are heterozygous. The values of all the traits in girls are highest in homozygous individuals. In order to reduce the number of variables the principal component analysis is applied. Boys and girls with average level of heterozygosity turned out to be closest to the corresponding population averages of morphological traits. The results are discussed in terms of 3 models: Lerner's concept of genetical homeostasis, additive and overdominance polygenic models. It is concluded that an average level of heterozygosity is optimal for a population.     

Patterns of DNA Variability at X-Linked Loci in Mus Domesticus

Introns of four X-linked genes (Hprt, Plp, Glra2, and Amg) were sequenced to provide an estimate of nucleotide diversity at nuclear genes within the house mouse and to test the neutral prediction that the ratio of intraspecific polymorphism to interspecific divergence is the same for different loci. Hprt and Plp lie in a region of the X chromosome that experiences relatively low recombination rates, while Glra2 and Amg lie near the telomere of the X chromosome, a region that experiences higher recombination rates. A total of 6022 bases were sequenced in each of 10 Mus domesticus and one M. caroli. Average nucleotide diversity (π) for introns within M. domesticus was quite low (π = 0.078%). However, there was substantial variation in the level of heterozygosity among loci. The two telomeric loci, Glra2 and Amg, had higher ratios of polymorphism to divergence than the two loci experiencing lower recombination rates. These results are consistent with the hypothesis that heterozygosity is reduced in regions with lower rates of recombination, although sampling of additional genes is needed to establish whether there is a general correlation between heterozygosity and recombination rate as in Drosophila melanogaster.     

Correlations between fitness and heterozygosity at allozyme and microsatellite loci in the Atlantic salmon, Salmo salar L

The relationship between heterozygosity at genetic markers (six allozyme and eight microsatellite loci), and fluctuating asymmetry (FA), length and weight was investigated in two samples of Atlantic salmon (Salmo salar L.) with different timings of first active feeding (early (EA) and late (LA) salmon). This trait had previously been related to fitness. EA fish show smaller values of FA, are longer, heavier and are more heterozygous at allozyme loci than are conspecific LA fish. Also within both samples, heterozygosity at allozyme loci was inversely related to FA and was positively related to weight and length. However, no significant differences in microsatellite diversity (heterozygosity and mean d2 measurements) were observed between samples (EA vs LA). Furthermore, no association was observed between the variability at microsatellite loci and FA, weight or length within each sample. These results suggest that allozyme loci, in themselves, influence fitness components, rather than associations arising from associative overdominance.     

New microsatellite loci confirm hybrid origin,parthenogenetic inheritance,and mitotic gene conversion in the gynogenetic Amazon molly (Poecilia formosa)

We describe the first microsatellite loci for the gynogenetic Amazon molly, Poecilia formosa, an all‐female species arisen through hybridization of the bisexual species Poecilia mexicana and Poecilia latipinna. The loci showed one to six alleles and an expected heterozygosity between zero and 0.75. As expected with parthenogenetic inheritance, most loci were either constantly homozygous (five loci) or constantly heterozygous (eight loci). For six loci, both heterozygotes and homozygotes occurred. This and the fact that some loci only showed alleles of one of the ancestral species could indicate genome homogenization through mitotic gene conversion. Our new loci conformed to the hybrid origin of Amazon molly and are also applicable to both ancestral bisexual species.     

Toward the development of highly homozygous diploid potato lines using the self-compatibility controlling Sli gene.

Cultivated diploid potatoes (2n = 2x = 24) are self-incompatible, but can be altered to become self-compatible using the Sli gene. Previously, a diploid clone 97H32-6 was selfed up to S3 using the Sli gene. To explore the usefulness of the Sli gene for the production of highly homozygous diploid potatoes, 2 S4 families from the above 97H32-6 derived S3 lines (inbred series A) and 3 S5 families by continuous selfings from a different F1 (= S0) plant (inbred series B) were developed. The level of heterozygosity and the location of heterozygous loci on the genetic map were investigated using RFLP and AFLP markers. The average heterozygosity levels of the originally heterozygous loci decreased from 100% in S0 to 10.7% in S4 and 8.6% in S5 (inbred series A and B, respectively). The average rate of reduction in heterozygosity per generation (38.4% and 38.5% for inbred series A and B, respectively) was lower than the theoretically expected rate (50%). However, none of the loci or chromosome sections was exclusively heterozygous in the advanced self-progeny. Thus, highly homozygous and seed-propagated diploid potatoes could be obtained by repeated selfing using the Sli gene.     

微卫星评价牙鲆雌核发育二倍体纯合性

采用8个微卫星座位分别对牙鲆减数雌核发育二倍体家系和卵裂雌核发育二倍体家系的纯合性进行检验。卵裂雌核发育二倍体在所有检测座位全部纯合。减数雌核发育二倍体在部分座位发生纯合,但未发现在所有座位全部纯合的个体,在Poli9TUF、Poli9-8TUF、Poli11TUF、Poli13TUF、Poli23TUF、Poli30TUF、Poli123TUF和Poli130TUF座位,杂合子比例分别为1·0000、1·0000、0·1944、0·9459、0·8611、1·0000、0·7778和0·8000,平均杂合子比例为0·8224。由此表明,牙鲆除了Poli11TUF外,在其余7个座位均具有很高的重组率。研究结果显示,牙鲆卵裂雌核发育二倍体一代即可形成纯合子;而减数雌核发育二倍体由于具有较高的重组率,使其与母本的遗传同质性较高。     

Mining and validating grape (<Emphasis Type="Italic">Vitis</Emphasis> L.) ESTs to develop EST-SSR markers for genotyping and mapping

Grape expressed sequence tags (ESTs) are a new resource for developing simple sequence repeat (SSR) functional markers for genotyping and genetic mapping. An integrated pipeline including several computational tools for SSR identification and functional annotation was developed to identify 6,447 EST-SSR sequences from a total collection of 215,609 grape ESTs retrieved from NCBI. The 6,447 EST-SSRs were further reduced to 1,701 non-redundant sequences via clustering analysis, and 1,037 of them were successfully designed with primer pairs flanking the SSR motifs. From them, 150 pairs of primers were randomly selected for PCR amplification, polymorphism and heterozygosity analysis in V. vinifera cvs. Riesling and Cabernet Sauvignon, and V. rotundifolia (muscadine grape) cvs. Summit and Noble, and 145 pairs of these primers yielded PCR products. Pairwise comparisons of loci between the parents Riesling and Cabernet Sauvignon showed that 72 were homozygous in both cultivars, while 70 loci were heterozygous in at least one cultivar of the two. Muscadine parents Noble and Summit had 90 homozygous SSR loci in both parents and contained 50 heterozygous loci in at least one of the two. These EST-SSR functional markers are a useful addition for grape genotyping and genome mapping.     

Modification du caryotype par une inversion péricentrique à l'état homozygote chez l'Amphibien Urodèle Pleurodeles waltlii Michahelles

A cytogenetic study on four generations of the newt Pleurodeles waltlii has resulted in a stock homozygous for a pericentric inversion in chromosomes no. 6.-The chromosomal rearrangement has first been detected at the heterozygous state in a female resulting from a cross between a normal female and a male treated with X rays. — The rearranged chromosome is very easily recognizable under direct microscopic investigation. The heterozygotes and the homozygotes for the aberration grow normally; thus, the inversion constitutes a nuclear marker which can be readily used.     

The components of life-history traits variation in Daphnia magna population

The variation of six growth and reproduction traits in the parthenogenetic clones of Daphnia magna and its relationships with the genotypes at 5 isozyme loci were studied under controlled conditions at three food concentrations. A significant genetic component of age at maturity, growth rate and fecundity variation was detected. Nested ANOVA revealed the influences of the genotypes of the isozyme loci, that are more pronounced at the high food concentration. In some cases the genotype-environment interactions were found.The variation of body length at 6 days and total number of offspring includes a significant heterozygosity — environment interaction. The most heterozygous clones show the least differences in life history traits between food conditions.Life-history traits heritability, genotype-environment interactions and different reproductive strategies of the clones are discussed.     

Tissue Matching and Early Rejection of Cadaveric-Donor Renal Allografts: The Importance of Unidentified Donor Antigens

Tissue typing has been reviewed in a series of 100 technically successful cadaveric-donor kidney grafts. The criterion of transplant failure was immunological rejection causing total loss of function within three months of operation.No significant correlation was observed between matching grade and graft failure due to early acute rejection. This is attributed to the failure to detect at least one “LA” or “4” antigen (as defined in our laboratory), representing a potential incompatibility, in 89% of the grafts, and in the remaining 11% to the lack of an available recipient with identical “LA” and “4” typing. Undetected antigens on the donor are usually incompatible, and probably these incompatibilities unfavourably influence early graft survival.If the results of cadaveric-donor renal transplantation are to equal those of transplantation from well-matched living related donors it will be necessary to type with sera which can recognize individually all HL-A antigens, including those not yet identified, and to create an international pool of over 1,000 potential recipients.     

Identification of one X‐linked and five autosomal microsatellite loci in Carabus violaceus (Coleoptera,Carabidae) and their applicability to related taxa

We characterize six microsatellite loci from the ground beetle Carabus violaceus. The polymorphism of the loci was assessed in 46 individuals from one population. The number of alleles ranges between three and eight, and the observed heterozygosities between 0.46 and 0.76. All males are homozygous for locus CVI08106CMPG, whereas most females are heterozygous. This suggests that this locus is situated on the X chromosome. Tests in eight different species of ground beetles showed that four loci could be amplified in C. coriaceus and one each in C. glabratus, C. nemoralis, C. problematicus and Abax parallelepipedus.     

Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays

Loss of heterozygosity (LOH) of chromosomal regions bearing tumor suppressors is a key event in the evolution of epithelial and mesenchymal tumors. Identification of these regions usually relies on genotyping tumor and counterpart normal DNA and noting regions where heterozygous alleles in the normal DNA become homozygous in the tumor. However, paired normal samples for tumors and cell lines are often not available. With the advent of oligonucleotide arrays that simultaneously assay thousands of single-nucleotide polymorphism (SNP) markers, genotyping can now be done at high enough resolution to allow identification of LOH events by the absence of heterozygous loci, without comparison to normal controls. Here we describe a hidden Markov model-based method to identify LOH from unpaired tumor samples, taking into account SNP intermarker distances, SNP-specific heterozygosity rates, and the haplotype structure of the human genome. When we applied the method to data genotyped on 100 K arrays, we correctly identified 99% of SNP markers as either retention or loss. We also correctly identified 81% of the regions of LOH, including 98% of regions greater than 3 megabases. By integrating copy number analysis into the method, we were able to distinguish LOH from allelic imbalance. Application of this method to data from a set of prostate samples without paired normals identified known regions of prevalent LOH. We have developed a method for analyzing high-density oligonucleotide SNP array data to accurately identify of regions of LOH and retention in tumors without the need for paired normal samples.     

The cytogenetic systems of grasshoppers and locusts

The australian plague locust (2n=23 male, 24 female) is distinctive in possessing three pairs of two-armed, short autosomes (S₉, S₁₀ and S₁₁). In two of these pairs (S₉, S₁₀) these arms are a constant feature but in the shortest (S₉) pair most individuals are either heterozygous for them or else are homozygous telocentric. Coupled with this five of the heterozygous individuals give evidence of occasional short-arm detachment.—In all the S-pairs the shorter of the two arms is invariably heterochromatic in character and in the S₉ and S₁₁ shows a bi- or tri-partite sub-structure which suggests they may have originated by tandem duplication. — Three of the other autosomes (L₂, M₃ and M₆) also have small heterochromatin(het)-blocks associated with them. At first meiotic prophase these frequently associate with the univalent X chromosome which itself displays an unconventional pattern of allocycly, its centric end appearing negatively heteropycnotic from leptotene through diplotene.—At metaphase I the het-blocks on the telocentric autosomes sometimes transform into swollen, negatively heteropycnotic, segments equivalent in appearance to that shown by the entire X at this stage. It is suggested that these puff-like structures represent an inter-chromosomal position effect conditional upon prior X/A het-association at first prophase.