Preliminary evidence of segregation distortion in the SLA system

The segregation of 11 well-defined SLA haplotypes was investigated in 40 Land-race and 48 Large White Danish and Swiss litters. Among the 11 haplotypes, the segregation of one (SLA 20–8.2.11) deviated significantly from the expected 1: 1 segregation ratio in back-cross families. Tests indicated that these families were homogeneous with respect to segregation distortion, although the distortion was more pronounced in litters sired by heterozygous Danish boars than by heterozygous Swiss boars and Danish and Swiss sows. The data presented do not allow any definite conclusion about the cause of the segregation distortion. The possibility of the distortion being caused either by a complex similar to the T/t-complex found in mouse and contemplated in man or directly by the SLA region is discussed.     

The swine histo compatibility system SLA: serological studies in the common Swiss and Danish swine breeds

Alloantisera were produced in common Swiss and Danish swine breeds by immunization with leucocytes or skin-grafts. Out of the 126 antisera, 66 were chosen for further study based on titrations employing lymphocytes from unrelated pigs typed with French SLA antisera (Vaiman, Chardon & Renard, 1979). The 66 selected antisera and the French reagents defining 26 SLA specificities were used to type lymphocytes from 595 unrelated pigs of the common Swiss and Danish breeds. The reaction-patterns of the French, Swiss and Danish antisera were adequately correlated for the French SLA specificities Nos FJ 2, 3, 6, 7, 8, 9, 11, 14, 19, 20 and 24 and for the haplotypes FJ 15.1.18 and FJ 5.4. In addition, a cluster of correlated Danish and Swiss antisera characterized a new specificity, provisionally designated CPH 31. This specificity was frequent in the Danish Landrace pigs.
Using the reagents identified in this report, the segregation of SLA markers was studied. Back-cross families demonstrated segregation of 15 distinct SLA haplotypes of which 14 are common in French Landrace or Large White. Differences were found in haplotype frequencies in both the Swiss and the Danish Landrace and Large White breeds.     

The swine histocompatibility system SLA: serological studies in the common Swiss and Danish swine breeds

Alloantisera were produced in common Swiss and Danish swine breeds by immunization with leucocytes or skin-grafts. Out of the 126 antisera, 66 were chosen for further study based on titrations employing lymphocytes from unrelated pigs typed with French SLA antisera (Vaiman, Chardon & Renard, 1979). The 66 selected antisera and the French reagents defining 26 SLA specificities were used to type lymphocytes from 595 unrelated pigs of the common Swiss and Danish breeds. The reaction-patterns of the French, Swiss and Danish antisera were adequately correlated for the French SLA specificities Nos FJ 2, 3, 6, 7, 8, 9, 11, 14, 19, 20 and 24 and for the haplotypes FJ 15.1.18 and FJ 5.4. In addition, a cluster of correlated Danish and Swiss antisera characterized a new specificity, provisionally designated CPH 31. This specificity was frequent in the Danish Landrace pigs. Using the reagents identified in this report, the segregation of SLA markers was studied. Back-cross families demonstrated segregation of 15 distinct SLA haplotypes of which 14 are common in French Landrace or Large White. Differences were found in haplotype frequencies in both the Swiss and the Danish Landrace and Large White breeds.     

Evidence for the Tf locus being associated with an early lethal factor in a strain of pigs

The frequencies of three co-dominant alleles Tf ^A, Tf ^B and Tf ^c controlling the serum transferrin locus in native and exotic breeds of pig in the United Kingdom are shown. Matings between different transferrin genotypes and segregation of the transferrin alleles in piglets from 131 litters are also recorded.
In eleven litters from matings within a closely related group of animals heterozygous for the Tf ^c allele, no offspring of the Tf ^c/ Tf ^c genotype were born. Matings between heterozygous related boars believed to be carrying a lethal factor linked to the Tf locus and heterozygous unrelated sows of the Saddleback breed, resulted in offspring of the Tf ^c/ Tf ^c genotype being born.
An excess of heterozygote genotypes was found in all litters from matings between animals heterozygous for the Tf ^c allele. In all these litters the average litter size was 0.5 piglets less per litter than the average for all other litters studied. For the eleven litters from matings involving closely related animals heterozygous for the Tf ^c allele, the average litter size was 1.4 piglets less per litter than the average for all other litters.
The possibility of an early lethal factor being linked to the Tf locus in this family of pigs is discussed.     

RFLP analysis of SLA haplotypes in Swiss large white and American Hampshire pigs using SLA class I and class II probes

Summary

Restriction fragment length polymorphism (RFLP) analyses of swine leukocyte antigen (SLA) class I and class II genes from Swiss Large White and American Hampshire families were performed using porcine DNA probes. Class I and class II RFLPs associated with the serologically‐defined haplotypes SLA H1, H8, H16 and H24 and with serotypes SLA 15, 16; SLA 14; and SLA 6, SB 19, were identified. Seven allelic class I RFLP patterns were observed. For genes in the SLA class II region, six allelic RFLP patterns of DQA and DQB; five allelic RFLP patterns of DRA; and seven allelic RFLP patterns of DRB were observed. The serologically‐defined H8 haplotype was subtyped based on differences in class II RFLPs.     

Assignment of MHC in swine to chromosome 7 by in situ hybridization and serological typing

Mapping of the MHC in swine (SLA) was achieved by direct in situ hybridization to chromosome preparations. We took advantage of the fact that the cDNA probe coding for class I HLA-B7 antigen cross-hybridizes with swine genomic DNA. By nick-translation, 35S nucleotides were incorporated to a specific activity of 2,7 10(7) cpm/ug. Analysis of 91 randomly selected labeled metaphases revealed highly significant labeling on chromosome 7. The SLA complex is most probably located at the proximal half of the long arm, as indicated in families carrying a modified chromosome 7 and heterozygous for SLA. The abnormal chromosome was always inherited with a specific haplotype whereas the other parental haplotypes were found in association with the normal 7.     

Microsatellite diversity and crossover regions within homozygous and heterozygous SLA haplotypes of different pig breeds

Our aim was to investigate microsatellite (MS) diversity and find crossover regions at 42 polymorphic MS loci in the swine leukocyte antigen (SLA) genomic region of 72 pigs with different well-defined homozygous and heterozygous SLA haplotypes. We analyzed the genetic polymorphisms of 42 MS markers in 23 SLA homozygous-heterozygous, common pig breeds with 12 SLA serological haplotypes and 49 National Institutes of Health (NIH) and Clawn homozygous-heterozygous miniature pigs with nine SLA serological or genotyped haplotypes including four recombinant haplotypes. In comparing the same and different haplotypes, both haplospecific patterns and allelic variations were observed at the MS loci. Some of the shared haplotype blocks extended over 2 Mb suggesting the existence of strong linkage disequilibrium (LD) in the entire SLA region. Crossover regions were easily defined by the MS markers within the class I and/or III region in the NIH and Clawn recombinant haplotypes. The present haplotype comparison shows that our set of MS markers provides a fast and cost-efficient alternative, or complementary, method to the serological or sequence-based determination of the SLA alleles for the characterization of SLA haplotypes and/or the crossover regions between different haplotypes.     

Testing Two Possible Mechanisms for Gametic Association in Human: Frozen Haplotypes and Segregation Distortion

Two possible mechanisms for the development and maintenance of gametic association have been subject to test using family studies (HLA typed) and direct analysis of two linked markers in individual sperm. The mechanisms are: (1) haplotypes frozen against recombination and (2) balanced segregation distortion. In the study of 1320 families, 86 individuals were identified in the offspring of whom recombination was confirmed or suspected. These individuals displayed allele frequencies of HLA similar to the others in the study, but had significantly different haplotype frequencies. In general, they displayed reduced (or absent) frequencies for the more common haplotypes. Similarly, in the study of meiotic products, recombination was observed in the individual whose HLA phenotypes suggested rare haplotypes, but not in the other individual. Both results were of marginal significance. When the family data were used to test for segregation distortion at HLA-DR, only a marginally significant result was found. However, when the data were classified according to the sex of the parent, a highly significant result was found in females, but not in males. Male segregation distortion was found in the sperm analysis, but was only of marginal statistical significance. The concordant results of two different experimental systems suggest that both mechanisms remain feasible explanations of the gametic associations in this area of the genome, although of the two, segregation distortion is preferable on theoretical grounds.     

Low Frequency of Mouse T Haplotypes in Wild Populations Is Not Explained by Modifiers of Meiotic Drive

t haplotypes are naturally occurring forms of mouse chromosome 17 that show non-Mendelian transmission from heterozygous +/t males. In laboratory studies, transmission ratios of >=0.90 or higher are typically observed. With transmission ratios of this level, theoretical analyses predict high frequencies of t haplotypes (~ 75%) in wild populations. In contrast, empirical frequencies of only 15-25% are typically found. This has led to the suggestion that modifiers of drive may play a role in reducing t frequencies. We have measured transmission ratio distortion (TRD) levels in wild +/t mice to examine this hypothesis. TRD was very high in both litters collected from wild-caught pregnant females, and in wild litters bred in the laboratory (mean = 0.9). Contrary to the results of other studies, we found no difference in TRD levels between semilethal and lethal t haplotypes nor between litters conceived from cycling or postpartum estrus. We found three litters with aberrantly low TRDs that were all multiply sired, although the role this might play in natural populations is unknown. These findings show a general absence of modifiers of drive in natural populations and suggest that other factors are responsible for the low observed frequencies of wild t haplotypes.     

Molecular characterization of swine leukocyte antigen gene diversity in purebred Pietrain pigs

The porcine major histocompatibility complex (MHC) harbors the highly polymorphic swine leukocyte antigen (SLA) class I and II gene clusters encoding glycoproteins that present antigenic peptides to T cells in the adaptive immune response. In Austria, the majority of commercial pigs are F ₂ descendants of F ₁ Large White/Landrace hybrids paired with Pietrain boars. Therefore, the repertoire of SLA alleles and haplotypes present in Pietrain pigs has an important influence on that of their descendants. In this study, we characterized the SLA class I ( SLA‐1 , SLA‐2 , SLA‐3 ) and class II ( SLA‐DRB1 , SLA‐DQB1 , SLA‐DQA ) genes of 27 purebred Pietrain pigs using a combination of the high‐resolution sequence‐based typing (SBT) method and a low‐resolution (Lr) PCR‐based method using allele‐group, sequence‐specific primers (PCR‐SSP). A total of 15 class I and 13 class II haplotypes were identified in the studied cohort. The most common SLA class I haplotype Lr‐43.0 ( SLA‐1 *11XX– SLA‐3 *04XX– SLA‐2 *04XX) was identified in 11 animals with a frequency of 20%. For SLA class II, the most prevalent haplotype, Lr‐0.14 [ SLA‐DRB1 *0901– SLA‐DQB1 *0801– SLA‐DQA *03XX], was found in 14 animals with a frequency of 26%. Two class II haplotypes, tentatively designated as Lr‐Pie‐0.1 [ SLA‐DRB1 *01XX/be01/ha04– SLA‐DQB1 *05XX– SLA ‐ DQA*blank] and Lr‐Pie‐0.2 [ SLA‐DRB1 *06XX– SLA‐DQB1 *03XX– SLA‐DQA *03XX], appeared to be novel and have never been reported so far in other pig populations. We showed that SLA genotyping using PCR‐SSP‐based assays represents a rapid and cost‐effective way to study SLA diversity in outbred commercial pigs and may facilitate the development of more effective vaccines or identification of disease‐resistant pigs in the context of SLA antigens to improve overall swine health.     

Rapid assignment of swine leukocyte antigen haplotypes in pedigreed herds using a polymerase chain reaction-based assay

We present a simple assay to determine the swine leukocyte antigen (SLA) haplotypes of animals within two experimental populations of MHC defined miniature pigs. The Yucatan miniature pigs have four founder haplotypes ( w, x, y, z) and one recombinant haplotype ( q). The NIH miniature pigs have three founder haplotypes ( a, c, d) and two recombinant haplotypes ( f, g). Because most crossovers occur between the class I and class II regions, haplotypes can be assigned by typing one class I locus and one class II locus for practical purposes. We have previously characterized these seven founder haplotypes by sequencing the cDNA of three SLA class I loci, designated as SLA-1, SLA-3 and SLA-2 and four SLA class II loci, SLA-DQA1, SLA-DQB1, SLA-DRA1 and SLA-DRB1. These sequences were used to design allele-specific primers to amplify one MHC class I and one MHC class II gene for each haplotype. Primers were tested for specificity in homozygous and heterozygous animals. Positive control primers were also designed to amplify a portion of the E-selectin or alpha-actin gene and multiplexed with the allele-specific primers to check for false negatives. This combination of allele-specific and positive control primers produced specific and robust PCR-site-specific primer assays for assigning SLA haplotypes in the two populations.     

Investigation of SLA class I and II haplotypes in the NIH miniature pigs

Xenotransplantation involves the transplantation of organs, tissues and cells from one species to another. A major barrier to successful xenotransplantation is the rejection of the donor tissue by the recipient immune system. Swine leukocyte antigens (SLA) are important molecules within the immune system and play an essential role in fighting infectious diseases and viruses. The present study investigated three SLA class I (SLA-1, SLA-3 and SLA-2) and three SLA class II (DRB1, DQB1 and DQA) alleles in 60 NIH miniature pigs using PCR with sequence-specific primers (PCR-SSP). As the results, nine combinations of SLA class I and II haplotypes, comprising of three homozygous and six heterozygous haplotypes, were examined. The SLA homozygous haplotype Lr-2.4/2.4 was the most prevalent, with an overall frequency of 28.3% (17/60) and heterozygous haplotype Lr-2.2/4.4 was the second most common (20.0%; 12/60), followed by haplotype Lr-4.2/4.2 (16.7%; 10/60), Lr-2.2/2.4 (15.0%; 9/60), Lr-2.2/2.2 (5.0%; 3/60), Lr-2.2/4.2 (5.0%; 3/60), Lr-2.4/4.4 (5.0%; 3/60) and Lr-2.2/3.3 (3.3%; 2/60), Lr-4.2/4.4 (1.7%; 1/60), respectively. These results provide useful information that can be used to establish highly inbred pig lines with fixed SLA homozygous alleles and haplotypes.     

Effect of swine lymphocyte antigen haplotypes on birth and weaning weights in pigs

Birth weights of 708 live piglets and weaning weights of 566 piglets were used to investigate the effect of the swine lymphocyte antigen (SLA) complex on these traits in Large White pigs. Piglets were from litters of a long-term selection experiment to measure response for selection to increase litter size. SLA haplotypes were determined using conventional class I antisera. A total of 14 haplotypes were detected. The effect of SLA haplotype on birth and weaning weights was investigated using a statistical model that included the effects of experimental group, sire, dam, sex and SLA haplotype. Results indicated that SLA class I haplotype 13.1.3 increased birth weights (P less than 0.10) and significantly increased weaning weights (P less than 0.01). This effect of haplotype 13.1.3 on weaning weight was 605 +/- 215 g (0.3 standard deviations). SLA class I homozygosity did not appear to affect birth and weaning weights. These results suggest that the SLA complex plays an important role in early growth in the pig and that further study of SLA effects on growth and reproduction are warranted.     

Human BF*F-subtypes: segregation analysis with inclusion of MHC haplotypes

Summary The segregation of factor B(BF)F subtypes was analyzed in conjunction with other MHC markers in 15 families with 89 offspring. Informative data for BF F subtypes were obtained from 11 families, 6 of them with known recombinant individuals for the HLA-B/DR/GLO region. The subtypes did not contribute further to the localization of the cross-overs, but followed the known segregation of conventional BF allotypes. In 2 families of one kinship, the recognition of heterozygous BF^*FAFB individuals could be established following the inclusion of three generations. The rarer of the two BF F subtype alleles, BF^*FA, is positively associated with the HLA haplotypes BW62, CW3, C4A^*3 and A29, CWX, B44, C4A^*3, B^*1, DR7. BF F subtypes are regarded as a very useful additional tool for studies of MHC organization and disease association.     

Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley

Segregation distortion can negatively impact on gains expected using selection. In order to increase our understanding of genetic factors that may influence the extent and direction of segregation distortion, segregation distortion analyses were conducted in four different doubled haploid (DH) populations. A high-density composite map of barley was then constructed by integrating information from the four populations. The composite map contained 2,111 unique loci, comprising RFLP, SSR and DArT markers and spanned 1,136 cM. In the four populations investigated, the proportion of markers with segregation distortion ranged from 15 to 38%, depending on the population. The highest distortion was observed in populations derived by the microspore culture technique. Distorted loci tended to be clustered, which allowed definition of segregation distortion regions (SDRs). A total of 14 SDRs were identified in the 4 populations. Using the high-density composite map, several SDRs were shown to have consistent map locations in two or more populations; one SDR on chromosome 1H was present in all four populations. The analysis of haplotypes underlying seven SDRs indicated that in three cases the under-represented haplotypes were common across populations, but for four SDRs the under-represented haplotypes varied across populations. Six of the seven centromeric regions harboured SDRs suggesting that genetic processes related to position near a centromere caused the segregation distortion in these SDRs. Other SDRs were most likely due to the methods used to produce the DH populations. The association of the SDRs identified in this study and some of the genes involved in the process of haploid production described in other studies were compared. The composite map constructed in this study provides an additional resource for the barley community via increased genome coverage and the provision of additional marker options. It has also enabled further insights into mechanisms that underpin segregation distortion.     

Possible relationships between SLA and porcine reproduction

The possible influence of the pig major histocompatibility complex on reproductive traits is reviewed. Among the parameters investigated, significant associations were observed between SLA and genital tract development in males. Several SLA haplotypes affected either positively or negatively the development of testes, the epididymes and the Cowper's glands, whereas the influence of these haplotypes on androsterone tissue content was limited. The impact of the SLA complex on female reproductive performance has been more difficult to ascertain, although some results suggest that the SLA region may interfere with ovulation rates. The influence on prolificacy of SLA sharing between sires and dams was also investigated. Even if fertilization rate is not affected, embryonic mortality and preimplantation embryo development might be influenced by the pig MHC region. Although the litter size was not only marginally affected by the SLA complex, there is one case where SLA identity between the boar and several related sows led to significantly reduced litter size. In these families piglets homozygous for a particular SLA haplotype were almost absent, suggesting the existence of a recessive lethal gene linked to SLA.     

Segregation of HLA A,B haplotypes and the distribution of antigen mismatches between mother and offspring in Hutterite families

Segregation of HLA haplotypes and offspring genotype distributions were analyzed in families from an inbred Caucasoid population, the Dariusleut Hutterite Brethren. Both parents and from one to 12 offspring were typed for HLA-A and -B antigens in 108 families. Segregation of paternal haplotypes was analyzed conditional on sibship size in 95 sibships (a total of 547 offspring), and segregation of maternal haplotypes, in 90 sibships (a total of 515 offspring). The distribution of the number of different genotypes among the offspring was analyzed conditional on sibship size in 90 families (515 offspring) where four equiprobable genotypes were expected. The distribution of the number of antigenic differences or mismatches for broad specificities between mother and offspring was analyzed in pooled family data consisting of a total of 377 offspring comprising 68 families. Compared with the multinomial distribution of segregation classes of haplotypes, there was no significant departure (probability .05 or less) from the expected segregation ratio for either paternal or maternal haplotypes. Compared with the multinomial distribution of the number of genotypes among the offspring, only two of the 11 sibship sizes had configurations that exceeded the 5% level of significance. Given the number of statistical tests performed, it is likely that these results could be explained by chance variation. Finally, there was no relative deficiency of offspring who were less mismatched with their mother for HLA-A and -B broad specificities. Therefore, if HLA-A,B region variation does have a major effect on the differential survival of fetuses in some families, it is an uncommon factor among fertile couples from this inbred population.     

Microsatellite–Centromere Mapping in Large Yellow Croaker (<Emphasis Type="Italic">Pseudosciaena crocea</Emphasis>) Using Gynogenetic Diploid Families

The large yellow croaker (Pseudosciaena crocea) is an economically important marine fish in China. Inheritance of 22 heterozygous microsatellite loci was examined in normal crossed diploid families and meio-gynogenetic families in P. crocea. Two gynogenetic families were produced via inhibition of the second polar body in eggs fertilized with UV-irradiated sperm. The ratio of gynogenesis was proven to be 100% and 96.9% in the two families, respectively. Of the 22 examined loci, 4 showed a segregation distortion in both control and gynogenetic families. Microsatellite–centromere (M–C) map distances were examined using 18 loci with normal Mendelian segregation. Estimated recombination rates ranged between 0 and 1.0 under the assumption of complete interference. High recombinant frequencies between heterozygous markers and the centromere were found in large yellow croaker, as in other teleosts. The average recombination frequency was 0.586. Ten loci showed high M–C recombination with frequency greater than 0.67. M–C distances provide useful information for gene mapping in large yellow croaker.     

Distorted segregation resulting from pea chromosome reconstructions with alien segments from Pisum fulvum

Pea (Pisum sativum L.) satellited chromosome reconstructions were analyzed by cytologic markers to identify segregation distortion events. The presence of modified chromosomes was evaluated on the basis of additional rDNA genes, an extra and a longer satellite, all derived from chromosome 5 and chromosome 7 from P. fulvum Sibth. & Sm. The segregation of modified satellited chromosome 5 was monitored through fluorescent in situ hybridization with rDNA probe; it fitted the expected 1:2:1 ratio after self-pollination of a heterozygous genotype for modified chromosome 5. In different genotypes, which were heterozygous for both modified chromosomes 5 and 7, the combined segregation of these chromosomes showed the occurrence of seven karyotype classes instead of the expected nine. The classes with modified chromosome 7 and without modified chromosome 5, whether heterozygous or homozygous, were absent. The hypothesis of gamete selection was rejected since the expected segregation ratio of 5:3:1 was significant by chi-square test. Based on the other hypothesis of postzygotic selection, the segregation ratio did not show a significant deviation from the expected 9:3:1 ratio, thereby indicating that embryo abortion caused the segregation distortion (SD). The hypothesis of the SD system involving two loci carried by the alien satellites of modified chromosomes 5 and 7 is discussed in relation to the evolution of the P. fulvum genome.     

Distortion of the maternal segregation of the silent alleles of complement factor 4 in normal and diabetic families

54 normal Caucasian families and 169 families in whom at least one child had type I diabetes (IDDM) were genotyped for HLA-A, B, C, DR and for the complement factors Bf and C4. The paternal and maternal transmission of the different alleles and of haplotypes and complotypes in linkage desequilibrium have been analysed. No distortion of the paternal transmission has been observed in the offspring of the two series of families. On the contrary, a distortion of the maternal segregation of the silent alleles at the complement factor C4A and B locus was found: mothers transmitted C4AQ0 more often than expected to their male offspring (p less than 0.04 in normal families, p less than 0.001 in IDDM families) while they transmitted C4BQ0 in excess to their female offspring (p less than 0.01 and p less than 0.03 in normal and IDDM families, respectively).