Revisiting the number of self-incompatibility alleles in finite populations: from old models to new results

Under gametophytic self-incompatibility (GSI), plants are heterozygous at the self-incompatibility locus (S-locus) and can only be fertilized by pollen with a different allele at that locus. The last century has seen a heated debate about the correct way of modeling the allele diversity in a GSI population that was never formally resolved. Starting from an individual-based model, we derive the deterministic dynamics as proposed by Fisher (1958), and compute the stationary S-allele frequency distribution. We find that the stationary distribution proposed by Wright (1964) is close to our theoretical prediction, in line with earlier numerical confirmation. Additionally, we approximate the invasion probability of a new S-allele, which scales inversely with the number of resident S-alleles. Lastly, we use the stationary allele frequency distribution to estimate the population size of a plant population from an empirically obtained allele frequency spectrum, which complements the existing estimator of the number of S-alleles. Our expression of the stationary distribution resolves the long-standing debate about the correct approximation of the number of S-alleles and paves the way to new statistical developments for the estimation of the plant population size based on S-allele frequencies.

Wild and Rare Self-Incompatibility Allele S17 Found in 24 Sweet Cherry (Prunus avium L.) Cultivars

The pollination of self-incompatible diploid sweet cherry is determined by the S-locus alleles. We resolved the S-alleles of 50 sweet cherry cultivars grown in Estonia and determined their incompatibility groups, which were previously unknown for most of the tested cultivars. We used consensus primers SI-19/20, SI-31/32, PaConsI, and PaConsII followed by allele-specific primers and sequencing to identify sweet cherry S-genotypes. Surprisingly, 48% (24/50) of the tested cultivars, including 17 Estonian cultivars, carry the rare S-allele S17, which had initially been described in wild sweet cherries in Belgium and Germany. The S17-allele in Estonian cultivars could originate from ‘Leningradskaya tchernaya’ (S6|S17), which has been extensively used in Estonian sweet cherry breeding. Four studied cultivars carrying S17 are partly self-compatible, whereas the other 20 cultivars with S17 have not been reported to be self-compatible. The recommended pollinator of seven self-incompatible sweet cherries is of the same S-genotype, including four with S17-allele, suggesting heritable reduced effectiveness of self-infertility. We classified the newly genotyped sweet cherry cultivars into 15 known incompatibility groups, and we proposed four new incompatibility groups, 64–67, for S-locus genotypes S3|S17, S4|S17, S5|S17, and S6|S17, respectively, which makes them excellent pollinators all across Europe. Alternatively, the frequency of S17 might be underestimated in Eastern European populations and some currently unidentified sweet cherry S-alleles might potentially be S17.

Alpha-1 Antitrypsin and Hepatocellular Carcinoma in Liver Cirrhosis: SERPINA1 MZ or MS Genotype Carriage Decreases the Risk

Heterozygotes for Z or S alleles of alpha-1-antrypsin (AAT) have low serum AAT levels. Our aim was to compare the risk of hepatocellular carcinoma (HCC) in patients with liver cirrhosis carrying the SERPINA1 MM, MZ and MS genotypes. The study groups consisted of 1119 patients with liver cirrhosis of various aetiologies, and 3240 healthy individuals served as population controls. The MZ genotype was significantly more frequent in the study group (55/1119 vs. 87/3240, p < 0.0001). The MS genotype frequency was comparable in controls (32/119 vs. 101/3240, p = 0.84). MZ and MS heterozygotes had lower serum AAT level than MM homozygotes (medians: 0.90 g/L; 1.40 g/L and 1.67 g/L; p < 0.001 for both). There were significantly fewer patients with HCC in the cirrhosis group among MZ and MS heterozygotes than in MM homozygotes (5/55 and 1/32 respectively, vs. 243/1022, p < 0.01 for both). The risk of HCC was lower in MZ and MS heterozygotes than in MM homozygotes (OR 0.3202; 95% CI 0.1361–0.7719 and OR 0.1522; 95% CI 0.02941–0.7882, respectively). Multivariate analysis of HCC risk factors identified MZ or MS genotype carriage as a protective factor, whereas age, male sex, BMI and viral aetiology of cirrhosis increased HCC risk.

GT-Repeat Polymorphism in the HO-1 Gene Promoter Is Associated with Risk of Liver Cancer: A Follow-Up Study from Arseniasis-Endemic Areas in Taiwan

The induction of heme oxygenase-1 (HO-1) has been shown to have therapeutic potential in experimental models of hepatitis and liver fibrosis, which are closely related to liver cancer. In humans, HO-1 induction is transcriptionally modulated by the length of a GT-repeat [(GT)n] in the promoter region. We aimed to investigate the effect of HO-1 (GT)n variants on liver cancer in a human population. We determined the HO-1 genotype in 1153 study subjects and examined their association with liver cancer risk during a 15.9-year follow-up. Allelic polymorphisms were classified as short [S, <27 (GT)n] or long [L, ≥27 (GT)n]. Newly developed cancer cases were identified through linkage to the National Cancer Registry of Taiwan. Multivariate Cox regression analysis was used to evaluate the effect of the HO-1 (GT)n variants. Alpha-fetoprotein (AFP) and cirrhosis history were also examined. The S/S genotype was found to be significantly associated with liver cancer risk, compared to the L/S and L/L genotypes. The S/S genotype group also had a higher percentage of subjects with abnormal AFP levels than other groups. There were significant percentages of cirrhosis among groups who carried S-alleles. Our findings indicate that short (GT)n variants in the HO-1 gene may confer susceptibility to rather than protection from liver cirrhosis/cancer.

Self-incompatibility characterization in segregating populations of apple trees with DNA markers for S-alleles

The objective of this study was to characterize the parents and respective populations of apple trees regarding S-alleles to confirm their genealogy and to evaluate the efficiency of the molecular markers used. Sixteen specific sets of primers were used for identification of apple S-alleles by PCR. Two segregating populations of the Epagri Apple Breeding Program resulting from crosses between ‘Fred Hough’ × ‘Monalisa’ and ‘M-11/00’ × ‘M-13/91’ were evaluated. The expected segregations are 1:1:1:1 for full compatibility and 1:1 for semi-compatibility, which can be confirmed by the X2 test. The ‘Fred Hough’ (S5S19) × ‘Monalisa’ (S2S10) cross proved to be fully compatible; and two triploids were identified among the hybrids as well. The ‘M-11/00’ (S3S19) × ‘M-13/91’ (S3S5) cross was characterized as semi-compatible based on DNA markers, and the segregation of the S-alleles in the hybrids was 1:1, as expected. The segregation of the DNA markers occurred together with their respective S-alleles: S2, S3, S5, S10, and S19. Thus, characterization of the S-alleles not only allowed identification of compatibility between parents but also identified contaminations in segregating populations.

Deciphering S-RNase Allele Patterns in Cultivated and Wild Accessions of Italian Pear Germplasm

The genus Pyrus is characterized by an S-RNase-based gametophytic self-incompatibility (GSI) system, a mechanism that promotes outbreeding and prevents self-fertilization. While the S-genotype of the most widely known pear cultivars was already described, little is known on the S-allele variability within local accessions. The study was conducted on 86 accessions encompassing most of the local Sicilian varieties selected for their traits of agronomic interest and complemented with some accessions of related wild species (P. pyrifolia Nakai, P. amygdaliformis Vill.) and some national and international cultivars used as references. The employment of consensus and specific primers enabled the detection of 24 S-alleles combined in 48 S-genotypes. Results shed light on the distribution of the S-alleles among accessions, with wild species and international cultivars characterized by a high diversity and local accessions showing a more heterogeneous distribution of the S-alleles, likely reflecting a more complex history of hybridization. The S-allele distribution was largely in agreement with the genetic structure of the studied collection. In particular, the “wild” genetic background was often characterized by the same S-alleles detected in P. pyrifolia and P. amygdaliformis. The analysis of the S-allele distribution provided novel insight into the contribution of the wild and international cultivars to the genetic background of the local Sicilian or national accessions. Furthermore, these results provide information that can be readily employed by breeders for the set-up of novel mating schemes.

ELEMENTS OF DNA-TECHNOLOGY FORMING QUALITY AND SAFE RAW MATERIALS

It is known that cows high milk productivity is associated with decrease in resistance to various diseases, including bovine leukosis, in resistance formation to which the BoLA-DRB3 gene plays role, whose alleles are associated with resistance (R-alleles *7, *11, *23, *28), sensitivity (S-alleles *8, *16, *22, *24) or are defined as neutral (N) in relation to the disease. Researchers also established association of BoLA-DRB3-alleles *8, *11, *23 with an increased milk yield volume, and the *22 allele - with reduced milk yield volume. The aim of research was to study associative communication of servicing bulls BoLA-DRB3 genotypes groups with their breeding value by female ancestor’s dairy productivity indicators. As a result, we studied associative communication of servicing bulls BoLA-DRB3 genotypes groups with their breeding value by female ancestor’s dairy productivity indicators with identification of reduced milk productivity with genetic resistance to bovine leukemia virus infection and bovine leukosis disease relationship, as well as observation of positive correlation between increased milk productivity and genetic predisposition to increased milk yield volumes. The obtained information will be taken into account in breeding during dairy herds reproduction with genetic resistance to bovine leukosis.