Allele Pool Research Articles

Breeding work with kazakh horses Zhabe type

Background and Aim. Kazakh horses of Zhabе type differ from local horses in their higher live weight and larger body measurements. Breeding work with Kazakh horses of the Zhabе type is carried out at Tailak farm in Zharminsky district of East Kazakhstan through targeted reproduction, cultivation, and widespread use of the best individuals based on their origin, exterior, productivity, adaptation to year-round grazing, and quality of offspring from stallions and mares. Individuals that are not up to these standards are strictly culled. The aim of the research is to determine meat productivity and study genetic characteristics of a sample of modern population of Kazakh horses of Zhabe type using DNA markers.Materials and Methods. The material for the study was DNA genotyping data from 20 horses of the Kazakh breed type Zhabe. The horses were genotyped according to 17 STR lоci rеcommended by the Internаtional Sоciety for Animаl Gеnetics (ISАG). The international alphabetical code was used to identify alleles. Genetic and population analyses were performed using the GenAIEx software 6.5. The follоwing indicаtors wеre calculаted: the averаge numbеr of allеles per lоcus (Na), the effеctive numbеr of allеles (Ne), levеls of expеcted (He) and obsеrved heterozygоsity (Ho), and inbreеding cоefficient (FIS) .Results. A study on 17 STR loci of DNA in Kazakh horses Zhabе type has shown that they have a unique allele pool with a significant number of identified alleles and high genetic variability. The average inbreeding coefficient (FIS) is negative (-0.059), indicating that the genetic diversity of this breed is preserved within this group.Conclusion. The improvement of these horses is achieved through breeding and cultivation of animals with high genetic potential for productivity, which is passed down through generations of descendants. This is done by carefully selecting horses with desirable traits for breeding.

Assessment of the genetic similarity between the novoaltayskaya horse breed and the original breeds by microsatellite DNA loci

The research was carried out for the purpose of a comparative assessment of the allele pool of the Novoaltayskaya horse breed and the breeds that participated in its creation. The experimental sample included 5736 horses, including: Novoaltayskaya breed – 363, Altai – 39, Lithuanian Heavy Draft – 159, Russian Heavy Draft – 617, Soviet d Heavy Draft – 288, Orlov trotter – 4,177, Budenny – 93. Population genetic analysis was performed using generally accepted methods. The following indicators were determined: the total number of alleles at 17 loci, the average number of alleles per locus, the level of polymorphism, observed and expected heterozygosity, coefficients of intrapopulation inbreeding, genetic similarity and genetic distances. It was established that horses of the Novo-Altai breed had the highest level of genetic diversity (154 alleles) and polymorphism (Ae = 4,909). Analysis of genetic differentiation showed the absence of intrapopulation inbreeding in the groups of Altai, Lithuanian Heavy Draft and Budenny breeds. Groups of horses of the Novoaltayskaya, Orlov trotter, Russian Heavy Draft and Soviet Heavy Draft breeds were distinguished by a slight deficiency of heterozygotes. It has been established that horses of the Novoaltayskaya and Heavy Draft breeds are characterized by a high frequency of occurrence of the HTG6 O allele, and the Altai breed is characterized by a high frequency of occurrence of the HTG4 M allele. A number of loci of alleles identical in spectrum to those of the Altai, Russian Heavy Draft and Soviet Heavy Draft breeds were identified in the Novoaltayskaya horse. Cluster analysis demonstrated a high level of genetic similarity of horses of the Novoaltayskaya breed with the Russian Heavy Draft (0,903) and Altai (0,899) breeds. As part of the study, using molecular genetic markers, new data was obtained on horses of seven breeds, with the help of which it is possible to improve breeding programs in horse breeding, allowing to control the biodiversity and genetic similarity of populations, preserving the originality and heterogeneity of the allele pool of horses of different breeds.

The human SMAD9 (GCC) repeat links to natural selection and late-onset neurocognitive disorders.

Whereas (GCC)-repeats are overrepresented in genic regions, and mutation hotspots, they are largely unexplored with regard to their link with natural selection. Across numerous primate species and tissues, SMAD9 (SMAD Family Member 9) reaches highest level of expression in the human brain. This gene contains a (GCC)-repeat in the interval between + 1 and + 60 of the transcription start site, which is in the high-ranking (GCC)-repeats with respect to length. Here we sequenced this (GCC)-repeat in 396 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 181) and controls (N = 215). We detected two predominantly abundant alleles of 7 and 9 repeats, forming 96.2% of the allele pool. The (GCC)7/(GCC)9 ratio was in the reverse order in the NCD group versus controls (p = 0.005), resulting from excess of (GCC)7 in the NCD group (p = 0.003) and (GCC)9 in the controls (p = 0.01). Five genotypes, predominantly consisting of (GCC)7 and lacking (GCC)9 were detected in the NCD group only (p = 0.008). The patients harboring those genotypes received the diagnoses of Alzheimer's disease (AD) and vascular dementia (VD). Five genotypes consisting of (GCC)9 and lacking (GCC)7 were detected in the control group only (p = 0.002). The group-specific genotypes formed approximately 4% of the genotype pool in the human samples studied. We propose natural selection and a novel locus for late-onset AD and VD at the SMAD9 (GCC)-repeat in humans.

Investigating Genetic Diversity and Population Structure in Rice Breeding from Association Mapping of 116 Accessions Using 64 Polymorphic SSR Markers

Genetic variability in rice breeding programs plays a very crucial role. It provides an outstanding pool of superior alleles governing better agronomic and quality characters through association mapping. For a greater understanding of population structure, the genetic relationship among different rice lines is indispensable prior to the setting of a correlation among dynamic alleles and traits. In the present investigation, the genetic diversity and population structure of 116 rice accessions were studied to understand genetic relatedness and diversity among them using 64 polymorphic SSR markers. A genotyping assessment based on SSR markers revealed a total of 225 alleles, with an average PIC value of 0.755. The germplasm lines were classified into three distinct subgroups through population structure analysis, utilizing both model- and distance-based approaches. AMOVA analysis showed that 11% of the total variation could be attributed to differences between groups, while the remaining 89% was likely due to differences within groups. This study suggested that population structure and genetic relatedness should be considered to establish marker–trait associations for association mapping when working with the core collection of germplasm lines.

Allele mining for blast-resistance gene at Pi5 locus in rice

Rice plays a crucial role in global food security, serving as a staple for more than half of the world's population. Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most devastating fungal diseases, resulting in substantial economic losses in terms of rice yield and grain quality. The resistance provided by individual blast resistance genes tends to become ineffective within a few years of extensive agricultural use due to the rapid evolution of the fungus. Therefore, continuous efforts in resistance breeding in rice are required to enrich the pool of new resistance genes and alleles. A large-scale screening of new blast resistance alleles was conducted across 2000 rice accessions from major rice-producing areas in China. Field trials were employed in two rice uniform blast nurseries located in Enshi and Yichang. Approximately 153 rice accessions showed at least moderate resistance to the rice blast. Sequence-based allele mining was used to identify the allelic variants of major rice blast resistance genes at the Pi5 locus of chromosome 9. Six novel alleles were identified from 64 accessions. Field tests at five locations, including Enshi, Yichang, Lvtian, Taojiang, and Yaan, and greenhouse inoculation using 33 blast strains from Hubei, Hunan, Guangzhou, and Sichuan, were employed to verify the resistance of these six alleles. Three near-isogenic lines (types 2, 4, and 6) were constructed and inoculated with 31 blast isolates from Heilongjiang to evaluate their blast resistance. Furthermore, bulk segregant analysis was used to confirm that Pi5-type2 and Pi5-type6 are dominant alleles in the analyzed populations. These novel alleles expand the allelic series, enriching the genetic resources for rice blast resistance breeding programs, especially in the north of China. Furthermore, they provide valuable insights into the molecular interactions between rice and rice blast.

Characteristic of allele pool of sheep of the southern meat breed using microsatellite markers

Purpose: to characterize the allele pool of sheep of the southern beef breed using microsatellites.Materials and methods. The biomaterial was ear’s plucks from 80 sheep of the southern meat breed, selected from the Ladozhsky Breeding Plant. 20 East Friesian sheep, 33 Dorset sheep and 63 Romanov sheep were used for comparison. Nine microsatellite loci (INRA005, SPS113, INRA23, MAF65, McM527, OarCP49, HSC, OarAE129, MAF214) were selected as DNA markers. Microsatellite variability was analyzed using the ABI3130x1 Genetic Analyzer. The results were processed in the GenAIEx 6.503 program, with the help of which the main indicators characterizing the state of the allele pool and genetic diversity were calculated.Results. Analysis of the population genetic parameters of sheep of the southern meat breed showed that the average number of alleles per locus (Na) and the effective number of alleles per locus (Ne) exceed the sample average by 1,72 and 0,58 alleles, respectively. The expected heterozygosity (He) was 0,766, while the observed heterozygosity (Ho) was 0,741. The coefficient of inbreeding (Fis) was 0,03. The analysis of the principal components, carried out for the studied breeds in the planes of the first and third principal components, did not fundamentally change the nature of the spatial clustering of the studied groups of sheep. Analysis of the principal coordinates, performed on the basis of calculation of pairwise Fst values, showed that the southern meat breed is located in the upper left quadrant and is isolated from other breeds. The values of the Fst indicator indicate that there is moderate genetic differentiation between the southern meat and dorset breeds (Fst=0,116), and significant genetic differentiation between the southern meat and romanov breeds (Fst=0,161).Conclusion. An analysis of the population genetic parameters of sheep of the southern meat breed, in comparison with the east friesian, dorset and romanov breeds, showed that, in general, in terms of the total number of alleles per locus and the number of effective alleles per locus, it is characterized by a high level of genetic diversity. The presence of a tendency towards a deficiency of heterozygotes is probably explained by the limited population, represented by the only relict gene pool in Russia.

ДИНАМИКА АЛЛЕЛОФОНДА ЛИВЕНСКОЙ ПОРОДЫ СВИНЕЙ НА ОСНОВЕ МИКРОСАТЕЛЛИТНОГО АНАЛИЗА

Using a multilocus panel of microsatellites, the allele pool of Livni breed populations was assessed in five-year dynamics (from 2018 to 2022) and in comparison with commercial breeds (Large White and Landrace). We identified alleles, which were found in Livni breed and absent in commercial breeds. However, there was a tendency towards the loss of certain alleles in the dynamics of the analyzed period. It was shown that observed heterozygosity in the population of Livni breed in 2022 was significantly higher (P<0.05) compared to those estimated in commercial breeds. Based on principal component analysis, genetic network construction, and cluster analysis, the preservation of authentic genomic components, which were predominant in Livni breed, in the modern population is shown.

The spatio-temporal diversification of SRK alleles in an Arabidopsis polyploid hybrid and introgression zone

Reproductive barriers and directional geneflow may play a key role in maintaining genetic gradients, thereby allowing ecological differentiation along ecological clines. In Brassicaceae, a sporophytic incompatibility system (SI) contributes to such barriers to geneflow, with the maternal component represented by a large diversity of SRK (stigma-specific S locus receptor kinase) alleles at varying frequencies and levels of dominance. Such clinal genetic gradient along an ecological gradient following a shift towards much drier and warmer conditions and also the bedrock type shifts from calcareous to silicious has been found earlier in an Arabidopsis introgression system involving A. lyrata and A. arenosa. The metapopulation system spans from the northeastern Austrian forealps northward towards the Danube river and the Bohemian massif. Here we explore diversification of population-level SRK gene pools across these hybrid Arabidopsis tetraploid metapopulation system and its putative parental source populations. Since it has been demonstrated that A. lyrata served as the maternal parent and A. arenosa introgressed via pollen constituting a genetic cline with decreasing contribution of A. arenosa genetic background, we test the hypothesis that this cline can be also explained by SRK allelic differentiation. A total of 603 individuals from 45 populations of introgressed and non-introgressed A. lyrata and A. arenosa across a 80 km transect were analysed for SRK allele variation. In total, 22 alleles from all four previously described dominance classes have been documented. Although there is clinal morphological and genetic variation following the introgression zone, SRK alleles do not follow this signature of the paternal taxa. Furthermore, the functional SI system is fully maintained across the transect, and crossing experiments show that there is no decrease in fitness depending on varying distances between populations along the transect studied herein. We conclude that transmission and structure of the SRK allelic gene pool contributes to the postglacial colonization success along such a pronounced ecological gradient maintaining a functional SI system and counteracting genetic depletion.

Environmental and Socio-Cultural Factors Impacting the Unique Gene Pool Pattern of Mae Hong-Son Chicken.

Understanding the genetic diversity of domestic chicken breeds under the impact of socio-cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son Province, Thailand; however, its genetic characterization, origin, and diversity remain poorly understood. Here, we studied the socio-cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed and investigated its diversity and allelic gene pool. We genotyped 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data to evaluate genetic diversity and assessed spatial habitat suitability using maximum entropy modeling. Sequence diversity analysis revealed a total of 188 genotyped alleles, with overall nucleotide diversity of 0.014 ± 0.007, indicating that the Mae Hong Son chicken population is genetically highly diverse, with 35 (M1-M35) haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken. During domestication in the past 200-300 years after the crossing of indigenous chickens and red junglefowl, the Mae Hong Son chicken has adapted to the highland environment and played a significant socio-cultural role in the Northern Thai community. The unique genetic fingerprint of the Mae Hong Son chicken, retaining a high level of genetic variability that includes a dynamic demographic and domestication history, as well as a range of ecological factors, might reshape the adaptation of this breed under selective pressure.

Thai Local Chicken Breeds, Chee Fah and Fah Luang, Originated from Chinese Black-Boned Chicken with Introgression of Red Junglefowl and Domestic Chicken Breeds

Knowledge of the genetic characteristics, origin, and local adaptation of chickens is essential to identify the traits required for chicken breeding programs. Chee Fah and Fah Luang are black-boned chicken breeds reared in Chiang Rai, Thailand. Chickens are an important part of the local economy and socio-culture; however, the genetic diversity, characteristics, and origins of these two breeds have been poorly studied. Here, we investigated the genetic diversity, gene pool, and origin of the Chee Fah and Fah Luang chickens using mitochondrial DNA D-loop (mtDNA D-loop) sequencing and microsatellite genotyping, as well as habitat suitability analysis using maximum entropy modeling. The MtDNA D-loop sequencing and microsatellite genotype analyses indicated that the Chee Fah and Fah Luang chickens shared haplogroups A, B, and CD with Chinese black-boned chickens. Gene pool analysis revealed that the Chee Fah and Fah Luang chickens have distinct genetic patterns compared to Thai domestic chickens and red junglefowl. Some gene pools of red junglefowl and other Thai domestic chickens were observed within the Chee Fah and Fah Luang chicken gene pool structures, suggesting genetic exchange. The data indicate that the Chee Fah and Fah Luang chickens originated from Chinese indigenous black-boned chicken breeds and experienced crossbreeding/hybridization and introgression with red junglefowl and other domestic breeds during domestication. Interestingly, the Chee Fah and Fah Luang chickens from Chiang Rai shared the same allelic gene pool, which was not shared with the Chee Fah and Fah Luang chickens from Mae Hong Son, suggesting at least two gene pool origins in the Chee Fah and Fah Luang chicken populations. Alternatively, different gene pools in the Chee Fah and Fah Luang chickens from different localities might be caused by differences in environmental factors, especially elevation.

Crop Wild Relatives: A Valuable Source of Tolerance to Various Abiotic Stresses

Global climate change is one of the major constraints limiting plant growth, production, and sustainability worldwide. Moreover, breeding efforts in the past years have focused on improving certain favorable crop traits, leading to genetic bottlenecks. The use of crop wild relatives (CWRs) to expand genetic diversity and improve crop adaptability seems to be a promising and sustainable approach for crop improvement in the context of the ongoing climate challenges. In this review, we present the progress that has been achieved towards CWRs exploitation for enhanced resilience against major abiotic stressors (e.g., water deficiency, increased salinity, and extreme temperatures) in crops of high nutritional and economic value, such as tomato, legumes, and several woody perennial crops. The advances in -omics technologies have facilitated the elucidation of the molecular mechanisms that may underlie abiotic stress tolerance. Comparative analyses of whole genome sequencing (WGS) and transcriptomic profiling (RNA-seq) data between crops and their wild relative counterparts have unraveled important information with respect to the molecular basis of tolerance to abiotic stressors. These studies have uncovered genomic regions, specific stress-responsive genes, gene networks, and biochemical pathways associated with resilience to adverse conditions, such as heat, cold, drought, and salinity, and provide useful tools for the development of molecular markers to be used in breeding programs. CWRs constitute a highly valuable resource of genetic diversity, and by exploiting the full potential of this extended allele pool, new traits conferring abiotic-stress tolerance may be introgressed into cultivated varieties leading to superior and resilient genotypes. Future breeding programs may greatly benefit from CWRs utilization for overcoming crop production challenges arising from extreme environmental conditions.

Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula

“Occasional” sexuality occurs when a species combines clonal reproduction and genetic mixing. This strategy is predicted to combine the advantages of both asexuality and sexuality, but its actual consequences on the genetic diversity and species longevity are poorly understood. Androgenesis, a reproductive mode in which the offspring inherits its entire nuclear genome from the father, is often reported as a strictly clonal reproductive mode. Androgenesis is the predominant reproductive mode within the hermaphroditic, invasive lineages of the mollusk genus Corbicula. Their ability to reproduce clonally through androgenesis has been determinant in their invasive success, having colonized during the 20th century American and European freshwater systems, where they became notorious invaders with a widespread, global distribution. However, in androgenetic Corbicula clams, occasional genetic mixing between distinct lineages has also been observed when the sperm of one lineage fertilizes the oocyte of another one. Because of these occasional introgressions, the genetic relationships between Corbicula species remained unclear, and the biogeographic origins of the invasive androgenetic lineages have been challenging to identify. To address these issues, we analyzed the patterns of allele sharing for several nuclear and mitochondrial molecular markers among Corbicula individuals collected across both the native and invasive range. Our results show the occurrence of an allelic pool encompassing all Corbicula freshwater species worldwide, including sexual and androgenetic ones, which highlights the substantial genetic mixing within this genus. However, the differences in allele sharing patterns between invasive lineages, and the low diversity within each lineage, suggest recent, distinct biogeographic origins of invasive Corbicula androgenetic lineages. Finally, the polyploidy, high heterozygosity, and hybrid phenotypes and genotypes found in our study probably originated from hybridization events following egg parasitism between distinct Corbicula lineages. This extensive cross-lineage mixing found in Corbicula may generate nuclear diversity in an otherwise asexually reproducing species.

Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits

BackgroundIn medical genetics, discovery and characterization of disease trait contributory genes and alleles depends on genetic reasoning, study design, and patient ascertainment; we suggest a segmental haploid genetics approach to enhance gene discovery and molecular diagnostics.MethodsWe constructed a genome-wide map for nonallelic homologous recombination (NAHR)-mediated recurrent genomic deletions and used this map to estimate population frequencies of NAHR deletions based on large-scale population cohorts and region-specific studies. We calculated recessive disease carrier burden using high-quality pathogenic or likely pathogenic variants from ClinVar and gnomAD. We developed a NIRD (NAHR deletion Impact to Recessive Disease) score for recessive disorders by quantifying the contribution of NAHR deletion to the overall allele load that enumerated all pairwise combinations of disease-causing alleles; we used a Punnett square approach based on an assumption of random mating. Literature mining was conducted to identify all reported patients with defects in a gene with a high NIRD score; meta-analysis was performed on these patients to estimate the representation of NAHR deletions in recessive traits from contemporary human genomics studies. Retrospective analyses of extant clinical exome sequencing (cES) were performed for novel rare recessive disease trait gene and allele discovery from individuals with NAHR deletions.ResultsWe present novel genomic insights regarding the genome-wide impact of NAHR recurrent segmental variants on recessive disease burden; we demonstrate the utility of NAHR recurrent deletions to enhance discovery in the challenging context of autosomal recessive (AR) traits and biallelic variation. Computational results demonstrate new mutations mediated by NAHR, involving recurrent deletions at 30 genomic regions, likely drive recessive disease burden for over 74% of loci within these segmental deletions or at least 2% of loci genome-wide. Meta-analyses on 170 literature-reported patients implicate that NAHR deletions are depleted from the ascertained pool of AR trait alleles. Exome reanalysis of personal genomes from subjects harboring recurrent deletions uncovered new disease-contributing variants in genes including COX10, ERCC6, PRRT2, and OTUD7A.ConclusionsOur results demonstrate that genomic sequencing of personal genomes with NAHR deletions could dramatically improve allele and gene discovery and enhance clinical molecular diagnosis. Moreover, results suggest NAHR events could potentially enable human haploid genetic screens as an approach to experimental inquiry into disease biology.

A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder

The human SBF1 (SET binding factor 1) gene, alternatively known as MTMR5, is predominantly expressed in the brain, and its epigenetic dysregulation is linked to late-onset neurocognitive disorders (NCDs), such as Alzheimer’s disease. This gene contains a (GCC)-repeat at the interval between + 1 and + 60 of the transcription start site (SBF1-202 ENST00000380817.8). We sequenced the SBF1 (GCC)-repeat in a sample of 542 Iranian individuals, consisting of late-onset NCDs (N = 260) and controls (N = 282). While multiple alleles were detected at this locus, the 8 and 9 repeats were predominantly abundant, forming > 95% of the allele pool across the two groups. Among a number of anomalies, the allele distribution was significantly different in the NCD group versus controls (Fisher’s exact p = 0.006), primarily as a result of enrichment of the 8-repeat in the former. The genotype distribution departed from the Hardy–Weinberg principle in both groups (p < 0.001), and was significantly different between the two groups (Fisher’s exact p = 0.001). We detected significantly low frequency of the 8/9 genotype in both groups, higher frequency of this genotype in the NCD group, and reverse order of 8/8 versus 9/9 genotypes in the NCD group versus controls. Biased heterozygous/heterozygous ratios were also detected for the 6/8 versus 6/9 genotypes (in favor of 6/8) across the human samples studied (Fisher’s exact p = 0.0001). Bioinformatics studies revealed that the number of (GCC)-repeats may change the RNA secondary structure and interaction sites at least across human exon 1. This STR was specifically expanded beyond 2-repeats in primates. In conclusion, we report indication of a novel biological phenomenon, in which there is selection against certain heterozygous genotypes at a STR locus in human. We also report different allele and genotype distribution at this STR locus in late-onset NCD versus controls. In view of the location of this STR in the 5′ untranslated region, RNA/RNA or RNA/DNA heterodimer formation of the involved genotypes and alternative RNA processing and/or translation should be considered.

De novo assembly of two chromosome-level rice genomes and bin-based QTL mapping reveal genetic diversity of grain weight trait in rice.

Following the “green revolution,” indica and japonica hybrid breeding has been recognized as a new breakthrough in further improving rice yields. However, heterosis-related grain weight QTLs and the basis of yield advantage among subspecies has not been well elucidated. We herein de novo assembled the chromosome level genomes of an indica/xian rice (Luohui 9) and a japonica/geng rice (RPY geng) and found that gene number differences and structural variations between these two genomes contribute to the differences in agronomic traits and also provide two different favorable allele pools to produce better derived recombinant inbred lines (RILs). In addition, we generated a high-generation (> F15) population of 272 RILs from the cross between Luohui 9 and RPY geng and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA, indica and Z7A, japonica). Based on three derived populations, we totally identified eight 1,000-grain weight (KGW) QTLs and eight KGW heterosis loci. Of QTLs, qKGW-6.1 and qKGW-8.1 were accepted as novel KGW QTLs that have not been reported previously. Interestingly, allele genotyping results revealed that heading date related gene (Ghd8) in qKGW-8.1 and qLH-KGW-8.1, can affect grain weight in RILs and rice core accessions and may also play an important role in grain weight heterosis. Our results provided two high-quality genomes and novel gene editing targets for grain weight for future rice yield improvement project.

Identification of S-genotypes and a novel S-RNase in 84 native Chinese pear accessions

The Chinese pear (Pyrus spp.) exhibits typical gametophytic self-incompatibility (GSI), which inhibits self-crossing and promotes out-crossing, similar to other fruit species in the Rosaceae family. Thus, S-compatible cultivars are required in pear orchards to ensure successful pollination and stable yields. In this study, 84 native Chinese pear accessions were genotyped by allele-specific PCR using one pair allele consensus primers and 29 pairs of S-allele-specific primers that were designed in this study. After cloning and sequencing the PCR products, the S-genotypes of all 84 pear accessions, including wild and cultivated accessions, were determined. The reported 34 S-alleles and a novel S-allele were isolated from these pear accessions. These S-alleles were expressed specifically in the style. Sequence analysis identified that six pear cultivars originated in China shared the same S-RNases with P. communis (Pc). These findings supported the hypothesis that oriental and occidental Pyrus spp. may share the same pool of alleles at the S-locus. A novel S-RNase was isolated in ‘Putiandouli’, ‘Daguoshanli’, ‘Yunhongli 1′, and ‘Dianli’ and deposited as S67-RNase under accession number MT773568. Furthermore, the deduced amino acid sequences exhibited high similarity (99.56%) to S32-RNase in Malus. The high similarity between S-RNase in Pyrus and Malus indicated that the existence of S-RNase could have predated speciation between Pyrus and Malus. Furthermore, S-allele information was rearranged in Asian and European pears to provide information for selecting the best pollinator for widely cultivated pear cultivars in China. This information is useful for pear production, cross-breeding, and understanding the mechanism of the self-incompatibility reaction.

Genetic specificity of the white-headed ukrainian breed according to the BоLA-DRB3 gene

The study of the genetic specificity of local breeds is a promising direction in the context of preserving the biodiversity of cattle breeds in the world. The purpose of research was to analyze the allelic polymorphism of the BoLA-DRB3 gene of the White-Headed Ukrainian breed. The study was carried out with blood samples from 49 animals (11 bulls and 38 cows) of this breed. The allelic spectrum of the BoLA-DRB3 gene was detected based on two-step PCR (primers HLO-30, HLO-31 and HLO-32). Restriction was performed with endonucleases RsaI, HaeIII, BstYI. Restriction fragments were separated by electrophoresis in 9-12 % polyacrylamide gel. According to the test results, 29 alleles were detected. Seven alleles (*03, *11, *13, *15, *22, *23 and *24) were determined with a frequency of over 5 %, that was 65.3 % of the allele pool of the breed. The most common was allele *24 with a frequency of 15.3%. In the experimental sample, 37 genotypes were identified. The predominant variant was *11/*24 (16.2%). A slight excess of heterozygotes was detected (Fis = – 0.035). White-Headed Ukrainian breed is characterized by a significant level of differentiation (or specificity) according to the BoLA-DRB3 gene (Wright fixation index He = 0.959, Shannon-Wiener index H` = 2.93), that confirms the thesis of the important role of local breeds in preserving the biodiversity of genetic resources of cattle.

Hanges in the occurrence of alleles of the EAB-locus of blood groups in cattle of the kholmogorsky breed due to holsteinization

The aim of the research was to analyze the allele pool and its changes in the EAB locus of blood groups of cattle of the Kholmogory breed using absorption crosses with bulls of the Holstein breed. The study was carried out by the method of immunological testing according to the agglutination reaction. The choice of locus is not accidental, because it is currently the most informative in terms of the nomenclature of alleles. The predominance of alleles of the Kholmogory breed (A2'O', E3'G'G'') is noted with an increase in the frequency of occurrence (G2Y2E1'Q') and the appearance of new alleles specific of the Holstein breed (O1A'2J'2K'O', B2Q 'G'G”, E'3G'Q', B1O2B', O4Y2A2', O4D'E3'F2'G'O'G”). Over the past 5 years, the index of genetic similarity between herds of Kholmogory cattle in the Komi Republic has twofold. It was revealed that in the population of Komi Republic introduced new alleles of the Holstein breed, but at the same time, part of the alleles of Kholmogory cattle, originally obtained from the breeding reserve, are conserved. Such alleles are transfered between generations of animals and may indicate the preservation of the genome structure of the original mother breed under conditions of intensive selection. As well as alleles are transmitted when using purebred, as well as Holsteinized sires of the Pechora type of breed. The gene pool of the native Kholmogory breed is unique and requires further study. Groups of antigens form a unique genetic structure of herds, which can serve to identify animals by relationship, as well as breed affiliation, as it is similarly made by microsatellite loci and SNP markers (ISAG standard). Testing was carried out as sires in the amount of &gt;30 heads, and their breeding reserve for more than 5 years (&gt;5925 cows of breeding herds). Groups of antigens make it possible to evaluate the change in the genetic structure of the population of the Kholmogory breed and other breeds of cattle in time slices and obtain information about the breeder's actions when focusing on specific genetic traits and their genetic variability, breeding traits and evaluate inbreeding (antigenic similarity), and not only to determine the relationship of animals

СВЯЗЬ СОДЕРЖАНИЯ ЖИРА В МОЛОКЕ КОБЫЛ ТЯЖЕЛОВОЗНЫХ ПОРОД С ГРУППАМИ КРОВИ, АЛЛЕЛЯМИ И АНТИГЕНАМИ ЭРИТРОЦИТОВ

Studies on the influence of blood groups, alleles and antigens of erythrocytes on the fat content in the milk of mares of heavy draft breeds were carried out on the basis of the dairy farm of the Semyonovskiy breeding plant CJSC and in the laboratory of clinical diagnostics and biochemical research of the Gary State University, Department of Livestock Production Technology. The chemical composition of milk from mares of heavy draft breeds was determined in the laboratory of the breeding kumys complex of ZAO PZ "Semyonovsky". The analysis of milk for fat content was carried out on the device "Klever-1M". The allele pool was determined according to the D blood group system of the Lithuanian and Russian heavy draft breeds, bred in ZAO PZ "Semyonovskiy". According to the D blood group system, 19 out of 36 possible genotypes have been established in Russian and Lithuanian mares. The highest fat content was observed in Lithuanian heavy draft mares with DdkDcgm genotypes and Russian heavy draft mares with DcgmDdghm genotypes. The share of genotypic influence on the fat content in milk was 0.1227 (p&gt;0.95) and 0.1881 (p&gt;0.95), respectively for breeds. Taking into account the revealed positive relationships of immunogenetic parameters with the content of fat in the milk of mares, it is possible to recommend the use of the results obtained to adjust the selection in terms of selection and breeding work.

Characteristics of the Allele Pool and the Genetic Differentiation of Goats of Different Breeds and their Wild Relatives by Str-Markers.

Based on 16 STR-loci, the allele pool and interbreed differentiation of goat breeds of Russian and foreign breeding were investigated in this study. These breeds included Karachai (KRCH-K, n=73, mountain zone; KRCH-Z, n=33, foothill zone), Dagestan Downy (DAGD, n=30), Dagestan Wool (DAGW, n=30), Soviet Wool (SOVW, n=30), Saanen (SAAN, n=34), Murciano-Granadina (MURS, n=37), as well as wild goats, represented by three species of mountain goats (n=52): Siberian Capricorn (Capra sibirica) of Altai (CSIB-S, n=6), Tajikistan (CSIB-T, n=4), Kyrgyzstan (CSIB-K, n=6), and the Himalayas (CSIB-H, n=4); Bezoar goat (Capa aegagrus) of Turkey (CAEG, n=3) and Pakistan (CAEG-S, n=3); West Caucasian tur (Capra caucasica): western Caucasian (Kuban, CCAU-K, n=10), central Caucasian (CCAU-M, n=8), and eastern Caucasian (Dagestan, CCAU-D, n=8). The highest genetic diversity was observed in the North Caucasus breeds, such as Karachai, Dagestan Downy, and Dagestan Wool. The mean numbers of alleles per locus and allelic diversity were 7.385-9.154 and 7.353-7.713, respectively. The genetic proximity of Caucasian breeds was confirmed by cluster analysis, and they formed a common branch with the highest genetic affinity, while the Orenburg and Soviet Wool breeds formed another branch, and the third branch with the least affinity was the dairy breed of foreign selection.The analysis of the phylogenetic tree of domestic and wild species established the formation of three clusters formed by the subspecies of the West Caucasian tur, Siberian ibex, and breeds of domestic goats. At the same time, populations of the Bezoar goats were localized at the root of the last cluster, which confirmed their role as the ancestors of domestic goats.