Degree Of Homozygosity Research Articles

Assessment and preservation of the gene pool of the domestic <i>Kholmogorsk</i> cattle breed in the Arkhangelsk region

The article presents the results of monitoring immunogenetic studies on the origin of Kholmogory cattle to establish their breed genetic passport for the EAB locus of blood groups. The importance of determining of the breeding animals statute taking into account the forms of the identified state of erythrocyte antigens for the purpose of registration in the federal state information and analytical system of breeding resources of the Russian Federation is noted. In breeding farms of the Arkhangelsk region over the past 29 years, the total number of animals tested for the reliability of origin was 57,311. The percentage of reliability in the monitored livestock numbers varied from 86.95% (1995-2000) to 97.28% (2016-2020). To establish the genetic passport of breeding female tribal species of the breed with up to 75% Holstein bloodline approved for breeding purposes when working with Kholmogory cattle, we conducted immunogenetic testing, which revealed 46 alleles of the EAB locus. The total frequency of the EAB locus alleles in animals of groups 1-2 with specific (typical) for the Kholmogory breed and with unique alleles was 69.38%. In group 3 of animals with alleles of the approved Holstein breed, the total frequency was set at 30.6%, in group 4 with alleles of unapproved breeds – 0.02%. It was established that the concentration of alleles G2O2, B2O2, B2G2KA’B’G’O’G’’, B2E’2G’, B2O2Y2D’, Q is very low, they are found only in some individuals. The degree of homozygosity (theoretical) is 5.6%, the number of effective alleles is 17.9.

Phenotypic correlates between clock genes and phenology among populations of Diederik cuckoo, Chrysococcyx caprius.

The Diederik cuckoo, Chrysococcyx caprius, is a small Afrotropical bird in the family Cuculidae. It is taxonomically related to 13 other species within the genus Chrysococcyx and is migratory in sub-Saharan Africa. It has a unique breeding behaviour of being a brood parasite: Breeding pairs lay their eggs in the nests of a host species and hatchlings expel the eggs of the host species. The aim of the present study was to investigate diversity in two circadian clock genes, Clock and Adcyap1, to probe for a relationship between genetic polymorphisms and their role in circannual timing and habitat selection (phenology) in intra-African migrants. DNA extracted from blood was used for the PCR amplification and sequencing of clock genes in 30 Diederik cuckoos. Three alleles were detected for Clock with similar genotypes between individuals from the Northern and Southern breeding ranges while 10 alleles were detected for Adcyap1, having shorter alleles in the North and longer alleles in the South. Population genetic analyses, including allele frequency and zygosity analysis, showed distinctly higher frequencies for the most abundant Clock allele, containing 10 polyglutamine repeats, as well as a high degree of homozygosity. In contrast, all individuals were heterozygous for Adcyap1 and alleles from both regions showed distinct differences in abundance. Comparisons between both clock genes and phenology found several phenotypic correlations. This included evidence of a relationship between the shorter alleles and habitat selection as well as a relationship between longer alleles and timing. In both instances, evidence is provided that these effects may be sex-specific. Given that these genes drive some of the synchronicity between environments and the life cycles of birds, they provide valuable insight into the fitness of species facing global challenges including climate change, urbanisation and expanding agricultural practices.

A novel tomato interspecific (Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium) MAGIC population facilitates trait association and candidate gene discovery in untapped exotic germplasm.

We developed a novel eight-way tomato multiparental advanced generation intercross (MAGIC) population to improve the accessibility of tomato relatives genetic resources to geneticists and breeders. The interspecific tomato MAGIC population (ToMAGIC) was obtained by intercrossing four accessions each of Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium, which are the weedy relative and the ancestor of cultivated tomato, respectively. The eight exotic ToMAGIC founders were selected based on a representation of the genetic diversity and geographical distribution of the two taxa. The resulting MAGIC population comprises 354 lines, which were genotyped using a new 12k tomato single primer enrichment technology panel and yielded 6488 high-quality single-nucleotide polymorphism (SNPs). The genotyping data revealed a high degree of homozygosity, an absence of genetic structure, and a balanced representation of the founder genomes. To evaluate the potential of the ToMAGIC population, a proof of concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness. Genome-wide association studies identified strong associations for the studied traits, pinpointing both previously identified and novel candidate genes near or within the linkage disequilibrium blocks. Domesticated alleles for fruit size were recessive and were found, at low frequencies, in wild/ancestral populations. Our findings demonstrate that the newly developed ToMAGIC population is a valuable resource for genetic research in tomato, offering significant potential for identifying new genes that govern key traits in tomato. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding.

Development of near homozygous lines for diploid hybrid TPS breeding in potatoes

Diploid inbred-based F1 hybrid True Potato Seed (DHTPS) breeding is a novel technique to transform potato breeding and cultivation across the globe. Significant efforts are being made to identify elite diploids, dihaploids and develop diploid inbred lines for heterosis exploitation in potatoes. Self-incompatibility is the first obstacle for developing inbred lines in diploid potatoes, which necessitates the introgression of a dominant S locus inhibitor gene (Sli) for switching self-incompatibility to self-compatibility. We evaluated a set of 357 diploid clones in different selfing generations for self-compatibility and degree of homozygosity using Kompetitive Allele Specific PCR (KASP) Single Nucleotide Polymorphism (SNP) markers. A subset of 10 KASP markers of the Sli candidate region on chromosome 12 showed an association with the phenotype for self-compatibility. The results revealed that the selected 10 KASP markers for the Sli gene genotype could be deployed for high throughput rapid screening of self-compatibility in diploid populations and to identify new sources of self-compatibility. The homozygosity assessed through 99 KASP markers distributed across all the chromosomes of the potato genome was 20–78 % in founder diploid clones, while different selfing generations, i.e., S0, S1, S2 and S3 observed 36.1–80.4, 56.9–82.8, 59.5–85.4 and 73.7–87.8 % average homozygosity, respectively. The diploid plants with ∼80 % homozygosity were also observed in the first selfing generation, which inferred that homozygosity assessment in the early generations itself could identify the best plants with high homozygosity to speed up the generation of diploid inbred lines.

Genetic aspects in working with the kholmogory cattle breed in the arkhangelsk region

Monitoring of the genetic structure of cattle breeds allows conducting studies that provide information about the cross-section in the timeline by the frequencies of genotypes of blood groups. In particular, the study was carried out on 10 time intervals of observations in herds for the Kholmogorsky breed of breeding plants of the Arkhangelsk region (n = 10983). The dynamics is shown by the decrease and increase in the frequencies of individual alleles. The genetic structure of the herd becomes more homozygous, as the loss of alleles goes on. A similar situation has developed in the samples of cows of the first and ninth generations, their genetic structures are sharply different. According to the results of the research, it was found that the quantitative and qualitative composition of the allelofund of the Kholmogorsky cattle of the Arkhangelsk region has changed under the influence of breeding processes. It was found that the degree of homozygosity (theoretical) tends to decrease from 10.5% (3rd generation) to 6.5% (9th, 10th generation) in the context of the analyzed generations of females, and the number of effective alleles, respectively, increases from 9.4% to 15.4%. At the same time, it was revealed that the breeding stock of the herds of breeding plants of the Arkhangelsk region was heterogeneous according to the genetic panel of the EAV locus. The greatest genetic distance is shown by purebred cows of the Kholmogorsky breed of cattle of the 1-2 observation intervals with Holstein in the 9-10 intervals. Breeding work and assessment of genetic variability is a tool for successful breeding in cattle herds of breeding plants by generations. The event to create new and improve existing factory lines using genetic markers of breed affiliation is promising. This will reduce the negative consequences of related mating of parent pairs, as well as avoid an increase in the level of homozygosity in the controlled herds of the Arkhangelsk population of the Kholmogorsky cattle breed.

Impact of predicted HLA class I immunopeptidome on viral reservoir in a cohort of people living with HIV in Italy.

The class I HLA genotype has been widely recognized as a factor influencing HIV disease progression in treatment-naïve subjects. However, little is known regarding its role in HIV disease course and how it influences the size of the viral reservoir once anti-retroviral therapy (ART) is started. Here, leveraging on cutting-edge bioinformatic tools, we explored the relationship between HLA class I and the HIV reservoir in a cohort of 90 people living with HIV (PLWH) undergoing ART and who achieved viral suppression. Analysis of HLA allele distribution among patients with high and low HIV reservoir allowed us to document a predominant role of HLA-B and -C genes in regulating the size of HIV reservoir. We then focused on the analysis of HIV antigen (Ag) repertoire, by investigating immunogenetic parameters such as the degree of homozygosity, HLA evolutionary distance and Ag load. In particular, we used two different bioinformatic algorithms, NetMHCpan and MixMHCpred, to predict HLA presentation of immunogenic HIV-derived peptides and identified HLA-B*57:01 and HLA-B*58:01 among the highest ranking HLAs in terms of total load, suggesting that their previously reported protective role against HIV disease progression might be linked to a more effective viral recognition and presentation to Cytotoxic T lymphocytes (CTLs). Further, we speculated that some peptide-HLA complexes, including those produced by the interaction between HLA-B*27 and the HIV Gag protein, might be particularly relevant for the efficient regulation of HIV replication and containment of the HIV reservoir. Last, we provide evidence of a possible synergistic effect between the CCR5 ∆32 mutation and Ag load in controlling HIV reservoir.

The genetic landscape of inherited retinal dystrophies in Arabs

Inherited retinal dystrophies (IRDs) are a major cause of vision loss. Altogether are highly heterogeneous genotypically and phenotypically, exhibiting substantial differences worldwide. To shed more light on these conditions, we investigated the genetic and phenotypic landscape of IRDs in the Arabs globally and per country.We analyzed 1,621 affected individuals from 16 Arabic countries reported in 198 articles. At the phenotypic level, rod-cone dystrophy (RCD) and Usher syndrome were the most prevalent conditions among non-syndromic and syndromic IRDs. At the gene level, TULP1, ABCA4, RP1, CRB1, MYO7A, RPE65, KCNV2, and IMPG2 were the most mutated genes. Interestingly, all except CRB1 were highly prevalent because they harbored founder mutations, implying that consanguinity is a major determinant in Arab countries. Of note, ~ 93% of the investigated individuals carried homozygous mutations. The country analysis for the IRDs conditions and their associated genotypes revealed that whereas Leber Congenital Amaurosis, RCD, and USHER syndrome were widely distributed, bestrophinopathies and non-syndromic hearing loss were restricted to specific countries (till now).This study could be a starting point for initiating suitable health policies towards IRDs in the Arab world. The high degree of homozygosity urges the need for genetic counsellors to provide personalized information and support the affected individuals.

The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India.

Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders. The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes. For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (FROH) and homozygous loci-based inbreeding estimate (FHOM). A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of FROH, FHOM, and pedigree-based inbreeding estimate (FPED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity. This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.

COMPARATIVE CHARACTERISTIC OF GENETIC PARAMETERS OF D -SYSTEM BLOOD GROUP OF NOVOALEXANDROVSKAYA DRAFTER AND TORIAN BREEDS STALLIONS

In Ukraine, the Novoalexandrovskaya and Torian drafter horse breeds belong to breeds with a limited genetic resources. This creates a problem of conservation and efficient breeding of these breeds. One of the priority tasks of modern work with the Novoalexandrovskaya drafter and Torian horse breeds is to preserve the unique genetic resource, improve breeding qualities and working efficiency. Therefore, it is relevant to study the genetic features of these breeds. The article presents the results of research of the immunogenetic structure of Novoalexandrovskaya and Torian horse breeds of different farms of Ukraine on D-system of blood groups. The aim of the work was to identify genetic markers inherent in the Novoalexandrovskaya drafter and Torian horse breeds, which make it possible to solve breeding and genetic issues in the preservation and improvement of the breeds. A high frequency of alleles was found in Novoalexandrovskaya drafter horse breed, there are Ddg (0,230), Dad (0,202), Dde (0,174), Dd (0,115). The alleles Dcgm (0,080), Dbcm (0,048), Ddk (0,024), Dcеgm (0,017) Dd (0,015) were found relatively less common. The allele Dcegm (0.017) was the rarest allele among the Novoalexandrovskaya drafter horse breed and it was 14.78% less common than the allele Dd (0.115). The Torian horse breed has the high frequency of occurrence of alleles Dcgm (0,25), Dd (0,112) Ddg (0,097), Dbcm (0,073), Ddk (0,225). Less common alleles are Dde (0,048), Dcеgm (0,016), Dad (0,032). The actual degree of homozygosity of Novoalexandrovskaya grafter horse breed is G (0.132), the expected degree is Ca (0.148), the Torian horse breed degrees are G (0.064) and Ca (0.144) accordingly. The polymorphism level of Ae of the breeds is 6.75 and 6.919 accordingly, indicating homozygote deficiency and low level of consolidation. The actual degree of heterozygosity of Novoalexandrovskaya drafter horse breed is 0.867, while the expected degree is 0.871. The actual degree of heterozygosity of Torian horse breed is 0.935, while the expected degree is 0.855. Thus, the level of genetic diversity in the examined horses is rather high, which indicates a significant reserve of variability and avoids innbreeding depression. Keywords: allele, horses, Novoalexandrovskaya grafter horse breed, Torian breed, genetic frequency, genetic variability.

STUDY OF BETA-CASEIN GENE POLYMORPHISM AND ITS RELATIONSHIP WITH MILK COMPOSITION IN SIMMENTAL COWS

STUDY OF BETA-CASEIN GENE POLYMORPHISM AND ITS RELATIONSHIP WITH MILK COMPOSITION IN SIMMENTAL COWS

Influence of the degree of homozygosity of STR-loci on the fertility of thoroughbred horses

Purpose: to study the effect of the level of homozygosity and inbreeding on the fecundity of thoroughbred mares.Materials and methods. A total of 3662 heads of breeding sows from leading stud farms of the Russian Federation were selected for the analysis. The influence of the homozygosity level on 17 microsatellite DNA loci on the main indices of reproduction of thoroughbred mares, such as the safe yield of foals and the number of fetal years, was analyzed in the article. All mares in the experimental sample had at least three years of breeding use. Individual fecundity rates and the number of homozygous loci in the STR profile were calculated for each horse.Results. The highest live foal yields (75.92%) had sows with homozygosity levels of 62.78-69.02%, and the lowest foal yields (45.73%) were recorded in mares with the highest homozygosity levels (75.28-76.92%). The maximum foal yield (65.85%) was determined in sows with an inbreeding rate of 4.1% or more, with a productive longevity of 6.26 fetal years on average. Analysis of the data showed that the level of inbreeding had almost no effect on the yield of live foals (R=0.010 at P>0.05), but had a negative correlation with the number of fruiting years (R=-0.092 at P<0.005).Conclusion. Estimation of homozygosity level of thoroughbred horses is especially relevant, as this breed has been perfected by purebred breeding method only for more than thirty years. In the thoroughbred horse breed, it is necessary to create a system of maintaining heterozygosity as well as the diversity of genotypes through the organization of breeding work.

Analysis of dairy productivity of cows of ukrainian brown dairy breed of different genotypes by kappa-casein

In the herd of cattle of the Ukrainian Brown Dairy breed studies were conducted, the purpose of which was to study the influence of the genotype of cows by kappa-casein on the indicators of their milk productivity. Genotyping of 29 heads of cattle. Determination of the polymorphism of the kappa-casein gene was performed in the genetic laboratory of the Institute of Physiology n.a. Bogomolets of NAS using molecular biological analysis of allele recognition by polymerase chain reaction (PCR) in real time. Allele A had a slightly higher frequency - 0.517 compared to allele B - 0.483 at the locus of the kappa-casein gene, although it was not significant. As a result, the proportions of AA and BB genotypes were high (38 and 34%, respectively). The performed genetic-statistical analysis revealed an excess in the kappa-casein locus of homozygous variants AA and BB and a lack of heterozygous AB. The degree of homozygosity, which is 50.1%, indicates a sufficient level of consolidation in the studied population of cattle. The number of effective active alleles in the kappa-casein locus of cows of the Ukrainian Brown Dairy breed is 1.99, with the maximum value of the level of polymorphism possible at a two-allele locus of 2. A negative heterozygosity test (HT) indicates a lower proportion of actual heterozygotes relative to the proportion of theoretical heterozygotes. The reason for the existing genetic structure of the herd of Ukrainian Brown Dairy breeds by the kappa-casein locus was the use of Swiss cattle breeders, most of which were not evaluated by the genotype of the kappa-casein gene. Studies of the level of milk productivity of cows of different genotypes by kappa-casein in the first lactation did not reveal a significant difference. At the same time, heterozygous (AB) animals were inferior to homozygous (AA and BB) in terms of milk yield, and animals with AA and AB genotypes were preferred in terms of quality. For the best lactation, a significant difference was found in the amount of milk yield and the amount of milk fat. Homozygous animals (AA and BB) significantly (p <0.05) outperformed heterozygous (AB) in milk yield, by 1091 and 922 kg, respectively. Animals with heterozygous AB genotype in terms of the average amount of milk fat were significantly inferior to homozygous AA and BB animals (p <0.05). The small number of experimental animals was one of the reasons for the discrepancy between the results of research and the data of other scientists. Key words: breed, milk yield, fat content, protein content, kappa casein, genotype, allele.

The use of modern biotechnology of reproduction to improve the Hereford gene pool

The gene pool improvement of North Caucasian population is carried out through artificial insemination of herds with sperm from sires carrying the desired alleles of genes associated with meat productivity and beef quality. The frequency of homozygotes in CAPN1 gene was found in Stavropol population of Hereford sires: CC – 6 %, GG – 88 % and more. This indicator was 50.0 % in the LL genotype of somatotropin gene (GH), which is 22-28 % more than that in hetero and homozygotes LV and VV. The frequency of CC genotype was 61 % higher in TG5 DNA-marker than that of the heterozygous CT form. The use of modern biotechnological methods of herd reproduction made it possible to reduce the degree of homozygosity in CAPN1 and TG5 genes by 28.8% and by 18.1% in the next generation. The homozygosity degree in CAPN1 and TG5 genes were less by 28.8 % and 18.1 % in progeny than that in sires. However, the number of effective alleles was higher by 0.53 % and 0.41 % for CAPN1 and TG5 SNP markers in progeny bulls. The observed heterozygosity varied in the range of 0.281-0.344 for gene markers CAPN1, GH and TG5 in the sire group. A high genetic similarity was established between sires and progeny – an average of 0.973. This indicator was 0.999 and 0.970 for GH and TG5 gene-markers. The largest genetic distance was determined in CAPN1 gene – 0.044. Thus, the high plasticity of the gene pool in North Caucasian Herefords population has been proved under the influence of a targeted mating system of parental pairs based on the improvement of herd reproduction biotechnology. The progeny bulls from sires-carriers of the desired alleles had an advantage over peers in growth rate at the age of 3-7 months and 12-15 months, it amounted to 163.9 g (17.7 %; P <0.05) and 160.3 g (14.5 %; P <0.05) respectively.

Differentiation of lines of Sychevka cattle using marker genes

The results of genetic differentiation of 10 main genealogical groups of sires of the breed of Sychevka cattle of the Smolensk region, using as genetic markers the genes of the B-locus of erythrocyte antigens of blood groups (n = 2949). At the present stage of breed improvement, 56 marker genes of the EAB locus were found in the studied animals, of which 16 are common to all lines and related groups. The most common are: b, G2Y2E'1Q', I1Y2E'3G'G'', I1Y2I', O1I'Q', O2A'2J'2K'O', Q', Y1A'1. Lines and related groups were differentiated by the level of marker gene concentration, degree of homozygosity, and genetic similarity. The coefficient of genetic similarity (r) between different lines ranged from 0.58 to 0.85. The high similarity between animals of individual lines and the wide distribution of identical inherited material marked with the G2Y2E'1Q' allele indicate that there are no genetic differences between them. The lines that originate from sires of Sychevska and Holstein origin do not have significant genetic differences between them (r = 0.9). It is proposed to direct breeding work using genetic markers to increase the genetic differentiation of existing and breeding new lines.

Dynamics of the Inbreeding Coefficient and Homozygosity in Thoroughbred Horses in Russia.

Simple SummaryThe Thoroughbred horse breed provides a unique model for studying the theoretical bases and practical methods of selection in horse breeding. To assess the diversity in the modern population of Russian Thoroughbred horses, we used classic parameters, such as Wright’s inbreeding coefficient, the heterozygosity level, and population inbreeding level, over the period 1990–2018. The average inbreeding coefficient of the Thoroughbred horses was 0.83% and slowly increased over the past three decades. The individual observed heterozygosity levels of the tested horses varied within 23.1–100%, and the population’s parameters of observed heterozygosity tended to decrease. The relationship between the level of inbreeding and the rate of homozygosity was not significant (r = 0.022; p > 0.05).The Thoroughbred (TB) horse has hugely impacted the development of horse breeding around the world. This breed has unique genetic qualities due to having had a closed studbook for approximately 300 years. In Russia, TBs have been bred since the second half of the 18th century. Here, we analyzed the genetic diversity and the inbreeding level in TB horses (n = 9680) for the period from 1990 to 2018 using polymorphisms of 17 microsatellite loci. We found that the genetic structure of the TB breed in Russia is represented by 100 alleles of panel STR (short tandem repeat) loci and has been stable for the past three decades. The conducted monitoring revealed a slight increase in the Wright’s inbreeding coefficient in all age and sex groups of TB horses (stallions, broodmares, and foals) from 0.68% to 0.90%, which was followed by a decrease in the degree of heterozygosity, Ho, from 68.5% to 67.6%. The Spearman’s rank correlation coefficient between the level of inbreeding and the degree of homozygosity was estimated (r = 0.022; p > 0.05). The obtained data on the DNA genotypes of horses of different breeds provide a unique base for the evaluation of genetic variability and the control of genetic variability of horses in selection programs.

Review: Understanding Rare Genetic Diseases in Low Resource Regions Like Jammu and Kashmir - India.

Rare diseases (RDs) are the clinical conditions affecting a few percentage of individuals in a general population compared to other diseases. Limited clinical information and a lack of reliable epidemiological data make their timely diagnosis and therapeutic management difficult. Emerging Next-Generation DNA Sequencing technologies have enhanced our horizons on patho-physiological understanding of many of the RDs and ushered us into an era of diagnostic and therapeutic research related to this ignored health challenge. Unfortunately, relevant research is meager in developing countries which lack a reliable estimate of the exact burden of most of the RDs. India is to be considered as the “Pandora’s Box of genetic disorders.” Owing to its huge population heterogeneity and high inbreeding or endogamy rates, a higher burden of rare recessive genetic diseases is expected and supported by the literature findings that endogamy is highly detrimental to health as it enhances the degree of homozygosity of recessive alleles in the general population. The population of a low resource region Jammu and Kashmir (J&K) – India, is highly inbred. Some of its population groups variably practice consanguinity. In context with the region’s typical geographical topography, highly inbred population structure and unique but heterogeneous gene pool, a huge burden of known and uncharacterized genetic disorders is expected. Unfortunately, many suspected cases of genetic disorders remain undiagnosed or misdiagnosed due to lack of appropriate clinical as well as diagnostic resources in the region, causing patients to face a huge psycho-socio-economic crisis and many a time suffer life-long with their ailment. In this review, the major challenges associated with RDs are highlighted in general and an account on the methods that can be adopted for conducting fruitful molecular genetic studies in genetically vulnerable and low resource regions is also provided, with an example of a region like J&K – India.

IMPACT OF HLA-DPB1 MATCHING ON CLINICAL OUTCOMES AFTER HAPLOIDENTICAL-RELATED HEMATOPOIETIC STEM CELL TRANSPLANTATION.

The impact of HLA-DPB1 compatibility and its role as a transplantation antigen in haploidentical-related hematopoietic stem cell transplant (haplo-R-HSCT) have not been established, and a negative effect on survival has been suggested. The objective of the determine was to study the frequency and clinical effects of incompatibility at the HLA-DPB1 locus in the haplo-R-HSCT setting. Clinical records and electronic files of 91 patients with a hematological disease who underwent haplo-HSCT from January 2009 to October 2017 in a university medical center were scrutinized. Overall survival (OS) was estimated by the Kaplan-Meier method; the cumulative incidence of transplant-related mortality (TRM) and relapse rates was determined. Acute graft-versus-host disease was assessed by binary logistic regression. Cox regression model with a 95% confidence interval was used to examine the association between the different variables and their effect on OS. Of the 91 donor-recipient pairs, 24 (26.37%) shared complete DPB1 identity, 60 (65.93%) had a mismatch at one allele, and 7 (7.70%) were mismatched at two alleles. Twenty-four different HLA-DPB1 alleles were found; the most frequent were DPB1*04:01 (34.1%) and DPB1*04:02 (27.5%). Two-year OS, the cumulative incidence of TRM and relapse was 51.3 ± 6.8%, 28 ± 6% and 60 ± 7.8% for all haplo-related transplants, respectively, with no statistical difference between HLA-DPB1 matched and partially matched patients. In Cox regression analysis, no risk factors associated with OS, TRM, or relapses were identified. HLA-DPB1 mismatching in the haplo-R-HSCT setting did not influence transplant outcomes and was clinically tolerable. A high degree of homozygosity was found.

Biotechnological methods as a tool for efficient sugar beet breeding.

Here we consider aspects of the application of biotechnological methods to rapid creation, propagation, and maintenance of plants with improved or new traits in sugar beet breeding. The results of the works carried out in these fields by the Federal State Budgetary Scientific Institution “The A.L. Mazlumov All-Russia Research Institute of Sugar Beet” are reviewed. A close association between morphological and physiological changes in in vitro cultured organs and tissues, on the one hand, and breeding traits, on the other hand, which allows the development of experimental systems for non-amphimictic plant reconstruction is shown. The influence of in vitro growth conditions on haploid cells of unfertilized sugar beet ovules in the course of obtaining doubled haploid lines with high degree of homozygosity and maintenance of valuable breeding properties is considered. As compared to common inbreeding, this method shortens the time for development of homozygous material from 10–12 to 3–5 years, which is of great importance for speeding-up the breeding process. The results of studies on the culturing of mature sugar beet zygotic embryos based on in vitro selective systems have made it possible to improve the adaptive potential of plants and to provide complex resistance to environmental stress factors. Strict selection under abiotic stress conditions allowed creation of sugar beet isogenic lines with tolerance of drought, salinity, and soil acidity. It is shown that the proposed original design of mass-scale microclonal in vitro reproduction and deposition of elite plants as components of highly productive hybrids can be used to obtain seeds of uniform high-quality breeding material. The technologies developed by biotechnological methods are a topical and innovative direction of inquiry, since the application of these techniques to sugar beet breeding will promote obtaining of competitive hybrids with a set of commercially valuable traits. The combination of biotechnology methods, including tissue culture, and traditional breeding techniques is expected to provide an opportunity to obtain a new starting material to develop domestic varieties and hybrids of new generation with heterosis effect and a wide resistance spectrum persisting across generations.

Screening of 31 genes involved in monogenic forms of obesity in 23 Pakistani probands with early-onset childhood obesity: a case report

BackgroundConsanguine families display a high degree of homozygosity which increases the risk of family members suffering from autosomal recessive disorders. Thus, homozygous mutations in monogenic obesity genes may be a more frequent cause of childhood obesity in a consanguineous population.MethodsWe identified 23 probands from 23 Pakistani families displaying autosomal recessive obesity. We have previously excluded mutations in MC4R, LEP and LEPR in all probands. Using a chip-based, target-region capture array, 31 genes involved in monogenic forms of obesity, were screened in all probands.ResultsWe identified 31 rare non-synonymous possibly pathogenic variants (28 missense and three nonsense) within the 31 selected genes. All variants were heterozygous, thus no homozygous pathogenic variants were found. Two of the rare heterozygous nonsense variants identified (p.R75X and p.R481X) were found in BBS9 within one proband, suggesting that obesity is caused by compound heterozygosity. Sequencing of the parents supported the compound heterozygous nature of obesity as each parent was carrying one of the variants. Subsequent clinical investigation strongly indicated that the proband had Bardet-Biedl syndrome.ConclusionsMutation screening in 31 genes among probands with severe early-onset obesity from Pakistani families did not reveal the presence of homozygous obesity causing variants. However, a compound heterozygote carrier of BBS9 mutations was identified, indicating that compound heterozygosity must not be overlooked when investigating the genetic etiology of severe childhood obesity in populations with a high degree of consanguinity.

Polymorphism of Keratin - Associated Protein (KAP) 6.1 gene and its association with wool traits of Sandyno and Nilagiri breeds of sheep

Polymorphic variants of keratin-associated protein (KAP) 6.1 gene with wool traits of Sandyno and Nilagiri breeds of sheep were investigated in this study. Genomic DNA was isolated from blood samples of 125 Sandyno, Nilagiri and Dorset x Nilagiri breeds of sheep along with 76 numbers of wool samples. A 528 bp segment was amplified by PCR using ovine specific primers for KAP 6.1 gene. SSCP analysis of KAP 6.1 gene in Dorset x Nilagiri crossbred sheep resulted in two genotypes for the A/B with no polymorphism. KAP 6.1 gene locus revealed allele frequencies of A, B, C, D and E in Sandyno sheep were 0.67, 0.23, 0.04, 0.01 and 0.04 and in Nilagiri were 0.75, 0.06, 0.11, 0.04 and 0.04 respectively. KAP 6.1 gene revealed departure from Hardy-Weinberg equilibrium. KAP 6.1 genes were found to have high degree of homozygosity (0.6667) in Nilagiri sheep. The effective number of alleles (Ne) for KAP 6.1 gene was 1.1690 and 1.7006 respectively in Sandyno and Nilagiri breeds of sheep. The PIC values for KAP 6.1 gene was 0.1341 and 0.3909 in Sandyno and Nilagiri breeds of sheep respectively. FIS values for KAP 6.1 gene was positive (0.1909) in Nilagiri breed and it was negative (– 0.0110) in Sandyno breed. Least squares analysis of variance showed significant (P less than 0.05) effect between genotypes and between sexes for wool traits like GFW (kg), CWY (%) and FD (µ). Significant (P less than 0.05) effect of breed (Sandyno and Nilagiri) was observed for all the wool traits (GFW, CWY, FD, SL and Medullation %). Significant (p less than 0.05) higher CWY production was recorded for AC genotype (62.00 ± 1.73 %) while low value was recorded for BB genotype (56.25 ± 1.74 %). FD was found to be high in genotype AC (24.29 ± 1.17 µ) than in AA genotype (23.24 ± 0.49 µ). The homozygote AA was found to have more Medullation (%) and SL. Genotypes BB had higher GFW and lower CWY. The heterozygous genotype AC yielded more FD and CWY with lower most Medullation (%) and SL values. From the study, it may be concluded that KAP 6.1 gene might be a potential molecular marker for genetic selection of wool traits in Sandyno and Nilagiri breeds of sheep.