Levels Of Homozygosity Research Articles

Jan and mini-Jan, a model system for potato functional genomics.

Potato (Solanum tuberosum) is the third-most important food crop in the world. Although the potato genome has been fully sequenced, functional genomics research of potato lags behind that of other major food crops, largely due to the lack of a model experimental potato line. Here, we present a diploid potato line, 'Jan,' which possesses all essential characteristics for facile functional genomics studies. Jan exhibits a high level of homozygosity after seven generations of self-pollination. Jan is vigorous, highly fertile and produces tubers with outstanding traits. Additionally, it demonstrates high regeneration rates and excellent transformation efficiencies. We generated a chromosome-scale genome assembly for Jan, annotated its genes and identified syntelogs relative to the potato reference genome assembly DMv6.1 to facilitate functional genomics. To miniaturize plant architecture, we developed two 'mini-Jan' lines with compact and dwarf plant stature through CRISPR/Cas9-mediated mutagenesis targeting the Dwarf and Erecta genes involved in growth. One mini-Jan mutant, mini-JanE, is fully fertile and will permit higher-throughput studies in limited growth chamber and greenhouse space. Thus, Jan and mini-Jan offer a robust model system that can be leveraged for gene editing and functional genomics research in potato.

Jan and mini-Jan, a model system for potato functional genomics.

Potato ( Solanum tuberosum ) is the third most important food crop in the world. Although the potato genome has been fully sequenced, functional genomics research of potato lags relative to other major food crops due primarily to the lack of a model experimental potato line. Here, we present a diploid potato line, 'Jan', which possesses all essential characteristics for facile functional genomics studies. Jan has a high level of homozygosity after seven generations of self-pollination. Jan is vigorous and highly fertile with outstanding tuber traits, high regeneration rates, and excellent transformation efficiencies. We generated a chromosome-scale genome assembly for Jan, annotated genes, and identified syntelogs relative to the potato reference genome assembly DMv6.1 to facilitate functional genomics. To miniaturize plant architecture, we developed two "mini-Jan" lines with compact and dwarf plant stature using CRISPR/Cas9-mediated mutagenesis targeting the Dwarf and Erecta genes related to growth. Mini-Jan mutants are fully fertile and will permit higher-throughput studies in limited growth chamber and greenhouse space. Thus, Jan and mini-Jan provide an outstanding model system that can be leveraged for gene editing and functional genomics research in potato.

Strategy for early selection for grain yield in soybean using BLUPIS

In soybean breeding programs, a great deal of time is devoted to the use of methods that perform selection of individual plants during the initial generations. Our hypothesis is that BLUPIS (simulated individual BLUP) can be efficient when applied in the initial stages of soybean breeding programs. This study aimed to explore the potential of BLUPIS in the early generations of a soybean breeding program, as well as to assess the viability of the strategy of dividing the useful area of experimental plots for estimating genotypic effects and plant selection. The experiment involved 84 segregating populations and 15 soybean parents in the F2 and F3 generations. Yield data was collected from the 2019/2020 and 2020/2021 cropping seasons. In the F2 generation, different data exploration methods were applied to determine the most suitable adaptation to be used in the F3 generation. The individual BLUP (BLUPI) was compared with BLUPIS using information from different replications and/or equal to the information used in BLUPI. The selection conducted by BLUPIS and BLUPI showed high concordance regarding the selected plants. In the F3 generation, segregating populations were selected based on positive genotypic effects, and individual plants within these populations were further selected according to the number of plants determined by BLUPIS. The division of the plot area was an efficient strategy for selecting segregating populations and individual plants within superior populations in the F3 generation, resulting in genetic gains of approximately 1.56 g per plant. When combined with the strategy of advancing generations in the off-season, the BLUPIS approach reduces the time required to achieve a high level of homozygosity. Therefore, BLUPIS proved to be a powerful statistical tool for early selection based on grain yield in soybeans.

Runs of Homozygosity Islands in Autochthonous Spanish Cattle Breeds.

Understanding the genetic architecture of autochthonous European cattle breeds is important for developing effective conservation strategies and sustainable breeding programs. Spanish beef cattle, which trace their origins to ancient migrations from the Near East with later admixture from African populations, exhibit a rich genetic diversity shaped by environmental adaptation and selective breeding. Runs of Homozygosity (ROH) are extended stretches of identical genetic material inherited from both parents. They serve as indicators of inbreeding and selection signatures within populations. ROH islands, or regions of the genome where ROH segments are highly concentrated across individuals within a breed, indicate genomic regions under selective pressure. This study explores the distribution of ROH islands across seven Spanish beef cattle breeds (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Retinta, Pirenaica, and Rubia Gallega). By analyzing high-density SNP data, we characterized ROH patterns and identified genomic regions with high levels of homozygosity, which may indicate selection pressures or common ancestry. Our findings revealed breed-specific ROH patterns as well as shared ROH islands, underscoring genetic relationships and differentiation among the breeds. Notably, Morucha displayed the highest number of ROH, while Asturiana de los Valles had the fewest. FROH values, which indicate genomic inbreeding, varied among the breeds, with Morucha and Retinta being associated with higher values. We identified 57 ROH islands, with shared regions among populations that suggest common ancestral selection pressures. Key genes within these regions, like MSTN, are associated with muscle growth, body weight, and fertility. This study offers valuable insights for breeding strategies and conservation efforts, highlighting the genetic diversity and historical background of Spanish cattle breeds.

Genome-wide scan for selection signatures in Mexican Sardo Negro Zebu cattle.

The Sardo Negro cattle (SN) is the only zebu cattle breed developed in Mexico. Since its development, the selection could have led to an increase in the homozygosity level in some regions of the genome and made differentiation with other cattle populations. We aimed to identify and characterize selection signatures in SN using medium-density SNP data using four approaches: 1) Runs of homozygosity (ROH) 2) Nucleotide Diversity 3) Tajima's D and 4) the Wright's fixation index (FST). A sample of 555 SN animals genotyped for 65k SNPs was used to obtain ROH segments considered regions under selection. The FST values were estimated by comparing the sample of genotyped SN animals with samples of genotyped animals from the Gir, Brahman, and Ongole breeds. Only one region mapped to 35.78-42.51 Mb on BTA6 was considered a selection signature by the ROH method. This selection signature overlapped with the lowest diversity, negative values of Tajima's D and a diversification region between SN and the other Zebu breeds by FST. We found several candidate genes (LCORL, NCAPG, and SLIT2) related to growth and other economically important productive traits in this common region. Using the FST method, different regions, such as regions on BTA8 (8:93.4-93.9 Mb), BTA11 (11:99.2-99.7), and BTA14 (14: 26.1-26.8) related to growth and milk traits also were defined as candidate selection signatures. The selective signals identified in this study reflected the direction of the selection pressure that primarily involves the increase of live weight traits in the Sardo Negro cattle breeding program.

A genome assembly and transcriptome atlas of the inbred Babraham pig to illuminate porcine immunogenetic variation.

The inbred Babraham pig serves as a valuable biomedical model for research due to its high level of homozygosity, including in the major histocompatibility complex (MHC) loci and likely other important immune-related gene complexes, which are generally highly diverse in outbred populations. As the ability to control for this diversity using inbred organisms is of great utility, we sought to improve this resource by generating a long-read whole genome assembly and transcriptome atlas of a Babraham pig. The genome was de novo assembled using PacBio longreads and error-corrected using Illumina shortreads. Assembled contigs were then mapped to the porcine reference assembly, Sscrofa11.1, to generate chromosome-level scaffolds. The resulting TPI_Babraham_pig_v1 assembly is nearly as contiguous as Sscrofa11.1 with a contig N50 of 34.95 Mb and contig L50 of 23. The remaining sequence gaps are generally the result of poor assembly across large and highly repetitive regions such as the centromeres and tandemly duplicated gene families, including immune-related gene complexes, that often vary in gene content between haplotypes. We also further confirm homozygosity across the Babraham MHC and characterize the allele content and tissue expression of several other immune-related gene complexes, including the antibody and T cell receptor loci, the natural killer complex, and the leukocyte receptor complex. The Babraham pig genome assembly provides an alternate highly contiguous porcine genome assembly as a resource for the livestock genomics community. The assembly will also aid biomedical and veterinary research that utilizes this animal model such as when controlling for genetic variation is critical.

CARBONIC ANHYDRASE FREQUENCY AND POPULATION STABILITY AMONG BREEDS OF NIGERIAN GOAT.

Using 900 goats of the three breeds in Nigeria from Borno, Sokoto and Ogun States with equal number across breed, blood was collected from each animal by means of jugular venipuncture and placed in heparinized tubes to prevent coagulation. It was then refrigerated at 8°C for two hours and thereafter carried into the laboratory. Carbonic anhydrase polymorphism from blood plasma and blood hemolysate were analysed by the method of starch gel electrophoresis using direct current electric source Multidrive XL. Gene, genotypic frequencies, allelic frequencies and genetic distance among the breeds were estimated for this locus. Carbonic anhydrase presented two alleles, Ca-S and Ca-F. The (Ca-F) was the predominant alleles in all the studied breeds. West African Dwarf breed recorded the highest frequency (0.9900) for (Ca-F) while the least value (0.9868) for (Ca-F) was observed in Red Sokoto goat. Considering the pattern of genotype within the sample population for carbonic anhydrase, it was observed that the average heterozygosity for all the breeds was 0.0000. This is a marker that the population has high level of homozygosity for carbonic anhydrase. UPMGA cluster showing relationship between populations at CA locus indicated similar distance value (0.0000) for the populations. It was recommended from observed result that the high level of homozygosity observed for this locus indicates that it is not a suitable candidate for selection and breeding purposes.

Exploring molecular, morphological, and biochemical diversity of Phaeolus vulgaris landraces cultivated in the Aniene Valley (Lazio region, Italy)

The cultivation of common beans has long been integral to rural economies in Italy, particularly in mountainous regions along the Apennine ridge, where the production focuses on local landraces grown by smallholder farmers using low-input methodologies. However, recent socioeconomic changes in rural communities pose a threat of genetic erosion to these landraces. This study examines the genetic diversity, structure, and uniqueness of common bean landraces in the Aniene Valley of the Lazio region to develop preservation strategies. Seventy-three accessions were investigated using morphological (seed traits), biochemical (phaseolin and phytohemagglutinin patterns), and molecular (microsatellite loci) analyses. These analyses revealed significant genetic variability within morphologically uniform seed materials and highlighted cases of homonymy and the inadvertent introduction of foreign genetic material. Among the 292 samples analyzed (four per accession), a clear differentiation between Mesoamerican and Andean gene pools was observed, with the Andean pool being predominant. Despite high levels of homozygosity and uniform seed morphotypes, genetic variability was detected in sixteen of the twenty-one landraces, suggesting that analyzing only a single or few plants per landrace may yield incomplete genetic information. The extensive morphological, biochemical, and genetic characterization of the P. vulgaris collection from the Aniene Valley provides insights for planning effective conservation strategies. These findings emphasize the importance of both in situ/on-farm and ex-situ conservation to preserve the genetic diversity and heritage of these local landraces.

Genetic characteristic of holstein cattle bred at Rakovskoye LLC of Primorsky Territory

The immunogenetic strucrure of Holstein cattle being imported from Germany and Hungary is determined. The presence of antigenes being met seldom – Z’ (EAA-locus), P2, T2, Q, I′, J′2, K′, P′, Y′, B′′ (EAB-locus), R1 (EAC- locus) and M (EAM-locus) is characteristic of the researched group of animals (1116 heads). Their summary frequency of being met made 17,64%. The antigenes – A2 (EAA-locus), G2, G3, Y2, E′2, E′3, G′, Q′ (EAB-locus), C1, C2, E, W, X2 (EAC-locus), F (EAF-locus), H′ (EAS-locus) are met with high frequency.They have been discovered in 40,05–98,39% of animals. Analysis of distribution of the genotypes in EAF-locus. pointed to the breach of genetic balance, that is caused by oversurplus of homozygous genotypes V/V and shortage of heterozygous F/V. Analysis of distribution of EAB-alleles exposed the high frequency of being met of the allele G2Y2Eʹ2Qʹ (q=0,2711), and also a presence in the researched group of animals the alleles typical for the black and white cattle, red steppe and other breeds of cattle. The level of homozygosity (Са) concerning EAB-locus. made 10,9%. The received materials. will be used in future for the improvement of selection and breeding work with the imported Holstein cattle.

A Case Study from the Overexpression of OsTZF5, Encoding a CCCH Tandem Zinc Finger Protein, in Rice Plants Across Nineteen Yield Trials

BackgroundDevelopment of transgenic rice overexpressing transcription factors involved in drought response has been previously reported to confer drought tolerance and therefore represents a means of crop improvement. We transformed lowland rice IR64 with OsTZF5, encoding a CCCH-tandem zinc finger protein, under the control of the rice LIP9 stress-inducible promoter and compared the drought response of transgenic lines and nulls to IR64 in successive screenhouse paddy and field trials up to the T6 generation.ResultsCompared to the well-watered conditions, the level of drought stress across experiments varied from a minimum of − 25 to − 75 kPa at a soil depth of 30 cm which reduced biomass by 30–55% and grain yield by 1–92%, presenting a range of drought severities. OsTZF5 transgenic lines showed high yield advantage under drought over IR64 in early generations, which was related to shorter time to flowering, lower shoot biomass and higher harvest index. However, the increases in values for yield and related traits in the transgenics became smaller over successive generations despite continued detection of drought-induced transgene expression as conferred by the LIP9 promoter. The decreased advantage of the transgenics over generations tended to coincide with increased levels of homozygosity. Background cleaning of the transgenic lines as well as introgression of the transgene into an IR64 line containing major-effect drought yield QTLs, which were evaluated starting at the BC3F1 and BC2F3 generation, respectively, did not result in consistently increased yield under drought as compared to the respective checks.ConclusionsAlthough we cannot conclusively explain the genetic factors behind the loss of yield advantage of the transgenics under drought across generations, our results help in distinguishing among potential drought tolerance mechanisms related to effectiveness of the transgenics, since early flowering and harvest index most closely reflected the levels of yield advantage in the transgenics across generations while reduced biomass did not.

Analysis of the level of inbreeding and relatedness of Bull Terrier dogs – the popular stud dog effect

The aim of the study was to analyze the level of homozygosity of a bull terrier dog population due to its small size, forcing mating in kinship and, possibly, overuse of popular stud dogs. The pedigrees of 107 bull terrier dogs (35 males and 72 females), born in 2008-2016 were used to obtain the inbreeding coefficients for all animals and relatedness coefficients between dogs, between bitches and between bitches and dogs. Pedigrees of bull terriers were also analyzed for occurrence the most common stud dogs. The frequency of occurrence of a popular sire was found according to its position in the pedigree. For the most common stud dog, a list of his sons and their progeny was created. In total about 75% of individuals from the studied population were inbred and their average inbreeding was over 0.04. Almost 95% of bull terriers were related with the average relatedness amounting to over 0.07. The highest value of an individual's inbreeding was almost 0.18, and the highest relationship coefficient was between bitches (over 0.61). There was a popular stud dog in the analyzed population that appeared 113 times in the pedigrees of 107 tested animals and his genes were passed on by his 10 sons as well. It should be noticed that the studied population requires constant monitoring of genetic variability and limiting the overuse of popular stud dogs, which should lead to maintain the variability.

Genome-wide diversity, population structure and signatures of inbreeding in the African buffalo in Mozambique

The African buffalo, Syncerus caffer, is a key species in African ecosystems. Like other large herbivores, it plays a fundamental role in its habitat acting as an ecosystem engineer. Over the last few centuries, African buffalo populations have declined because of range contraction and demographic decline caused by direct or indirect human activities. In Mozambique, historically home to large buffalo herds, the combined effect of colonialism and subsequent civil wars has created a critical situation that urgently needs to be addressed. In this study, we focused on the analysis of genetic diversity of Syncerus caffer caffer populations from six areas of Mozambique. Using genome-wide SNPs obtained from ddRAD sequencing, we examined the population structure across the country, estimated gene flow between areas under conservation management, including national reserves, and assessed the inbreeding coefficients. Our results indicate that all studied populations of Syncerus caffer caffer are genetically depauperate, with a high level of inbreeding. Moreover, buffaloes in Mozambique present a significant population differentiation between southern and central areas. We found an unexpected genotype in the Gorongosa National Park, where buffaloes experienced a dramatic population size reduction, that shares a common ancestry with southern populations of Catuane and Namaacha. This could suggest the past occurrence of a connection between southern and central Mozambique and that the observed population structuring could reflect recent events of anthropogenic origin. All the populations analysed showed high levels of homozygosity, likely due to extensive inbreeding over the last few decades, which could have increased the frequency of recessive deleterious alleles. Improving the resilience of Syncerus caffer caffer in Mozambique is essential for preserving the ecosystem integrity. The most viable approach appears to be facilitating translocations and re-establishing connectivity between isolated herds. However, our results also highlight the importance of assessing intraspecific genetic diversity when considering interventions aimed at enhancing population viability such as selecting suitable source populations.

Performance of Convergent Breeding Wheat (Triticum aestivum L.) Lines in the Lowlands

The development of tropical wheat in Indonesia is currently confined to the availability of wheat’s optimal environments in the highlands. Wheat competes with major highland crops, such as vegetables, which also have high economic values. Despite this, the demand for wheat in Indonesia remains high, whether in the form of wheat flour, wheat meal, or oats. Wheat breeders are actively working to create various crossbreeds so that wheat can adapt and perform effectively in lowland areas. The convergent breeding method is one of the strategies employed to produce genotypes with superior performance. Convergent breeding enhances genetic diversity by incorporating superior traits from all parent plants. The breeding results expedite the emergence of genetic combinations between selected parents. This method involves combining several parent varieties with various traits, with the hope that their offspring will inherit all the characteristics of the crossed parents. Our study with wheat convergent breeding has reached the F6 generation, and in this current study we evaluated the performance of each observed trait in different environments, with the goal of determining the levels of homogeneity and homozygosity. The study utilized a randomized complete block design with three replications, and the crops were planted in various locations. The planting locations selected were those that are >1000 m above sea level (asl), and at a lowland of ± 250 m asl. Wheat performance based on stomatal characteristics showed a reduction in the lowland, which indicates a response to climatic conditions in a particular environment. The higher the environmental temperatures, the smaller the stomatal size, which reduces plant water loss. Noteworthy findings include the tallest plant in CBF-6. CAMN23(265), the highest number of tillers in CBF-6. CAMN233 and CBF-6.CAMN8(4), the largest flag leaf area in CBF-7.CAMN60, and the highest 100-seed weight, as well as overall yield in CBF-7.CAMN119. An analysis of the lowland sensitivity index identified ten moderate genotypes that could potentially adapt well and achieve optimal yields.

Investigating the genetic makeup of the major histocompatibility complex (MHC) in the United Arab Emirates population through next-generation sequencing

The Human leukocyte antigen (HLA) molecules are central to immune response and have associations with the phenotypes of various diseases and induced drug toxicity. Further, the role of HLA molecules in presenting antigens significantly affects the transplantation outcome. The objective of this study was to examine the extent of the diversity of HLA alleles in the population of the United Arab Emirates (UAE) using Next-Generation Sequencing methodologies and encompassing a larger cohort of individuals. A cohort of 570 unrelated healthy citizens of the UAE volunteered to provide samples for Whole Genome Sequencing and Whole Exome Sequencing. The definition of the HLA alleles was achieved through the application of the bioinformatics tools, HLA-LA and xHLA. Subsequently, the findings from this study were compared with other local and international datasets. A broad range of HLA alleles in the UAE population, of which some were previously unreported, was identified. A comparison with other populations confirmed the current population’s unique intertwined genetic heritage while highlighting similarities with populations from the Middle East region. Some disease-associated HLA alleles were detected at a frequency of > 5%, such as HLA-B*51:01, HLA-DRB1*03:01, HLA-DRB1*15:01, and HLA-DQB1*02:01. The increase in allele homozygosity, especially for HLA class I genes, was identified in samples with a higher level of genome-wide homozygosity. This highlights a possible effect of consanguinity on the HLA homozygosity. The HLA allele distribution in the UAE population showcases a unique profile, underscoring the need for tailored databases for traditional activities such as unrelated transplant matching and for newer initiatives in precision medicine based on specific populations. This research is part of a concerted effort to improve the knowledge base, particularly in the fields of transplant medicine and investigating disease associations as well as in understanding human migration patterns within the Arabian Peninsula and surrounding regions.

Reproductive traits in Pura Raza Española mares manifest inbreeding depression from low levels of homozygosity.

Inbreeding depression is a genetic phenomenon associated with the loss of fitness and mean phenotypic performance due to mating between relatives. Historically, inbreeding coefficients have been estimated from pedigree information. However, the onset of genomic selection programs provides large datasets of individuals genotyped using SNP arrays, enabling more precise assessment of an individual's genomic-level inbreeding using genomic data. One of the traits most sensitive to issues stemming from increased inbreeding is reproduction. This is particularly important in equine, in which fertility is only moderate compared to other livestock species. To explore this further, we evaluated the effect of inbreeding on five reproductive traits (age at first foaling (AFF), average interval between foalings (AIF), total number of foalings (NF), productive life (PL) and reproductive efficiency (RE)) in Pura Raza Español mares using genomic data. Residual predicted phenotypes were obtained by purging these traits through the REML (wgResidual ) and ssGREML (gResidual ) approaches in reproductive data of 29,847 PRE mares using the BLUPF90+ program. Next, we used pedigree-based (Fped ) and ROH-based genomic (FROH ) inbreeding coefficients derived from 1018 animals genotyped with 61,271 SNPs to estimate the inbreeding depression (linear regression). Our results indicated significant levels of inbreeding depression for all reproductive traits, with the exception of the AIF trait when Fped was used. However, all traits were negatively affected by the increase in genomic inbreeding, and FROH was found to capture more inbreeding depression than Fped . Likewise, REML models (ssGREML) using genomic data for estimated predicted residual phenotypes resulted in higher variance explained by the model compared with the models not using genomics (REML). Finally, a segmented regression analysis was conducted to evaluate the effect of inbreeding depression, revealing that the levels of genealogical and genomic homozygosity do not manifest uniformly in reproductive traits. In contrast, the levels of inbreeding depression ranged from low to high as homozygosity increased. This analysis also showed that reproductive traits are very sensitive to inbreeding depression, even with relatively low levels of homozygosity.

Facultative parthenogenesis discovered for the first time in Jamaican boa (Chilabothrus subflavus) using novel microsatellite markers.

The mode of reproduction most often seen in snakes is sexual, but studies have noted facultative parthenogenesis in at least six families. Here, we provide evidence for the first observed case of facultative parthenogenesis in a captive Jamaican boa (Chilabothrus subflavus). A 7-year-old female Jamaican boa, isolated since birth, was found to have produced a litter of 15 offspring. To provide molecular DNA evidence of parthenogenesis, 13 new microsatellite loci were isolated in the species. All offspring were found to be homozygous at each locus and only possess alleles found in the dam, implicating that they were born from asexual reproduction. Several developmental abnormalities, including stillbirths and spinal deformities, were noted in the litter which may be explained by their increased level of homozygosity. To preserve genetic diversity in the captive population, research should be conducted to understand the prevalence of this mode of reproduction and to guide future management decisions of this IUCN listed Vulnerable species.

Genetic diversity of a recovering European roller (Coracias garrulus) population from Serbia.

The European Roller (Coracias garrulus), a long-distance migratory bird, faced a considerable decline in breeding pairs throughout Europe at the end of the 20th century. Due to conservation efforts and the installation of nesting boxes, the population of the European Roller in Serbia has made a remarkable recovery. Here, we used the variability of nucleotide sequences of the mitochondrial DNA (mtDNA) control region and 10 microsatellite loci to assess the genetic diversity and structuring, phylogeographic patterns and demographic history of this species using 224 individuals from Serbia. Our results showed moderate level of genetic diversity (HO = 0.392) and a slightly elevated level of inbreeding and homozygosity (FIS = 0.393). Genetic structuring based on microsatellite data indicated three genetic clusters, but without a clear spatial pattern. High haplotype diversity (Hd = 0.987) of the mtDNA control region sequences was detected, and neutrality tests indicated a recent demographic expansion. The phylogeographic analysis, which also included previously published sequences of the mtDNA control region, supported the subdivision into two distinct European and Asian haplogroups (ΦST = 0.712). However, the results of our study showed that a larger number of haplotypes sampled in Serbia are clustered in the Asian haplogroup as compared to previous studies, indicating a historically continuous distribution of this species and possibly a wider distribution of the subspecies Coracias garrulus semenovwi. Our results suggest that the European Roller population in Serbia is genetically stable, with no evidence of recent bottlenecks, and emphasize the importance of artificial nest boxes for promoting and maintaining population dynamics of European Rollers.

DArTseq-based SNP markers reveal high genetic diversity among early generation fall armyworm tolerant maize inbred lines.

Diversity analysis using molecular markers serves as a powerful tool in unravelling the intricacies of inclusivity within various populations and is an initial step in the assessment of populations and the development of inbred lines for host plant resistance in maize. This study was conducted to assess the genetic diversity and population structure of 242 newly developed S3 inbred lines using 3,305 single nucleotide polymorphism (SNP) markers and to also assess the level of homozygosity achieved in each of the inbred lines. A total of 1,184 SNP markers were found highly informative, with a mean polymorphic information content (PIC) of 0.23. Gene diversity was high among the inbred lines, ranging from 0.04 to 0.50, with an average of 0.27. The residual heterozygosity of the 242 S3 inbred lines averaged 8.8%, indicating moderately low heterozygosity levels among the inbred lines. Eighty-four percent of the 58,322 pairwise kinship coefficients among the inbred lines were near zero (0.00-0.05), with only 0.3% of them above 0.50. These results revealed that many of the inbred lines were distantly related, but none were redundant, suggesting each inbred line had a unique genetic makeup with great potential to provide novel alleles for maize improvement. The admixture-based structure analysis, principal coordinate analysis, and neighbour-joining clustering were concordant in dividing the 242 inbred lines into three subgroups based on the pedigree and selection history of the inbred lines. These findings could guide the effective use of the newly developed inbred lines and their evaluation in quantitative genetics and molecular studies to identify candidate lines for breeding locally adapted fall armyworm tolerant varieties in Ghana and other countries in West and Central Africa.

Identification on SNP polymorphisms associated with meat productivity in the local Kazakh horse breed

The aim of our study was to genotype local horses of the Kazakh breed, including the Zhabe u types from the Pavlodar and Zhetysu regions, as well as the Adai type from the Mangystau region, using PCR-RFLP methods for the LCORL and PRKAG3 gene loci. A total of 41 horses were included in the study. The results showed that the frequency of the homozygous genotype TT at the LCORL locus was 81.25% in Zhabe Pavlodar horses, with a heterozygous genotype TC of 18.75%. In Kazakh horses of the Adai type from Mangystau and Zhabe type from Zhetysu, no genetic polymorphism was detected, and all individuals had a homozygous genotype – TT. For the PRKAG3 locus, genetic polymorphism was only found in Adai type horses, with one mare out of 17 tested horses having a heterozygous genotype – CT (5.89%). Horses of the Zhabe type in Pavlodar and Zhetysu regions had a single homozygous CC genotype. The level of homozygosity for the LCORL gene locus in the three studied groups was: 81.25, 100.0 100.0. For the PRKAG3 gene is 100.0, 94.11, 100.0. The level of heterozygosity for the LCORL gene locus in horses of Pavlodar region was 18.75%, for the PRKAG3 gene locus in horses of Mangistau region 5.89%. Thus, LCORL and PRKAG3 gene polymorphisms play a significant role in determining the development of muscle mass, skeletal structure, chest circumference, and growth rate in horses. Therefore, these SNP polymorphisms can potentially serve as DNA markers for evaluating meat production in horses.

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.