High Levels Of Heterozygosity Research Articles

Genetic diversity of meat quality related genes in Argentinean pigs

Genetic influence on pork quality exists between breeds and within a breed. The variation is caused by a large set of genes, and pork quality traits have a multifactorial background. Research into the genetics of meat quality found causative mutations associated with marked effects on pig meat value. This study aimed to investigate the segregation of meat quality-related SNPs and compare their diversity and genetics in commercial and Creole pigs from different farms in the North-West of Argentina. A screen for SNPs in RYR1, PRKAG3, CAST, and SOX6 candidate genes and the differentiation of their genotypes by PCR–RFLP was conducted. All genes were characterized by a high level of polymorphism and heterozygosity, and populations showed no differences in the genetic structure for the analyzed SNPs. These results highlighted the role of pig genotypes as a source of basic variability potentially affecting processed meat products and fresh meat.

Highly efficient CRISPR systems for loss-of-function and gain-of-function research in pear calli.

CRISPR/Cas systems have been widely used for genome engineering in many plant species. However, their potentials have remained largely untapped in fruit crops, particularly in pear, due to the high levels of genomic heterozygosity and difficulties in tissue culture and stable transformation. To date, only a few reports on the application of the CRISPR/Cas9 system in pear have been documented, and have shown very low editing efficiency. Here we report a highly efficient CRISPR toolbox for loss-of-function and gain-of-function research in pear. We compared four different CRISPR/Cas9 expression systems for loss-of-function analysis and identified a potent system that showed nearly 100% editing efficiency for multi-site mutagenesis. To expand the targeting scope, we further tested different CRISPR/Cas12a and Cas12b systems in pear for the first time, albeit with low editing efficiency. In addition, we established a CRISPR activation (CRISPRa) system for multiplexed gene activation in pear calli for gain-of-function analysis. Furthermore, we successfully engineered the anthocyanin and lignin biosynthesis pathways using both CRISPR/Cas9 and CRISPRa systems in pear calli. Taking these results together, we have built a highly efficient CRISPR toolbox for genome editing and gene regulation, paving the way for functional genomics studies as well as molecular breeding in pear.

Detecting Structural Variants and Associated Gene Presence-Absence Variation Phenomena in the Genomes of Marine Organisms.

As complete genomes become easier to attain, even from previously difficult-to-sequence species, and as genomic resequencing becomes more routine, it is becoming obvious that genomic structural variation is more widespread than originally thought and plays an important role in maintaining genetic variation in populations. Structural variants (SVs) and associated gene presence-absence variation (PAV) can be important players in local adaptation, allowing the maintenance of genetic variation and taking part in other evolutionarily relevant phenomena. While recent studies have highlighted the importance of structural variation in Mollusca, the prevalence of this phenomenon in the broader context of marine organisms remains to be fully investigated.Here, we describe a straightforward and broadly applicable method for the identification of SVs in fully assembled diploid genomes, leveraging the same reads used for assembly. We also explain a gene PAV analysis protocol, which could be broadly applied to any species with a fully sequenced reference genome available. Although the strength of these approaches have been tested and proven in marine invertebrates, which tend to have high levels of heterozygosity, possibly due to their lifestyle traits, they are also applicable to other species across the tree of life, providing a ready means to begin investigations into this potentially widespread phenomena.

Genomic Prediction of Complex Traits in Forage Plants Species: Perennial Grasses Case.

The majority of forage grass species are obligate outbreeders. Their breeding classically consists of an initial selection on spaced plants for highly heritable traits such as disease resistances and heading date, followed by familial selection on swards for forage yield and quality traits. The high level of diversity and heterozygosity, and associated decay of linkage disequilibrium (LD) over very short genomic distances, has hampered the implementation of genomic selection (GS) in these species. However, next generation sequencing technologies in combination with the development of genomic resources have recently facilitated implementation of GS in forage grass species such as perennial ryegrass (Lolium perenne L.), switchgrass (Panicum virgatum L.), and timothy (Phleum pratense L.). Experimental work and simulations have shown that GS can increase significantly the genetic gain per unit of time for traits with different levels of heritability. The main reasons are (1) the possibility to select single plants based on their genomic estimated breeding values (GEBV) for traits measured at sward level, (2) a reduction in the duration of selection cycles, and less importantly (3) an increase in the selection intensity associated with an increase in the genetic variance used for selection. Nevertheless, several factors should be taken into account for the successful implementation of GS in forage grasses. For example, it has been shown that the level of relatedness between the training and the selection population is particularly critical when working with highly structured meta-populations consisting of several genetic groups. A sufficient number of markers should be used to estimate properly the kinship between individuals and to reflect the variability of major QTLs. It is also important that the prediction models are trained for relevant environments when dealing with traits with high genotype×environment interaction (G×E). Finally, in these outbreeding species, measures to reduce inbreeding should be used to counterbalance the high selection intensity that can be achieved in GS.

Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family.

Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple.

Genotyping pigs of Ukrainian breeds by microsatellite loci with a tetranucleotide motif

The aim of the research was genotyping animals of Ukrainian pig breeds according to microsatellite loci of the genome for further creation and implementation of the methodology for determining gene complexes of pig adaptability. Research methods: zootechnical – the analysis of genealogy and the productivity indexes of animals of different breeds; bioinformation - work with databases of the primary genome sequences for the design of oligonucleotide primers; molecular genetic - nucleic acid extraction, the determination of purity and concentration of DNA preparations, the amplification of microsatellite loci in PCR with subsequent electrophoretic separation of the amplification products in denaturing gel; statistical – the determination of population-genetic parameters on the basis of typing data on microsatellite loci, the relationship of microsatellite loci with performance indexes, the search for adaptive complexes. It was carried out genotyping animals of the Ukrainian meat breed in SE “RF Elita MIW named after V. M. Remeslo NAAS "of Kyiv region for 6 microsatellite loci with tetranucleotide repeats, a panel of primers of its own design. It was found the fact that the average number of alleles per locus was 5.2 alleles. The level of actual heterozygosity was 0.830, while the expected heterozygosity was 0.780. However, this difference is not significant. DNA typing animals for 6 loci of microsatellite DNA of 17 heads of Poltava meat breed of SE "EB Nadiia" was carried out. As a result of genotyping, the average number of alleles per locus was 3.8. The actual and expected heterozygosity levels were 0.680 and 0.730, respectively. By loci of microsatellite DNA, we found in animals of Myrhorod breed: for locus FH3628 – 5 alleles of 200-228 nucleotides, FH1865 – 5 alleles (size from 109 to 129 nucleotides), FH4219 – 2 alleles of 80 and 92 nucleotides, FH1885 – 4 alleles from 205 up to 213 nucleotides, FH3764 – 2 alleles 138 and 146 nucleotides, and for FH4231 – 2 alleles 116 and 120 nucleotides. The level of actual heterozygosity was 0.860, while the expected heterozygosity was 0.810. Thus, in three breeds of Ukrainian selection for 6 loci of microsatellite DNA with tetranucleotide repeat, the level of actual heterozygosity was in the range of 0.680 in animals of Poltava meat breed to 0.860 in animals of Myrhorod breed. The level of expected heterozygosity is 0.730 in animals of Poltava meat breed to 0.810 in Myrhorod breed. The high level of heterozygosity, as well as the average number of alleles per locus allows to search for alleles and genotypes associated with the adaptability of animals in breeds of pigs of Ukrainian selection. Key words: pigs, microsatellite loci, genome, average number of alleles, level of heterozygosity, population, variability.

Genome features of common vetch (Vicia sativa) in natural habitats.

Wild plants are often tolerant to biotic and abiotic stresses in their natural environments, whereas domesticated plants such as crops frequently lack such resilience. This difference is thought to be due to the high levels of genome heterozygosity in wild plant populations and the low levels of heterozygosity in domesticated crop species. In this study, common vetch ( Vicia sativa ) was used as a model to examine this hypothesis. The common vetch genome (2n = 14) was estimated as 1.8 Gb in size. Genome sequencing produced a reference assembly that spanned 1.5 Gb, from which 31,146 genes were predicted. Using this sequence as a reference, 24,118 single nucleotide polymorphisms were discovered in 1243 plants from 12 natural common vetch populations in Japan. Common vetch genomes exhibited high heterozygosity at the population level, with lower levels of heterozygosity observed at specific genome regions. Such patterns of heterozygosity are thought to be essential for adaptation to different environments. The resources generated in this study will provide insights into de novo domestication of wild plants and agricultural enhancement.

Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding

Guava (Psidium guajava L.), a rich source of nutrients, is an important tropical and subtropical fruit of the Myrtaceae family and exhibits magnificent diversity. Genetic diversity analysis is the first step toward the identification of parents for hybridization, genetic mapping, and molecular breeding in any crop species. A diversity analysis based on whole-genome functional markers increases the chances of identifying genetic associations with agronomically important traits. Therefore, here, we sequenced the genome of guava cv. Allahabad Safeda on an Illumina platform and generated a draft assembly of ~304 MB. The assembly of the Allahabad Safeda genome constituted >37.95% repeat sequences, gene prediction with RNA-seq data as evidence identified 14,115 genes, and BLAST n/r, Interproscan, PfamScan, BLAST2GO, and KEGG annotated 13,957 genes. A comparative protein transcript analysis of tree species revealed the close relatedness of guava with Eucalyptus. Comparative transcriptomics-based SSR/InDel/SNP-PCR ready genome-wide markers in greenish-yellow skinned and white fleshed-Allahabad Safeda to four contrasting cultivars viz apple-color-skinned and white-fleshed-Lalima, greenish-yellow-skinned and pink-fleshed-Punjab Pink, purple-black-skinned and purple-fleshed-Purple Local and widely used rootstock-Lucknow-49 were developed. The molecular markers developed here revealed a high level of individual heterozygosity within genotypes in 22 phenotypically diverse guava cultivars. Principal coordinate, STRUCTURE clustering, and neighbor-joining-based genetic diversity analysis identified distinct clusters associated with fruit skin and flesh color. The genome sequencing of guava, functional annotation, comparative transcriptomics-based genome-wide markers, and genetic diversity analysis will expand the knowledge of genomes of climacteric fruits, facilitating trait-based molecular breeding and diversifying the nutritional basket.

Analysis of Genetic Diversity in the Traditional Chinese Medicine Plant 'Kushen' (Sophora flavescens Ait.).

Kushen root, from the woody legume Sophora flavescens, is a traditional Chinese medicine that is a key ingredient in several promising cancer treatments. This activity is attributed in part to two quinolizidine alkaloids (QAs), oxymatrine and matrine, that have a variety of therapeutic activities in vitro. Genetic selection is needed to adapt S. flavescens for cultivation and to improve productivity and product quality. Genetic diversity of S. flavescens was investigated using genotyping-by-sequencing (GBS) on 85 plants grown from seeds collected from 9 provinces of China. DArTSeq provided over 10,000 single nucleotide polymorphism (SNP) markers, 1636 of which were used in phylogenetic analysis to reveal clear regional differences for S. flavescens. One accession from each region was selected for PCR-sequencing to identify gene-specific SNPs in the first two QA pathway genes, lysine decarboxylase (LDC) and copper amine oxidase (CAO). To obtain SfCAO sequence for primer design we used a targeted transcript capture and assembly strategy using publicly available RNA sequencing data. Partial gene sequence analysis of SfCAO revealed two recently duplicated genes, SfCAO1 and SfCAO2, in contrast to the single gene found in the QA-producing legume Lupinus angustifolius. We demonstrate high efficiency converting SNPs to Kompetitive Allele Specific PCR (KASP) markers developing 27 new KASP markers, 17 from DArTSeq data, 7 for SfLDC, and 3 for SfCAO1. To complement this genetic diversity analysis a field trial site has been established in South Australia, providing access to diverse S. flavescens material for morphological, transcriptomic, and QA metabolite analysis. Analysis of dissected flower buds revealed that anthesis occurs before buds fully open suggesting a potential for S. flavescens to be an inbreeding species, however this is not supported by the relatively high level of heterozygosity observed. Two plants from the field trial site were analysed by quantitative real-time PCR and levels of matrine and oxymatrine were assessed in a variety of tissues. We are now in a strong position to select diverse plants for crosses to accelerate the process of genetic selection needed to adapt kushen to cultivation and improve productivity and product quality.

Estimation of Genome Size in the Endemic Species Reseda pentagyna and the Locally Rare Species Reseda lutea Using comparative Analyses of Flow Cytometry and K-Mer Approaches.

Genome size is one of the fundamental cytogenetic features of a species, which is critical for the design and initiation of any genome sequencing projects and can provide essential insights in studying taxonomy, cytogenetics, phylogenesis, and evolutionary studies. However, this key cytogenetic information is almost lacking in the endemic species Reseda pentagyna and the locally rare species Reseda lutea in Saudi Arabia. Therefore, genome size was analyzed by propidium iodide PI flow cytometry and compared to k-mer analysis methods. The standard method for genome size measures (flow cytometry) estimated the genome size of R. lutea and R. pentagyna with nuclei isolation MB01 buffer were found to be 1.91 ± 0.02 and 2.09 ± 0.03 pg/2 °C, respectively, which corresponded approximately to a haploid genome size of 934 and 1.022 Mbp, respectively. For validation, K-mer analysis was performed on both species’ Illumina paired-end sequencing data from both species. Five k-mer analysis approaches were examined for biocomputational estimation of genome size: A general formula and four well-known programs (CovEST, Kmergenie, FindGSE, and GenomeScope). The parameter preferences had a significant impact on GenomeScope and Kmergenie estimates. While the general formula estimations did not differ considerably, with an average genome size of 867.7 and 896. Mbp. The differences across flow cytometry and biocomputational predictions may be due to the high repeat content, particularly long repetitive regions in both genomes, 71% and 57%, which interfered with k-mer analysis. GenomeScope allowed quantification of high heterozygosity levels (1.04 and 1.37%) of R. lutea and R. pentagyna genomes, respectively. Based on our observations, R. lutea may have a tetraploid genome or higher. Our results revealed fundamental cytogenetic information for R. lutea and R. pentagyna, which should be used in future taxonomic studies and whole-genome sequencing.

Exploring genetic diversity and population structure of Punjab goat breeds using Illumina 50K SNP bead chip.

Pakistan has 35 goat breeds. Moreover, the province of Punjab has highest goat population constituting 37% of country's total population with seven goat breeds including Beetal, Daira Deen Panah, Nachi, Barbari, Teddi, Pahari, and Pothwari. The diversity study of breeds warrants the documentation of breeds particularly using genome wide panel of markers, i.e., SNP chip. The objective of the current study was to fill this gap of information. Therefore, in current study we collected total of 879 unrelated goat blood samples along with data on body weight measurements; genomic DNA was extracted, and genotyping was carried out using 50K SNP bead chip. Quality control measures were performed in Plink 1.07. Genetic diversity was observed among studied populations using heterozygosity and pairwise FST estimates, principal component analysis, admixture analysis in Plink software with visualization in Clumpak, and constructing phylogenetic tree in Mega 7 software. Moderate to high level of heterozygosity was observed among the studied populations. Coefficient of inbreeding varied from 0.0186 ± 0.0327 in Pahari to 0.183 ± 0.0715 in Barbari. Barbari and Daira Deen Panah had quite higher level of inbreeding coefficient as compared to all other breeds with value of 0.183 ± 0.0715 and 0.1378 ± 0.0741, respectively. PCA identified three steps of subdividing the seven goat breeds at various levels of K. All the seven breeds made independent clusters at various levels of PCA. Admixture analysis revealed the distinctness of Teddi and Barbari breeds. Genetic sub-structuring was observed in the admixture patterns of Beetal breed. Moreover, high level of genetic admixture was observed in Nachi, Pahari, Pothwari, and Daira Deen Panah breeds. Admixture results were further interpreted by calculating pairwise FST values. Our results provided first insights about genetic diversity of Pakistani goat breeds based on genomic data. To conclude, the enriched goat breed diversity in Pakistan could provide valuable genetic reservoir for national breeding schemes.

Genetic Variability of Nile Tilapia Strains as Determined by Microsatellite DNA Markers

AbstractThe main purpose of the present study was to investigate the genetic variability of Nile Tilapia Oreochromis niloticus strains by using microsatellite DNA markers and to compare these data with those previously obtained with single‐nucleotide polymorphisms (SNPs). Five mixed‐sex strains and four YY‐male strains were analyzed. All nine microsatellite loci were polymorphic; the number of unique alleles per locus varied from 6 at UNH216 to 33 at UNH880. Strong correspondence was observed between the level of expected heterozygosity (He) or observed heterozygosity and the number of alleles per locus (A) or the number of private alleles. Strains with high levels of heterozygosity typically had higher values of A and the presence of private alleles. In general, mixed‐sex strains had higher genetic variability than YY‐male strains. Four mixed‐sex strains (GIFT, Ismailia Canal, LSA hybrid, and Miami) had the highest level of genetic variability, with mean He ranging from 0.630 to 0.798 and mean A ranging from 5.11 to 9.78. Three YY‐male strains (Fishgen YY Dark–Group 2, Fishgen YY Red, and Til‐Aqua YY) had low genetic variability, with mean He ranging from 0.282 to 0.367 and mean A ranging from 1.89 to 3.56. All investigated strains demonstrated low values of the inbreeding coefficient FIS (from –0.266 to 0.014), suggesting that mating of closely related individuals is being avoided during maintenance of these strains. Pairwise genetic differentiation index FST values had a broad range (from 0.0915 to 0.6063), indicating different levels of genetic differentiation between strains. A dendrogram constructed according to shared allele distance showed the existence of two distinct clusters among strains. The present data on genetic variability of Nile Tilapia strains demonstrated substantial similarity with data from a previous study of SNPs in the same populations.

Description of the growth hormone gene of the Australasian snapper, Chrysophrys auratus, and associated intra- and interspecific genetic variation.

The growth hormone (GH) gene of the marine teleost, the Australasian snapper (Chrysophrys auratus), was identified and characterized from the reference genome showing it was approximately 5577 bp in length and consisted of six exons and five introns. Large polymorphic repeat regions were found in the first and third introns, and putative transcription factor binding sites were identified. Phylogenetic analysis of the GH genes of perciform fish showed largely conserved coding regions and highly variable noncoding regions among species. Despite some exon sequence variation and an amino acid deletion identified between C. auratus and its sister species Chrysophrys/Pagrus major, the amino acid sequences and putative secondary structures were largely conserved across the Sparidae. A population-level assessment of 99 samples caught at five separate coastal locations in New Zealand revealed six variable alleles at the intron 1 site of the C. auratus GH gene. A population genetic analysis suggested that C. auratus from the five sample locations were largely panmictic, with no evidence for departure from the Hardy-Weinberg equilibrium, and have a high level of heterozygosity. Overall these results suggest that the GH gene is largely conserved across the coding regions, but some variability could be detected.

Analysis of allele frequencies of the selected 15 autosomal STR markers in Tikrit population – Iraq with comparison to Middle Eastern, African, and Europeans

Short tandem repeats (STRs) have been recommended as the highest polymorphic loci among the humana DNA regions. Therefore, STRs are agreeable to many genetic fields like forensic, population genetics and anthropological studies. The main aim of this research is to evaluate the autosomal STRs in Tikrit city-Iraq, to expand the human genetics database and forensic genetics analysis. The DNA database was obtained from 306 unrelated volunteers from native Tikrit population-Iraq, using 15 autosomal STR loci. The current study determined the allele frequencies in the Tikrit population and then compared them with other national Iraqi populations as well as with populations in the Middle East, Africa, and Europe. The highest level of heterozygosity was observed in D8S1179 and TH01 loci (0.797), while the less level was shown by CSF1PO (0.48). The departure from HWE Equilibrium was recorded in only 3 STR loci from a total of 15 loci analyzed (p<0.003). The Combined Match Probability (CMP) for 15 autosomal STR was 1 in 7.89208×10-19 and the Combined Discrimination Power (CDP) was 0.9999999997. The discrimination power (DP) was especially high in D2S1338, D18S51, D19S433 and D21S11. Based on the results observed in a Dendrogram, Tikrit population was clustered with other populations, likely reflecting the historical and geographical factors. D2S1338, D18S51, D19S433 and D21S11 markers were recognized as suitable for forensic genetics analysis in Tikrit population. Also, the 15 STRs markers provide information for the studies of genetic distances between the current study and other included populations to be compared with this study.

Single-nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana).

PremiseProgeny of avocado (Persea americana) are highly variable due to high levels of heterozygosity. Breeding programs need molecular resources to allow the assessment of genetic differences and the selection of genotypes. Polymorphisms that uniquely identify different avocado cultivars provide a valuable tool to accelerate avocado research and development, including, for example, genotype selection.MethodsA double‐digest restriction site–associated DNA sequencing (ddRADseq) approach was used to screen 10 avocado cultivars for single‐nucleotide polymorphisms (SNPs). The fragments were size selected with Blue Pippin and PCR using universal Illumina primers, and catalog tags were then created with de novo alignment using Stacks software. Catalog tags were tabulated and filtered to identify alleles unique to each cultivar.ResultsA total of 104 million sequences were collected, and 52 homozygous SNPs were identified that uniquely distinguished nine avocado cultivars. The cultivars Carmen Hass and Hass have a strong genetic similarity and no homozygous SNPs distinguishing these cultivars could be identified; therefore, both cultivars were grouped together.DiscussionThe resource described here for cultivars of P. americana presents a new and significant molecular resource that can enable targeted genotype selection, paternity analysis, germplasm genotyping, pollination dynamics investigation, and crop improvement.

ASSESSMENT OF THE GENETIC VARIABILITY OF DIFFERENT AGE GROUPS OF SILVER AND BIGHEAD CARPS BY BIOCHEMICAL POLYMORPHISM

Goal. The study aimed to analyze and assess the genetic variability of different age groups of silver and bighead carps by the polymorphism of protein and enzyme systems.
 Methods. Blood samples were taken from silver (Hypophthalmichthys molitrix) and bighead (Aristichthys nobilis) carps of "Sunpoint Ukraine" LLC, Slobozhanske, Zmiiv district, Kharkiv region.
 Blood from the tail vein was collected from age-2 and age-3 fish in vivo and placed into tubes with an anticoagulant. Whole blood samples were separated into fractions by centrifugation and as a result plasma and erythrocytes were packed into separate tubes. The methods of vertical polyacrylamide and horizontal starch electrophoresis were used for the electrophoretic separation of proteins and enzymes of silver and bighead carps blood. Histochemical staining of the gel plates was carried out with t) and bighead he following genotyping of allelic variants of protein and enzyme systems. Biochemical systems such as loci of prealbumin (Pralb), esterase (EST, K.F. 3.1.1.1), malate dehydrogenase (MDH, K.F. 1.1.1.37), enzyme malic (ME, K.F. 1.1.1.40) and carbonic anhydrase (CA, K.F. 4.2.1.1) were investigated. Statistical processing of experimental data was performed using Biosys-1. Cluster analysis was carried out using MEGA-X.
 Results. Analysis of the peculiarities of the distribution of allele frequencies and the genotypic composition of Pralb, EST, MDH, ME, and CA loci was carried out in the age-2 and age-3 groups of silver and bighead carps. The prevalence of the frequency of the fast migrating allelic variant F was revealed in comparison with the slow migrating gene at EST locus in the age-3 group of silver carp (Est F = 0.620). The prevalence of the frequency of the fast allelic variant Pralb A in comparison with the slow Pralb B was observed in the silver carp groups (Pralb A = 0.812 in the age-2 and Pralb A = 0.726 in the age-3 groups. According to the genotypic composition of the studied loci, there was an excess of heterozygous individuals in the age-2 group of silver carp, which indicates their genetic imbalance. The formation of breeding stocks of silver and bighead carps requires control of the level of genetic variability of different age groups to monitor changes in the genetic structure and maintain the optimal level of heterozygosity in stocks. The highest level of average heterozygosity (79.4%) was found in the age-2 group of silver carp, which prevailed over the expected average heterozygosity with a value of 49.4%. In comparison with other studied groups, the age-2 group of bighead carp had the lowest level of average heterozygosity of 59.1% versus the theoretically calculated level of 45.5%. The age-2 and age-3 groups of bighead carp had the highest level of heterozygosity at Ca locus at the level of 82.8 and 78.6% respectively, in contrast to the expected heterozygosity at this locus at the level of 49.9 and 49.7%. A dendrogram of the genetic relationships of different age groups of silver carp was constructed based on the values of genetic distances. The formed clusters indicated the formation of the genetic structure of the silver and bighead carps by species affiliation.
 Conclusions. The analysis of the genetic structure of different age groups of the silver and bighead carps was performed by the polymorphism of protein and enzyme systems such as Pralb, EST, MDH, ME, CA loci. The study describes the features of the distribution of allelic frequencies and genotypic variants of the aforementioned loci. The level of average heterozygosity, observed and expected heterozygosity at loci in age-2 and age-3 groups of silver and bighead carps were determined. The high genetic variability of an age-2 group of silver carp at the level of 79.4% indicates the need to stabilize their genetic structure. As a result of the cluster analysis, it was determined that the formation of the genetic structure of the silver carp groups of the "Sunpoint Ukraine" farm in the Kharkiv region occurs by species affiliation. The study and use of biochemical markers will allow differentiating stocks of silver and bighead carps. As well as in complex analysis with other molecular genetic markers will allow them to develop a genetic passport.

Whole-genome assembly of Corylus avellana cv "Tonda Gentile delle Langhe" using linked-reads (10X Genomics).

The European hazelnut (Corylus avellana L.; 2n = 2x = 22) is a worldwide economically important tree nut that is cross-pollinated due to sporophytic incompatibility. Therefore, any individual plant is highly heterozygous. Cultivars are clonally propagated using mound layering, rooted suckers, and micropropagation. In recent years, the interest in this crop has increased, due to a growing demand related to the recognized health benefits of nut consumption. C. avellana cv “Tonda Gentile delle Langhe” (“TGdL”) is well-known for its high kernel quality, and the premium price paid for this cultivar is an economic benefit for producers in northern Italy. Assembly of a high-quality genome is a difficult task in many plant species because of the high level of heterozygosity. We assembled a chromosome-level genome sequence of “TGdL” with a two-step approach. First, 10X Genomics Chromium Technology was used to create a high-quality sequence, which was then assembled into scaffolds with cv “Tombul” genome as the reference. Eleven pseudomolecules were obtained, corresponding to 11 chromosomes. A total of 11,046 scaffolds remained unplaced, representing 11% of the genome (46,504,161 bp). Gene prediction, performed with Maker-P software, identified 27,791 genes (AED ≤0.4 and 92% of BUSCO completeness), whose function was analyzed with BlastP and InterProScan software. To characterize “TGdL” specific genetic mechanisms, Orthofinder was used to detect orthologs between hazelnut and closely related species. The “TGdL” genome sequence is expected to be a powerful tool to understand hazelnut genetics and allow detection of markers/genes for important traits to be used in targeted breeding programs.

DNA Markers for Meat Quality of Pigs

This paper presents the results of determining genotypes of 3-breed pig hybrids (Landrace x Yorkshire x Duroc) by marker genes MC4R (melanocortin receptor-4 gene), IGF2 (insulinoid growth factor-2), POU1F1 (pituitary transcription factor), H-FABP (protein gene binding fatty acids), GH (growth hormone gene), LEP (leptin gene) and their interrelation with meat productivity. Allele frequencies for the studied genes were determined (MC4R: А = 0.58, G = 0.42; IGF2: Q = 0.96, q = 0.04; POU1F1: Е = 0.66, F = 0.34; H-FABP: D = 0.38, d = 0.62; GH: А = 0.26, G = 0.74; LEP: С = 0.27, Т = 0.73). The study showed that 3-breed hybrids did not have the highest level of heterozygosity in most allelic genes. MC4R (AG = 48%), POU1F1 (EF = 68%) and H-FABP (Dd = 52%) genes had the greatest number of heterozygotes; IGF2 (QQ = 92%), GH (GG = 58%) and LEP (TT = 56%) genes had the greatest number of homozygotes. The data showed that the breeds used to obtain three-breed hybrids were selected for analogous (meat quality) traits and that they had a higher frequency of the desired Q (IGF2), G (GH) and T (LEP) gene alleles, which were lost from hybrids in the homozygous condition. We identified the most desirable genotypes for the studied genes (GGMC4R, AGMC4R, QQIGF2, EFPOU1F1, DDH-FABP, AAGH, CTLEP) which are recommended for pig selection as well as for selection of parent pairs for producing commercial hybrids with high meat productivity.
 Keywords: gene-dependent selection, slaughter and meat qualities of pigs, marker genes, MC4R, IGF2, POU1F1, H-FABP, GH, LEP

Distribution, Genetic Diversity and Population Structure of Aegilops tauschii Coss. in Major Wheat-Growing Regions in China

Aegilops tauschii Coss. is known as a noxious grass weed seriously affecting wheat quality and yield. To investigate its present occurrence in wheat fields and the potential genetic diversity of the grass weed in China, a filed survey covering major wheat production regions was conducted during 2017–2019. Seeds of different Ae. tauschii populations collected from the survey were analyzed with Simple Sequence Repeats (SSRs) technique. Results showed that Ae. tauschii was occurring in each of the provinces surveyed with varied occurrence frequency ranging from 0.91% in Sichuan Province to 92.85% in Henan Provinces. Eighty alleles with size ranging from 98 bp to 277 bp were detected from the 192 collected Ae. tauschii populations with 17 SSR markers. Ae. tauschii, in this study, exhibited a moderately high level of genetic diversity, high differentiation, deficient heterozygosity and limited gene flow. Compared with other provinces, Hubei populations possessed relatively low genetic diversity. Dendrogram analysis showed that genetic distance did not seem to be related to geographic distribution. Additionally, STRUCTURE analysis suggested that Ae. tauschii populations in wheat fields of China can be divided into three groups, which was further supported by cluster analysis. Among the three groups, solely 7% of the total variation was detected, whereas the majority variation (67%) occurred among different populations within same group. Undoubtedly, such information will help us to better understand population relationships and spread of Ae. tauschii in China and will provide a new perspective for its integrated management.

Genetic analysis of a potato (Solanum tuberosum L.) breeding collection for southern Colombia using Single Nucleotide Polymorphism (SNP) markers.

Detailed knowledge on genetic parameters such as diversity, structure, and linkage disequilibrium (LD) and identification of duplicates in a germplasm bank and/or breeding collection are essential to conservation and breeding strategies in any crop. Therefore, the potato genetic breeding collection at the Universidad de Nariño in Colombia, which is made up of diploid and tetraploid genotypes in two of the more diverse genebanks in the world, was analyzed with 8303 single nucleotide polymorphisms (SNP) from SolCAP version 1. In total, 144 genotypes from this collection were analyzed identifying an 57.2% of the polymorphic markers that allowed establishing two and three subpopulations that differentiated the diploid genotypes from the tetraploids. These subpopulations had high levels of heterozygosity and linkage disequilibrium. The diversity levels were higher in the tetraploid genotypes, while the LD levels were higher in the diploid genotypes. For the tetraploids, the genotypes from Peru had greater diversity and lower linkage disequilibrium than those from Colombia, which had slightly lower diversity and higher degrees of LD. The genetic analysis identified, adjusted and/or selected diploid and tetraploid genotypes under the following characteristics: 1) errors in classification associated with the level of ploidy; 2) presence of duplicates; and 3) genotypes with broad genetic distances and potential use in controlled hybridization processes. These analyses suggested that the potato genetic breeding collection at the Universidad de Nariño has a genetic base with a potential use in breeding programs for this crop in the Department of Nariño, in southern Colombia.