Genetic Similarity Index Research Articles

Evaluation of Genetic Diversity in Sorghum Genotypes via Simple Sequence Repeat (SSR) Markers

This study aimed to evaluate the genetic diversity of 20 sorghum [Sorghum bicolor (L.) Moench] genotypes via simple sequence repeat (SSR) markers, with a focus on identifying drought-tolerant varieties. Leaf samples were collected from three-week-old seedlings, and genomic DNA was extracted via the CTAB method, a widely recognized protocol for obtaining high-quality DNA. The DNA samples were quantified to ensure consistent template concentrations for amplification via 25 SSR primers. PCR amplification was performed, followed by agarose gel electrophoresis to separate and visualize the SSR band patterns, which were then recorded in a binary matrix format on the basis of the presence or absence of bands. Among the SSR primers used, nine were polymorphic, generating 13 scorable markers, highlighting the genetic variability among the genotypes. The polymorphic information content (PIC) values ranged across the SSR loci, with the Xtxp145 locus exhibiting the highest PIC value of 0.998, indicating its high discriminatory power and informativeness in differentiating between genotypes. Genetic similarity indices were calculated via Jaccard's similarity coefficient [1], and the data were subjected to cluster analysis via the unweighted pair group method with arithmetic mean (UPGMA) method. The resulting dendrogram grouped the genotypes into seven main clusters at a 50% similarity threshold, underscoring the genetic diversity present within the sorghum genotypes studied. Cluster I contained a single genotype, SVD-1272R, whereas, Cluster II included seven genotypes with subcluster formation. Cluster III comprised one ungrouped genotype, SPV-486. Cluster IV included eight genotypes, whereas Clusters V, VI, and VII each contained a single ungrouped genotype. This dendrogram illustrates the genetic diversity and relationships among the sorghum genotypes on the basis of similarity indices. The findings of this study confirmed the efficacy of SSR markers in assessing genetic diversity and emphasized their potential utility in breeding programs aimed at improving drought tolerance.

Screening of among seventeen sunflowers (Helianthus annuus L.) genotypes for oil content and the first flowering day using random amplified polymorphic DNA markers

Background Sunflower refers to the tribe Helianthus, subtribe Helianthinae, and family Asteraceae, which collectively contains 20 genera and 400 species. An important oilseed crop that yields edible oil is Helianthus annuus L. Objective The primary goal of the current study was to assess the genetic diversity of 17 genotypes of sunflower (Helianthus annuus L) To measure the oil content during the initial flowering period and to reach the highest percentage of oil can be obtained from the first flowering day. Materials and methods Five RAPD (random amplified polymorphic DNA) primers were used to detect the genetic diversity of the 17 sunflower hybrid genotypes obtained from Spain. Phylogenetic relationships of 17 sunflower genotypes were determined using three replications and 6 m lines on August 15, 2019, at the National Research Centre farm in Nubaria as part of a donation from the German corporation (strobe), Spain. To analyze the genetic diversity and phylogenetic linkages in sunflower germplasm, DNA fingerprinting and the Random Amplified Polymorphic DNA (RAPD) molecular marker approach were also used. Results and conclusion The oil content of 17 sunflower genotypes (Helianthus annuus L.) was assessed, with values ranging from 46 to 50%, with the highest values falling into five genotypes. However, the two genotypes were found to have the lowest oil percentage (46%). The early age and oil percentage differed among the varieties. In the Tornado and Elves genotypes, the longest and shortest days were 59 and 47, respectively. The means and standard errors for all statistical data are reported. Statistical significance was evaluated using the LSD. P values were considered statistically significant at P less than or equal to 0.05. According to the findings, RAPD primers generated 49 bands with a size range of 0.1–3 kb and an 87.75% polymorphism percentage. For RAPD, 43 polymorphic bands with distinct bands were observed. Morphological features and RAPD analysis separated the UPGMA Dendrogram into three groups. Jaccard’s coefficient was used to analyze the genetic similarity matrix, and a morphological study revealed that Tornado and Elvas, both from Spain, shared the most genetic similarity (0.970). RAPD analysis and morphological features are useful in identifying genetic variants. Conclusion, according to our findings, Helianthus annuus L. has a significant variation ratio. Indicating substantial diversity across the 17 sunflower genotypes, the genetic similarity index calculated using pooled data from RAPD markers showed an extensive range from 0.645 to 0.986. This study may be a reference for future research on Helianthus annuus L. and may support breeding initiatives and species concepts.

Genetic Diversity of Bio-fortified Lentils (Lens culinaris Medik.) through Simple Sequence Repeat Markers

Nepalese lentils are comparatively rich in iron and zinc, making it a potential crop of whole food solution to aid in the global battle against the micronutrient malnutrition. Understanding the genetic basis for uptake of grain iron and zinc is required to increase their stable concentrations along with these minerals in lentils. This study aimed at characterizing genetic variation in micronutrient high grain iron and zinc concentrations and exploring the potential in lentil accessions. A set of 25 lentil accessions was evaluated in two seasons across the three locations and genotyped by using 40 simple sequence repeat (SSR) markers that are linked with lentil iron and zinc concentrations. Out of the 40 SSR markers, 23 markers were found polymorphic while 12 were monomorphic, and 5 markers were null. These 23 polymorphic markers produced a total of 584 alleles, of which 52 were polymorphic alleles, and average alleles per locus was 11.49. The linkage disequilibrium (LD) analysis was done using a mixed linear model (MLM) that identified three SSR markers, PBALC 13, PBALC 206, and GLLC 563, associated with grain Fe concentration, explaining 9% to 11% phenotypic variation, respectively, and four SSR markers (PBALC 353, SSR 317–1, PLC 62, and PBALC 217) associated with grain Zn concentration, explaining 14% to 21% phenotypic variation, respectively. The pairwise genetic similarity index among 25 lentil accessions varied from 0.16 to 0.83. The identified SSRs exhibited consistent performance across two seasons and have potential for utilization in lentil molecular breeding program. SAARC J. Agric., 21(2): 27-40 (2023)

Immunogenetic characteristics of sheep breeds of the Siberian-Far Eastern region

A comparative analysis of eight breeds of sheep (medium-wool, coarse-wooled, semifine-wool and fine-wool) bred in the Siberian-Far Eastern region was carried out. The research used the data on immunogenetic testing of sheep in breeding farms for a number of years. The testing was performed using 14 specific sera – reagents. The allelic profile of sheep, their similarities and differences related to phylogeny and previous selection were studied. All breeds studied had a distinctive allelic profile. Both frequent and infrequent antigens were identified in each breed. Based on antigen frequencies, an index of genetic similarity (r) was calculated, which was higher in the breeds of the same productivity direction, e.g. between Buubei and Edilbaevskaya breeds (r = 0.912), and lower between the breeds that were selected in isolation from each other. The lowest index of genetic similarity was found between the Buryat and West Siberian meat breeds (r = 0.707). Breeds of the same productivity direction from different regions also have distinctive features. The index of genetic similarity between coarse-wooled breeds (Buubei and Edilbaevskaya) is 0.912; between medium-wool breeds (Buryat and Aginskaya) it is at the level of 0.739; between semifine-wool breeds (Gorno Altai and West Siberian meat breeds) – 0.845; between fine-wool breeds (Kulunda and Zabaikalskaya) – 0.902. Using the cluster analysis of genetic distances, the relationships of breeds, their origin, and phylogeny were determined. West Siberian Meat and Kulunda breeds formed one cluster, Buubei and Buryat breeds were also included in one cluster. More distant breeds were Aginskaya (Zugalai type) and Edilbaevskaya.

Genetic monitoring cattle a herd of the sychev breed

According to the results of immunogenetic studies (2006-2020), the dynamics of changes in the herd allelofond according to genetic markers of blood groups with a period of five years was studied in JSC Smolenskoye for breeding work. A reduction in the number of EAB alleles in breeding bulls from 29 to 16, in cows from 39 to 33 was revealed. The frequency of occurrence of 12-13 main EAB alleles in the herd is 0.737 - 0.753, in the breed - 0,778. During all monitoring periods, the EAB alleles - G2Y2E/1Q/, Y1A/1, E/3G/G//, Q/ were found with a frequency of 4% and higher. There was an increase in the level of homozygosity for dam stock by 1.1%, for producing bulls - by more than 3%. It was found that in the herd for 2020 with a total frequency of 0.318, there are alleles of the EAB locus B2±G2O1Y2D/E/2G//, E/3G/, E/3G/G//, G2T2Y2A/1B/G/I/Q/Y/B//, G1A/1. The frequency of their occurrence by breed is 0.120. In 13% of cows of the herd, there are EAB alleles A1B/, B1I1Q, O1I/Q/, G3O1T1A/2E/3F/2K/G//, I1Y2I/, in the breed they occur in 22.3% of animals. It was revealed that alleles of the Holstein breed in different periods were found, respectively, in 43.3, 25.9, 61.7 percent of cows, alleles of the breed of Sychevka - in 19.2, 36.0, 23.2%. The index of genetic similarity between the breeding farms of the breed of Sychevka varied from 0.632-0.884, between the animals of the herd and the breed it was 0.750-0.855. We note that in bulls evaluated by the quality of offspring, the difference in the productivity of daughters in favor of one or another preferential allele from the producer was 61-1403 kg of milk, 0,01-0,15% fat and up to 0.06 percent protein for the first lactation. According to the highest lactation, the differences in milk yield are 26-1083 kg of milk, in fat content - 0,02-0,19%, protein 0,01-0,06%.

Genetic characteristics of the herd of KP "Rybkovskoe" by alleles of the EAB-locus of blood groups

The analysis of the genetic structure of the herd to the marker alleles of the EAB locus - blood groups was according. The EAB-allele G2Y2E/1Q/according to the results of the study with a high frequency of 11.9 – 15.7%, in the herd, whereas its frequency is 18% for the breed was found. In the period 2011-2015 sixteen main alleles of the EAB-locus of blood groups with a total frequency of 0.802 in the herd were found. In 2016-2020, the main EAB-alleles were 12 and the frequency of their occurrence was equal 0,752. The number of four main alleles of the Red-and-White Holstein breed Y1A/1, O2A/2J/2K/O/, I1Y2E/3G/G//, B1O1 decreased from 0,213 to 0,102. With the highest frequency, totaling 40.6% marker EAB - alleles G2T2Y2A/1B/D/G/I/Q/Y/B// (0.052), E/3G/G// (0,070), B1I1Q (0,053), O1I/Q/ (0,080), B2G2O1Y2D/E/2G// (0,056), b (0.095) in KP "Rybkovskoe" are found. In the breed, these alleles occur with a frequency of 29.8%. There are no significant differences between the breed and the herd in the frequency of EAB alleles. The difference did not exceed 2.4 – 2.7%. From a genetic standpoint, the animals of the herd and the breed are close. The index of genetic similarity between them is 0.95. The level of homozygosity was 6.2% in the herd in the period 2016-2020, but its increase over the past five years was 1,2%, indicating a decrease in the genetic diversity of animals. The number of producer sires used by the pedigree farm decreased to 14 and the total diversity of their alleles decreased to 15. Comparative analysis showed that the difference in productivity of the daughters of bulls with alternative EAB-alleles was from 7 to 710 kg of milk, 0.01 – 0.19% fat and 0.02 – 0.09% protein for the first lactation in favor of one or another marker allele from the producer. By the highest lactation, the differences in milk yield are 55 – 1034 kg of milk, in fat content – 0.01 – 0.22%, protein – 0.02 – 0.14%.

Genetic diversity and population structure analyses in barley (Hordeum vulgare) against corn-leaf aphid, Rhopalosiphum maidis (Fitch).

Corn-leaf aphid (CLA), Rhopalosiphum maidis (Fitch) (Hemiptera: Aphididae) is a serious economic pest of barley worldwide. Breeding for aphid resistance in plants is considered a cost-effective and environmentally safe approach for aphid control, compared to the use of chemical pesticides. One of the challenges in breeding for aphid resistance is the identification of resistant plant genotypes, which can be achieved through the use of molecular markers. In the present study, a set of aphid specific 10 simple-sequence repeats (SSR) markers were used to investigate genetic diversity and population structure analyses in 109 barley genotypes against R. maidis. Three statistical methods viz., multivariate hierarchical clustering based on Jaccard's similarity coefficient, principal coordinate analysis (PCoA) and the Bayesian approach were utilized to classify the 109 barley genotypes. The analyses revealed four subpopulations i.e., SubPop1, SubPop2, SubPop3 and SubPop4 with 19, 46, 20 and 24 genotypes including admixtures, respectively and represented 17.43%, 42.2%, 18.34% and 22.01% genotypes of the total population size, respectively. The studied SSR markers produced 67 polymorphic bands, with an average of 6.7 and ranging from 3 to 12 bands. Heterozygosity (H) was found to be highest in SSR28 (0.64) and lowest in SSR27 (0.89). The observed genetic diversity index varied from 0.10 to 0.34 (with an average of 0.19). Major allele frequency varied from 74.08% to 94.80%. On an average, 87.52% of the 109 barley genotypes shared a common major allele at any locus. Based on the Aphid Infestation Index (AII), only 2 genotypes were found to be resistant against CLA. SubPop2 also had lowest mean aphid population (28.83), widest genetic similarity index (0.60-1.00) and highest genetic similarity coefficient (0.82), which highlighted its potential for inclusion in future CLA resistance breeding programs.

Families of Brown Swiss cows in breeding farms of the Smolensk region

Increasing the dairy productivity of cows is the main goal of breeding work in dairy cattle breeding. The main method of purebred cattle breeding is considered to be breeding by lines and families. In the herds of five padigree farms of the Smolensk region for the breeding of the Brown Swiss breed of cattle 160 main families with a total number of 2285 cows have been established. The number of families on farms ranged from 17 to 40 with the number of animals from 235 to 502, in each. The main indicators of dairy productivity of cows in individual families are determined, the most promising for further breeding work are identified. The best families were formed in the breeding reproducer of the SPC "Druzhba" with record indicators of dairy productivity of cows for the breed. So in the Nevesta's family 917 cows were received: Zlata 2259 (3 – 305 – 8953 -3.94% – 3.31%); Dona 313 (2 – 305 – 11184 – 3.76% – 3.64 %). The Index of genetic similarity between animals of individual families calculated using immunogenetic markers revealed significant differences in the hereditary characteristics of the compared groups.

De Novo Transcriptome Profiling for the Generation and Validation of Microsatellite Markers, Transcription Factors, and Database Development for Andrographis paniculata.

Andrographis paniculata belongs to the family Acanthaceae and is known for its medicinal properties owing to the presence of unique constituents belonging to the lactones, diterpenoids, diterpene glycosides, flavonoids, and flavonoid glycosides groups of chemicals. Andrographolide, a major therapeutic constituent of A. paniculata, is extracted primarily from the leaves of this plant and exhibits antimicrobial and anti-inflammatory activities. Using 454 GS-FLX pyrosequencing, we have generated a whole transcriptome profile of entire leaves of A. paniculata. A total of 22,402 high-quality transcripts were generated, with an average transcript length and N50 of 884 bp and 1007 bp, respectively. Functional annotation revealed that 19,264 (86%) of the total transcripts showed significant similarity with the NCBI-Nr database and were successfully annotated. Out of the 19,264 BLAST hits, 17,623 transcripts were assigned GO terms and distributed into three major functional categories: molecular function (44.62%), biological processes (29.19%), and cellular component (26.18%) based on BLAST2GO. Transcription factor analysis showed 6669 transcripts, belonging to 57 different transcription factor families. Fifteen TF genes that belong to the NAC, MYB, and bHLH TF categories were validated by RT PCR amplification. In silico analysis of gene families involved in the synthesis of biochemical compounds having medicinal values, such as cytochrome p450, protein kinases, heat shock proteins, and transporters, was completed and a total of 102 different transcripts encoding enzymes involved in the biosynthesis of terpenoids were predicted. Out of these, 33 transcripts belonged to terpenoid backbone biosynthesis. This study also identified 4254 EST-SSRs from 3661 transcripts, representing 16.34% of the total transcripts. Fifty-three novel EST-SSR markers generated from our EST dataset were used to assess the genetic diversity among eighteen A. paniculata accessions. The genetic diversity analysis revealed two distinct sub-clusters and all accessions based on the genetic similarity index were distinct from each other. A database based on EST transcripts, EST-SSR markers, and transcription factors has been developed using data generated from the present study combined with available transcriptomic resources from a public database using Meta transcriptome analysis to make genomic resources available in one place to the researchers working on this medicinal plant.

Studying of Polymorphism of Some Grain Crop from GenBank Collection of Armenia

During the research, 15 genotypes of grain crop (4 spiecies of Hordeum and 11 of Triticum) from the genbank collection of the Scientific Center of Agrobiotechnology were studied. The gluten locus of all studied cultivated and wild species is polymorphic consisting of GluA, GluB, GluC, GluD, GluE alleles. Moreover, GluB, GluC and GluD alleles have the highest meeting frequency, it is 82.35%. The GluE allele has the lowest frequency of occurrence at 41.17%. The following genotypes were formed in the gluten locus: GluAA, AB, BB, BC, CC, CD, DE, EE, EF, the frequency of which is equal to 47.05, 29.53, 70.58, 82.35, 76.47, 17.65, 52.94, 35.29, 23.53 and 23.53%. The highest frequency was recorded for GluBC genotype (82.35%), and the lowest for GluAB, EE, EF (25.53%) genotypes. In the studied species of wild barley, homozygosity is 60-100%, in the case of wild wheat - 66.7-71.42%. Indicators are close to the genetic makeup of free-breeding populations. It ranges from 50-80% in wheat amphidiploids and 25-60% in non-amphidiploids. The genetic similarity index of wild barley species ranges from 0.488 to 0.648, which indicates a unique and rich biodiversity. Meanwhile, it is quite high (r=0.844) in wild types of wheat. For amphidiploid x wild einkorn wheat, it is 0.982-0.982. In other cases, the genetic similarity index ranges from 0.488 to 0.648.

GENETIC DIVERSITY AND PHYLOGENETICS OF FOUR RELEASED COWPEA (Vigna unguiculata (L.) Walp) VARIETIES (FUAMPEA-1, FUAMPEA-2, FUAMPEA-3 AND FUAMPEA-4) USING SIMPLE SEQUENCE REPEATS MARKERS

Cowpea improvement has continued to play key roles in the quest for national food security. This work elucidated the molecular genetic diversity and phylogenetics among four released cowpea varieties (FUAMPEA-1, FUAMPEA-2, FUAMPEA-3 AND FUAMPEA-4). DNA was extracted from 14 day old seedlings using the CTAB method. A total of nine (9) SSR (Simple Sequence Repeats) markers were employed in DNA amplifications. Binary matrix was generated from banding profiles of gel images and uploaded into the Minitab 17.0 software for analysis. Polymorphic Information Content (PIC) was computed for the primers and cowpea varieties. Cluster analysis was carried out using the Single Linkage method measured on Euclidean Distance. Four primers (CLM1190, CLM0342, RB38 and RB7) produced maximum of two bands each resulting in 15.4% polymorphism and 0.977 Polymorphism Information Content (PIC). Varietal Polymorphic Content (VPC) varied from 15.4% in FUAMPEA-2 as the lowest to 38.5% in FUAMPEA-1 as the highest. FUAMPEA-1 had the lowest genetic similarity index (19.82). Dendrogram further showed that FUAMPEA-2 and FUAMPEA-3 were more closely related than others with about 46.55 similarity index. Therefore, FUAMPEA-1 was the most divergent and genetically diverse variety followed by FUAMPEA-4. These are potential genetic resource material that can used to develop more cultivars when their inherent agronomic traits and genes coding for the traits are identified and tapped.

Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index.

Clonal reproduction, the formation of nearly identical individuals via mitosis in the absence of genetic recombination, is a very common reproductive mode across plants, fungi and animals. To detect clonal genetic structure, genetic similarity indices based on shared alleles are widely used, such as the Jaccard index, or identity by state. Here we propose a new pairwise genetic similarity index, the SH index, based on segregating genetic marker loci (typically single nucleotide polymorphisms) that are identically heterozygous for pairs of samples (NSH ). To test our method, we analyse two old seagrass clones (Posidonia australis, estimated to be around 8500 years old; Zostera marina, >750 years old) along with two young Z. marina clones of known age (17 years old). We show that focusing on shared heterozygosity amplifies the power to distinguish sample pairs belonging to different clones compared to methods focusing on all shared alleles. Our proposed workflow can successfully detect clonemates at a location dominated by a single clone. When the collected samples involve two or more clones, the SH index shows a clear gap between clonemate pairs and interclone sample pairs. Ideally NSH should be on the order of approximately ≥3000, a number easily achievable via restriction-site associated DNA (RAD) sequencing or whole-genome resequencing. Another potential application of the SH index is to detect possible parent-descendant pairs under selfing. Our proposed workflow takes advantage of the availability of the larger number of genetic markers in the genomic era, and improves the ability to distinguish clonemates from nonclonemates in multicellular diploid clonal species.

Immunogenetic characteristics of sires of different breeds at OAO «Barnaulskoe» Bull stud

The purpose of the research was to study the frequency of erythrocyte antigens of 9 genetic systems, the number of genotypes and the frequency of alleles in the F-V system in sires of four breeds at the OAO “Barnaulskoe” Bull stud, as well as to establish indices of genetic similarity between them. The characteristics of 138 sires of Black-and-White breed, 103 of Red-and-White, 106 of Simmental and 270 sires of red breeds have been given. 53 antiserums were used in the tests. The high occurrence of blood factors A₂ (system A), B₂, G₂, O₁, Y₂, G’, O’ and Q’ (system B), C₂, E, W, X₂ (system C), H’ (system S) and Z (system Z) in sures of all four breeds ranged from 0,204 (O’ in sires of Red-and-White breed) to 0,825 (X₂ in the same breed). The frequency of the F antigen in all breeds was maximal and varied from 0,874 in sires of Red-and-White breed to 0,981 in sires of red breeds. On the contrary, the occurrence of blood factors B₁, I₁, I₂, P₁, P₂, Q, T₁, T₂, I’, J₂’, K’, P₁’, Y’, B” and R₁ was significantly lower and amounted to 0–0,130 in sires of Black-and–White breed, 0–0,087 in sires of Red-and-White breed, 0–0,094 in Simmental sires and 0,004–0,137 in sires of Red breeds. Sires of red breeds had all 53 antigens, Black-and-White sires did not have 8, Red-and-White sires did not have 11, and Simmental sires did not have 9 blood factors. There were no significant differences in the value of the genetic similarity index between the animals of the four breeds. However, there was a tendency to increase the similarity between the sires of Black-and-White and Simmental breeds on the one hand and the sires Red-and-White breed on the other (r=0,8837 and 0,8765). The least close breeds are Red-and-White and Simmental on the one hand and Red breeds on the other (r=0,8613 and 0,8585). This is also indicated by the occurrence of genotypes and alleles in the F-V genetic system. Thus, significant differences in the number of all genotypes and frequencies of alleles were revealed between sires of Simmental and Red breeds.

Construction and Characterization of an Intergeneric Fusant That Degrades the Fungicides Chlorothalonil and Carbendazim.

Bordetella sp. CTN-16 (GenBank FJ598326) can degrade chlorothalonil (CTN) but not carbendazim (MBC), and Microbacterium sp. MBC-3 (GenBank OK667229) can degrade MBC but not CTN. A functional strain BD2 was obtained by protoplast fusion of CTN-16 and MBC-3 to generate a fusant with improved degradation efficiency of CTN and MBC. Fusant-BD2 with eighth transfer on a medium containing CTN and two antibiotics was obtained. To identify and confirm the genetic relationship between parental strains and fusion strain BD2, scanning electron microscopy (SEM), random amplified polymorphic DNA (RAPD), and 16S ribosomal RNA (rRNA) gene sequences analysis were carried out. SEM analysis illustrated BD2 and its parents had some slight differences in the cell morphology. Fusant-BD2 not only possessed the same bands as parental strains but also had its specific bands analyzed through RAPD. The genetic similarity indices for BD2 and its parental strains CTN-16 and MBC-3 are 0.571 and 0.428, respectively. The degradation rates of CTN and MBC were 79.8% and 65.2% in the inorganic salt solution containing 50 mg·L−1 CTN and 50 mg·L−1 MBC, respectively, and the degradation efficiencies were better than the parental strains CTN-16 and MBC-3. This study provides a prospect for the application of fusion strain BD2 in bioremediation of CTN and MBC contaminated sites.

Genetic Diversity Analysis of Rice (Oryzae sativa L.) Landraces using SSR Markers in Bangladesh

It is necessary to assess genetic diversity and a molecular characteristic among Bangladesh’s local rice cultivars. The purpose of the study was to assess the genetic diversity and molecular characterization of 83 rice landraces in Bangladesh using nine (9) SSR markers. A total of 262 allels were identified using nine (9) polymorphic markers. The highest number alleles 34 were identified by RM336 while the lowest was 13 by RM262. Polymorphism information content (PIC) value of each marker was evaluated on the basis of the number of alleles and it varied greatly for all the SSR loci tested. The PIC value ranged from 0.951 to 0.766 and marker RM336 was found to be the most appropriate marker to discriminate among the rice genotypes owing to the highest PIC value of 0.951. The allele frequency ranged from 37.35% (RM262) to 10.84% (RM585, RM336) with an average of 18.47%. The genotypes G82, G77, G68, G50, and G1; G65, G37, and G10; G71 and G11; G25 and G14; G39 and G27 have 100% genetic similarity according to the pair wise genetic similarity indexes. Genotype G10 had the least similarity (0.44 percent) to genotype G9, G16 with G17, G22 with G29, G28 with G30, and so on. The dendrogram based on UPGMA and Nei’s genetic distance classified the 83 rice landraces into 5 clusters with a similarity coefficient of 0.6 Cluster 2 had maximum thirty-two genotypes followed by cluster 4. The landraces that were derivatives of genetically similar types were clustered together on the dendrogram. These landraces is showed wide genetic divergence among the constituent in it and in future it will be useful for hybridization programme in plant breeding. SAARC J. Agric., 19(2): 13-25 (2021)

Homogeneity of Arabian Peninsula dromedary camel populations with signals of geographic distinction based on whole genome sequence data

Dromedary camels in the Arabian Peninsula distribute along different geographical and ecological locations, e.g. desert, mountains and coasts. Here, we are aiming to explore the whole genome sequence data of ten dromedary populations from the Arabian Peninsula to assess their genetic structure, admixture levels, diversity and similarity indices. Upon including reference dromedary and Bactrian camel populations from Iran and Kazakhstan, we characterise inter-species and geographic genetic distinction between the dromedary and the Bactrian camels. Individual-based alpha genetic diversity profiles are found to be generally higher in Bactrian camels than dromedary populations, with the exception of five autosomes (NC_044525.1, NC_044534.1, NC_044540.1, NC_044542.1, NC_044544.1) at diversity orders (q ≥ 2). The Arabian Peninsula camels are generally homogenous, with a small degree of genetic distinction correlating with three geographic groups: North, Central and West; Southwest; and Southeast of the Arabian Peninsula. No significant variation in diversity or similarity indices are observed among the different Arabian Peninsula dromedary populations. This study contributes to our understanding of the genetic diversity of Arabian Peninsula dromedary camels. It will help conserve the genetic stock of this species and support the design of breeding programmes for genetic improvement of favorable traits.

ГЕНЕТИЧЕСКАЯ СТРУКТУРА ОВЕЦ ЗАПАДНО-СИБИРСКОЙ МЯСНОЙ И КУЛУНДИНСКОЙ ТОНКОРУННОЙ ПОРОД ПО ГЕНАМ CAST, GDF9 И KRT1.2

The purpose of the study is to analyze the genotypic structure and population-genetic parameters of the West Siberian meat and Kulunda fine-wool breed of sheep by the CAST, GDF9 and KRT1.2 genes and blood groups. Molecularnogenetic and immunogenetic studies were carried out in the SRIAH (Siberian Research Institute of Animal Husbandry SFSCA RAS) biotechnology laboratory. PCR-RFLP analysis to determine genotypes was performed according to the described and approved methods on a C1000 “BioRad” amplifier; the results were visualized using an E-Box-CX5.TS-20.M gel documentation system. It was found that the frequency of genotypes and alleles of the CAST gene of West Siberian meat and Kulunda fine-wool breeds have no significant differences. In both breeds, CASTMM was predominant, with a frequency of 69.0–75.0%, CASTNN carriers being only 1.6–5.1%. The Kulunda fine-wool breed is characterized by a very high frequency of the GDF9GG genotype 92.7%, which is higher than that of the West Siberian meat sheep by 26.3%. GDF9AA genotype is extremely rare in breeds (0–5%). The GDF9G allele in the compared breeds was found to range from 0.811–0.960 and the GDF9A allele from 0.189–0.040. There are differences in the ratio of genotypes of the KRT1.2 gene in the compared breeds. In the Kulunda fine-wool breed, the vast majority of animals have homozygous genotype KRT1.2MM (95.5%), whereas in the West Siberian meat breed such sheep constitute 32.8%. Consequently, the frequency of the KRT1.2M allele is 0.565–0.978 and the KRT1.2N allele is 0.435–0.022. The genetic balance in the studied genes is not disturbed, χ2 = 0,033–1,025. The index of genetic similarity between breeds, calculated on the basis of the frequencies of genotypes and blood groups is 0.901 ± 0.028 and 0.833 ± 0.024. Population and genetic characteristics are practically identical in the compared breeds, except for gene homozygosity (Ca), which is higher in the Kulunda fine-wool sheep breed by 24.3% for the GDF9 gene and KRT1.2 by 29.1%, compared to the West Siberian meat sheep breed. The number of effective alleles is insignificant (1.04–1.46). The genetic variability (V) by individual genes in the breeds varies from 5.0 to 49.6%. The negative value of the Fis coefficient indicates the absence of inbreeding in sheep the studied breeds.

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

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

Polyembryony in citrus: does the largest embryo in the seed develop a nucellar seedling?

A generalized concept in the Citrus genus is that highly polyembryonic varieties produce only a small number of hybrids. Small zygotic embryos congregate primarily near the micropyle, while nucellar embryos organize near or away from the micropyle. In the present study, the authors determined the number of polyembryonic seeds, embryos per seed, and the largest embryo (LE) position in five citrus cultivars: C35 citrange, Volkamer lemon, Amblycarpa mandarin, Minneola tangelo, and Valencia orange. The percentage of nucellar seedlings obtained exclusively from the LE per seed was then calculated. The polyembryony percentage varied largely between genotypes, from 65 to 98 %, and the mean number of embryos ranged from 2.9 to 4.6. The chalaza contained up to 87 % of the LE. Out of 30 primers, 17 Simple sequence repeats [SSRs] (AG14, ATC09, CAT01, CCSM147, CCSM18, CCSM13, CCSM4, F2, F4, F6, GT03, TAA41, TAA45, TAA1, F7, F11 and TAA52) identified nucellar plants identical to the female parent (genetic similarity index [GSI] value ≥ 0.95). This study establishes for the first time the relationship between the sexual or asexual origin of seedlings derived from LE embryos isolated from seeds and the SSR primers described above. While the five citrus cultivars had high polyembryony levels, 30 % of the resulting plants differed from the female parent in C35 Citrange, 45 % in Volkamer lemon, 15 % in Amblycarpa mandarin, 15 % in Valencia orange, and 45 % in Minneola tangelo. The largest seedling is not always nucellar: in the five citrus species studied, the LE produces 55 to 85 % of the nucellar embryos.

Genetic structure of population of the Kalmyk breed cattle

Blood groups, due to their irremovability and independence from gender, age, feeding conditions and maintenance, are widely used in animal breeding. The purpose of this study was to identify genetic markers of economically valuable traits of cattle of Kalmyk breed. Analysis of polymorphism of blood groups of Kalmyk cattle during the study period showed that there are antigens in the allelofond with a high concentration and frequency of occurrence: А1, A2, D', W, V, and Z, while G2I', C2 remain with low one. Analysis of the genetic status of different breeds revealed that there are obvious differences in frequencies. Antigens A1,A2,E’3,Z can serve as genetic markers of Kalmyk cattle purebred. The highest index of genetic distance was 0.1931 between the Kalmyk breed of the Republic of Kazakhstan and the Kazakh white-headed breed. The smallest genetic distance was found between the Simmental breed and the Kalmyk AO and is equal to 0.1166. The identification of the most effective method of selection, taking into account the index of genetic similarity, revealed the smallest number of parent pairs in the low (0.0-0.30) and high (0.61-0.90) indices of antigenic similarity and amounted to: “Agrofirma Aduchi” LLC – 24 pairs (16%) and 48 pairs (32%), “Sarpa” AO – 17 pairs (11%) and 21 pair (14%), A. A. Chapchayev AO PZ – 15 pairs (10%) and 9 pairs (6%), “Agribusiness” LLC – 8 pairs (5%) and 7 pairs (5%), respectively. When selecting parent pairs with an antigenic similarity index of 0.31-0.60, it allows to get bullheads with the highest live weight. Antigens marking the index value of 0,31-0,60, А1, А2, G2, E’3, C2, Z are considered genetic markers of the reproductive ability of Kalmyk breed cattle.