Effective Number Of Alleles Research Articles

Genetic diversity of Colletotrichum kahawae populations in Burundi

AbstractMicrosatellite markers were used to assess genetic diversity of Colletotrichum kahawae isolates from Burundi. Sampling was carried out through all coffee growing areas in Burundi. The indices of genetic diversity such as the number of different alleles (Na), the number of effective alleles (Ne) revealed low genetic diversity with an average of 1.900 and 1.196 respectively. Higher than expected heterozygosity and significant linkage disequilibrium are consistent with clonal reproduction. The results showed a weak genetic diversity between the populations from different region and the low value of Fst indicated that the C. kahawae populations of Burundi were weakly differentiated. Our results confirm the clonality of C. kahawae and its low dispersion ability. The weak differentiation between the populations and the occurrence of one clonal lineage in Burundi are consistent with previous study suggesting that the East African populations of C. kahawae are the most recently populations derived from the ancestral Angolan population.

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

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

Population structure and markers analysis associated with powdery mildew resistance in pumpkin, Cucurbita pepo L

Pumpkin (Cucurbita pepo L.) is an economically important vegetable and summer crop. The seeds have high nutritional value due to their edible oil and protein content with a high medicinal value. Pumpkin is attacked by several fungal diseases; one of which is powdery mildew (PM) caused by Podosphaera xanthii race-0. PM causes severe disease on pumpkin leading to major yield losses globally. In this study, we analyzed the genetic diversity and population structure of fourteen local pumpkin cultivars, all under Cucurbita pepo L. based on dominance in the region using 15 Inter-Simple-Sequence-Repeats-(ISSR) primer-pairs in association with resistance against PM as well as regulating the expression of three resistant marker genes i.e. SGT1, bHLH and PSK via qRT-PCR at three stages with 10 days' interval post-inoculation-stages-(SPI) with the powdery mildew agent, P. xanthii race-0. The results showed that ISSR markers demonstrated 13 primers out of 15 primers generated 169 distinct amplified bands, out of which 143 bands showed polymorphism. The mean polymorphism information content (PIC), marker index (MI), effective-number of alleles (I), expected heterozygosity (H), and Nei's gene diversity parameters were 0.354, 3.344, 0.334, 0.205 and 0.200, respectively. According to PIC, MI, I, H, and Nei indices evaluation, ISSR10 primer had the best performance in genetic diversity of the related pumpkin population. NTSYS pc 2.02e software and several similarity coefficients (r = 0.964), placed the related genotypes into five distinct groups. Of which, ‘Maragheh1′ and ‘Shahreza’ as resistant ones with 9.4 % and 6.1 % disease severity (DS), and ‘Gorgan’, ‘Urmia1′ and 3 and ‘Maragheh3’ with 79.6–84.8 % DS, as susceptible ones into two distinct groups, respectively. Further, the marker genes SGT1, bHLH and PSK expression level changes showed that the effect of variable factors including different genotypes (susceptible and resistant), disease-causing fungus, SPI, and the mutual effect of these factors is significant with the highest increase in resistant genotypes. Considering the relative compatibility in the classification of pumpkin genotypes in the dendrograms of DS and ISSR markers, it can be expected that increasing the number of markers in evaluating the genetic diversity of these genotypes makes it possible to differentiate pumpkin genotypes resistant and susceptible to PM disease based on the degree of disease resistance. The markers associated with resistance are recommended for use in marker assisted breeding.

The impact of LEP gene polymorphisms located at exon 2 (LEP-HinfI) and intron 2 (LEP-Sau3AI) on growth and reproductive traits in Saanen goats

Abstract. Leptin (LEP), alternatively recognized as the obesity gene, influences food consumption, energy balance, and lipid metabolism. Additionally, it plays a crucial role in energy metabolism, and variations in the LEP gene have been studied extensively among various livestock species. These investigations have unveiled correlations with traits such as meat quality, milk yield and composition, and growth characteristics. Nevertheless, the existing knowledge regarding its correlation with growth and reproductive traits in goats is comparatively limited, particularly when juxtaposed with studies of cattle. Hence, the objective of the current study was to investigate the relationship between polymorphisms in the intron 2 (Sau3AI) and exon 2 (HinfI) regions of the LEP gene and growth and reproductive traits in Saanen goats. The study comprised 185 Saanen goats in total. The PCR-RFLP (polymerase chain reaction restriction fragment length polymorphism) technique was employed to genotype these polymorphisms. Population genetic analysis included the number of effective alleles, heterozygosity, polymorphism information content, and compatibility with the Hardy–Weinberg equilibrium. The general linear model procedure's least-squares methods were used for the statistical analysis. The SNP (single-nucleotide polymorphism) located in exon 2 (LEP-HinfI) was monomorphic. Remarkably, the SNP located in intron 2 (LEP-Sau3AI) was associated with birth weight (p<0.05) and average daily weight gain (p<0.05). In this context, the AA genotype demonstrated higher birth weight and daily live weight gain means compared to other genotypes. No significant differences were observed in litter size, total weight gain, or morphometric measurements. The caprine LEP-Sau3AI polymorphism situated within intron 2 proved influential in traits critical for the profitability and sustainability of goat breeding. The findings of this study provide novel and valuable information for future research on the LEP gene in goats.

Genetic diversity and fingerprinting of Elaeagnus angustifolia based on SSR molecular markers

DNA fingerprinting can reveal the genetic diversity of Elaeagnus angustifolia germplasm resources and clarify the source and genetic background of E. angustifolia germplasm, which are the preconditions for the breeding of new varieties, the identification and protection of germplasm resources, and the comprehensive development of the E. angustifolia industry considering both ecological and economic benefits. We employed 11 pairs of primers with high polymorphism, clear bands, and high reproducibility to analyze the genetic diversity of 150 E. angustifolia germplasm accessions from Gansu and Beijing by the simple sequence repeat (SSR) molecular markers. We then employed the unweighted pair-group method with arithmetic means (UPGMA) to perform the cluster analysis based on genetic distance and analyzed the genetic structure of the 150 germplasm accessions based on a Bayesian model in Structure v2.3.3. The genetic diversity analysis revealed the mean number of alleles (Na) of 7.636 4, the mean number of effective alleles (Ne) of 2.832 6, the mean Shannon genetic diversity index (I) of 1.178 1, the mean Nei's gene diversity index (H) of 0.582 1, the mean observed heterozygosity (Ho) of 0.489 9, the mean expected heterozygosity (He) of 0.584 0, the mean polymorphism information content (PIC) of 0.535 4, and the mean genetic similarity (GS) of 0.831 5. These results suggested that the E. angustifolia germplasm resources we studied exhibited significant genetic differences and rich genetic diversity. The cluster analysis revealed that the tested materials can be classified into 3 groups, with the main genetic distance (GD) of 0.422 9. The clustering results were not completely consistent with the geographic origin. The population structure analysis classified the germplasm accessions into 2 populations. We used 8 pairs of primers with high PIC to construct the fingerprints of 150 E. angustifolia germplasm accessions. The present study successfully constructs the DNA fingerprints and clarified the genetic relationship of the E. angustifolia germplasm resources in Gansu and Beijing, providing a theoretical basis for germplasm resource identification, breeding of elite varieties, application in gardening, and molecular-assisted breeding of E. angustifolia.

Assessment of Genetic Diversity and Population Structure of Exotic Sugar Beet (Beta vulgaris L.) Varieties Using Three Molecular Markers.

Sugar beet (Beta vulgaris L.) is a biennial herb belonging to the Amaranthaceae family. It contributes to approximately 30% of the world's total sucrose production and is an economically important crop. In this study, we analyzed the genetic diversity and population structure of 132 exotic sugar beet varieties using three molecular makers: four pairs of simple sequence repeat (SSR) primers, three pairs of insertion-deletion sequence (InDel) primers, and 20 cis-element amplification polymorphism (CEAP) primers. The results indicated that the number of alleles (Na) was 298, among which the number of effective alleles (Ne) was 182.426 (accounting for approximately 61.2%). The mean value of the genetic diversity index was 0.836. The polymorphic information content (PIC) was 0.639-0.907 (mean = 0.819), indicating a high level of polymorphism. These sugar beet varieties were classified into six clusters using the UPGMA method of cluster analysis. Population structure analysis revealed that the most ideal K value was 6. This indicated that the test materials could be divided into six categories, consistent with the clustering results. The clustering results indicated that most sugar beet varieties from the same breeding company clustered together, and the genetic distance between them was small, indicating that they may share the same male and/or female parent. Some varieties from different companies clustered together, indicating a narrow genetic base and potential exchange of germplasm resources between breeding companies. This study revealed the genetic differences among exotic sugar beet varieties and characteristics of the population structure. It provided a scientific basis for the identification of sugar beet varieties and markers-assisted breeding in China in the future.

Bottleneck Effect Analysis in Indigenous Poonchi Chicken Located Near International Border of India and Pakistan

Background: Poonch is the remotest district of Jammu, India located near to line of control with Pakistan. Poonchi chicken is the first native poultry breed of Jammu region which is being characterized and registered with National Bureau of Animal Genetic Resources. Present study is the first study on genetic bottleneck assessment in Poonchi chicken population using recommended microsatellite markers. This study in Poonchi chicken would be of immense use in tracing evolutionary origin and formulating effective conservation strategies for genetic diversity within breeds. Methods: Blood samples were collected randomly from Poonch and Rajouri districts of Jammu for DNA extraction and analysis. Microsatellite markers selected for the analysis were ADL0268, MCW0206, MCW0081, ADL0278, MCW0069, MCW0248, MCW0111, MCW0222, MCW0016 and LEI0094. To evaluate the Poonchi chicken for mutation drift equilibrium, Bottleneck software was used. Infinite allele model (IAM), two phase model of mutation (TPM) and stepwise mutation model (SMM) tests were done. Mode shift test was also used as another method of qualitative test for allele frequency. Result: Total number of alleles observed were 72, with the total number alleles ranged from 6 to 9. The results of all three models (IAM, TPM, SMM) in Sign test depicted the heterozygosity was more in the expected number of loci in Poonchi chicken as 5.97 (P less than 0.05), 5.93 (P less than 0.05), 5.90 (P less than 0.05) respectively. Whereas for Wilcoxon rank test the IAM, TPM and SMM revealed significant values of (P less than 0.05) deviation indicating that all the loci deviate from mutation-drift equilibrium. Mode shift test graph obtained depicted a slight shift from normal L-shaped curve indicating recent bottleneck effect in Poonchi chicken. This might have resulted in the loss of number of effective alleles which suggests a need of planning and implementing an effective breeding policy in order to preserve and promote this native breed.

Evaluation of germplasm resources of Sarcomyxa edulis in the Changbai Mountains of Northeast China

ABSTRACT In this study, we evaluated 16 strains of Sarcomyxa edulis from the Changbai Mountains, China through antagonism tests and ISSR molecular marker technique for cytological and molecular biological evaluation. Q-type and R-type cluster analyses were utilised to evaluate and classify agronomic traits according to the test guidelines for distinctness, uniformity, and stability. The tested strains showed antagonistic reactions. The differences in antagonistic reactions among different germplasm resources are helpful for evaluating genetic diversity and provide a basis for better development and utilisation of fungal germplasm resources. A total of 330 bands were amplified by 21 ISSR primers, including 321 polymorphic bands. The percentage of polymorphic bands observed was 97.07%. Using PopGen32 software, the effective number of alleles (Ne), Nei's gene diversity index (H), and Shannon's diversity index (I) were calculated, yielding average values of 1.6638, 0.3796, and 0.5480, respectively. In addition, the genetic similarity coefficient of 16 strains ranged from 0.4306–0.7778. According to the Q-type clustering, the tested strains were classified into two categories based on the Euclidean distance of 8.52. While R-type cluster analysis revealed a significant correlation between the traits. At the Euclidean distance of 6.298, the traits could be classified into three distinct categories. According to the findings, all 16 strains demonstrated high genetic diversity. The ISSR clustering results revealed that strains with shorter genetic distances were more similar in specific traits. However, there were notable differences between the results of comprehensive trait clustering (Q-type clustering) and ISSR clustering.

Simple Sequence Repeat Marker-Based Genetic Diversity and Chemical Composition Analysis of Ancient Camellia sinensis in Jiulong County, Sichuan Province, China.

The ancient tea plant germplasm resources are rich in genetic diversity and provide an important basis for the genetic diversity in tea germplasm resources. To explore the genetic diversity of ancient tea plant germplasm resources in Jiulong County, Sichuan Province. 59 ancient tea tree germplasm resources were analyzed using simple sequence repeat (SSR) molecular markers and chemical composition analysis. The results showed that a total of 83 alleles were amplified by 23 pairs of SSR primers, with an average observed allele number (Na) of 3.6 and an effective allele number (Ne) of 2.335. The average Shannon information index (I) and the polymorphic information content (PIC) of the primers were 0.896 and 0.446, respectively. The results of the UPGMA cluster analysis showed that 59 ancient tea tree samples could be classified into five different subgroups. Based on the results of chemical composition analysis, two specific tea germplasm resources with high amino acid content, 10 excellent germplasm resources with tea polyphenol content over 20% and some other tea germplasm resources were identified. This study reveals that Jiulong's ancient tea tree germplasm exhibits significant genetic diversity and includes valuable tea tree planting resources. These findings provide a foundational framework for the conservation, detailed exploration and sustainable utilization of these resources.

Developmental and validation of a novel small and high-efficient panel of microhaplotypes for forensic genetics by the next generation sequencing

BackgroundIn the domain of forensic science, the application of kinship identification and mixture deconvolution techniques are of critical importance, providing robust scientific evidence for the resolution of complex cases. Microhaplotypes, as the emerging class of genetic markers, have been widely studied in forensics due to their high polymorphisms and excellent stability.Results and discussionIn this research, a novel and high-efficient panel integrating 33 microhaplotype loci along with a sex-determining locus was developed by the next generation sequencing technology. In addition, we also assessed its forensic utility and delved into its capacity for kinship analysis and mixture deconvolution. The average effective number of alleles (Ae) of the 33 microhaplotype loci in the Guizhou Han population was 6.06, and the Ae values of 30 loci were greater than 5. The cumulative power of discrimination and cumulative power of exclusion values of the novel panel in the Guizhou Han population were 1-5.6 × 10− 43 and 1-1.6 × 10− 15, respectively. In the simulated kinship analysis, the panel could effectively distinguish between parent-child, full-sibling, half-sibling, grandfather-grandson, aunt-nephew and unrelated individuals, but uncertainty rates clearly increased when distinguishing between first cousins and unrelated individuals. For the mixtures, the novel panel had demonstrated excellent performance in estimating the number of contributors of mixtures with 1 to 5 contributors in combination with the machine learning methods.ConclusionsIn summary, we have developed a small and high-efficient panel for forensic genetics, which could provide novel insights into forensic complex kinships testing and mixture deconvolution.

Genetic structure of cattle of the siberian branch by microsatellite loci

Molecular-genetic methods are essential tools for the utilization and conservation of animal genetic resources. These methods facilitate more efficient management and control of breeding programs within livestock production systems. For studying the genetic diversity of a population, the use of STR markers is relevant due to the high variability of repeats. This study presents a genetic characterization of a Holstein and Black Pied cattle population (n = 10233) in Western Siberia using 12 microsatellite loci (BM1818, BM1824, BM2113, ETH10, ETH225, ETH3, INRA023, SPS115, TGLA126, TGLA122, TGLA227, TGLA53). A total of 145 alleles were identified across all loci, with frequencies ranging from 0.00005 to 0.68961. The highest level of genetic diversity was observed at the TGLA122 locus (25 alleles) with an average number of effective alleles (Ne) of 4.5. The least polymorphic locus was BM1824 (7 alleles) with an average Ne of 3.27. The average observed (Ho) and expected (He) heterozygosity across all loci was 0.6. The highest variability was observed at the TGLA53 locus, with a Wright’s fixation index (Fis) of 0.161, indicating a heterozygote deficiency. A similar deficiency was observed at the BM1818 locus. All other loci exhibited a positive Fis, with the highest value observed at the ETH3 locus (-0.074), indicating an excess of heterozygotes. The average Fis across all loci was -0.02, suggesting a sufficient level of heterozygosity within the studied population. These findings provide valuable information for population studies and practical breeding programs aiming to manage genetic diversity and improve selection efficiency in this cattle population.

Assessing the population structure and genetic diversity of wheat germplasm with the iPBS-retrotransposons marker system

Context Wheat (Triticum aestivum L.) is an important crop that provides food to millions of people all over the world. Currently, wheat production is limited due to various biotic and abiotic stresses resulting from uneven patterns of climate change. Therefore, it is very important to develop climate-resilient wheat cultivars. Crop genetic diversity allows the scientific community to identify genetic variations that can be utilised in the development of improved cultivars. Aims This study planned to characterise the wheat germplasm with the iPBS-retrotransposons marker system. Methods A total of 30 iPBS-retrotransposons markers were screened and among these, the 12 most polymorphic markers were selected for further analysis. Key results Molecular characterisation yielded a total of 170 bands, of which 143 were polymorphic. A substantial level of genetic diversity was observed (mean effective number of alleles: 1.37, Shannon’s information index: 0.23, gene diversity: 0.35). Maximum genetic distance was observed in G9 and G60 genotypes. Analysis of molecular variance revealed that most genetic variation (95%) occurred within the populations. The model-based structure algorithm divided the studied germplasm into three populations based on their collection regions. Similarly, the neighbour-joining analysis also divided 70 tested wheat genotypes into three populations, whereas principal coordinate analysis divided the evaluated germplasm into four populations. Conclusions This study confirms the iPBS-retrotransposons as an ideal marker for the genetic diversity assessment studies for any crop, especially for wheat. Implications The results presented here will be helpful for the scientific community in the marker-assisted breeding of wheat.

Genetic characterisation of a recovered Italian chicken breed: the Millefiori Piemontese

The recent rediscovering of the Millefiori Piemontese breed, previously considered as extinct, has led to its genetic characterisation: establishing the basis for its recovery and preservation. This study describes the morpho-biometric traits and compares the genetic variability of the Millefiori Piemontese breed with that of other local chicken breeds using 26 microsatellite markers. A subset of 14 markers was used to compare the genetic variation of the Millefiori Piemontese breed with that of two other Piedmontese chicken breeds (Bionda Piemontese and Bianca di Saluzzo) as well as 17 Italian and 2 commercial hybrids, whose genetic variability has already been investigated. The present study confirmed the sexual dimorphism and assessed the genetic variability of the Millefiori Piemontese in terms of number of alleles/locus (Na = 4), the effective number of alleles (Nea = 3), observed (Ho = 0.56) and expected heterozygosity (He = 0.53), self-coancestry (IB = 0.65), potential extinction risk (ERI = 2), and its contribution to the Italian poultry biodiversity (GDT = −0.60). The results indicate that, despite its small population size (Ne = 56), the Millefiori Piemontese population exhibits significant genetic diversity, making it a valuable resource for breeding programs focused on preserving the breed and safeguarding its biodiversity. This study is the first to investigate the genetic variability of the Millefiori Piemontese breed and compare it with other local poultry breeds. The findings highlight the genetic uniqueness of the Millefiori breed and its significant contribution to the biodiversity of chickens in Piedmont and Italy, emphasising the importance of its conservation.

Screening a new set of microhaplotypes in exonic regions for sample identity testing and paternity testing during whole exome sequencing analysis.

Whole exome sequencing (WES) is widely used in clinical diagnosis. Before obtaining an accurate diagnosis, it is essential to conduct sample identity testing and paternity testing on trio samples. Currently, there is a lack of optimal genetic markers for these purposes, with limited literature available in this area. Microhaplotypes (MHs) are promising genetic markers due to their high polymorphism, low mutation rate, short amplified fragments, absence of stutter and amplification bias. These characteristics make them suitable for sample tracking and paternity testing during WES analysis. In this study, we screened out a set of polymorphic MHs in exonic regions for the above purposes. The results showed that the power of discrimination (PD) and probability of exclusion (PE) of this set of markers ranged from 0.2682 to 0.8878 and 0.0178 to 0.4583, respectively. Both the cumulative power of discrimination (CPD) and cumulative probability of exclusion (CPE) exceeded 0.999999, indicating the great value of these markers in paternity testing and individual identification in the study population. However, these markers had the effective number of alleles (Ae) values ranging from 1.1784 to 3.8727 (average 2.1805) and informativeness (In) values ranging from 0.0151 to 0.2209 (average 0.0766), showing limited value in DNA mixture analysis and biogeographical ancestry inference.

Genetic Diversity and Selection Signal Analysis of Hu Sheep Based on SNP50K BeadChip.

This research is designed to examine the genetic diversity and kinship among Hu sheep, as well as to discover genes associated with crucial economic traits. A selection of 50 unrelated adult male Hu sheep underwent genotyping with the SNP50K BeadChip. Seven indicators of genetic diversity were assessed based on high-quality SNP data: effective population size (Ne), polymorphic information content (PIC), polymorphic marker ratio (PN), expected heterozygosity (He), observed heterozygosity (Ho), effective number of alleles, and minor allele frequency (MAF). Plink software was employed to compute the IBS genetic distance matrix and detect runs of homozygosity (ROHs), while the G matrix and principal component analysis were performed using GCTA software. Selective sweep analysis was carried out using ROH, Pi, and Tajima's D methodologies. This study identified a total of 64,734 SNPs, of which 56,522 SNPs remained for downstream analysis after quality control. The population displayed relatively high genetic diversity. The 50 Hu sheep were ultimately grouped into 12 distinct families, with families 6, 8, and 10 having the highest numbers of individuals, each consisting of 6 sheep. Furthermore, a total of 294 ROHs were detected, with the majority having lengths between 1 and 5 Mb, and the inbreeding coefficient FROH was 0.01. In addition, 41, 440, and 994 candidate genes were identified by ROH, Pi, and Tajima's D methods, respectively, with 3 genes overlapping (BMPR1B, KCNIP4, and FAM13A). These results offer valuable insights for future Hu sheep breeding, genetic assessment, and population management.

Exploring Sampling Strategies and Genetic Diversity Analysis of Red Beet Germplasm Resources Using SSR Markers

By using 14 SSR primer pairs, we here analyzed and compared the amplification results of 534 DNA samples from six red sugar beet germplasm resources under three treatments. These data were used to explore the sampling strategy for the aforementioned resources. Based on the sampling strategy results, 21 SSR primer pairs were used to evaluate the genetic diversity of 47 red sugar beet germplasm resources. The six population genetic parameters used for exploring the sampling strategy unveiled that individual plants within the population had a relatively large genetic distance. The genetic parameters Ne, I, and Nei’s of the randomly mixed sampling samples increased rapidly between 10 and 30 plants before decreasing. Therefore, when SSR technology was used to analyze the genetic diversity of the red sugar beet germplasm resources, the optimal sampling gradient for each population was the adoption of a random single-plant mixed sampling sample of no less than 10 plants and no more than 30 plants. The 21 SSR primer pairs were used to detect genetic diversity in 30 random mixed samples of 47 resources. The average polymorphic information content (PIC) was 0.5738, the average number of observed alleles (Na) was 4.1905, the average number of effective alleles (Ne) was 2.8962, the average Shannon’s information index (I) was 1.1299, the average expected heterozygosity (Nei’s) was 0.6127, and the average expected heterozygosity (He) was 0.6127. The genetic distance of the 47 germplasm resources ranged from 0.0225 to 0.551 (average: 0.316). According to the population structure analysis, the most suitable K value was six, which indicated the presence of six populations. Based on the clustering analysis results, the 47 germplasm resources were segregated into six groups, with obvious clustering and some germplasm resources noted for having groups with close genetic relationships. We here established a more accurate and scientific sampling strategy for analyzing the genetic diversity of red sugar beet germplasm resources by using SSR molecular markers. The findings provide a reference for collecting and preserving red sugar beet germplasms and protecting their genetic diversity.

Genetic Diversity and Population Genetic Structure of Jatropha curcas L. Accessions from Different Provenances Revealed by Amplified Fragment-Length Polymorphism and Inter-Simple Sequence Repeat Markers

The genetic diversity and structure of 17 populations of J. curcas, including 92 accessions from different provenances (tropical and subtropical), were investigated and effectively evaluated using twelve inter-simple sequence repeats (ISSRs) and seven pairs of florescence-amplified fragment-length polymorphism (AFLP) primers. Genetic diversity, at the overall level among populations of J. curcas based on the ISSR markers, showed that the observed number of alleles (Na) was 1.593, the effective number of alleles (Ne) was 1.330, Nei’s gene diversity (H) was 0.200, Shannon’s information index (I) was 0.303, and the percentage of polymorphic loci was 59.29%, indicating moderate genetic diversity between and within the different populations of J. curcas. Based on the genetic diversity analysis of AFLP markers, there were 1.464 (Na) and 1.216 (Ne) alleles, Nei’s gene diversity (H) was 0.132, Shannon’s information index (I) was 0.204, and the percentage of polymorphic loci was 46.40%. The AMOVA analysis showed that this large variance was due to differences within the populations, with genetic distinctions and limited gene flow among those from varied regions. The 17 populations were clustered into five main groups via UPGMA clustering analysis based on Nei’s genetic distance, and the genetic relationships among the populations exhibited no significant correlations with geographical provenances. The genetic variation among Chinese populations of J. curcas distributed in dry-hot valley areas was remarkable, and the American germplasm presented with distinct genetic differentiation.

GENETIC DIVERSITY AND POPULATION STRUCTURE OF JUNIPERUS SERAVSCHANICA KOM. IN CENTRAL ASIA REVEALED BY MICROSATELLITE MARKERS

Juniperus seravschanica Kom. is a widely distributed and significant tree species in Central Asia, thriving in the mountain ranges from Oman to Uzbekistan, Kyrgyzstan, and Kazakhstan. It plays a vital role in forming shrub-forest massifs in mountainous regions, contributing to soil drainage and stabilization at medium to high altitudes. To gain a detailed understanding of the current status of J. seravschanica and to develop effective conservation strategies, a comprehensive study of the species' genetic diversity and population structure was conducted. Leaf samples were collected from 15 J. seravschanica populations across Uzbekistan, Kyrgyzstan, and Kazakhstan to assess genetic diversity and population structure. Using 11 polymorphic simple sequence repeat (SSR) markers, genetic diversity parameters such as the number of alleles, the number of effective alleles, the percentage of polymorphic loci, and Nei's genetic diversity index were evaluated. Nei's genetic diversity index for J. seravschanica populations averaged 0.450, ranging from 0.407 to 0.566. The AMOVA revealed that 90.3% of the total genetic variation was within populations, indicating a high level of genetic diversity within each population. Gene flow, calculated using alleles from all populations, was estimated at 4.654. Population structure analysis showed weak clustering among the studied populations, supporting the AMOVA findings. This study provides valuable insights into the genetic diversity and population structure of J. seravschanica in Central Asia. The high genetic diversity within populations suggests a strong adaptive capacity to environmental changes. These findings can be effectively utilized to develop conservation strategies for J. seravschanica, ensuring the long-term sustainability of this important tree species in Central Asia. This work was supported by Grant No.AP09259027 of the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan.

Detection of the effect of the KISS1 gene on reproductive parameters in Saanen goats

The KISS1 gene, which activates G protein-coupled receptor-54 (GPR54) and plays a crucial role in the neuroendocrine regulation of GnRH secretion, is known to encode a family of neuropeptides called kisspeptins. Therefore, the KISS1 gene is thought to be associated with sexual maturity, offspring development, and estrus. The g.2124T>A polymorphism of the KISS1 gene, is believed to affect the reproductive system, has been studied in Indonesian goat breeds, Damascus, Zarabi, Baladi, Gaddi, Kaligesing, Guanzong, Xinong Saanen and Boer goat breeds until now. These studies are generally related determining polymorphism frequencies or the effect of genotype on litter size. The study aims to determine the allele and genotype frequencies of the KISS1 gene g.2124T>A SNP by the PCR-RFLP method and define the relationship between the genotypic structures and reproductive parameters such as luteal growth, maximum corpus luteum diameter, and mating rate in Saanen goats (n=30). According to the results, the genotype frequencies in Saanen goats for the KISS1 gene g.2124T>A were 10.35%, 55.17%, and 34.48% for AA, TT and AT, respectively. Moreover, the genotypic structure did not have a statistically significant effect on the investigated fertility characteristics. The average values of expected heterozygosity (He), observed heterozygosity (Ho), the effective number of alleles (Ne), fixation index values (FIS), and the polymorphism information content (PIC) were 0.3996, 0.3448, 1.6655, 0.8629 and 0.855, respectively. The Hardy-Weinberg chi square (χ2) value was found to be 0.5435. In conclusion, it was found necessary to study the KISS1 - g.2124T>A polymorphism in larger herds with different gene pools as a reason for the existence of genotypic variation and the narrow population size.

Hemoglobin polymorphism and its association with morphometric and egg production traits in Ethiopian indigenous and Sasso chicken breeds.

The present study investigated the biochemical polymorphism of hemoglobin (Hb) and its relationship with performance traits of Ethiopian indigenous and Sasso chicken breeds. A total of 284 chickens reared in three agro-ecologies were examined for genetic diversity and associations with productive traits at Hb locus using agarose gel electrophoresis. The results showed that the HbA allele was dominant in both breeds, and a higher proportion of male chickens were HbAA genotypes, while females were predominantly HbBB types. In the highland agro-ecology, chickens with the HbAA genotype were the most dominant, whereas in mid- and low-land agro-ecologies, chickens with HbBB and HbAB genotypes were found to be more frequent. A moderate level of expected heterozygosity was obtained with 0.47 and 0.445 for indigenous and Sasso chickens, respectively, with an average effective number of alleles per locus of 1.89 and 1.80. Moreover, chickens with HbAA genotypes showed significantly (p ≤ 0.05) higher body weight and linear body measurements than those of HbAB and HbBB genotypes. However, for appendage body structures (comb and wattle dimensions), chickens with the HbAB and HbBB genotypes had higher mean values. Additionally, clutch size (14.2 ± 0.4), clutch length (21.8 ± 0.7), and eight-month egg production (84.1 ± 1.2) were significantly (p ≤ 0.05) higher for hens with HbBB genotypes, followed by those with HbAB-types. Therefore, the considerable hemoglobin variability and significant associations of Hb variants with the performance traits can be sought as guiding information for further genetic improvement interventions in the chicken breeds under investigation. Further microsatellite marker-based genotyping is recommended to validate the higher morphometric values for HbAA genotypes and the better egg production for HbBB and HbAB genotypes.