Polymorphism Information Content Research Articles

Comparative Analysis of Physical and Chemical Mutagenesis in Chrysanthemum cv. 'Candid': Assessing Genetic Variation and Breeding Potential.

In this study, we developed a mutagenesis protocol specifically designed for chrysanthemum cv. "Candid" in order to introduce genetic variation. By subjecting chrysanthemum shoots to different doses of physical and chemical mutagens, we successfully generated a total of 24 mutants, each with unique genetic compositions. We observed that the mortality rate was lowest when the shoots were exposed to 10 Gy gamma irradiation and 1.00% EMS. To assess the diversity and relatedness among the mutants, we employed RAPD and SSR markers. The combination of these markers allowed us to construct a dendrogram that effectively categorized the mutant population into distinct clusters based on the specific mutagen treatments. Interestingly, the mutants induced by 10 Gy gamma irradiation exhibited greater genetic diversity in terms of flower colors. On the other hand, mutants created with 1.00% EMS displayed a higher level of variation and yielded more viable mutants. To determine the optimal markers for studying genetic diversity, we analyzed the polymorphic information content (PIC) of different markers. Among the tested markers, OPA-07 (RAPD) and JH47 (SSR) showed the highest PIC values, indicating their effectiveness in capturing genetic variability within the mutant population. Conversely, the PIC values of OPD-07 and JH20 demonstrated the lowest among the markers tested. Our results revealed a percentage of polymorphism ranging from 81.81% to 100% for RAPD markers and 66.66% to 100% for SSR markers. These findings indicate that physical mutation induced by 10 Gy gamma irradiation can be clearly distinguished from chemical mutation induced by EMS at concentrations of 1% and 0.75% in chrysanthemum cv. "Candid.″ Overall, this study provides valuable insights into the genetic composition of the generated mutants and highlights their potential for enhancing chrysanthemum-breeding programs. The identified markers, particularly, OPA-07 and JH47, can serve as valuable tools for future studies aimed at exploring and exploiting the genetic diversity within the chrysanthemum population.

Genetic diversity, population structure, and DNA fingerprinting of Ailanthus altissima var. erythrocarpa based on EST-SSR markers

Ailanthus altissima var. erythrocarpa is an A. altissima variety with high economic, ecological and ornamental value, but there have been no reports on the development of SSR primers for it. According to the SSR primer information provided by the transcriptome of A. altissima var. erythrocarpa, 120 individuals with different redness levels were used to screen polymorphic primers. Transcriptomic analysis revealed 10,681 SSR loci, of which mononucleotide repeats were dominant (58.3%), followed by dinucleotide and trinucleotide repeats (16.6%, 15.1%) and pentanucleotide repeats (0.2%). Among 140 pairs of randomly selected primers, nineteen pairs of core primers with high polymorphism were obtained. The average number of alleles (Na), average number of effective alleles (Ne), average Shannon’s diversity index (I), average observed heterozygosity (Ho), average expected heterozygosity (He), fixation index (F) and polymorphic information content (PIC) were 11.623, 4.098, 1.626, 0.516, 0.696, 0.232 and 0.671, respectively. Nineteen EST-SSR markers were used to study the genetic diversity and population structure of A. altissima var. erythrocarpa. The phylogenetic tree, PCoA, and structure analysis all divided the tested resources into two categories, clearly showing the genetic variation between individuals. The population showed high genetic diversity, mainly derived from intraspecific variation. Among nineteen pairs of primers, 4 pairs (p33, p15, p46, p92) could effectively distinguish and be used for fingerprinting of the tested materials. This study is of great significance for genetic diversity analysis and molecular-assisted breeding of A. altissima var. erythrocarpa.

Evaluation of the Allelic Variations in Vernalisation (VRN1) and Photoperiod (PPD1) Genes and Genetic Diversity in a Spanish Spelt Wheat Collection.

Allelic variation within genes controlling the vernalisation requirement (VRN1) and photoperiod response (PPD1) determines the adaptation of wheat to different environmental growing conditions as well as influences other traits related to grain yield. This study aimed to screen a Spanish spelt wheat collection using gene-specific molecular markers for VRN-A1, VRN-B1, VRN-D1, and PPD-D1 loci and to phenotype for heading date (HD) in both field and greenhouse experiments under a long photoperiod and without vernalisation. Fifty-five spelt genotypes (91.7%) exhibited a spring growth habit, and all of them carried at least one dominant VRN1 allele, whereas five (8.3%) genotypes had a winter growth habit, and they carried the triple recessive allele combination. The Vrn-D1s was the most frequent allele in the studied set of spelt accessions, and it was found in combination with both the dominant Vrn-A1b and/or Vrn-B1a alleles in 88.3% of the spelt accessions tested. All spelt accessions carried the photoperiod-sensitive Ppd-D1b allele, which may explain the late heading of spelt germplasm compared to the commercial spring bread wheat Setenil used as a control. The least significant difference test showed significant differences between allelic combinations, the earliest accessions being those carrying two or three dominant alleles, followed by the one-gene combinations. In addition, the genetic diversity was evaluated through capillary electrophoresis using 15 wheat simple sequence repeat (SSR) markers. Most markers had high levels of polymorphism, producing 95 different alleles which ranged between 53 and 279 bp in size. Based on the polymorphic information content values obtained (from 0.51 to 0.97), 12 out of the 15 SSRs were catalogued as informative markers (values > 0.5). According to the dendrogram generated, the spelt accessions clustered as a separate group from the commercial bread wheat Setenil. Knowledge of VRN1 and PPD1 alleles, heading time, and genetic variability using SSR markers is valuable for spelt wheat breeding programs.

Genetic Diversity and Genetic Structure among Four Selected Strains of Whiteleg Shrimp (Litopenaeus vannamei) Using SSR Markers

The whiteleg shrimp (Litopenaeus vannamei) is one of the most economically important aquaculture species in China. Genetic diversity is crucial for maintaining the gene pool of farmed shrimp. In this study, the effects of artificial selection on the genetic structure of four whiteleg shrimp strains were evaluated using microsatellite sequences. The results showed that the observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) of the four selected strains ranged from 0.446 to 0.574, 0.450 to 0.566, and 0.435 to 0.509, respectively. All the selected strains maintained a moderate level of genetic diversity. Most inbreeding coefficients (Fis) in the four strains were positive but not significantly different from zero, indicating a relatively low degree of inbreeding within each strain. However, He and PIC in line 5 showed a decreasing trend from the 2017 to the 2019 generations, and Fis in line 10 showed a significant increasing trend across generations, indicating that measures must be taken to maintain the level of genetic diversity for lines 5 and 10. UPGMA cluster trees showed that the four breeding lines had apparent genetic differences, which could provide a genetic basis for studying crossbreeding between selective lines and the utilization of heterosis. This study will be useful for population genetic research and the breeding strategies of whiteleg shrimp.

Genetic diversity and population structure of Mastacembelus armatus in the river systems of southern China revealed by microsatellites

The Zig-zag eel (Mastacembelus armatus) is an economically important species in southern China. Its natural resources have declined year by year due to overfishing. Understanding its genetic diversity and population structure is very important for resource conservations. Here, we first successfully developed 28 polymorphic microsatellite markers for zig-zag eels and ten of them were used to examine the genetic diversity and differentiation of 7 populations collected from the major river systems of south China. In total, 224 alleles were found with the 10 microsatellite loci in 7 populations, ranging from 4.6 (Nandujiang: NDJ) to 11.1 (Xijiang, XJ), with an average of 8.871 alleles. The average observed and expected heterozygosity ranged from 0.550 (NDJ) to 0.964 (Yuangjiang, YJ) and from 0.537 (NDJ) to 0.775 (Tanjiang, TJ), respectively. The average polymorphism-information content ranged from 0.472 (NDJ) to 0.757 (TJ). Hardy–Weinberg equilibrium test results revealed the loci showed differing deviation in different populations. In total, low level of genetic diversity was only found in HJ (Hanjiang) and NDJ populations. Besides, evidence of recent bottleneck was found in the HJ populations. Analysis of molecular variation showed that the percent variation within individuals (75.00%) was higher than that among populations (25%). In addition, population structure and the pairwise FST revealed that there was low differentiation among XJ, TJ and YJ populations. These data provide important genetic resources for understanding the population differentiation and facilitating genetic conservation and utilization of this species.

Genetic Variation among Three Species of Genus <i>Erythroculter</i>

The genus Erythroculter (Cypriniformes, Cyprinidae, Abramidinae) is one of the most commercially important freshwater fish species inhabiting China. However, very limited information is available regarding genetic variation among Erythroculter species, therefore hindering their effective management. In this regard, microsatellite markers and sequences of mitochondrial COII and D-loop were analyzed to investigate the genetic variation among three species of genus Erythroculter. Results demonstrated that 11 microsatellite loci were amplified effectually, and the size of allele was 110–350, 94–338 and 86–384 bps in E. ilishaeformis, E. dabryi and E. mongolicus respectively. Average number of allele was 5.82, 5.73 and 6.45 per locus for E. ilishaeformis, E. dabryi and E. mongolicus respectively. Fragments of COII and D-loop was 675 and 929 bps respectively. On the basis of Shannon’s information index, heterozygosity, polymorphic information content and nucleotide diversity index (P), the microsatellite and nucleotide diversity of E. ilishaeformis was most abundant, and that of E. mongolicus was least abundant. Based on the haplotype distribution of D-loop or the allele size in microsatellite loci of EI19 or HWB05, it could be distinguished perfectly among E. ilishaeformis, E. dabryi and E. mongolicus. Some historical and environmental elements might result in the high genetic divergence and promote the speciation of E. ilishaeformis, E. dabryi and E. mongolicus. These results would be of avail in the conservation and sustainable utilization of these three species.

Construction of a genome-wide SSR marker library in Gerbera hybrida: Insights into genetic variation and germplasm resources

Gerbera hybrida is a highly sought-after cut flower globally, renowned for its diverse flower color and pattern resulting from its complex inflorescence meristem architecture. However, the scarcity of genomic information and molecular markers has impeded efforts to comprehend the genetic diversity of G. hybrida. To address this, our study aimed to construct genome-wide simple sequence repeat (SSR) markers in G. hybrida, utilizing genomic data from an inbred line. We employed 170 gerbera cultivars exhibiting distinct flower patterns and colors to analyze genetic variation and diversity. Our analyses revealed highly polymorphic SSR markers, a total of 69 alleles (Na) were amplified by 14 pairs of primers, in which polymorphic information content (PIC) ranging from 0.380 to 0.700 with an average value of 0.583. The polymorphic results of the observed heterozygosity (Ho) and Shannon's information index (I) were 0.499 and 1.195, respectively, showing a high level of genetic diversity within the enriched sequences of the G. hybrida genome. Leveraging these markers with strong differentiation, we successfully constructed a unique fingerprint map encompassing 170 gerbera germplasm lines. This study involved the construction of an SSR fingerprint library for G. hybrida germplasm resources, employing genetic analysis for screening and molecular-level identification. The findings provide valuable insights into the identification of gerbera germplasm resources and kinship studies among various groups. Moreover, this study lays a solid foundation for future advancements in molecular design breeding improvement and germplasm resource development in G. hybrida.

Analysis of genetic diversity and population structure of Magnaporthe grisea, the causal agent of foxtail millet blast using microsatellites.

Foxtail millet blast caused by Magnaporthe grisea is becoming a severe problem in foxtail millet growing regions of India. The genetic diversity and population structure of foxtail millet infecting M. grisea is crucial for developing effective management strategies, such as breeding blast-resistant cultivars. We analyzed thirty-two M. grisea isolates from ten foxtail millet-growing districts in Tamil Nadu, India for genetic diversity using twenty-nine microsatellite or simple sequence repeat (SSR) markers. A total of 103 alleles were identified with a mean of 3.55 alleles/locus. Gene diversity ranged from 0.170 to 0.717, while major allelic frequencies ranged from 0.344 to 0.906. The polymorphism information content (PIC) ranged from 0.155 to 0.680, with a mean value of 0.465. Population structure analysis of the genomic data sets revealed two major populations (SP1 and SP2) with different levels of ancestral admixture among the 32 blast isolates. Phylogenetic analysis classified the isolates into three major clusters. Analysis of molecular variance (AMOVA) showed high genetic variation among individuals and less among populations. Principal Coordinate Analysis (PCoA) revealed 27.16% genetic variation among populations. The present study provides the first report on the genetic diversity and population structure of the foxtail millet-infecting M. grisea population in Tamil Nadu, which could be useful for the development of blast-resistant foxtail millet cultivars.

Microsatellite-based diversity analysis and the development of core-set germplasm in Pakistani barley lines.

Illustrating the population structure and genetic diversity in selected germplasm resources (after three year multi locations trials) plays a key role which directly utilize the selection of lines in a population for accumulative trait breeding in crops. In order to further understand, the structure of population and genetic variability, we explored 100 selected lines, cultivated for three consecutive years (2016-2019) in swat, University of Malakand, Khyber Pakhtunkhwa Pakistan and Provinces of China (Chongqing and Beijing) with 33 mapped SSR markers. The integrated population structure analysis in a core of hundred germplasm with Pakistani origin with three approved commercial barley cultivars have strong stratification that allowed their division into four major subpopulations (i.e. PI, PII, PIII and PIV) and an admixture subpopulation, with 52, 9, 15 and 27 germplasm respectively. A total of 133 alleles were identified with mean value of 0.80 Polymorphic information content. The number of alleles detected by the system varied from two alleles amplified to as six with an average of 4.03 per SSR marker pair. The gene diversity ranged from 0.56 to 0.98 with an average of 0.82 in selected germplasm resources. Based on the SSR data, the 100 selected germplasm with three cultivars were classified into four main phylogenetic Linages (LI, LII, LIII and LIV) which corresponded to the phylogenic grouping in genotypes. We assembled a core set of 20 barley genotypes (~1/5 of original population size) to sustain sufficient mapping of SSR marker with Phenotype, in which we proposed four SSR markers, Bmac0040, Bmac0134, Bmag0125 and Bmag0211 for malt gene and marker (Bmac0399) for tolerance to salinity gene, which will be applicable for marker assisted breeding in barley gene resources.

AEGILOPS L. GENETIC DIVERSITY IN SOUTHWESTERN REGION OF UZBEKISTAN

As wheat donors, wild species of the genus Aegilops L. play a vital role in practical breeding to improve wheat production because of their strong relationship and wide genetic diversity. Using nine simple sequence repeat (SSR) markers helped assess the genetic diversity in 96 collected samples of four species belonging to the genus Aegilops, i.e., Aegilops tauschii Coss (D), Ae. cylindrica Host (CD), Ae. crassa Boiss (DDM), and Ae. triuncialis L. (UC). The said collection came from 21 sites of various expeditions located in three regions of Southwestern Uzbekistan (Samarkand, Urgut, Kitab, and Shakhrisabz regions). Generally, 102 distinct alleles were found, with an average of 11.33 alleles per primer. The total number of species-specific amplicons was 35. The polymorphism detected varied from 28.6% (for the WSP107 primer) to 77.0% (for the WSP130 and WSP192 primers). The mean values of polymorphism information content (PIC) and expected heterozygosity (Ho) for all samples were 0.675 and 0.527, respectively. Based on nine SSR markers, on average, the genetic distance indices (GD) varied from 0.63 to 0.77. The highest genetic similarity (GD = 0.77) recorded occurred between the species Ae. crassa and Ae. cylindrica, whereas the least (GD = 0.48), between Ae. cylindrica and Ae. triuncialis with their taxonomic classification. Genus Aegilops samples from the same region often attain an identical subgrouping, which might be due to relatedness by genetic parameters. The gene pool of native species of the genus Aegilops from the Southwestern region of Uzbekistan may provide suitable alleles for wheat improvement and adaptation in the future.

Development and Validation of Gene-Based SSR Markers in the Genus Mesembryanthemum.

Bioinformatics tools have been employed for the direct development of gene-based simple sequence repeat (SSR) markers. Through the analysis of 28,056 Mesembryanthemum expressed sequence tag (EST) sequences, a total of 5,851 ESTs containing SSRs were identified, amounting to approximately 17.07 Mb. Among these, 938 EST sequences harbored more than one SSR marker, and 788 EST-SSR sequences were found in compound form. The most prevalent types of SSR motifs were mononucleotide repeats (MNRs), accounting for 44%, followed by di-nucleotide repeats (DNRs) at 37%, and trinucleotide repeats (TNRs) at 16%. Notably, TNR or longer SSR motifs primarily consisted of shorter repeat lengths, with only 51 motifs containing 10 or more repeats. The BLASTX analysis successfully assigned functions to 4,623 (79%) of the EST sequences. Among the developed primer sets, 21 primers amplified a total of 65 alleles, with primer PMA79 EST-SSR exhibiting the maximum of six alleles. The polymorphic information content (PIC) values ranged from 0 to 0.76, with a mean of 0.47. The marker index (MI) and discriminating power (D) values reached 0.66 (primer PMA63) and 0.95 (primer PMA20), respectively. Utilizing the unweighted pair group method with arithmetic mean (UPGMA), a dendrogram was constructed, successfully segregating the 24 Mesembryanthemum genotypes into three distinct clusters, with a similarity coefficient ranging from 0.96 to 0.38. In this study, we have developed a total of 83 EST-SSR primer pairs specific to the Mesembryanthemum genus. These newly developed EST-SSRs will serve as valuable tools for researchers, particularly molecular breeders, enabling gene-based identification and trait selection through marker-assisted breeding approaches.

Genetic and phenotypic diversity of native potatoes (Solanum spp.) from the Central Andes of Peru

The diversity of native potatoes cultivated above 3500 masl in the Pasco region (Central Andes of Peru) has not been fully characterized. It is currently subject to constant genetic erosion caused by biotic and abiotic factors. The research aimed to characterize phenotypically and genotypically 40 native potato landraces representative of 4 Solanum species. Twenty phenotypic descriptors and 10 microsatellites were used for genetic evaluation. Likewise, the ploidy level was evaluated based on the number of chloroplasts in the stomata. The clustering analysis was performed using the Infostat software and the R program with the Adegenet and Polysat libraries. The phenotypic characterization allowed to obtain five groups with a distance coefficient of 9.5. The molecular characterization found seven groups and 58 alleles in total. The average number of alleles per microsatellite was 5.5. 13.2 % of duplicates were identified. The microsatellites STG001, STM1106, ST0032, and STM5127 with an average He of 0.8 and a polymorphism information content (PIC) of 0.5 - 0.8 were the most informative. Finally, the ploidy results were 13 % diploid, 35 % triploid, and 52 % tetraploid. It was evidenced low diversity when using a set of 10 SSR markers, which indicates limited applicability for studying the genetic diversity of local potato landraces. It is necessary to involve a broader range of markers and a more diverse set of genotypes from the Pasco region for further studies.

Unveiling the genetic landscape of high-altitude adaptive ethnic groups with polymorphic markers: Implications of comprehensive forensic appraisals and population genetic investigations

BackgroundDeletion/insertion polymorphisms (DIPs), a novel class of biomarker, have been widely utilized in forensic areas for individual identification, paternity tests, and ancestral origin inference due to its applicability to degraded samples and low mutation rates. Despite the availability of a well-established commercial kit, the Investigator® DIPplex kit (Qiagen), certain loci exhibit limited levels of polymorphisms in East Asian populations, particularly in Chinese populations. ObjectiveThis dissertation seeks to undertake a comprehensive evaluation about the forensic efficiency of a self-developed multiplex amplification system in high-altitude adaptive ethnic groups of China. Healthy unrelated Tibetan individuals residing in Tibet Autonomous Region and Qinghai Province were genotyped using previously reported 43 deletion/insertion polymorphism loci. Forensic statistical analyses including allele frequencies and forensic parameters were conducted in the two Tibetan groups, and the genetic relatedness of the studied groups with reference populations from the 1000 Genomes Project Phase 3 were investigated. ResultsForensic statistical results showed that the polymorphism information content values of the 43 deletion/insertion polymorphism loci in the two Tibetan groups exceeded 0.35. Moreover, the combined power of discrimination using the 43 deletion/insertion polymorphism loci was calculated to be 0.9999999999999999984 in the Qinghai Tibetan group and 0.9999999999999999921 in the Tibet Tibetan group. The cumulative power of exclusion using the 43 deletion/insertion polymorphism loci was calculated to be 0.999782512 in the Qinghai Tibetan group and 0.999886205 in the Tibet Tibetan group. Analysis of population genetics demonstrated that the two studied Tibetan groups shared close genetic relationships with East Asia populations. ConclusionThe set of 43 deletion/insertion polymorphism loci exhibited remarkable forensic efficacy, rendering it a promising tool for forensic practice. Population genetic analyses indicated that the two Tibetan groups had closer genetic affinities to East Asian populations.

Evaluation of Morpho-Physiological and Yield-Associated Traits of Rice (Oryza sativa L.) Landraces Combined with Marker-Assisted Selection under High-Temperature Stress and Elevated Atmospheric CO2 Levels.

Rice (Oryza sativa L.) is an important cereal crop worldwide due to its long domestication history. North-Eastern India (NEI) is one of the origins of indica rice and contains various native landraces that can withstand climatic changes. The present study compared NEI rice landraces to a check variety for phenological, morpho-physiological, and yield-associated traits under high temperatures (HTs) and elevated CO2 (eCO2) levels using molecular markers. The first experiment tested 75 rice landraces for HT tolerance. Seven better-performing landraces and the check variety (N22) were evaluated for the above traits in bioreactors for two years (2019 and 2020) under control (T1) and two stress treatments [mild stress or T2 (eCO2 550 ppm + 4 °C more than ambient temperature) and severe stress or T3 (eCO2 750 ppm + 6 °C more than ambient temperature)]. The findings showed that moderate stress (T2) improved plant height (PH), leaf number (LN), leaf area (LA), spikelets panicle-1 (S/P), thousand-grain weight (TGW), harvest index (HI), and grain production. HT and eCO2 in T3 significantly decreased all genotypes' metrics, including grain yield (GY). Pollen traits are strongly and positively associated with spikelet fertility at maturity and GY under stress conditions. Shoot biomass positively affected yield-associated traits including S/P, TGW, HI, and GY. This study recorded an average reduction of 8.09% GY across two seasons in response to the conditions simulated in T3. Overall, two landraces-Kohima special and Lisem-were found to be more responsive compared to other the landraces as well as N22 under stress conditions, with a higher yield and biomass increment. SCoT-marker-assisted genotyping amplified 77 alleles, 55 of which were polymorphic, with polymorphism information content (PIC) values from 0.22 to 0.67. The study reveals genetic variation among the rice lines and supports Kohima Special and Lisem's close relationship. These two better-performing rice landraces are useful pre-breeding resources for future rice-breeding programs to increase stress tolerance, especially to HT and high eCO2 levels under changing climatic situations.

Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea.

Psathyrostachys juncea is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restoration. Plant architecture, especially tillering traits, is critical for bunch grasses in breeding programs, and these traits in plants are mostly quantitative traits. In this study, the genetic diversity, population structure, and linkage disequilibrium of 480 individual lines were analyzed using 127 pairs of the EST-SSR marker, and a significant association between ten plant-architecture-related traits of P. juncea and molecular markers was found. The results of the genetic diversity analysis showed that the number of observed alleles was 1.957, the number of effective alleles was 1.682, Shannon's information index was 0.554, observed heterozygosity was 0.353, expected heterozygosity was 0.379, and the polymorphism information content was 0.300. A total of 480 individual lines were clustered into five groups based on population genetic structure, principal coordinate analysis, and unweighted pair group method with arithmetic mean analysis (UPGMA). The linkage disequilibrium coefficient (r2) was between 0.00 and 0.68, with an average of 0.04, which indicated a relatively low level of linkage disequilibrium among loci. The results of the association analysis revealed 55 significant marker-trait associations (MTA). Moreover, nine SSR markers were associated with multiple traits. This study provides tools with promising applications in the molecular selection and breeding of P. juncea germplasm.

Development of polymorphic simple sequence repeat markers in Agastache rugosa and their application in genetic evaluation and cross-taxon transferability of Agastache species

Agastache is a genus of perennial herbaceous plants belonging to the mint family, Lamiaceae. Several Agastache species are commercially cultivated and used as medicinal, culinary, and ornamental plants. However, information on the genetic diversity and population structure of the species remains unclear. In the present study, genetic diversity within Agastache species was analyzed using simple sequence repeat (SSR) markers. In this study, 249,746 SSRs were identified in the A. rugosa genome and primer pairs were designed for 56,675 SSRs. The majority of SSR repeat types were dinucleotides (60.65%), followed by trinucleotides (12.38%), and pentanucleotides (12.10%). PCR conditions were established for 250 primer pairs, 111 of which were found to be polymorphic in A. rugosa germplasm. The number of alleles (NA) ranged from 2 to 19, major allele frequency (MAF) ranged from 0.11 to 0.95, observed heterozygosity (HO) ranged from 0 to 0.89, and polymorphic information content (PIC) ranged from 0.09 to 0.92. Cross-species amplification of SSRs markers in other Agastache species showed amplification rates of 82.6% for A. foeniculum and 78.1% in A. urticifolia, with an average of 80.37%. Cluster analysis of the 19 A. rugosa accessions using SSRs markers revealed four major clusters, and population STRUCTURE analysis using 79 SSRs markers revealed three groups and three subgroups among the A. rugosa populations. The SSRs markers developed can contribute to applications such as varietal identification, genetic diversity analysis, and population structure analysis of A. rugosa germplasm.

Molecular Variations in Rabi Sorghum Varieties Using SSR Markers

Genetic diversity was assessed for 2 popular varieties and 5 promising lines of rabi sorghum by using11 SSR markers. The marker Xiabt312 reported 100% polymorphism rate followed by Xtxp15 (85.70%) and mSbCIR300 (85.71%). The sorghum varieties studied for this analysis showed the polymorphism information content (PIC) ranged from 0.25 to 0.87 with a mean of 0.67 indicates higher diversity within them. Clustering analysis based on the genetic dissimilarity grouped the 7 lines into 2 major and 4 sub clusters and grouping was in good agreement with pedigree. Cluster II was the largest cluster with 4 genotypes followed by cluster I with 3 genotypes. The rabi sorghum genotypes viz., M35-1, RSV-1876 and RSLG-2422 were placed in cluster I and Phule Anuradha, RSV-2371, RSV-1910 and RSV-1988 placed in cluster II. Clustering based on SSR molecular profile of the genotypes shows that there is a distinct variability among the genotypes under this study. The selected markers have great potential in DNA fingerprinting in sorghum which in future could be integrated with DUS data descriptors for effective cultivar identification and differentiation.

Genetic diversity and population structure of maize inbred lines using phenotypic traits and single nucleotide polymorphism (SNP) markers

Understanding germplasm’s genetic diversity is essential for developing new and improved cultivars with stable yields under diverse environments. The objective of this study was to determine the genetic diversity and population structure of 128 maize inbred lines sourced from the International Institute of Tropical Agriculture (IITA), the International Maize and Wheat Improvement Centre (CIMMYT), and the University of KwaZulu-Natal (UKZN) using 11,450 informative single nucleotide polymorphism (SNP) markers. The inbred lines revealed highly significant (p < 0.001) levels of variability for the key phenotypic traits. The SNP markers had a mean gene diversity (GD) and polymorphic information content (PIC) of 0.40 and 0.31, respectively, indicating the existence of substantial genetic variation across the germplasm panel. The model-based population structure analysis identified three subpopulations (K = 3) among the inbred lines. This corroborated the phylogenetic analysis using phenotypic traits and molecular markers which classified the inbred lines into three groups. The findings of this study identified considerable genetic diversity for the selection of inbred lines with favourable alleles for multiple traits and could be useful to initiate marker-assisted selection (MAS) to identify significant loci associated with agronomic performance and multiple-stress tolerance.

Establishment of AA-NAT, SCD, PROP1, and IGFBP3 gene frequency distributions in Karacabey Merino and Kivircik Sheep Breeds

Thus, the aim of the current study was to investigate the genotypic dispersion of AA-NAT, SCD, PROP1, and IGFBP3 genes in the target population. Primarily, the genomic DNA was isolated from blood samples by the phenol/chloroform method. The genomic analyses were performed on a total of 160 Karacabey Merino (KM) sheep (n=80) and Kivircik (n=80). The PCR-RFLP method was used to determine the genotype of the SNPs. Deviation from Hardy–Weinberg equilibrium (HWE) and population genetic assays such as observed (Ho) and expected (He) heterozygosities, effective allele numbers (Ne), and the polymorphism information content (PIC) were calculated for each gene in the population. As a result, there was no deviation from HWE was determined except SCD and PROP1 gene in KM. The most frequent genotypes were found AA (66,25% and 87,50%) for AA-NAT gene, CC (93,75% and 91,25%) for SCD gene and CC genotype (70,00% and 56,25%) for PROP1 gene in KM and Kivircik sheep. All breeds were detected monomorphic in terms of the IGFBP3 gene. In conclusion, the other regions of the IGFBP3 gene which were determined as monomorphic in the studied flock could be researched. Moreover, further studies should be necessary for defining the effects of investigated genes on related traits in KM and Kivircik sheep in terms of polymorphic genes specified.

Variation of Fruit Color in Cakra Hijau, G1/M8 and HV-149 Chilli Pepper Cultivar: Physiology and Molecular Approach

The fruit color of chili pepper is an important characteristic in identification and classification and is often used as the basis for determining consumer preferences. Information on the relationship between chili fruit color and its molecular profile is very important in supporting selection activities in plant breeding. This study aims to identify genetic diversity associated with the fruit color of three genotypes of chili (Capsicum frutescens L.): Cakra Hijau, HV-149 and G1/M8, using Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR). Morphological confirmation was carried out according to Capsicum descriptors. Nineteen RAPD markers and six SSR markers were used for genetic variability assessment. Genetic variation was analyzed using the unweighted pair group method with the arithmetic mean and the Jaccard similarity index. The three chili genotypes had different fruit colors at each maturation stage. The immature Cakra Hijau fruit is dark green and turns dark red as it ripens. The immature fruits of the G1/M8 line are light green and turn red when ripe. Finally, immature HV-149 fruits are dark green and yellow when ripe. The SSR markers used in this study were unable to show polymorphism. On the other hand, the RAPD marker successfully detected genetic variation in the three chili genotypes and resulted in a total of 49 alleles. The average value of polymorphic information content of the RAPD primers used ranged from 0 to 0.296, with the highest index indicated by OPA-1. The dendrogram shows the separation of the three genotypes into two main clusters, with the first cluster consisting of the HV-149 variety and the second cluster consisting of Cakra Hijau and G1/M8 lines. This study revealed that there are genetic variations based on the morphological characteristics of fruit color at each ripening stage and RAPD band profile. The RAPD marker was more effective than the SSR marker for identifying the genetic diversity of fruit color in the three chilies studied.