Polymorphism Information Content Values Research Articles

Assessment of Genetic Diversity of Bread Wheat Genotypes for Drought Tolerance Using Canopy Reflectance-Based Phenotyping and SSR Marker-Based Genotyping

This study investigated the genetic diversity of bread-wheat genotypes using canopy reflectance-based vegetation indices (VIs) and simple sequence repeat (SSR) marker-based genotyping for drought tolerance. A total of 56 wheat genotypes were assessed using phenotypic traits (combination of VIs and yield traits) and 30 SSR markers. The data of the phenotypic traits were averaged over two growing seasons under irrigated and drought-stressed conditions. The hierarchical clustering of the wheat genotypes unveiled three drought-tolerant groups. Cluster 1 genotypes showed minimal phenotypic alterations, conferring superior drought tolerance and yield stability than clusters 2 and 3. The polymorphism information content values for the SSR markers ranged from 0.434 to 0.932, averaging 0.83. A total of 458 alleles (18.32 alleles per locus) were detected, with the most polymorphic markers, wmc177 and wms292, having the most alleles (24). A comparative study of SSR diversity among phenotypic clusters indicated that genotypes under cluster 1 had higher genetic diversity (0.879) and unique alleles (47%), suggesting their potential in future breeding programs. The unweighted neighbor-joining tree grouped the wheat genotypes into five major clusters. Wheat genotypes from all phenotypic clusters were distributed throughout all SSR-based clusters, indicating that genetically heterogeneous genotypes were allocated to different drought-tolerant groups. However, SSR-based clusters and model-based populations showed significant co-linearity (86.7%). The findings of the present study suggest that combining reflectance-based indirect phenotyping with SSR-based genotyping might be an effective technique for assessing genetic diversity to improve the drought tolerance of bread-wheat genotypes.

Determining Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers

Assessment of genetic diversity among different varieties helps to improve desired characteristics of crops, including disease resistance, early maturity, high yield, and resistance to drought. Molecular markers are one of the most effective tools for discovering genetic diversity that can increase reproductive efficiency. Simple sequence repeats (SSRs), which are codominant markers, are preferred for the determination of genetic diversity because they are highly polymorphic, multi-allelic, highly reproducible, and have good genome coverage. This study aimed to determine the genetic diversity of 40 common bean (Phaseolus vulgaris L.) landraces collected from the Ispir district located in the Northeast Anatolia region of Türkiye and five commercial varieties using SSR markers. The Twenty-seven SSR markers produced a total of 142 polymorphic bands, ranging from 2 (GATS91 and PVTT001) to 12 (BM153) alleles per marker, with an average number of 5.26 alleles. The gene diversity per marker varied between 0.37 and 0.87 for BM053 and BM153 markers, respectively. When heterozygous individuals are calculated proportional to the population, the heterozygosity ranged from 0.00 to 1.00, with an average of 0.30. The expected heterozygosity of the SSR locus ranged from 0.37 (BM053) to 0.88 (BM153), with an average of 0.69. Nei’s gene diversity scored an average of 0.69. The polymorphic information content (PIC) values of SSR markers varied from 0.33 (BM053) to 0.86 (BM153), with an average of 0.63 per locus. The greatest genetic distance (0.83) was between lines 49, 50, 53, and cultivar Karacaşehir-90, while the shortest (0.08) was between lines 6 and 26. In cluster analysis using Nei’s genetic distance, 45 common bean genotypes were divided into three groups and very little relationship was found between the genotypes and the geographical distances. In genetic structure analysis, three subgroups were formed, including local landraces and commercial varieties. The result confirmed that the rich diversity existing in Ispir bean landraces could be used as a genetic resource in designing breeding programs and may also contribute to Türkiye bean breeding programs.

Disease Resistance and Molecular Variations in Irradiation Induced Mutants of Two Pea Cultivars.

Induced mutation is useful for improving the disease resistance of various crops. Fusarium wilt and powdery mildew are two important diseases which severely influence pea production worldwide. In this study, we first evaluated Fusarium wilt and powdery mildew resistance of mutants derived from two elite vegetable pea cultivars, Shijiadacaiwan 1 (SJ1) and Chengwan 8 (CW8), respectively. Nine SJ1 and five CW8 M3 mutants showed resistant variations in Fusarium wilt, and the same five CW8 mutants in powdery mildew. These resistant variations were confirmed in M4 and M5 mutants as well. Then, we investigated the genetic variations and relationships of mutant lines using simple sequence repeat (SSR) markers. Among the nine effective SSR markers, the genetic diversity index and polymorphism information content (PIC) values were averaged at 0.55 and 0.46, which revealed considerable genetic variations in the mutants. The phylogenetic tree and population structure analyses divided the M3 mutants into two major groups at 0.62 genetic similarity (K = 2), which clearly separated the mutants of the two cultivars and indicated that a great genetic difference existed between the two mutant populations. Further, the two genetic groups were divided into five subgroups at 0.86 genetic similarity (K = 5) and each subgroup associated with resistant phenotypes of the mutants. Finally, the homologous PsMLO1 cDNA of five CW8 mutants that gained resistance to powdery mildew was amplified and cloned. A 129 bp fragment deletion was found in the PsMLO1 gene, which was in accord with er1-2. The findings provide important information on disease resistant and molecular variations of pea mutants, which is useful for pea production, new cultivar breeding, and the identification of resistance genes.

Genetic analysis of X-chromosomal short tandem repeat (X-STR) frequencies in Arab Iraqi male population

BackgroundThe X-chromosome short tandem repeat (STR) polymorphisms are a particular tool in the fields of human population genetics and personal identification. It was necessary in investigating complex kinship or deficiency cases in conditions where information on mitochondrial DNA (mtDNA) or Y chromosome polymorphisms have been used to explore their direct paternal line. This study aimed to investigate the allele frequency of (12X-STR) of 200 unrelated males from different region of Baghdad City to serve as a reference data base for individual identification in Iraqi population. ResultsTwelve X-STR loci (DXS7424, HPRTB, DXS8377, GATA31E08, DXS7423, DXS8378, DXS9895, DXS10074, DXS6809, DXS7133, DXS101, DXS6807) were successfully amplified by multiplex PCR and divided into four groups. According to measures of allele frequency, the higher alleles frequency were 16, 11, 46, 11, 14, 10, 15, 15.2, 35, 11, 25, and 11 while the lowest alleles frequency were 11, 9, 52,53, 7, 17, 14, 13, 12.2,17, 36, 15, 16, 22, 29, and 17 that observed at the 12 loci respectively. Forensic efficiency parameter for DXS8377 locus in the first group showed highest polymorphic allele in the Iraqi Arab population with the frequencies ranging from 0.005 to 0.16%. The power of discrimination (PD) value ranged from 0.663 for DXS7423 locus and 0.9066 for DXS8377 locus. In addition, the polymorphism information content (PIC) value ranged from 0.602974 for DXS7423 locus to 0.899206 for DXS8377 locus. ConclusionsOverall the X-STR markers become used as an important source of information beside the autosomal and Y-STR markers, especially for kinship testing and haplotype analysis.

Development and verification of SSR markers from drought stress-responsive miRNAs in Dongxiang wild rice (Oryza rufipogon Griff.).

Rice production worldwide has continued to decline due to various environmental stresses, with drought stress being a prominent factor, as rice is a semi-aquatic plant. Thus, development of drought stress-resistant rice varieties is of great importance for rice production. In our previous study, we found that microRNAs (miRNAs) play a crucial role in the response to drought stress in Dongxiang wild rice (DXWR) (Oryza rufipogon Griff.). Developing drought stress-responsive miRNA-based single sequence repeat (SSR) markers for DXWR will be of great value for the efficient identification and utilization of miRNA genes to breed drought stress-resistant rice varieties. In this study, ninety-nine novel SSR markers were developed based on the drought stress-responsive miRNAs of DXWR. These markers were distributed in all 12 rice chromosomes, and most were in chromosomes 2 and 6, with di- and tri-nucleotides being the most abundant repeat motifs. Twelve out of fourteen synthesized markers displayed high levels of genetic diversity in the genomes of three populations of DXWR and 40 modern rice varieties worldwide. The number of alleles per locus ranged from 2 to 7, with an average of 4.67; the genetic diversity index ranged from 0.21 to 0.76, with an average of 0.58; and the polymorphism information content value ranged from 0.18 to 0.72, with an average of 0.53. These novel molecular markers developed from the drought stress-responsive miRNAs of DXWR could be additional tools for mapping elite miRNA genes and breeding drought stress-resistant rice varieties.

Genetic diversity and population structure of pigeonpea (Cajanus cajan [L.] Millspaugh) landraces grown in Benin revealed by Genotyping-By-Sequencing.

Genetic diversity studies provide important details on target trait availability and its variability, for the success of breeding programs. In this study, GBS approach was used to reveal a new structuration of genetic diversity and population structure of pigeonpea in Benin. We used a total of 688 high-quality Single Nucleotide Polymorphism markers for a total of 44 pigeonpea genotypes. The distribution of SNP markers on the 11 chromosomes ranged from 14 on chromosome 5 to 133 on chromosome 2. The Polymorphism Information Content and gene diversity values were 0.30 and 0.34 respectively. The analysis of population structure revealed four clear subpopulations. The Weighted Neighbor Joining tree agreed with structure analyses by grouping the 44 genotypes into four clusters. The PCoA revealed that genotypes from subpopulations 1, 2 and 3 intermixed among themselves. The Analysis of Molecular Variance showed 7% of the total variation among genotypes while the rest of variation (93%) was within genotypes from subpopulations indicating a high gene exchange (Nm = 7.13) and low genetic differentiation (PhiPT = 0.07) between subpopulations. Subpopulation 2 presented the highest mean values of number of different alleles (Na = 1.57), number of loci with private alleles (Pa = 0.11) and the percentage of polymorphic loci (P = 57.12%). We discuss our findings and demonstrate how the genetic diversity and the population structure of this specie can be used through the Genome Wide Association Studies and Marker-Assisted Selection to enhance genetic gain in pigeonpea breeding programs in Benin.

Genetic Diversity of Philippine Native Pigs (Sus scrofa L.) from Quezon and Marinduque Based on Morphological and Microsatellite Markers

Nine microsatellite markers recommended by the Food and Agriculture Organization were used to measure the genetic diversity of Quezon and Marinduque native pig populations – with a total of 37 and 40 individuals, respectively. All markers were discovered to be polymorphic, with a mean number of alleles per locus of 10. Marinduque native pigs were found to have a mean effective number of alleles (EA), mean observed heterozygosity (HO), mean expected heterozygosity (HE), and mean polymorphic information content (PIC) of 5.005 ± 0.547, 0.673 ± 0.040, 0.780 ± 0.024, and 0.76 ± 0.03, respectively. By contrast, Quezon native pigs had mean EA, mean HO, mean HE, and mean PIC values of 5.280 ± 0.787, 0.634 ± 0.044, 0.773 ± 0.035, and 0.75 ± 0.04, respectively. Between the two populations, the heterozygosity (HE > HO) and positive values of FIS (0.1714) and FIT (0.1868) indicated a low number of heterozygotes, suggesting the possibility of inbreeding. The test of Hardy-Weinberg equilibrium (HWE) showed that three loci each in the Quezon and Marinduque native pig populations deviated from HWE. Although morphological analysis revealed significant differences in snout shape, head profile, ear type, and all morphometric traits, a low level of genetic differentiation between the two populations was observed (FST = 0.0186; Nei genetic distance = 0.130; Nei unbiased genetic distance = 0.082). Overall, these findings imply that further studies on the genetic improvement and conservation of Philippine native pigs are required for the development of signature pig breeds across the country.

Exploring genetic diversity and Population structure of five Aegilops species with inter-primer binding site (iPBS) markers.

Turkey is not only a center of origin for wheat, but also contains wild forms of various cereals. Turkey, located in the Fertile Crescent, has conserved its genetic richness to the present day. The aim of the study was to investigate the genetic diversity of 70 wild wheat species, to evaluate the structure of diversity in germplasm and to generate useful data for further breeding programs. Genetic diversity and population structure of 70 wild wheat species (Ae. cylindrica, Ae. geniculata, Ae. triuncialis, T. dicocoides, Ae. columnaris) collected from Eastern and Southeastern Anatolia regions of Turkey were investigated in this study with the use of inter-primer binding site (iPBS) markers. Of 35 iPBS primers used, 11 yielded a total of 61 alleles. Number of alleles per marker varied between 2 (iPBS-2085) and 9 (iPBS-2394) with an average value of 5.55. Polymorphic information content (PIC) values varied between 0.22 and 0.47, with an average value of 0.35. Average number of effective alleles (Ne) was identified as 1.9488, Nei's genetic diversity (H) as 0,4861 and Shannon's information index (I) as 0.6791. Cluster analysis through unweighted pair-group mean average (UPGMA) method revealed that 70 wild wheats were divided into three main clusters. Genetic similarity between the genotypes, calculated with the use of NTSYS-pc software, varied between 19% (YB2 and YB70) and 98% (YB66 and YB67). Principal coordinate analysis (PCoA) revealed that three principal coordinates explained 62.33% of total variation. Moreover, population structure analysis showed that all genotypes formed three sub-populations. Expected heterozygosity values varied between 0.2666 (the first sub-population) and 0.2330 (third sub-population), with an average value of 0.2500. Average population differentiation measurement (Fst) was identified as 0.3716 for the first sub-population, 0.3930 for the second subpopulation and 0.4804 for the third sub-population. Based on present findings population structure of 70 wild wheat genotypes collected from Eastern and Southeastern Anatolia regions of Turkey were successfully characterized with the use of iPBS markers. Present findings suggested that iPBS-retrotransposon markers could reliably be used to elucidate genetic diversity of Aegilops genotypes.

Identification of heat-tolerant rice genotypes and their molecular characterisation using SSR markers

The effect of high-temperature stress has a critical impact in causing reduced crop yield. The focus of the current investigation is the identification of heat-tolerant rice varieties that can alleviate the effects of stress. Among the ten genotypes evaluated across various parameters such as leaf area, dry weight, photosynthetic rate, stomatal conductance and spikelet fertility, N-22 showed superior characteristics for the grain filling parameters along with CR-Dhan 307. The variety CR-Dhan 307 with significantly higher mean pollen viability (80.23%), spikelet fertility (81.18%) and 1000 grain weight (25.45 gm) can be utilized as a heat-tolerant variety. Other genotypes Ptb-7 and CR-Dhan 202 seemed to have tolerance traits beneficial at the vegetative stage. The genotype Rajalakshmi can be characterised as heat susceptible as it had significantly lower values for all parameters. Polymorphic analysis was carried out to validate SSR markers associated with heat tolerance. The polymorphic information content (PIC) was found to be the highest for RM236 and RM6100. The SSR marker RM6100 has been validated in the current investigation to be associated with heat tolerance. As the PIC value is an indication of the ability of the marker in indicating genetic diversity, the PIC values of the 11 polymorphic markers is useful for identify heat-tolerant genotypes. The genetic diversity analysis was carried out using DendroUPGMA to establish the relationship between the genotypes. The genotypes Ptb-7 and CR-Dhan 204 were thus found to be closely related to the heat-tolerant check variety, N-22 indicating genetically related traits for tolerance to heat.

Characterization of diverse sesame (Sesamum indicum L.) panel through morphological and molecular marker analysis

Sesame is one of the most important and ancient oilseeds crop with high and good quality oils content. Present Investigation was carried out for the assessment of the genetic diversity using 33 sesame genotypes through morphologically and 21 SSR markers. In the morphological diversity analysis, nine clusters were observed with 33 genotypes using all phenological, yield and its contributing attributes. Among the 9 clusters, cluster II had maximum number of genotypes (14) followed by cluster III (6), cluster IV (5), cluster I (3), cluster V, VI, VII, VIII and IX had one genotype to each cluster. The highest inter-cluster distance was observed between cluster VI and I (386.70), which indicates maximum diversity between the genotypes of these clusters, could be further used in crossing programme. However, SSR markers grouped 33 genotypes into six clusters at 0.51 dissimilarity index. In which cluster V had maximum (7) genotypes and cluster VI had minimum (3) genotypes. The results of genetic diversity tallied with the morphological diversity, such as BRT-04 are the farthest from BRT-08, BRT-09 and BRT-10, however BRT-08, BRT-09 and BRT-10 are in the same cluster in both morphological and molecular diversity analysis. The UPGMA dendrogramwas constructed using Jaccard's dissimilarity coefficients based on SSR markers score on thirty-three genotypes. Polymorphism information content (PIC) value varied between 0.15 and 0.36 with an average of 0.27. The genotypes from the distinct clusters can be utilized for hybridization programme to recover heterotic pools.

Genetic Diversity and Selection Signatures in Synthetic-Derived Wheats and Modern Spring Wheat.

Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan.

Genetic diversity and marker trait association for yellow mosaic virus disease ingreen gram, Vigna radiata (L.) Wilczek

Yellow mosaic virus (YMV) disease is known to cause severe damage in green gram in terms of yield loss. As the resistance is often governed by recessive genes, introgression of such resistance faces some difficulty. DNA molecular markers are reported to be effective in this process. However, validation of such markers is important. Here, we have made an attempt to validate DNA markers associated with YMV disease resistance gene from a diverse group of 26 green gram genotypes. A total of 19 molecular markers were used to assess the susceptibility or resistance against YMV disease. Results show that among the amplified 31 alleles, 21 were polymorphic, with a mean of 1.1.0 per locus. The polymorphism information content (PIC) values ranged from 0.32 to 0.80. Only five markers exhibited higher PIC value (>6.0) and were revealed to be polymorphic, suggesting its utility in marker assisted selection for breeding YMV resistant genotypes in greengram. Dice dissimilarity coefficient among the genotypes exhibited a range of 0.07 to 1.0 which show a wide genetic variation among the genotypes for YMV tolerance. Neighbor-joining cluster analysis has grouped 26 green gram genotypes into 4 main clusters which revealed the existence of genetic dissimilarities among the genotypes. The genotypes AUGG 6, VBN (Gg) 2 and CO (Gg) 8 carried the positive alleles for YMV disease resistance and the allele for susceptibility were found in the genotypes AUGG 12, AUGG 15, AUGG 17 and AUGG 19. Single marker analysis indicated that there was correlation between the markers and the disease reaction in the field with exceptions. The findings revealed that the SSR markers CEDG180 and YR4 could be used to screen germplasm in order to discriminate the YMV resistant genotypes from the susceptible genotypes in marker assisted selection.

Characterization of genetic diversity of citron watermelon landrace accessions of South Africa through simple sequence repeat markers

ABSTRACT Profiling the genetic diversity of germplasm collections is fundamental for selection programs and strategic conservation. Citron watermelon (Citrullus lanatus var. citroides [L.H. Bailey] Mansf. ex Greb.) is an under-researched cucurbit crop despite providing food and nutritional security in sub-Saharan Africa. There is limited information on genetic relationships of South African citron watermelon accessions for effective breeding. The objective of this study was to determine the extent of genetic diversity among 48 South African citron watermelon landrace accessions using selected simple sequence repeat (SSR) markers to identify genetically divergent accessions for trait integration and variety development. The SSR markers amplified a total of 24 alleles, with a mean expected heterozygosity value of 0.38, indicating moderate genetic diversity among the studied accessions. The mean polymorphic information content value of 0.21 indicated low discriminatory power of the SSR markers. Analysis of molecular variance attributed 8%, 75%, and 17% of the molecular variation between populations, among accessions and within accessions, respectively. Three distinctive genetic groups were identified based on cluster analysis, which aided the selection of genetically diverse citron watermelon accessions for breeding and cultivar development.

Assessing the molecular variability in Ustilaginoidea virens, the rice false smut pathogen with ISSR markers

Rice false smut disease is gaining importance because of its impact on the grain yield and its toxin production ability. Fifty-eight isolates of Ustilaginoidea virens were collected from different rice-growing regions of India. DNA of U. virens was isolated by the CTAB method and fifty ISSR primers were screened for molecular variability studies. Twelve primers viz., UBC series 807, 808, 809, 810, 811, 812, 834, 835, 836, 840, 841, and 842 were selected to study the genetic variability. Different parameters of tested primers viz., heterozygosity (Hn), polymorphism information content (PIC), effective multiplex ratio (EMR), marker Index (MI), and resolving power (RP) were calculated. Primers UBC 812 and UBC 809 recorded maximum heterozygosity (Hn). The PIC values ranged from 0.10 to 0.27 and UBC 807 recorded the maximum value of 0.27. The EMR value varied from 6.75 to 24.0, Similarly, UBC 807 recorded the highest value of MI (24) and RP (8.55). A dendrogram was generated using the DARwin software (version 6.0.21A) based on the unweighted neighbor-joining cluster method. All the fifty-eight U. virens isolates were grouped into three major clusters. Clusters I and II had 21 and 35 U. virens isolates respectively. Cluster III had only two isolates. The isolates showed genetic variations and there was no specific grouping based on the geographical distance.

Molecular Characterization of Tomato (Solanum lycopersicum L.) Accessions under Drought Stress

Exploring the genetic diversity among plant accessions is important for conserving and managing plant genetic resources. In the current study, a collection of forty-six tomato accessions from Jordan were evaluated based on their performance and their morpho-physiological, in addition to molecularly characterizing to detect genetic diversity. Tomato accessions seedlings were exposed to drought stress with 70% field capacity and 40% field capacity under field conditions in Jordan. Drought stress had significantly negatively influenced the dry root weight, fresh root weight, root growth rate, fresh shoot weight, dry shoot weight, and shoot growth rate. Moreover, proline content showed a highly significant increase of 304.2% in response to drought stress. The analysis of twenty morphological characters revealed a wide range of variations among tomato accessions. Accessions were screened with fourteen SSR primers; six primers were informative to explain the genetic diversity. Based on resolving power, primers LEct004 and LEat018 were most significant with all 46 accessions. Interestingly, polymorphic information content (PIC) values ranged from 0.00 (Asr2 marker) to 0.499 (LEct004), which confirms that the SSR markers are highly informative. Our findings provide new insights into using informative molecular markers to elucidate such wide genetic variation discovered in our collections from Afraa and Abeel (the southern part of Jordan). Interestingly, the SSR markers were associated with genes, e.g., LEat018 with ACTIN_RELATED PROTEIN gene, the LEct004 with the HOMEOBOX PROTEIN TRANSCRIPTION FACTORS gene, and Asr2 with ABA/WDS. Moreover, the AUXIN RESPONSE FACTOR8 gene was associated with the LEta014 SSR marker and the LEta020 with the THIOREDOXIN FAMILY TRP26 gene. Therefore, the genetic diversity analysis and functional annotations of the genes associated with SSR information obtained in this study provide valuable information about the most suitable genotype that can be implemented in plant breeding programs and future molecular analysis. Furthermore, evaluating the performance of the collection under different water regimes is essential to produce new tomato varieties coping with drought stress conditions.

Genetic Diversity and Structure of the Main Danubian Horse Paternal Genealogical Lineages Based on Microsatellite Genotyping

Simple SummaryThe Danubian horse was created on the former Klementina stud farm near Pleven to satisfy the demands of the Bulgarian Army for light draft horses and to improve the working capacity of the local horse population. The privatization of the Klementina stud farm in the late 1990s and the lack of economic activity have led to a sharp reduction in the number of mares and stallions and their sale to private owners. At present, only six of the main paternal lines which participated in the creation of the Danubian horse breed are preserved: Zdravko, NONIUS XVII-30, Torpedo, Lider, Kalifa, and Hrabar. This is the first study on the genetic and population diversity of the Danubian horse paternal lines based on microsatellite markers (STRs). The results showed that the studied Danubian horse population was characterized by a high level of genetic diversity with a medium value of 0.84. The fixation index (FST) was 0.08 for all studied markers, which is indicative of the low genetic differentiation of the Danubian horse population. Our analysis also confirmed the low level of inbreeding and heterozygous deficiency among the animals selected from the six paternal lineages of the Danubian horse. The present research could be helpful for the development of breeding and conservation programs for the Danubian horse, as well as for making informed decisions on the management of paternal lines.The Danubian horse, together with the Pleven and the Eastern Bulgarian horse breeds, is one of the modern breeds in Bulgaria. The objective of this study was to compare the genetic structure and genetic diversity of six paternal genealogical lineages of the Danubian horse breed (Zdravko, NONIUS XVII-30, Torpedo, Lider, Kalifa, and Hrabar). In total, 166 individuals from the six genealogical lines were investigated, based on 15 STR markers (short tandem repeats, also known as microsatellites). In total, 184 alleles were found in the six populations, using 15 microsatellite loci. The mean number of alleles, the effective number of alleles, and the polymorphic information content (PIC) values per locus were 12.28, 9.48, and 0.73, respectively. In a comparison of the allelic diversity among sire lineages, the highest genetic diversity (Na) was observed in Lider and Kalifa (14.60 ± 0.21), while the lowest value of this parameter was observed in the Zdravko lineage 4.20 ± 0.35. The largest genetic diversity was found in loci HMS3 and HMS7, with 13 alleles, and the smallest polymorphism was noted for the locus ASB17, with 10 alleles. The level of observed heterozygosity was in the range of 0.65 ± 0.069 for the Zdravko lineage to 0.93 ± 0.01 for the Torpedo lineage. The expected heterozygosity level range was from 0.57 ± 0.048 to 0.91 ± 0.01 for all horse lineages. Structure analysis revealed three main gene pools in the study population. The first pool included the Zdravko lineage; the second had the NONIUS XVII-30, Torpedo, Lider, and Kalifa lineages; and the third defined the Hrabar lineage, which was significantly differentiated from the other genealogical lineages.

Molecular genetic diversity in dual purpose and land races of pigeonpea (Cajanus cajan (L.) Millsp.)

Molecular genetic diversity was assessed among 32 dual purpose and land races of pigeonpea using 20 pigeonpea specific SSR markers. Among 20 markers, 15 markers revealed polymorphism, while five markers exhibited a monomorphic banding pattern. The polymorphic markers produced a total of 43 alleles with an average of 2.15 alleles per marker. The markers CcM 0008 and CcM 1026 produced the highest number of alleles (4). The Polymorphic Information Content (PIC) value of the markers ranged from 0.06 (PGM 16) to 0.64 (CcM 0008) with an average of 0.19. A dendrogram constructed using UPGMA distinguished 32 genotypes into 10 clusters. Cluster I was the largest with 15 genotypes followed by cluster V with five genotypes. The Neighbour- joining tree produced based on the weighted average for dissimilarity matrix grouped the 32 genotypes into eight groups. Among them group II was the largest comprising of 10 genotypes. Based on the molecular genetic diversity study using SSR markers, the genotypes Kunnathur local, CRG 13-01, BSR 1 and Pillayakothur local were found diverse among the genotypes and had good grain and vegetable pigeonpea traits could be used in the breeding programme. The results indicated that SSR markers provide a more definitive separation of clusters indicating a higher level of efficiency for determining the relationship among pigeonpea genotypes. Keywords:  Pigeonpea, Dual purpose, Land races, Genetic diversity   &nbsp

Structural analysis of Actinidia arguta natural populations and preliminary application in association mapping of fruit traits

The fruit of Actinidia arguta are currently receiving much attention owing to their various colors in green or purple and fully edible smooth skin with unique shapes, taste appeal and rich nutritional value. A. arguta is now, after A. chinensis var. chinensis and A. chinensis var. deliciosa, the third most widely planted member of the Actinidia genus in commercial orchards. In order to improve our understanding of A. arguta and to plan future use of the germplasm for breeding elite cultivars, 189 accessions (including 14 cultivars) collected were analyzed with 200 simple sequence repeats (SSR) to explore their molecular diversity and population structure, and to identify elite alleles. The results showed all these markers used were polymorphic and generated 2496 allele loci with a polymorphism information content (PIC) value of 0.658. Through population structure analysis, the accessions have been divided into four subpopulations (K = 4), each subpopulation corresponding well with the distance-based clustering. Eleven traits were associated using MLM (mixed linear model) with markers. Marker-trait association analysis identified 43 significant associations involving the 35 SSRs for the 11 traits, including some important and interesting traits in breeding such as gender and fruit quality like flesh color. Through transient expression, LR71 discovered in this study is a marker significantly associated with fruit flesh color, belongs to a gene encoding an MYB transcription factor that regulates the accumulation of anthocyanins, and causes red pigmentation. This study revealed the extent of genetic diversity and the population structure of A. arguta germplasm collected. The trait-marker pairs obtained from association mapping have potential value in molecular marker-assisted breeding, and genomics studies with gene mapping. The relationships among the natural populations touched and the origin of the cultivars mainly used are discussed, all of these help us to further understand and analyze the natural evolution of A. arguta.

DNA marker based diversity across rice genotypes and advanced breeding lines bred for temperate regions of North-West India.

Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes. This study involves the agro-morphological and cooking quality besides, molecular characterization of 51 genotypes/advance breeding lines of rice from Kashmir Himalayas. Significant variability was observed for all agro-morphological and cooking quality traits among all the studied genotypes. Cluster analysis using UPGMA method divided the genotypes into two major clusters having 15 and 36 genotypes. Thirty eight genotypes screened using 24 SSR markers detected 48 alleles with 2.0 alleles for each locus with average polymorphism information content (PIC) of 0.37. High polymorphism information content (PIC) values was observed for the primers RM263 (0.67), RM159 (0.59) and RM333 (0.50). Furthermore, out of 38 SSR markers screened on 192 temperate rice germpalsm lines, R4M17 accurately differentiated indica and temperate japonica genotypes amplifying 220bp and 169bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types. The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing. Also the analysis was useful to classify the temperate germplasm into indica and temperate japonica. The classification could be helpful to devise a strategy for inter-sub species hybridization to breed for improved rice varieties.

Elucidating the Population Structure and Genetic Diversity of Indian Puccinia striiformis f. sp. tritici Pathotypes Based on Microsatellite Markers

In India, systematic wheat yellow rust survey and pathotype (race) analysis work began in 1930. However, information on population structure and genetic diversity of yellow rust pathogen has not been available. To address this, we conducted studies on population structure and genetic diversity of Puccinia striiformis f. sp. tritici (Pst) pathotypes using 38 simple sequence repeat primer-pairs. Bayesian assignment and discriminant analysis of principal components indicated the presence of two distinct Pst subpopulations (Pop1 and Pop2) along with 37.9% admixed pathotypes. The unweighted pair-group method with arithmetic mean also categorized these pathotypes into two major clusters. Principal coordinates analysis explained 20.06 and 12.50% variance in horizontal and vertical coordinates, respectively. Index of association (IA) and the standardized index of association ([Formula: see text]) values showed that Pst subpopulations reproduced asexually (clonally). In total, 102 alleles were detected, with the expected heterozygosity (Hexp) per locus ranging from 0.13 to 0.73, with a mean of 0.47. The average polymorphic information content value of 0.40 indicated high genetic diversity among pathotypes. Analysis of molecular variance revealed 12% of the total variance between subpopulations, 11% among the pathotypes of each subpopulation, and 77% within pathotypes. A significant moderate level of genetic differentiation (FST = 0.122, P < 0.001) and gene flow (Nm = 1.80) were observed between subpopulations. The Pst virulence phenotypes showed a weak positive correlation (R2 = 0.027, P < 0.02) with molecular genotypes.