Mean Polymorphic Information Content Value Research Articles

Effect of Chromosomal Localization of NGS-Based Markers on Their Applicability for Analyzing Genetic Variation and Population Structure of Hexaploid Triticale.

This study aimed to determine whether using DNA-based markers assigned to individual chromosomes would detect the genetic structures of 446 winter triticale forms originating from two breeding companies more effectively than using the entire pool of markers. After filtering for quality control parameters, 6380 codominant single nucleotide polymorphisms (SNPs) markers and 17,490 dominant diversity array technology (silicoDArT) markers were considered for analysis. The mean polymorphic information content (PIC) values varied depending on the chromosomes and ranged from 0.30 (2R) to 0.43 (7A) for the SNPs and from 0.28 (2A) to 0.35 (6R) for the silicoDArTs. The highest correlation of genetic distance (GD) matrices based on SNP markers was observed among the 5B-5R (0.642), 5B-7B (0.626), and 5A-5R (0.605) chromosomes. When silicoDArTs were used for the analysis, the strongest correlations were found between 5B-5R (0.732) and 2B-5B (0.718). A Bayesian analysis showed that SNPs (total marker pool) allowed for the identification of a more complex structure (K = 4, ΔK = 2460.2) than the analysis based on silicoDArTs (K = 2, ΔK = 128). Triticale lines formed into groups, ranging from two (most of the chromosomes) to four (7A) groups depending on the analyzed chromosome when SNP markers were used for analysis. Linkage disequilibrium (LD) varied among individual chromosomes, ranging from 0.031 for 1A to 0.228 for 7R.

Genetic diversity of Sinapis arvensis L. (wild mustard) in Türkiye determined by microsatellite markers

Wild mustard (Sinapis arvensis L.) is a self-fertilizing weed species that exerts negative impacts on wheat production and herbicides are intensively used to manage it. Cross-fertilization may lead to genetic differentiation in this species. Therefore, this study investigated genetic diversity among wild mustard populations collected from wheat fields across various regions in Türkiye. Genetic variation was evaluated using 5 simple sequence repeat (SSR) markers in populations collected from 30 different locations. Populations were analyzed using UPGMA (unweighted pair group method with arithmetic mean) and principal component analysis (PCA). The mean genetic diversity (GD) and polymorphism information content (PIC) values were 0.752 and 0.844, respectively. High genetic variability was recorded among populations within geographic locations. The populations were categorized into two major groups by UPGMA. There was no apparent geographic isolation among tested populations, which displayed a high degree of variability. The primary source of this variability is thought to be the adaptability of wild mustard seeds dispersed through various methods across diverse locations. Despite being a predominantly self-pollinating species, wild mustard may also employ some cross-pollination mechanisms. In conclusion, SSR markers proved useful in determining genetic diversity in outcrossing species, especially where no prior genotypic information is available. The study suggests that genetic diversity is maintained in wild mustard populations even with rotational farming practices and intensive use of herbicides.

Genetic variation among Brassica rapa subsp. rapa genotypes growing in Malatya/Türkiye

AbstractIn this study, the genetic variation of 18 Brassica rapa subsp. rapa genotypes grown in Malatya was determined using the inter simple sequence repeat - polymerase chain reaciton (ISSR-PCR). Using nine ISSR primers, a total of 73 bands were obtained and the polymorphism rate was 91.78%. The mean polymorphism information content value was determined as 0.3319. The mean gene diversity (H) value was determined as 0.4276. The mean major allele frequency value was determined as 0.6531. Similarity index values were determined to be between 0.0928 and 1.0924. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram consisted of two groups. Principal component analysis analysis and UPGMA dendrogram were compatible. In addition, the groups in the phylogenetic trees were partially compatible with geographical distribution. Our results suggest that ISSR-PCR analysis is a suitable approach for breeding Brassica rapa subsp. rapa genotypes and developing different cultivars.

SSR-marker Assisted Evaluation of Genetic Diversity in Greengram [Vigna radiata (L.) Wilcezk

Background: Assessing genetic diversity in greengram is a prerequisite for its genetic improvement for yield and quality. DNA markers such as simple sequence repeats (SSRs) have been preferred in this crop for the analysis of genetic diversity because SSR markers are locus-specific, widely dispersed throughout the genome, highly polymorphic due to variation in repeat units, highly informative because of co-dominant nature, high reproducibility and ease of assay by PCR (Polymerase chain reaction). The current study aimed to study the genetic diversity among the mutants of greengram at the molecular level using SSR markers. Methods: In this study, twenty-five SSR markers were used to analyze the genetic diversity amongst twenty mutant genotypes of greengram along with their parents. Genomic DNA was isolated from the leaves by using the standard CTAB DNA extraction method. Then DNA purification and PCR amplifications were carried out. The genetic variability and diversity among genotypes was examined by assessing the scoring of the amplified bands by SSR -PCR amplification. Result: Seventeen SSR primers generated 102 polymorphic bands with an average of the six polymorphic bands per primer. The number of alleles per locus ranged from four to nine. The size of amplification product varied for each primer and the range found to be 100bp to 2000bp. The mean polymorphic information content (PIC) value for SSR markers was found to be 0.6335. The value of Jaccard’s similarity coefficient had ranged from 0.07-0.70 with an average value of 0.38. The dendrogram constructed on SSR molecular markers data through the unweighted pair group method with arithmetic averages (UPGMA) method had enabled grouping of the genotypes into thirteen clusters. The results indicate the usefulness of SSR markers in the assessment of genetic variability and diversity among the mutant genotypes of greengram.

Genetic Diversity and Population Structure Analyses in Bitter Gourd (Momordica charantia L.) Based on Agro-Morphological and Microsatellite Markers.

Bitter gourd (Momordica charantia L.) is an important vine crop of the Cucurbitaceae family and is well known for its high nutritional and medicinal values. However, the genetic variation remains largely unknown. Herein, 96 diverse bitter gourd genotypes were undertaken for diversity analysis using 10 quantitative traits, and 82 simple sequence repeat (SSR) markers. Out of 82 SSRs, 33 were polymorphic and the mean polymorphism information content (PIC) value was 0.38. Marker, JY-003 revealed a maximum (0.81) PIC value and, the number of alleles per locus ranged from 2 to 7 (average 3.46). The value of gene diversity showed the presence of a significant level of polymorphism among these genotypes. The unweighted pair group method (UPGMA) cluster analysis grouped the genotypes into two major clusters of which Cluster I comprised mostly small and medium-fruited genotypes of both M. charantia var. charantia and M. charantia var. muricata, whereas Cluster II included mostly long and extra-long fruited genotypes. Furthermore, these genotypes were divided into six distinct groups based on population structure analysis. The diversity analysis based on 10 quantitative traits revealed that earliness and high-yielding ability were exhibited by the predominantly gynoecious line DBGS-21-06 followed by DBGS-48-00. The principal component analysis (PCA) revealed that the first two components exhibited more than 50% of the total genetic variation. The present study deciphered a higher magnitude of agro-morphological and genetic diversity in 96 bitter gourd genotypes. Therefore, trait-specific genotypes identified in this study could be utilized in breeding programmes directed towards the development of improved cultivars and hybrids of bitter gourd.

Morpho-physiological traits and SSR markers-based analysis of relationships and genetic diversity among fodder maize landraces in India.

Maize is an excellent fodder crop due to its high biomass, better palatability, succulency, and nutrition. Studies on morpho-physiological and biochemical characterization of fodder maize are limited. The present study aimed to explore the genetic variation in fodder maize landraces for various morpho-physiological traits and estimation of genetic relationship and population structure. The study on 47 fodder maize landraces revealed significant variation for all morpho-physiological traits except leaf-stem ratio. Plant height, stem girth, leaf-width and number of leaves showed positive correlation with green fodder yield. Morpho-physiological traits-based clustering grouped the landraces into three major clusters, whereas neighbour joining cluster and population structure analysis using 40 SSR markers revealed four and five major groups, respectively. Most landraces of Northern Himalaya-Kashmir and Ludhiana fall into a single group, whereas rest groups mainly had landraces from North-Eastern Himalaya. A total of 101 alleles were generated with mean polymorphic information content value of 0.36 and major allele frequency of 0.68. The pair wise genetic dissimilarity between genotypes ranged from 0.21 to 0.67. Mantel test revealed weak but significant correlation between morphological and molecular distance. Biochemical characterisation of superior landraces revealed significant variation for neutral detergent fibre, acid detergent fibre, cellulose and lignin content. Interestingly, significant, and positive correlation of SPAD with lignin content can be explored to bypass the costly affair of invitro quality assessment for digestibility parameters. The study identified superior landraces and demonstrated the use of molecular markers in genetic diversity assessment and grouping of genotypes for fodder maize improvement.

황해쑥 품종 구별을 위한 유전체 염기서열 기반 genomic SSR marker 개발

Background: Artemisia argyi is an economically important medicinal plant with in the genus of Artemisia. However, the lack of the molecular markers hinders the understanding of genetic diversity and cultivar discrimination. Therefore, the main objectives of this study were to characterize the SSRs of Artemisia argyi in the reference genome, and to developed polymorphic SSRs for cultivar discrimination and population genetic studies.BRMethods and Results: Novel 100 simple sequence repeat (SSR) markers were designed based on the whole-genome sequence data of Artemisia argyi, and selected 78 polymorphic markers were selected. Upon the assessment of the five accessions with the full set of 78 SSR, the major allele frequency (MAF) ranged from 0.20 to 1, with an average of 0.36. In addition, the number of alleles per locus ranged from 2 to 9 alleles with a mean value of 5.2 alleles per locus. The polymorphism information content (PIC) values ranged from 0.27 to 0.87 with a mean PIC value of 0.69.BRConclusions: The Artemisia argyi alleles were detected in 5 accessions, among them six primers (argyi-gSSR003, argyi-gSSR014, argyi-gSSR035, argyi-gSSR036, argyi-gSSR093, argyigSSR094) produced five cultivar-specific loci, therefore very promising for cultivar identification, genetic diversity and breeding studies in Artemisia argyi.

Genetic dissection, relationship and population structure of drumstick (Moringa oleifera Lam.) using Agro-morphological and SCoT markers

Drumstick (Moringa oleifera Lam.) is an economically important multipurpose perennial vegetable and every part of this plant contain essential properties for nutritional and medicinal values. Specially its leave can be used as an ideal remedy to combat micronutrient-related malnutrition. However, the assessment of genetic diversity is necessitated to isolate rich nutrient dense genotypes for improving culinary, pharmaceutical, and industrial demands. Therefore, In the present study, a total of 52 accessions collected from diversified areas of southern (Tamil Nadu, Kerala, Karnataka, and Andhra Pradesh); western (Maharashtra, Gujarat), and eastern state (Orissa) of India were assessed for morpho-molecular genetic diversity using 10 morphological traits and 36 Start Codon Targeted (SCoT) markers. Out of 36 SCoT primers, 20 primers were polymorphic, and the polymorphic information content (PIC) value ranged from (0.01–0.36) with mean PIC value of 0.21. The neighbor-joining (N-J) tree grouped the 52 accessions into three major distinct clusters (CI-CIII) and the population structure analysis divided these accessions into two pure population groups (probability score ≥ 0.80). Molecular variance using principal component analysis (PCA) showed 30.25% variations in the first three axes (axis 1–13.33%, axis 2–9.33%, and axis 3–7.59%, respectively). Analysis of molecular variance (AMOVA) indicated that 17% variance observed among the population and the remaining 83% variance attributed to variation within individuals. The present investigation elucidates a high genetic diversity among the drumstick accessions, and some distinct accessions could be utilized for crop improvement programmes in trait-specific breeding.

Molecular characterization and genetic diversity analysis in Indian mustard (Brassica juncea L. Czern & Coss.) varieties using SSR markers.

In this study, we evaluated genetic diversity in a panel of 87 Indian mustard varieties using 200 genomic-SSR markers. A total of 189 SSRs resulted into positive amplification with 174 (92.06%) SSRs generating polymorphic products and 15 (7.94%) SSRs producing monomorphic amplicons. A total of 552 alleles were obtained and allele number varied from 2–6 with an average number of 3.17 alleles per SSR marker. The major allele frequency ranged from 0.29 (ENA23) to 0.92 (BrgMS841) with an average value of 0.58 per SSR locus. The polymorphic information content (PIC) value ranged from 0.10 (BrgMS841) to 0.68 (BrgMS519) with 0.39 as mean PIC value. The gene diversity per locus ranged from 0.13 (BrgMS841) to 0.72 (ENA23 & BrgMS519) with a mean value of 0.48 per SSR primer pair. Both Unweighted Neighbor Joining-based dendrogram and population structure analysis divided all the 87 varieties into two major groups/subpopulations. Analysis of molecular variance (AMOVA) inferred the presence of more genetic variation (98%) among individuals than among groups (2%). A total of 31 SSRs produced 36 unique alleles for 27 varieties which will serve as unique DNA-fingerprints for the identification and legal protection of these varieties. Further, the results obtained provided a deeper insight into the genetic structure of Indian mustard varieties in India and will assist in formulating future breeding strategies aimed at Indian mustard genetic improvement.

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.

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.

Morphological and molecular characterization of some pumpkin (Cucurbita pepo L.) genotypes collected from Erzincan province of Turkey

Plant genetic resources constitute the most valuable assets of countries. It is of great importance to determine the genetic variation among these resources and to use the data in breeding studies. To determine the genetic diversity among genotypes of Cucurbita pepo L. species of pumpkin, which is widely grown in Erzincan, 29 different pumpkin genotypes collected were examined based on the morphological parameters and molecular characteristics. SSR (Simple Sequence Repeat) markers were used to determine genetic diversity at the molecular level. The analysis of morphological characterization within genotypes showed a wide variability in morphological traits of plant, flower, fruit, and leaf. In the evaluation performed using SSR markers, all primers exhibited polymorphism rate of %100. Seven SSR markers yielded a total of 15 polymorphic bands, the number of alleles per marker ranged from 2 to 3, and the mean number of alleles was 2.14. Polymorphic information content (PIC) ranged from 0.06 (GMT-M61) to 0.247 (GMT-P41), and the mean PIC value per marker was 0.152. Cluster analysis using Nei's genetic distance determined that 29 genotypes were divided into 4 major groups. The present findings have revealed the genetic diversity among pumpkin genotypes collected from Erzincan province and may form the basis for further breeding studies in pumpkin.

Morphometric and Microsatellite Diversity in Seabuckthorn (Hippophae rhamnoides L.) Natural Populations Originating from the Different Geographical Regions of the Indian Himalayas.

Seabuckthorn (Hippophae rhamnoides L.), an upcoming superfood plant, has attracted researchers’ attention worldwide for its medicinal, nutritional, and socio-economic value, along with its characteristic features to sustain extreme climatic conditions. We have studied microsatellite marker–based genetic and morphometric diversity in 93 collections of H. rhamnoides from different geographic sites representing two regions, namely Leh and Lahaul of the Indian Himalayas. Microsatellite markers were isolated using two different approaches, including screening of microsatellite-enriched genomic library, and in silico screening of in-house developed seabuckthorn EST database and whole transcriptome assembly. In Leh and Lahaul collections, 32 and 30 microsatellite markers were found polymorphic, respectively. All the markers developed for H. rhamnoides showed cross-species transferability to H. salicifolia and H. tibetana. Two to six alleles were recorded in the two sets of collections with an average of 3.71 and 3.53 alleles per locus in Leh and Lahaul collections, respectively. Mean polymorphic information content (PIC) values for microsatellite markers were 0.39 and 0.41 for Leh and Lahaul collections, respectively. The average expected heterozygosity was less than the observed heterozygosity. Wright’s fixation index (FIS) varied from (−)0.2045 to 1.0 and (−)0.1688 to 1.0 for Leh and Lahaul collections, respectively. Shannon’s informative index (I) remained in the range of 0.6745 to 1.8621, and 0.6824 to 1.6308 for Leh and Lahaul collections, respectively. The UPGMA-based combined dendrogram showed clear demarcation between Leh and Lahaul collections, although a few ecotypes were regrouped with collections from the other region. No significant relationship was observed between the morphological distance matrix and molecular marker distance matrix. The findings of the present study may prove helpful in future breeding and conservation strategies aiming for seabuckthorn improvement.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11105-022-01338-6.

Development and application of a duplex simple sequence repeat panel for outcrossing fertility evaluation in red clover (Trifolium pratense) under open-pollination conditions†

Context Red clover (Trifolium pratense L.) is an important legume forage in temperate agricultural zones. Evaluation of self- and cross-pollination fertility is important for setting up an effective breeding-program scale. However, the outcrossing rate of red clover under open-pollination conditions is not certain. Development of a reliable and time-saving marker system is needed to quantify and characterise outcrossing rates. Aim We aimed to develop a duplex PCR-based protocol based on a genome-wide simple sequence repeat (SSR) screen, and to determine the outcrossing rate of red clover under open-pollination environments. Methods We screened 209 SSR markers with pooled DNA samples of 60 plants from 20 red clover accessions, and selected 185 SSR markers that produced clear scorable bands for testing with 24 individual DNA samples to determine polymorphism. We selected 70 primer pairs, and then assembled a core set of 24 loci into 12 sets of duplex markers, which were used for outcrossing behaviour analysis of 60 maternal parents and their respective 22 half-sib progenies. Key results Mean polymorphic information content (PIC) for the 70 markers was 0.490 (range 0.117–0.878). Minimum, mean and maximum PIC values for the 24 markers constituting the 12 duplexes were 0.226, 0.594 and 0.781, respectively. The outcrossing rate was identified as 99.4% for red clover in a natural environment. Conclusion We successfully developed a duplex SSR-based PCR protocol consisting of 24 markers. This SSR system was applied to determine the outcrossing rate of red clover in a natural environment.

Genetic Diversity and Population Structure of Didymellarabiei Affecting Chickpea in Ethiopia.

Ascochyta blight, also known as chickpea blight, which is caused by the fungal pathogen, Didymella rabiei, is an important disease affecting chickpea (Cicer arietinum L.) in many countries. We studied the genetic diversity and population structure of 96 D. rabiei isolates collected from three geographic populations in Ethiopia using simple sequence repeat (SSR) markers. We confirmed the genetic identity of 89 of the D. rabiei isolates by sequencing their rRNA internal transcribed spacer region genes. The chickpea blight pathogen isolates were genetically diverse, with a total of 51 alleles identified across 6 polymorphic SSR loci, which varied from 3 to 18 (average 8.5) alleles per SSR marker. The observed heterozygosity and expected heterozygosity ranged from 0.01 to 0.92 and 0.19 to 0.86, respectively. The mean polymorphic information content value of the D. rabiei populations was 0.58, with a mean gene diversity of 0.61 among loci. Gene flow (Nm = number of migrants) for the three populations of D. rabiei isolates ranged from 1.51 to 24.10 (average 6.2) migrants/cluster. However, the genetic variation between the D. rabiei populations was small (8%), with most of the variation occurring within populations (92%). Principal component analysis to visualize genetic variation showed that the D. rabiei isolates obtained from most of the chickpea samples formed roughly three groups on a two-dimensional coordinate plane. Similarly, the clustering of individuals into populations based on multi-locus genotypes (using Clumpak) grouped isolates into three clusters but with individual isolate admixtures. Hence, no clear geographic origin-based structuring of populations could be identified. To our knowledge, this is the first report of D. rabiei diversity in Ethiopia. Virulence studies should be conducted to develop chickpea varieties that are resistant to more aggressive pathogen populations.

ISSR analysis of Tulipa suaveolens (Liliaceae) populations from throughout the European part of the species range reveal genetic patterns shaped by Pleistocene transgressions of the Caspian Sea

Tulipa suaveolens Roth is a decorative bulbous, polycarpic species in the Liliaceae family. Currently, the species populations are declining due to the degradation of natural steppes. In the present article, we evaluated the genetic diversity of 216 specimens from 22 natural T. suaveolens localities in the European part of the species range using 10 inter simple sequence repeat (ISSR) markers. The polymerase chain reaction (PCR) yielded 250 unambiguous and reproducible polymorphic bands with a mean polymorphism information content (PIC) value of 0.27. Neither the principal component analysis nor the clustering method split the dataset. However, the Bayesian model‐based STRUCTURE analysis detected two genetic clusters of T. suaveolens. The analysis of the biogeographical distributional pattern of the revealed genetic groups confirmed our hypothesis that the evolution and distribution of T. suaveolens were likely affected by the Early Khvalynian transgression of the Caspian Sea and the following Enotayevsk regression. Furthermore, this hypothesis was supported by the results of the NEW HYBRIDS analysis identifying the specimens from the populations located outside the Early Khvalynian flooding limit as pure parents, while the specimens of the populations within the flooding limit were classified as backcrosses and second generation hybrids.

Screening for drought tolerance and molecular variability among some sugar beet cultivars

Drought is one of the significant abiotic stress factors that affect plant development and productivity. Screening and producing of more tolerant genotypes with higher yield capacity is the breeders' principal purpose. Therefore, this work was carried out to evaluate the performance of four sugar beet cultivars (Top, Hossam, Hercules and Kawamera) under water limitation. The drought stress experiment was applied based on three water regimes, 25%, 50% and 75% (severe, moderate and non-stress conditions, respectively) of relative water capacity (RWC). The study incorporated some productivity and quality traits. The results showed that drought stress has a significant effect on all studied traits. Whereas, increasing of water deficiency led to decrease of the productivity traits and increasing of quality parameters. Kawamera cultivar has superior performance in all the studied traits under all three different levels of water regime. Besides, the four cultivars were assessed by both SSR and ISSR molecular markers. SSR marker exhibited a higher polymorphism percentage (71.43%) than ISSR marker (44.26%). In addition, the mean polymorphism information content (PIC) value was higher for the SSR marker (0.25) than the ISSR marker (0.18) too. Moreover, the constructed dendrograms revealed that the SSR marker was able to separate the cultivars according to their drought-tolerance, where the highest drought-tolerant cultivar (Kawamera) was classified alone in the main cluster. However, the superiority of Kawamera cultivar under drought stress indicated that it could be utilized in breeding programs for developing more drought-tolerant sugar beet cultivars.

Genetic Diversity of Ancient Camellia sinensis (L.) O.Kuntze in Sandu County of Guizhou Province in China

The ancient tea plant germplasm is an important resource for breeding new tea plant varieties and has great economic value. However, due to man-made and natural disturbances, it has become endangered. In order to have a better management of the conserved tea plant germplasm, it is a requirement to understand the genetic and phenotypic diversity. The aim of this study was to evaluate the genetic and phenotypic diversity of 145 ancient tea plant germplasm resources from five populations in Sandu County of Guizhou province in China. To explore the population genetics of tea plant, we successfully identified 15 simple sequence repeat (SSR) markers, which were highly polymorphic. Additionally, we applied traditional phenotypic methods to evaluate the tea plant diversity. The results suggested that the genetic and phenotypic diversity were relatively high. A total of 96 alleles were identified, and the mean polymorphic information content (PIC) value was found to be 0.66. The analysis of molecular variance (AMOVA) showed that genetic variation within the populations was greater than among the populations. Overall, our results are the valuable baseline data in developing more efficient management and breeding plans for one of the most popular non-alcoholic beverage crops, the tea plant species.

Genetic Diversity among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

Deriving tropical gynoecious inbred backcross lines from exotic pickling cucumber using marker assisted backcross breeding

Indian cucumber cultivars are basically monoecious and vigorous in nature with many lateral branches but they are poor in productivity. The present study was aimed to introgress gynoecious trait (F locus) from pickling cucumber line (Gy14) into elite Indian cultivar Pusa Uday using marker assisted backcross breeding. Based on allelic diversity analysis, the allele numbers per locus ranged from 2 to 3 in BC1F3 and the observed heterozygosity (Ho) was ranged from 0.01 to 0.55. The heterozygosity expected (He) mean was 0.28 (range 0.03 to 0.50) which was higher than mean Ho (0.18) and mean polymorphic information content (PIC) for 87 markers was 0.23. Whereas the allele numbers per locus was 2 in BC2F2 and the observed heterozygosity (Ho) was ranged from 0.01 to 0.56. The mean expected heterozygosity (He) was 0.24 which was higher than mean Ho (0.17) and the mean PIC value was 0.19. The gynoecism (F locus) was introgressed in the Indian slicing cucumber cv. Pusa Uday though backcross breeding accompanied by foreground and background selections. The foreground selection was performed with one dominant SCAR marker, and 3 SSR markers (SSR 00233, SSR 15516 and SSR13251). A total of 87 polymorphic markers spanning genetic distance of 1031 cM with an average distance of 12.9 cM between adjacent markers were used for background selection. The genome recovery of the individuals in BC1F3 population was ranged from 62.64% to 93.10% while among BC2F2 plants it was ranged from 89.66% to 95.40%. Four inbred backcross lines (IBL) were selected from backcross populations (BC1F4 and BC2F3) those were purely gynoecious even at 45°C with more than 5 lateral branches. Hence, marker assisted backcross breeding served as a potential approach for precise introgression of the gynoecy (F locus) from picking cucumber to Indian slicing cucumber.