Percentage Of Polymorphic Loci Research Articles

SSR and 18S rDNA based molecular profiling of Neopyropia yezoensis (Rhodophyta) in China: insight into genetic impact of laver aquaculture on wild resource

Neopyropia yezoensis is a typical intertidal seaweed and an indispensable species for conservation of seaweed resources. As one of the most important marine vegetables, the cultivation area of N. yezoensis has been largely increasing in the past decade and ranked the second highest among all the farmed seaweeds in China. It remains unknown whether large-scale cultivation of N. yezoensis has a genetic impact on wild populations. In this study, SSR markers and 18S rDNA were applied for diversity and genetic structure analysis of 22 N. yezoensis populations from North China. Twenty-two haplotypes were generated from 352 18S rDNA sequences and only three haplotypes were shared by both cultivated and wild populations. Based on 11 polymorphic SSR markers developed, the average polymorphism of the cultivated N. yezoensis populations was higher than that of the wild populations, with the percentage of polymorphic loci being 90.91% in most cultivated populations. The cultivated populations were clustered separately from the wild ones based on the population phylogenetic tree. This indicates that cultivated N. yezoensis populations are diverse and divergent from wild populations in China. However, there were cultivated individuals mixed with the wild ones based on the individual phylogenetic tree and STRUCTURE analysis. The genetic differentiation between cultivated and wild populations decreased with increasing cultivation time, suggesting a possible long-term and slow process of genetic introgression between cultivated N. yezoensis and the wild resource. The wild populations were grouped into two distinct clades by SSRs, with one distributed around the intersection between the Yellow Sea and the Bohai Sea, where the populations were characterized by a specific 18S rDNA haplotype. These findings provide useful insights into germplasm conservation, genetic breeding and improvement of N. yezoensis farming practices.

MOLECULAR DIVERSITY IN POPULATIONS OF CHILI (CAPSICUM ANNUUM L.)

Chili (Capsicum annuum L.) is a self-pollinated crop, with natural cross-pollination occurring below 4%–5%. It intends to have low heterosis. Developing cross-pollination in chili currently receives much attention to achieve diversity in trait improvement. Double-crossing becomes one of the alternatives to achieving this goal. In this study, three different parental chili genotypes (K, B, and T) gained crossing, with four populations (S2 K, F3 KB, F2 BTKB, and F2 KBBT) developed. Using 11 selected sequence-related amplified polymorphism (SRAP) combination markers that target Open Reading Frame (ORF) regions assessed molecular diversity in these chili populations. Results revealed the possibility of identifying diversity using SRAP markers based on primer profile information. The iMEC analysis showed high values of PIC (0.3381), discriminant power (0.882), and mean polymorphic value (97.88%). The highest similarity emerged between the populations BTKB and KBBT as the reciprocal. Then, the smallest similarity appeared between K and the double cross. Compared with the self-pollinated genotype, SRAP primers discovered that double crosses provided more variation based on Shannon’s index (I) and percentage of polymorphic loci (PPL). The genetic distance denotes maternal inheritance or extraneous involvement in progeny. However, multiple-parent hybridization authenticated the boost in genetic diversity.

Infraspecific genetic diversity and seed fatty acid composition in Sesamum indicum L. populations (Pedaliaceae) in Iran

Sesamum indicum L. of the Pedaliaceae family is considered an economically important oil-bearing plant that has been cultivated for more than 5000 years. In this research, we examined genetic diversity and seed fatty acid composition in 11 Iranian populations of S. indicum. We extracted the nuclear DNA using the CTAB protocol and then amplified the genomes using 10 SCoT molecular primers. For the phytochemical study, the seed fatty acid methyl esters were subjected to a GC apparatus and their composition was determined. The data were then analyzed using PAST, POPGENE, Geno-Dive, and STRUCTURE software. We determined that the percentage of polymorphic loci was 62%. According to the AMOVA test and estimated genetic diversity parameters, high genetic differentiation occurred between the examined populations, which was followed by a low rate of gene flow and Hs. Based on the Nei's genetic distance and Structure analysis, the populations were divided into seven genotype groups. Most identified genotypes had homogeneous genetic structures indicating a limited genetic flow rate. The phytochemical evaluation revealed that a great part of the seed oils was composed of unsaturated fatty acids with linoleic and oleic acids as the main compounds. We detected palmitic acid as the major saturated fatty acid. The populations were divided into four chemotype groups based on the seed oil fatty acids composition. However, the population clustering patterns in the molecular genetic and seed fatty acid analyses were not identical. These results indicated that some environmental parameters strongly affect the seed oil fatty acids composition. We suppose that the populations under study are comprised of several genotypes or cultivars grown in various Iranian locations.

Genetic variation of Limnophora marginata Stein, 1904 (Diptera: Muscidae), associated with an altitudinal gradient in Pedro Moncayo Canton, Pichincha, Ecuador

Abstract. Aguilar KEV, Vivas AYS, Acosta-López C. 2023. Genetic variation of Limnophora marginata Stein, 1904 (Diptera: Muscidae), associated with an altitudinal gradient in Pedro Moncayo Canton, Pichincha, Ecuador. Biodiversitas 24: 269-275. Analyzing heterogeneity in insect populations is relevant to understanding its biology. Thus, we analyzed the genetic variability of two populations of “hunter-flies”, Limnophora marginata Stein, 1904 associated with an altitudinal gradient in the Tocachi and Jerusalem localities, in the Pedro Moncayo Canton, Ecuador, using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) of the mitochondrial Cytochrome oxidase I gene. Thirty alleles were detected from analysis with five restriction enzymes; the percentage of polymorphic loci was higher in Tocachi (96.67%) than in Jerusalem (80%). Haplotypes were generated with the corresponding alleles, resulting in a different haplotype for each analyzed individual. Several estimators were used to characterize the population structure. The Analysis of Molecular Variance (AMOVA) evidenced the existence of higher intra-population variability (94%) than inter-population (6%), showing similar information to that found through haplotype analysis. The Fst fixation index indicated that there is no genetic difference between populations (0.056, P<0.05). Nei's genetic distance and Nei's similarity index indicated that L. marginata populations did not show differences between populations. From the results we deduce that the evolutionary force that may be modelling the existent genetic variability may be gene flow, thus establishing a low inter-population genetic structure. The mitochondrial DNA Cytochrome oxidase I gene was an advantageous molecular marker to obtain results that established intra and inter population variability. The characteristics of the mitochondrial DNA were useful to successfully apply the PCR-RFLP technique. Our findings highlight the existence of ecosystem connectivity between L. marginata populations despite altitudinal and habitat differences.

Evaluation of genetic diversity and production adaptability in different germplasms of Paspalum dilatatum

AbstractPaspalum dilatatum is an excellent warm‐season forage grass and soil conservation plant in subtropical regions. However, information on P. dilatatum cultivation in southwestern China is limited. A preliminary evaluation of the genetic diversity and adaptability of six P. dilatatum germplasms was conducted in Guizhou based on inter simple sequence repeat (ISSR) markers and field trials. Fifteen polymorphic primers were screened from 50 ISSR primers. A total of 141 bands were generated, 124 of which were polymorphic, yielding 88.63% polymorphic bands. The number of polymorphic loci detected for the different germplasms ranged from 23 to 61, and the percentage of polymorphic loci was 40.67%. The mean number of alleles was 1.23, and the effective allele number was 1.15. Nei's genetic diversity index was 0.08. The Shannon information index was 0.12, and the genetic similarity coefficient (GSC) ranged from 0.6002 to 0.8955, indicating a relatively rich genetic base among the germplasms. The unweighted pair group method with arithmetic mean approach was used to construct the clustering map. Using a GSC of 0.83 as the threshold value, the six germplasm materials were divided into four clusters, indicating that ISSR molecular markers can be effectively applied to analyze the genetic diversity of P. dilatatum germplasms. Cluster analysis of 12 growth characteristics of the germplasms of P. dilatatum showed that germplasm 4 exhibited strong tillering ability and a high crude protein content. Germplasm 3 showed high plant height, fresh yield and hay yield. Germplasm 1 showed the lowest forage yield and crude protein content. Germplasms 2, 5 and 6 showed excellent crude protein and crude fat contents; the remaining indicators showed intermediate performance. This study provides important references for the utilization and variety selection of introduced P. dilatatum resources in the karst areas of Guizhou.

The assessment of genetic diversity and population structure of endemic Scutellaria yildirimlii (Lamiaceae) for conservation purposes

Scutellaria yildirimlii is an endangered perennial endemic species from Turkey and belongs to the family Lamiaceae, which has a high number of medicinal and aromatic plants. It is crucial to determine genetic diversity and population structure of this species for its conservation measures; therefore, 111 individuals from five natural populations of S. yildirimlii were investigated by using 15 inter simple sequence repeats (ISSR) primers. The percentage of polymorphic loci (PPL), Nei?s gene diversity (H), and Shannon?s information index (I) at the species and population-level were determined as 93.9%, 0.183, 0.292 and 56.5%, 0.158, 0.242, respectively. The analysis of molecular variance (AMOVA) showed that there is more genetic variation within populations (84%) than among populations (16%). Nei?s differentiation coefficient (GST = 0.144) was determined to be moderate, which was confirmed by the level of genetic differentiation among populations. Gene flow (Nm = 2.984) showed high genetic exchange among populations. Pairwise genetic distance values among populations ranged from 0.0219 to 0.0512. The Mantel test revealed a statistically significant positive correlation between genetic and geographical distance (r = 0.493, p < 0.001). The Unweighted Pair Group Method with Arithmetic Averages (UPGMA) dendrogram and Principal Coordinate Analysis (PCoA) showed similar results. STRUCTURE analysis (?K = 3) revealed that the K test yielded maximum peaks for 3 clusters. Based on the findings, measures for genetic conservation and management of this species were presented.

Padrão de diversidade genética de Passiflora spp. em Boyacá, Colômbia

Abstract The objective of this work was to characterize the genetic diversity, using ISSR markers, of 70 genotypes of five species of Passiflora spp. in Boyacá, Colombia. For molecular characterization, samples of young leaves were collected from 11 municipalities of the Boyacá department. Genetic similarity was used to cluster the genotypes by the UPGMA method, and genetic structure was evaluated by the Bayesian model. Eight ISSR primers produced 138 loci. The formed cluster consists of two populations, with most individuals of the same species but from different geographic origins. The percentage of polymorphic loci is higher than 80%. The average value of heterozygosity is between 0.29 and 0.36 for population I and II, respectively, and the values of polymorphic information content are low. A moderate genetic differentiation (0.16) and high gene flow (3.35) are observed.

Molecular Characterization of the Honeybee (Apis mellifera) from two Vegetational Zones in Nigeria

The genetic structure and diversity of Apis mellifera from eight populations across two vegetational zones of Nigeria was investigated in order to provide base line information that will enhance its conservation, genetic improvement and sustainable yield. Genomic DNA was extracted from 40 specimens randomly selected from eight colonies in derived savannah and tropical rainforest regions of Nigeria. The specimens were amplified using five Random Polymorphic DNA (RAPD) primers and the amplicons generated were assessed using appropriate statistical indices. Results generated revealed significant genetic polymorphisms among the eight populations of A. mellifera ranging from 38.89 to 68.52% with a total of 281 bands amplified from 54 loci in all samples. The derived savannah population (Offa) had a greater amount of genetic diversity than the rest seven (7) populations as revealed by the percentage of polymorphic loci, expected heterozygosity and Shannon information index (I). The genetic structure as revealed by the Neighbour-Joining dendrogram showed that the eight populations studied represent two major genotypic groups with intra-group relationships. Eleyoka and Offa populations were the genetically closest in the first group while Ayetoro-Gbede and Ayegunle-Gbede populations were the genetically closest in the second group. The study suggests that the two major genotypic groups represent two distinct genetic stocks and can thus be managed accordingly.

Molecular characterization and diversity analysis of some local potato (Solanum tuberosum L.) genotypes of Bangladesh by RAPD markers

Genetic identification of cultivars and varieties is useful in preserving endangered potato germplasm and planning for new breeding programs. Molecular characterization and genetic diversity of 10 local potato genotypes of Bangladesh were investigated with five RAPD primers, namely OPA-18, OPB-06, OPC-01, OPD-02 and OPW. Genomic DNA was extracted from young leaves and PCR reactions were performed with selected primers. The selected primers generated 33 distinct and differential amplified bands (size ranged from 131-1188 bp), out of which 28 were polymorphic. The percentage of polymorphic loci was valued from 33.33% to 100%. Gene frequency was ranged from 0.300 to 1 and gene diversity was from 0 to 0.70. The inter-varietal similarity indices was ranged from 42.45% to 92.67%. Pair-wise comparisons of Nei's genetic identity value was from 0.4848 to 0.9394. The highest Nei's genetic identity (0.9394) was observed in Sheel Bilati and SAU Promising Genotype-5 genotype pair. Nei's (1972) genetic distance was from 0.0625 to 0.7239. Dendrogram based on Nei's genetic distance using Unweighted Pair Group Method with Arithmetic Means (UPGMA) indicated the segregation of studied potato genotypes into two main clusters. It was found that RAPD markers are sensitive enough to identify genetic variation in a variety of germplasm, which will be helpful for choosing genetically unique germplasm in potato breeding programs. SAARC J. Agric., 20(2): 43-55 (2022)

Genetic diversity and population structure of Irvingia species using DArTseq generated markers

ABSTRACT Irvingia gabonensis and Irvingia wombolu trees indigenous to West and Central Africa are economically important owing to their valuable kernels. Massive fruit harvesting and reduction of forests land area has threatened their genetic diversity thus warranting conservation. This study reports the genetic diversity and population structure based on dominant markers of Irvingia accessions from Nigeria, Cameroon and Gabon held at World Agroforestry field genebanks. A total of 60 samples and 6532 SilicoDArT markers revealed high genetic differentiation among populations (phiPT = 0.301, P = .001). The overall genetic diversity revealed by Nei’s gene diversity (He = 0.117) and percentage of polymorphic loci (39.60%) was low. I.gabonensis provenances from Cameroon and Nigeria were more diverse than Gabonese populations. Pairwise phiPT values calculated from AMOVA variances delineated I. wombolu and I. gabonensis. Population structure and cluster analysis based on Bayesian algorithm, DAPC and UPGMA methods placed Cameroon at the center of distribution of I. gabonensis accessions from Nigeria and Gabon. Gabonese accessions tend to cluster independent of Nigerian accessions while I. wombolu formed a distinct cluster from I. gabonensis. SilicoDArT markers were found suitable for population structure and differentiation analysis of Irvingia accessions and can guide future recollections to enrich genebank diversity and materials for domestication events.

Pineapple genetic diversity in Riau peat land assessed by Random Amplified Polymorphic DNA (RAPD) marker

Riau is one of the centers for pineapple production in Indonesia and harbored many local cultivar that have been cultivated for generations. The purpose of this study was to investigate the genetic diversity and genetic similarity between local cultivar in Riau based on RAPD (Random Amplified Polymorphic DNA) markers. Diversity analysis was carried out on ten local pineapple cultivar from five districts, namely Kampar, Indragiri Hilir, Siak, Bengkalis, and Dumai, using 11 RAPD primers. The PCR amplification result of the 11 RAPD primers selected generated a total 77 loci and the percentage of polymorphic loci was 96.42%. The high value of percentage of polymorphic loci reflected high diversity of pineapple in Riau propince. The values of genetic similarity coefficient of the pineapple genotypes in Riau Province ranged from 53% to 91%. The UPGMA dendrogram displayed that the Queen and Smooth Cayenne cultivars were separated in different cluster, while the Gemilang cultivar (GT) was placed between the Smooth Cayenne and Queen groups. This finding confirmed that Gemilang cultivar was the result of the natural crossing pollination between Smooth Cayenne and Queen pineapple.

Characterization of assembled clones of Pongamia pinnata (L.) Pierre for its genetic variability using ISSR

Genetic diversity of Pongamia pinnata within and among 5 populations collected and assembled from two different agroclimatic zones of Tamil Nadu, India. Totally 25 accesions were examined with eight inter simple sequence repeat (ISSR) primers. A total of 120 scorable bands were generated, among which 80% were polymorphic. Jaccard similarity coefficient was calculated for pairwise comparisons. Within all 25 accessions and ranged from 0.30 to 0.88 while average within population similarity ranged from 0.50 to 0.60. Within populations variability was estimated as percentage polymorphic loci (ranging from 50% to 80%). Shannon’s information index among two zones were detected. Between and within accessions relatedness was estimated among populations with a principal coordinate analysis and also estimated with cluster analysis (UPGMA). These estimation depicts outcrossing rates both within population and between-population diversity. Molecular marker characterization can however be used to identify the most suitable zone for collection of high polymorphic accessions for tree improvement program with the yield.

Assessment of the Genetic Relationship and Population Structure in Oil-Tea Camellia Species Using Simple Sequence Repeat (SSR) Markers.

Oil-tea camellia trees, the collective term for a class of economically valuable woody oil crops in China, have attracted extensive attention because of their rich nutritional and pharmaceutical value. This study aimed to analyze the genetic relationship and genetic diversity of oil-tea camellia species using polymorphic SSR markers. One-hundred and forty samples of five species were tested for genetic diversity using twenty-four SSR markers. In this study, a total of 385 alleles were identified using 24 SSR markers, and the average number of alleles per locus was 16.0417. The average Shannon's information index (I) was 0.1890, and the percentages of polymorphic loci (P) of oil-tea camellia trees were 7.79-79.48%, indicating that oil-tea camellia trees have low diversity. Analysis of molecular variance (AMOVA) showed that the majority of genetic variation (77%) was within populations, and a small fraction (23%) occurred among populations. Principal coordinate analysis (PCoA) results indicated that the first two principal axes explained 7.30% (PC1) and 6.68% (PC2) of the total variance, respectively. Both UPGMA and PCoA divided the 140 accessions into three groups. Camellia oleifera clustered into one class, Camellia vietnamensis and Camellia gauchowensis clustered into one class, and Camellia crapnelliana and Camellia chekiangoleosa clustered into another class. It could be speculated that the genetic relationship of C. vietnamensis and C. gauchowensis is quite close. SSR markers could reflect the genetic relationship among oil-tea camellia germplasm resources, and the results of this study could provide comprehensive information on the conservation, collection, and breeding of oil-tea camellia germplasms.

Application of MaxEnt Modeling and HRM Analysis to Support the Conservation and Domestication of Gevuina avellana Mol. in Central Chile.

The Chilean hazelnut (Gevuina avellana Mol., Proteaceae) is a native tree of Chile and Argentina of edible fruit-type nut. We applied two approaches to contribute to the development of strategies for mitigation of the effects of climate change and anthropic activities in G. avellana. It corresponds to the first report where both tools are integrated, the MaxEnt model to predict the current and future potential distribution coupled with High-Resolution Melting Analysis (HRM) to assess its genetic diversity and understand how the species would respond to these changes. Two global climate models: CNRM-CM6-1 and MIROC-ES2L for four Shared Socioeconomic Pathways: 126, 245, 370, and 585 (2021–2040; 2061–2080) were evaluated. The annual mean temperature (43.7%) and water steam (23.4%) were the key factors for the distribution current of G. avellana (AUC = 0.953). The future prediction model shows to the year 2040 those habitat range decreases at 50% (AUC = 0.918). The genetic structure was investigated in seven natural populations using eight EST-SSR markers, showing a percentage of polymorphic loci between 18.69 and 55.14% and low genetic differentiation between populations (Fst = 0.052; p < 0.001). According to the discriminant analysis of principal components (DAPC) we identified 10 genetic populations. We conclude that high-priority areas for protection correspond to Los Avellanos and Punta de Águila populations due to their greater genetic diversity and allelic richness.

Variation of Genetic Diversity of Ralstonia Solanacearum In Tomato And Egg Plant of Bangladesh

Genetic diversity of Ralstonia solanacearum, on seeds of tomato and brinjal from different seed sources in Bangladesh were studied with Random Amplified Polymorphic DNA (RAPD) marker. The primers viz., OPA02, OPA08, OPA09, OPA10, OPA18 and OPE19 were used in this study and were also evaluated on the basis of intensity and resolution of the band. The genetic variations in 24 isolates of R. solanacearum were analyzed with (OPA18) RAPD marker in Polymerase Chain Reaction (PCR). The percentage of polymorphic loci was 100.00 for both tomato and brinjal. Combined Dendrogram based on Nei’s (1972) genetic distance in Unweighted Pair Group Method of Arithmetic Means (UPGMA) segregated the 24 isolates of R. solanacearum into two main clusters: RsT-6, RsB-2 and RsB-3 in cluster 1, and rest of the 24 isolates were grouped in cluster 2. The isolate of brinjal (RsB-8) was close to the isolate RsB-12 and the isolate RsB-11 was near to RsT-5 (tomato) with the least genetic distance (0.000), while the brinjal isolate RsB-4 was also close to RsB-5 with the low genetic distance (0.0606). The coefficient of gene differentiation (Gst) was obtained at 1.0000 which reflects the existence of higher genetic variations among 24 isolates of R. solanacearum. Comparatively higher genetic distance (1.7346) and the lower genetic identity (0.1765) were observed in RsB-1 vs. RsT-12, whilst the higher genetic identity (1.000) and the lower genetic distance (0.000) were estimated in RsB-8 vs. RsB-12 and RsB-11 vs. RsT-5, respectively. Consequently, interactive significant genetic variations in 24 isolates of R. solanacearum of tomato and brinjal seed sources were found to be evident in both the crop species’ of diversified different varieties as the genetic variability of specific crop species. Bangladesh J. Bot. 51(3): 519-526, 2022 (September)

Population genetic of the Indonesian rosewood (Dalbergia latifolia) from Java and West Nusa Tenggara revealed using sequence-related amplified polymorphism

Dalbergia latifolia is commercial tropical tree species known for its beautiful heartwood, mainly used for furniture and musical instrument. High market demand has put concerns on its sustainability and conservation aspects in Indonesia. Ninety-five specimens of D. latifolia were collected from eight populations of Java, Lombok, and Sumbawa Island to study intraspecific variability and diversity using SRAP. One hundred and eighty SRAP loci with 54.03% ± 4.35% polymorphism obtained from PCR amplification of 10 primer combinations, with the average PIC for these primers of 0.28. Genetic diversity and variability measures were calculated using GenAlEx software indicating a relatively low-mid level of percentage of polymorphic loci (PPL) (54.03%), effective number of alleles (Ne) (1.255), Shannon information index (I) (0.242), and heterozygosity (He) (0.156) on average. The highest value (I = 0.309, He = 0.196) was observed in population P2CJ (Central Java), followed by West Java of P1WJ (I = 0.300, He = 0.191) and West Sumbawa of P7Wsumb (I = 0.257, He = 0.169), while the lowest (I = 0.202, He = 0.129) was found in West Lombok (P4WL). The genetic relationships were measured from genetic distance and identity from the two-pairwise calculation, PCoA, and STRUCTURE analysis. The relative homologous population is found between populations Central and West Java of P2CJ and P1WJ (Nei uD = 0.031), suggesting these populations have the same origin and formed one population, while the most distinct (Nei uD = 0.157) was recorded between Sumbawa regency (P6Sumb) and East Java (P3EJ). The results from PCoA showed that all individuals are placed in three groups almost in accordance with their respective islands, i.e. a group comprised inclusively trees from Sumbawa island, a group of Lombok and some Central Java trees, and a group of trees from Java with the exclusion of some trees of Central Java that were clustered with trees from Lombok island. This result was also supported by STRUCTURE analysis, which showed that Sumbawa, Lombok, and West-East Java populations formed their respective clusters, and Central Java population contains a mixture of West-East Java and Lombok populations. This may suggest evidence of complex origin, thus needing further study to clarify. It is recommended that the populations with the highest value of genetic diversity (Central and East Java) are to be maintained as the source of the gene pool for genetic enrichment programs.

Assessment of Genetic Diversity for Cercospora Leaf Spot (CLS) Resistance in Mung Bean [Vigna radiata (L.) Wilczek] using SSR Markers

Background: CLS causes severe yield loss in mung bean. To sustain mung bean health, it is vital to include alleles that may be useful in resisting CLS. Therefore, in the present study, 90 mung bean genotypes were included for assessing genetic diversity using 66 SSR markers for CLS resistance. Methods: The mung bean crop was regularly monitored for the presence of pathogen and development of CLS disease in natural field conditions during pre rabi 2018 and pre rabi 2019. CLS screening assessments of germplasms were carried out using a 1-5 rating scale. Total genomic DNA was isolated from the leaf samples of all the genotypes and SSR genotyping was performed. The genotyping data were analysed by using GenAlEx 6.51b2 and TASSEL 5.0 software programme for genetic diversity parameters. Result: A moderate molecular diversity was observed in the panel population as a wide variation in alleles showed a range of 80 bp to 300 bp with the average PIC value of 0.40. The maximum percentage of polymorphic loci was 75.76% in the resistance genotypes followed by 56.06% in moderately resistant genotypes. The percentages of Shannon information among and within the population were found to be 44% and 56%, respectively. The archaeopterx tree differentiated the panel population into two major clusters, i.e., cluster I and cluster II, which were again sub divided into different sub-clusters and sub-sub clusters. These findings indicate that, the mung bean germplasm panel used in the present study could enrich the local gene pool and provide information for CLS resistance breeding.

Identification, Genetic Diversity, and Chemical Control of Xanthomonas arboricola pv. pruni in China.

Peach bacterial spot caused by Xanthomonas arboricola pv. pruni has become widespread in most peach-producing areas of China and has caused devastating losses to the peach industry. However, little is known about the population biology and epidemiology of X. arboricola pv. pruni in China, thus no effective management strategy is available. Altogether, 321 symptomatic samples of peach bacterial spot from 12 provinces in China were collected from which 612 bacterial isolates were obtained. Based on 16S rDNA sequence comparison in GenBank, the obtained isolates were identified as Pantoea spp. (514) and Xanthomonas spp. (98). The pathogenicity test demonstrated that the causal agent of the peach bacterial spot was the Xanthomonas spp. instead of the Pantoea spp. Based on morphological observation, physiological and biochemical characterization, and molecular identification, the Xanthomonas spp. were further identified to be X. arboricola pv. pruni. Then, 41 X. arboricola pv. pruni isolates representing different populations were selected and analyzed with repetitive element sequence based-PCR and intersimple sequence repeat markers to understand the genetic diversity and population structure along with four X. arboricola pv. pruni isolates from plum and three isolates of X. arboricola pv. juglandis as comparison. A total of 98 polymorphic alleles were identified, with a mean value of percentage of polymorphic loci of 14. Genetic diversity and phylogenetic analysis revealed the profound heterogeneity between X. arboricola pv. juglandis and X. arboricola pv. pruni, moderate genetic differentiation within X. arboricola pv. pruni, and obvious host specificity but weak geographical differentiation in X. arboricola population. Finally, the efficiency of bactericides on X. arboricola pv. pruni was evaluated invitro and invivo. The parallel repeated field trials in two orchards demonstrated that 80% Mancozeb (1:800) and 47% Kocide (1:800, 1:1,500, and 1:2,000) had excellent control efficacies for X. arboricola pv. pruni, especially as the control efficacy of Kocide could even reach 90%. This study conducted a systematic investigation for the occurrence, population variance, and chemical control of X. arboricola pv. pruni. It improved the understanding of the pathogen populations of peach bacterial spot in China and provided solid theoretical and practical guidance for X. arboricola pv. pruni control.

Identification and Validation of Microsatellite Markers in &lt;i&gt;Rhododendron campanulatum&lt;/i&gt; D. Don through cross transferability

The genetic diversity maintained by Forest Genetic Resources (FGRs) bestow them the capability for survival, adaptation and evolution in response to the changing climatic conditions. Population genetic studies based on DNA based marker may aid in understanding the actual level of diversity and its distribution within and among the populations, gene flow, allele fixation, structuring etc. that could be wisely used in their conservation and management. Rhododendron campanulatum is a medicinally, horticulturally and ecologically important tree species growing at tree line throughout the Himalayas. In the present study, efforts were carried out to identify simple sequence repeat (SSR) markers in R. campanulatum through cross species amplification. In total, 15 SSR markers developed in R. arboreum (Choudhary et al., 2014) were tested for cross transferability and polymorphism in R. campanulatum. Of these, 12 primer pairs were positively amplified but only 5 (SSR-7, SSR-8, SSR-11, SSR-25 and SSR-29) showed polymorphism across the populations. Mean Polymorphic Information Content (PIC), expected heterozygosity (H ) and observed heterozygosity (H ) of these markers were e o recorded as 0.609, 0.360 and 0.343, respectively. Other measures such as genetic differentiation (F ) and gene flow (N ) were recorded as 0.467 and ST m 0.486, respectively. Population of Valley of Flowers had the highest percentage of polymorphic loci (100.0%). Analysis of molecular variance (AMOVA) revealed about 25% among the populations and 75% within population. The markers identified in the study could be highly useful for detailed population genetic analysis of this species.

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.