Gene Diversity Index Research Articles

Genetic diversity and population structure of sorghum [Sorghum bicolor (L.) Moench] genotypes in Ethiopia as revealed by microsatellite markers

In the tropical and semi-arid regions of Africa, sorghum [Sorghum bicolor (L.) Moench] is mainly grown as a major food security crop. Understanding the extent and pattern of genetic variability is a prerequisite criterion for sorghum improvement and conservation. The genetic diversity and population structure of 100 genotypes of sorghum were profiled using 15 microsatellite loci. A total of 108 alleles, with an overall mean of 7.2 alleles per locus, were produced by all of the microsatellite loci used due to their high polymorphism. Polymorphic information content values ranging from 0.68 to 0.89 indicated that all of the loci are effective genetic tools for analysing the genetic structure of sorghum. Different diversity metrics were used to evaluate genetic diversity among populations, and Nei's gene diversity index ranged from 0.74 to 0.81 with an overall mean of 0.78. Poor genetic differentiation (FST: 0.02; p < 0.0001) was found, where 98% of entire variability was accounted by the within populations genetic variability, leaving only 2.32% among populations. The highest genetic differentiation and Nis's genetic distance were observed between the sorghum populations of the Southern Nation and Nationalities Peoples and Dire Dawa regions. Due to increased gene flow (Nm = 10.53), the clustering, principal coordinate analysis and STRUCTURE analysis failed to categorize the populations into genetically different groups corresponding to their geographic sampling areas. In general, it was found that the microsatellite loci were highly informative and therefore valuable genetic tools to unfold the genetic diversity and population structure of Ethiopian sorghum genotypes. Among the five populations studied, sorghum populations from Amhara and Oromia had the highest genetic variation, indicating that the regions could be perhaps hotspots for useful alleles for the development of better-performing genotypes, and also for designing appropriate germplasm management strategies.

Start codon-targeted marker evaluation of genetic relationship and population structure in southern Nigerian fluted pumpkin (Telfairia occidentalis Hook F.) collection

AbstractFluted pumpkin (Telfairia occidentalis Hook F.) is an underutilized indigenous leafy vegetable with enormous prospects for food security in sub-Saharan Africa. However, relatively little is known about genetic relationships and population structure in the species. In this study, 32 landraces of fluted pumpkin collected across three southern geographical regions in Nigeria were assessed for genetic diversity and population structure using 8 start codon-targeted (SCoT) makers. The polymorphic information content of the SCoT markers ranged from 0.48 in SCoT36 to 0.94 in SCoT28, with an average of 0.77. Hierarchical cluster dendrogram based on Ward's method and principal component analysis grouped the landraces into four clusters without affiliation to provenance. Overall, the mean values of the population genetic diversity parameters – Nei's gene diversity (H) and Shannon's information index (I) showed values of 0.28 ± 0.01 and 0.43 ± 0.02, respectively, implying a narrow genetic base for the landraces. The result was further corroborated by a very close Nei's genetic distance and identity among populations of the landraces. Furthermore, the south-west population exhibited the higher genetic diversity (H = 0.31 ± 0.02 and I = 0.45 ± 0.03). Population structure analysis inferred three subpopulations for the accessions with varying degrees of allelic admixture. An analysis of molecular variance revealed that almost all the genetic variation occurred within (99%) than between (1%) populations. The findings shed light on the genetic diversity of southern Nigerian fluted pumpkin and have significant implications for the characterisation, conservation, exploitation and improvement of the species.

Study on the “Space Gene” Diversity of Traditional Dong Villages in the Southwest Hunan Province of China

Traditional villages are essential carriers of traditional culture and ethnic culture. Hence, it is of great significance to study and protect them in the context of urban–rural integration. From the perspective of the “Space Gene”, this study proposes the identification and extraction of the space gene. Then, we examine six traditional Dong villages in the Pingtan River Basin selected as cases to quantify their space gene diversity. The results show that (i) traditional Dong villages are rich and diverse in terms of their space types. (ii) The important value of the public space reflects the social cohesion of the Dong people. (iii) However, the sample villages still have differences in their space gene diversity index values. (iv) The characteristic culture encapsulated by the spaces of traditional Dong villages is facing disappearance. Furthermore, we propose a conservation strategy for traditional villages. Through the space gene diversity index, we can examine the current state of the protection and development of the village. The main objective of this study was to deepen our interpretation of the space in order to study the cultural value behind it.

Correlations among population genetic structure, geographic origin, growth rate, and fungicide resistance of Rhizoctonia solani AG 1-IA, the pathogen of rice sheath blight

Rhizoctonia solani AG1-IA is a necrotrophic fungus that causes rice sheath blight and results in severe yield and quality reductions in rice worldwide. Differences of genetic structure and fungicide sensitivity of the pathogen have significant effects on the severity and control effect of this disease in the field. To determine correlations among population genetic structure, geographic origin, growth rate, and fungicide resistance of the pathogen, 293 strains of R. solani were isolated from diseased rice collected from 13 cities of Jiangsu Province and five regions of China. Simple sequence repeat (SSR) molecular marker technology was used to analyze the genetic diversity of these strains, and a total of 74 bands were amplified by nine pairs of primers. Population genetic structure analysis showed that strains from Central China and northern Jiangsu had the highest Nei’s gene diversity index and Shannon diversity index. The vast majority of strains grew fast with colony diameters of more than 60.0 mm cultured at 28 °C for 36 h. The half-maximal effective concentration (EC50) of them to tebuconazole, thifluzamide, and propiconazole varied ∼16.2-, 3.8-, and 7.5-fold. However, the genetic diversity of R. solani had no significant correlation with their geographic origin, growth rate or fungicide sensitivity.

Cross transferability of barley nuclear SSRs to pearl millet genome provides new molecular tools for genetic analyses and marker assisted selection

AbstractPearl millet (Pennisetum glaucum(L.) R. Br.) is a valuable agronomic and industrial promising crop with high adaptation potentials considered as understudied species and is not attributed the interest it deserves. This investigation reports for the first time the transferability of barley nuclear microsatellites to pearl millet genome. This allowed the inference of the considerable potential of transferability of the nuclear simple sequence repeats (nSSRs) mapped fromHordeum vulgareL. genome toP. glaucumspecies. Out of the 42 tested SSRs, ten were found to be transferable, giving a transferability rate of 23.8%. These latter markers enabled the molecular characterization of the nine barley and nine pearl millet autochthonous landraces and revealed high levels of polymorphism and discriminatory powers. All the microsatellites were proved to be highly informative with an average polymorphic information content value of 0.74. The gene diversity index revealed a high level of diversity encompassed in both germplams with a meanHevalue of 0.80. At the species level, comparable amounts of genetic variability were detected forH. vulgareandP. glaucumlandraces. Furthermore, the set of ten transferable nSSRs exhibited high ability in revealing the genetic structure, differentiation and phylogenetic relationships among the studied germplasms. The new available nSSRs present an additional informative and discriminant set of molecular markers which will be useful in further genetic studies concerning the multipurpose speciesP. glaucumL. such as molecular fingerprinting, genetic purity assessment, genome mapping, marker-assisted breeding and conservation programs.

Diversity and Population Structure of Local Rice Varieties from Indonesia Revealed by SSR Markers

Indonesia's local rice varieties (Oryza sativa L.) have a wide range of diversity that can be valuable sources for crop improvement with molecular markers. This study investigated local rice varieties' genetic diversity and population structure using simple sequence repeat (SSR) markers. The SSR markers demonstrated their informativeness for genotypic characterization as represented by the gene diversity indices and polymorphic information content. The UPGMA dendrogram divided 63 varieties into two distinct clusters with different levels of sub-grouping and the tendency according to their origins, as supported by PCoA. In contrast, PCA of these varieties according to agro-morphological traits was scattered in all quadrants. Thus, DNA level variation analyzed by SSR seems to complement the phenotypic traits, which were not well structured and revealed significant genetic diversity among varieties, within, and among populations (P&lt;0.01). The pattern of grouping structure analysis of total varieties into two subpopulations is similar to the dendrogram according to SSR markers but better resembles the pedigree information of the set local varieties. These findings have implied their importance in rice breeding for genetic improvement, maintenance, and management of local genetic resources in Indonesia.

Genetic diversity of Prunus armeniaca L. var. ansu Maxim. germplasm revealed by simple sequence repeat (SSR) markers.

The genetic diversity and genetic structure of P. armeniaca var. ansu were analyzed based on SSR markers. The aim was to provide scientific basis for conservation, efficient utilization, molecular marker assisted breeding and improved variety selection of P. armeniaca var. ansu germplasm resources. The results showed that the level of genetic diversity within the population was high. Among the 30 SSR markers, the mean number of observed alleles was 11.433, the mean number of effective alleles was 4.433, the mean of Shannon information index was 1.670, and the mean of polymorphic information content was 0.670. Among the eight provenances, Tuanjie Township, Xinyuan County, Xinjiang had the highest genetic diversity. The observed alleles, effective alleles, Shannon information index and Nei’s gene diversity index among provenances were higher than those within provenances. Based on Bayesian mathematical modeling and UPGMA cluster analysis, 86 P. armeniaca var. ansu accessions were divided into three subpopulations and four groups, which reflected individual differences in provenances. Subpopulations classified by Bayesian mathematical modeling and groups classified by UPGMA cluster analysis were significantly correlated with geographical provenance (Sig<0.01) and the provenances significantly impacted classification of groups. The provenances played an important role in classification of groups. The genetic distance between Tuanjie Township of Xinyuan County and Alemale Township of Xinyuan County was the smallest, while the genetic relationship between them was the closest and the degree of genetic differentiation was small.

Genetic diversity in populations of Girardinia diversifolia from Nepal Himalaya using ISSR markers

Girardinia diversifolia (Link) Friis from Urticaceae family is a perennial herb, commonly known as the Himalayan giant nettle. It has cultural, medicinal, and economic values among the indigenous peoples and local communities living in the mountains of Nepal and India. Prior knowledge of genetic diversity in plant species may contribute to conservation and sustainable utilization of important genotype. The aim of this study is to assess the genetic diversity within and among different populations of the 45 accessions of G. diversifolia collected from Far-western, Central, and Eastern regions of Nepal. The amplification of genomic deoxyribonucleic acid (DNA) with ten inter-simple sequence repeat (ISSR) primers yielded 131 clear DNA bands, of which 98.09% were found to be polymorphic. The mean effective number of alleles (ne), Nei's gene diversity (h) and Shannon's information index (I) were 1.598, 0.349, and 0.523, respectively. The total genetic diversity Ht (0.350 ± 0.04), low intrapopulation genetic diversity Hs (0.141 ± 0.03) and low estimated gene flow Nm (0.355 ± 0.11) reflected high genetic differentiation among population Gst (0.594 ± 0.08). The analysis of molecular variance among and within five populations of G. diversifolia showed that the value of genetic variation among the population was 60% whereas the value of genetic variation within the population was 40%. The results show that the ISSR markers are informative for the study of genetic diversity, which may help in the conservation and sustainable utilization of G. diversifolia and allied taxa.

Polymorphism analysis of Valsa mali isolated from Xinjiang Province using ISSR markers

AbstractApple quality and quantity is reduced by valsa canker (caused by Valsa mali Miyabe et Yamada) in Xinjiang, China. To develop treatment options, we need to understand its genetic diversity, which was assessed at the molecular level. Eight primers were selected for ISSR‐PCR analysis of 44 strains of apple valsa canker in Xinjiang. The results showed that eight primers amplified a total of 80 clear and reproducible bands including 80 polymorphic loci; the polymorphic loci rate was 100%. Nei's gene diversity index and Shannon's information index were both higher than 0.2 and 0.4 in different geographical regions, which indicated that the genetic diversity of V. mali in Xinjiang was very abundant. The cluster analysis indicated that there was no significant correlation between the genetic relationships and their geographical originals.

Development of DNA molecular ID card in hog millet germplasm based on high motif SSR

<p id="C3">In order to identify hog millet (<italic>Panicum miliaceum</italic>) germplasm rapidly, to establish a big data management platform, to provide a theoretical basis for germplasm identification and traceability management, 130 germplasms from four ecological cultivation areas were used as materials to construct a molecular ID based on 35 high-motif SSRs (21, 10, and 4 with four-, five-, and six-nucleotide repeats, respectively). The results showed that 30 out of the 35 SSRs could be used as core markers for the construction of molecular ID cards. Ninety allelic variants were detected; effective allelic variants (<italic>Ne</italic>) ranged from 2.3186 to 2.9982 with an average of 2.7607; Shannon diversity index (<italic>I</italic>) ranged from 0.9158 to 1.0873 with an average of 1.0472. The observed heterozygosity (<italic>Ho</italic>) was 0.5000-0.8678 with a mean of 0.7168; the expected observed heterozygosity (<italic>He</italic>) was 0.5710-0.6691 with a mean of 0.6386; the Nei’s gene diversity index (<italic>Nei</italic>) was 0.5687-0.6665 with a mean of 0.6360; the polymorphism information content (PIC) was 0.5151-0.7898, with a mean of 0.6966. All accessions were divided into three groups (Group I, II, and III) according to UPGMA analysis. In terms of Shanxi accessions, landraces and breeding varieties were classified into Group I and III, respectively, and farmers materials were distributed into three groups. Based on PCA analysis, all accessions were classified into four clusters, which were related to their geographical origin. As for the rule that the most germplasms were determined using the least markers, 3 markers were excluded due to their high similarity coefficient with others, namely RYW23, RYW49, and RYW51. Screening the remaining 27 markers, the combinations of 17 SSR (RYW35, RYW40, RYW37, RYW18, RYW30, RYW16, RYW20, RYW19, RYW8, RYW5, RYW3, RYW7, RYW1, RYW14, RYW9, RYW6, and RYW10) could identify all hog millet accessions. The DNA molecular identifications of character strings, bar code, and quick response (QR) codes were constructed via ID analysis 4.0, software online of bar code and QR codes technique (<uri>http://barcode.cnaidc.com/app/html/bcgcode128.php</uri> and <uri>https://cli.im/</uri>).

Elucidating genetic diversity and population structure of Pyricularia oryzae isolates causing wheat blast in Bangladesh.

Wheat blast, caused by Pyricularia oryzae pathotype Triticum, is one of the most notorious diseases of wheat. In this study, a total of twenty-four monoconidial isolates representing four major wheat blast affected districts, namely Chuadanga, Meherpur, Kustia and Jhenaidah of Bangladesh were analyzed. Eight RAPD and four ISSR primers being used for genetic diversity assay produced a total of 94 bands of which 85% were polymorphic. UPGMA dendrogram based on combined dataset (RAPD and ISSR) separated all the isolates into two main clusters having similarity ranged from 64 to 93%. Principal coordinate analysis showed congruent result with cluster analysis. However, clustering of the isolates according to their origin and plant part sampled was not apparent in the dendrogram. The genetic diversity indices unveiled that genetic diversity in P. oryzae populations is low. Average Nei's gene diversity (h) and Shannon's Information Index (I) calculated for isolates from each district were found 0.16 and 0.24, respectively. The population structure analysis of the isolates revealed the presence of two sub-populations with admixture of alleles. Analysis of molecular variance indicated that significantly higher level of variation (96%) in the population was present within districts while a relatively low proportion (4%) of the variation was detected among districts. Knowledge generated in this study will give a pace in the development of appropriate wheat blast management strategies to control this disease in Bangladesh.

Analysis of Genetic Diversity and Relationship of &lt;i&gt;Jacaranda mimosifolias&lt;/i&gt; Based on ISSR Molecular Markers Technique

The genetic diversity and relationship of Jacaranda mimosifolias &nbsp;from 19 provenances including 21 germplasms in China were studied by ISSR molecular markers&nbsp;technique. 53 bands were amplified by using 10 selected primers from all the 33 primers, of which 44 bands were polymorphic, with the polymorphism ratio of 83.02%. Each primer could amplify 5.3 bands in average. The average number of tested alleles (Na) , effective alleles (Ne) , Nei&rsquo;s gene diversity index &nbsp;(H) &nbsp;and Shannon&rsquo;s information index (I) &nbsp;were 1.83, 1.45, 0.27, 0.40, respectively.&nbsp;ISSR molecular marker cluster analysis research shows 21 J. mimosifolias &nbsp;germplasm resources could be divided into two groups, and the genetic diversity is high. Their genetic relationship is not strongly related to geographical origin of cultivation area. In this study, the relatively accurately molecular identification of the germplasm resources of J. mimosifolias &nbsp;was carried out, which will provide a theoretical basis for the breeding of the improved varieties.

Assessment of Genetic Diversity and Population Structure of the Endangered Astragalus exscapus subsp. transsilvanicus through DNA-Based Molecular Markers.

Astragalus exscapus L. subsp. transsilvanicus (Schur) Nyár. (Fabaceae) is a rare plant endemic to the Transylvanian Plateau, represented by 24 identified populations. Limited information on the genetic variation and population structure is available, which obstructs efficient measures for conservation strategy. The present study aimed to analyze the genetic diversity and population structure of eight populations of A. exscapus subsp. transsilvanicus revealed by sequence-related amplified polymorphism (SRAP) markers. A total of 164 bands were amplified, 96.7% of which (159) were polymorphic. Nei’s gene diversity index (He) was estimated to be 0.228 at the population level and 0.272 at the subspecies level. The genetic differentiation among populations (Gst) was 0.165, which indicated a low proportion of total genetic diversity. The analysis of molecular variance (AMOVA) indicated that 17% of the total variation of A. exscapus subsp. transsilvanicus is found among the populations, while 83% was found within the populations. A UPGMA dendrogram, principal coordinate analysis, and the STRUCTURE software grouped the populations into two clusters uncorrelated with the provenience of the 125 individuals, which might be attributed to fragmentation processes, insect pollination, population size, and specific environmental conditions of the habitats.

Genetic diversity of common reed in the southern Baltic Sea region – Is there an influence of disturbance?

European populations of common reed (Phragmites australis) are considered to build a single metapopulation with an extensive gene pool. Here we characterise the pattern of genetic diversity of 24 common reed populations in northeastern Germany and test how a disturbance by water salinity and mowing influences population genetic and morphological parameters. The investigation of in total 720 samples revealed them as uniformly tetraploid. The four haplotypes found and a set of eight SSR loci combined freely corroborating the hypothesis of a single large metapopulation. A MEMGENE plot based on pairwise genetic and geographic distances explained only 3.27% of genetic variation. Most of the genetic diversity was found within populations implying that gene flow over distances exceeding 10 km seems to be effectively mediated via seeds and pollen. Only in two cases, we encountered spread via rhizomes among different populations. Populations influenced by brackish water salinity show consistently higher values for Nei's unbiased gene diversity index, which we explain by higher disturbance (water salinity, water currents, stronger winds) creating more room for seedling establishment, and/or lower extension of clones. A structural equation model revealed both mowing and water salinity, but not genetic parameters, to have a negative effect on stem width, and put an effect on haplotype composition. Our results point towards a very effective gene flow in this species, a high degree of plasticity, and the importance of disturbance for the accumulation of genetic diversity, perhaps via seedling recruitment. Data Availability StatementSequence data that support the findings of this research have been deposited in GenBank with the accession code OK666430. Raw data for all samples, used in this study, and the quality plots of assignment loci as isoloci, have been deposited in Figshare [DOI: 10.6084/m9.figshare.16438668; 10.6084/m9.figshare.16438812].

DNA barcode reference library construction and genetic diversity and structure analysis of Amomum villosum Lour. (Zingiberaceae) populations in Guangdong Province.

BackgroundAmomum villosum Lour. is the plant that produces the famous traditional Chinese medicine Amomi Fructus. Frequent habitat destruction seriously threatens A. villosum germplasm resources. Genetic diversity is very important to the optimization of germplasm resources and population protection, but the range of inherited traits within A. villosum is unclear. In this study, we analyzed the genetic diversity and genetic structures of A. villosum populations in Guangdong and constructed a local reference DNA barcode library as a resource for conservation efforts.MethodsDNA barcoding and Inter-Simple Sequence Repeat (ISSR) markers were used to investigate the population genetics of A. villosum. Five universal DNA barcodes were amplified and used in the construction of a DNA barcode reference library. Parameters including percentage of polymorphic sites (PPB), number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity index (H), and Shannon’s polymorphism information index (I) were calculated for the assessment of genetic diversity. Genetic structure was revealed by measuring Nei’s gene differentiation coefficient (Gst), total population genetic diversity (Ht), intra-group genetic diversity (Hs), and gene flow (Nm). Analysis of molecular variance (AMOVA), Mantel tests, unweighted pair-group method with arithmetic mean (UPGMA) dendrogram, and principal co-ordinates (PCoA) analysis were used to elucidate the genetic differentiation and relationship among populations.ResultsA total of 531 sequences were obtained from the five DNA barcodes with no variable sites from any of the barcode sequences. A total of 66 ISSR bands were generated from A. villosum populations using the selected six ISSR primers; 56 bands, 84.85% for all the seven A. villosum populations were polymorphic. The A. villosum populations showed high genetic diversity (H = 0.3281, I = 0.4895), whereas the gene flow was weak (Nm = 0.6143). Gst (0.4487) and AMOVA analysis indicated that there is obvious genetic differentiation amongA. villosum populations and more genetic variations existed within each population. The genetic relationship of each population was relatively close as the genetic distances were between 0.0844 and 0.3347.

Genetic diversity of mangrove tree species Avicennia marina in eco-geographic regions of Kerala coast, Southern India

The genetic assembly of Avicennia marina (Forsk.) Vierh, Avicenniaceae within and between the three natural mangrove forests of Kerala coast belonging to the districts of Kochi, Kozhikode and Kannur was investigated using Inter Simple Sequence Repeat (ISSR) markers to provide coherent scientific conservation practices. The ten selective ISSR primer combinations of 60 genotypes of Avicennia marina ensured a total of 171 bands of which 84.5% were polymorphic. Gene diversity index H varied from 0.142 Kochi to 0.195 Kozhikode. The mean gene diversity H S was 0.169 and the total gene diversity H T was 0.262 which showed a moderate level of genetic diversity in the studied population. The mangrove Avicennia marina populations showed large genetic difference G ST = 0.3849, indicating that 38% of the total genetic diversity was among the populations and the rest 62% resides within the population. The gene flow estimates Nm = 0.79 shown that natural mangroves of Kerala are in the course of differentiation due to genetic drift. We investigated the genetic distinctiveness of taxonomically confusing species, Avicennia marina and Avicennia officinalis , and resulted in clear demarcation between the two. There is a significant correlation between dendrogram and PCoA designated that extensive distant spreading of seeds between populations of Avicennia marina is comparatively low. The genetic study contributed relatively high diversity and strong differentiation across the three eco-geographic locations. The best remedy to preserve coastal mangrove species like Avicennia marina is to plant the identical species in its respective habitat. Launch, on-site protection zones to safeguard the species and to decrease the impact of human activities would allow its habitats to increase in size through natural regeneration.

Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

Assessment of genetic diversity and wilt disease resistance in hot pepper (Capsicum annuum) germplasm from Ethiopia

Abstract Hot pepper (Capsicum annuum L.) is an economically important crop in Ethiopia. Wide variability in hot pepper germplasm in Ethiopia is expected due to the presence of diverse environmental conditions and variation in farming systems. The present study was carried out to evaluate the resistance of 75 hot pepper accessions to wilt disease and assess their genetic diversity using SSR markers. Out of 75 accessions tested, the present study identified 23 accessions that showed resistance (R) with the value of 1-10% disease incidence. The genetic diversity assessment using 13 polymorphic SSR markers allowed the detection of 111 clear and scorable bands. The number of alleles per locus ranged from 5 to 13, with an average of 8.54. The PIC value ranged from 0.27 to 0.87 with an average of 0.59. The gene diversity indices were highly variable across SSR loci and ranged from 0.29 to 0.88 with mean genetic diversity of 0.62. Observed heterozygosity was also highly variable between loci (0.01-0.45) indicating that the accessions were not fixed to homozygosity. Furthermore, genetic diversity parameters were estimated among populations by grouping accessions based on their origin. Within populations, the PIC value ranged from 0.31 to 0.77. The genetic distances among the eight populations ranged from 0.15 to 0.48. The observed highest genetic diversity (0.80) in the Amhara region (Gojam) may indicate this area as the primary site for designing in situ conservation for this crop in Ethiopia. The research findings provide baseline information on disease resistance germplasm sources to be used for the breeding program, as well as the status of genetic diversity of the accessions for efficient conservation and proper utilization of the existing genetic resources in the country.

Genetic diversity and population structure of Euscaphis japonica, a monotypic species.

BackgroundUnderstanding plant genetic diversity is important for effective conservation and utilization of genetic resources. Euscaphis japonica (Thunb.) Dippel, is a monotypic species with high phenotypic diversity, narrow distribution, and small population size. In this study, we estimated the genetic diversity and population structure of E. japonica using nine natural populations and inter-simple sequence repeat (ISSR) markers. Our results could provide a theoretical reference for future conservation and utilization of E. japonica.ResultsWe obtained a total of 122 DNA bands, of which 121 (99.18%) were polymorphic. The average number of effective alleles (Ne = 1.4975), Nei’s gene diversity index (H = 0.3016), and Shannon’s information index (I = 0.4630) revealed that E. japonica possessed a high level of genetic diversity. We observed that E. japonica consisted of both deciduous and evergreen populations. UPGMA tree showed that the evergreen and deciduous E. japonica form a sister group. There is little genetic differentiation among geographic populations based on STRUCTURE analysis. The Dice’s similarity coefficient between the deciduous and evergreen populations was low, and the Fst value was high, indicating that these two types of groups have high degree of differentiation.ConclusionRich genetic diversity has been found in E. japonica, deciduous E. japonica and evergreen E. japonica populations, and genetic variation mainly exists within the population. The low-frequency gene exchange between deciduous and evergreen populations may be the result of the differentiation of deciduous and evergreen populations. We suggest that in-situ protection, seed collection, and vegetative propagation could be the methods for maintenance and conservation of E. japonica populations.

Genome-Wide Assessment of Population Structure and Genetic Diversity of the Global Finger Millet Germplasm Panel Conserved at the ICRISAT Genebank.

Finger millet [Eleusine coracana (L.) Gaertn.] is an important climate-resilient nutrient-dense crop grown as a staple food grain in Asia and Africa. Utilizing the full potential of the crop mainly depends on an in-depth exploration of the vast diversity in its germplasm. In this study, the global finger millet germplasm diversity panel of 314 accessions was genotyped, using the DArTseq approach to assess genetic diversity and population structure. We obtained 33,884 high-quality single nucleotide polymorphism (SNP) markers on 306 accessions after filtering. Finger millet germplasm showed considerable genetic diversity, and the mean polymorphic information content, gene diversity, and Shannon Index were 0.110, 0.114, and 0.194, respectively. The average genetic distance of the entire set was 0.301 (range 0.040 – 0.450). The accessions of the race elongata (0.326) showed the highest average genetic distance, and the least was in the race plana (0.275); and higher genetic divergence was observed between elongata and vulgaris (0.320), while the least was between compacta and plana (0.281). An average, landrace accessions had higher gene diversity (0.144) and genetic distance (0.299) than the breeding lines (0.117 and 0.267, respectively). A similar average gene diversity was observed in the accessions of Asia (0.132) and Africa (0.129), but Asia had slightly higher genetic distance (0.286) than African accessions (0.276), and the distance between these two regions was 0.327. This was also confirmed by a model-based STRUCTURE analysis, genetic distance-based clustering, and principal coordinate analysis, which revealed two major populations representing Asia and Africa. Analysis of molecular variance suggests that the significant population differentiation was mainly due to within individuals between regions or between populations while races had a negligible impact on population structure. Finger millet diversity is structured based on a geographical region of origin, while the racial structure made negligible contribution to population structure. The information generated from this study can provide greater insights into the population structure and genetic diversity within and among regions and races, and an understanding of genomic-assisted finger millet improvement.