Genetic Diversity Values Research Articles

Genetic Diversity and Food Value of Black Soybean (Glycine max (L.) Merr.) in Uttarakhand Hills, North-Western India

Genetic Diversity and Food Value of Black Soybean (Glycine max (L.) Merr.) in Uttarakhand Hills, North-Western India

Uncovering inbreeding, small populations, and strong genetic isolation in an Australian threatened frog, Litoria littlejohni

AbstractThe status of many amphibian populations remains unclear due to undetected declines driven by disease and difficulties in obtaining accurate population estimates. Here, we used genome complexity reduction-based sequencing technology to study the poorly understood Littlejohn’s treefrog, Litoria littlejohni across its fragmented distribution in eastern Australia. We detected five identifiable genetic clusters, with moderate to strong genetic isolation. At a regional scale, population isolation was likely driven by population crashes, resulting in small populations impacted by founder effects. Moderate genetic isolation was detected among populations on the Woronora Plateau despite short distances between population clusters. Evidence of recent declines was apparent in three populations that had very small effective population size, reduced genetic diversity and high inbreeding values. The rates of inbreeding detected in these populations combined with their small size leave these populations at elevated risk of extinction. The Cordeaux Cluster was identified as the most robust population as it was the largest and most genetically diverse. This study exemplifies the value of employing genetic methods to study rare, cryptic species. Despite low recapture rates using traditional capture-recapture demographic methods, we were able to derive population estimates, describe patterns of gene flow, and demonstrate the need for urgent conservation management.

The role of niche breadth in oak phylogeography: Quercus glaucoides as a study case

AbstractAimThe extent of genetic diversity and its distribution among populations have been associated with species attributes such as mating system, dispersal ability and geographic range size. Another attribute that could contribute to intraspecific phylogeographic patterns is niche breadth, but this has rarely been tested. Here, we ask whether a Mexican oak with a comparatively narrow climatic niche breadth has distinct genetic diversity patterns compared to other codistributed oaks with a broader climatic niche.LocationMexico.TaxonQuercus glaucoides M. Martens & Galeotti (Fagaceae).MethodsDescriptors of genetic diversity and structure were calculated for 21 Q. glaucoides populations using chloroplast DNA (cpDNA) and nuclear microsatellites (nSSRs). Historical demographic dynamics were inferred with approximate Bayesian computation (ABC) and past potential distribution models. To test for an association between niche breadth and phylogeographic patterns, we used genetic diversity and differentiation values of Q. glaucoides plus those previously published for 10 other Mexican oak taxa. Niche breadth was estimated for all taxa and linear regressions were performed.ResultsGenetic diversity calculated from nSSRs (HO = 0.539; HE = 0.714) was among the lowest and cpDNA differentiation (NST = 0.88) was the highest so far obtained for comparable Mexican oaks. Moderate changes in demographic size and distribution shifts throughout the last glacial cycle were inferred, explaining some of the observed genetic patterns. A positive correlation of HO and a negative correlation of NST with niche breadth were detected across taxa.Main ConclusionsDistinct phylogeographic patterns in Q. glaucoides could be explained because a narrower niche may cause lower historical effective population sizes and more fragmented distributions in comparison to species with a wider niche breadth, even with similar range sizes. Our results indicate that niche breadth would be an interesting ecological attribute to be included in future comparative phylogeographic studies.

Assessment of genetic diversity based on agro-morphological traits and ISSR molecular markers in einkorn wheat (Triticum monococcum ssp. monococcum) landrace populations from Turkey

The aim of this study is to investigate genetic diversity in 48 einkorn (Triticum monococcum L. ssp. monococcum) landraces grown in agricultural areas of Bolu and Kastamonu. Therefore, variation in seven agro-morphological traits was investigated. Agro-morphological traits such as leaf weight (mg), coleoptile length (cm), root number (n), root length (cm), fresh root weight (mg), and dry root weight (mg) were examined by the coefficient of variation, ANOVA, and principal components analysis. The highest coefficient of variation (%) was observed in fresh root weight (FRW = 52.09%), while the lowest was in leaf weight (LW = 8.9%). Principal Component Analysis (PCA) was calculated as 76.93% variation in two main components. For molecular characterization, data obtained with iSSR primers were analyzed with the population genetics analysis program PopGene (ver. 1.32). According to PopGene results, the mean number of alleles, the mean number of effective alleles, and average genetic diversity values were calculated as na = 2, nea = 1.33, and h = 0.13, respectively. Among the agro-morphological traits, germination power, root number, and coleoptile length appeared to be reliable traits. The results show that the use of morphological characters alone for genetic diversity in populations is not sufficient to determine the difference between populations and their genetic structure.

PENDUGAAN KERAGAMAN GENETIK DAN HERITABILITAS MUTAN PADI HITAM (Oryza sativa L.) GENERASI M2 HASIL IRADIASI SINAR GAMMA

The low productivity and long harvesting period of local black rice causes this plant to be rarely cultivated by farmers in Indonesia. One way to increase the genetic diversity of black rice is by using gamma ray irradiation. This study aims to determine the genetic diversity and heritability value of M2 generation black rice resulting from gamma-ray irradiation. The research was conducted in February - June 2021 at the Screenhouse Universitas Perjuangan Tasikmalaya. The genetic material used was black rice M2 generation resulting from gamma ray irradiation with doses 200 gy and PH5 as a control. The research was conducted in 2 experimental stages. The first experiment was in the nursery where M2 seeds were planted with 1000 seeds and 200 seeds for the control. In the second study, the M2 generation black rice mutant was planted with 250 seedlings without replication and the control 10 plants were repeated three times. The results showed that there was a chlorophyll mutation in the M2 generation lines which produced color variations including albino 0.5%, xantha 42%, viridis 5%, tigrina 0.5%, normal 52% at 21 HSS. The survival ability of the black rice mutant was smaller than that of the control. The heritability values in the broad sense of the high category and high genetic diversity were found in the number of productive tillers, the number of total grain, and the number of empty grain. M2 generation black rice irradiated with 200 gy gamma rays was able to provide a response of longer flowering time, narrower flag leaves, lower weight per plant, less filled grain, and increased number of empty grain compared to control (PH5).

Molecular assessment of the taxonomic status of pine vole species Microtus subterraneus and Microtus majori in southeastern Europe and Turkey

Intra– and inter–specific phylogenetic relationships and the taxonomic status of pine vole populations have been controversial for years, and cryptic species are thought to exist, especially concering the species' distribution area. To clarify the taxonomic status of Turkish populations we analysed mitochondrial (cytochrome–b and cytochrome oxidase–I) and nuclear (interphotoreceptor retinoid binding protein) gene markers, adding GenBank data from Europe and Caucasia. Considering the data obtained based on mean genetic distance, genetic diversity and fixation index values, Bayesian trees and Median–joining networks, we found that M. subterraneus and M. majori are valid species which have diverged since 1.28 Mya. Findings also suggested that although Anatolian, Thracian (Turkish Thrace and Greece) and European populations of M. subterraneus and Anatolian and Caucasian populations of M. majori have been in the process of divergency since 0.528–0.337 Mya correspond to the Pleistocene glacial periods, these intrapopulations do not appear to be different species.Besides, considering the high intraspecific variation in M. subterraneus, it remains likely that new species could be identified in future studies.

Molecular and morphological analyses disclose the existence of three species of Dolichopoda (Orthoptera: Rhaphidophoridae) in the Calabria region (Italy)

ABSTRACT For a long time, Dolichopoda palpata was the only species of this genus thought to live in the cave habitats of the Calabrian region. The results of our study, based on morphological and molecular data, highlight the existence of three species in the Calabria region. In particular, our data demonstrate the occurrence of two well-separated species, one in the northern Tyrrhenian area and one in the Calabrian Ionian area, attesting to the validity of D. calabra Galvagni 1968, and the discovery of a new species, D. apollinea sp. nov. Both species appear to be geographically very limited. Dolichopoda calabra occurs in the mountain region between Scalone Pass in the north and the Savuto Valley in the south (a district called ‘Catena Costiera’), whereas D. apollinea sp. nov. appears to be distributed on the eastern slope of Pollino Massif. On the other hand, D. palpata shows a vast distribution, occurring in caves from La Sila in the north to the Aspromonte Massif in the extreme south of Calabria. About 1/3 of the Italian Dolichopoda species are present in this relatively small geographical area, supporting the importance of Calabria as a geographical region characterised by a high level of biodiversity. It shows the maximum values of genetic diversity and species richness in comparison with the rest of the Italian peninsula. This fact could be related to the palaeogeological and palaeoclimatic history of the region, as it was affected by glaciation events and eustatic movements. The combination of these two conditions that occurred during the Pliocene and Pleistocene transformed the Calabria into a vast archipelago of little islands, favouring the isolation of populations and the consequent speciation processes. http://www.zoobank.org/urn:lsid:zoobank.org:pub:AB64936E-EAEF-4730-A517-4F0C11226A94

A genetic warning system for a hierarchically structured wildlife monitoring framework.

Genetic variation is a well-known indicator of population fitness yet is not typically included in monitoring programs for sensitive species. Additionally, most programs monitor populations at one scale, which can lead to potential mismatches with ecological processes critical to species' conservation. Recently developed methods generating hierarchically nested population units (i.e., clusters of varying scales) for greater sage-grouse (Centrocercus urophasianus) have identified population trend declines across spatiotemporal scales to help managers target areas for conservation. The same clusters used as a proxy for spatial scale can alert managers to local units (i.e., neighborhood-scale) with low genetic diversity, further facilitating identification of management targets. We developed a genetic warning system utilizing previously developed hierarchical population units to identify management-relevant areas with low genetic diversity within the greater sage-grouse range. Within this warning system we characterized conservation concern thresholds based on values of genetic diversity and developed a statistical model for microsatellite data to robustly estimate these values for hierarchically nested populations. We found that 41 of 224 neighborhood-scale clusters had low genetic diversity, 23 of which were coupled with documented local population trend decline. We also found evidence of cross-scale low genetic diversity in the small and isolated Washington population, unlikely to be reversed through typical local management actions alone. The combination of low genetic diversity and a declining population suggests relatively high conservation concern. Our findings could further facilitate conservation action prioritization in combination with population trend assessments and (or) local information, and act as a base-line of genetic diversity for future comparison. Importantly, the approach we used is broadly applicable across taxa.

Genetic Diversity and Population Structure of Scots Pine (Pinus sylvestris L.) in Middle Siberia

Scot pine (Pinus sylvestris L.) is one the main forest-forming tree species in Russia, and is of great ecological, economic and social value. In order to manage the genetic resources of this important forest tree species efficiently, knowledge of its genetic diversity and structure is needed. Here, we assessed the genetic variation of 17 populations representing different parts of Scots pine range in Russia by using nuclear microsatellite markers (nSSR). Specifically, 14 populations were chosen within the natural distribution range of the species in Middle Siberia and three distant populations were sampled from the European part of Russia, the West Siberia and the Russian Far East. All populations showed high values of genetic diversity (HE = 0.514) and AR = 4.150. However, the easternmost population has shown the lowest level of genetic diversity (HE = 0.433) and allelic richness (AR = 3.505). Five genetic groups could be detected that correspond to: the European part of Russia, the south of Middle Siberia, the northwest of Middle Siberia, West and Middle Siberia, and the Russian Far East. However, the European population was the most genetically distinct one. The variation among Scots pine populations accounted for only 5% of the total variance. The highest level of genetic differentiation was found only between westernmost and easternmost populations (FST = 0.097). Our genetic data may contribute to a better understanding of the pattern of genetic diversity of Scots pine populations in Middle Siberia and help the conservation efforts of these genetic resources.

Genetic diversity and population structure assessment of Western Canadian barley cooperative trials.

Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r2, declined to below the critical r2 = 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.

Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders.

Merino sheep are a breed of choice across the world, popularly kept for their wool and mutton value. They are often reared as a pure breed or used in crossbreeding and are a common component in synthetic breed development. This study evaluated genetic diversity, population structure, and breed divergence in 279 animals of Merino and Merino-based sheep breeds in South Africa using the Illumina Ovine SNP 50K BeadChip. The sheep breeds analysed included the three Merino-derived breeds of Dohne Merino (n = 50); Meatmaster (n = 47); and Afrino (n = 52) and five presumed ancestral populations of Merinos (Merino (n = 46); South African Merino (n = 10); and South African Mutton Merino (n = 8)); and the non-Merino founding breeds of Damara (n = 20); Ronderib Afrikaner (n = 17); and Nguni (n = 29). Highest genetic diversity values were observed in the Dohne Merino (DM), with H o = 0.39 ± 0.01, followed by the Meatmaster and South African Merino (SAM), with H o = 0.37 ± 0.03. The level of inbreeding ranged from 0.0 ± 0.02 (DM) to 0.27 ± 0.05 (Nguni). Analysis of molecular variance (AMOVA) showed high within-population variance (>80%) across all population categories. The first principal component (PC1) separated the Merino, South African Mutton Merino (SAMM), DM, and Afrino (AFR) from the Meatmaster, Damara, Nguni, and Ronderib Afrikaner (RDA). PC2 aligned each Merino-derived breed with its presumed ancestors and separated the SAMM from the Merino and SAM. The iHS analysis yielded selection sweeps across the AFR (12 sweeps), Meatmaster (four sweeps), and DM (29 sweeps). Hair/wool trait genes such as FGF12; metabolic genes of ICA1, NXPH1, and GPR171; and immune response genes of IL22, IL26, IFNAR1, and IL10RB were reported. Other genes include HMGA, which was observed as selection signatures in other populations; WNT5A, important in the development of the skeleton and mammary glands; ANTXR2, associated with adaptation to variation in climatic conditions; and BMP2, which has been reported as strongly selected in both fat-tailed and thin-tailed sheep. The DM vs. SAMM shared all six sweep regions on chromosomes 1, 10, and 11 with AFR vs. SAMM. Genes such as FGF12 on OAR 1:191.3-194.7Mb and MAP2K4 on OAR 11:28.6-31.3Mb were observed. The selection sweep on chromosome 10 region 28.6-30.3Mb harbouring the RXFP2 for polledness was shared between the DM vs. Merino, the Meatmaster vs. Merino, and the Meatmaster vs. Nguni. The DM vs. Merino and the Meatmaster vs. Merino also shared an Rsb-based selection sweep on chromosome 1 region 268.5-269.9Mb associated with the Calpain gene, CAPN7. The study demonstrated some genetic similarities between the Merino and Merino-derived breeds emanating from common founding populations and some divergence driven by breed-specific selection goals. Overall, information regarding the evolution of these composite breeds from their founding population will guide future breed improvement programs and management and conservation efforts.

Genetic polymorphisms and phylogenetic characteristics of Tibeto-Burman-speaking Lahu population from southwest China based on 41 Y-STR loci

Background Male sex-linked Y-chromosome short tandem repeats (Y-STRs) have been widely used in forensic cases and population genetics research. At present, the forensic-related Y-STR data in the Chinese Lahu population are still poorly understood. Aim To enrich the available Y-STR data of this Chinese minority population and investigate its phylogenetic relationships with other reported populations. Subjects and methods The genetic polymorphisms of 41 Y-STR loci were analysed in 299 unrelated healthy Lahu male individuals from Southwest China. Phylogenetic analyses were performed by multidimensional scaling analysis and neighbor-joining phylogenetic tree construction. Results A total of 379 alleles were observed at the 41 Y-STR loci. The allele frequencies ranged from 0.0033 to 0.9666. The genetic diversity values ranged from 0.0653 to 0.9072. A total of 254 different haplotypes of the 41 Y-STR loci were observed in 299 individuals. The values of haplotype diversity, haplotype match probability, and discrimination capacity were 0.9987, 0.0047, and 0.8495, respectively. The phylogenetic analysis indicated that the Tibeto-Burman-speaking Lahu population showed a close genetic relationship with the Yunnan Yi population. Conclusions The haplotype data of the present study can enrich the forensic databases of this Chinese minority population and will be useful for population genetics and forensic DNA application.

Genetic diversity of six populations of Ajamaru rainbowfish (Melanotaenia ajamaruensis) with different breeding ratios

The Ajamaru rainbowfish (Melanotaenia ajamaruensis) is a West Papuan endemic and has been successfully cultured. The study aims to determine the genetic diversity of the Ajamaru rainbowfish ornamental fish populations that breed with differences in the breeding ratio to offspring. Tail fin samples were taken from six populations of Ajamaru rainbowfish consisting of 2 generations for DNA extraction. Three-broodstock populations (1:1, 1:2, and 3:1) spawn at seven months old, and three offspring populations. The method used was Randomly Amplified Polymorphic DNA (RAPD) analysis, primary screening using 20 primers, and four selected primers (OPG 2, OPB 6, OPH 5, and OPZ 9). Data analysis used TFPGA software to generate genetic diversity values in heterozygosity and polymorphism. The results showed the lowest genetic diversity in population 1, with polymorphism (46.99%) and heterozygosity 0.1894. The highest genetic diversity was in population 4, with descendants with polymorphism (78.31%) and heterozygosity of 0.2922. Relationships among 6 Ajamaru rainbowfish populations formed two clades based on their generation. Improving genetic quality in the breeding of Ajamaru rainbowfish can be done through selective breeding with a breeding ratio of 1:1 or the full-sib broodstock for higher genetic diversity values.

Genome-wide data suggest a revision in management of the Caspian Sea trout Salmo caspius.

Salmo caspius Kessler, 1877 is one of the most commercially important species of Salmonidae in the southern basin of the Caspian Sea. The occurrence of its wild populations has undergone sever reduction during the last years. In spite of the yearly restocking activity, still no progress on the recovery of its wild population has been observed. Hence, the present study was done in order to assess the efficiency of the current restocking activity in the southern Caspian basin in term of genetic diversity. DNA extracts of 32 S. caspius from four different groups were screened using 62621 genome-wide single nucleotide polymorphisms (SNP). The overal genetic diversity and Fst values were 0.18 and 0.08, respectively. Considering the observed admixture pattern and the positive values for inbreeding coeficient it seems that S. caspius suffers from its small effective population size. In order to obtain the maximum performance, alonside with expanding the size of brood stocks, rehabilitation of the habitats and spawning rivers of this nationally endangered species is of great importance.

Diversidade genética, produtividade e qualidade de frutos de caqui nos trópicos

Abstract The objective of this work was to determine the genetic diversity, yield, and fruit quality of persimmon genotypes grown in the tropics, in order to select promising genetic materials. DNA extraction was performed on young leaves of 19 persimmon genotypes. For pomological characterization, 15 genotypes were selected. From each genotype, 50 fruit at the physiological maturity stage were harvested in the morning, in order to determine the following parameters: physicochemical characteristics; and the productive variables number of fruit per plant, average fruit fresh mass, average yield, and estimated average yield in two seasons. Twenty SSR markers were tested, out of which 12 were selected to evaluate genetic similarity, which allowed of the identification of distinct groups. The mean genetic diversity value found was 0.41, which is an indicative of low diversity among the analyzed persimmon genotypes. The 'Guiombo', 'Iapar 125', 'Kakimel', 'Mikado RJ', 'Rama Forte Tardio', and 'Taubaté' genotypes show a high yield. The genotypes classified as pollination-constant astringent ('Pomelo', 'Regina', 'Rubi', and 'Taubaté') and those classified as pollination-variant astringent ('Rama Forte', 'Guiombo', and 'Cereja') are potential materials for selection and genetic breeding programs due to their excellent fruit physicochemical characteristics. The investigation through molecular markers is an efficient approach to study the genetic diversity of persimmon genotypes grown in the tropics.

Genetic Diversity and Structure of Natural, Planted and Selected Populations of Tree Bean (Parkia timoriana (DC.) Merr.) in North East India

Planted populations of indigenous fruit trees (IFTs) in the tropics may be the link towards efficient utilization and conservation of its genetic resources, but little is known of the genetic diversity they harbor. Tree bean ( Parkia timoriana ) is an economically important IFT that is cultivated and planted on and off farm in tropical regions of Northeast India. Using 3-microsatellite markers, we compared the genetic variation and structure of five-planted populations and a farmer-selected with three natural populations within northeast India. Pooled planted and selected populations showed marginal reduction in genetic diversity values compared to natural populations. Individually, cultivated populations from Manipur had higher Shannon diversity index (I=1.30 and 1.32) compared to wild populations (I= 1.30, 1.08 and 1.12). The farmer selected population displayed appreciable levels of diversity (Na= 5.33 and I=1.12). Structure analysis revealed high degree of admixture in natural and two planted populations and PCA depicted close congruence with the geographical distribution of populations. The present study reveals that famer driven selection process has not resulted to any major reduction in genetic diversity. There is ample diversity with natural as well as planted populations of the species, which shall be crucial components for trait improvement in tree breeding programs.

Epigenetic and Genetic Variability in Contrasting Latitudinal Fagus sylvatica L. Provenances

The adaptive capacity of a species and its population is determined by both genetic and epigenetic variation, which defines the potential for adaptive evolution and plastic response to environmental changes. In this study, we used Methylation Sensitive Amplified Polymorphism (MSAP) and Amplified Fragment Length Polymorphism (AFLP), similar genome-wide profiling techniques, to analyze the epigenetic and genetic variability in European beech provenances from Germany (DE), Spain (ES) and Sweden (SE), representing the latitudinal distribution of the species. In addition, we evaluated the effect of moderate water stress on cytosine methylation dynamics by comparing two latitudinal contrasting provenances. Our analysis revealed that trees from ES showed lower values of epigenetic and genetic diversity than those from DE and SE. Analyses of molecular variance for MSAPs and AFLPs showed that 16% and 15% of the among population variations were associated with epigenetic and genetic variation, respectively. The study of the effect of water stress on cytosine methylation dynamics in seedlings from ES and SE revealed no significant levels of epigenetic differentiation between well-watered and stressed plants. Only 2% of the epigenetic variation was explained by the watering regime in ES without changes in SE. The results support that DNA methylation may play a role in the local adaptation of Fagus sylvatica to environmental variation.

Development of the maize 5.5K loci panel for genomic prediction through genotyping by target sequencing.

Genotyping platforms are important for genetic research and molecular breeding. In this study, a low-density genotyping platform containing 5.5K SNP markers was successfully developed in maize using genotyping by target sequencing (GBTS) technology with capture-in-solution. Two maize populations (Pop1 and Pop2) were used to validate the GBTS panel for genetic and molecular breeding studies. Pop1 comprised 942 hybrids derived from 250 inbred lines and four testers, and Pop2 contained 540 hybrids which were generated from 123 new-developed inbred lines and eight testers. The genetic analyses showed that the average polymorphic information content and genetic diversity values ranged from 0.27 to 0.38 in both populations using all filtered genotyping data. The mean missing rate was 1.23% across populations. The Structure and UPGMA tree analyses revealed similar genetic divergences (76-89%) in both populations. Genomic prediction analyses showed that the prediction accuracy of reproducing kernel Hilbert space (RKHS) was slightly lower than that of genomic best linear unbiased prediction (GBLUP) and three Bayesian methods for general combining ability of grain yield per plant and three yield-related traits in both populations, whereas RKHS with additive effects showed superior advantages over the other four methods in Pop1. In Pop1, the GBLUP and three Bayesian methods with additive-dominance model improved the prediction accuracies by 4.89-134.52% for the four traits in comparison to the additive model. In Pop2, the inclusion of dominance did not improve the accuracy in most cases. In general, low accuracies (0.33-0.43) were achieved for general combing ability of the four traits in Pop1, whereas moderate-to-high accuracies (0.52-0.65) were observed in Pop2. For hybrid performance prediction, the accuracies were moderate to high (0.51-0.75) for the four traits in both populations using the additive-dominance model. This study suggests a reliable genotyping platform that can be implemented in genomic selection-assisted breeding to accelerate maize new cultivar development and improvement.

Genetic diversity and population structure analyses of South African Bambara groundnut (Vigna subterranea [L]. Verdc.) collections using SNP markers

• Bambara groundnut productivity in South Africa is low (0.62 t/ha) compared to the attainable yield of the crop reaching up to 3 t/ha. • The low productivity is attributable to a lack of improved and high yielding cultivars that are locally bred and adapted in the country. • This paper presents baseline information on Bambara groundnut genetic profile of South African collections for effective breeding and conservation. • The magnitude of the genetic diversity and population structure of Bambara groundnut collections of South Africa using high throughput single nucleotide polymorphisms (SNP) markers are highlighted to guide current and future Bambara groundnut research and development by selection genetically unique genotypes for breeding. Bambara groundnut ( Vigna subterranea [L.] Verdc) is a highly nutritious grain legume with a significant potential to develop various commercial food and feed products. It is a resilient crop able to grow under harsh climates and poor soil conditions. Bambara groundnut productivity in South Africa is low (0.62 t/ha) compared to the attainable yield of the crop reaching up to 3 t/ha. The low productivity is attributable to a lack of improved and high yielding cultivars that are locally bred and adapted in the country. Genetically diverse and locally adapted Bambara groundnut landrace varieties and exotic collections are present in South Africa for strategic breeding to improve yield and yield-related traits and nutritional quality. The objective of this study was to determine the magnitude of the genetic diversity and population structure of Bambara groundnut collections of South Africa using high throughput single nucleotide polymorphisms (SNP) markers. Ninety-three genotypes were assessed using genotyping with 2286 SNP markers and some unique complementary morpho-agronomic traits of the crop. The mean genetic diversity value was 0.32, revealing moderate genetic differences among the assessed genotypes. Cluster and structure analyses grouped the test genotypes into two distinct categories. Further, the analysis of molecular variance partitioned the total genetic variation into among genotypes (90%), within genotypes (8%) and among populations (2%). The results revealed two heterotic groups for hybridization and selection programs. The following unique genotypes were selected: ARC Bamb 37 (with spreading growth type), ARC Bamb 49 (bunch type), ARC Bamb 61 (semi-bunch) and ARC Bamb 83 (spreading) using the SNP markers and desirable agronomic traits. The study provided new insight on Bambara groundnut genetic profiles of South African collections which will assist in conservation strategy and management of the crop for effective breeding.

GENETIC DIVERSITY OF NEPENTHES GRACILIS IN HEATH FOREST IN SOUTH AND CENTRAL PARTS OF KALIMANTAN

Nepenthes gracilis is found in the lowlands in the form of peat swamp forest, heath forests and is widely distributed in Thailand, Sumatra, Peninsular Malaysia, Singapore, Kalimantan, and Sulawesi. The unique characteristics of the plant, potential benefits and threats of declining population of N. gracilis impacted this plant as a conservation priority in the heath forest. Characterization of N. gracilis applied before implementing conservation actions. The conservation approach proceeded by analyzing the genetic diversity of N. gracilis from various types of heath forest. The research object used as genetic material was the leaf part of N. gracilis. The sampling locations of N. gracilis were in the heath forest of Guntung Ujung village, Gambut sub-district, Banjar regency, South Kalimantan (Location 1), heath forest in Tabalong Regency, South Kalimantan (Location 2), heath forest in East Kotawaringin Regency, Central Kalimantan (Location 3), heath forest of the Nyaru Menteng Arboretum, Palangkaraya, Central Kalimantan (Location 4). The tools and materials used for genetic analysis with PCR-RAPD markers are divided into several stages of work: DNA extraction, DNA quality and quantity testing, DNA visualization, and data analysis. The results show that OPP-09 and OPBH-20 were the primers with the highest amplification success for N. gracilis plants from the heath forest and the amplification values are 52.5% and 51.25%. The percentages of polymorphism bands were 97.62% and 95.24%, respectively. Disturbed heath forest with open canopy cover showed an indication of low genetic diversity shown by N. gracilis originating from location 1 and location 4 of heath forests and the highest genetic diversity value, and the highest percentage of locus polymorphism value (79%) was shown by N. gracilis location 3 with relatively undisturbed forest cover and classified as old growth. It is crucial to preserve the heath forest cover from damage to maintain high genetic diversity of N. gracilis. Genetic relationships between populations can be a barometer in conservation programs for N. gracilis.