Single Nucleotide Polymorphism Markers Research Articles

Extent and patterns of morphological and molecular genetic diversity and population structure of Nigerian Taro cultivars.

Genetic diversity is crucial for conservation efforts as well as breeding programs targeted at the development of improved varieties. Taro, a climate-resilient crop, plays a vital role in the nutritional and economic livelihoods of many households in Nigeria, but its yield is very low due to inadequate genetic improvement efforts. A diversity assessment of Nigerian taro is therefore required to create a premise for its improvement in yield, quality and disease tolerance. In this study, the genetic diversity and population structure of 490 taro cultivars comprising two main gene pools: Dasheen (215) and Eddoe (275), collected from farmers and marketers across seven states in Nigeria was assessed using 3047 Diversity Array Technology single nucleotide polymorphism (DArT-SNP) markers. A subset of 114 taro cultivars, comprising 30 Dasheens and 84 Eddoes were further phenotyped using 24 agro-morphological descriptors. Both phenotypic and molecular characterization revealed higher genetic diversity among the Eddoes than Dasheens. Estimates of gene flow (Nm = 0.353) revealed intermixing of cultivars among the States of collection, with the highest gene flow occurring between cultivars from Anambra and Ondo states and the lowest between Anambra and Kwara states. Population structure and Ward's minimum variance hierarchical cluster based on DArT-SNPs identified four groups, one comprising Dasheen and three comprising Eddoe cultivars. Hierarchical clustering based on phenotypic traits delineated three clusters. Variation between gene pools (49%) was higher than within gene pools (32%). Variation among States of collection was high (41%), while variation among individuals within gene pools (18%) and States of collection (19%) was relatively low. Correlation between phenotypic and genotypic diversity assessments was low (r = 0.01), indicating that both approaches were necessary for assessing genetic diversity in taro. However, genotypic assessment provided better information about genetic diversity of the taro cultivars. This is the first study that represented germplasm collection across the major taro growing regions of Nigeria. The findings from this study based on agro-morphological characterization and DArT-SNP genotyping are critical for genetic characterization, conservation and breeding of taro in Nigeria, mainly initiating hybridization between the two genepools after careful assessment of ploidy levels of the accessions collected in this study. This will facilitate in developing improved taro varieties with desirable traits, such as higher yield, better disease resistance, and improved nutritional quality.

Genetic Diversity and Population Structure Analysis in Guar

Guar [Cyamopsis tetragonoloba (L.) Taub] was domesticated in India and Pakistan. It is mainly self-pollinated, bushy, and deeply tap-rooted. Guar seed endosperm contains galactomannan gum, which is used in many food products, pharmaceuticals, cosmetics, explosives, meat products, and pet foods, and in the textile industry, yet its genetic diversity remains largely underexplored. Using 7000 high-quality single nucleotide polymorphism (SNP) markers acquired from genotyping by sequencing (GBS), we analyzed the genetic diversity and population structure in 225 guar accessions from India, Pakistan, and the United States. Structure Harvester revealed that K = 3 had the best delta K, whereas K = 2 had the second-highest delta K. Three major genetic clusters (K = 3) were identified using population structure analysis, utilizing an admixture model: 156 accessions (69.3%) were classified into Q1, 23 accessions (10.2%) in Q2, and 16 accessions (7.1%) in Q3. The remaining 30 accessions (13.3%) were included in the admixture. In all three of the subpopulations at K = 3, most of the guar accessions came from India. We also found that these clusters mostly correlated with geographic origins. Results showed that the Q2 and Q3 subpopulations included only guar accessions from India. Genetic resources from Q2 and Q3 may represent an untapped reservoir for introducing beneficial variety into the U.S. breeding populations. This genetic diversity and population structure analysis of the guar gene pool will be of interest to conduct allele mining and donor parent selection for the development of new and better guar germplasm for desired traits.

Genome‐wide association study for powdery mildew resistance in CIMMYT's spring wheat germplasm

AbstractPowdery mildew (PM), caused by Blumeria graminis f. sp. tritici (Bgt), is a foliar disease of wheat (Triticum aestivum) that adversely affects both grain yield and quality. Growing resistant cultivars offers an effective and environmentally sustainable solution to managing PM. However, relying on the same genetic source of resistance can lead to resistance breakdown as Bgt isolates rapidly evolve. To mitigate this, identifying novel resistance sources is crucial. In this study, 225 diverse wheat genotypes were evaluated at adult plant stage in disease nurseries over the three crop seasons (2018/2019, 2019/2020 and 2020/2021). Using disease and genotyping data from 12,160 single‐nucleotide polymorphism (SNP) markers, a genome‐wide association study (GWAS) was conducted to identify novel resistance loci. We identified 22 marker loci significantly (at p < 0.005) associated with PM resistance, distributed across 14 wheat chromosomes (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 5D, 6A, 7A and 7B). Of these, seven loci overlap with previously identified regions, while the remaining 15 loci represent novel regions reported for the first time in this study. The identified SNP markers have significant potential for wheat breeding programmes, as they can accelerate the development of PM‐resistant cultivars through marker‐assisted selection.

From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis?

AbstractPremiseLeveraging DNA markers, particularly single‐nucleotide polymorphisms (SNPs), in parentage analysis, sib‐ship reconstruction, and genomic relatedness analysis can enhance plant breeding efficiency. However, the limited availability of genomic information, confined to the most commonly used species, hinders the broader application of SNPs in species of lower economic interest (e.g., most tree species). We explored the possibility of using universal target capture probes, namely Angiosperms353, to identify SNPs and assess their effectiveness in genomic relatedness analysis.MethodsWe tested the approach in 11 tree species, six of which had a half‐sib family structure. Variants were called within species, and genomic relatedness analysis was conducted in species with two or more families. Scalability via amplicon sequencing was tested by designing primers and testing them in silico.ResultsAdequate SNPs for relatedness analysis were identified in all species. Relatedness values from Angiosperms353‐based SNPs highly correlated with those from thousands of genome‐wide DArTseq SNPs in Cordia africana, one of the species with a family structure. The in silico performance of designed primers demonstrated the potential for scaling up via amplicon sequencing.DiscussionUtilizing universal target capture probes for SNP identification can help overcome the limitations of genomic information availability, thereby enhancing the application of genomic markers in breeding plant species with lower economic interest.

Genetic Diversity and Genome-Wide Association Study of Pleurotus pulmonarius Germplasm

Pleurotus pulmonarius is prized by consumers for its distinct flavor, strong aroma, and dense, crispy texture. Although China has extensive germplasm resources for P. pulmonarius, only a limited number of cultivars are commercially available. A comprehensive evaluation and detailed analysis of P. pulmonarius germplasm, alongside the exploration of superior germplasm resources, are essential for developing new varieties. In this study, we resequenced the genomes of 47 P. pulmonarius strains collected nationwide, identifying a total of 4,430,948 single nucleotide polymorphism (SNP) loci. After filtering based on minor allele frequency and data integrity, 181,731 high-quality SNP markers were retained. Phylogenetic analysis grouped the strains into six clusters, with strains from similar geographical regions clustering together. Most CBS strains formed a single cluster; cultivated varieties exhibited higher genetic similarity, whereas wild strains displayed greater diversity. Principal component analysis (PCA) and population structure analyses, using the same SNP markers, corroborated the phylogenetic findings. DNA fingerprinting, derived from 369 core SNPs, further underscored the genetic diversity among strains. Significant morphological variation was observed, with strains in groups ZP, CBS, and WHLJ exhibiting notably higher yields and cap widths compared to other groups. Correlation analysis revealed associations among various phenotypes, while genome-wide association study (GWAS) identified multiple SNP markers within candidate genes linked to agronomic traits, most of which were controlled by multiple genes. This research offers a molecular-level characterization and evaluation of P. pulmonarius germplasm resources, providing a scientific basis for enriching available germplasm and advancing breeding materials.

Virulence and Diversity of Puccinia striiformis f. sp. tritici Populations in Northwestern and Southwestern Oversummering Regions of China.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is the most devastating fungal disease affecting wheat in China, particularly in the northwestern (Qinghai, Gansu, and Ningxia) and southwestern (Sichuan, Yunnan, and Guizhou) oversummering regions. In this study, 302 isolates collected from these six provinces were analyzed using virulence testing and single-nucleotide polymorphism (SNP) markers. Virulence testing on 19 Chinese differentials identified 38 previously reported and 49 novel races. CYR34 was the most prevalent race in both the northwestern and southwestern oversummering regions, with frequencies of 24.00% and 21.05%, respectively. In the northwestern oversummering region, the prevalence of CYR32 (10.70%) and G22-14 (10.67%) was nearly identical, whereas in the southwestern oversummering region, CYR32 (13.20%) and G22-14 (9.87%) exhibited significant differences. Additionally, 112 races were identified using 18 Yr single-gene differentials, although none of the isolates showed virulence to either Yr5 or Yr15. The virulence diversity of Pst populations was greater in the southwestern than in the northwestern oversummering region, as indicated by the differential sets. Further molecular analysis with 20 pairs of polymorphic KASP-SNP markers confirmed that the southwestern Pst population exhibited higher genetic diversity than the northwestern population. Both virulence phenotypes and genotype data demonstrated that the Pst population was more diverse in the southwestern oversummering region, despite presence of the exchange of Pst sources between regions. In addition, mutant isolates indicating resistance to tiadimefon fungicide were detected in both regions. This study provides a systematic comparison of Pst populations in the northwestern and southwestern oversummering regions based on virulence phenotyping and SNP marker genotyping, and the findings are crucial for the integrated management of wheat stripe rust in these regions and across the country.

DurdusTools—An Online Genetic Distance Calculation Tool for Efficient Variety Testing in Durum Wheat (Triticum turgidum L. subsp. durum (Desf.) Husn.)

The management of variety collections can be supported by integrating molecular data into Distinctness, Uniformity, and Stability (DUS) testing. DurdusTools is a genetic distance (GD) calculation tool that supports planning field trials in durum wheat. A commercially available single-nucleotide polymorphism (SNP) wheat microarray is used to profile varieties and candidate varieties. Their molecular profiles are stored in a database. SNP markers selected based on quality parameters are used to calculate the pairwise genetic distance (GD) between the varieties. Combining molecular and variety information creates a downloadable, user-friendly Excel-based output. The file shows the pairwise GD of the varieties most similar to the candidate variety of interest and selected variety information. After the first year of field trials, the DUS experts use the phenotypic assessment data together with the GD information to select genotypes to be grown in the field for side-by-side comparisons. The principles of DurdusTools allow for an easy integration of molecular data into DUS testing. Using the tool requires neither specific infrastructure nor molecular expert knowledge and was developed by its users for DUS testing purposes. This makes DurdusTools an easily accessible and user-friendly tool that supports variety selection for DUS field trials through an improved data basis.

Evaluation of population genetics of Moringa oleifera Provenances from Coastal Kenya using Single Nucleotide Polymorphism (SNPs) markers

Population genetics analysis is a prerequisite to understanding how and why genotypes and allele frequencies and change over time between and within populations. Consequently, it offers insight into the process of evolutionary change and makes it possible to map variants linked to traits that differ among populations. In the present study, Single Nucleotide Polymorphisms (SNPs) markers were utilized to study the genetic characterization of 17 provenances from the Coast region of Kenya. 164 genotypes of Moringa oleifera were selected from 17 populations and genome sequencing undertaken utilizing genotyping by sequencing (GBS). Identification of polymorphisms (SNP Calling) in the selected genotypes and population genetic studies were carried out. SNP calling was done by Illumina’s SNP caller algorithm in the CASAVA software. 20,921 SNPs were called with an average call rate of 0.82. Average polymorphsm content (PIC) for the SNPs was 0.24 and reproducibility was 0.98. A phenetic tree was constructed using a neighbor-joining approach using DArT R. For the population genetics analysis, F statistic (Fst) utilising the functions StAMPP package in DArT R was performed whereby Gede and Samburu exhibited the least heterozygosity/correlation with a value of 0.0003 whereas Pwani University and Samburu had the highest correlation of genes at 0.37. Euclidean was used as a measure distance, and the average distance between the populations was 33.024. The molecular variance analysis (AMOVA) described a lower, 2.55%, variation within the population and 2.73% among the populations. The high similarity between the genotypes could be attributed to the Moringa plants in the various provenances having the same ancestry. This study may help identify links between gene allelic forms and phenotypes, allowing the alleles to be connected to desired characteristics such as rapid growth and high yield (functional analysis), because of the high frequency of SNPs and their role as a source of allele variations.

Comprehensive overview of host plant resistance and its progress in wilt resistance in castor bean (Ricinus communis L.)

Castor bean, a non-edible monotypic species known for its unique hydroxy fatty acid, is susceptible to a range of pathogens. Wilt caused by Fusarium oxysporum f. sp. ricini is the most complex and destructive disease. Chemical control of wilt has proven ineffective due to the systemic nature of the disease and the seed and soil borne nature of the pathogen. Physical, chemical, biological, and integrated management methods have shown only limited success in controlling wilt. Host plant resistance, however, stands out as the most promising strategy, offering a viable pathway for the genetic improvement of castor beans for wilt resistance. Screening techniques are well established, and several resistant donors have already been identified. While significant progress has been made in understanding the inheritance of wilt resistance, a complete understanding of its genetic mechanisms still requires further research. Single Nucleotide Polymorphism (SNP) markers and genomic regions linked to wilt resistance have been successfully identified. Reniform nematode (Rotylenchulus reniformis) has been identified as a predisposing factor for wilt, and genomic regions linked to nematode resistance have also been identified. However, Marker-assisted selection has not yet been utilized to develop wilt-resistant castor varieties. Further research is required to explore the pathogen diversity, host-pathogen interactions, and mechanisms underlying wilt resistance including the metabolites responsible for preventing the emergence of new pathogenic races and ensuring long-term protection against wilt.

Characterization of a new barley greenbug resistance gene Rsg4 in the Chinese landrace CI 2458.

Barley (Hordeum vulgare) is a climate-resilient crop widely cultivated in both highly productive and suboptimal agricultural systems, and its ability to adapt to multiple biotic and abiotic stresses has contributed significantly to food security. Greenbug is a destructive insect pest for global barley production, and new greenbug resistance genes are needed to overcome the challenges posed by diverse greenbug biotypes in fields. CI 2458 is a Chinese landrace exhibiting a unique resistance profile to a set of 14 greenbug biotypes, which suggests the presence of a new greenbug resistance gene in CI 2458. A recombinant inbred line population from the cross Weskan × CI 2458 was developed, evaluated for responses to greenbug biotype F, and genotyped using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing. Linkage analysis revealed a single gene, designated Rsg4, conditioning greenbug resistance in CI 2458. Rsg4 was delimited to a 1.14 Mb interval between SNP markers S3H_666512114 and S3H_667651446 in the terminal region of chromosome arm 3HL, with genetic distances of 1.2 cM proximal to S3H_667651446 and 1.1 cM distal to S3H_666512114. Allelism tests confirmed that Rsg4 is a new greenbug resistance gene independent of Rsg1 and Rsg3, which reside in the same chromosome arm. Rsg4 differs from Rsg1 alleles and Rsg3 in its resistance to greenbug biotype TX1, one of the most widely virulent biotypes. The introgression of Rsg4 into locally adapted barley cultivars is of agronomic importance, and kompetitive allele-specific polymerase chain reaction (KASP) markers flanking Rsg4, KASP-Rsg336-1 and KASP-Rsg336-2, enable rapid pyramiding of Rsg4 with other resistance genes to develop durable greenbug-resistant cultivars.

Construction of a high-density genetic map using specific-locus amplified fragment sequencing and quantitative trait loci analysis for tillering related traits in Psathyrostachys juncea perennial grass.

Russian wildrye (RWR, Psathyrostachys juncea) is an outcrossing perennial grass that plays a crucial role in foragaing and rangeland restoration due to its tiller producing capabilities, nevertheless, a genetic map has yet to be constructed due to a shortage of efficient and reliable molecular markers. This also limits the identification, localization, and cloning of economically important traits related to tiller density during breeding. Therefore, this study aimed to create a F1 mapping population with 147 individual lines and their two parents, which were selected based on varying tiller densities. We then used this mapping population to conduct specific-locus amplified fragment sequencing (SLAF-seq) to generate SLAF markers and discover single nucleotide polymorphisms (SNPs). Initially, we generated a total of 1,438.38 million pair-end reads with an average sequencing depth of 84.92 in the maternal line, 79.34 in the parental line, and 27.05 in each F1 individual line, respectively. Following the filtering of low-depth SLAF tags, a total of 558,344 high-quality SLAFs were identified. A total of 1,519,903 SNP markers were obtained, and 62,424 polymorphic SNPs were discovered. From these, 4,644 polymorphic SNPs were selected and used for the construction of a genetic map encompassing seven linkage groups. The genetic map spanned 1,416.60 cM with an average distance of 0.31 cM between adjacent markers. Comparative analysis between the seven linkage groups of RWR SLAF tag and the whole-genome sequences in barley (Hordeum vulgare L.) revealed homology values ranging from 17.5% to 34.6%, and the collinearity between the RWR linkage groups and the barley homology groups ranged from 0.6787 to 0.9234, with an average value of 0.8158. Additionally, 143 significant quantitative trait locus (QTLs) with Logarithm of Odds (LOD) value greater than 2.5 for five tiller related traits were detected using three consecutive years of phenotypic trait data from the F1 population, further verifying the map's reliability.

Assessment of genetic diversity and heterotic alignment of CIMMYT and IITA maize inbred lines adapted to sub‐Saharan Africa

AbstractDespite the breeding efforts by many institutions, maize (Zea mays L.) productivity in sub‐Saharan Africa is still low. A limited number of productive maize hybrids have been developed partly due to a lack of knowledge on the diversity and heterotic relationship of the germplasm, especially in public breeding programs. Understanding the extent of diversity, structure, and heterotic grouping of available maize germplasm originating from different breeding programs is important to enhance long‐term genetic gain in hybrid maize breeding programs by optimizing heterotic pools using modern breeding tools. Information about the genetic structure of the available germplasm could help breeders design effective breeding strategies to improve yield. This study was conducted to determine the genetic diversity, population structure, and heterotic alignment among 187 elite maize inbred lines from the IITA (International Institute of Tropical Agriculture) and CIMMYT (International Maize and Wheat Improvement Center) maize breeding programs. The inbred lines were genotyped with 9857 Diversity Array Technology sequencing based single nucleotide polymorphism markers. Hierarchical clustering revealed three major groups, with some subgroups consistent with the selection history, and pedigree of the inbred lines. Three broad groups were detected: two consisting of CIMMYT lines and a mixed group consisting of both CIMMYT and IITA inbred lines. The STRUCTURE analysis revealed six subpopulations (fixation index value = 0.58), which depicts a moderate genetic diversity among the materials. Population 2 comprises the highest number of genotypes (102) from both programs. More than 89% of the elite lines had homozygosity exceeding 95%, with the remaining lines requiring further inbreeding through repeated self‐pollination. There was inconsistency in the predetermined heterotic groups' alignment between CIMMYT and IITA elite inbred lines. Analysis of molecular variance revealed that 96% of the total variation was accounted for by differences within groups, with the remaining 4% representing the variation between groups. This suggests that the two programs can benefit from germplasm exchange for the improvement of maize productivity.

Genetic variation and population structure of the rice accessions maintained in the AfricaRice genebank using DArTseq

AbstractUtilizing the full potential of rice collections mainly depends on an in‐depth exploration and understanding of the vast diversity in its germplasm. The AfricaRice genebank holds the largest collection of rice germplasm originating from the African continent. In the present study, we comprehensively characterized a collection of 9013 accessions, including Oryza barthii A. Chev., Oryza glaberrima Steud., Oryza longistaminata A. Chev. & Roehr., Oryza sativa L. ssp. indica, and Oryza sativa L. ssp. japonica, for genetic diversity and population structure using genotyping‐by‐sequencing through DArTseq analysis. We identified 27,718 high‐quality single nucleotide polymorphism markers after the genotypic data were filtered. Based on the analyses, the collection has extensive genetic diversity, and the average genetic distance of the entire set was 0.267 (range 0.001–0.469), with 45.1% of pairs of accessions being highly distant and 40.1% moderately distant from each other. Neighbor‐joining tree, principal component, and Bayesian population structure analyses clustered the 9013 accessions into six groups, based roughly on their taxonomic and biological status. The first, second, and third groups consisted of accessions belonging to O. glaberrima, O. barthii, and O. longistaminata, respectively. The fourth, fifth, and sixth groups were improved‐indica, japonica, and traditional‐indica accessions, respectively. The highest value of genetic variance proportion (PhiPT) was found in the species group followed by groups based on cluster analysis and on Bayesian population structure at K = 6. These results allow us to better understand the genetic diversity present in 9013 rice accessions maintained in the AfricaRice genebank and offer a valuable tool for pre breeding, breeding, and further genetic applications.

Genetic diversity, population structure, and phylogeny of insular Spanish pepper landraces (Capsicum annuum L.) through phenotyping and genotyping-by-sequencing.

Pepper (Capsicum spp.) is one of the most important crops worldwide. Understanding the species' genetic background is key to preserve agrodiversity on-farm, to contribute to a more diverse and resilient agrifood sector, and to find new sources of variation that could be useful in future breeding programs. In this regard, varietal groups bred in insular environments have gained special interest as they have evolved quite isolated from continental forms, with a limited genetic exchange. The present work explores the diversity of a plethora of Balearic landraces, corresponding to different local varietal types, through phenotyping and genotyping-by-sequencing (GBS). Mallorca and Eivissa landraces were phenotyped according to a comprehensive list of descriptors for plant, leaf, flower, fruit, pollen, and seed and were genotyped with single nucleotide polymorphism (SNP) markers; population structure and their patterns of diversity were studied. The results showed a considerable morphological diversity for most traits analyzed, within and between landraces. On the whole, in regard to genetic patterns, relatively low levels of heterozygosity and moderate genetic diversity for the studied landraces were found although some of them exhibited diverse patterns. The materials were not grouped in specific clusters associated with each island, but mainly according to varietal types. These findings can serve as the basis for studying divergent evolutionary patterns associated with the corresponding populations. Finally, the results can contribute to further elucidation of the genetic basis of Balearic landraces and serve as an inspiring case of study for other insular endemisms of cultivated species.

Distinct management units for the Critically Endangered angelshark (Squatina squatina) revealed in the Canary Islands

AbstractThe angelshark, Squatina squatina, is listed as Critically Endangered on the IUCN Red List of Threatened Species, and remaining populations are highly fragmented throughout its historical distribution. The Canary Islands archipelago in the North East Atlantic has been identified as a uniquely large stronghold for the species. In the present study, we compared the population genetic structure of S. squatina across different islands of the Canary Island archipelago using both microsatellite and single nucleotide polymorphism (SNP) markers. Both markers revealed significant differentiation of angelsharks between islands in the archipelago, with three main genetic units at: (1) Tenerife, (2) Gran Canaria and (3) the island group consisting of La Graciosa, Lanzarote and Fuerteventura. Our results imply a connectivity barrier between some adjacent islands, most likely driven by abyssal depths, and varying geological history and formation of each island and oceanographic patterns (i.e. seasonal coastal upwellings off the African coast). Therefore, we suggest that in the Canary Islands, S. squatina populations should be managed locally, with conservation and research priorities designed and implemented specifically for each of the three genetic units.

Genotyping-by-sequencing shows high genetic diversity in Corylus avellana germplasm resistant to eastern filbert blight

European hazelnut (Corylus avellana) is an anemophilous, dichogamous, self-incompatible tree nut species. It is native to a large portion of Europe, Turkey, and the Caucasus region, across which a wealth of plant genetic resources is present. The objective of this study was to evaluate the genetic diversity of a core set of C. avellana representing the world’s germplasm using genotyping-by-sequencing derived single nucleotide polymorphism (SNP) markers and to classify novel eastern filbert blight (EFB) resistant or tolerant accessions. Two-hundred-twenty-two accessions underwent next-generation sequencing (NGS) to generate SNP markers. From this, 1,250 SNP markers were used to construct a neighbor-joining (NJ) dendrogram and perform a STRUCTURE and discriminant analysis of principal coordinates (DAPC) analyses. In the dendrogram, five major groups were established, which generally corresponded to geographic origins of the plant materials studied. In STRUCTURE, support was found for groupings at (K) = 3, (K) = 6, and (K) = 10 populations, with the greatest Δ-(K) value occurring at (K) = 10. Although the three different analyses indicated slightly different solutions, the overall results were generally consistent from the standpoint of identifying similar accession groupings. For many of the accessions, recorded origins tended to correspond with their genetic grouping, although there was also evidence of intermixing and likely movement of plant materials. Interestingly, in all three analyses, a vast majority of the new accessions from the Republic of Georgia formed their own distinct group, highlighting this geographic region as a unique pool of C. avellana genetic resources. Overall, EFB resistant/tolerant accessions were placed across a wide range of genetic backgrounds. Thus, our results indicate EFB resistance/tolerance is present across a wide spectrum of C. avellana genetic resources, with the Georgian accessions representing a new and relatively unique germplasm pool that can be incorporated into hazelnut breeding programs.

Genetic Diversity and Population Structure Analysis of Soybean [Glycine max (L.) Merrill] Genotypes Using Agro-Morphological Traits and SNP Markers

Background/Objectives: Understanding the genetic diversity of soybean genotypes can provide valuable information that guides parental selection and the design of an effective hybridization strategy in a soybean breeding program. In order to identify genetically diverse, complementary, and prospective parental lines for breeding, this study set out to ascertain the genetic diversity, relationships, and population structure among 35 soybean genotypes based on agro-morphological traits and Single Nucleotide Polymorphic (SNP) marker data. Methods/Results: Cluster analysis, based on agro-morphological traits, grouped the studied genotypes into four clusters. The first two principal components accounted for 62.8% of the total phenotypic variation, where days to 50% flowering, days to 95% maturity, grain yield, shattering score, and lodging score had high and positive contributions to the total variation. Using the SNP marker information, mean values of 0.16, 0.19, 0.067, and 0.227 were obtained for minor allele frequency (MAF), polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He), respectively. Using different clustering approaches (admixture population structure, principal component scatter plot, and hierarchical clustering), the studied genotypes were grouped into four major clusters. Conclusions:The agro-morphological and molecular analysis results indicated the existence of moderate genetic diversity among the studied genotypes. The traits identified to be significantly related to yield provide valuable information for the genetic improvement of soybeans for yield.

RNA-seq and whole-genome re-sequencing reveal Micropterus salmoides growth-linked gene and selection signatures under carbohydrate-rich diet and varying temperature

This study was performed on Micropterus salmoides to determine growth-linked gene and single nucleotide polymorphism (SNP) markers under carbohydrate diet and varying temperature through RNA-seq and whole-genome re-sequencing. The results showed that growth-related genes were primarily enriched in the fat digestion and absorption signaling pathway, playing a role in lipid transport and metabolism. Fatty acid binding protein 6, bile salt-activated lipase-like, lysophosphatidylcholine acyltransferase 2, phospholipase A2, minor isoenzyme-like, and phospholipase A2, group IB (pancreas) were identified as the crucial genes. The differentially expressed genes between high and low temperatures were enriched in the pentose phosphate pathway, with carbohydrate transport and metabolism were most affected by temperature. Major facilitator superfamily domain containing 10, phosphogluconate dehydrogenase, fructose-1,6-bisphosphatase 1a, and spinster homolog 3 transcript variant X1(spns3) were the shared genes affected by temperature. From all the common genes, 10 growth-associated SNP markers were identified. The TT genotype at rs7781 was associated with lower body weight, while AA genotype at rs31434173 and CC genotype at rs31435313 showed positive correlation with body weight. Analogously, the GG genotype at rs31436887 and AA genotype at rs31438769 also found to characterize better growth performance. At low temperature, individuals with the AA genotype at rs11506587 and rs31435313 exhibited the slowest growth. For the genotypes labeled with rs11510589, the GG individual grew faster than the AA individual, whereas the opposite phenomenon occurred in these genotypes when labeled with rs11511314. The genotypes at rs32970704 and rs32967921 showed no growth correlation. The AA genotype at rs31435313 in spns3 had the slowest growth under a carbohydrate-rich diet regardless of the temperature. Our study presents candidate genes and SNP markers associated with growth influenced by carbohydrate and temperature, providing basis for the development of M. salmoides strain that better accepts carbohydrate diets at varying temperature.

Genetic Diversity and Population Structure of Cacao (Theobroma cacao L.) Germplasm from Sierra Leone and Togo Based on KASP–SNP Genotyping

Cacao (Theobroma cacao L.) is a tropical tree species belonging to the Malvaceae, which originated in the lowland rainforests of the Amazon. It is a major agricultural commodity, which contributes towards the Gross Domestic Product of West African countries, where it accounts for about 70% of the world’s production. Understanding the genetic diversity of genetic resources in a country, especially for an introduced crop such as cacao, is crucial to their management and effective utilization. However, very little is known about the genetic structure of the cacao germplasm from Sierra Leone and Togo based on molecular information. We assembled cacao germplasm accessions (235 from Sierra Leone and 141 from Togo) from different seed gardens and farmers’ fields across the cacao-producing states/regions of these countries for genetic diversity and population structure studies based on single nucleotide polymorphism (SNP) markers using 20 highly informative and reproducible KASP–SNPs markers. Genetic diversity among these accessions was assessed with three complementary clustering methods, including model-based population structure, discriminant analysis of principal components (DAPC), and phylogenetic trees. STRUCTURE and DAPC exhibited some consistency in the allocation of accessions into subpopulations or groups, although some discrepancies in their groupings were noted. Hierarchical clustering analysis grouped all the individuals into two major groups, as well as several sub-clusters. We also conducted a network analysis to elucidate genetic relationships among cacao accessions from Sierra Leone and Togo. Analysis of molecular variance (AMOVA) revealed high genetic diversity (86%) within accessions. A high rate of mislabeling/duplicate genotype names was revealed in both countries, which may be attributed to errors from the sources of introduction, labeling errors, and lost labels. This preliminary study demonstrates the use of KASP–SNPs for fingerprinting that can help identify duplicate/mislabeled accessions and provide strong evidence for improving accuracy and efficiency in cacao germplasm management as well as the distribution of correct materials to farmers.

Identification of Candidate Genes for Soybean Storability via GWAS and WGCNA Approaches

Soybean (Glycine max (L.) Merr.) is an important crop for both food and feed, playing a significant role in agricultural production and the human diet. During long-term storage, soybean seeds often exhibit reduced quality, decreased germination, and lower seedling vigor, ultimately leading to significant yield reductions in soybean crops. Seed storage tolerance is a complex quantitative trait controlled by multiple genes and is also influenced by environmental factors during seed formation, harvest, and storage. This study aimed to evaluate soybean germplasms for their storage tolerance, identify quantitative trait nucleotides (QTNs) associated with seed storage tolerance traits, and screen for candidate genes. The storage tolerance of 168 soybean germplasms was evaluated, and 23,156 high-quality single nucleotide polymorphism (SNP) markers were screened and analyzed through a genome-wide association study (GWAS). Ultimately, 14 QTNs were identified as being associated with seed storage tolerance and were distributed across the eight chromosomes of soybean, with five QTNs (rs25887810, rs27941858, rs33981296, rs44713950, and rs18610980) being newly reported loci in this study. In the linkage disequilibrium regions of these SNPs, 256 genes were identified. By combining GWAS and weighted gene co-expression network analysis (WGCNA), eight hub genes (Glyma.03G058300, Glyma.04G1921100, Glyma.04G192600, Glyma.04G192900, Glyma.07G002000, Glyma.08G329400, Glyma.16G074600, Glyma.16G091400) were jointly identified. Through the analysis of expression patterns, two candidate genes (Glyma.03G058300, Glyma.16G074600) potentially involved in seed storage tolerance were ultimately identified. Additionally, haplotype analysis revealed that natural variations in Glyma.03G058300 could affect seed storage tolerance. The findings of this research provide a theoretical foundation for understanding the regulatory mechanism underlying soybean storage.