Germplasm Characterization Research Articles

Sensory characterization of the Ethiopian germplasm of Coffea arabica L. conserved in the Colombian Coffee Collection

The sensory quality of coffee (Coffea arabica L.) has become increasingly important and is considered the best way to increase the competitiveness and profitability of the sector. Given the narrow genetic base cultivated, the use of its genetic resources conserved in germplasm banks is particularly relevant, especially for germplasm collected in Ethiopia, the country from which coffee originated and the center of its diversity of profiles. However, the potential benefits of using these resources is unknown. Therefore, the objective of this study was to characterize the sensory quality of the Ethiopian germplasm conserved in the Colombian Coffee Collection (CCC) to determine its variability and potential for use. The sensory qualities of drinks from 378 accessions of CCC were characterized. The results showed that 34% of the accessions evaluated presented sensory descriptors different from those of the traditional varieties. For the Global Impression attribute, the highest scores were associated with citrus, spice and floral notes. Additionally, prospecting rather than the area of origin of the germplasm influenced its sensory diversity, possibly due to the established objectives of the collection. The conserved germplasm exhibited important sensory variability, which is linked to rare descriptors in traditional varieties. Characterization activities of genetic resources, such as those conducted in this study, add value and serve as an initial step toward their application in breeding. The results obtained allow the selection of genotypes with distinct sensory profiles, which can be incorporated into genetic improvement programs aimed at developing future varieties with these attributes.

Study on Genetic Variation, Trait Association and PCA of Different Quantitative Traits in Local Maize Germplasm

Background: Maize has wider adaptability and high yielding ability among the cereals. North-East India is a hotspot of the biodiversity of maize. Lots of local germplasms are distributed throughout various eco-geographic situations of hills and the plains of the entire region. Characterization of local germplasm of maize helps to identify genotypes with different features and also depicts a picture on genetic variability in the genetic resources studied. Methods: The present investigation comprised of a set of thirty five local germplasm along with five check hybrids in the crop was raised in augmented randomized block design duing rabi 2019 at Assam Agricultural University, Jorhat. Observation was recorded for twenty three quantitative characters. Analysis of variance and estimation of genetic parameter were done by using R software. Result: The present study revealed that the genotypes differed significantly among themselves for all the characters except ear leaf width and leaf width. Moderate to high estimates of GCV and PCV were recorded for all the traits except days to 75% dry husk, days to maturity and moisture content. Moderate to high estimates of heritability and genetic advance percent of mean were observed for all the traits. Grain yield per plant exhibited positive and highly significant correlation with traits namely ear length, ear diameter, kernel rows per ear, kernels per row, kernel length, kernel width and 100 kernel weights. PCA generated four principal components with an eigen value of more than 1.0 accounting for 67.74% of the overall variation present in maize germplasm.

Estimates of Genetic Variability on Agro-Morphological Parameters of Newly Selected Maize [<i>Zea mays L.</i>] Landraces in Nigeria

Agro-morphological characterizations offer resilient and strong means for the precise characterization of germplasm to be used in breeding programs. Here, agro-morphological parameters were analyzed to figure out the genetic variability within 23 maize accessions commonly grown in the maize producing states. A total of 12 important agro-morphological traits were determined in the field trails at Agas research farm, kwara state Nigeria during 2023 planting season. The experiment was conducted in a complete randomized design with three replications. The highest plant height was recorded in the Accession NG03 (187.45), thenumber of leaves per plant was highest in the accessions BA-02 and KW-03 with the mean value (17.27) respectively. The length of cob was highest in the accessions NG-03 and JG-04 (21.60). The length of husk was lowest in the accession JG-04 (24.40). The accession NG-03 can serve as a breeding tool in breeding programmes as it showed highest in some morphological parameters. Other agro-morphological parameters showed significant differences as revealed by ANOVA statistically. This study revealed some accessions with diverse morphological traits that might be used as promising parents for maize in current and future biotechnology research and breeding programmes.

Securing nature’s pharmacy: investigating conservation and drug discovery potential in Curcuma caesia through germplasm characterization and threatened status analysis

Securing nature’s pharmacy: investigating conservation and drug discovery potential in Curcuma caesia through germplasm characterization and threatened status analysis

Application of a Multi-Spectral UAV Imagery in Germplasm Characterization: Prediction of Forage Biomass and Growth Patterns of Cicer Milkvetch (Astragalus cicer L.) Populations

Unmanned aerial vehicles (UAV)-based multi-spectral imaging could reduce the intensive labour required in phenotyping germplasm in crop breeding. The objectives of this study were to examine if UAV-based imaging could differentiate cicer milkvetch (Astragalus cicer L.) germplasm and identify UAV-based vegetation indices with correlations to its dry matter yield (DMY). A spaced nursery from 27 cicer milkvetch populations was established near Saskatoon, SK, Canada, in 2019. From 1 June to 15 October in 2020 and 2021, phenotypic traits including maximum stem length, leaf number per stem, rhizome spread rate, and stem density, along with two UAV-measured traits, green area and canopy volume, were measured bi-weekly. Forage DMY was determined in late June and mid-October of each year. In this study, normalized difference vegetation index (NDVI) green area and NDVI canopy volume data differentiated the three selected populations. NDVI green area had the highest correlation with forage DMY among the traits (June harvest: r = 0.91, October harvest: r = 0.77). Among measured phenotypic traits, maximum stem length had the highest correlation with forage DMY (June harvest: r = 0.74, October harvest: r = 0.83), which was significantly correlated to NDVI green area. The results indicated potential use of UAV-phenotyping in single plant evaluation in plant breeding.

Germplasm characterization of Coffea arabica L. accessions based on agronomic traits

Germplasm characterization of Coffea arabica L. accessions based on agronomic traits

Characterisation of Tomato (Solanum lycopersicon Mill.) Genotypes for Morphological and Disease Resistance Traits through Cluster Analysis

The characterization of germplasm is crucial for breeding and developing improved seed varieties. In this study, seed material was collected from M/s. Noble Seeds Pvt. Ltd., Yelhanka, focusing on genotypes with varying resistance to Tomato Leaf Curl Virus (ToLCV). The research was conducted during the Kharif seasons of 2021 and 2022 in Kestur Village, Doddballapura. Morphological characterization was performed according to DUS guidelines set by PPV&FRA, assessing 20 qualitative and 22 quantitative traits. The genotypes were grown in a randomized complete block design for reliability. Multivariate cluster analysis was employed to group the genotypes based on the morphological traits assessed, enabling the identification of patterns and relationships among them. This analysis facilitated the formation of distinct clusters, highlighting the genetic diversity and similarities among the genotypes, which are crucial for targeted breeding strategies. Through multivariate cluster analysis, two main clusters (A and B) were identified, each further divided into two sub-clusters (C and D). Overall, 66.67% of the 30 genotypes (20 in total) were grouped in Cluster E, while 5 genotypes were placed in Cluster C, 3 in Cluster D, and only 2 in Cluster F. The analysis revealed that NBLTM-22 and NBLTM-11 exhibited the highest variation between them, while genotypes within clusters demonstrated greater similarity. These findings underscore the importance of genetic diversity in breeding programs, highlighting that closer proximity in clustering correlates with trait similarity among genotypes. This information can guide further breeding efforts aimed at developing ToLCV-resistant varieties.

Exploring Italian Autochthonous Punica granatum L. Accessions: Pomological, Physicochemical, and Aromatic Investigations.

Autochthonous Italian pomegranate accessions are still underexplored, although they could be an important resource for fresh consumption, processing, and nutraceutical uses. Therefore, it is necessary to characterize the local germplasm to identify genotypes with desirable traits. In this study, six old Italian pomegranate landraces and a commercial cultivar (Dente di Cavallo) were investigated, evaluating their fruit pomological parameters, physicochemical (TSS, pH, TA, and color) characteristics, sugar content, and aromatic profiles (HeadSpace Solid-Phase MicroExtraction (HS-SPME)) coupled with Gas Chromatographyass Spectrometry (GC-MS) of pomegranate juices. Significant differences were observed in the size and weight of the seed and fruits (127.50-525.1 g), as well as the sugar content (100-133.6 gL-1), the sweetness (12.9-17.6 °Brix), and the aroma profiles. Over 56 volatile compounds, predominantly alcohols (56%), aldehydes (24%), and terpenes (9%), were simultaneously quantified. Large variability among the genotypes was also statistically confirmed. The results indicate a strong potential for commercial exploitation of this germplasm, both as fresh and processed fruit, and highlight its versatility for diverse applications. The genetic diversity of the autochthonous pomegranate accessions represents a precious heritage to be preserved and enhanced. This work represents a preliminary step toward a more comprehensive characterization and qualitative valorization of the Italian pomegranate germplasm.

The genetic characterization of germplasm and identification of the litter size trait associated candidate genes in Dexin mutton and fine-wool sheep.

Xinjiang is a major province of sheep breeding in China, which plays an important role in meeting people's needs for meat products, increasing farmers' income and sustainable development of animal husbandry. However, the genetic differentiation relationship between breeds was not clear, and most sheep had low fecundity, which seriously restricted the efficient development of sheep industry. Therefore, this study used the whole genome resequencing to detect the genetic variation of Dexin mutton and fine-wool sheep, explored the selected regions and important genes of the litter size traits, analyzed the genetic mechanism of reproductive traits, and provided new insights for the high fecundity breeding of sheep. A total of 5,236.338 G genome data and 35,884,037 SNPs were obtained. Furthermore, we identified 39 selection signals spanning candidate genes, 99 genes were significantly associated related to growth, reproduction and immunity, among which, BRIP1, BMPR1B, BMP4, NGF, etc. genes, and MAKP signaling pathway, Fanconi anemia pathway and Thyroid hormone signaling pathway and other signaling pathways were significantly correlated with litter size trait. Among them, we identified NGF, TrKA and BRIP1 genes was the important genes for sheep litter size traits and the mutation frequencies of 9 SNPs in BRIP1 gene were significantly different in domestic sheep in the world. The research provided new insights for the breeding of self-cultivated meat fine-wool sheep.

Efficient vegetation indices for phenotyping of abiotic stress tolerance in tea plant (Camellia sinensis (L.) Kuntze)

Early non-destructive detection of stress effect is crucial for efficient breeding strategies and germplasm characterization. Recently developed hyperspectral technologies allow to perform fast real-time phenotyping through reflectance-based vegetation indices. However, efficiency of these vegetation indices has to be validated for each crop in different environment. The aim of this study was to reveal efficient vegetation indices for phenotyping of abiotic stress (cold, freezing and nitrogen deficiency) response in tea plant. Among 31 studied VIs, few indices were efficient to distinguish tolerant and susceptible tea plants under abiotic stress: ZMI (Zarco-Tejada & Miller Index), VREI1,2,3 (Vogelmann Red Edge Indices), RENDVI (Red Edge Normalized Difference Vegetation Index), CTR1 and CTR2 (Carter Indices). Most of these indices are calculated based on reflectance in near-infrared area at 705–760 nm, indicating this range as promising for tea germplasm characterization under abiotic stresses. Tolerant tea plants showed the following values under freezing: ZMI ≥1.90, VREI1 ≥ 1.40, RENDVI ≥0.38, Ctr1 ≤ 1.74. The leaf N-content was positively correlated (Pearson's) with the following indices ZMI, VREI1, RENDVI, while negatively correlated with CTR, and VREI2,3. These results will be useful for tea germplasm management, genomics and breeding research aimed at abiotic stress tolerance of tea plant.

Principal component analysis of foxtail millet accessions under rainfed condition

Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest cultivated millet for grain, hay and silage. There is wide genetic diversity available in foxtail millet and characterization of available germplasm is a pre-requisite for the genetic improvement of any crop. Keeping the above fact in view 30 foxtail germplasm lines were evaluated during kharif 2020 and 2021 for morphological traits, stover yield, dry fodder yield and seed yield under rainfed conditions of Haryana. The results (based on pooled data of two years) revealed that enough variability was present among germplasm lines for further exploitation. High heritability and positive correlation was reported between traits like plant height, leaf length, leaf stem ratio, stover yield, grain yield etc. Principal component analysis also revealed that PC1, PC2, PC3, PC4 and PC5 contributed for 31.8%, 15.05%, 12.31%, 11.43% and 10.14%, respectively to the total variation. Five foxtail accessions viz., SEA8, SEA12, SEA48, SEJ184 and SEA37 were identified promising for yield and related traits under rainfed conditions of Haryana.

Exploring crop genomics: role of molecular markers in identifying genetic diversity and characterization

and facilitating germplasm characterization for crop improvement. Understanding and harnessing crop genetic diversity are paramount with the escalating demand for sustainable agricultural practices and the need to address global food security challenges. Molecular markers have emerged as powerful tools enabling precise identification, characterization, and utilization of genetic resources for crop enhancement. The paper provides an in-depth analysis of various molecular marker techniques, encompassing DNA-based markers such as single nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs), and amplified fragment length polymorphisms (AFLPs), as well as RNA-based markers like expression sequence tags (ESTs) and microRNAs. By elucidating genetic relationships, population structure, and phylogenetic analysis, these markers facilitate the conservation and utilization of crop germplasm. Moreover, the review highlights recent advancements in high-throughput genotyping technologies and bioinformatics tools, which have revolutionized crop genomic research. These advancements enable comprehensive genome-wide analyses, accelerating breeding efforts for the development of improved crop varieties with enhanced traits such as yield, quality, and stress tolerance. Integration of molecular marker-assisted selection (MAS) into breeding programs further enhances the efficiency and precision of crop improvement strategies. Despite the significant contributions of molecular markers to crop genomics, challenges persist. The review addresses these challenges and discusses potential solutions, emphasizing the importance of collaborative efforts, data sharing, and interdisciplinary research endeavors. By overcoming these hurdles, the agricultural community can fully harness the potential of genomics for sustainable crop improvement, thus addressing global food security challenges in the face of changing environmental conditions and population growth. In conclusion, understanding the role of molecular markers in crop genomics is crucial for optimizing breeding strategies, conserving genetic resources, and developing resilient crop varieties to meet the demands of a growing population and ensure food security in a changing world.

SNP genotyping Dutch heritage apple cultivars allows for germplasm characterization, curation, and pedigree reconstruction using genotypic data from multiple collection sites across the world

The curation and preservation of Dutch apple germplasm depends on reliable accession level information. However, many accessions of Dutch heirloom apple cultivars maintained publicly by the “Centre for Genetic Resources, the Netherlands” (CGN) and privately by Dutch pomological societies lack information regarding true-to-typeness and pedigree ancestry. The aim of this study was to address this knowledge gap by genotyping 652 apple accessions maintained in the CGN collection and Dutch private collections, compare their genotypic information to each other and to a large database of apple cultivars from around the world to identify genotypic duplicates and pedigree relationships for the Dutch apple cultivars. Towards this aim, accessions were genotyped on the 20 K Illumina Infinium(R) apple SNP array and with 15 SSR markers. Each accession was assigned to a genotypic profile code (MUNQ codes, as used in previous studies) facilitating communication regarding genotypic duplicates. There were 211 (51.1%) genotypic profiles in the Dutch germplasm which were not identified in other germplasm collections. Private collections maintained many of these unique accessions, including important pedigree ancestors. The study identified a number of common pedigree ancestors of Dutch cultivars, such as ‘Herfst Bloem Soete’, ‘Huismanszoet’ (2), and ‘Reinette Rouge Étoilée’. The duplicate and pedigree reconstruction results and relevant literature descriptions were used to pomologically verify the identity of relevant accessions. The results of this study resolved identity disputes, helped to decide which accessions should be retained or included in the CGN collection, and benefited ongoing pomological studies in ancestry and provenance of traditional Dutch cultivars.

Phaseolus coccineus L. Landraces in Greece: Microsatellite Genotyping and Molecular Characterization for Landrace Authenticity and Discrimination.

Phaseolus coccineus L. is a highly valuable crop for human consumption with a high protein content and other associated health benefits. Herein, 14 P. coccineus L. landraces were selected for genetic characterization: two Protected Geographical Indication (PGI) landraces from the Prespon area, namely "Gigantes" ("G") and "Elephantes" ("E"), and 12 additional landraces from the Greek Gene Bank collection of beans (PC1-PC12). The genetic diversity among these landraces was assessed using capillary electrophoresis utilizing fluorescence-labeled Simple Sequence Repeat (SSR) and Expressed Sequence Tag (EST); Simple Sequence Repeat (SSR) is a molecular marker technology. The "G" and "E" Prespon landraces were clearly distinguished among them, as well as from the PC1 to PC12 landraces, indicating the unique genetic identity of the Prespon beans. Overall, the genetic characterization of the abundant Greek bean germplasm using molecular markers can aid in the genetic identification of "G" and "E" Prespon beans, thus preventing any form of fraudulent practices as well as supporting traceability management strategies for the identification of authenticity, and protection of the origin of local certified products.

Genetic Diversity of the Mango Plant Based on Rapd Marks: Random Amplification of Polymorphic DNA

Mangosteen is a tropical fruit commodity that is Indonesia's leading export. The location and characterization of mangosteen germplasm and protective relatives are key in the conservation and use of genetic and mangosteen resources. Genetic improvement programs rely heavily on existing genetic resources. This research aims to analyze the genetic diversity of mangosteen plants based on RAPD markers. This research was carried out in Bulukumba Regency through genotypic observation and evaluation in the laboratory, as well as genetic observation through DNA band pattern analysis using the RAPD technique in the laboratory. The results of this research obtained information on phenotypic and genetic diversity, as well as obtaining superior candidate parents for mangosteen, obtaining information about the consistency of genetic variability between parent and progeny of Bulukumba mangosteen, recommending the most effective mangosteen characterization method in describing genetic variability and grouping mangosteen accessions and relatives involved.

Unlocking Genetic Diversity and Germplasm Characterization with Molecular Markers: Strategies for Crop Improvement

Molecular markers have emerged as the most useful tools in assessment of genetic diversity and characterizing germplasm, for crop improvement. This review paper comprehensively analyzes the applications of molecular markers in diversity analysis and germplasm characterization. It underscores the significance of genetic diversity as the bedrock for plant breeding programs, enabling the development of improved varieties with desirable attributes such as higher yields, stress tolerance, and enhanced nutritional profiles. The paper provides an overview of various types of molecular markers, including hybridization-based markers (e.g., RFLPs) and PCR-based markers (e.g., RAPDs, AFLPs, SSRs, and SNPs). It discusses marker selection strategies, emphasizing the consideration of factors like polymorphism, informativeness, and the potential for multiplexing and high-throughput genotyping. Diversity analysis techniques, including principal component analysis (PCA), cluster analysis methods (UPGMA and Neighbor-Joining), and population structure analysis (model-based approaches like STRUCTURE), are detailed. These methods enable the assessment of genetic relationships, identification of subpopulations, and selection of diverse parents based on molecular marker data. The review further explores the applications of molecular markers in germplasm management, conservation, and utilization. It discusses the role of markers in targeted introgression of desirable traits from diverse sources, as well as the integration of genotypic and phenotypic data for association mapping, genomic prediction, and selection. Additionally, the paper addresses emerging technologies, such as next-generation sequencing (NGS) and the integration of molecular markers with other omics data. It also highlights the practical applications and impact of molecular markers in crop improvement programs, including marker-assisted selection (MAS), genomic selection, and the development of genetically modified crops. Finally, the review outlines challenges and future perspectives, including limitations0 of current technologies, the potential of emerging techniques like NGS, and the integration of molecular markers with other omics approaches for a comprehensive understanding of complex traits.

KERAGAMAN PLASMA NUTFAH TANAMAN DURIAN (DURIO ZIBETHINUS MURR) DI PULAU BANGKA

Durians In Bangka island have potensials of the diversity which has not been identified yet. The protection of the genetical plants of durian resources have been done by exploration and identification activities. The aim of this research are to discover the amount of Germplasm, the relationship, and the diversity of phenotype of durians in Bangka island. This research started from December 2020 to March 2021. The determination of location has been done by purposive sampling and the technique of taking samples also has been done by convenience sampling. Germplasm characterization consists of qualitative and quantitative characters. The analysis of relationships were used by dendogram according to UPGMA method. The results have discovered over 14 germplasm of durian in Bangka island. Those are Belo,Bujang Kuning, Mangga, Rudal, Katon, Sihijua, Sibola Emas, Putri Dewa, Petaling, Burak 1, Burak 2, Burak 3, T 9, and Simanis. The results of the relationships qualitative analysis were obtained 5 clusters in the level of coefficient similarities 0.49 or 49%. Meanwhile, quantitative were obtained 7 clusters in the level of coefficient 0.31 or 31% and the combined were obtained 5 clusters in the level of coefficient 0.45 or 45%.

Genetic analysis and molecular validation of gene conferring petal spot phenotype in interspecific crosses of cotton

Cotton (Gossypium species) has received considerable interest from the geneticists, cytologists and evolutionary biologists since the last more than a century. Here, we explore the genetics of petal spot in the interspecific derivatives involving tetraploid and diploid cottons; and confirm the location of gene governing petal spot phenotype on chromosome A7 by demonstrating co-segregation of SSR marker NAU 2186 with petal spot phenotype. The presence of petal spot was observed to be dominant over its absence. Petal spot inheritance showed significant deviation from the expected Mendelian ratio in all the segregating populations indicating segregation distortion. The distortion was biased towards the hirsutum parent which has important implications from introgression point of view. We also report a strong association between petal spot and petal margin coloration phenotypes. Extant American cotton varieties generally lack petal spot and margin coloration phenotypes. These petal characteristics can serve as morphological markers during germplasm characterization.

Morphological, phenotypic and nutritional characterization of exotic and local tomato germplasm under tunnel

Tomato (Solanum lycopersicum L.) is one of the most important and widely cultivated fruit. By characterizing local germplasm, exclusive breeding material is successfully identified and improved varieties could be created. The research conducted between November 2020 and 2021 at the Ayub Agricultural Research Institute (AARI) in Pakistan used developmental, vegetative and fruit traits to individualize sixty tomato inbred lines for 17 morphological traits. The study showed that 6 qualitative and 11 quantitative morphological traits exhibited a wide range of variation, while 8 traits showed a high coefficient of variation among genotypes according to biplot principal component analysis (PCA). According to biplot PCA, the first component contributed 17.6% of the variation, while the second component contributed 13.0%. Together, the first and second components explained 30.6% of the variation. A correlation analysis was performed to determine the relationship between genotypic traits and phenotypic traits. A very positive correlation was observed between inter-nodal distance, flower per cluster and immature fruit color. The morphological data for firmness, pericarp thickness, fruit width, TSS, inter-nodal distance, number of flowers and fruits per cluster showed specific characteristics that can be used to distinguish the genotypes. The highest value of lycopene of 21.2 mg kg−1 fresh weight was observed among the genotypes. We conclude the results of this study, presenting the crop quality and yield characteristics that could be used in future plant breeding and genetic enhancement of tomato germplasm for improved food security. Based on yield characteristics, Nyagous, Korneseivje and Earliana were selected as the best and most promising genotypes.

The Musa Marker Database: A Comprehensive Genomic Resource for the Improvement of the Musaceae Family

Molecular markers, including Simple Sequence Repeat (SSR), Single Nucleotide Polymorphism (SNP), and Intron Length Polymorphism (ILP), are widely utilized in crop improvement and population genetics studies. However, these marker resources remain insufficient for Musa species. In this study, we developed genome-wide SSR, SNP, and ILP markers from Musa and its sister species, creating a comprehensive molecular marker repository for the improvement of Musa species. This database contains 2,115,474 SSR, 63,588 SNP, and 91,547 ILP markers developed from thirteen Musa species and two of its relative species. We found that 77% of the SSR loci are suitable for marker development; 38% of SNP markers originated from the genic region, and transition mutations (C↔T; A↔G) were more frequent than transversion. The database is freely accessible and follows a ‘three-tier architecture,’ organizing marker information in MySQL tables. It has a user-friendly interface, written in JavaScript, PHP, and HTML code. Users can employ flexible search parameters, including marker location in the chromosome, transferability, polymorphism, and functional annotation, among others. These distinctive features distinguish the Musa Marker Database (MMdb) from existing marker databases by offering a novel approach that is tailored to the precise needs of the Musa research community. Despite being an in silico method, searching for markers based on various attributes holds promise for Musa research. These markers serve various purposes, including germplasm characterization, gene discovery, population structure analysis, and QTL mapping.