Germplasm Collection Research Articles

Molecular Characterization of Rice Genotypes Using Molecular Markers

Rice, (Oryza sativa L. 2n=24) belongs to the family Gramineae and subfamily Oryzoideae. Oryza has two cultivated species: Oryza sativa and Oryza glaberrima. Breeding for good-quality traits requires the selection of parents with a wider genetic diversity. Molecular markers are used in molecular biology and biotechnology to identify a sequence of DNA. Molecular markers have played an increasing role in rice breeding for cultivar improvement, screening, selection, and germplasm collections. The present investigation is undertaken to study the genetic diversity among thirty rice genotypes using the ISSR marker.
 Out of 40 ISSR primers, 9 amplified and showed polymorphism, viz., ISSR 807, ISSR 808, ISSR 809, ISSR 811, ISSR 816, ISSR 823, ISSR 826, ISSR 827 and ISSR 829. A total of 76 loci were generated by amplification with 9 polymorphic primers, out of which 66 loci were polymorphic with an average of 86.84 percent polymorphism. Among ISSR primers, ISSR 807 produced the maximum number of 11 loci. A dendrogram constructed using NTSYSpc 2.02i software grouped all 30 genotypes into two major clusters (clusters A and B). Cluster A Kalbhat alone is present in one sub-cluster at 69.2% similarity with Karjat 2, Jaya, Sairam, Saubhagya Dhan, RPBIO 226, Karjat 6, Ratnagiri 1, DRR Dhan 44, DRR Dhan 45, DRR Dhan 46, MTU 10010, Karjat 7, Swarna Shreya, Sugandha, and Madhumati. In Cluster B Karjat 3 alone forms one sub- cluster and has 70 % similarity with MTU 1001, PKVHMT, JGL 1798, Indrayani, Phule Samruddhi, Phule Maval, Sonsal, Pavana, DRR Dhan 41, kundalika, Bhogawati, Ambemohar, and Phule Radha.

Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum.

Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species Fagopyrum esculentum and Fagopyrum tataricum (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei's expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (p = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (p < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for F. esculentum and F. tataricum. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among F. esculentum and F. tataricum accessions and pointed to future directions for genomics-based breeding programs and germplasm management.

Genome-wide association mapping in a sweet cherry germplasm collection (Prunus avium L.) reveals candidate genes for fruit quality traits.

In sweet cherry (Prunus avium L.), large variability exists for various traits related to fruit quality. There is a need to discover the genetic architecture of these traits in order to enhance the efficiency of breeding strategies for consumer and producer demands. With this objective, a germplasm collection consisting of 116 sweet cherry accessions was evaluated for 23 agronomic fruit quality traits over 2-6 years, and characterized using a genotyping-by-sequencing approach. The SNP coverage collected was used to conduct a genome-wide association study using two multilocus models and three reference genomes. We identified numerous SNP-trait associations for global fruit size (weight, width, and thickness), fruit cracking, fruit firmness, and stone size, and we pinpointed several candidate genes involved in phytohormone, calcium, and cell wall metabolisms. Finally, we conducted a precise literature review focusing on the genetic architecture of fruit quality traits in sweet cherry to compare our results with potential colocalizations of marker-trait associations. This study brings new knowledge of the genetic control of important agronomic traits related to fruit quality, and to the development of marker-assisted selection strategies targeted towards the facilitation of breeding efforts.

Conservation and Global Distribution of Onion (Allium cepa L.) Germplasm for Agricultural Sustainability.

Onion (Allium cepa L.) is recognized globally as a crucial vegetable crop, prized not only for its culinary applications but also for its numerous health-promoting properties. With climate change relentlessly exerting mounting challenges to agriculture, the preservation and deployment of onion germplasm has become critical to ensuring sustainable agriculture and safeguarding food security. Global onion germplasm collections function as repositories of genetic diversity, holding within them an extensive array of valuable traits or genes. These can be harnessed to develop varieties resilient to climate adversities. Therefore, detailed information concerning onion germplasm collections from various geographical regions can bolster their utility. Furthermore, an amplified understanding of the importance of fostering international and inter-institutional collaborations becomes essential. Sharing and making use of onion genetic resources can provide viable solutions to the looming agricultural challenges of the future. In this review, we have discussed the preservation and worldwide distribution of onion germplasm, along with its implications for agricultural sustainability. We have also underscored the importance of international and interinstitutional collaboration in onion germplasm collecting and conservation for agricultural sustainability.

Cryopreservation of Duckweed Genetic Diversity as Model for Long-Term Preservation of Aquatic Flowering Plants.

Vegetatively propagating aquatic angiosperms, the Lemnaceae family (duckweeds) represents valuable genetic resources for circular bioeconomics and other sustainable applications. Due to extremely fast growth and laborious cultivation of in vitro collections, duckweeds are an urgent subject for cryopreservation. We developed a robust and fast DMSO-free protocol for duckweed cryopreservation by vitrification. A single-use device was designed for sampling of duckweed fronds from donor culture, further spin-drying, and subsequent transferring to cryo-tubes with plant vitrification solution 3 (PVS3). Following cultivation in darkness and applying elevated temperatures during early regrowth stage, a specific pulsed illumination instead of a diurnal regime enabled successful regrowth after the cryopreservation of 21 accessions of Spirodela, Landoltia, Lemna, and Wolffia genera, including interspecific hybrids, auto- and allopolyploids. Genome size measurements revealed no quantitative genomic changes potentially caused by cryopreservation. The expression of CBF/DREB1 genes, considered as key factors in the development of freezing tolerance, was studied prior to cooling but was not linked with duckweed regrowth after rewarming. Despite preserving chlorophyll fluorescence after rewarming, the rewarmed fronds demonstrated nearly zero photosynthetic activity, which did not recover. The novel protocol provides the basis for future routine application of cryostorage to duckweed germplasm collections, saving labor for in vitro cultivation and maintaining characterized reference and mutant samples.

Fine-Scale analysis of both wild and cultivated horned galls provides insight into their quality differentiation

BackgroundGalla chinensis is a traditional Chinese medicine (TCM) produced due to the interaction between the Fordinae aphids and the Rhus plant species. Horned galls with high tannin content are the most widely cultivated gall type, and Wufeng county of Hubei province in China is the center of cultivation. However, long-term artificial cultivation and domestication of horned galls to meet the increasing production demand have led to quality degradation. Understanding the reasons underlying quality degradation is urgent for horned gall production and application. The present study used a combination of metabolic, genetic, and ecological analyses to investigate the quality and genetic differentiation of the horned galls under long-term domestication as well as the potential relationships between them.ResultsAnalysis of gallic acid content and other three phenotypic traits (fresh weight, gall size, and wall thickness) revealed quality differentiation of horned galls collected from five locations in Wufeng, in which the cultivated samples from Wang Jiaping (WJP) showed the highest degradation. Genetic differentiation between the cultivated and wild Rhus chinensis trees in WJP, and between WJP and the other populations was detected based on SSR molecular markers, however, no significant difference in genetic structure was seen for the aphid populations. Among the various ecological factors examined, temperature was identified as the primary one affecting the quality of horned galls.ConclusionsBoth genetic and ecological factors caused quality differentiation of horned galls. The collection of diverse germplasm of host trees and aphids will help reduce the quality degradation of horned galls in Wufeng.

Identification of Soybean Germplasm and Associated Molecular Markers with Resistance to Fusarium graminearum

Soybean ranks second by total production of all crops grown in the United States. From surveys of soybean production regions in the US and Canada, seedling diseases have been consistently identified as one of the top five biotic limitations on yield for over two decades. The role of Fusarium graminearum as an aggressive member of this complex was unknown until relatively recently and, consequently, publicly and commercially available varieties with resistance to this pathogen are unavailable. To address the need for resistant germplasm and to improve our understanding of the genetic basis underlying the resistance, we screened a set of 208 accessions of soybean from the United States Department of Agriculture Soybean Germplasm Collection (USDA-SGC) under controlled greenhouse conditions. A ratio of the root weight of inoculated plants compared to mock-inoculated controls was used to evaluate the degree of resistance. A linear mixed model identified eight resistant accessions (PI 548311, PI 438500, PI 561318 A, PI 547690, PI 391577, PI 157484, PI 632418, and PI 70466 -3) with significantly higher resistance than the population mean. Previous genotyping publicly available through the SoyBase database was used in a genome-wide association study (GWAS) to determine single nucleotide polymorphism (SNP) markers associated with resistant and susceptible phenotypes. A total of five significant marker-trait associations (MTAs) were discovered on chromosomes Gm02, Gm03, Gm06, Gm07, and Gm13, each accounting for 4.8, 4.3, 3.8, 4.1, and 3.0% of the phenotypic variance, respectively. This study, thus, lays a foundation for the better dissection of germplasm resistant to F. graminearum.

Ex situ germplasm collections of exceptional species are a vital part of the conservation of Australia's national plant treasures

Societal Impact StatementConservation seed banks maintain collections of many seed‐bearing plant species, providing germplasm and data to support management of wild populations. However, a proportion of plant species produce seeds that are difficult to collect, dry, store and utilise; these are known as ‘exceptional’ species. Here we tested a framework for identifying exceptional species, to document examples and provide case studies within the Australian flora. We present a workflow that may be used to identify additional exceptional species, and direct efforts to establish appropriate collection types (seeds and/or living collections, tissue culture or cryopreservation) for their ex situ conservation.SummarySeed banking is well established to contribute to the conservation of many seed‐bearing plant species ex situ for future use in restoration, translocation, agriculture and horticulture. In Australia, over 67% of currently listed threatened plants are represented in conservation seed banks. However, there are challenges to conserving the full extent of plant diversity in seed banks, with growing recognition that we need to think beyond conventional seed banking methods to conserve ‘exceptional’ plant species that are difficult to collect, store and germinate. We examine how the framework for identification of such species can be applied to the Australian flora, using examples from the recently published guidelines for ‘Plant Germplasm Conservation in Australia’ and case studies and data arising from the Australian Academy of Science Fenner Conference on the Environment ‘Exceptional Times, Exceptional Plants’. We present a workflow to assist conservation decision‐makers and practitioners in identifying exceptional species and overcoming barriers to storage of germplasm, enabling appropriate ex situ collection types to be established via seeds, living collections, tissue culture, cryopreservation or a combination of these. Australia's seed conservation sector continues to expand, with increasing expertise, facilities and networks established to conserve a diversity of plant species; however, resolving the challenges relating to each exceptionality factor requires significantly more time, labour and collaboration than current capacity allows. Understanding the barriers to conservation and production of healthy plants, via germination or other methods of propagation, is a critical component of conserving species long‐term and ultimately returning plants to the landscape.

Analysis of global Napier grass (Cenchrus purpureus) collections reveals high genetic diversity among genotypes with some redundancy between collections

Genetic diversity amongst genotypes of several Napier grass collections was analyzed and compared with the diversity in a set of open pollinated progeny plants. A total of 114,881 SNP and 46,293 SilicoDArT genome-wide markers were generated on 574 Napier grass genotypes. Of these, 86% of the SNP and 66% of the SilicoDArT markers were mapped onto the fourteen chromosomes of the Napier grass genome. For genetic diversity analysis, a subset of highly polymorphic and informative SNP markers was filtered using genomic position information, a maximum of 10% missing values, a minimum minor allele frequency of 5%, and a maximum linkage-disequilibrium value of 0.5. Extensive genetic variation, with an average Nei’s genetic distance value of 0.23, was identified in the material. The genotypes clustered into three major and eleven sub-clusters with high levels of genetic variation contained both within (54%) and between (46%) clusters. However, we found that there was low to moderate genetic differentiation among the collections and that some overlap and redundancy occurred between collections. The progeny plants were genetically diverse and divergent from the germplasm collections, with an average FST value of 0.08. We also reported QTL regions associated with forage biomass yield based on field phenotype data measured on a subset of the Napier grass collections. The findings of this study offer useful information for Napier grass breeding strategies, enhancement of genetic diversity, and provide a guide for the management and conservation of the collections.

Data-driven approaches to improve water-use efficiency and drought resistance in crop plants

With the increasing population, there lies a pressing demand for food, feed and fibre, while the changing climatic conditions pose severe challenges for agricultural production worldwide. Water is the lifeline for crop production; thus, enhancing crop water-use efficiency (WUE) and improving drought resistance in crop varieties are crucial for overcoming these challenges. Genetically-driven improvements in yield, WUE and drought tolerance traits can buffer the worst effects of climate change on crop production in dry areas. While traditional crop breeding approaches have delivered impressive results in increasing yield, the methods remain time-consuming and are often limited by the existing allelic variation present in the germplasm. Significant advances in breeding and high-throughput omics technologies in parallel with smart agriculture practices have created avenues to dramatically speed up the process of trait improvement by leveraging the vast volumes of genomic and phenotypic data. For example, individual genome and pan-genome assemblies, along with transcriptomic, metabolomic and proteomic data from germplasm collections, characterised at phenotypic levels, could be utilised to identify marker-trait associations and superior haplotypes for crop genetic improvement. In addition, these omics approaches enable the identification of genes involved in pathways leading to the expression of a trait, thereby providing an understanding of the genetic, physiological and biochemical basis of trait variation. These data-driven gene discoveries and validation approaches are essential for crop improvement pipelines, including genomic breeding, speed breeding and gene editing. Herein, we provide an overview of prospects presented using big data-driven approaches (including artificial intelligence and machine learning) to harness new genetic gains for breeding programs and develop drought-tolerant crop varieties with favourable WUE and high-yield potential traits.

Genetic Diversity of New Almond Accessions from Central Asian and Cold-adapted North American Germplasm

We evaluated the genetic diversity of a newly available collection of 94 almond [Prunus dulcis (Mill.) D.A. Webb] accessions from the former Improving Perennial Plants for Food and Bioenergy (IPPFBE) Foundation. Most of the collection (87 accessions) were collected as seeds from trees growing in the central Asian nations of Kyrgyzstan, Tajikistan, and Uzbekistan, and included several examples of Prunus bucharica (Korsh.) Hand.-Mazz, and related wild species. Of the remaining accessions, six were sourced from a nursery in northern Utah in the United States, and one was a seedling of ‘Nonpareil’, a major commercial cultivar. DNA fingerprints were generated from 10 simple sequence repeat markers. To evaluate the comparative diversity of these new accessions, 66 accessions from the US Department of Agriculture, National Plant Germplasm System (NPGS) almond germplasm collection near Davis, CA, USA, were also included. These NPGS accessions were chosen to represent those collected in similar regions of Central Asia and the Caucasus. The fingerprints were analyzed via hierarchical clustering, principal components analysis (PCA), and discriminant analysis of principal components (DAPC). Hierarchical clustering suggested that half of the Utah-sourced accessions are closely related to each other and to the ‘Nonpareil’ seedling. Additional close relationships were detected (including at least one duplication or mislabeling), and two P. bucharica accessions from the IPPFBE collection were separated from the rest of the collection. A plot of the first two principal components clearly separated wild almond relatives (P. bucharica and Prunus fenzliana Fritsch) from the remaining accessions. PCA after removal of the wild species separated the ‘Nonpareil’ seedling, the Utah-sourced accessions, and many of the IPPFBE accessions (mostly from Uzbekistan) from nearly all other individuals. The third principal component identified an additional population structure that separated groups of predominantly IPPFBE or NPGS accessions. DAPC showed a considerable admixture of accessions from Azerbaijan, and a little to no admixture of accessions from Georgia and Tajikistan. These results suggest that central Asian/Caucasian almond germplasm is generally distinct from ‘Nonpareil’ and its relatives, and that although there is overlap between the NPGS and IPPFBE collections from this region, the IPPFBE collection does enhance the diversity of available almond germplasm.

Androgenic response of spring barley (Hordeum vulgare L.) varieties and lines – sources of high grain protein content

Aim. Protein content is known to be one of the most important characters of grain quality. Investigation was aimed to determine the capability to haploid production in anther culture in vitro of spring barley accessions which are the sources of high protein content in grain. Methods. Infrared spectroscopy was used for evaluation of variability of barley genotypes in protein content. Anthers isolated from cold-pretreated spikes were cultivated on agar solidified nutrient medium containing N6 macro-and MS micronutrients, physiologically active substances and maltose (9.0 %). Results. Three years testing showed that mean grain protein contents in six spring barley accessions varied from 12.6 to 19.1 %. Commercial variety Yavir, accessions IR06605 and DD-21 from germplasm collection of the National Plant Gene Pool of Ukraine were selected as genotypes with a stable expression of this char-acter. Response to androgenesis in vitro varied from 6.9 to 45.9 % of morphogenic anthers and from 0.64 до 14.7 green plants per 100 cultivated anthers in dependence of genotype and donor plant growth conditions. Conclusions. Because of association between high protein content in grains and a relatively high androgenic response, varieties Velikan and Yavir were considered to be the most valuable ones for use in spring barley breeding for improvement of protein content via anther culture in vitro.

Seed Germination and Seedling Growth Influenced by Genetic Features and Drought Tolerance in a Critically Endangered Maple.

Understanding the adaptation of plant species will help us develop effective breeding programs, guide the collection of germplasm, and improve the success of population restoration projects for threatened species. Genetic features correlate with species adaptation. Acer yangbiense is a critically endangered plant species with extremely small populations (PSESP). However, no information was available on its seed germination and seedling growth in populations with different genetic characteristics. In this study, we investigated seed germination and compared the performance of 566 seedlings in 10 maternal half-sib families cultivated in Kunming Botanical Garden. The results showed that A. yangbiense seeds required an average of 44 days to start germinating, with a 50% germination rate estimated to take about 47-76 days, indicating slow and irregular germination. There is a trade-off between the growth and survival in A. yangbiense seedlings, with fast growth coming at the cost of low survival. Groups that were able to recover from a recent bottleneck consistently had higher relative growth rates. High genetic diversity and low levels of inbreeding are likely to be responsible for their improved survival during drought conditions and rapid growth under optimal environmental conditions. Our results suggest that maternal genetic traits might be used as indicators for conservation and population restoration. These findings provide us with new information that could be applied to support ex situ conservation and reintroduction of threatened species.

Phenotypic diversity among cowpea mutants and accessions for grain yield and yield components

Phenotypic characterization of cowpea germplasm collections is an essential step for the cowpea genetic improvement. The objectives of the study were to determine the phenotypic diversity and characterize cowpea mutants and accessions for grain yield and yield components, to identify their superiority, and to determine the correlation between measured characteristics. Thirty-one cowpea genotypes (16 Namibian mutants, seven International Institute of Tropical Agriculture (IITA) genotypes and eight South Africa genotypes) were planted in five different environments in South Africa during the 2021/2022 cropping season. Significant (P ≤ 0.05) genotype, environment and genotype by environment interaction effects were observed for all grain yield and yield components. Moderate to high broad-sense heritability (H2) (> 50%) was observed for all yield components. Superior Namibian Mutants (ShR10P12, ShR3P4, ShR4P1 and BrR11P2), IITA genotype (98K-476-8) and South African genotype (Enchore) were identified for grain yield (GY), number of seeds per plant (NSPPx), pod weight per plant (PWP) and number of pods per plant (NPP). There were significant positive correlations between most of the yield components. In the principal component analysis, Namibian mutant genotypes ShL2P7, ShR4P1, NKR1P3 and BrR11P2 were associated with high NSPPx, PWP and GY. The clustered heat map identified a group of Namibian mutants (NKR1P3, BrR11P2, ShL2P7, ShR2P11 and ShR10P12), IITA genotype (98K-47-8) and South African genotypes (Glenda, Dr Saunders, Enchore, and Oloyin) which was associated with high GY, PWP, NSPPx, NPP, seed weight per plant (SWP) and harvest index (HI). The identified superior cowpea mutants for grain yield and yield components can be used for cowpea improvement.

Positioning Portugal in the Context of World Almond Production and Research

Almond production plays a very significant role in the Portuguese socio-economic context, especially with regard to dried fruit production. Indeed, Portugal is the third largest almond producer in Europe, producing 41,450 t of almonds in shells in 2021. This is due to its edaphoclimatic conditions that are favorable for its production. Traditionally, the north region of “Trás-os-Montes” has stood out as one of the most relevant for Portuguese almond production and bioeconomy. However, production in “Alentejo“ and “Beira Interior” will surpass the northern region in a short time as a result of the installation of new orchards. Despite its importance, there is a need to uncover genetic traits underlying phenotypic desirable traits needed to improve yield and quality but also cope and mitigate the impacts of climate change on their production. To address this, it is important to characterize the genetic resources available and the germplasm collection since they are crucial players for conservation and breeding initiatives. In this review, we describe the main cultivars of almonds cultivated in Portugal and their productive challenges. We also provide an overview of the main genetic resources available, breeding goals, and accomplishments regarding their improvement towards biotic and abiotic constraints in both Portugal and the rest of the world.

‘Newell’ bermudagrass: A public release from the USDA Cynodon collection

AbstractWarm‐season perennial grasses are the backbone of the pasture‐based livestock industry in the lower southeastern United States, and bermudagrass (Cynodon spp.) is the most widely planted forage species, covering ∼15 million ha. The genus Cynodon is native to southern Africa, and germplasm collections possess high genetic and phenotypic variability. The USDA National Plant Germplasm System maintains a collection of bermudagrass plant introductions (PIs) in Griffin, GA, and USDA‐ARS, Tifton, GA, maintains additional germplasm. Multi‐location trials were established in four states (Florida, Georgia, North Carolina, and Oklahoma) to screen Cynodon germplasm for herbage accumulation (HA), nutritive value (NV), and bermudagrass stem maggot (BSM) (Atherigona reversura Villeneuve). Due to the large genotype × environment interaction for HA, we focused on selecting accessions adapted to South Georgia and Florida, and further studies were performed in Florida. Several PIs showed improved HA and NV compared with ‘Tifton 85’. PI 316510, originally introduced from Ingelheim, Germany, produced high HA in Citra, FL, and Tifton, GA, with improved NV traits. In addition, PI 316510 had faster establishment and similar BSM tolerance to Tifton 85. We confirmed PI 316510 as tetraploid (2n = 4x = 36) through chromosome counts and flow cytometry, and it is genetically distinct from other commercial cultivars. PI 316510 has been publicly released under the name ‘Newell’, and it is vegetatively propagated. Planting material can be requested from the UF‐IFAS Forage Breeding program.

Elucidation of the Genetic Diversity within Some In Situ Shea Germplasm in Ghana

Shea is an agroforestry tree species known primarily for its rich butter, which contains stearin and tocopherol, and has ultraviolet ray absorption property; it is used in cooking, body care and traditional medicines. This tree is, however, uncultivated and collection of its nuts by rural dwellers is threatened by increased urbanization with its accompanying land use pressure and the need for fuel wood for rural households. There is also increased demand for shea products worldwide necessitating the need for shea improvement strategies. At the apex of this improvement program lies the need for germplasm collection, characterization, conservation and utilization. In order to conserve elite shea materials amidst dwindling shea populations threatened by climate change, there is a need to develop shea germplasm banks based on the representation of genetic and phenotypic variation focusing on known traits. The objective of the study was to evaluate 282 shea accessions for germplasm conservation and to determine the genetic diversity of the collected materials to inform future collections and drive crop improvement strategies. Leaf traits were used to differentiate and group the selected materials. Leaf length ranged between 16.83 cm and 30.85 cm, and leaf blade length ranged between 12.28 cm and 20.68 cm. Petiole length varied between 5.53 cm and 10.2 cm and the blade to petiole ratio was from 1.41 to 2.69. Correlation studies revealed significant negative correlation between the latitude of collection and all leaf traits measured. There was significant positive correlation between blade length and petiole length (0.57), blade length and total leaf length (0.87) and petiole length and breadth (0.49). The collected materials were grouped at 90% into two, based on the morphological descriptors studied. Three different approaches were employed to genetically analyze the materials based on single nucleotide polymorphic markers (SNP). A phylogenetic tree was constructed based on the SNPs generated; this grouped the materials into three, with various subgroups. Principal coordinate analysis also produced three distinct groups with groupings not based on geographical area of collection. Discriminant analysis of principal components (DAPC) also confirmed three groupings. The genetic diversity of the collection was very low (Hs) = 0.0406, which is an indication of potential inbreeding within the shea populations. To conclude, there was higher variation within locations than between locations.

Genomic predictions to leverage phenotypic data across genebanks.

Genome-wide prediction is a powerful tool in breeding. Initial results suggest that genome-wide approaches are also promising for enhancing the use of the genebank material: predicting the performance of plant genetic resources can unlock their hidden potential and fill the information gap in genebanks across the world and, hence, underpin prebreeding programs. As a proof of concept, we evaluated the power of across-genebank prediction for extensive germplasm collections relying on historical data on flowering/heading date, plant height, and thousand kernel weight of 9,344 barley (Hordeum vulgare L.) plant genetic resources from the German Federal Ex situ Genebank for Agricultural and Horticultural Crops (IPK) and of 1,089 accessions from the International Center for Agriculture Research in the Dry Areas (ICARDA) genebank. Based on prediction abilities for each trait, three scenarios for predictive characterization were compared: 1) a benchmark scenario, where test and training sets only contain ICARDA accessions, 2) across-genebank predictions using IPK as training and ICARDA as test set, and 3) integrated genebank predictions that include IPK with 30% of ICARDA accessions as a training set to predict the rest of ICARDA accessions. Within the population of ICARDA accessions, prediction abilities were low to moderate, which was presumably caused by a limited number of accessions used to train the model. Interestingly, ICARDA prediction abilities were boosted up to ninefold by using training sets composed of IPK plus 30% of ICARDA accessions. Pervasive genotype × environment interactions (GEIs) can become a potential obstacle to train robust genome-wide prediction models across genebanks. This suggests that the potential adverse effect of GEI on prediction ability was counterbalanced by the augmented training set with certain connectivity to the test set. Therefore, across-genebank predictions hold the promise to improve the curation of the world's genebank collections and contribute significantly to the long-term development of traditional genebanks toward biodigital resource centers.

RGB image-based method for phenotyping rust disease progress in pea leaves using R

BackgroundRust is a damaging disease affecting vital crops, including pea, and identifying highly resistant genotypes remains a challenge. Accurate measurement of infection levels in large germplasm collections is crucial for finding new resistance sources. Current evaluation methods rely on visual estimation of disease severity and infection type under field or controlled conditions. While they identify some resistance sources, they are error-prone and time-consuming. An image analysis system proves useful, providing an easy-to-use and affordable way to quickly count and measure rust-induced pustules on pea samples. This study aimed to develop an automated image analysis pipeline for accurately calculating rust disease progression parameters under controlled conditions, ensuring reliable data collection.ResultsA highly efficient and automatic image-based method for assessing rust disease in pea leaves was developed using R. The method’s optimization and validation involved testing different segmentation indices and image resolutions on 600 pea leaflets with rust symptoms. The approach allows automatic estimation of parameters like pustule number, pustule size, leaf area, and percentage of pustule coverage. It reconstructs time series data for each leaf and integrates daily estimates into disease progression parameters, including latency period and area under the disease progression curve. Significant variation in disease responses was observed between genotypes using both visual ratings and image-based analysis. Among assessed segmentation indices, the Normalized Green Red Difference Index (NGRDI) proved fastest, analysing 600 leaflets at 60% resolution in 62 s with parallel processing. Lin’s concordance correlation coefficient between image-based and visual pustule counting showed over 0.98 accuracy at full resolution. While lower resolution slightly reduced accuracy, differences were statistically insignificant for most disease progression parameters, significantly reducing processing time and storage space. NGRDI was optimal at all time points, providing highly accurate estimations with minimal accumulated error.ConclusionsA new image-based method for monitoring pea rust disease in detached leaves, using RGB spectral indices segmentation and pixel value thresholding, improves resolution and precision. It rapidly analyses hundreds of images with accuracy comparable to visual methods and higher than other image-based approaches. This method evaluates rust progression in pea, eliminating rater-induced errors from traditional methods. Implementing this approach to evaluate large germplasm collections will improve our understanding of plant-pathogen interactions and aid future breeding for novel pea cultivars with increased rust resistance.

Determining Genetic Markers and Seed Compositions Related to High Test Weight in Glycine max.

Test weight, one of the primary indicators of soybean seed quality, is measured as the amount of soybean seeds in kilograms that can fit into one hectoliter. The price that growers receive for their soybean is dependent on test weight. Over the past 50 years, growers have observed a decreasing trend in test weight. Therefore, it is imperative to understand better the relationship between soybean test weight and other traits to enable breeders to select parental lines with high test weights in breeding programs to ensure the grower's profitability. The objectives of the study were to identify genetic markers associated with high test weight in soybean and to determine the correlation between high test weight and five important seed composition traits (protein, oil, sucrose, raffinose, and stachyose content). Maturity group IV and V germplasms from the USDA soybean germplasm collection were grown in Blacksburg and Warsaw in Virginia from 2019 to 2021 and were measured for all of the above traits. Results show that test weight values ranged from 62-77 kg/hL over the three years. Multiple single-nucleotide polymorphisms (SNPs) significantly associated with high test weight were found on chromosome (Chr.) 15 along with a couple on chromosome 14, and 11 candidate genes were found near these SNPs. Test weight was found to be significantly negatively correlated with oil content, inconsistently correlated with protein content in all environments, and negatively correlated but not significantly with all three sugars except for raffinose in Blacksburg 2019. We concluded that the genes that underlie test weight might be on chromosome 15, and the validated associated SNPs might be used to assist breeding selection of test weight. Breeders should pay special attention to test weight while selecting for high oil content in soybean due to their negative correlation.