Germplasm Collection Research Articles

Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics.

The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.

Agro-morphological Characterization and Digitization of Job’s Tears (Coix lacryma-jobi L.) Germplasm: A Minor Cereal Crop of Northeastern India

Thirty-seven Job’s tears accessions of India’s northeastern hill region (NEH) were characterized for nine quantitative and eight qualitative traits. Prominent furrow and elliptic shape of grain in soft-shelled types are supposed to be the most important trait that indicates the domestication trend of the crop in NEH region. Principal component analysis showed that agro-morphological traits, namely time for first heading, days to 80% maturity, seed yield/plant (g), number of culms, and length of culm (cm) have significantly contributed to the diversity. Correlation analysis has shown significant correlations between different yield-contributing traits. Diversity and potential traits in each cluster were also identified through cluster analysis. Grid mapping was done to identify the areas for collection of trait-specific germplasm like higher number of culms, length of culm and hundred seed weight. The germplasm accessions IC0332644, IC0416831 and IC0540173 were identified as promising genotypes

Determining morphological and biochemical indices to select for smut-resistant sugarcane varieties

ABSTRACT In Sri Lanka, smut in sugarcane (Saccharum spp. hybrid) is caused by Sporisorium scitamineum and results in significant crop yield and economic losses. Current field evaluation methods to identify smut resistance in sugarcane are time consuming and do not show an association between disease resistance and the resistance mechanisms. This research was conducted to identify morphological and biochemical characters as selection indices of smut-resistant varieties to strengthen the existing varietal selection program. Fifty accessions were selected from the sugarcane germplasm collection and tested for their resistance to S. scitamineum by the standard inoculation method. The disease incidence and Area Under Disease Progress Curve (AUDPC) were assessed in the first two crop cycles. Pearson correlation coefficients were used to identify relationships of AUDPC with evaluated nine morphological and biochemical characteristics. Principal component analysis (PCA) was used to identify the indices associated with smut resistance and select the superior sugarcane varieties. Significant negative correlations (P < 0.05) were detected between AUDPC and total phenols in the leaves, bud hardness, foliage inclination angle (FIA) and number of scale leaves in the buds. The tested nine morphological and biochemical indices formed four major clusters by PCA with a cumulative contribution rate of 66%. The findings revealed that total phenols in the leaf, bud hardness, FIA and the number of scale leaves in the bud are useful, simple and non-laborious indices to determine sugarcane smut resistance in varietal selection.

Assessment of Genetic Divergence through Principal Component Analysis and Clustering in Tomato Germplasm Accessions

The base material of this study comprises of 104 tomato accessions including local landraces, varieties and germplasm collections. The collected tomato accessions were evaluated using 13 quantitative traits by Principal Component Analysis (PCA) and Hierarchial clustering. PCA was done to quantify diversity among the germplasm accessions and also the contribution of individual traits towards diversity. In our study, only the first four (PC1, PC2, PC3 and PC4) of the thirteen principal components yielded eigen value more than one indicating the greater influence of identified traits under study. The first six PCs accounts for 84% of variability whereas, PC1 exhibited 41% of total variability. Cluster analysis aids to classify the genotypes based on the grouping pattern of the accessions under evaluation. According to the dendrogram obtained, cluster analysis grouped 104 tomato accessions into two significant clusters. The first cluster consists of 16 genotypes whereas, the second cluster consists of 88 genotypes. Among the genotypes used in this study EC617055, EC617061, EC638302, Periakulam local and EC631390 were found to be best performing in terms of yield and quality. These accessions can be used as a base material in future breeding programs.

Diversity and structure assessment of the genetic resources in a germplasm collection from a vanilla breeding programme in Madagascar

AbstractA breeding programme of aromatic vanilla, dating back to 1944, was conducted in Ambohitsara, Antalaha, SAVA (Sambava, Antalaha, Vohemara, Andapa) – Madagascar. Imported, local, wild and cultivated vanillas were used as progenitors and thousands of hybrids were generated. However, this germplasm has not undergone any genetic evaluation, and it appears that these valuable genetic resources have been dispersed or lost after the end of the programme (2000). This study aims to investigate the genetic diversity and structure of rescued genotypes currently held in a local collection in Antalaha. Double digest restriction associated-site (RAD)-seq (ddRAD)-seq protocol was applied, providing 865 million read sequences from 56 accessions. The ddRAD sequences have been deposited to the SRA archive of NCBI. From the data, 23,701 filtered concordant common Single Nucleotide Polymorphisms (SNPs) were identified using the three widely used tools (Stacks, BCFtools, Genome Analysis ToolKit - GATK) for short-read library sequencing. These SNPs were used for germplasm evaluation. Clustering analysis segregated samples into five genetic groups: Vanilla planifolia, Vanilla pompona, hybrid Tsitaitra, Vanille Banane and the phenotype Tsivaky. Our analysis revealed distinct subgroups within V. pompona and Tsitaitra, emphasizing the importance of further characterization to accurately reflect the genetic diversity and facilitate better utilization of these accessions in future research and germplasm management. The presence of private alleles in all groups (from 487 to 2866) indicated that populations were diverging and represented a large gene pool that could be useful for future breeding efforts. The genetic data obtained from this study offers valuable insights into the genetic diversity and structure of the vanilla population, with potential applications in breeding and conservation efforts.

Biodiversity of hot pepper germplasm collection from Vegetable Research Development Station Buzau, Romania

Biodiversity of hot pepper germplasm collection from Vegetable Research Development Station Buzau, Romania

Phenotypic Plasticity Index as a Strategy for Selecting Water-Stress-Adapted Coffee Genotypes

The adaptive potential of plants is commonly used as an indicator of genotypes with higher breeding program potential. However, the complexity and interaction of plant metabolic parameters pose a challenge to selection strategies. In this context, this study aimed to explore phenotypic plasticity within the germplasm of Hybrid Timor coffee. Additionally, we assessed the utility of the multivariate phenotypic plasticity index (MVPi) as a promising tool to predict genotype performance across diverse climatic conditions. To achieve this, we evaluated the performance of seven accessions from the Hybrid Timor germplasm in comparison to the Rubi and IPR 100 cultivars, known for their susceptibility and resistance to drought, respectively. The experiment took place in a greenhouse under two conditions: one with normal soil moisture levels near maximum capacity, and the other with a water deficit scenario involving a period of no irrigation followed by rehydration. Data on physiological and biochemical factors were collected at three stages: before applying the water deficit, during its imposition, and after rehydration. Growth data were obtained by the difference between the beginning and end of the experimental period Furthermore, field evaluations of the productivity of the same genotypes were carried out over two consecutive seasons. Based on physiological and biochemical assessments, the MVPi was computed, employing Euclidean distance between principal component multivariate analysis scores. Subsequently, this index was correlated with growth and productivity data through linear regressions. Our findings reveal that the plastic genotypes that are capable of significantly altering physiological and biochemical parameters in response to environmental stimuli exhibited reduced biomass loss in both aerial and root parts. As a result, this positively influenced their productivity. Enhanced plasticity was particularly prominent in accessions from the MG Germplasm Collection: MG 311—Hybrid Timor UFV 428-02, MG 270—Hybrid Timor UFV 377-21, and MG 279—Hybrid Timor UFV 376-31, alongside the Rubi MG 1192 cultivar. The MVPi emerged as a valuable instrument to assess genotype adaptability and predict their performance under varying climatic scenarios.

Identification and mapping of a recessive allele, dt3, specifying semideterminate stem growth habit in soybean

Key messageA locus, dt3, modulating semideterminancy in soybean, was discovered by a combination of genome-wide association studies and linkage mapping with multiple distinct biparental populations.Stem growth habit is a key architectural trait in many plants that contributes to plant productivity and environmental adaptation. In soybean, stem growth habit is classified as indeterminate, semideterminate, or determinate, of which semideterminacy is often considered as a counterpart of the “Green Revolution” trait in cereals that significantly increased grain yields. It has been demonstrated that semideterminacy in soybean is modulated by epistatic interaction between two loci, Dt1 on chromosome 19 and Dt2 on chromosome 18, with the latter as a negative regulator of the former. Here, we report the discovery of a third locus, Dt3, modulating soybean stem growth habit, which was delineated to a ~ 196-kb region on chromosome 10 by a combination of allelic and haplotypic analysis of the Dt1 and Dt2 loci in the USDA soybean Germplasm Collection, genome-wide association studies with three subsets of the collection, and linkage mapping with four biparental populations derived from crosses between one of two elite indeterminate cultivars and each of four semideterminate varieties possessing neither Dt2 nor dt1. These four semideterminate varieties are recessive mutants (i.e., dt3/dt3) in the Dt1/Dt1;dt2/dt2 background. As the semideterminacy modulated by the Dt2 allele has unfavorable pleotropic effects such as sensitivity to drought stress, dt3 may be an ideal alternative for use to develop semideterminate cultivars that are more resilient to such an environmental stress. This study enhances our understanding of the genetic factors underlying semideterminacy and enables more accurate marker-assisted selection for stem growth habit in soybean breeding.

SSR Genotyping and Marker-Trait Association with Yield Components in a Kazakh Germplasm Collection of Chickpea (Cicer arietinum L.).

Genetic diversity and marker-trait association with yield-related components were assessed in 39 chickpea accessions from a germplasm collection with either spring or autumn-sown seeds in South-Eastern Kazakhstan. Chickpea accessions originated from Azerbaijan, Germany, Kazakhstan, Moldova, Russia, Türkiye, Ukraine, Syria, and the International Center for Agricultural Research in the Dry Areas (ICARDA). Eleven SSR markers were used for molecular genotyping. Yield and yield components were evaluated in nine traits in experiments with spring and autumn seed sowing. The number of alleles of polymorphic markers varied from 2 to 11. The greatest polymorphism was found in the studied chickpea genotypes using SSR marker TA22 (11 alleles), while NCPGR6 and NCPGR12 markers were monomorphic. In the studied chickpea accessions, unique alleles of the SSR loci TA14, TA46, TA76s, and TA142 were found that were not previously described by other authors. An analysis of correlation relationships between yield-related traits in chickpea revealed the dependence of yield on plant height, branching, and the setting of a large number of beans. These traits showed maximal values in experiments with chickpea plants from autumn seed sowing. An analysis of the relationship between the SSR markers applied and morphological yield-related traits revealed several informative markers associated with important traits, such as plant height, height to first pod, number of branches, number of productive nodes, number of pods per plant, hundred seed weight, seed weight per plant, and seed yield.

Recovery of Neglected Species with Cloud Water Micro Condense Capacity as a Response to Climate Change: The Case of Sclerophyllous Boxwoods of Buxus balearica Lam. in the Southern Spanish Mediterranean

Understanding the survival needs of neglected or underutilized species (NUS) in agroforestry can offer valuable insights to mitigate climate change and biodiversity loss. This paper analyses the habitat heterogeneity of Buxus balearica populations (palaeorelict of the Mediterranean Basin) using a methodology that integrates four approaches: ecological profiling, multivariate analysis, and the clustering of populations according to environmental variables and suitability. The habitat analysis was conducted on 240 occurrence points, integrating open-source databases and germplasm collection field work. Results reveal that the distribution of B. balearica in the south of the Iberian Peninsula is mainly conditioned by thermal variations, the humidity regime, and microtopography, which makes it very vulnerable to current and future climate change scenarios. The analysis of habitat heterogeneity demonstrates its capacity to estimate genetic diversity, which provides a solid basis for future research and conservation actions. The rapid extinction process of these boxwoods is evident by comparing the suitability model under different climate scenarios. There is an urgent need to improve the current status of the species and associated landscapes, considering B. balearica as an underutilized species, and establishing a sound management plan to reinforce its populations and protect its natural habitat.

Microsatellite Markers: A Tool to Assess the Genetic Diversity of Yellow Mustard (Sinapis alba L.)

Microsatellite markers were used for the assessment of genetic diversity and genetic structure in a germplasm collection of yellow mustard, Sinapis alba L. The comprehensive collection of genetic resources represented 187 registered varieties, landraces, and breeding materials. Microsatellites generated 44 polymorphic alleles in 15 loci. Eleven of them were medium to highly polymorphic, and the high levels of observed heterozygosity (0.12–0.83) and Nei’s gene diversity index (0.11–0.68) indicated a high level of polymorphism. Based on PCoA and neighbor joining analyses, the genetic resources were divided into two groups. The range of genetic dissimilarity in the analysed collection was in the range of 0.00–1.00. The high level of dissimilarity between the accessions was documented by the high WAM value (33.82%). Bayesian clustering algorithms were performed in the STRUCTURE 2.3.4 software. The number of clusters was estimated at K = 2. The accessions were classified according to Q1/Q2 values. The low average values of the parameters Fst_1 (0.3482), Fst_2 (0.1916), and parameter alpha (0.0602) indicated substantial mating barriers between varieties and reproductive isolation due to the limited exchange of genetic resources between breeders. These results demonstrated the importance of extensive collections of genetic resources for the maintenance of genetic diversity and indicated considerable genetic differentiation among accessions.

Genome-Wide Association Mapping and Genomic Prediction of Fusarium Wilt Race 2 Resistance in the USDA Citrullus amarus Collection.

Fusarium wilt caused by Fusarium oxysporum f. sp. niveum (Fon) race 2 is a serious disease in watermelon and can reduce yields by 80%. Genome-wide association studies (GWAS) are a valuable tool in dissecting the genetic basis of traits. Citrullus amarus accessions (n = 120) from the USDA germplasm collection were genotyped with whole-genome resequencing, resulting in 2,126,759 single nucleotide polymorphic (SNP) markers that were utilized for GWAS. Three models were used for GWAS with the R package GAPIT. Mixed linear model (MLM) analysis did not identify any significant marker associations. FarmCPU identified four quantitative trait nucleotides (QTN) on three different chromosomes (i.e., chromosomes 1, 5, and 9), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) identified one QTN on chromosome 10 as significantly associated with Fon race 2 resistance. FarmCPU identified four QTN that explained 60% of Fon race 2 resistance, and the single QTN from BLINK explained 27%. Relevant candidate genes were found within the linkage disequilibrium (LD) blocks of these significant SNPs, including genes encoding aquaporins, expansins, 2S albumins, and glutathione S-transferases which have been shown to be involved in imparting resistance to Fusarium spp. Genomic predictions (GP) for Fon race 2 resistance using all 2,126,759 SNPs resulted in a mean prediction accuracy of 0.08 with five-fold cross-validation employing genomic best linear unbiased prediction (gBLUP) or ridge-regression best linear unbiased prediction (rrBLUP). Mean prediction accuracy with gBLUP leave-one-out cross-validation was 0.48. Thus, along with identifying genomic regions associated with Fon race 2 resistance among the accessions, this study observed prediction accuracies that were strongly influenced by population size.

Biotechnological Strategies Adopted for Sugarcane Disease Management in Tucumán, Argentina

Sugarcane diseases can be controlled by an integrated management approach where biotechnological tools can successfully contribute. The Obispo Colombres Agroindustrial Experimental Station (EEAOC) in Tucumán (Argentina’s main sugarcane producer) has successfully implemented multiple strategies that greatly enhance the productivity of sugarcane fields. The local breeding program develops resistant varieties by applying molecular markers to reveal the presence of Bru1 gene for brown rust resistance throughout the EEAOC germplasm collection. In addition, SNP alleles linked to novel sources of resistance were identified following a selective genotyping strategy. Another strategy is the implementation of a seed cane sanitation project using hydrothermal therapy, an in vitro culture technique, molecular diagnosis of diseases, and bionanoparticles. As a result, the incidence of systemic diseases has significantly decreased in the production fields. More recently, the use of biological products has shown to be effective for disease control in EEAOC varieties. In summary, several biotechnological strategies including molecular markers associated with resistant sources, in vitro culture of apical meristems, molecular diagnostic techniques, and the use of bioproducts are being successfully used for the sustainable management of sugarcane diseases in Tucumán, Argentina.

Assessment of the chemical and genetic variability among accessions of Cicerbita alpina (L.) Wallr., an alpine plant with anthelmintic properties

Cicerbita alpina(L.) Wallr, is a perennial alpine plant and a member of theAsteraceaefamily, typically found at altitudes above 1000 meters in the Italian Alps. Although previously utilized primarily as a local delicacy, recent studies have revealed strong antiparasitic activity throughin vitroexperiments. In Europe, numerous chemical drugs employed to combat nematodes — helminths that infest the digestive tract of livestock — are banned due to their environmental harm or show only reduced efficiency because of the development of resistance. Consequently, there is a growing demand for new alternative anthelmintic treatments in agricultural practices. Specialized metabolites found in the extracts ofC. alpinacould offer a sustainable and biological alternative to chemical drugs, specifically for nematode control. For this purpose, a unique germplasm collection originating from eight distinct natural populations in the Italian Alps was analyzed for its chemical diversity using state-of-the-art targeted LC-MS/MS spectrometry, including quantification based on multiple reaction monitoring. The predominant metabolites identified from the species were the caffeic acid derivatives chicoric acid, chlorogenic acid, and 3. 5-dicaffeoylquinic acid, the sesquiterpene lactone derivative 8-O-acetyl-15-ß-D-glucopyranosyl lactucin and the flavone glycosides, apigenin-7-O-glucoside and luteolin-7-O-glucoside, alongside their precursors apigenin and luteolin, respectively. Additionally, the genetic diversity of eighty individual plants within the germplasm collection was evaluated using ten DNA molecular markers (Simple Sequence Repeats), successfully transferred from two closely related species (Cichorium intybusandTanacetum parthenium). This investigation unveiled a significant range of genetic diversity within the examined populations, resulting in the establishment of three distinct genetic groups. The findings were further correlated with the original ecological environment and local climate conditions spanning a biennial period, indicating substantial variations among the different accessions and the intricate interplay between genetic background and environmental factors. These results could serve as a basis for future domestication of the species through plant breeding programs ensuring product quality, but also facilitating the cultivation ofC. alpinain more diverse geographic regions.

Characterization of agronomic traits and genomic diversity in a newly assembled radish core collection

AbstractCrop breeding programs are reliant on the genetic diversity of varieties and germplasm collections. Raphanus sativus L. is a root crop species of the Brassicaceae family that accounts for ∼2% of global vegetable production. We recently reported the assembly of a new radish core collection consisting of 125 accessions obtained from worldwide germplasm banks. To develop a comprehensive plant resource for radish research and breeding, we characterized the agronomic traits of 83 accessions and analyzed their genome‐wide DNA variations along with 17 previously analyzed accessions. A total of 14 agronomically important root, leaf, and flower phenotypic traits were examined according to the guidelines of the International Union for the Protection of New Plant Varieties. Chemical diversity in radish roots was investigated by measuring their sugar, glucosinolate, and anthocyanin contents. Through high‐depth whole‐genome resequencing of 100 accessions and multi‐sample genotyping analysis using the Rs2.0 genome assembly as a reference, we identified a total of 796,294 homozygous high‐quality single‐nucleotide polymorphisms. Genetic structural analysis using a neighbor‐joining algorithm and multi‐dimensional scaling analysis of the variations were applied to classify the accessions into three major groups, including 37 and 55 accessions of European and Asian cultivated radishes, respectively, and eight wild radish accessions. For each accession, the mitochondria‐encoded Ogura cytoplasmic male‐sterility determinant orf138 and nuclear fertility restorer PPR‐B genes were reconstructed by reference‐guided assembly. It is anticipated that these genetic diversity and agronomic properties of the radish core collection will facilitate breeding programs to develop new radish cultivars with desirable profiles.

Accelerating genetic gains for quantitative resistance to verticillium wilt through predictive breeding in strawberry.

Verticillium wilt (VW), a devastating vascular wilt disease of strawberry (Fragaria ananassa), has caused economic losses for nearly a century. This disease is caused by the soil-borne pathogen Verticillium dahliae, which occurs nearly worldwide and causes disease in numerous agriculturally important plants. The development of VW-resistant cultivars is critically important for the sustainability of strawberry production. We previously showed that a preponderance of the genetic resources (asexually propagated hybrid individuals) preserved in public germplasm collections were moderately to highly susceptible and that genetic gains for increased resistance to VW have been negligible over the last 60 years. To more fully understand the challenges associated with breeding for increased quantitative resistance to this pathogen, we developed and phenotyped a training population of hybrids ( ) among elite parents with a wide range of resistance phenotypes. When these data were combined with training data from a population of elite and exotic hybrids ( ), genomic prediction accuracies of 0.47-0.48 were achieved and were predicted to explain 70%-75% of the additive genetic variance for resistance. We concluded that breeding values for resistance to VW can be predicted with sufficient accuracy for effective genomic selection with routine updating of training populations.

Promoter insertion leads to polyembryony in mango — a case of convergent evolution with citrus

Abstract Sexual reproduction in plants is the main pathway for creating new genetic combinations in modern agriculture. In heterozygous plants, after the identification of a plant with desired traits, vegetative propagation (cloning) is the primary path to create genetically uniform plants. Another natural plant mechanism that creates genetically uniform plants (clones) is apomixis. In fruit crops like citrus and mango, sporophytic apomixis results in polyembryony, where seeds contain multiple embryos, one of which is sexually originated and the others are vegetative clones of the parent mother tree. Utilizing the mango genome and genetic analysis of a diverse germplasm collection, we identified MiRWP as the gene that causes polyembryony in mango. There is a strong correlation between a specific insertion in the gene’s promoter region and altered expression in flowers and developing fruitlets, inducing multiple embryos. The MiRWP gene is an ortholog of CitRWP that causes polyembryony in citrus. Based on the data, we speculate that promoter insertion events, which occurred independently in citrus and mango, induced nucellar embryogenesis. The results suggest convergent evolution of polyembryony in the two species. Further work is required to demonstrate the utility of these genes (mango and citrus) in other biological systems as a tool for the clonal production of other crops.

Multi-environment screening of Linum germplasm collection for dissecting the potential of bud fly (Dasyneura lini Barnes) resistance and assembling a reference set for efficient utilization in genetic improvement

Linseed or flaxseed (Linum usitatissimum L.) is one of the most ancient industrial crops domesticated for oil and natural fiber. Bud fly (Dasyneura lini Barnes) susceptibility is serious biotic stress affecting its production both quantitatively and qualitatively. It has economic significance particularly in Asian countries, causing substantial crop damage leading to significant yield penalty and deterioration of seed quality. In the present study, a large collection of 2598 linseed germplasm accessions from the Indian National Genebank were screened for bud fly infestation at two natural hot-spot locations in India. The maximum bud fly incidence across all four environments ranged from 47.93% to 90.47%. Based on average bud fly infestation over the environments, a reference set comprising 195 accessions including 46 resistant, 94 moderately resistant and 55 moderately susceptible/susceptible germplasm was developed. Further, a selected subset of 26 accessions having a common reaction against linseed bud fly at both locations was validated for resistance over multi-location-year environments (four environments over two years) through GGE biplot analysis. The GGE biplot revealed that two accessions, G22 (EC0993391) and G23 (IC0633096) were highly resistant (<10% bud fly damage) and most stable over the tested environments against bud fly infestation. Additionally, two accessions namely G15 (IC0498795) and G24 (EC0099001) were considered resistant as they showed consistent performance and low bud fly infestation in comparison to the resistant check (Neela). Moreover, these accessions had a great buffering capacity to perceive environmental signals for developing adaptive capacities in a wide range of environments. The identified germplasm accessions may serve as potential donors for accelerating the resistance breeding programme to impart a long-lasting, broad-spectrum resistance against linseed bud fly.

A comprehensive lettuce variation map reveals the impact of structural variations in agronomic traits

BackgroundAs an important vegetable crop, cultivated lettuce is grown worldwide and a great variety of agronomic traits have been preserved within germplasm collections. The mechanisms underlying these phenotypic variations remain to be elucidated in association with sequence variations. Compared with single nucleotide polymorphisms, structural variations (SVs) that have more impacts on gene functions remain largely uncharacterized in the lettuce genome.ResultsHere, we produced a comprehensive SV set for 333 wild and cultivated lettuce accessions. Comparison of SV frequencies showed that the SVs prevalent in L. sativa affected the genes enriched in carbohydrate derivative catabolic and secondary metabolic processes. Genome-wide association analysis of seven agronomic traits uncovered potentially causal SVs associated with seed coat color and leaf anthocyanin content.ConclusionOur work characterized a great abundance of SVs in the lettuce genome, and provides a valuable genomic resource for future lettuce breeding.

Efforts to cryopreserve shrimp (Penaeid) genetic resources and the potential for a shrimp germplasm bank in the United States

Shrimp are an important global protein source and the most consumed seafood in the United States. Despite the importance of shrimp to the United States and to global food production, genetic diversity and germplasm preservation has not received critical attention. At this time, shrimp genetic resources have not been added to the USDA National Animal Germplasm Program gene bank in the United States. Here we summarize the importance of shrimp genetic resources to US and global food production and describe the need for shrimp germplasm cryopreservation. We also describe past and current research efforts to cryopreserve shrimp germplasm in the forms of embryos, larvae, and spermatophores. While early work has focused on protocol development, these protocols have not been successfully implemented on a commercial scale. It has also not been documented that cryopreserved larvae can reach reproductive maturity. Therefore, additional research and stakeholder efforts are needed to develop and validate larval cryopreservation methods capable of producing larvae reaching reproductive maturity. Finally, we discuss the necessary material needed to establish a shrimp germplasm collection in the USDA repository. We describe the numbers of larvae or families needed to reconstitute a breeding population given varying levels of cryopreservation success. Early work relating to shrimp germplasm cryopreservation is laying the foundation for the successful cryopreservation of larvae and spermatophores as well as the establishment of a national germplasm bank for shrimp larvae within the United States.