Germplasm Collection Research Articles

First report of sweepoviruses infecting Ipomeas batatas L. cultivars and landraces in Trinidad.

Root crops, referred to as ground provisions in the Caribbean, are traditional staples in Trinidad. One widely consumed example is sweet potato (Ipomeas batatas L.). The crop is mainly produced by subsistence farming which together with imports from neighboring Caribbean countries meet domestic demand (Singh et al. 2008). The Central Experiment Station, situated in the eastern part of Trinidad, maintains a sweet potato germplasm collection comprising both imported and locally-sourced landraces for cultivar development and distribution of propagules. In May 2017 chlorosis and leaf curling symptoms, typically associated with sweepoviruses, were observed on imported cultivars, Centennial, Jewel, 86 BM 31, TIB 313, TIB 8 21 1, and S128, and the landraces, Kick Up Jenny, John, and Carrot. Leaf samples from these nine symptomatic plants were collected for analysis, along with samples from the asymptomatic landrace, Chickenfoot. Total nucleic acids were extracted (Sharma et al. 2008) and the samples were assayed by PCR using degenerate primers SPG1 and SPG2 (Li et al. 2004) that target the replication associated protein gene (ORF C1), a highly conserved region of sweepoviruses. Amplicons of 912-bp were obtained from two of the nine symptomatic plants (TIB 8 21 1, Kick Up Jenny), but not from the asymptomatic Chickenfoot. The same samples were assayed by PCR amplification using primers SpvF and SpvR (Avelar 2015) which are specific to a highly conserved 632-bp region of the coat protein gene (ORF V1) of sweet potato leaf curl virus (SPLCV). All 10 samples tested positive for SPLCV, including the asymptomatic landrace, Chickenfoot. The ORF V1 PCR products from three of the 10 samples, namely Chickenfoot, TIB 8 21 1, and Kick Up Jenny, were cloned and sequenced (two clones per sample). Comparison of the sequences (GenBank accession nos. OR882007 [Chickenfoot], OR913125 [TIB 8 21 1] and OR913126 [Kick Up Jenny]) identified up to 4% nt sequence variability between samples. In BLASTn analysis, they were most closely related to the SPLCV isolate China:Sichuan (GenBank accession no. KJ013557), sharing 94 to 98% nt identity. Total nucleic extracts from one representative sample (TIB 8 21 1) was used as template for rolling circle amplification (RCA, TempliPhi Amplification Kit, GE Healthcare Life Sciences, Piscataway, NJ, USA). Digestion of the RCA product with StuI (Thermo Scientific, MA, USA) yielded ~2.8 kb DNA fragments indicative of monomeric full length genomes. Digested fragments were cloned, completely sequenced and deposited in GenBank under the accession nos. OR866202 (2,821 nts) and OR866203 (2,828 nts). Two species of sweepoviruses were detected. In BLASTn analysis, OR866202 showed 95% nt identity with sweet potato golden vein associated virus (SPGVaV) US:MS:1B-3 (GenBank accession no. HQ333143.1) which is a recombinant virus comprised of SPLCV and sweet potato leaf curl Georgia virus (SPLCGV) (Zhang and Ling 2011) and in BLASTx analysis OR866202 was most similar (92-99%) to SPLCV isolates from Brazil (GenBank accession nos. ACI23475.1, AGW16179.1, ACY79479.1), Peru (GenBank accession no. ACY79466.1) and China (GenBank accession nos. ACY79439.1). OR866203 shared 96% nt identity with SPLCV China:Henan25(8):2012 (GenBank accession no. KF040465.1) in BLASTn analysis and BLASTx analysis revealed ≥ 94% aa sequence identity with SPLCV from Brazil (GenBank accession nos. ACI23475.1, AGW16179.1, ADZ96559.1), Peru (GenBank accession no. ACY79479.1), China (GenBank accession no. ACY79466.1). and Spain (GenBank accession no. QWQ56365.1). Both Trinidad isolates also showed 90-96% nt identity with SPLCV from Korea (GenBank accession no.s KT992061.1, KT992064.1, unpublished). This is the first detection of sweepoviruses in Trinidad. SPGVaV has been reported in Brazil, the United States and Korea (Kil et al. 2014), while SPLCV has been described in other Caribbean islands, including Cuba, Jamaica, Puerto Rico, St. Vincent (Cuellar et al. 2015), and Barbados (Alleyne et al. 2019), as well as several countries in South America. Although Koch's postulates were not completed, our findings suggest that sweet potato crops in Trinidad harbor sweepoviruses, notwithstanding efforts to distribute pathogen-free materials and, in some instances, the apparent absence of visible symptoms on infected plants. Further studies on the management and impact of these viruses are necessary, including their prevalence in the sweet potato production regions of Trinidad.

Variation in plant morphology and leaf essential oil composition of a representative <em>Cinnamomum verum</em> collection from Sri Lanka

Sri Lankan cinnamon germplasm is an underexploited genetic resource of high breeding potential. A representative collection of a cultivated cinnamon germplasm with 48 accessions, is established at the University of Ruhuna, Sri Lanka. From that collection, 40 three-year-old vegetative-propagated accessions, were used in this study to study the variations in plant morphology and leaf oil composition. Flush colour was determined as four main categories of pink, red, brown, and green in all 48 accessions. Leaf length, leaf width, leaf length to width ratio and petiole length varied from 7.9 to 14.5 cm, 3.8 to 7.3 cm, 1.8 to 3.07 cm, and 1 to 2.2 cm, respectively, in the selected 40 accessions. Both the good fragrant aroma category of bark fragrance and the sweet pungent category of bark taste were recorded in 21 of the 40 accessions. Twenty (20) accessions from above collection were selected for leaf oil analysis. Gas chromatography-mass spectrometry (GC-MS) of leaf oil revealed the presence of 146 chemical compounds. Eugenol was the major compound of 17 accessions (52.2% to 79.5%). Two accessions with zero eugenol contained 86.8% and 91.9% of benzyl benzoate (BB), in contrast to that of 0%-0.65% from other accessions. One accession produced 16.6% eugenol and 22.3% BB. A green flush colour associated with a higher BB percentage suggested a potential morphological marker for BB. The PCA for 20 accessions explained 88.11% of total variance. The cinnamon accessions with high BB, KA11 and GB17, were clustered together, and HB12 was isolated on a different cluster. Positive correlations were detected between linalool and β-caryophyllene (0.649), linalool and BB (0.770) (p < 0.01), and negative correlations between eugenol and linalool (-0.630) and eugenol and BB (-0.886) (p <0.01).

Genome‐wide association study of adult plant resistance to spot blotch in an elite Canadian two‐row barley germplasm collection

AbstractSpot blotch, caused by Bipolaris sorokiniana, is a growing concern for barley (Hordeum vulgare) production in most humid, temperate growing regions of the world. Under epidemic conditions, this disease can reduce yields significantly. Reduction of kernel plumpness is associated with lower malt extract and consequently grain quality. Enhanced resistance to this disease is a major goal of western Canadian two‐row barley breeding programmes; however, two‐row barley is considered to be more susceptible than six‐row barley. Plant–pathogen interactions observed for Canadian germplasm are polygenic, where quantitative breeding methods could be beneficial for the development of resistant germplasm. A germplasm panel consisting of 200 two‐row, spring barley genotypes with differential reaction to spot blotch was evaluated at Brandon, Manitoba (MB), and Melfort, Saskatchewan (SK), over eight site years. Genome‐wide association study was conducted using a 50k single‐nucleotide polymorphism (SNP) Illumina iSelect genotyping array. The most‐resistant germplasm was found to carry Midwest Six‐rowed Durable Resistant Haplotype (MSDRH) alleles at the loci located on chromosomes 1H (Rcs‐qtl‐1H‐11_10764), 3H (Rcs‐qtl‐3H‐11_10565) and 7H (Rcs‐qtl‐7H‐11_20162, Rcs5 locus), where the 3H locus was found to be the most under‐represented in Canadian germplasm. Additional marker‐trait associations within nurseries were identified on chromosomes 1H, 2H and 4H. Several of the SNP markers identified were found to be polymorphic within the Canadian two‐row germplasm panel and thus could be useful for enhancing spot blotch resistance in two‐row barley for development of resistant cultivars.

Phenotyping Peanut Drought Stress with Aerial Remote-Sensing and Crop Index Data

Peanut (Arachis hypogaea L.) plants respond to drought stress through changes in morpho-physiological and agronomic characteristics that breeders can use to improve the drought tolerance of this crop. Although agronomic traits, such as plant height, lateral growth, and yield, are easily measured, they may have low heritability due to environmental dependencies, including the soil type and rainfall distribution. Morpho-physiological characteristics, which may have high heritability, allow for optimal genetic gain. However, they are challenging to measure accurately at the field scale, hindering the confident selection of drought-tolerant genotypes. To this end, aerial imagery collected from unmanned aerial vehicles (UAVs) may provide confident phenotyping of drought tolerance. We selected a subset of 28 accessions from the U.S. peanut mini-core germplasm collection for in-depth evaluation under well-watered (rainfed) and water-restricted conditions in 2018 and 2019. We measured morpho-physiological and agronomic characteristics manually and estimated them from aerially collected vegetation indices. The peanut genotype and water regime significantly (p < 0.05) affected all the plant characteristics (RCC, SLA, yield, etc.). Manual and aerial measurements correlated with r values ranging from 0.02 to 0.94 (p < 0.05), but aerially estimated traits had a higher broad sense heritability (H2) than manual measurements. In particular, CO2 assimilation, stomatal conductance, and transpiration rates were efficiently estimated (R2 ranging from 0.76 to 0.86) from the vegetation indices, indicating that UAVs can be used to phenotype drought tolerance for genetic gains in peanut plants.

Analyzing the response of rice to tefuryltrione herbicide: Haplotype variation and evolutionary dynamics of the HIS1 gene

Weeds pose multifaceted challenges in rice cultivation, leading to substantial economic losses through reduced yield and poor grain quality. Harnessing the natural genetic diversity in germplasm collections becomes crucial for identifying novel herbicide resistance loci in crops. A comprehensive analysis was conducted on 475 rice accessions from the KRICE depository, assessing their response to TFT (tefuryltrione) and probing the underlying HIS1 (HPPD INHIBITOR SENSITIVE 1) genotypic variations. The HIS1 gene, responsible for detoxifying benzobicyclon (BBC) and imparting broad-spectrum herbicide resistance, holds significant promise in rice breeding. This study explores the genetic landscape of HIS1 within Korean rice collection (KRICE), aiming to unveil genetic variations, haplotype diversity, and evolutionary relationships across diverse rice ecotypes. The indica ecotype showed the highest nucleotide diversity, while the wild and temperate japonica groups exhibited low diversity, hinting at selective sweeps and possible population expansion. Negative Tajima's D values in temperate japonica and wild groups indicate an excess of low-frequency mutations, potentially resulting from selective sweeps. In contrast, with positive Tajima's D values, admixture, indica, and aus groups suggest balancing selection. Furthermore, haplotype analysis uncovered 42 distinct haplotypes within KRICE, with four shared haplotypes between cultivated and wild accessions, four specific to cultivated accessions, and 34 specific to wild types. Phenotypic assessments of these haplotypes revealed that three haplotypes, viz., Hap_1 (predominant in japonica), Hap_2 (predominant in indica), and Hap_3 (specific to indica), displayed significant differences from aus-specific Hap_4 and indica-specific Hap_5. This study offers insights into genetic diversity, selective pressures, and ecotype-specific responses, ultimately paving the way for developing HPPD-inhibiting herbicide-resistant rice cultivars.

Investigating Phenotypic Diversity in a Germplasm Collection of Scarlet Eggplant under Mediterranean Conditions

This study aimed to determine phenotypic diversity in the germplasm collection of Solanum aethiopicum, also known as scarlet eggplant, under Mediterranean conditions. Two different experiments were established in which morphological and valuable agronomic traits were employed to measure diversity among 57 and 55 accessions, respectively. The experiments were carried out in a greenhouse and open field, and descriptors designated by the European Cooperative Program for Plant Genetic Resources (ECPGR) and the International Board for Plant Genetic Resources (IBPGR) were used to measure the plants and fruits. The results from descriptive statistics on quantitative traits data of plants and fruits show a great variation among accessions of Solanum aethiopicum. Multiple correlation analysis in the two distinct experiments shows that the highly correlated variables/descriptors represented fruit quantitative traits. Finally, results from principal component analysis (PCA) confirm that the overall differences observed in the germplasm collection of Solanum aethiopicum were mainly due to fruit quantitative traits, which are decisive for phenotypic characterization of this eggplant.

Selective Genotyping and Phenotyping for Optimization of Genomic Prediction Models for Populations with Different Diversity.

To overcome the different challenges to food security caused by a growing population and climate change, soybean (Glycine max (L.) Merr.) breeders are creating novel cultivars that have the potential to improve productivity while maintaining environmental sustainability. Genomic selection (GS) is an advanced approach that may accelerate the rate of genetic gain in breeding using genome-wide molecular markers. The accuracy of genomic selection can be affected by trait architecture and heritability, marker density, linkage disequilibrium, statistical models, and training set. The selection of a minimal and optimal marker set with high prediction accuracy can lower genotyping costs, computational time, and multicollinearity. Selective phenotyping could reduce the number of genotypes tested in the field while preserving the genetic diversity of the initial population. This study aimed to evaluate different methods of selective genotyping and phenotyping on the accuracy of genomic prediction for soybean yield. The evaluation was performed on three populations: recombinant inbred lines, multifamily diverse lines, and germplasm collection. Strategies adopted for marker selection were as follows: SNP (single nucleotide polymorphism) pruning, estimation of marker effects, randomly selected markers, and genome-wide association study. Reduction of the number of genotypes was performed by selecting a core set from the initial population based on marker data, yet maintaining the original population's genetic diversity. Prediction ability using all markers and genotypes was different among examined populations. The subsets obtained by the model-based strategy can be considered the most suitable for marker selection for all populations. The selective phenotyping based on makers in all cases had higher values of prediction ability compared to minimal values of prediction ability of multiple cycles of random selection, with the highest values of prediction obtained using AN approach and 75% population size. The obtained results indicate that selective genotyping and phenotyping hold great potential and can be integrated as tools for improving or retaining selection accuracy by reducing genotyping or phenotyping costs for genomic selection.

Flooding stress and responses to hypoxia in plants.

In recent years, research on flooding stress and hypoxic responses in plants has gathered increasing attention due to climate change and the important role of O2 in metabolism and signalling. This Collection of Functional Plant Biology on 'Flooding stress and responses to hypoxia in plants' presents key contributions aimed at progressing our current understanding on how plants respond to low-O2 conditions, flooding stress and a combination of stresses commonly found in flooded areas. The Collection emphasises the characterisation of diverse plant responses across different developmental stages, from seed germination to fully developed plants, and under different water stress conditions ranging from waterlogging to complete submergence, or simply low-O2 conditions resulting from limited O2 diffusivity in bulky tissues. Additionally, this Collection highlights diverse approaches, including eco-physiological characterisation of plant responses, detailed descriptions of root anatomical characteristics and their surrounding microenvironments, evaluation of the seed microbiota under flooding stress, the modification of gene expression, and evaluations of diverse germplasm collections.

Prediction accuracy of genomic estimated breeding values for fruit traits in cultivated tomato (Solanum lycopersicum L.)

BackgroundGenomic selection (GS) is an efficient breeding strategy to improve quantitative traits. It is necessary to calculate genomic estimated breeding values (GEBVs) for GS. This study investigated the prediction accuracy of GEBVs for five fruit traits including fruit weight, fruit width, fruit height, pericarp thickness, and Brix. Two tomato germplasm collections (TGC1 and TGC2) were used as training populations, consisting of 162 and 191 accessions, respectively.ResultsLarge phenotypic variations for the fruit traits were found in these collections and the 51K Axiom™ SNP array generated confident 31,142 SNPs. Prediction accuracy was evaluated using different cross-validation methods, GS models, and marker sets in three training populations (TGC1, TGC2, and combined). For cross-validation, LOOCV was effective as k-fold across traits and training populations. The parametric (RR-BLUP, Bayes A, and Bayesian LASSO) and non-parametric (RKHS, SVM, and random forest) models showed different prediction accuracies (0.594–0.870) between traits and training populations. Of these, random forest was the best model for fruit weight (0.780–0.835), fruit width (0.791–0.865), and pericarp thickness (0.643–0.866). The effect of marker density was trait-dependent and reached a plateau for each trait with 768−12,288 SNPs. Two additional sets of 192 and 96 SNPs from GWAS revealed higher prediction accuracies for the fruit traits compared to the 31,142 SNPs and eight subsets.ConclusionOur study explored several factors to increase the prediction accuracy of GEBVs for fruit traits in tomato. The results can facilitate development of advanced GS strategies with cost-effective marker sets for improving fruit traits as well as other traits. Consequently, GS will be successfully applied to accelerate the tomato breeding process for developing elite cultivars.

Mutations overlying the miR172 target site of TOE-type genes are prime candidate variants for the double-flower trait in mei

Mutations affecting flower shape in many plants have been favored by human selection, and various fruit trees are also grown for ornamental purposes. Mei (Prunus mume) is a dual purpose tree originated in China well known in the Western world for its generous early blooms, often bearing double flowers. Building on the knowledge of its genomic location, a candidate gene approach was used to identify a 49 bp deletion encompassing the miR172 target site of the euAP2 gene pmTOE (PmuVar_Ch1_3490) as a prime variant linked to flower doubleness. Searching within a large dataset of genome sequencing data from Eastern germplasm collections demonstrated a tight variant-trait association, further confirmed in a panel of commercial and non-commercial varieties available in Italy. Moreover, two SNP mutations in the miR172 target site of pmPET (PmuVar_Ch1_1333) were identified in some double flower accessions. The mei orthologue of PETALOSA genes already found responsible for the phenotype in other plants suggests that independent variants may have been selected throughout mei domestication history.

Millet production, challenges, and opportunities in the Asia-pacific region: a comprehensive review

Global warming, water scarcity, population growth, rising food prices, urbanization, and other socio-economic factors pose significant threats to agriculture and food security in the 21st century. This situation is particularly grave for low-income individuals in the Asia-Pacific region. To tackle this challenge and eradicate hunger and poverty, it is imperative for scientists to explore alternative food sources, covering all stages from production through processing to consumption. Cereal grains serve as a crucial food source and hold substantial importance in human diets. Therefore, revamping the food system becomes crucial to achieve food and nutritional security. A pragmatic approach toward reaching this goal involves ensuring universal access to affordable, wholesome, and nourishing food through the utilization of millets—nutrient-dense grains (often referred to as Nutri-cereals) that offer a rich array of vital macronutrients, micronutrients, carbohydrates, protein, dietary fiber, lipids, and phytochemicals. Leveraging these grains holds the potential to significantly alleviate the challenges of food insecurity and malnutrition. Millet, a drought-resistant grain, constitutes a primary source of carbohydrates and proteins for populations residing in semi-arid regions of Africa and Asia. Given its crucial contribution to national food security and potential health advantages, there is a growing focus among food scientists. Additionally, the United Nations designated 2023 as the International Year of Millet, underscoring its importance. This article delves into various methods of production and processing, highlighting opportunities to enhance the production and nutritional qualities of millet. We attribute millets to inadequate rainfall distribution, poor crop management high prices of farm inputs such as fertilizer and pesticides and low adoption of improved varieties by the farmers. It also outlines the constraints, challenges, and future prospects associated with promoting millet as a viable food source for the burgeoning population. Despite the promise that millets hold, they have not received adequate research attention. Therefore, increased research efforts on integrating genomics in genome-wide marker-trait association are imperative, encompassing germplasm collection, protection, evaluation, consumption patterns, development of high-yielding cultivars, processing techniques, and policy interventions. Such initiatives are necessary to bolster the cultivation of millets and harness their potential to address the escalating global food challenge.

Exploitation of the Genetic Variability of Diverse Metric Traits of Durum Wheat (Triticum turgidum L. ssp. durum Desf.) Cultivars for Local Adaptation to Semi-Arid Regions of Algeria.

Abiotic stresses pose significant challenges to wheat farming, yet exploiting the genetic variability within germplasm collections offers an opportunity to effectively address these challenges. In this study, we investigated the genetic diversity of key agronomic traits among twenty durum wheat cultivars, with the intention to pinpoint those better suited to semi-arid conditions. Field trials were conducted at the ITGC-FDPS Institute, Setif, Algeria, during the winter season of 2021/22. A completely randomized design was used with three replicates. Statistical analyses revealed significant variation among the genotypes for most of the studied traits, with some cultivars exhibiting a superior performance in a stressful environment. Notably, traits like the number of grains per spike (NGS) and the grain yield (GY) displayed high genotypic coefficients of variation (CVg). Except for membrane thermostability (MT) and biological yield (BY), the majority of the assessed traits exhibited moderate-to-high heritability estimates. Genotypic and phenotypic correlation studies have confirmed the importance of many yield-related traits in the expression of GY. The harvest index (HI) underscored the highest genotypic direct effect on GY, followed closely by spike number (SN), serving as consistent pathways through which most of the measured traits indirectly influenced GY. The cluster analysis categorized the durum wheat cultivars into seven distinct clusters. The largest inter-cluster distance was observed between clusters G3 and G4 (D2 = 6145.86), reflecting maximum dissimilarity between the individuals of these clusters. Hybridizing divergent clusters may benefit future breeding programs aiming to develop potential durum wheat varieties through cross combinations. This study's findings contribute to sustainable agriculture efforts by facilitating the selection of genotypes with enhanced resilience and productivity, particularly for cultivation in challenging semi-arid regions.

Variability in seed quality traits in castor germplasm

Castor is an industrial oilseed crop with great potential for biorefineries. However, little is known about the variability in the bioactive compounds in castor germplasm. This study evaluated seed weight, oil content, fatty acid profile, tocopherols, and phytosterols in 160 accessions of the USDA-ARS castor germplasm collection. The accessions were grown in Cordoba, Spain, under three different environmental conditions. Environmental and genotype-by-environment interaction effects were predominant for most traits, resulting in moderate to low broad-sense heritabilities, which ranged from 0.12 for total tocopherol content to 0.88 for hundred-seed weight. The genetic variability in the seed quality traits identified in the collection was lower than that reported previously for the germplasm of wild and semi-wild accessions from Spain, which is attributed to the lower genetic diversity in cultivated than in wild forms. The variation in seed quality traits in castor germplasm can be exploited to improve the concentration of bioactive compounds in castor cultivars.

Protection of cowpea seeds and toxicity against cowpea weevils by the essential oils from Lippia alba (verbenaceae) and Schinus terebinthifolius (anacardiaceae)

Alternative methods have been widely studied to mitigate problems arising from the use of pesticides in agriculture. Among them is the use of essential oils to control stored grain pests. In this context, the aim of this study was to evaluate the effect of fumigation of cowpeas with 12 essential oils having different chemical profiles, derived from the germplasm collection of Schinus terebinthifolius and Lippia alba at Rio de Janeiro Federal Rural University. These oils were applied at various concentrations (0.1–1.0 mg/mL of air) against cowpea weevils (Callosobruchus maculatus). The chemotypes evaluated included citral, citral/limonene, carvone/limonene, and linalool from the essential oils of L. alba, as well as α-pinene, sabinene, α-phellandrene/α-pinene, β-pinene/α-pinene, δ-carene/α-pinene, limonene, α-phellandrene/sabinene, and myrcene from the essential oils of S. terebinthifolius. Various aspects of the insects' reproductive cycle were evaluated, including mortality, egg laying, emergence of new adults, emergence rate, and larval hatching, along with grain mass loss. The results indicated life cycle inhibition of all evaluated oils, with the essential oil from the UFRRJ ECB028 (linalool CT) genotype having the lowest LC50 (0.10 mg/mL of air), completely halting the insects’ life cycle and totally preventing seed mass loss. Overall, the results pointed to certain genotypes as promising for the development of technologies aimed at seed protection.

Genetic diversity and candidate genes for transient waterlogging tolerance in mungbean at the germination and seedling stages.

Mungbean [Vigna radiata var. radiata (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini-core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome-wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully-expanded). In a temperature-controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high-quality DArTseq-derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain-containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad-sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker-trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker-assisted selection of tolerance traits to accelerate breeding of climate-resilient mungbean varieties.

Multi-omics profiling reveals an extensive regulation network shift in the domestication process of the traditional Chinese medicinal herb Rehmannia glutinosa Liboschitz (Orobanchaceae)

Plant domestication plays a vital role in human evolution and society development. Contrasted to the major crops, the domesticated procedure of medicinal herbs remains largely unknown. Here we analyzed the epigenomic, transcriptomic, and metabolomic profiling of three wild and nine cultivated samples of Dihuang (Rehmannia glutinosa Liboschitz), a well-known traditional Chinese medicinal herb, to elucidate the genetic differentiation and regulation mechanism during domestication. The results unraveled that tremendous differentiation existed among wild and cultivated types from genomes to metabolites. The cultivars presented significantly more methylated sites than the wild type and conjoint analyses indicated that hypermethylation of key genes was generally related to their down-regulated expressions and up-regulated metabolites in the pathways of monoterpenoid biosynthesis and carbohydrate metabolism involved in main components production and tuberous root enlargement. We also identified the key gene related to plant circadian rhythms and potential adaptation in the domestication of Dihuang. This work unveiled the systematic transformation from wild to cultivated Dihuang and provides new insights into the regulatory networks of genetic architectures, benefiting germplasm collection, cultivation, and utilization in the future.

Greater ecophysiological stress tolerance in the core environment than in extreme environments of wild chickpea (Cicer reticulatum)

Global climate change and land use change underlie a need to develop new crop breeding strategies, and crop wild relatives (CWR) have become an important potential source of new genetic material to improve breeding efforts. Many recent approaches assume adaptive trait variation increases towards the relative environmental extremes of a species range, potentially missing valuable trait variation in more moderate or typical climates. Here, we leveraged distinct genotypes of wild chickpea (Cicer reticulatum) that differ in their relative climates from moderate to more extreme and perform targeted assessments of drought and heat tolerance. We found significance variation in ecophysiological function and stress tolerance between genotypes but contrary to expectations and current paradigms, it was individuals from more moderate climates that exhibited greater capacity for stress tolerance than individuals from warmer and drier climates. These results indicate that wild germplasm collection efforts to identify adaptive variation should include the full range of environmental conditions and habitats instead of only environmental extremes, and that doing so may significantly enhance the success of breeding programs broadly.

GENETIC DIFFERENTIATION OF CULTIVATED CITRUS FRUITS (Citrus spp.) IN COLOMBIA USING SSR MOLECULAR MARKERS

Citrus is the second most important fruit crop in Colombia after bananas, with production taking place in 26 of the country’s 32 departments. Oranges, sour limes, and mandarins are the most economically important crops in terms of area planted and production. Microsatellites were used to assess the genetic differentiation of oranges, mandarins, tangelos, grapefruits, and acid limes from the Colombian Agricultural Research Corporation AGROSAVIA germplasm bank and collection of micro-grafted plants at Palmira Research Center in Colombia. A total of 121 samples from eight citrus groups were analyzed with 30 fluoromarked simple sequence repeats (SSR) microsatellites. The mean expected heterozygosity and mean observed heterozygosity were 0.58 and 0.57, respectively, and the coefficient of genetic differentiation was 0.558, confirming very high genetic differentiation among the citrus groups evaluated. Microsatellites mCrCIR01B02, AMB5, Ci01C09, mCrCIR08B08, and Ci01C07 were the most informative, presenting a high number of alleles and polymorphic loci percentages of more than 45 %; in addition, they allowed the identification of unique alleles, which can be used to establish the genetic fingerprint of citrus. Genetic differentiation was achieved for seven out of the eight groups evaluated. The SSRs used failed to differentiate the orange groups, possibly due to genetic origin; for this group, other molecular markers are recommended.

An international breeding project using a wild potato relative Solanum commersonii resulted in two new frost-tolerant native potato cultivars for the Andes and the Altiplano.

This breeding project, initiated at the United States Potato Genebank (USPG) in collaboration with Peruvian partners Instituto Nacional de Innovacion Agraria (INIA), International Potato Center, Peru (CIP), and local farmers, sought to enhance cold hardiness and frost tolerance in native potato cultivars in Peru. The Andes and Altiplano are often affected by frost, which causes significant reduction in yield; creating varieties with superior resilience is a critical undertaking. The goal was to transfer outstanding non-acclimated cold tolerance and acclimation capacity found in wild potato species Solanum commersonii (cmm). Breeding families segregating for cold hardiness were created using (a) a somatic hybrid cmm + haploid Solanum tuberosum (tbr) (cv. Superior, US variety from Wisconsin) as male and (b) seven cultivars native to Peru of the species S. tuberosum sbsp. andigenum (adg) as females. All plant materials were part of the USPG germplasm collection. Sexual seeds of each family were sent to Peru for evaluations under the natural conditions of the Andean highlands and Altiplano. The plants were assessed for their response to frost, and genotypes showing exceptional tolerance were selected. Plants were also evaluated for good tuber traits and yield. Initial planting involving ~2,500 seedlings in five locations resulted in selecting 58 genotypes with exceptional frost tolerance, good recovery capacity after frost, and good tuber traits. Over the years, evaluations continued and were expanded to replicated field trials in the harsher conditions of the Altiplano (Puno). All trials confirmed consistency of frost tolerance over time and location, tuber quality, and yield. After 8 years, two advanced clones were considered for cultivar release because of their exceptional frost tolerance and superior field productivity that outyielded many of the established cultivars in the region. In November 2018, a new native cultivar named Wiñay, a Quechua word meaning "to grow" was released in Peru. In 2022, a second cultivar followed with the name Llapanchispaq (meaning "for all of us"). This project evidenced that a multinational and all-encompassing approach to deploy valuable genetic diversity can work and deliver effective results. This is even more significant when outcomes can promote food security and sustainability in very vulnerable regions of the world.

A Novel Sorbitol-Based Flow Cytometry Buffer Is Effective for Genome Size Estimation across a Cypriot Grapevine Collection.

Flow cytometry (FCM) is a widely used technique to study genome size (C-value), but recalcitrant metabolites in grapevines often hinder its efficiency in grapevine research. The aim of the present study was (i) to develop a novel buffer tailormade for the nuclei isolation of grapevines and (ii) to characterize a Cypriot germplasm collection based on C-values. A local cultivar "Xinisteri" was used as a pilot test to evaluate a Sorbitol-based buffer, while sprouting, young, and fully matured leaves were examined to evaluate the developmental parameter. The novel Sorbitol buffer was shown to have a coefficient of variation (CV) of 4.06%, indicating improved properties compared to other commonly used FCM buffers [WPB (7.69%), LB01 (6.69%), and LB (7.13%), respectively]. In addition, a significant variation in genome size between genotypes was found in a comprehensive application with 24 grape varieties. Nucleic content (2C) ranged from 0.577/1C pg for the "Assyrtiko" cultivar up to 0.597/1C pg for the "Spourtiko" cultivar, revealing a 17.6/1C Mbp difference. The lowest coefficient of variation (CV) across all entries was found in the variety "Ofthalmo" (2.29%), while the highest was observed in "Pinot Noir" (3.44%). Anova analysis revealed several distinct clusters, showing that in several cases, C-values can be used as a simple method to distinguish grapevine cultivars.