Crop Germplasm Research Articles

A comprehensive review on impact of climatic change on adaptability and mitigation in fruit crop

Global warming and climate change are among the most pressing challenges confronting humanity in the 21st century. Climate change will result in rising temperatures, changes in rainfall patterns and an increased occurrence of extreme weather events, such as heatwaves, cold spells, frost days, droughts and floods. The effects of climate change have recently become more evident, with rising temperatures, altered and irregular precipitation patterns and increased extreme weather events. These changes are directly impacting the maturity and development of fruit crops. Heat stress during flowering and fruit set can greatly reduce fruit production, while irregular rainfall may disrupt pollination and heighten the risk of pests and diseases. Furthermore, increased carbon dioxide levels can influence the quality characteristics of fruits. To maintain the ongoing production and sustainability of fruit crops, it is vital to enhance resilience. Focusing on developing new varieties that offer higher yield potential and resistance to various stresses, such as drought, flooding and salinity, is crucial for sustaining crop yields. Additionally, breeding programs should aim to enhance the germplasm of key tropical and subtropical fruit crops to improve heat stress tolerance. Recent advancements in genetic editing technologies present substantial opportunities for the agricultural sector, especially in enhancing fruit crop traits. These innovations can be precisely tailored to meet consumer preferences, which is crucial for driving commercial success. In this review, we strive to provide a comprehensive overview of the current understanding of this important topic, along with recommendations for future research.

The Regulation of ROS and Phytohormones in Balancing Crop Yield and Salt Tolerance.

Salinity affects crop growth and productivity, and this stress can be increased along with drought or high temperature stresses and poor irrigation management. Cultivation of salt-tolerant crops plays a critical role in enhancing crop yield under salt stress. In the past few decades, the mechanisms of plant adaptation to salt stress have been described, especially relying on ionic homeostasis, reactive oxygen species (ROS) scavenging, and phytohormone signaling. The studies of these molecular mechanisms have provided a basis for breeding new salt-tolerant crop germplasm and have facilitated the entry into the era of molecular breeding of salt-tolerant crops. In this review, we outline the recent progress in the molecular regulations underlying crop salt tolerance, focusing on the double-edged sword effect of ROS, the regulatory role of phytohormones, and the trade-off effects of ROS and phytohormones between crop yield and salt tolerance. A future challenge is to identify superior alleles of key salt-tolerant genes that will accelerate the breeding of high-yield and salt-tolerant varieties.

The transcription factor FcMYB3 responds to 60Co γ-ray irradiation of axillary buds in Ficus carica L. by activating the expression of the NADPH oxidase, FcRbohD.

Plant irradiation has been used to induce genetic variation in crop germplasm. However, the underlying mechanisms of plant responses to ionizing radiation stress are still unclear. In plants, reactive oxygen species (ROS) are produced with abiotic stress. Respiratory burst oxidative homologs (Rboh) genes are important regulators of plant ROS stress responses, but little is known of their involvement in the response to ionizing radiation stress. In this study, young branches of Ficus carica L. were irradiated with 60Co γ-rays and axillary buds were collected after 3- 48 h after irradiation. The differentially expressed genes (DEGs; p< 0.05) detected included an early (6 h) and sustained increase in member of the MAPK signaling pathway. The activities of superoxide dismutase SOD, POD and CAT in fig axillary buds showed a trend of first decrease and then increase with time, while the contents of MDA and H2O2 maintained an overall upward trend. The analysis of differentially expressed genes (DEGs; p < 0.05) indicated an early (6 h) and sustained increase in member of the MAPK signaling pathway. DEGs for glutathione-s-transferase and genes involved in phenylpropanoid and flavonoid biosynthesis pathways were detected at all time points, indicating that γ-irradiation induced an increased capacity for in ROS-scavenging. Substantial changes in the expression of MYB, NAC and bHLH transcription factor family members were also seen to occur within 6 h after irradiation. Taking Rboh-derived ROS signaling pathway as the entry point, the MYB transcription factor, FcMYB3, was identified as an potential upstream regulator of FcRbohD in a yeast one hybrid assay and this interaction verified by LUC and EMSA experiments. The knock-down and overexpression of FcMYB3 indicated that FcMYB3 is a positive regulator of ROS accumulation in response to γ-ray radiation stress responses in fig. Our results will provide a better understanding of the mechanisms of radiation tolerance in plant materials.

Seeing the Forest for the Trees: Threats, Vulnerabilities, and Opportunities for Woody Landscape Plant Genetic Resources

Genetic resources are the foundation of American agriculture’s ongoing success—the diversity, security, health, and genetic integrity of these resources must be safeguarded. However, in contrast to other crops, protecting, managing, and using collections of woody landscape plant genetic resources present significant challenges. These include conservation of at-risk populations that have high genetic diversity, evaluation of taxa with an unknown potential to invade, and management of large specimens that have long generation times and often recalcitrant or difficult-to-store seeds. The wide diversity of taxa and the limited number of specialist curators and scholars present further challenges. Thus, effective collection, preservation, evaluation, and distribution of woody landscape plant germplasm require substantial and specialized resources. The most fundamental challenge is simple: too many built landscapes have low taxonomic diversity and are often dominated by a single taxon, or monoculture. In turn, these taxonomically and genetically depauperate landscapes are vulnerable to a host of biotic and abiotic threats and are less likely to provide ecosystem and societal services for which they were designed. To develop more resilient landscapes, there is an urgent need to expand taxonomic diversity, which requires the horticultural community to effectively acquire, curate, evaluate, distribute, and use diverse woody landscape plant genetic resources. The role of the US Department of Agriculture-Agricultural Research Service (USDA-ARS) National Plant Germplasm System (NPGS) Woody Landscape Plant Crop Germplasm Committee (WLPCGC) is to identify vulnerabilities and threats that compromise WLP crops in the United States and make recommendations for prioritization of germplasm acquisition, evaluation, research, and management priorities through regular interaction with stakeholders. Due to the breadth of genera and shifting plant genetic resource needs of the nursery industry, it is impractical to list specific threatened or priority genera in a broadly applicable crop vulnerability statement. Instead, the WLPCGC has identified themes of threats and vulnerabilities providing a foundation upon which to support prioritization as threats to specific genera emerge.

Marker Assisted Selection (MAS) and It's Application in Vegetable Crop Improvement

Vegetable crop breeding has changed dramatically since the early 1980s due to technological breakthroughs, especially high-throughput sequencing and molecular marker technologies, which have made it possible to sequence many plant genomes, create dense genetic maps, and identify important genes and QTLs linked to traits like yield and disease resistance. ..These instruments have expedited genetic research and breeding programs in crops including tomato, pepper, eggplant, and cucumber, establishing marker-assisted selection (MAS) as a crucial component of contemporary breeding. The use of these technologies has improved crop characteristics significantly and is still influencing the development of vegetable crops in the future. .. For instance, in the majority of private and public tomato breeding projects, major-gene disease resistance traits like verticillium wilt and anthracnose are selected for using PCR-based markers such as SCAR and CAPS.Bs5 and Bs6 have broad-spectrum resistance against Xanthomonas spp. against chilli leaf spot thanks to marker-assisted gene pyramiding. Major QTLs associated to SSR marker CAMS451 on chromosome 1 (from Capsicum accession LS2341) and marker ID10-194305124 on chromosome 10 (from C. annuum BVRC1) have been mapped for resistance to Ralstonia bacterial wilt.Constantly searching crop germplasm for new resistance genes or alleles is essential to diversify the gene pool and stop resistance from breaking down. By using marker-assisted selection (MAS), it is possible to combine genes for resistance to different pathogens or several sources of resistance to the same pathogen to create novel cultivars.

Analysis of geographical origin of solar terms based on the STTMD method

The 24 solar terms are a significant component of traditional Chinese culture. Amid global warming climate change, research on the Solar Terms has gained increasing prominence. Identifying the geographical origins of the Solar Terms not only provides evidence for studies on the origins of Chinese agricultural civilization but also serves as a critical foundation for the innovative utilization of traditional culture in the modern era. Previous research has primarily relied on historical records, literature review, and field investigation, often challenged by the vast and complex data, the difficulty distinguishing authenticity, the time-consuming nature of the work, and the need for direct scientific evidence. The STTMD (Solar Terms Typical Meteorological Day) method was used for typifying solar term meteorological data sequences, supplemented by isothermal estimation and clustering analysis. This approach was further validated using key crop germplasm sites, phenological indicators, and phenological observation contour maps. The results derived from statistical methods are cross-referenced with historical documents to infer the geographical origins of the 24 Solar Terms. The findings indicate that: (1)On a larger spatial scale, the Solar Terms originated in the middle and lower reaches of the Yellow River; (2)On a smaller spatial scale, the "Luoyang-Zhengzhou-Anyang" triangle is the most probable origin area; (3)The core area of origin is hypothesized to be in present-day Xingyang, Henan Province, or slightly further north. These results are consistent with historical literature and phenological records of crops, offering a novel analysis and transformative insights into the knowledge of Solar Terms. The study provides valuable evidence or methodological inspiration for historical agricultural research in China and offers references for agricultural production and the environmental impacts of global warming.

Machine learning prediction of stalk lignin content using Fourier transform infrared spectroscopy in large scale maize germplasm

Lignin has been recognized as a major factor contributing to lignocellulosic recalcitrance in biofuel production and attracted attentions as a high-value product in the biorefinery field. As the traditional wet chemical methods for detecting lignin content are labor-intensive, time-consuming and environment-toxic, it is an urgent need to develop high-throughput and environment-friendly techniques for large-scale crop germplasms screening. In this study, we conducted a Fourier transform infrared (FTIR) assay on 150 maize germplasms with a diverse lignin composition to build predictive models for lignin content in maize stalk. Principal component analysis (PCA) was applied to the FTIR spectra for use as model inputs. Classification and advanced gradient boosting machine (GBM) algorithms demonstrated higher predictive accuracy (0.82–0.96) compared to traditional linear and regularization algorithms (0.03–0.04) in the training set. Notably, two optimal models, built using the extreme gradient boosting (XGBoost) and light gradient boosting machine (LightGBM) algorithms, achieved R2 values of over 0.91 in the training set and over 0.82 in the test set. Overall, the combination of FTIR and machine learning (ML) algorithms offers a high-throughput and efficient method for predicting lignin content. This approach holds significant potential for genetic breeding and the effective utilization of maize in industrial production.

Agro-morphological evaluation of gamma ray-induced mutant populations and isolation of harder grain mutants in wheat (Triticum aestivum L.)

AbstractGamma ray-induced mutations have been widely used to improve existing crop germplasm and create novel genetic variation. In the current study, a multi-year experiment was carried out to induce and isolate mutants with desirable agro-morphological traits and improved grain hardness through evaluation of induced mutant populations generated in soft-textured wheat variety HPW 89 irradiated with gamma ray dose of 250, 300 and 350 Gy. Mutagen sensitivity studies revealed a higher frequency of biological damage and seedling mortality for doses beyond 300 Gy in the M1 generation. However, the mutagenic treatments in the M2–3 populations significantly altered the magnitude of the biometrical traits. Results from the variability and association studies among traits showed that biological yield per plant, 1000-grain weight, spike length, grains per spike and plant height may be prioritized for higher genetic gain and could be used as selection criteria parameters. Multivariate analysis indicated induction of heterogeneity among mutant populations. Overall, 250–300 Gy doses were found ideal for a successful wheat mutation programme and 293 agro-morphologically superior wheat mutants were identified, out of which 108 had semi-hard grain texture based on single kernel characterization system. Among these, nine mutants were found to have the highest grain hardness index due to induced changes in one or both puroindoline genes. Hence, these mutants identified for several traits along with harder grain texture will serve as important genetic resource in future wheat-breeding programmes.

Training set optimization is a feasible alternative for perennial orphan crop domestication and germplasm management: an Acrocomia aculeata example.

Orphan perennial native species are gaining importance as sustainability in agriculture becomes crucial to mitigate climate change. Nevertheless, issues related to the undomesticated status and lack of improved germplasm impede the evolution of formal agricultural initiatives. Acrocomia aculeata - a neotropical palm with potential for oil production - is an example. Breeding efforts can aid the species to reach its full potential and increase market competitiveness. Here, we present genomic information and training set optimization as alternatives to boost orphan perennial native species breeding using Acrocomia aculeata as an example. Furthermore, we compared three SNP calling methods and, for the first time, presented the prediction accuracies of three yield-related traits. We collected data for two years from 201 wild individuals. These trees were genotyped, and three references were used for SNP calling: the oil palm genome, de novo sequencing, and the A. aculeata transcriptome. The traits analyzed were fruit dry mass (FDM), pulp dry mass (PDM), and pulp oil content (OC). We compared the predictive ability of GBLUP and BayesB models in cross- and real validation procedures. Afterwards, we tested several optimization criteria regarding consistency and the ability to provide the optimized training set that yielded less risk in both targeted and untargeted scenarios. Using the oil palm genome as a reference and GBLUP models had better results for the genomic prediction of FDM, OC, and PDM (prediction accuracies of 0.46, 0.45, and 0.39, respectively). Using the criteria PEV, r-score and core collection methodology provides risk-averse decisions. Training set optimization is an alternative to improve decision-making while leveraging genomic information as a cost-saving tool to accelerate plant domestication and breeding. The optimized training set can be used as a reference for the characterization of native species populations, aiding in decisions involving germplasm collection and construction of breeding populations.

Integrating NIR spectroscopy with machine learning and heuristic algorithm-assisted wavelength selection algorithms for protein content prediction in rice bean (Vigna umbellata L.)

Protein-energy malnutrition (PEM) is a global concern, particularly in underdeveloped and underprivileged regions dependent on plant-based diets. Plant-based meat alternatives offer a potential solution, with rice bean emerging as a promising crop due to its high protein content. However, traditional methods for determining protein content in rice bean are labor-intensive, costly, and time-consuming, thus necessitating more efficient approaches. This study addresses the need for efficient, rapid technique by integrating Near-Infrared Spectroscopy (NIRS) with machine learning models to predict protein content in rice bean (Vigna umbellata L.) germplasm. We developed predictive models using Support Vector Regressor (SVR), Random Forest Regressor (RFR), and Modified Partial Least Square (MPLS) coupled with key wavelengths selection algorithms including Genetic Algorithm (GA), Ant Colony Optimization (ACO), Particle Swarm Optimization (PSO), and Competitive Adaptive Reweighted Sampling (CARS). The MPLS model demonstrated superior performance, achieving an R² (Coefficient of Determination) of 0.81 and an RPD (Residual Prediction Deviation) of 2.14 when combined with the ACO algorithm. The SVR model also performed well when combined with ACO and PSO, yielding an R² of 0.78, an RPD of ∼1.95. In contrast, the RFR model showed relatively lower performance (R² of ∼0.45 and RPD ≤ 1.74). These results indicate that MPLS and SVR, combined with selected wavelength selection algorithms significantly improves prediction accuracy. The study highlights the importance of appropriate model and algorithm selection in enhancing predictive performance of protein content. The developed technology provides a rapid and efficient method for selecting nutritionally superior crop germplasm present in global respositories.

Exotic alleles from the wild Hordeum spontaneum contribute to drought tolerance and grain quality in modern Hordeum vulgare

Conventional breeding relies on genetic variability in crop germplasm and wild species. This study evaluated 137 barley Recombinant Chromosome Substitution Lines (RCSLs), originating from crossing a drought and salinity-tolerant wild Hordeum spontaneum with the high-quality malting H. vulgare cv. Harrington. The objectives of this work were to i) improve understanding of the genetic diversity and introgression levels in RCSLs using a comprehensive set of high-density single nucleotide polymorphism (SNP) markers; ii) investigate the phenotypic variability of physiological, agronomic, and malting quality traits in RCSLs under rainfed and fully irrigated conditions; iii) unravel the relationship between these traits and the resilience of crops in drought-prone regions; and iv) identify specific SNPs associated with both drought tolerance indices and malting quality traits. Variability in physiological, agronomic, and malting quality traits was examined under rainfed and irrigated conditions, aiming to identify specific SNPs associated with both drought tolerance indices and malting quality traits. Additionally, a subset of three recombinant lines and the parent cv. Harrington was tested in growth chambers under well-watered and water-limited conditions. Agronomic traits were influenced by genotype-by-environment interaction, with notable drought tolerance lines. The grain yield was significantly correlated with yield-related traits and carbon isotope discrimination in grains. Drought stress impacted agronomic and physiological traits, with a strong reduction in leaf gas exchange and chlorophyll and protein content. The H. spontaneum genome introgression into H. vulgare cv. Harrington varied across 137 RCSLs, averaging 13.0 %. Associations between traits and genetic markers were found, particularly for the stress tolerance index in chromosome 1H and for grain quality traits (alfa-amylase, wort color, and protein) in chromosomes 1H, 4H, and 5H. These findings uncovered valuable barley RCSLs that demonstrate drought tolerance, offering promising prospects for breeding programs targeted at improving stress resilience.

Genetic diversity and population structure of wheat landraces in Southern Winter Wheat Region of China

BackgroundWheat landraces are considered a valuable source of genetic diversity for breeding programs. It is useful to evaluate the genetic diversity in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. In addition, constructing a core germplasm set that represents the genetic diversity of the entire variety set is of great significance for the efficient conservation and utilization of wheat landrace germplasms.ResultsTo understand the genetic diversity in wheat landrace, 2,023 accessions in the Jiangsu Provincial Crop Germplasm Resource Bank were used to explore the molecular diversity and population structure using the Illumina 15 K single nucleotide polymorphism (SNP) chip. These accessions were divided into five subpopulations based on population structure, principal coordinate and kinship analysis. A significant variation was found within and among the subpopulations based on the molecular variance analysis (AMOVA). Subpopulation 3 showed more genetic variability based on the different allelic patterns (Na, Ne and I). The M strategy as implemented in MStratv 4.1 software was used to construct the representative core collection. A core collection with a total of 311 accessions (15.37%) was selected from the entire landrace germplasm based on genotype and 12 different phenotypic traits. Compared to the initial landrace collections, the core collection displayed higher gene diversity (0.31) and polymorphism information content (PIC) (0.25), and represented almost all phenotypic variation.ConclusionsA core collection comprising 311 accessions containing 100% of the genetic variation in the initial population was developed. This collection provides a germplasm base for effective management, conservation, and utilization of the variation in the original set.

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

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

Data blanks by design: Intellectual property and restrictions on genetic diversity assessments of the maize standing crop in the USA Upper Midwest

Societal Impact StatementAll US commercial maize (Zea mays) is a single race, “Corn Belt Dent,” and its genetic base has been in decline for at least 40 years. Independent genotyping can only be conducted after patent and licensing restrictions have expired, a period of 20 years. These restrictions also impede a molecular based assessment of the standing crop by the United States Department of Agriculture (USDA) as recommended by experts. Data blanks about landscape vulnerability put farmers at risk of crop failure and the public at risk of food insecurity. Understanding maize diversity experts' perspectives and analysis helps describe the contours of these data blanks and inform policy recommendations.Summary Recommendations by the Maize Crop Germplasm Committee to the United States Department of Agriculture (USDA) for a molecular based vulnerability assessment on the US standing maize (Zea mays) crop have not been acted on because of intellectual property and licensing restrictions. This research explores maize diversity experts' access to data and perceptions and analysis of the standing crop. The data come from semi‐structured interviews conducted with 44 maize diversity experts in the public and private sectors. Experts explain that genetic data blanks restrict non‐industry research, describe public sector concerns that standing diversity is narrow(ing), and find historic sources of pedigree data in Plant Variety Protection and patent records are no longer reliable. Some interviewees perceive that industry monitoring of standing diversity is in their best financial interest. Industry participants describe concentration in US maize allows them to control diversity over time, while public researchers discuss efficiency of scale narrowing genetic diversity and global concentration spreading this trend. Knowledge gaps about genetic diversity in US commercial maize are designed through patents, contracts, non‐disclosure agreements, and confidentiality agreements by patent holders who do not want their inbred lines genotyped by competitors. This restricts research and knowledge flow about genetic information into public networks. The Maize Crop Germplasm Committee is a node for knowledge flow; however, the lack of mechanisms for action suggests it is performative. We recommend all protections used on seed include exemptions for research, breeding, and seed saving; an independent assessment of how industry monitors standing diversity; and a molecular analysis of the standing crop conducted by the USDA.

Spontaneous chromosome instability and tissue culture-induced karyotypic alteration in wheat-Thinopyrum intermedium alien addition lines.

Wheat lines harboring wild-relative chromosomes can be karyotypically unstable during long-term maintenance. Tissue culture exacerbates chromosomal instability but appears inefficient to induce somatic homoeologous exchange between alien and wheat chromosomes. We assessed if long-term refrigerator storage with regular renewal via self-fertilization, a widely used practice for crop germplasm maintenance, would ensure genetic fidelity of alien addition lines, and explored the possibility of inducing somatic homoeologues exchange by tissue culture. We cytogenetically characterized sampled stock seeds of originally confirmed 12 distinct wheat-Thinopyrum intermedium alien addition lines (dubbed TAI lines), and subjected immature embryos of the TAI lines to tissue culture. We find eight of the 12 TAI lines were karyotypically departed from their original identity as bona fide disomic alien addition lines due to extensive loss of whole-chromosomes of both Th. intermedium and wheat origins during the ca. 3-decade storage. Rampant numerical chromosome variations (NCVs) involving both alien and wheat chromosomes were detected in regenerated plants of all 12 studied TAI lines, but at variable rates among the wheat sub-genomes and chromosomes. Compared with NCVs, structural chromosome variations (SCVs) occurred at substantially lower rates, and no SCV involving the added alien chromosomes was observed. The NCVs manifested only moderate effects on phenotypes of the regenerated plants under field conditions.

Anthracnose and bean common mosaic necrosis virus resistance in wild and landrace Phaseolus vulgaris (L.) genetic stocks

AbstractWild crop germplasm and landrace varieties have long been considered as a source of novel genetic variation for improving domesticated crops. Due to genetic bottlenecks that occurred during domestication, dissemination, and subsequent crop improvement, many beneficial genes are absent from commercial varieties and elite breeding germplasm, yet are still present in wild populations. To catalog potential novel disease resistance genes useful for breeding more resilient dry beans, we screened wild and landrace Phaseolus vulgaris L. accessions archived in the USDA GRIN seed bank for untapped resistance to anthracnose (Colletotrichum lindemuthianum) and bean common mosaic necrosis virus (BCMNV). A population of 194 wild and 55 landrace accessions were screened for resistance to two highly virulent races of anthracnose (race 2047 and race 3481) and for resistance to the BCMNV strain NL‐3. Thirteen accessions, all wild, were resistant to both anthracnose races, with MX‐QT‐3 and PI 661812 displaying complete resistance with no disease symptoms across all replications. Surprisingly, no natural resistance to BCMNV strain NL‐3 was detected in the wild germplasm. PI 442541, PI 661891, and W6 10164 were the only three accessions that expressed the I‐gene phenotype and all three have some history of cultivation. This study provides a resource for introgression of genetic diversity for anthracnose resistance into cultivated beans and reveals that innate resistance to BCMNV may not exist in wild populations of P. vulgaris.

Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.

An Optimized Protocol for Comprehensive Evaluations of Salt Tolerance in Crop Germplasm Accessions: A Case Study of Tomato (Solanum lycopersicum L.)

The comprehensive evaluation of crop germplasm serves to scientifically and objectively assess the quality of different genetic accessions against certain standards. Here, we propose an optimized approach to enhance the result’s stability when assessing salt tolerance in crop germplasm. This protocol was applied to a case study involving 249 tomato genotypes, systematically refining the processes involved in constructing an evaluation index system, data preprocessing, statistical method selection, and weight calculation. The optimization process reduced the system variance of salt tolerance evaluation results and achieved an 85.42% concordance with a classical approach, across a tomato population covering 241 genotypes, suggesting the improved stability and high accuracy of the optimized protocol. Moreover, an 83.82% consistency rate between pre- and post-optimization results also suggested the high accuracy of the optimized protocol. The enhanced stability was further confirmed by a secondary validation on a subpopulation (covering 39 genotypes), which demonstrated a consistency rate of 83.87% between the two populations. The study identified 8.43% of the evaluated germplasm as salt-tolerant accessions, providing valuable parental materials for breeding programs. The findings underscore the potential of our protocol for the precise identification of stress-resistant germplasm, contributing to the development of stress-tolerant crop varieties.

KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance.

Advances in plant molecular breeding have resulted in the development of new varieties with superior traits, thus improving the crop germplasm. Breeders can screen a large number of accessions without rigorous and time-consuming phenotyping by marker-assisted selection (MAS). Molecular markers are one of the most imperative tools in plant breeding programmes for MAS to develop new cultivars possessing multiple superior traits. Single nucleotide polymorphisms (SNPs) are ideal for MAS due to their low cost, low genotyping error rates, and reproducibility. Kompetitive Allele Specific PCR (KASP) is a globally recognized technology for SNP genotyping. KASP is an allele-specific oligo extension-based PCR assay that uses fluorescence resonance energy transfer (FRET) to detect genetic variations such as SNPs and insertions/deletions (InDels) at a specific locus. Additionally, KASP allows greater flexibility in assay design, which leads to a higher success rate and the capability to genotype a large population. Its versatility and ease of use make it a valuable tool in various fields, including genetics, agriculture, and medical research. KASP has been extensively used in various plant-breeding applications, such as the identification of germplasm resources, quality control (QC) analysis, allele mining, linkage mapping, quantitative trait locus (QTL) mapping, genetic map construction, trait-specific marker development, and MAS. This review provides an overview of the KASP assay and emphasizes its validation in crop improvement related to various biotic and abiotic stress tolerance and quality traits.

Diversity, conservation and utilization of grain legumes: A potential source for food and nutritional security in Nepal

Grain legumes are precious crops of Nepal in terms of the dietary protein supplement ample concentration of micronutrients, and role in crop intensification and ameliorating soil fertility. About 11% of the cultivated area is occupied by grain legumes that include lentil, chickpea, grasspea, fieldpea, fababean, pigeonpea, soybean, blackgram, horsegram, ricebean, cowpea, and mungbean. About 100 genera and 379 species of legumes are distributed in diverse agroecological zones ranging from terai to the alpine region of Nepal, with growth habits ranging from annual to perennial shrubs. Out of the 379 species of legumes which include grain, vegetable, and forage legumes, 262 are native, and 20 species belonging to the sub-group Papilionacae are used as food legumes. Highest food legume species diversity has been recorded in Macrotyloma (34 spp.), followed by Crotalaria (18 spp.), Vigna (15 spp.), Lathyrus (7 spp.), Vicia (6 spp.), Cajanus (5 spp.), Trigonella (5 spp.) and Phaseolus (4 spp.). Other genus having 1-3 species includes Cicer (3 spp.), Mukuna (3 spp.), Glycine (2 spp.), Canavila (2 spp.), Pisum (2 spp.), Lablab (2 spp.), Pachyrrhizus (1 sp.), Psophocarpus (1 sp.), Lens (1 sp.) and Cyamopsis (1 sp.). Research on grain legumes was initiated in 1976 and a systematic collection of grain legume landraces was done in 1987 by the Grain Legumes Research Program (GLRP). Past collection missions organized in collaboration with the International Development Research Centre (IDRC), the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the International Center for Agricultural Research in the Dry Areas (ICARDA), and other institutes have resulted in the collection of 1107 landraces and provided an opportunity for their inclusion in the variety improvement program. National Agricultural Genetic Resources Center (NAGRC) has conserved 2936 landraces of different legumes, 951 landraces have been kept in gene banks of ICARDA center, while GLRP Khajura has active collections of 218 landraces and 627 exotic germplasm of various legume crops. Varietal improvement programs resulted in the development of 51 varieties, while 6 varietes were registered and two varieties were de-notified in food legumes (lentil, chickpea, soybean, cowpea, black gram, mungbean, pigeon pea, rice bean, faba bean, grass pea, and kidney bean).