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Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, "PolyHighResolution" (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.

Soybean seed-protein content and composition is important because it contributes over half the value of this $61 billion crop. Historic negative correlation between seed-protein content and oil have been reported. Similarly, negative correlation between seed-protein content and yield have been reported but may be at least in part mitigated by increasing the genetic diversity of the elite soybean germplasm. Improvements in amino acid composition of seed-protein would increase the value of soybean meal and protein for animal and human consumption. We have identified a genetic resource in wild soybean germplasm, PI424025B, with elevated seed-protein, elevated cysteine in the seed and increased sulfur content in the seed. We have developed a population of Recombinant Inbred Lines derived from a cross between NC-Raleigh and PI424025B. We evaluated the carbon, nitrogen and sulfur (C, N and S) content of seeds from the progeny, the parents and other high-seed protein soybean lines. N content and C/N (ratio of C to N) were well correlated with protein content measured by NIR. PI424025B had a N content comparable to high-protein soybean lines and a superior N/S. These traits were inherited by some of the progeny. Quantitative Trait Loci (QTL) associated with high-seed protein were identified on chr2, chr20 and chr15 and colocalizes with well characterized loci on chr 15 and chr 20 known to affect seed-protein content and quality. A potentially unique QTL was identified on Chr15. Unlike the chr20 QTL, the chr15 QTL improved S content relative to N content and was superior to other high seed-protein phenotypes tested. These data indicate that PI424025B is a valuable resource to diversify the genetics of soybean while improving soybean seed-protein content and composition. [ABSTRACT FROM AUTHOR]

The goal of transgenesis in plant breeding is to make step‐change improvements in traits of interest. However, improving quantitative traits, such as yield in maize (Zea mays L.), with transgenes has been difficult. Traditionally, transgene testing is done on a few isogenic lines, and results are extrapolated to entire breeding populations. Testing on limited germplasm does not provide a robust estimate of a transgene's value. Incorporating transgenes directly into breeding populations could increase genetic variance and the rate of genetic gain. Here, we used a transgene that reduces ethylene as a case study and investigated event, transgene, family, and environment effects and their interactions. We also determined whether introduction of the transgene into a breeding population would result in transgenic lines being preferentially selected over nontransgenic lines for yield. We found significant variation in transgene effects across clustered environments and families for multiple traits including yield. In environmental Cluster 2, the transgenic lines yielded 0.4 Mg ha−1 more than nontransgenic lines in family KC22; yet, in family QY43, transgenic lines yielded 0.3 Mg ha−1 less. Similarly, within Cluster 4, the QY43 family had preferential selection of transgenic over nontransgenic lines, whereas in families YE41 and AY91, nontransgenic lines were selected more frequently. These results show the critical importance of evaluating transgenes across broad germplasm diversity to assess their general value to a program. Integrating transgenes, or using gene editing, directly in a breeding program can expand genetic variation for quantitative traits and potentially accelerate genetic gain. [ABSTRACT FROM AUTHOR]

Understanding the genetic diversity of crops is of fundamental importance for the efficient use and improvement of germplasm resources. Different molecular genotyping systems have been implemented for population structure and phylogenetic relationships analyses, among which, microsatellites (SSRs) and single nucleotide polymorphisms (SNPs) markers have been the most widely used. This study reports the efficacy of SNPs detected via double-digest restriction-site-associated DNA sequencing (ddRADseq) and SSRs analyzed via capillary electrophoresis (CE) and high-resolution melting (HRM) in tomato. In total, 21,020 high-quality SNPs, 20 CE-SSRs, and 17 HRM-SSR markers were assayed in a panel of 72 accessions that included a diversified set of landraces, long-shelf-life cultivars and heirlooms with different origins and fruit typology. The results showed how the population structure analysis was consistent using the three genotyping methods, although SNPs were more efficient in distinguishing cultivar types and in measuring the degree of accessions' similarity. Compared to CE-SSR, the analysis of microsatellites via HRM yielded a slightly higher number of alleles (98 vs. 96). HRM-SSR demonstrated a distinction between European and non-European germplasm, better resolving the collection's diversity and being more consistent with SNP data. Phylogenetic trees drawn with independent marker data, detected specific groups of accessions showing robust clusters, highlighting how heirlooms were less heterogeneous than landraces. In addition, the fixation index (FST) revealed a high genetic differentiation between heirlooms and long-shelf-life cultivars, with SNP and SSR-HRM data emphasizing the distinction between cherry and plum types and CE-SSR data between cherry and oxheart types. In all instances, a greater molecular variance was found within the different considered biological statuses, provenances, and typologies rather than among them. This work presents the first attempt to compare the three tomato genotyping techniques in tomato. Findings highlighted how the markers used are complementary for genetic diversity analysis, with SNPs providing better insight and HRM-SSR as a viable alternative to capillary electrophoresis to dissect the genetic structure. [ABSTRACT FROM AUTHOR]

ABSTRACT The present study aims to enrich the genetic marker resources that are amenable for future trait mapping and quality improvement programmes in pomegranate. We analysed 140 well‐characterized genes that belonged to seven important gene families involved in the growth and development of pomegranate. We retrieved 140 representative genes for seven gene families from four draft genomes of pomegranate, cvs. Tunisia, Dabenzi, Taishanhong and Bhagawa, using BLASTn homology search. A total of 245 InDel primers were designed based on the comparison among four pomegranate genomes for the representative gene sequences, focusing on a size difference of at least 8 base pairs (bp). One hundred forty‐eight (60.41%) markers were in silico verified through e‐PCR on the Tunisia genome and further confirmed on the other three genomes, and we identified 107 polymorphic markers with an average PIC value of 0.62. By using 148 InDel markers physically mapped on the genome, we found that Tunisia had the highest syntenic relations with the Bhagawa (100%), Dabenzi (97.97%) and Taishanhong (97.30%) genomes. Experimental validation of 54 InDel primers on six pomegranate genotypes identified a set of 37 (71.15%) polymorphic markers, 24 of which had PIC values of ≥ 0.48. An investigation on genetic diversity and phenotype correlations in 16 pomegranate genotypes using 16 InDel markers demonstrated the utility of these markers. The developed InDel markers are an excellent resource for diverse applications in pomegranate including genetic diversity, trait mapping, gene discovery and gene editing. [ABSTRACT FROM AUTHOR]

The All of Us Research Program (AoU) is an initiative designed to gather a comprehensive and diverse dataset from at least one million individuals across the USA. This longitudinal cohort study aims to advance research by providing a rich resource of genetic and phenotypic information, enabling powerful studies on the epidemiology and genetics of human diseases. One critical challenge to maximizing its use is the development of accurate algorithms that can efficiently and accurately identify well-defined disease and disease-free participants for case-control studies. This study aimed to develop and validate type 1 (T1D) and type 2 diabetes (T2D) algorithms in the AoU cohort, using electronic health record (EHR) and survey data. Building on existing algorithms and using diagnosis codes, medications, laboratory results, and survey data, we developed and implemented algorithms for identifying prevalent cases of type 1 and type 2 diabetes. The first set of algorithms used only EHR data (EHR-only), and the second set used a combination of EHR and survey data (EHR+). A universal algorithm was also developed to identify individuals without diabetes. The performance of each algorithm was evaluated by testing its association with polygenic scores (PSs) for type 1 and type 2 diabetes. We demonstrated the feasibility and utility of using AoU EHR and survey data to employ diabetes algorithms. For T1D, the EHR-only algorithm showed a stronger association with T1D-PS compared to the EHR + algorithm (DeLong p-value = 3 × 10−5). For T2D, the EHR + algorithm outperformed both the EHR-only and the existing T2D definition provided in the AoU Phenotyping Library (DeLong p-values = 0.03 and 1 × 10−4, respectively), identifying 25.79% and 22.57% more cases, respectively, and providing an improved association with T2D PS. We provide a new validated type 1 diabetes definition and an improved type 2 diabetes definition in AoU, which are freely available for diabetes research in the AoU. These algorithms ensure consistency of diabetes definitions in the cohort, facilitating high-quality diabetes research. [ABSTRACT FROM AUTHOR]

Multiparent advanced generation intercross (MAGIC) populations are a new genetic resource for high‐resolution mapping of quantitative traits and as a source of new germplasm or improved cultivars for breeding due to the high level of recombination events in the population. Here, we have developed an eight‐founder MAGIC population for peanut (Arachis hypogaea L.) (PeanutMAGIC). Eight diverse founders were intercrossed using a simple funnel mating design to ensure that the MAGIC population would possess equal representation from each founder. This was followed by advancement using small family plot and single‐seed descent, resulting in 3187 F2:7 recombinant inbred lines (RILs). The objective of this study was to introduce this PeanutMAGIC as a new resource for genetic and genomic studies. We randomly selected a smaller subset of 310 RILs (MAGIC Core) from PeanutMAGIC and conducted genotyping using whole genome sequencing and phenotyping over two growing seasons for seed and pod traits. Whole genome characterization of the MAGIC Core demonstrated that PeanutMAGIC harbors a balanced and evenly differentiated mosaic of genomic blocks from eight founders, providing unique recombination events for high‐resolution mapping of quantitative traits. Using 2‐year phenotypic data, we showed that PeanutMAGIC can improve genetic mapping power of a spectrum of qualitative, like seed coat color, to quantitative traits such as pod weight, seed weight, shelling percentage, pod constriction, and pod reticulation. These findings show that the PeanutMAGIC population can be used by the peanut research community as a new resource for genetic and genomic studies and for cultivar improvement. [ABSTRACT FROM AUTHOR]

Shade has a direct impact on photosynthesis and production of plants. Exposure to shade significantly reduces crops yields. Identifying shade-tolerant genomic loci and soybean varieties is crucial for improving soybean yields. In this study, we applied a shade treatment (30% light reduction) to a natural soybean population consisting of 264 accessions, and measured several traits, including the first pod height, plant height, pod number per plant, grain weight per plant, branch number, and main stem node number. Additionally, we performed GWAS on these six traits with and without shade treatment, as well as on the shade tolerance coefficients (STCs) of the six traits. As a result, we identified five shade-tolerance varieties, 733 SNPs and four candidate genes over two years. Furthermore, we developed four kompetitive allele-specific PCR (KASP) makers for the STC of S18_1766721, S09_48870909, S19_49517336, S18_3429732. This study provides valuable genetic resources for breeding soybean shade tolerance and offers new insights into the theoretical research on soybean shade tolerance. [ABSTRACT FROM AUTHOR]

Introduction: Verticillium dahliae causes a serious decline in cotton yield and quality, posing a serious threat to the cotton industry. However, the mechanism of resistance to V. dahliae in cotton is still unclear, which limits the breeding of resistant cultivars. Methods: To analyze the defense mechanisms of cotton in response to V. dahliae infection, we compared the defense responses of two upland cotton cultivars from Xinjiang (JK1775, resistant; Z8,susceptible) using transcriptome sequencing at different infection stages. Results: The results revealed a significant differential expression of genes in the two cotton cultivars post V. dahliae infection, with the number of DEGs in JK1775 being higher than that in Z8 at different infection stages of V. dahliae. Interestingly, the DEGs of both JK1775 and Z8 were enriched in the MAPK signaling pathway in the early and late stages of infection. Importantly, the upregulated DEGs in both cultivars were significantly enriched in all stages of the phenylpropanoid metabolic pathway. Some of these DEGs were involved in the regulation of lignin and coumarin biosynthesis, which may be one of the key factors contributing to the resistance of upland cotton cultivars to V. dahliae in Xinjiang. Lignin staining experiments further showed that the lignin content increased in both resistant and susceptible varieties after inoculation with V. dahliae. Discussion: This study not only provides insights into the molecular mechanisms of resistance to Verticillium wilt in Xinjiang upland cotton but also offers important candidate gene resources for molecular breeding of resistance to Verticillium wilt in cotton. [ABSTRACT FROM AUTHOR]

The simplified question on the genetic change of a conserved plant germplasm accession over time is raised for a better understanding of the challenging mission of conserving more than 7.4 million germplasm accessions in 2000 genebanks worldwide for generations to come. Its answer will influence how these genebanks operate to ensure the continued survival and availability of the conserved plant genetic resources for future food security. Here, we explore the expected impact of evolutionary forces on plant germplasm in genebanks, search for the theoretical expectations and empirical evidence for such impacts from the literature, and discuss the ramifications of the evidence for long-term plant germplasm management and conservation. It is expected that genetic changes of long-term conserved germplasm under genebank conditions will occur commonly as an evolutionary rule, not as an exception. Incorporating evolutionary biology into the Genebank Standards and operational procedures will benefit the mission of long-term germplasm conservation. [ABSTRACT FROM AUTHOR]

Excellent germplasm resources are the foundation for cultivating high-quality, disease-resistant, and stress-tolerant varieties. In this study, simple sequence repeat (SSR) markers were used to identify 138 potato accessions collected from worldwide, and genetic cluster analysis was used to characterize the genetic diversity of the tested germplasm resources. The Potato virus Y (PVY) resistance of these potato accessions was identified by artificial friction inoculation combined with molecular marker detection, and potato accessions with different PVY resistance were screened based on disease index and incidence rate. Using SSR markers, 138 potato accessions were identified, and the results showed that the genetic distances between the tested potato germplasm resources ranged from 0.025 to 0.660, and the genetic similarity coefficients ranged from 0.489 to 0.975. The 138 accessions could be clustered into five subgroups using Unweighted Pair-Group Method with Arithmetic Mean (UPGMA). Among them, Z173, Biyin No. 4, Suyin No. 2, XN995, XN987, Biyin No 22, Bibiao104, Sarpo mira, XN996, XN979, Desiree, RUNSHI, Actrice, Jia 1219, Heyin No 12, and Moyin No.1 have relatively distant genetic relationship with another 122 accessions. Based on the disease index, the following different accessions were screened: five highly resistant, 11 resistant, 45 moderately resistant, 35 susceptible, and 42 highly susceptible. Fourteen resource materials with good resistance (disease index ≤ 33.74%, and a grading of high resistance (HR) or medium resistance (MR); incidence rate ≤ 67.58%) were identified. By combining genetic cluster analysis and PVY resistance identification, six accessions showed PVY resistance and had distant genetic relationships with other accessions selected which provided important materials for disease resistance breeding and quality improvement of potato. In this study, the genetic diversity and PVY resistance of global potato germplasm resources was explored, and potato germplasm materials with important utilization value were screened. The results obtained in this study could provide important references for the research and utilization of global potato germplasm resources. [ABSTRACT FROM AUTHOR]

Seed vigor is an important trait closely related to improved seed quality and long-term germplasm conservation, and it gradually decreases during storage, which has become a major concern for agriculture. However, the underlying regulatory mechanisms of seed vigor loss in terms of genes remain largely unknown in quinoa. Here, two cultivars of quinoa seeds with different storage performance, Longli No.4 (L4) and Longli No.1 (L1), were subjected to transcriptome sequencing to decipher the pathways and genes possibly related to vigor loss under artificial aging. Multispectral imaging features and germination phenotypes showed significantly less seed vigor loss in L1 than in L4, indicating L1 seeds having stronger aging resistance and storability. Totally, 272 and 75 differentially expressed genes (DEGs) were, respectively, identified in L4 and L1 during aging. Transcriptomic analysis further revealed the differences in metabolic pathways, especially, flavonoid biosynthesis, TCA cycle, and terpenoid backbone biosynthesis were significantly enriched in L4 seeds, while carbon metabolism in L1 seeds, which involved key genes such as CHS , CHI , AACT , ENO1 , IDH , NADP-ME , and HAO2L. It indicated that the adverse effects on flavonoids and terpenoids induced by aging might be the significant reasons for more vigor loss in storage sensitive seeds, whereas storage tolerant seeds had a stronger ability to maintain carbon metabolism and energy supply. These findings elucidated the underlying molecular mechanism of seed vigor loss in quinoa, which also provided novel insights into improving seed vigor through modern molecular breeding strategies. [ABSTRACT FROM AUTHOR]

Abscisic acid (ABA) is a key plant hormone that regulates plant growth and response to stress. Pyrabactin resistance 1-like (PYR/PYL) proteins are ABA receptors involved in the initial steps of ABA signaling. Triticum monococcum L. subsp. aegilopoides is an important germplasm resource for wheat. In this study, we identified 15 PYL genes from T. monococcum L. subsp. aegilopoides and found that they were distributed across five chromosomes. Based on phylogenetic analysis, we classified these genes into three subfamilies. Members of each subfamily have similar gene structures and contain a common motif. Further analysis revealed that the promoters have multiple hormone-related elements. We found 7, 33, and 49 collinear gene pairs in three different ploidy wheat species (T. urartu, T. turgidum and T. aestivum), indicating that PYL genes are relatively conserved during the process of wheat polyploidization. Additionally, interaction networks and miRNA targets were predicted, revealing interactions between PYL proteins and key components of the abscisic acid signaling network. miR9666b-3p may serve as a central factor in PYL involvement in the abscisic acid network. Through RNA-seq analysis and qPCR validation, three genes (TbPYL2, TbPYL5, and TbPYL12) were found to potentially play a role in cold stress. These findings lay the groundwork for further research on PYL genes in T. monococcum L. subsp. aegilopoides. [ABSTRACT FROM AUTHOR]

Background: Foxtail millet [Setaria italica (L.) Beauv] is a C4 graminoid crop cultivated mainly in the arid and semiarid regions of China for more than 7000 years. Its grain highly nutritious and is rich in starch, protein, essential vitamins such as carotenoids, folate, and minerals. To expand the utilisation of foxtail millet, efficient and precise methods for dynamic phenotyping of its growth stages are needed. Traditional foxtail millet monitoring methods have high labour costs and are inefficient and inaccurate, impeding the precise evaluation of foxtail millet genotypic variation. Results: This study introduces a high-throughput imaging system (HIS) with advanced image processing techniques to enhance monitoring efficiency and data quality. The HIS can accurately extract a range of key growth feature parameters, such as plant height (PH), convex hull area (CHA), side projected area (SPA) and colour distribution, from foxtail millet images. Compared with traditional manual measurements, this HIS improved data quality and phenotyping of the key foxtail millet growth traits. High-throughput phenotyping combined with a genome-wide association study (GWAS) revealed genetic loci associated with dynamic growth traits, particularly plant height (PH), in foxtail millet. The loci were linked to genes involved in the gibberellic acid (GA) synthesis pathway related to PH. Conclusion: The HIS developed in this study enables the efficient and dynamic monitoring of foxtail millet phenotypic traits. It significantly improves the quality of data obtained for phenotyping key growth traits. The integration of high-throughput phenotyping with GWAS provides new insights into the genetic underpinnings of dynamic growth traits, particularly plant height, by identifying associated genetic loci in the GA synthesis pathway. This methodological advancement opens new avenues for the precise phenotyping and exploration of genetic resources in foxtail millet, potentially enhancing its utilisation. [ABSTRACT FROM AUTHOR]

SUMMARY Wheat growth process has been experiencing severe challenges arising from the adverse environment. Notably, the incidence of Fusarium crown rot (FCR), a severe soil‐borne disease caused by Fusarium pseudograminearum (Fp), has significantly intensified in various wheat‐growing regions, resulting in a decline in grain yield. However, the identification of wheat varieties and the exploration of effective gene resources resistant to FCR have not yet been accomplished. Here, we screened and identified the tryptophan metabolism pathway to participate in wheat resistance to FCR by correlation analysis between transcriptome and metabolome, and found that indole‐3‐acetaldehyde (IAAld) and melatonin, two key metabolites in the tryptophan metabolic pathway, were significantly accumulated in Fp‐induced wheat stem bases. Interestingly, exogenous application of these two metabolites could significantly enhance wheat resistance against Fp. Additionally, we observed that the activity of TaALDHase, a crucial enzyme responsible for catalyzing IAAld to produce indole‐3‐acetic acid (IAA), was inhibited. Conversely, the activity of TaMTase, a rate‐limiting involved in melatonin biosynthesis, was enhanced in the Fp‐induced wheat transcriptome. Further analysis showed that TaWRKY24 could regulate IAA and melatonin biosynthesis by inhibiting the expression of TaALDHase and enhancing the transcription of TaMTase, respectively. Silencing of TaALDHase could significantly increase wheat resistance to FCR. However, interference with TaWRKY24 or TaMTase could decrease wheat resistance to FCR. Collectively, our findings demonstrate the crucial role of the tryptophan metabolism pathway in conferring resistance against FCR in wheat, thereby expanding its repertoire of biological functions within the plant system. [ABSTRACT FROM AUTHOR]

Ceratostigma willmottianum Stapf is a unique chalk gland (salt‐excreting) plant from China, with a salt gland structure that excretes white crystals of calcium carbonate (CaCO3), which has potential biomineralization and carbon sequestration functions. Due to the narrow distribution of wild germplasm resources, there is a lack of diversity of new varieties to satisfy commercial development and scientific exploration. Therefore, we used ethyl methanesulfonate (EMS) mutagenesis to obtain new dwarf mutant germplasm, and analysed it in terms of morphology, growth, photosynthesis, salt glands, and excretion traits. All four dwarfing mutant strains (DM1, DM2, DM3, and DM4) exhibited extreme dwarfing (62.28%, 62.28%, 74.55% and 61.68% reduction in plant height, respectively), faster growth, increased belowground root biomass, and earlier bud differentiation and flowering. Photosynthetic capacity was enhanced: chlorophyll content, maximum quantum yield of PSII (Fv/Fm), effective quantum yield of PSII (ΦPSII), photochemical quenching coefficient (qP), electron transfer rate (ETR), net photosynthesis (Pn), intercellular CO2 concentration (Ci), stomatal conductance (Gs), and transpiration (Tr), were significantly higher in leaves of DM mutants. The density of salt glands per unit leaf area and average Ca2+ excretion rate of individual salt glands increased significantly (especially in DM2), and CaCO3 accumulation per unit leaf area was 28.57% higher than that of the wild type. Pearson correlation analysis showed that photosynthetic capacity was significantly and positively correlated with CaCO3 excretion. The above study not only provided enriched new germplasm of C. willmottianum, but also important research material for studying the mechanism of CaCO3 excretion by salt glands and carbon sequestration capacity of biomineralization. [ABSTRACT FROM AUTHOR]

With global warming, heat stress has been recognized as a significant factor limiting grapevine development and fruit quality. MicroRNAs (miRNAs) are a class of small non-coding RNAs known to play crucial regulatory roles in stress resistance. Hence, there is an immediate requirement to cultivate and identify grapevine varieties that are resistant to heat and explore miRNA-mediated heat stress defense mechanisms. In this study, we assessed the thermal resistance of 38 grape germplasm resources and identified a series of miRNAs involved in heat stress resistance. The CK (25°C) and HS (45°C) groups of "Shenyue" cuttings of grapes were used as experimental materials for next-generation sequencing and construct libraries of small RNAs. A total of 177 known and 20 novel miRNAs were detected in the libraries. Differential expression analysis identified 65 differentially expressed miRNAs (DEMs) using the DE-Seq procedure. Furthermore, RT-qPCR validation confirmed complementary expression profiles of eight DEMs and their target genes between the HS and CK groups. Heterologous transformation further identified the function of Vvi-miR3633a downregulated under heat stress in Arabidopsis. In the heterologous expression lines, the survival rate was reduced by high temperature treatment indicating the ability of Vvi-miR3633a to regulate heat resistance. Assessing the heat resistance of grape species and the expression patterns of miRNA in response to high temperatures may reveal the molecular processes of heat resistance regulation mediated by miRNA in grapes under heat stress. [ABSTRACT FROM AUTHOR]

Nitrogen (N) is the most essential element for growth, development, and grain yield determination in crops. However, excessive nitrogen application can result in environmental pollution and greenhouse gas emissions that contribute to climate change. In this study, we used 158 rice genetic resources to evaluate the relationships between the soil and plant analysis development (SPAD) value and grain yield (GY) and its components. The SPAD value ranged between 30.5 and 55.8, with a mean of 41.7 ± 5.3, under normal nitrogen conditions (NN, 9 kg/10a), and between 27.5 and 52.3, with a mean of 38.6 ± 4.8, under low nitrogen conditions (LN, 4.5 kg/10a). Under NN conditions, the SPAD values were in the following order: japonica (43.5 ± 5.8), Tongil -type (41.7 ± 2.5), others (41.7 ± 5.2), and indica (38.3 ± 3.8). By contrast, under LN conditions, the SPAD values were in the following order: Tongil -type (40.4 ± 2.1), others (40.1 ± 4.5), japonica (39.6 ± 5.2), and indica (35.6 ± 3.9). The 158 genetic resources showed no correlation between SPAD and yield. Therefore, the low-decrease rate (LDR) and high-decrease rate (HDR) SPAD groups were selected to reanalyze the relationships between the surveyed traits. The SPAD values were positively correlated with 1000-grain weight (TGW) for both LDR and HDR groups (NN: 0.63, LN: 0.53), However, SPAD and GY were positively correlated only in the LDR group. For TGW, the coefficient of determination (R 2) was 20% and 13% under NN and LN conditions, respectively. For GY, R 2 values of 32% and 52% were observed under NN and LN conditions, respectively. Genetic resources with higher SPAD values in the LDR group exhibited the highest yield (NN: 1.19 kg/m2, LN: 1.04 kg/m2) under both NN and LN conditions. In conclusion, we selected 10 genetic resources that exhibited higher GY under both NN and LN conditions with minimal yield reductions. These genetic resources represent valuable breeding materials for nitrogen deficiency adaptation. [ABSTRACT FROM AUTHOR]

Saline-alkali soils limit rice growth and production. With an increasing global population, enhancing rice salt tolerance is crucial for improving yields in these areas. This study investigated the developmental characteristics of young panicles and pollen fertility in two rice varieties, 58M and 58L, under salt stress. Results showed that 58M had more substantial salt tolerance during panicle development. RNA sequencing of 18 samples from both varieties under high salt stress (0 h, 6 h, and 24 h) identified 469 common differentially expressed genes (DEGs) and 2,308 DEGs between the varieties. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment highlighted significant pathways such as phenylpropanoid biosynthesis, protein processing, and flavonoid biosynthesis. Six gene co-expression modules related to salt tolerance were identified, with six candidate genes (LOC_Os05g38530, LOC_Os04g07920, LOC_Os12g02105, LOC_Os01g06580, LOC_Os06g49250, and LOC_Os06g48300) potentially linked to salt tolerance. These findings provide insights into rice salt tolerance mechanisms and offer new genetic resources for breeding salt-tolerant rice. [ABSTRACT FROM AUTHOR]

Polygonatum rhizome is a traditional Chinese medicine of the same origin as food and medicine, and it has high economic value and social benefits. To screen the excellent germplasm resources of Polygonatum kingianum (P. kingianum) and clarify the nutritional and medicinal value of the rhizome of P. kingianum, we used widely targeted metabolomics to analyze the traits and metabolomics of rhizomes of different germplasms of P. kingianum from different growth years. The results showed that different germplasms and growth years of P. kingianum were rich in different nutritional and medicinal components. Among them, Polygonatum kingianum 'Linyun 1′ rhizome (PWR) was richer in amino acids and derivatives, alkaloids, and phenolic acids, while Polygonatum kingianum rhizome (PRR) was richer in flavonoids, organic acids, and phenolic acids. Most of the differential compounds were mainly enriched in PRR when the growth year was one, and PWR had a greater variety and higher content of differential compounds in the third year, which also reflected the advantages of Polygonatum kingianum 'Linyun 1′ (P. kingianum 'Linyun 1′) as an excellent new variety of P. kingianum. The Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis showed that in P. kingianum with the same age and different germplasms, the significantly enriched metabolic pathway was more active in biosynthesis in PWR. In the same germplasm of P. kingianum from different years, the metabolites involved in PRR were mainly the highest in one-year-old P. kingianum (PR-1) or three-year-old P. kingianum (PR-3), and the metabolites involved in PWR were mainly the highest in three-year-old P. kingianum 'Linyun 1′ (PW-3). The above results showed that the three-year-old PWR had more advantages based on chemical substances. Therefore, this study provided a new theoretical reference for the development of P. kingianum products and the breeding of new varieties. [ABSTRACT FROM AUTHOR]

Saccharina japonica is one of the most productive aquatic plants in the world, widely used in food, feed, medicine, and other industries. Predominantly inhabiting temperate marine environments in mid- to high-latitude regions of the Northern Hemisphere, the growth of S. japonica is significantly limited by high-temperature stress. Abscisic acid (ABA) plays an important role in plant growth and development and stress responses. However, the role of ABA on high-temperature stress tolerance in S. japonica still needs to be further elucidated. Here, we found that exogenous ABA significantly alleviated disease and decay in S. japonica under high-temperature stress while also increasing the relative growth rate, chlorophyll fluorescence parameters, photosynthetic pigment, and osmotic substance content. Meanwhile, exogenous ABA enhanced the activity of protective enzymes and up-regulated the transcript levels of antioxidant-related genes, thereby reducing oxidative damage. Most importantly, we observed a significant increase in ABA content and the transcript levels of key genes involved in ABA synthesis in S. japonica under high-temperature stress, which were further amplified by the addition of exogenous ABA. In conclusion, this study provides evidence that ABA can moderate the detrimental effects of high-temperature stress and provides a theoretical basis for the screening of S. japonica germplasm resources and the cultivation of new stress-resistant varieties. [ABSTRACT FROM AUTHOR]

Ubiquitin-specific proteases (UBPs), the largest subfamily of deubiquitinating enzymes (DUBs), are critical for plant growth and development as well as abiotic-stress responses. In this study, we discovered that the expression of the ubiquitin-specific protease 15 (UBP15) gene of the gene ubiquitin-specific protease 15 (UBP15) was induced by salt, mannitol and abscisic acid (ABA) treatments. Further research revealed that UBP15 is involved in modulation of salt, drought tolerance and ABA signaling during seed germination, early seedling development, post-germination root growth or adult-plant stage. Enrichment analysis showed that many genes related to abiotic stresses and metabolic pathways were altered in the ubp15-1 mutant. Through the joint analysis of the quantitative real-time polymerase chain reaction (qRT-PCR) and differentially-expressed gene relationship network, we found that UBP15 may mainly regulate salt-stress tolerance by modulating the dwarf and delayed flowering 1 (DDF1) pathway through a cascade reaction. In the regulation of drought-stress responses, ring domain ligase1 (RGLG1) may be a direct substrate of UBP15. Moreover, we cannot exclude the possibility that UBP15 acts in a feed-forward loop mechanism in the regulation of drought-stress responses via ethylene response factor 53 (ERF53) and its ubiquitin (Ub) ligase RGLG1. In ABA signal transduction, UBP15 may play a role in at least three aspects of the ABA signaling pathway: ABA synthesis, stomatal closure regulated by ABA signaling, and transcription factors in the ABA pathway. Taken together, our results suggest that UBP15 is involved in salt, osmotic, and drought-stress tolerance and the ABA signaling pathway by directly regulating the stability of key substrates or indirectly affecting the expression of genes related to abiotic stresses in Arabidopsis thaliana. Our research provides new germplasm resources for stress-resistant crops cultivation. These results demonstrate that UBP15 is a key regulator of salt, drought and ABA tolerance in Arabidopsis. [ABSTRACT FROM AUTHOR]

Gentiana rigescens, an alpine plant with significant medicinal value, possesses a complex genetic background. However, comprehensive genomic research on G. rigescens is still lacking, particularly concerning its organelle genome. In this study, G. rigescens was studied to sequence the mitochondrial genome (mitogenome) and ascertain the assembly, informational content, and developmental expression of the mitogenome. The mitogenome of G. rigescens was 393,595 bp in length and comprised four circular chromosomes ranging in size from 6646 bp to 362,358 bp. The GC content was 43.73%. The mitogenome featured 30 distinct protein-coding genes, 26 tRNA genes, and 3 rRNA genes. The mitogenome of G. rigescens also revealed 70 SSRs, which were mostly tetra-nucleotides. In addition, 48 homologous fragments were found between the mitogenome and the chloroplast genome, with the longest measuring 23,330 bp. The documentation of the mitochondrial genome of G. rigescens is instrumental in advancing the understanding of its physiological development. Decoding the G. rigescens mitogenome will offer valuable genetic material for phylogenetic research on Gentianaceae and enhance the use of species germplasm resources. [ABSTRACT FROM AUTHOR]

Cryopreservation allows for the long-term storage of biological materials, ensuring their viability for future use and preserving biodiversity. This study aimed to develop an efficient protocol for the long-term in vitro conservation of fegra fig. In vitro precultured shoot tips of fegra fig with 0.3 M sucrose showed the highest regrowth percentage (100%) before plunging into liquid nitrogen. After plunging into liquid nitrogen, the regrowth percentage was 43.33%. Following cryopreservation, the recovered shoots were rooted and acclimatized to ex vitro conditions. The genetic fidelity of the acclimatized 8-week-old fegra fig plantlets after cryopreservation with their mother plant was tested using randomly amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR), and start codon targeted (SCoT) molecular markers. Genetic similarity between the stored plantlets with their mother plant was 100% ensuring uniformity and true-to-type regenerated plants following cryopreservation. This study presents, for the first time, an efficient protocol for the genetic conservation of fegra fig. [ABSTRACT FROM AUTHOR]

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level. [ABSTRACT FROM AUTHOR]

As a major staple food crop for the global human population, climate-resilient wheat is the key to global food security. In this context, there is an urgent need to combine advances in genomic technologies and cutting-edge tools in the crop breeding pipelines. The genetic improvement of wheat starts with a clear understanding of genes and genomic components. The past 4–5 years have seen unprecedented growth in wheat genomes, pangenomes, and functional genomics studies. More than 50 reference-level genome assemblies are available for wheat and its wild and related species. Wheat's wild and related species provide a rich source of new genes and alleles to improve wheat. Reference genome assemblies of wheat's wild and related progenitor species have provided a new, helpful resource for targeted gene discovery for wheat improvement. This review explores the journey of wheat genomics starting in 2003. There is an urgent need to improve wheat for upcoming challenges, including biotic and abiotic stresses. Sustainable wheat improvement requires the introduction of new genes and alleles in high-yielding wheat cultivars. Using new approaches, tools, and technologies to identify and introduce new genes in wheat cultivars is critical. High-quality genomes, transcriptomes, and pangenomes provide essential resources and tools to examine wheat closely to identify and manipulate new and targeted genes and alleles. Wheat genomics has improved excellently in the past 5 years, generating multiple genomes, pangenomes, and transcriptomes. Leveraging these resources allows us to accelerate our crop improvement pipelines. This review summarizes the progress made in wheat genomics and trait discovery in the past 5 years. [ABSTRACT FROM AUTHOR]

Molecular studies have contributed to the taxonomy of carrageenan-producing Kappaphycus spp. and Eucheuma denticulatum. However, unresolved species complexes and the lack of standardization in the use of genetic markers impede the identification of specimens and the delineation of a robust taxonomic framework. Here, nine molecular markers (cox1, cox2–3 spacer, cox2, cox3, COB, ITS, psbA, UPA and rbcL) were used to generate a multilocus phylogeny for 113 fresh eucheumatoid samples and four herbarium specimens. Analyses of species delineation and genetic distances confirmed the monophyly of currently accepted taxa. These analyses suggest that clades previously reported as K. striatus KS1 and KS2 are conspecific, and that E. denticulatum EDA 'spinosum' and EDB 'endong/cacing' are also conspecific. The results also unveiled possible new taxa from Hawaii and Indonesia. Each molecular marker and combinations thereof were assessed with regard to species identification, ease of amplification and sequencing, and haplotype characterization. All genetic markers recorded at least 94% success in the amplification and sequencing of fresh specimens, with cox1 being the most phylogenetically informative. Automatic partitioning, phylogenetic and tree-based assessments showed cox1, cox2–3 spacer, cox2 and rbcL were able to correctly identify species while cox1+ rbcL, COB+rbcL, cox2+ rbcL or cox1+ COB+rbcL trees best represented the phylogeny with consistently high nodal support. Among individual markers, cox1 identified the greatest number of haplotypes, while UPA, partial rbcL (750 bp), ITS, cox3 and cox2–3 spacer were able to retrieve information from herbarium specimens of 12–16 years of age. These molecular results provide a basis for a database essential for the taxonomic framework, cultivar development and germplasm conservation of eucheumatoids. Highlights: Mitochondria cox1, cox2–3 spacer, cox2 and plastid rbcL can be used for species identification and cox1 for haplotype detection of eucheumatoids. cox1+rbcL, COB+rbcL, cox2+rbcL or cox1+COB+rbcL are the most cost-effective molecular markers for phylogenetic inference. The most comprehensive up to date multilocus phylogeny of Kappaphycus spp. and Eucheuma denticulatum is presented. [ABSTRACT FROM AUTHOR]

Summary: Germplasm resources serve as the foundations of advancements in breeding and are crucial for maintaining food security. Wild rice species of the genus Oryza include rich sources of genetic diversity and high adaptability, making them a substantial resource for rice breeding. The discovery of wild‐type cytoplasmic male sterility resources enabled the achievement of the 'three lines' goal in hybrid rice, significantly increasing rice yields. The application of resistance alleles from wild rice enables rice production to withstand losses caused by stress. Reduced genetic diversity due to rice breeding poses a significant limitation to further advances and can be alleviated through a systematic use of wild genetic resources that integrate geographic, climatic and environmental data of the original habitat, along with extensive germplasm collection and identification using advanced methods. Leveraging technological advancements in plant genomics, the understanding of genetic mechanisms and the application of artificial intelligence and gene editing can further enhance the efficiency and accuracy of this process. These advancements facilitate rapid isolation and functional studies of genes, and precise genome manipulation. This review systematically summarizes the utilization of superior genes and germplasm resources derived from wild rice sources, while also exploring the collection, conservation, identification and utilization of further wild rice germplasm resources. A focus on genome sequencing and biotechnology developments is leading to new breeding and biotechnology opportunities. These new opportunities will not only promote the development of rice varieties that exhibit high yields, superior stress resistance and high quality but also expand the genetic diversity among rice cultivars. [ABSTRACT FROM AUTHOR]

Summary: Cold stress is a major abiotic stress that threatens maize (Zea mays L.) production worldwide. Understanding the molecular mechanisms underlying cold tolerance is crucial for breeding resilient maize varieties. Tonoplast intrinsic proteins (TIPs) are a subfamily of aquaporins in plants. Here, we report that TIP family proteins are involved in maize cold tolerance. The expression of most TIP genes was responsive to cold stress. Overexpressing TIP2;1, TIP3;2 or TIP4;3 reduced the cold tolerance of maize seedlings, while loss‐of‐function mutants of TIP4;3 exhibited enhanced cold tolerance. Candidate gene‐based association analysis revealed that a 328‐bp transposon insertion in the promoter region of TIP4;3 was strongly associated with maize cold tolerance. This transposon insertion conferred cold tolerance by repressing TIP4;3 expression through increased methylation of its promoter region. Moreover, TIP4;3 was found to suppress stomatal closure and facilitate reactive oxygen species (ROS) accumulation under cold stress, thereby inhibiting the expression of cold‐responsive genes, including DEHYDRATION‐RESPONSIVE ELEMENT BINDING FACTOR 1 (DREB1) genes and a subset of peroxidase genes, ultimately attenuating maize cold tolerance. This study thus elucidates the mechanism underlying TIP‐mediated cold tolerance and identifies a favourable TIP4;3 allele as a potential genetic resource for breeding cold‐tolerant maize varieties. [ABSTRACT FROM AUTHOR]

Nepal has 15 distinct agroecosystems spread across three major agroecozones: Tarai, Mid Hill, and High Hill. These regions support a rich variety of agrobiodiversity. This paper examines the significance of native agrobiodiversity within each of these agroecosystems for diversified food, nutrition, health, business and environment. The information presented is derived from various literature sources, discussions with key experts, and the authors' own experiences. Each of these agroecosystems has cultivated and preserved numerous unique species, landraces, and genotypes of agrobiodiversity, including crops, forages, livestock, agro-insects, agro-microorganisms, and aquatic genetic resources. This agrobiodiversity is deeply connected with local cultures, traditional knowledge, and skills. The high diversity of agricultural genetic resources (AGRs) within Nepal's relatively small area is a crucial factor for ensuring food security, nutrition, health, business opportunities, and environmental sustainability. Many niche products, prized for their purity, quality, taste, health benefits, and nutritional value, are sold at premium prices. However, the focus on production-centric agricultural programs over the years has led to the replacement of many niche-specific varieties by more uniform and limited ones. Introducing new genotypes into a particular agroecosystem may undermine the principles of ecological agriculture. Therefore, it is essential to enhance the competitiveness of native AGRs and associated indigenous technologies within each agroecosystem. [ABSTRACT FROM AUTHOR]

Leaf blotch, caused by Zymoseptoria tritici , is a fungal disease that poses a severe threat to wheat production worldwide. Knowledge of virulence variability is crucial in choosing effective control measures. However, there have only been a few studies of the pathogenic variability and pathotypes within Ethiopian isolates. Hence, the objective of this study was to assess the virulence spectrum and variability of Z. tritici isolates. Forty-three isolates were tested for their virulence and pathotype against 7 wheat differential lines that have different resistance genes. A pathogenicity assay detected 41 differential line-specific virulent isolates among 301 interactions between a host and pathogen based on the percentage coverage of the leaf area by pycnidia. Some isolates were virulent against 50 %–60 % of the resistant genes, but most of them were virulent against some differential lines. Isolates such as EtA-11, EtSh-1, EtSh-2, EtSh-4, and EtA-19 expressed broad-spectrum virulence, highlighting that such isolates are useful for germplasm screening. The isolates were classified into 25 pathotypes, defined by their differential virulence responses. They were also assigned to two clusters according to their mean pycnidia percent. Pathotypes and principal component analysis detected 58.1 % and 62.2 % pathogenic diversity in Ethiopian isolates, respectively. The current findings provide information that breeders can use to identify and select more resistant varieties for farmers. [ABSTRACT FROM AUTHOR]

Powdery mildew is a serious fungal disease in protected melon cultivation that affects the growth, development and production of melon plants. Previous studies have shown that red light can improve oriental melon seedlings resistance to powdery mildew. Here, after inoculation with Podosphaera xanthii, an obligate fungal pathogen eliciting powdery mildew, we found that red light pretreatment increased ethylene production and this improved the resistance of melon seedlings to powdery mildew, and the ethylene biosynthesis gene CmACS10 played an important role in this process. By analysing the CmACS10 promoter, screening yeast one‐hybrid library, it was found that CmERF27 positively regulated the expression of CmACS10, increased powdery mildew resistance and interacted with PHYTOCHROME INTERACTING FACTOR8 (CmPIF8) at the protein level to participate in the regulation of ethylene biosynthesis to respond to the red light‐induced resistance to P. xanthii, Furthermore, CmPIF8 also directly targeted the promoter of CmACS10, negatively participated in this process. In summary, this study revealed the specific mechanism by which the CmPIF8‐CmERF27‐CmACS10 module regulates red light‐induced ethylene biosynthesis to resist P. xanthii infection, elucidate the interaction between light and plant hormones under biological stress, provide a reference and genetic resources for breeding of disease‐resistant melon plants. Summary Statement: We found that ethylene was induced by red light and plays a positive role in the resistance of melon to powdery mildew. CmERF27 and CmPIF8 activate and inhibit the transcription of CmACS10, respectively, and regulate ethylene biosynthesis. Moreover, CmERF27 and CmPIF8 proteins interact, and this interaction interferes with the transcriptional activation of CmACS10 by CmERF27. [ABSTRACT FROM AUTHOR]

Ruffled vegetables, having wrinkled leaves with a crispy and tender texture, are highly favored by consumers. However, the genetic resources of crinkled leaf vegetables in the Brassica genus are limited. In this study, distant hybridization was performed between 'Mottle-leaf Tai-cai' (Brassica campestris L. ssp. chinensis (L.) Makino var. tai-tsai Hort. AA, 2n = 20) and 'Big Yellow Flower Chinese Kale' (B. oleracea var. alboglabra Bailey. CC, 2n = 18) by hand emasculation followed by tissue culture. As a result, all obtained three embryos were identified as true hybrids (AC, 2n = 19) through morphology, cytology, and molecular markers. After chromosome doubling, an allotetraploid hybrid (AACC, 2n = 38) was obtained with a giant leaf, serrated leaf margin, and wrinkled leaf surface; therefore, its most agronomical characters were biased toward the female parent of 'Mottle-leaf Tai-cai'. In comparison with diploid hybrid, the pollen stainability of allotetraploids were significantly improved and similar to their parents. Additionally, all 5 pairs of SSR primers showed the authenticity of the hybrids. Furthermore, the contents of soluble sugar, vitamin C, and cellulose in the hybrids increased when compared with their parents. Briefly, the obtained hybrid is interspecific euhybrid, and has wrinkle-leaf characteristics, improved nutritional quality, so it is a novel Brassica wrinkle-leaf vegetable germplasm. [ABSTRACT FROM AUTHOR]

Genebanks serve as both providers of valuable traits for breeding programs and repositories of diverse crop genetic material representing society's agricultural heritage. In this study, we use a Becker‐DeGroot‐Marschak mechanism to elicit the willingness‐to‐pay of rice farmers in Côte d'Ivoire for small amounts of African rice (Oryza glaberrima) landraces held by the genebank of the Rice Biodiversity Center for Africa, and for seed of newly developed ARICA rice varieties bred using genebank materials. Using a field experiment, we additionally investigate how randomized exposure to and experimentation with small amounts of African rice landrace seed or seed of advanced rice varieties developed by AfricaRice affect how smallholder rice farmers value these novel genetic resources. Surprisingly, we find that farmers generally value having access to African rice landraces at approximately the same level as for advanced rice varieties (and far above market rates for improved seed), and that those farmers who grew landrace seed in the offseason were willing to pay more than those who did not. Our results demonstrate the additional value provided by the conservation of African rice landrace varieties (apart from their use in breeding) and highlight the importance of experimentation in the adoption process. [ABSTRACT FROM AUTHOR]

Grasspea (Lathyrus sativus L.) is a climate-smart legume crop with adaptation to fragile agroecosystems. The genus Lathyrus is recognized for its vast genetic diversity, encompassing over 160 species, many of which are cultivated for various purposes across different regions of the world. Among these, Lathyrus sativus is widely cultivated as food, feed, and fodder in South Asia, Sub-Saharan Africa, and the Central and West Asia and North Africa (CWANA) regions. Its global cultivation has declined substantially due to the stigma posed by the presence of neurotoxin β-N-oxalyl-L-α, β-diaminopropionic acid (β-ODAP) in its seeds and green foliage. Overconsumption for a longer period of grasspea seeds harvested from landraces may lead to a neurological disorder called neurolathyrism in humans. ODAP is an obstacle for grasspea expansion, but crop wild relatives (CWRs) have been found to offer a solution. The incorporation of CWRs, particularly Lathyrus cicera, and landraces into breeding programs may reduce the ODAP content in grasspea varieties to a safer level. Recent advances in genomics-assisted breeding have expanded the potential for utilizing challenging CWRs to develop grasspea varieties that combine ultra-low ODAP levels with improved yield, stability, and adaptability. Further progress in omics technologies—such as transcriptomics, proteomics, and metabolomics—along with genome sequencing and editing, has greatly accelerated the development of grasspea varieties with reduced or zero ODAP content, while also enhancing the plant's agronomic value. This review highlights the significance of utilizing CWRs in pre-breeding programs, and harnessing advanced tools and technologies to enhance the performance, adaptability, and resilience of grasspea in response to changing environmental conditions. [ABSTRACT FROM AUTHOR]

Salt stress has become a major environmental problem affecting plant growth and development. Some WRKY transcription factors have been reported to be involved in the salt stress response in plants. However, there are few studies on the involvement of WRKYs in the salt stress response in Rosa rugosa. In this study, we isolated a salt tolerance gene, RrWRKY1, from R. rugosa. RrWRKY1 was found to belong to Group I of the WRKY family, and it was specifically expressed in leaves and petals. RrWRKY1 expression was upregulated under NaCl stress in rose leaves. After silencing RrWRKY1 in R. rugosa, transgenic plants showed dry leaves and black and brown veins, indicating sensitivity to salt stress. At the same time, the transcription levels of the salt tolerance-related genes RrNHX1, RrABF2, RrRD22, RrNCED1, and RrHKT1 also changed significantly. The superoxide dismutase (SOD) and peroxidase (POD) activities decreased, the proline content decreased, and the malondialdehyde (MDA) content in the gene-silenced plants increased, indicating that RrWRKY1 regulates the salt tolerance of R. rugosa. In addition, the overexpression of RrWRKY1 in Arabidopsis thaliana improved the germination rate and the average of the main root and lateral root lengths, and the transgenic plants had a larger number of lateral roots than the WT plants under salt stress. This study provides candidate gene resources for salinity tolerance breeding and a theoretical basis for analyzing the salinity tolerance mechanism of the WRKY gene. [ABSTRACT FROM AUTHOR]

Dendrobium officinale Kimura & Migo (D. officinale) is a well-recognized traditional Chinese medicinal herb that is both medicinal and edible. Contemporary pharmacological studies have revealed that D. officinale contains abundant bioactive compounds, including polysaccharides, flavonoids, alkaloids, and dendrobine, exhibiting diverse pharmacological properties such as antioxidant, anti-inflammatory, and immunomodulatory effects. However, the industrial application of D. officinale faces many problems, such as the scarcity of wild resources, low natural reproduction rate, and slow growth rate as well as the lack of relevant industrial standards. Nevertheless, substantial advancements, including the exploitation of artificial propagation techniques and breeding of new varieties, have been achieved in recent years. These developments have effectively addressed the challenges associated with its low natural reproduction rate and the scarcity of wild resources. This review summarizes the progress in the industrial development, seedling cultivation, and pharmacological exploration of D. officinale in recent years. Furthermore, it analyzes current research inadequacies and offers strategic solutions to enhance its application in healthcare and medicine. [ABSTRACT FROM AUTHOR]

Sugar beet (Beta vulgaris L.) is a biennial herb belonging to the Amaranthaceae family. It contributes to approximately 30% of the world's total sucrose production and is an economically important crop. In this study, we analyzed the genetic diversity and population structure of 132 exotic sugar beet varieties using three molecular makers: four pairs of simple sequence repeat (SSR) primers, three pairs of insertion–deletion sequence (InDel) primers, and 20 cis-element amplification polymorphism (CEAP) primers. The results indicated that the number of alleles (Na) was 298, among which the number of effective alleles (Ne) was 182.426 (accounting for approximately 61.2%). The mean value of the genetic diversity index was 0.836. The polymorphic information content (PIC) was 0.639–0.907 (mean = 0.819), indicating a high level of polymorphism. These sugar beet varieties were classified into six clusters using the UPGMA method of cluster analysis. Population structure analysis revealed that the most ideal K value was 6. This indicated that the test materials could be divided into six categories, consistent with the clustering results. The clustering results indicated that most sugar beet varieties from the same breeding company clustered together, and the genetic distance between them was small, indicating that they may share the same male and/or female parent. Some varieties from different companies clustered together, indicating a narrow genetic base and potential exchange of germplasm resources between breeding companies. This study revealed the genetic differences among exotic sugar beet varieties and characteristics of the population structure. It provided a scientific basis for the identification of sugar beet varieties and markers-assisted breeding in China in the future. [ABSTRACT FROM AUTHOR]

Polyphenols are important functional components that have anti-cancer and anti-inflammatory effects. Apple fruit is rich in polyphenols and is one of the dietary sources of polyphenols. The polyphenol components and contents of the peel and pulp of 74 Malus sieversii (Led.) Roem. and 26 Chinese Malus germplasm resources were determined using ultra-high-phase chromatography (UPLC) and liquid chromatography–mass spectrometry (LC–MS). The results showed that 34 components were detected in the peel and 30 in the flesh, and that the polyphenol components and contents of the different germplasm resources were significantly different; the polyphenol content of Malus sieversii (Led.) Roem. was significantly higher than that of the other local varieties, and the polyphenol content in the peel was also higher than that in the flesh. Rutin, quercetin 3-O-arabopyranoside, kaempferol 3-O-rutinoside, and peonidin 3-O-galactoside were detected only in the peel. The total polyphenol content in the peel ranged from 949.76 to 5840.06 mg/kg, and the polyphenol content in the pulp ranged from 367.31 to 5123.10 mg/kg. The cluster analysis of polyphenol components and contents in peel and pulp showed that 100 Malus germplasm resources could be grouped into four categories. Principal component analysis of 34 kinds and 30 kinds of polyphenols in peel and pulp of 100 resources was performed. If the eigenvalue is greater than 1, eight and seven principal components are extracted, respectively. Five Malus resources with high polyphenol content in the peel and pulp were selected: 'XY-77' (peel: 5840.06 mg/kg, pulp: 5123.10 mg/kg; 'LF-09' (peel: 4692.63 mg/kg, pulp: 3729.79 mg/kg); '2012-5' (peel: 4377.61 mg/kg, pulp: 3847.54 mg/kg); '29028' (peel: 5088.05 mg/kg, pulp: 3994.61 mg/kg); and '11-01' (peel: 5154.45 mg/kg, pulp: 3616.15 mg/kg). These results provide us with information regarding the polyphenol composition and content of the wild apple resources and local cultivars. The high polyphenol content resources obtained by screening can be used as raw materials for the extraction of polyphenol components and functional fruit juice processing and can also be used as parents for functional fruit creation and variety breeding. [ABSTRACT FROM AUTHOR]

Flowering time of crops is critical for maximizing yield, quality and regional adaptability under target environments. In rice, Heading date 3a (Hd3a) and Rice Flowering Locus T 1 (RFT1) proteins are the key factors of flowering time regulation in the florigen activation complex. However, effects of hd3a and rft1 mutations on the flowering time under long-day conditions are not clear. In this study, we generated single and double mutants of Hd3a and RFT1 in japonica varieties Shen Nong 9816 (SN9816) background, termed hd3a-SNs, rft1-SNs and doub-SNs, by using CRISPR/Cas9 system. The flowering time of hd3a-SN mutants was similar to wild-type (WT); but mutations of RFT1 delayed flowering time by 11 to 14 days comparing to WT under nature long day (NLD) conditions. Double mutants of Hd3a and RFT1 (doub-SNs) exhibited an extremely late flowering phenotype, and they did not flower up to 365 days after regeneration under either NLD or short-day conditions. The leaf emergency rate of RFT1 mutants was similar to WT, suggesting that the late flowering phenotype of rft1-SNs was caused by delayed floral transition, but not by retarded growth. The expression of the key floral organ identity genes was significantly decreased in rft1-SN and doub-SN mutants, resulting in late flowering phenotypes. The expression profiles, evolution and haplotypes of Hd3a and RFT1 was also analyzed. Our studies provide insight into the potential utilization of Hd3a and RFT1 gene resources to improving growth period and regional adaptability in rice breeding. [ABSTRACT FROM AUTHOR]

Background: Rice ECQ (eating and cooking quality) is an important determinant of rice consumption and market expansion. Therefore, improvement of ECQ is one of the primary goals in rice breeding. However, ECQ-related quantitative trait loci (QTL) have not yet been fully revealed. The present study aimed to identify a major effect QTL for rice taste, an important component of ECQ via genotyping-by-sequencing, to reveal the associated molecular mechanisms, and to predict key candidate genes. Results: A population of F9 recombinant inbred lines resulting from a cross between R668 (national standard of high-quality third class) and R838 (common edible rice) was used to construct a high-density genetic map (2,295.062 cM). The map comprises 639,504 markers distributed on 12 linkage elements with an average genetic distance of 0.004 cM. We detected a major taste-related QTL, qECQ8, which explained 41.4% of phenotypic variance and had LOD values of 4.42–7.73. Using a five-generation NIL population from the backcross of "Ganxiangzhan No. 1" carrying qECQ8 with the recurrent parent R838 (without qECQ8), we narrowed qECQ8 to a 187.5 kb interval between markers M33 and M37 on Chr8. Comparative transcriptomic analysis revealed that photosynthesis, glyoxylate and dicarboxylate metabolism, carbon fixation in photosynthetic organisms, and alpha-linolenic acid metabolism were induced in developing seeds of lines containing qECQ8. Furthermore, we identified two candidate genes in the qECQ8 region, including LOC_Os08g30550 (zinc knuckle family protein), a major candidate for genetic-assisted breeding of high-quality rice. Conclusion: Our findings provide important genetic resources for targeted improvement of rice taste quality and may facilitate the genetic breeding of rice ECQ. [ABSTRACT FROM AUTHOR]

ABSTRACT African horned melon (Cucumis metuliferus E. Meyer ex Naudin, 2n = 2x = 24) is an under‐researched and under‐utilised cucurbit crop primarily grown for its nutritious fruit. In its centre of diversity, the crop is valued for its relatively high tolerance to insect pests, diseases, drought and heat stress. It is a potential opportunity crop and a valuable source of genes to major Cucumis species, including cucumber (Cucumis sativas L.) and melon (C. melo L.). Its climate resilience and nutrient‐rich fruit provide niche market opportunities. Hence, production and value‐adding will make African horned melon a crop of choice globally. There is a need for an in‐depth investigation into the genetic diversity, breeding and food composition of the crop. Therefore, the objective of this review was to provide perspectives on the production and breeding status of African horned melon to appraise its genetic value for human welfare, strategic production, genetic conservation and breeding of market‐preferred varieties, including closely related Cucumis species. The first section described the botany, production status, germplasm resources and characterisation based on phenotypic and genetic markers. This is followed by breeding progress for biotic and abiotic stress tolerance, utilities and challenges of gene transfer and potential rootstock to Cucumis species, especially cucumber and melon. The review summarised the main breeding goals and approaches, including mutation breeding to fast‐track the development of new varieties. Information presented in the review will guide cultivar design in African horned melon or related cucurbits, aiming for superior agronomic and nutritional quality traits and tolerance to biotic and abiotic stresses. [ABSTRACT FROM AUTHOR]

Leaf heading is an important agronomic trait of Chinese cabbage, which directly affects its yield. Leaf heading formation in Chinese cabbage is controlled by its internal genotype and external environmental factors, the underlying mechanism of which remains poorly understood. To discover the leaf heading formation mechanism more deeply, this study analyzed the correlation between proteomic and transcriptomic data in the leaf heading formation mutant fg-1 generated by EMS. iTRAQ-based quantitative proteomics techniques were performed to identify the protein expression profiles during the key periods of the early heading stage in the section of the soft leaf apical region (section a) and the whole leaf basal region (section d). We first identified 1,246 differentially expressed proteins (DEPs) in section a and 1,055 DEPs in section d. Notably, transcriptome–proteome integrated analysis revealed that 207 and 278 genes showed consistent trends at the genes’ and proteins’ expression levels in section a and section d, respectively. KEGG analyses showed that the phenylpropanoid biosynthesis pathway was enriched in both sections a and d. Furthermore, 86 TFs exhibited co-upregulation or co-downregulation, and seven out of 86 were involved in plant hormone synthesis and signal transduction pathways. This indicates that they are potentially related to the leaf heading formation in Chinese cabbage. Taken together, we have identified several key earlyheading-formation-related factors via integration analysis of the transcriptomics and proteomics data. This provides sufficient gene resources to discover the molecular mechanism of leaf heading formation. [ABSTRACT FROM AUTHOR]

Cucumis melo L., commonly known as melon, is a crucial horticultural crop. The selection and breeding of superior melon germplasm resources play a pivotal role in enhancing its marketability. However, current methods for melon appearance phenotypic analysis rely primarily on expert judgment and intricate manual measurements, which are not only inefficient but also costly. Therefore, to expedite the breeding process of melon, we analyzed the images of 117 melon varieties from two annual years utilizing artificial intelligence (AI) technology. By integrating the semantic segmentation model Dual Attention Network (DANet), the object detection model RTMDet, the keypoint detection model RTMPose, and the Mobile-Friendly Segment Anything Model (MobileSAM), a deep learning algorithm framework was constructed, capable of efficiently and accurately segmenting melon fruit and pedicel. On this basis, a series of feature extraction algorithms were designed, successfully obtaining 11 phenotypic traits of melon. Linear fitting verification results of selected traits demonstrated a high correlation between the algorithm-predicted values and manually measured true values, thereby validating the feasibility and accuracy of the algorithm. Moreover, cluster analysis using all traits revealed a high consistency between the classification results and genotypes. Finally, a user-friendly software was developed to achieve rapid and automatic acquisition of melon phenotypes, providing an efficient and robust tool for melon breeding, as well as facilitating in-depth research into the correlation between melon genotypes and phenotypes. [ABSTRACT FROM AUTHOR]

Hazelnuts are traditional woody oilseed plants. Corylus L. resources are rich in variety and widely distributed in China. However, the identification of germplasm varieties and the selection of superior varieties remain quite limited. This study aimed to analyze the genetic diversity of 331 Corylus L. germplasms using 16 simple sequence repeat (SSR) markers. Based on this, 11 pairs of core primers were selected, a fingerprint database of germplasm resources was constructed, and a primary core collection was screened. The results indicated that these tested Corylus L. germplasms exhibited a high level of genetic diversity, with an average number of alleles (Na) per locus of 14.5 and a polymorphic information content of 0.777. The phylogenetic relationships among various hazelnut cultivars were characterized by complexity, and they were delineated into four distinct groups facilitated by genetic distance analyses. An SSR fingerprint database for 331 Corylus L. germplasms was successfully constructed using the 11 obtained core SSR markers to increase the discrimination efficiency. Ultimately, 127 primary core accessions of Corylus L. were selected. The retention rate for the observed Na and MAF (the minor allele frequency) in the primary core germplasm constructed based on a sampling proportion of 38.36% was 100% and 94.7%, respectively. Shannon's information index (I) was highly consistent between the core and original germplasms, indicating that the core germplasm could fully represent the genetic diversity of the original germplasm. Additionally, the principal coordinate analysis of the selected primary core germplasm was essentially consistent with that of the entire original germplasm, further supporting the broad representativeness of the core germplasm. This study provided a basis for precisely identifying and efficiently utilizing Corylus L. accession. [ABSTRACT FROM AUTHOR]

SUMMARY Dormancy is an essential characteristic that enables seeds to survive in unfavorable conditions while germinating when conditions are favorable. Myosin‐binding proteins (MyoBs) assist in the movement of organelles along actin microfilaments by attaching to both organelles and myosins. In contrast to studies on yeast and metazoans, research on plant MyoBs is still in its early stages and primarily focuses on tip‐growing cells. In this study, we found that Arabidopsis MyoB13 is highly expressed in dry mature seeds. The myob13 mutant, created using CRISPR/Cas9, exhibits a preharvest sprouting phenotype, which can be mitigated by after‐ripening treatment, indicating that MyoB13 plays a positive role in primary seed dormancy. Furthermore, we show that MyoB13 negatively regulates ABA biosynthesis and signaling pathways. Notably, the expression of MyoB13 orthologs from maize and soybean can completely restore the phenotype of the Arabidopsis myob13 mutant, suggesting that the function of MyoB13 in ABA‐induced seed dormancy is evolutionarily conserved. Therefore, the functional characterization of MyoB13 offers an additional genetic resource to help prevent vivipary in crop species. [ABSTRACT FROM AUTHOR]

ABSTRACT The past decade has witnessed rapid developments in gene discovery, biological big data (BBD), artificial intelligence (AI)‐aided technologies, and molecular breeding. These advancements are expected to accelerate crop breeding under the pressure of increasing demands for food. Here, we first summarize current breeding methods and discuss the need for new ways to support breeding efforts. Then, we review how to combine BBD and AI technologies for genetic dissection, exploring functional genes, predicting regulatory elements and functional domains, and phenotypic prediction. Finally, we propose the concept of intelligent precision design breeding (IPDB) driven by AI technology and offer ideas about how to implement IPDB. We hope that IPDB will enhance the predictability, efficiency, and cost of crop breeding compared with current technologies. As an example of IPDB, we explore the possibilities offered by CropGPT, which combines biological techniques, bioinformatics, and breeding art from breeders, and presents an open, shareable, and cooperative breeding system. IPDB provides integrated services and communication platforms for biologists, bioinformatics experts, germplasm resource specialists, breeders, dealers, and farmers, and should be well suited for future breeding. [ABSTRACT FROM AUTHOR]

ABSTRACT Soybean (Glycine max) is an important crop for its nutritional value. Its wild relative, Glycine soja, provides a valuable genetic resource for improving soybean productivity. Root development and differentiation are essential for soybean plants to take up water and nutrients, store energy and anchor themselves. Long noncoding RNAs (lncRNAs) have been reported to play critical roles in various biological processes. However, the spatiotemporal landscape of lncRNAs during early root development and differentiation in soybeans is scarcely characterized. Using RNA sequencing and transcriptome assembly, we identified 1578 lncRNAs in G. max and 1454 in G. soja, spanning various root portions and time points. Differential expression analysis revealed 82 and 69 lncRNAs exhibiting spatiotemporally differential expression patterns in G. max and G. soja, respectively, indicating their involvement in the early stage of root architecture formation. By elucidating multiple competitive endogenous RNA (ceRNA) networks involving lncRNAs, microRNAs and protein‐coding RNAs, we unveiled intricate regulatory mechanisms of lncRNA in early root development and differentiation. Our efforts significantly expand the transcriptome annotations of soybeans, unravel the dynamic landscapes of lncRNAs during early root development and differentiation, and provide valuable resources into the field of soybean root research. [ABSTRACT FROM AUTHOR]

Background: Fusarium head blight (FHB), a devastating disease of wheat production, is predominantly elicited by Fusarium graminearum (Fg). The tetraploid Thinopyrum elongatum is a tertiary gene resource of common wheat that possesses high affinity and displays high resistance traits against multiple biotic and abiotic stress. We aim to employ and utilize the novel FHB resistance resources from the wild germplasm of common wheat for breeding. Results: Durum wheat-tetraploid Th. elongatum amphiploid 8801 was hybridized with common wheat cultivars SM482 and SM51, and the F5 generation was generated. We conducted cytogenetically in situ hybridization (ISH) technologies to select and confirm a genetically stable 7E(7D) substitution line K17-1069-5, which showed FHB expansion resistance in both field and greenhouse infection experiments and displayed no significant disadvantage in agronomic traits compared to their common wheat parents in the field. The F2 segregation populations (K17-1069-5 × SM830) showed that the 7E chromosome conferred dominant FHB resistance with dosage effect. We developed 19 SSR molecular markers specific to chromosome 7E, which could be conducted for genetic mapping and large breeding populations marker-assisted selection (MAS) during selection procedures in the future. We isolated a novel Fhb7 allele from the tetraploid Th. elongatum chromosome 7E (Chr7E) using homology-based cloning, which was designated as TTE7E-Fhb7. Conclusions: In summary, our study developed a novel wheat-tetraploid Thinopyrum elongatum 7E(7D) K17-1069-5 substitution line which contains stable FHB resistance. [ABSTRACT FROM AUTHOR]

SUMMARY The BonnMu resource is a transposon tagged mutant collection designed for functional genomics studies in maize. To expand this resource, we crossed an active Mutator (Mu) stock with dent (B73, Co125) and flint (DK105, EP1, and F7) germplasm, resulting in the generation of 8064 mutagenized BonnMu F2‐families. Sequencing of these Mu‐tagged families revealed 425 924 presumptive heritable Mu insertions affecting 36 612 (83%) of the 44 303 high‐confidence gene models of maize (B73v5). On average, we observed 12 Mu insertions per gene (425 924 total insertions/36 612 affected genes) and 53 insertions per BonnMu F2‐family (425 924 total insertions/8064 families). Mu insertions and photos of seedling phenotypes from segregating BonnMu F2‐families can be accessed through the Maize Genetics and Genomics Database (MaizeGDB). Downstream examination via the automated Mutant‐seq Workflow Utility (MuWU) identified 94% of the presumptive germinal insertion sites in genic regions and only a small fraction of 6% inserting in non‐coding intergenic sequences of the genome. Consistently, Mu insertions aligned with gene‐dense chromosomal arms. In total, 42% of all BonnMu insertions were located in the 5′ untranslated region of genes, corresponding to accessible chromatin. Furthermore, for 38% of the insertions (163 843 of 425 924 total insertions) Mu1, Mu8 and MuDR were confirmed to be the causal Mu elements. Our publicly accessible European BonnMu resource has archived insertions covering two major germplasm groups, thus facilitating both forward and reverse genetics studies. [ABSTRACT FROM AUTHOR]