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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.

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]

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]

ABSTRACT Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of P. davidiana makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype‐resolved genome assembly of P. davidiana. Genomic comparisons of the two haplotypes revealed 18,152 structural variations, 2,699 Pda_hap1‐specific and 2,702 Pda_hap2‐specific genes, and 1,118 allele‐specific expressed genes. Genome composition indicated 4.1% of the P. davidiana genome was non‐peach origin, out of which 94.5% was derived from almond. Based on the haplotype genome, the aphid resistance quantitative trait locus (QTL) was mapped at the end of Pda03. From the aphid resistance QTL, PdaWRKY4 was identified as the major dominant gene, with a 9‐bp deletion in its promoter of the resistant phenotype. Specifically, PdaWRKY4 regulates aphid resistance by promoting PdaCYP716A1‐mediated anti‐aphid metabolite betulin biosynthesis. Moreover, we employed a genome design to develop a breeding workflow for rapidly and precisely producing aphid‐resistant peaches. In conclusion, this study identifies a novel aphid resistance gene and provides insights into genome design for the development of resistant fruit cultivars. [ABSTRACT FROM AUTHOR]

Adopted in 2010 as a supplementary agreement to the 1992 Convention on Biological Diversity, the Nagoya Protocol (NP) mandates the fair and equitable sharing of benefits arising from the use of genetic resources provided by Indigenous peoples. Member states must newly enact or amend domestic laws to align with the NP. Consequently, many countries are currently implementing legislative, administrative, and policy measures to ensure fair benefit sharing from the use of Indigenous genetic resources. We examined the inclusion of intellectual property (IP) protection in the sharing of benefits from research and development that utilizes Indigenous genetic resources. The NP does not specify guidelines for IP‐related benefit sharing, leaving each member state to establish its own rules. We used an economics‐based approach to explore the optimal scope and duration of IP protection for maximizing stakeholder interests, including those of Indigenous peoples, at the national level. The optimal duration of IP protection was when the marginal social cost and benefit of IP protection were equal. When this point occurred varied depending on various factors, such as the type of genetic resources in the country, existence of alternatives, number of users, and competing actors. The optimal scope of IP protection was when the social benefit of investment in fundamental research equaled the social benefit of application development. Likewise, this point of implementation also varied based on various factors, such as the type, uniqueness, potential for further discovery, and diversity of providers in the country. [ABSTRACT FROM AUTHOR]

A gene bank for farm animal genetic resources (FAGR) is an important facility for the diversity conservation of FAGR. The primary purpose of gene banks for FAGR is the reconstruction of those breeds. With the advent of the post-genomic era, gene banks for FAGR have increasingly become an infrastructure for the support of livestock research and animal breeding, and a platform for international research collaboration. China is one of the richest countries in the world in terms of FAGR. Chinese National Gene Banks for FAGR (CNGBFs) have an important legal status and play an important function in the Chinese FAGR protection system. In this paper, we reviewed the current situation of CNGBFs construction, and systematically collected and analyzed legal rules related to CNGBFs. As results, those legal rules were categorized into two types: (a) organization and management, (b) activities. We summarized problems existing in the current legal rules for CNGBFs from three levels: institution, practical operation, and digital development. Improvement directions of legal rules regarding CNGBFs are proposed. They include clarifying the utilization function of CNGBFs and the ownership of FAGR in CNGBFs. Moreover, improving the mechanism of administrative management, rules on domestic and international access and benefit-sharing, and the system of digital sequence information management are also suggested. The improvements in those legal rules will contribute to the appropriate utilization of Chinese FAGR and international collaborations. [ABSTRACT FROM AUTHOR]

Sea cucumbers are deposit feeding members of marine benthic communities. The over-exploitation of sea cucumber natural stocks, especially in the Mediterranean basin, is having negative impacts on the marine ecosystem. This concerns had led the Italian government to take legal actions to preserve these important marine resources. The aim of this study was to evaluate the level of genetic diversity and population structures within two sympatric Holothuria sea cucumber species, H. polii and H. tubulosa, across ten Mediterranean areas along Italy. A 323 bp portion of the COI mitochondrial gene was sequenced in a total of 441 holothurians (251 H. polii, 177 H. tubulosa and 13 from other species). Genetic diversity analyses and analysis of molecular variance (AMOVA) suggest that H. polii and H. tubulosa species are distinct, but within and among populations are homogeneous, indicating active gene flows across the Mediterranean areas investigated. H. polii showed a lower genetic diversity than H. tubulosa, probably related to differences in life history traits. Phylogenetic analyses showed a clear differentiation between the two species, even if six specimens morphologically assigned to a species clustered within the other species, indicating a possible occurrence of hybridization events. These data will be useful in implementing conservation actions for these holothurian genetic resources. [ABSTRACT FROM AUTHOR]

Bract coloration is one of the key ornamental traits in Bougainvillea, yet research has predominantly focused on phenotypic color traits and pigment composition, with limited understanding of the molecular mechanisms underlying color formation. This gap hinders the improvement and innovation in bract coloration. To elucidate the regulatory mechanisms of bract coloration in Bougainvillea and to enhance the utilization of its germplasm resources, this study employed the Illumina Novaseq 6000 sequencing platform to conduct transcriptomic sequencing on 21 samples of bracts exhibiting seven distinct phenotypes. Comparative analysis against Nr, Pfam, EggNOG, GO, and KEGG databases annotated 90,279 unigenes. The highest annotation rates were achieved with the Nr (40.13%), GO (30.44%), and EggNOG (25.64%) databases. Among the species annotated, Beta vulgaris (20.08%) and Chenopodium quinoa (14.58%) shared the highest homology with Bougainvillea bract transcriptomes. WGCNA analysis identified 12 positively correlated tissue-specific modules, of which 2 are related to bract color formation. By comparing transcriptome data and genes within these specific modules against the KEGG database, a total of 321 unigenes associated with bract color formation in Bougainvillea were discovered. Among these, 220 unigenes are involved in anthocyanin synthesis, 43 unigenes are involved in betalain synthesis, 23 unigenes are annotated as Chlorophyll a-b binding protein genes, and 35 unigenes participate in carotenoid synthesis. Quantitative real-time PCR (qRT-PCR) validation of 16 differentially expressed genes (DEGs) including PAL2, CHS1, ANS, BZ1, 6GT, CDOPA5GT, ANR, CHS2, and DOPA, revealed significant expression differences among magenta, yellow, white, and cherry-colored bracts, suggesting their potential as candidate genes for bract color development. This study not only enriches the transcriptomic data of Bougainvillea but also identifies genes associated with bract coloration, providing a valuable theoretical basis for future gene cloning, genetic engineering, and breeding efforts in Bougainvillea. [ABSTRACT FROM AUTHOR]

The new landmark BBNJ Treaty (Marine Biodiversity of Areas beyond National Jurisdiction Agreement) emphasises applying the notion of ‘common heritage of humankind’ to conserve and sustainably use marine biological diversity in areas beyond national jurisdiction (ABNJ). Existing regulatory gaps and loopholes in international law, biodiversity law, and intellectual property rights (IPR) hinder sustainable use and equitable sharing of benefits from marine genetic resources (MGRs). Effective management of MGR-based patents and digital sequence information is essential for regulating access to and use of biological materials. To foster innovation and regulate bioprospecting, a sui generis IPR regime for inventions derived from ABNJ genetic resources is necessary, potentially including regulations on MGR discoveries. This article argues that IPR considerations significantly impact commercialisation, monetary benefit-sharing from MGR utilisation, as well as the regulation of digital sequence information, capacity-building, technology transfer, and marine scientific research in ABNJ. [ABSTRACT FROM AUTHOR]

Background: Castor is an important industrial raw material. Drought-induced oxidative stress leads to slow growth and decreased yields in castor. However, the mechanisms of drought-induced oxidative stress in castor remain unclear. Therefore, in this study, physiological, biochemical, and RNA-seq analyses were conducted on the roots of castor plants under PEG-6000 stress for 3 d and 7 d followed by 4 d of hydration. Results: The photosynthetic rate of castor leaves was inhibited under PEG-6000 stress for 3 and 7 d. Biochemical analysis of castor roots stressed for 3 d and 7 d, and rehydrated for 4 d revealed that the activities of APX and CAT were highest after only 3 d of stress, whereas the activities of POD, GR, and SOD peaked after 7 d of stress. RNA-seq analysis revealed 2926, 1507, and 111 differentially expressed genes (DEGs) in the roots of castor plants under PEG-6000 stress for 3 d and 7 d and after 4 d of rehydration, respectively. GO analysis of the DEGs indicated significant enrichment in antioxidant activity. Furthermore, KEGG enrichment analysis of the DEGs revealed significantly enriched metabolic pathways, including glutathione metabolism, fatty acid metabolism, and plant hormone signal transduction. WGCNA identified the core genes PP2C39 and GA2ox4 in the navajowhite1 module, which was upregulated under PEG-6000 stress. On the basis of these results, we propose a model for the response to drought-induced oxidative stress in castor. Conclusions: This study provides valuable antioxidant gene resources, deepening our understanding of antioxidant regulation and paving the way for further molecular breeding of castor plants. [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]

Ulomoides dermestoides, a member of the Tenebrionidae family, is known by various common names such as Chinese beetle, Chinese weevil, peanut beetle, cancer beetle, or asthma beetle. Despite its origin in Asia, it has achieved global distribution owing to its perceived medicinal properties. In this study, we employed a combination of Illumina short-read, PacBio long-read, and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to produce a high-quality, chromosome-scale genome assembly of U. dermestoides. The assembled genome spans 253.38 Mb across 11 chromosomes, including the two sex chromosomes, X and Y. Key metrics include contig and scaffold N50 values of 9.83 Mb and 28.62 Mb, respectively, with an estimated genome completeness of 99.62%. Annotation efforts identified 15,553 protein-coding genes and revealed that 48.11% of the genome comprises repetitive sequences. This meticulously assembled genome serves as a pivotal resource for elucidating the genetic determinants underlying the species' ecological habits and potential medicinal properties. [ABSTRACT FROM AUTHOR]

Reaumuria soongarica is a xerophytic shrub belonging to the Tamaricaceae family. The species is widely distributed in the deserts of Central Asia and is characterized by its remarkable adaptability to saline and barren desert environments. Using PacBio long-read sequencing and Hi-C technologies, we assembled a chromosome-level genome of R. soongarica. The genome assembly has a size of 1.28 Gb with a scaffold N50 of 116.15 Mb, and approximately 1.25 Gb sequences were anchored in 11 pseudo-chromosomes. A completeness assessment of the assembled genome revealed a BUSCO score of 97.5% and an LTR Assembly Index of 12.37. R. soongarica genome had approximately 60.07% repeat sequences. In total, 21,791 protein-coding genes were predicted, of which 95.64% were functionally annotated. This high-quality genome will serve as a foundation for studying the genomic evolution and adaptive mechanisms to arid-saline environments in R. soongarica, facilitating the exploration and utilization of its unique genetic resources. [ABSTRACT FROM AUTHOR]

In this study, we evaluated 16 strains of Sarcomyxa edulis from the Changbai Mountains, China through antagonism tests and ISSR molecular marker technique for cytological and molecular biological evaluation. Q-type and R-type cluster analyses were utilised to evaluate and classify agronomic traits according to the test guidelines for distinctness, uniformity, and stability. The tested strains showed antagonistic reactions. The differences in antagonistic reactions among different germplasm resources are helpful for evaluating genetic diversity and provide a basis for better development and utilisation of fungal germplasm resources. A total of 330 bands were amplified by 21 ISSR primers, including 321 polymorphic bands. The percentage of polymorphic bands observed was 97.07%. Using PopGen32 software, the effective number of alleles (Ne), Nei's gene diversity index (H), and Shannon's diversity index (I) were calculated, yielding average values of 1.6638, 0.3796, and 0.5480, respectively. In addition, the genetic similarity coefficient of 16 strains ranged from 0.4306–0.7778. According to the Q-type clustering, the tested strains were classified into two categories based on the Euclidean distance of 8.52. While R-type cluster analysis revealed a significant correlation between the traits. At the Euclidean distance of 6.298, the traits could be classified into three distinct categories. According to the findings, all 16 strains demonstrated high genetic diversity. The ISSR clustering results revealed that strains with shorter genetic distances were more similar in specific traits. However, there were notable differences between the results of comprehensive trait clustering (Q-type clustering) and ISSR clustering. [ABSTRACT FROM AUTHOR]

Human genomics research with indigenous peoples has often been characterised by tension between the ‘western’ science ideologies and indigenous peoples’ cultural beliefs in relation to their human genetic resources and data. This article explores this tension from the lens of the concept of indigenous peoples’ human genomic sovereignty and tests the applicability of the concept in Africa. The article achieves this by first highlighting the tension between ‘western’ science and indigenous peoples through three case studies from Canada, the USA, and South Africa. It then analyses indigenous peoples’ human genomic sovereignty in the USA and Canada and compares it with the notion of indigenous peoples’ sovereignty in Africa. The article concludes by highlighting lessons that indigenous groups in Africa can draw from the USA and Canada in their quest for human genomic sovereignty. [ABSTRACT FROM AUTHOR]

Global climate change poses challenges to agricultural production and food security. Assessing the adaptive capacity of crop wild relatives to future climate is important for protecting key germplasm resources and breeding new crops. We performed population genomics, genotype-environment association analyses, and genomic offset assessment of Chinese wild rice, Zizania latifolia, a crop wild relative and potential new grain crop, based on 168 individuals from 42 populations. We found two genetic lineages in Z. latifolia, corresponding to the south and north of its range, that diverged during the Late Pleistocene. We also identified lineage-specific positively selected genes associated with flower development and flowering, seed shattering, pathogen defense response and cold tolerance. We further found that populations from southeastern China are the most maladapted to future climate and should be prioritized for conservation. Our findings provide important clues for leveraging existing genetic diversity to identify important germplasm resources and create climate-resilient crops. A landscape genomics analysis of Chinese wild rice identifies signatures of local adaptation in its two lineages and the most maladapted populations under future climate conditions, and provides important clues for its conservation and use. [ABSTRACT FROM AUTHOR]

ABSTRACT Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) has decimated kiwifruit orchards growing susceptible kiwifruit Actinidia chinensis varieties. Effector loss has occurred recently in Psa3 isolates from resistant kiwifruit germplasm, resulting in strains capable of partially overcoming resistance present in kiwiberry vines (Actinidia arguta, Actinidia polygama, and Actinidia melanandra). Diploid male A. melanandra recognises several effectors, sharing recognition of at least one avirulence effector (HopAW1a) with previously studied tetraploid kiwiberry vines. Sequencing and assembly of the A. melanandra genome enabled the characterisation of the transcriptomic response of this non‐host to wild‐type and genetic mutants of Psa3. A. melanandra appears to mount a classic effector‐triggered immunity (ETI) response to wildtype Psa3 V‐13, as expected. Surprisingly, the type III secretion (T3SS) system‐lacking Psa3 V‐13 ∆hrcC strain did not appear to trigger pattern‐triggered immunity (PTI) despite lacking the ability to deliver immunity‐suppressing effectors. Contrasting the A. melanandra responses to an effectorless Psa3 V‐13 ∆33E strain and to Psa3 V‐13 ∆hrcC suggested that PTI triggered by Psa3 V‐13 was based on the recognition of the T3SS itself. The characterisation of both ETI and PTI branches of innate immunity responses within A. melanandra further enables breeding for durable resistance in future kiwifruit cultivars. [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]

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]

In genomic selection (GS), the prediction accuracy is heavily influenced by the composition of the training set (TS). Currently, two primary strategies for building TS are used: one involves accumulating historical phenotypic records from multiple years, while the other is the “test‐and‐shelf” approach. Additionally, studies have suggested that optimizing TS composition using genetic algorithms can improve the accuracy of prediction models. Most breeders operate in open systems, introducing new genetic variability into their populations as needed. However, the impact of elite germplasm introduction in GS models remains unclear. Therefore, we conducted a case study in self‐pollinated crops using stochastic simulations to understand the effects of elite germplasm introduction, TS composition, and its optimization in long‐term breeding programs. Overall, introducing external elite germplasm reduces the prediction accuracy. In this context, test and shelf seem more stable regarding accuracy in dealing with introductions despite the origin and rate, being useful in programs where the introductions come from different sources over the years. Conversely, using historical data, if the introductions come from the same source over the cycles, this negative effect is reduced as long as the cycles and this approach become the best. Thus, it may support public breeding programs in establishing networks of collaborations where the exchange of germplasm will occur at a predefined rate and flow. In either case, the use of algorithms of optimization to trim the genetic variability does not bring a substantial advantage in the medium to long term. [ABSTRACT FROM AUTHOR]

Societal Impact Statement Summary Bananas are nutritious fruits of major importance worldwide. Characterizing their diversity is essential to ensure their conservation and use. A catalog showcasing cultivated bananas genomic diversity was compiled and is to be used as a tool to support the classification of banana cultivars. This research revealed that cultivated banana groups are not all made of identical clones. Materials from recent collecting missions indicated that more banana diversity is expected to be found as the exploration of the banana gene pool continues. These discoveries will drive dynamic conservation strategies for banana genetic resources and should increase their use. Banana is an important food crop cultivated in many tropical and subtropical regions around the world. Because banana cultivars often have low fertility, they are typically propagated clonally, which maintains desirable traits across generations. However, different factors, such as synonymy, incomplete passport data, and environmental effects, complicate the morphological‐based assignment of banana cultivars to specific clones or cultivar groups. In this study, we applied a previously developed genomic‐based tool for fine‐scale characterization of banana ancestry, known as in silico chromosome painting, to high‐throughput genotyping data from 317 banana accessions. This dataset covers most of the globally conserved, studied, and cultivated cultivar groups and includes both genebanks and new, uncharacterized materials. By comparing curated morphological assignation to the genomic patterns resulting from in silico chromosome painting, we compiled a diversity catalog referencing curated passport data, pictures, and chromosome painting patterns of the cultivar groups. Examining the genomic patterns obtained, intra‐cultivar group variability was discovered. In some cultivar groups, mitotic recombination or deletions accumulated clonally. In addition, at least four cultivar groups encompassed cultivars from distinct sexual events co‐existing, notably Pisang Awak with five distinct patterns across two ploidy levels. Finally, additional patterns were discovered in the newest materials of the set, showing that a wider diversity of clones still exists on farm. [ABSTRACT FROM AUTHOR]

Societal Impact Statement Summary Despite strong historical declines, Guadeloupe and Haiti's coffee sectors remain important to rural communities' livelihood and resilience. Coffee also holds value as part of the islands' historical legacy and cultural identities. Furthermore, it is often grown in agroforestry systems providing important ecosystem services, which will become more important as these vulnerable islands work to adapt to a changing climate. Current efforts to revitalize coffee farms and target strategically important specialty markets would benefit from understanding existing genetic resources and the historical factors that shaped them. Our study reveals the rich history reflected in current coffee stands on the islands. The West Indies, particularly former French colonies like Haiti and Guadeloupe, were central to the spread of coffee in the Americas. The histories of these Islands are shared until the 19th century, where they diverged significantly. Still, both Islands experienced a strong decline in their coffee sector. Characterizing the genetic and varietal diversity of their coffee resources and understanding historical factors shaping them can help support revitalization efforts. To that end, we performed Kompetitve Allele‐Specific PCR (KASP) genotyping of 80 informative single nucleotide polymorphism (SNP) markers on field samples from across main coffee‐growing region of Guadeloupe, and two historically important ones in Haiti, as well as 146 reference accessions from international collections. We also compared bioclimatic variables from sampled geographic areas and searched for historical determinants of present coffee resources. At least five Coffea arabica varietal groups were found in Haiti, versus two in Guadeloupe, with admixed individuals in both. The traditional Typica variety is still present in both islands, growing across a variety of climatic environments. We also found Coffea canephora on both islands, with multiple likely origins, and identified C. liberica var. liberica in Guadeloupe. These differences are explained by the Islands' respective histories. Overall, Guadeloupe experienced fewer, but older introductions of non‐Typica coffee. By contrast, several recent introductions have taken place in Haiti, driven by local and global factors and reflecting the history of Arabica varietal development and spread. Diversity on these islands is dynamic, and our results reveal opportunities and limits to the future of Guadeloupean and Haitian coffee. [ABSTRACT FROM AUTHOR]

Longstanding negotiations on the status of marine genetic resources beyond national jurisdiction under a new UN treaty oscillated between the common heritage of mankind and the freedom of the high seas. The final text of the new Biodiversity Beyond National Jurisdiction (BBNJ) Treaty bridges the normative dissonance by crafting a freedom of marine scientific research juxtaposed with the common heritage of humankind. This article argues that the principle is a specific carve‐out from the freedom of scientific research in the United Nations Convention on the Law of the Sea (UNCLOS), enumerated as one of the freedoms of the high seas. The principle of freedom of marine scientific research is best conceived as a property‐protected activity tethered to marine genetic resources where the scope and consequences of the activity demarcate the commons resource. It derives legitimacy and content from the common heritage regimes in UNCLOS as well as the operative elements of Part II of the BBNJ Treaty that address the equitable use of marine genetic resources and digital sequence information on marine genetic resources. As such, this element in the Treaty and the explanation set out here introduces a new and unprecedented constitutionalising norm in global biodiversity governance. [ABSTRACT FROM AUTHOR]

Black pepper (Piper nigrum L.), a highly valued spice crop, is economically significant as one of the most widely traded spices in the world. The global yield and quality of black pepper (Piper nigrum L.) are affected by foot rot-causing soilborne oomycete pathogen Phytophthora capsici. To gain initial insights toward developing an approach that utilizes microbial genetic resources for controlling foot rot disease in black pepper, we mapped the rhizobiome communities in susceptible Piper nigrum L. and wild-resistant Piper colubrinum. The analysis showed compositional differences in the rhizobiome of two Piper species, which revealed higher diversity and the presence of more differentially abundant genera in P. colubrinum. Furthermore, P. colubrinum rhizobiome had a significantly higher abundance of known anti-oomycete genera, such as Pseudomonas, and a higher differential abundance of Janthinobacterium, Variovorax, and Comamonas, indicating their probable contribution to pathogen resistance. Predictive functional profiling in P. colubrinum rhizobiome showed highly enriched functional gene orthologs (KOs), particularly chemotaxis proteins, osmoprotectants, and other transport systems that aid in pathogen resistance. Similarly, pathways such as phenylpropanoid biosynthesis and other antimicrobial synthesis were enriched in P. colubrinum rhizobiome. The culturable diversity of the resistant root endosphere, which harbors efficient biocontrol agents such as Pseudomonas, strengthens the possible role of root microbiome in conferring resistance against soil-borne pathogens. Our results depicted a clear distinction in the rhizobiome architecture of resistant and susceptible Piper spp., suggesting its influence in recruiting bacterial communities that probably contribute to pathogen resistance. [ABSTRACT FROM AUTHOR]

Background: Plant mutagenesis creates novel alleles, thereby increasing genetic and phenotypic diversity. The availability of the faba bean (Vicia faba L.) reference genome and a growing set of additional genomic resources has increased the scientific and practical value of mutant collections. We aimed to genotype and morphologically phenotype a historical faba bean mutant collection developed and characterized by Jan Sjödin (1934–2023) over half a century ago in order to increase its value to researchers. The collection was genotyped using high-throughput single-primer enrichment technology (SPET) assays. Results: We used 11,073 informative single nucleotide polymorphism (SNP) markers spanning the faba bean genome to genotype 52 mutant lines along with the background line, cv. Primus. A range of flower, seed, leaf, and stipule mutations were observed. The analysis of population structure revealed a shallow structure with no major subpopulations. Principal component and cluster analyses revealed, to a minor extent, that the mutants clustered by their phenotype. Conclusions: The mutants' phenotypic variation and shallow structure indicate that the Sjödin faba bean collection has the potential to play a significant role in faba bean breeding and in genetic and functional studies. [ABSTRACT FROM AUTHOR]

Pampus argenteus is a highly commercial marine fish whose population is declining sharply. Here, we generated a female P. argenteus genome, spanning 536.33 Mb with contig N50 of 1.79 Mb; 24070 genes (99.50% of 24,182) were functionally annotated. To improve quality of it, we assembled a 553.79 Mb genome of male fish with contig N50 of 24.75 Mb through HiFi and ultra-long ONT sequence technologies; 550.82 Mb were anchored onto 24 gap-free chromosomes; 22,892 genes (98.1% of 23,346) were functionally annotated; the QV value was 51.55 with 98.9% of BUSCO and 99.39% coverage of Illumina reads. Finally, we compared this genome with previous published one, revealing 37,301 SVs. 52.82 Mb and 18.05 Mb SDs were characterized in our and published assemblies, respectively, and 48.96 Mb PURs were constructed. Thus, this genome assembly exhibits excellent completeness, continuity and accuracy comparing to the published one, which can be current preferred reference genome. Overall, these works help aquaculture and wild resources recovery of P. argenteus and provide a valuable genetic resource for study. [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]

The genetic analysis of potato is hampered by the complexity of tetrasomic inheritance. An ongoing effort aims to transform the clonally propagated tetraploid potato into a seed-propagated diploid crop, which would make genetic analyses much easier owing to disomic inheritance. Here, we construct and report the large-scale genetic and heterotic characteristics of a diploid F2 potato population derived from the cross of two highly homozygous inbred lines. We investigate 20,382 traits generated from multi-omics dataset and identify 25,770 quantitative trait loci (QTLs). Coupled with gene expression data, we construct a systems-genetics network for gene discovery in potatoes. Importantly, we explore the genetic basis of heterosis in this population, especially for yield and male fertility heterosis. We find that positive heterotic effects of yield-related QTLs and negative heterotic effects of metabolite QTLs (mQTLs) contribute to yield heterosis. Additionally, we identify a PME gene with a dominance heterotic effect that plays an important role in male fertility heterosis. This study provides genetic resources for the potato community and will facilitate the application of heterosis in diploid potato breeding. An ongoing effort aims to transform the clonally propagated tetraploid potato to a seed-propagated diploid crop, but our understanding of it disomic inheritance is limited. Here, the authors report genetic basis of heterosis in the elite hybrid potato and identify a male fertility-related PME gene with dominance heterotic effect. [ABSTRACT FROM AUTHOR]

To explore the morphological differences among different geographic populations of Gymnocypris chilianensis, 29 measurable traits and 13 landmarks on 191 individuals of 10 geographic populations were collected from three different inland water systems, i.e., Shiyang River, Heihe River, and Shule River, in Qilian Mountains, China. Multivariate statistical methods were used to compare morphological differences among the populations, such as principal component analysis, cluster analysis, discriminant analysis, and visual analysis of landmark data. The results showed that: (1) There were significant morphological differences between groups of G. chilianensis. The Shiyang River basin differs significantly from populations in the other two basins. (2) The inter-population differences were mainly reflected in the length of the trunk and tail, and the difference between trunk and caudal fin had the most obvious characteristics, proving the tail being the main direction of variation. This research provides an effective theoretical basis for the fine management and accurate protection of G. chilianensis germplasm resources. [ABSTRACT FROM AUTHOR]

To protect the germplasm resources of Gymnodiptychus dybowskii (Kessler, 1874), a species endemic to Xinjiang, the key stages of embryonic development of G. dybowskii were studied. From May to July 2021, the artificial breeding of G. dybowskii was carried out at the fish breeding station of the Kenswart Water Conservancy Project. The embryos and early larvae were obtained using temperature promotion, water stimulation, hormone induction, and dry insemination techniques. their development process was observed, and morphological characteristics of each developmental stage were recorded. The results showed that the mature oocyte was round, heavy, and light yellow, with an egg diameter of (2.32 ± 0.21) mm. The fertilized egg was slightly viscous, and the viscosity disappeared after water absorption. Under the temperature of 15.6-17.7 °C (16.23 ± 0.52) °C, the embryonic development of G. dybowskii lasted for 142 h and 33 min and went through 7 stages of fertilization, cleavage, blastula, gastrula, neurula embryo, organ formation, and membrane hatching, with a total of 26 periods. The membrane broke after 2376.724 °C-h. The embryonic development of G. dybowskii follows the rule of freshwater bony fish, but it differs from other Schizothorax species in the muscular effect period and membrane emergence mode. In addition, differences in hatching water temperature among different geographic populations lead to differences in embryo development duration and accumulated temperature, which further proves that G. dybowskii is highly adaptive to the ecological environment of its habitat water, and these characteristics together constitute its survival and reproduction strategy in the natural environment. In this study, through the artificial breeding experiment of G. dybowskii, the characteristics of its embryonic development were explored, which laid the foundation for the cultivation of unique fish seedlings, enriched the early life history data of G. dybowskii, and further provided basic data for its resource protection. [ABSTRACT FROM AUTHOR]

The pathogen Plasmopara halstedii, causing downy mildew (DM), is a widespread sunflower disease which can be controlled by single dominant genes. Wild Helianthus annuus have been a valuable source of vertical resistance to control P. halstedii, but such resistance may eventually be overcome by new races of the pathogen. Alternatively, quantitative, or partial resistance, is more stable and may be combined with vertical resistance to prevent DM outbreaks. We assessed the responses of six populations of wild H. annuus naturalized in Argentina to race 710 of P. halstedii. We examined: 1) the aerial phenotype (including seedling death) using two damage scales and three disease indices, 2) the growth of the pathogen along the hypocotyls, and 3) the presence of the pathogen in the root system. We found that the evaluated sunflower wild populations had lower disease levels than the susceptible cultivated controls. A histologic analysis showed that the wild H. annuus seedlings showed cellular reactions (e.g. necrosis and the deposit of materials on the walls of invaded cells) to restrict the pathogen's growth, allowing the identification of two possible types of resistance: type I, when the growth of the pathogen was limited to the base of the hypocotyls, and type II, when the pathogen managed to invade the entire length of the hypocotyls. The wild sunflower populations also showed differential responses to root infections. A quantitative or partial genetic resistance, rather than resistance based on major genes, seems to be operating in the sampled populations. The individuals found to be resistant in each population represent promising germplasm for sunflower breeding. [ABSTRACT FROM AUTHOR]

Haliotis midae is one of the most important molluscs in South African commercial aquaculture. In this study, a high‐resolution integrated linkage map was constructed, and QTL identified using 2b‐RADseq for genotyping SNPs in three families. The final integrated linkage map was composed by merging the individual family maps, resulting in 3290 informative SNPs mapping to 18 linkage groups, conforming to the known haploid chromosome number for H. midae. The total map spanned 1798.25 cM with an average marker interval of 0.55 cM, representing a genome coverage of 98.76%. QTL analysis, across all three families, resulted in a total of five QTL identified for growth‐related traits, shell width, shell length, and total body weight. For shell width and total body weight, one QTL was identified for each trait respectively, whilst three QTL were identified for shell length. The identified QTL respectively explained between 7.20% and 11.40% of the observed phenotypic variance. All three traits were significantly correlated (r = 0.862–0.970; p < 0.01) and shared overlapping QTL. The QTL for growth traits were mapped back to the H. midae draft genome and BLAST searches revealed the identity of candidate genes, such as egf‐1, megf10, megf6, tnx, sevp1, kcp, notch1, and scube2 with possible functional roles in H. midae growth. The constructed high‐density linkage map and mapped QTL have given valuable insights regarding the genetic architecture of growth‐related traits and will be important genetic resources for marker‐assisted selection. It remains, however, important to validate causal variants through linkage disequilibrium fine mapping in future. [ABSTRACT FROM AUTHOR]

Covering two-thirds of the ocean and half of the planet's surface, the high seas are increasingly the focus of commercial activity and conservation ambitions. Contrary to narratives of a lawless frontier, they are governed by a dense network of sectoral institutions for shipping, fisheries, and other industries, although these collectively deal with conservation and sustainable use of biodiversity in a fragmented and uneven manner. These gaps were the subject of nearly 20 years of negotiation, resulting in the adoption of the Agreement on Conservation and Sustainable Use of Marine Biological Diversity of Areas Beyond National Jurisdiction in June 2023. The Agreement was designed to address access and benefit sharing associated with marine genetic resources; the establishment of area-based management tools such as marine protected areas, Environmental Impact Assessments, and capacity building; and the transfer of marine technology. Achieving coherence across public and private governance mechanisms will be a significant challenge as human activity increases on the high seas, but it is key to achieving ocean sustainability goals. [ABSTRACT FROM AUTHOR]

Context: Brassica juncea germplasm exhibits significant variations in flowering timing and vernalisation requirements. However, knowledge gaps exist with respect to variations in expression and the divergent evolution of flowering genes in B. juncea subgenomes. Aims: This study aims to examine the role of flowering genes in defining trait variation and to identify indications of directional selection on these genes. Methods: Employing a combination of genome-wide association studies, functional genomics and population genetic assays, we explored the genetic architecture underlying flowering time variation within expansive germplasm collections of this allopolyploid and its progenitor species. Key results: Genome-wide association studies aided in predicting 17 and 34 candidate genes in B. rapa and B. juncea , respectively. Seven of these (FT , FLC , BAG4 , ELF4-L2 , EFM , SEP4 , and LSH6) were predicted in both B. juncea and B. rapa. Some genes, GA20OX3 , NF-YA1 , PI , MMP , RPS10B , CRY2 , AGL72 , LFY , TOC1 , ELF5 , EFM , FLC and TFL1 exhibited directional selection as inferred from negative Tajima's D and Fu's Fs statistics. Conclusions: Common predicted genes are known influencers of flowering time and phenological changes between species as well as across zones of adaptation. An analysis of gene expression patterns indicates that the gene expression bias in resynthesised B. juncea could be influenced by the cytoplasmic background. Most expression variants are found in B genome copies. Some genes lacked expression variation in their diploid progenitors, whereas these genes exhibit expression variation in polyploid species. Implications: This study highlights that integrating genome-wide association studies with molecular signals of natural selection can effectively contribute to our understanding of the ecological genetics of adaptive evolution. Brassica juncea is farmed around the world, and varies widely in flowering time and the need for cold temperatues to trigger flowering. We used a range of molecular techniques to understand the genetics and evolution underpinning that variation, in contemporary breeds and ancestor species. This article belongs to the Collection Plant breeding- and genetics-based tools for food security under changing climate. [ABSTRACT FROM AUTHOR]

Context: Wheat (Triticum aestivum L.) is an important crop that provides food to millions of people all over the world. Currently, wheat production is limited due to various biotic and abiotic stresses resulting from uneven patterns of climate change. Therefore, it is very important to develop climate-resilient wheat cultivars. Crop genetic diversity allows the scientific community to identify genetic variations that can be utilised in the development of improved cultivars. Aims: This study planned to characterise the wheat germplasm with the iPBS-retrotransposons marker system. Methods: A total of 30 iPBS-retrotransposons markers were screened and among these, the 12 most polymorphic markers were selected for further analysis. Key results: Molecular characterisation yielded a total of 170 bands, of which 143 were polymorphic. A substantial level of genetic diversity was observed (mean effective number of alleles: 1.37, Shannon's information index: 0.23, gene diversity: 0.35). Maximum genetic distance was observed in G9 and G60 genotypes. Analysis of molecular variance revealed that most genetic variation (95%) occurred within the populations. The model-based structure algorithm divided the studied germplasm into three populations based on their collection regions. Similarly, the neighbour-joining analysis also divided 70 tested wheat genotypes into three populations, whereas principal coordinate analysis divided the evaluated germplasm into four populations. Conclusions: This study confirms the iPBS-retrotransposons as an ideal marker for the genetic diversity assessment studies for any crop, especially for wheat. Implications: The results presented here will be helpful for the scientific community in the marker-assisted breeding of wheat. Wheat, a vital global food source, faces production limitations due to climate-induced stresses. Developing resilient cultivars is crucial. Genetic diversity aids in identifying variations for improved cultivars. This study utilised iPBS-retrotransposons to characterise wheat germplasm, yielding 170 bands. Genetic distance highlighted G9 and G60 as genetically distinct genotypes. Different methods identified three or four distinct groups of genotypes amongst the studied germplasm. This informs targeted breeding strategies for enhanced wheat varieties. This article belongs to the Collection Plant breeding- and genetics-based tools for food security under changing climate. [ABSTRACT FROM AUTHOR]

In the current context of climate change, marked by severe drought and heat stresses, we hypothesized that the trait plasticity, opposite of stability, could be an important mechanism of reaching adaptability and therefore enhancing resilience. To assess this, we tested 10 promising genotypes under three environments (E1, E2, and E3) for yield and its components: Number of Spikes per m2 (NS/m2), Number of Spikelets per Spike (NSpk/S), Number of Grains per Spikelet (NG/Spk), Number of Grains per Spike (NG/S), Number of Grains per m2 (NG/m2); and Thousand Grain Weight (TGW). A highly significant effect (p < 0.01) of the environment (E) was observed for all traits. Additionally, a significant effect (p < 0.05) of genotype (G) was identified in all traits except TGW. While a significant effect (p < 0.05) of genotype by environment interaction (G×E) was noted for NSpk/S and TGW. The stability and plasticity criteria were reported as a positive way to achieve adaptability when they reflect a high yielding potential of stable or plastic traits. As depicted by GGE- analysis, the best stable genotypes with high performance were Kharouba for NS/m2, NG/S, and NG/m2, Amal for NG/S, 15/42, Malika, and 90-55-17 for NSpk/S, Achtar for NG/Spk, and 15/49 for TGW. While the plastic genotypes with high performance were 15/42 for NS/m2, Achtar for NG/S and NG/m2, Amal for NSpk/S and NG/Spk, and 90–55-17 for TGW. These genotypes that combine stability or plasticity criteria with high yielding performances hold promise as potential genetic resources in breeding programs aiming to achieve desirable yield component structure for better adaptability and resilience. [ABSTRACT FROM AUTHOR]

In order to determine the diversity in local seedling origin mango genotypes from different five districts (Navsari, Valsad, Dang, Tapi and Surat) of South Gujarat region during 2021–2023, which have been found in orchards or backyards by using IPGRI mango descriptor. The exploration of genetic resources was carried out to find alternative genotype against prevailing varieties in the state and it sustain mango production in future. A total of 113 mango seedlings were identified and characterized on basis of 7 qualitative, 12 quantitative and 6 biochemical parameters using Completely Randomized Design with three replications of quantitative characteristics. High variation among genotypes was observed with respect qualitative, quantitative and biochemical parameters. Ten superior genotypes were identified based on five commercially important traits viz., fruit weight (> 200 g), pulp percentage (> 60.00%), TSS (> 20 °Brix), shelf life (> 7 days) and overall acceptability (> 7 point). The genetic variability revealed that higher heritability coupled with higher genetic advance as per cent of mean for 12 quantitative characteristics namely mature fruit weight, fruit length, fruit width, pulp weight, peel weight, stone weight, TSS, acidity, ascorbic acid, total sugars, reducing sugars and non-reducing sugars. The First three Principal component contributed 70.21% of total variation and characters such as mature fruit weight, fruit length, fruit width, pulp weight, peel weight and stone weight most contributing towards diversity in germplasm. Hierarchical cluster analysis resulted the genotypes was grouped into three clusters and genotypes present in cluster III (20) and cluster I (39) had found most divers from each other. [ABSTRACT FROM AUTHOR]

Safflower oil with high oleic is an important source of oil due to its oxidative stability and nutritional value as well as its industrial benefits. Identification of molecular markers associated with oil quality traits may aid in genotype selection in breeding efforts of safflower. To determine the genetic basis of seed oil, oleic acid, and linoleic acid content in safflower seeds, a recombinant inbred population was developed from a cross between Goldasht (low oleic line) and Mex 22–191 (high oleic line) by individual self-pollinated plants in each generation (from F2 to F9). Fatty acid components were detected by gas chromatography and subsequently analyzed by QTL analysis. The high variability in fatty acid composition was demonstrated and the first high-oleic safflower genotype was generated. A new linkage map with 69 AFLP and 45 ISSR polymorphic markers was made, covering 1472,441 cM of the safflower genome. A total of 63 individual QTLs and 238 epistatic QTLs, related to oil quality, were detected in 14 genomic regions. Some major QTLs with phenotypic variation greater than 10% were identified for the measured traits. These results demonstrate that major QTL may play an important role in increase the oleic acid of the genetic material used. Furthermore, the larger number of minor QTLs and epistatic QTLs, both of which have additive effects, indicates that the expression of these traits is also influenced by interactions between multiple genes. Our results provide additional genetic resources that can be used to precisely breed these traits in the future. [ABSTRACT FROM AUTHOR]

A comprehensive genetic diversity analysis of 87 Passiflora germplasm accessions domesticated and cultivated for several years in the karst region of Guizhou, China, was conducted utilizing simple sequence repeat (SSR) fluorescent markers. These Passiflora species, renowned for their culinary and medicinal value, could bring significant economic and ecological benefits to the region. This study aimed to assess the genetic resources of these species and facilitate the selection of superior cultivars adapted to the karst environment. Our analysis revealed an abundance of SSR loci within the Passiflora transcriptome, with single-base repeats being the most prevalent type. Through rigorous primer screening and amplification, we successfully identified 27 SSR primer pairs exhibiting robust polymorphisms. Further interrogation at eight microsatellite loci revealed 68 alleles, underscoring the high level of genetic diversity present in the cultivated accessions. The average expected heterozygosity was 0.202, with the ssr18 locus exhibiting the highest value of 0.768, indicating significant genetic variation. The mean polymorphic information content (PIC) of 0.657 indicates the informativeness of these SSR markers. Comparative analyses of the cultivated and potential wild progenitors revealed distinct genetic variations among the different Passiflora types. Genetic structure and clustering analyses of the 87 accessions revealed seven distinct groups, suggesting gene flow and similarities among the resources. Notably, a DNA fingerprinting system was established using eight SSR primer pairs, effectively distinguishing the selected cultivars that had adapted to the karst mountainous region. This study not only deepens our understanding of Passiflora genetic resources in the karst environment but also provides a valuable reference for conservation, genetic improvement, and cultivar selection. The rich genetic diversity of the Passiflora germplasm underscores their potential for sustainable utilization in breeding programs aimed at enhancing the economic and ecological viability of these valuable plant species. [ABSTRACT FROM AUTHOR]

Clubroot, a significant soil-borne disease, severely impacts the productivity of cruciferous crops. The identification and development of clubroot resistance (CR) genes are crucial for mitigating this disease. This study investigated the genetic inheritance of clubroot resistance within an F2 progeny derived from the cross of a resistant parent, designated "377", and a susceptible parent, designated "12A". Notably, "377" exhibited robust resistance to the "KEL-23" strain of Plasmodiophora brassicae, the causative agent of clubroot. Genetic analyses suggested that the observed resistance is controlled by a single dominant gene. Through Bulked Segregant Analysis sequencing (BSA-seq) and preliminary gene mapping, we localized the CR gene locus, designated as BraPb8.3, to a 1.30 Mb genomic segment on chromosome A08, flanked by the markers "333" and "sau332-1". Further fine mapping precisely narrowed down the position of BraPb8.3 to a 173.8 kb region between the markers "srt8-65" and "srt8-25", where we identified 22 genes, including Bra020861 with a TIR-NBS-LRR domain and Bra020876 with an LRR domain. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses confirmed that both Bra020861 and Bra020876 exhibit increased expression levels in the resistant parent "377" following inoculation with P. brassicae, thereby underscoring their potential as key genes implicated in BraPb8.3-mediated clubroot resistance. This study not only identifies molecular markers associated with BraPb8.3 but also enriches the genetic resources available for breeding programs aimed at enhancing resistance to clubroot. [ABSTRACT FROM AUTHOR]

Plant stomata play a crucial role in photosynthesis by regulating transpiration and gas exchange. Meanwhile, environmental cues can also affect the formation of stomata. Stomatal formation, therefore, is optimized for the survival and growth of the plant despite variable environmental conditions. To adapt to environmental conditions, plants open and close stomatal pores and even regulate the number of stomata that develop on the epidermis. There are great differences in the leaf structure and developmental origin of the cell in the leaf between Arabidopsis and grass plants. These differences affect the fine regulation of stomatal formation due to different plant species. In this paper, a comprehensive overview of stomatal formation and the molecular networks and genetic mechanisms regulating the polar division and cell fate of stomatal progenitor cells in dicotyledonous plants such as Arabidopsis and Poaceae plants such as Oryza sativa and Zea mays is provided. The processes of stomatal formation mediated by plant hormones and environmental factors are summarized, and a model of stomatal formation in plants based on the regulation of multiple signaling pathways is outlined. These results contribute to a better understanding of the mechanisms of stomatal formation and epidermal morphogenesis in plants and provide a valuable theoretical basis and gene resources for improving crop resilience and yield traits. [ABSTRACT FROM AUTHOR]

The Chinese rare minnow (Gobiocypris rarus), an important model fish in China, faces endangerment in the wild. Sperm cryopreservation facilitates the development of new strains and germplasm conservation, but the quality of its cryopreserved sperm remains low. This study evaluates the protective effects of different concentrations of antifreeze proteins (AFP I and AFP III) on the cryopreservation of Chinese rare minnow sperm. Cryopreserved sperm showed significant declines in progressive motility, curvilinear velocity (VCL), average path velocity (VAP), and lifespan compared to fresh sperm, except for straight-line velocity (VSL). The cryomedium containing 10 μg/mL AFP I improved these parameters to their highest levels. However, no significant difference was found in progressive motility and kinetic parameters between cryopreserved sperm with and without AFPs. Cryopreserved sperm with 10 μg/mL AFP I showed the highest plasma membrane integrity, mitochondrial activity, and DNA integrity, significantly better than without AFPs; importantly, the fertilization rate of cryopreserved sperm with 10 μg/mL AFP I was not significantly different from that of fresh sperm. These results indicate that the addition of 10 μg/mL AFP I to the cryomedium for Chinese rare minnow sperm does not improve kinetic parameters but significantly enhances sperm quality, aiding in its new strain development and germplasm conservation. [ABSTRACT FROM AUTHOR]

Rind thickness (RT) is an important agronomic trait in watermelon [Citrullus lanatus (Thunb.) Mansf.] and affects watermelon storability. However, genetic studies on this trait, as well as gene regulation studies, are scarce and of limited production significance. We constructed a temporary F2 generation using the highly differentiated thick-rind watermelon 'XiaoXiGua-4' and the thin-rind watermelon 'DuanMan' as parents and localized the Cla97C02G044120 gene, which controls the thickness of watermelon rind, to the intervals of chromosome 2, CL2-32303995 and CL2-32316840, through 2 years of genetic analysis. No exonic mutations were found in this gene, but two promoter mutations resulted in changes in the promoter progenitor. Fluorescence quantitative PCR analysis revealed highly significant differences in expression at 1 d and 28 d, and the expression was significantly lower in thick-skinned watermelon varieties. Marker-assisted selection (MAS) for this trait was performed using the Caps marker CL2-32303995 and the InDel marker CL2-32316840, which not only verified the stability of the localization interval but also distinguished thick rind from thin rind. These results can be used for germplasm resource screening and have strong breeding significance. [ABSTRACT FROM AUTHOR]