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Background: Germin-like proteins (GLPs) are ubiquitous plant proteins, which play significant role in plant responses against various abiotic stresses. However, the potential functions of GLPs in rice (Oryza sativa) against salt and drought stress are still unclear., Methods and Results: In this study, transcriptional variation of eight OsGLP genes (OsGLP3-6, OsGLP4-1, OsGLP8-4, OsGLP8-7, OsGLP8-10, OsGLP8-11 and OsGLP8-12) was analyzed in leaves and roots of two economically important Indica rice cultivars, KS282 and Super Basmati, under salt and drought stress at early seedling stage. The relative expression analysis from qRT-PCR indicated the highest increase in expression of OsGLP3-6 in leaves and roots of both rice varieties with a significantly higher expression in KS282. Moreover, relative change in expression of OsGLP8-7, OsGLP8-10 and OsGLP8-11 under salt stress and OsGLP8-7 under drought stress was also commonly higher in leaves and roots of KS282 as compared to Super Basmati. Whereas, OsGLP3-7 and OsGLP8-12 after salt stress and OsGLP8-4 and OsGLP8-12 after drought stress were observed with higher relative expression in roots of Super Basmati than KS282. Importantly, the OsGLP3-6 and OsGLP4-1 from chromosome 3 and 4 respectively showed higher expression in leaves whereas most of the OsGLP genes from chromosome 8 exhibited higher expression in roots., Conclusion: Overall, as a result of this comparative analysis, OsGLP genes showed both general and specific expression profiles depending upon a specific rice variety, stress condition as well as tissue type. These results will increase our understanding of role of OsGLP genes in rice crop and provide useful information for the further in-depth research on their regulatory mechanisms in response to these stress conditions., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)

The root system architecture is an important complex trait in rice. With changing climatic conditions and soil nutrient deficiencies, there is an immediate need to breed nutrient-use-efficient rice varieties with robust root system architectural (RSA) traits. To map the genomic regions associated with crucial component traits of RSA viz. root length and root volume, a biparental F 2 mapping population was developed using TI-128, an Ethyl Methane Sulphonate (EMS) mutant of a mega variety BPT-5204 having high root length (RL) and root volume (RV) with wild type BPT-5204. Extreme bulks having high RL and RV and low RL and RV were the whole genome re-sequenced along with parents. Genetic mapping using the MutMap QTL-Seq approach elucidated two genomic intervals on Chr.12 (3.14-3.74 Mb, 18.11-20.85 Mb), and on Chr.2 (23.18-23.68 Mb) as potential regions associated with both RL and RV. The Kompetitive Allele Specific PCR (KASP) assays for SNPs with delta SNP index near 1 were associated with higher RL and RV in the panel of sixty-two genotypes varying in root length and volume. The KASP_SNPs viz. Chr12_S4 (C→T; Chr12:3243938), located in the 3' UTR region of LOC_Os12g06670 encoding a protein kinase domain-containing protein and Chr2_S6 (C→T; Chr2:23181622) present upstream in the regulator of chromosomal condensation protein LOC_Os2g38350. Validation of these genes using qRT-PCR and in-silico studies using various online tools and databases revealed higher expression in TI-128 as compared to BPT- 5204 at the seedling and panicle initiation stages implying the functional role in enhancing RL and RV., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

Introduction: Peanut is susceptible to infection of Aspergillus fungi and conducive to aflatoxin contamination, hence developing aflatoxin-resistant variety is highly meaningful. Identifying functional genes or loci conferring aflatoxin resistance and molecular diagnostic marker are crucial for peanut breeding., Objectives: This work aims to (1) identify candidate gene for aflatoxin production resistance, (2) reveal the related resistance mechanism, and (3) develop diagnostic marker for resistance breeding program., Methods: Resistance to aflatoxin production in a recombined inbred line (RIL) population derived from a high-yielding variety Xuhua13 crossed with an aflatoxin-resistant genotype Zhonghua 6 was evaluated under artificial inoculation for three consecutive years. Both genetic linkage analysis and QTL-seq were conducted for QTL mapping. The candidate gene was further fine-mapped using a secondary segregation mapping population and validated by transgenic experiments. RNA-Seq analysis among resistant and susceptible RILs was used to reveal the resistance pathway for the candidate genes., Results: The major effect QTL qAFTRA07.1 for aflatoxin production resistance was mapped to a 1.98 Mbp interval. A gene, AhAftr1 (Arachis hypogaea Aflatoxin resistance 1), was detected structure variation (SV) in leucine rich repeat (LRR) domain of its production, and involved in disease resistance response through the effector-triggered immunity (ETI) pathway. Transgenic plants with overexpression of AhAftr1 (ZH6) exhibited 57.3% aflatoxin reduction compared to that of AhAftr1 (XH13) . A molecular diagnostic marker AFTR.Del.A07 was developed based on the SV. Thirty-six lines, with aflatoxin content decrease by over 77.67% compared to the susceptible control Zhonghua12 (ZH12), were identified from a panel of peanut germplasm accessions and breeding lines through using AFTR.Del.A07., Conclusion: Our findings would provide insights of aflatoxin production resistance mechanisms and laid meaningful foundation for further breeding programs., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Production and hosting by Elsevier B.V.)

Sweetpotato, Ipomoea batatas (L.) Lam., is an important worldwide crop used as feed, food, and fuel. However, its polyploidy, high heterozygosity and self-incompatibility makes it difficult to study its genetics and genomics. Longest vine length (LVL), yield per plant (YPP), dry matter content (DMC), starch content (SC), soluble sugar content (SSC), and carotenoid content (CC) are some of the major agronomic traits being used to evaluate sweetpotato. However limited research has actually examined how these traits are inherited. Therefore, after selecting 212 F 1 from a Xin24 × Yushu10 crossing as the mapping population, this study applied specific-locus amplified fragment sequencing (SLAF-seq), at an average sequencing depth of 26.73 × (parents) and 52.25 × (progeny), to detect single nucleotide polymorphisms (SNPs). This approach generated an integrated genetic map of length 2441.56 cM and a mean distance of 0.51 cM between adjacent markers, encompassing 15 linkage groups (LGs). Based on the linkage map, 26 quantitative trait loci (QTLs), comprising six QTLs for LVL, six QTLs for YPP, ten QTLs for DMC, one QTL for SC, one QTL for SSC, and two QTLs for CC, were identified. Each of these QTLs explained 6.3-10% of the phenotypic variation. It is expected that the findings will be of benefit for marker-assisted breeding and gene cloning of sweetpotato., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

Background: Genome Mapping Technologies (optical and electronic) use ultra-high molecular weight DNA to detect structural variation and have application in constitutional genetic disorders, hematological neoplasms, and solid tumors. Genome mapping can detect balanced and unbalanced structural variation, copy number changes, and haplotypes. The technique is analogous to chromosomal microarray analysis, although genome mapping has the added benefit of being able to detect and ascertain the nature of more abnormalities in a single assay than array, karyotyping, or FISH alone., Key Messages: This paper describes a specific nomenclature for genome mapping that can be used by diagnostic and research centers to report their findings accurately. An international nomenclature is essential for patient results to be understood by different healthcare providers as well as for clear communication in publications and consistency in databases., Summary: Genome mapping can detect aneuploidy, balanced and unbalanced structural variation, as well as copy number changes. The Standing Committee for the International System for Human Cytogenomic Nomenclature (ISCN) recognised there was a need for a specific nomenclature for genome mapping that encompasses the range of abnormalities detected by this technique. This paper explains the general principles of the nomenclature as well as giving specific ISCN examples for the different types of numerical and structural rearrangements., (© 2024 S. Karger AG, Basel.)

Single-cell sequencing provides a new level of granularity in studying the heterogeneous nature of cancer cells. For some cancers, this heterogeneity is the result of copy number changes of genes within the cellular genomes. The ability to accurately determine such copy number changes is critical in tracing and understanding tumorigenesis. Current single-cell genome sequencing methodologies infer copy numbers based on statistical approaches followed by rounding decimal numbers to integer values. Such methodologies are sample dependent, have varying calling sensitivities which heavily depend on the sample's ploidy and are sensitive to noise in sequencing data. In this paper we have demonstrated the concept of integer-counting by using a novel bioinformatic algorithm built on our library construction chemistry in order to detect the discrete nature of the genome., (© 2021. The Author(s).)

Choroidal neovascularization (CNV) is a type of eye disease that can cause vision loss. In recent years, many studies have attempted to investigate the major pathological processes and molecular pathogenic mechanisms of CNV. Because many diseases are related to genes, the genes associated with CNV need to be identified. In this study, we proposed a network-based approach for identifying novel CNV-associated genes. To execute such method, we first employed a protein-protein interaction network reported in STRING. Then, we applied a network diffusion algorithm, Laplacian heat diffusion, on this network by selecting validated CNV-related genes as the seed nodes. As a result, some novel genes that had unknown but strong relationships with validated genes were identified. Furthermore, we used a screening procedure to extract the most essential genes. Eleven latent CNV-related genes were finally obtained. Extensive analyses were performed to confirm that these genes are novel CNV-related genes., Competing Interests: The authors declare that there is no conflict of interest regarding the publication of this paper., (Copyright © 2021 Minjie Sheng et al.)