Rice (Oryza sativa L.) is an important food crop. The appearance of lesion mimics in rice leads to phytohormone disorders, which affects rice adaptation to environmental stresses and ultimately reduces the yield and quality. To explore whether the changes in the adaptability of rice lesion-mimic mutants to stressful environments are caused by the disorder of phytohormone metabolism in plants. In this study, we screened an ethyl methane sulfonate-treated population of the japonica cultivar 'Taipei 309' for a mutant with rust-like spots on leaves at the early tillering stage and brown-red spots at maturity and named it rsl1 (rust spotted leaf 1). Compared with the wild type, rsl1 showed decreases in plant height, panicle length, primary branch number, secondary branch number, filled grains per panicle, seed-setting rate, and 1 000-grain weight, and an increase in number of effective panicles. Genetic analysis indicated that rsl1 was controlled by a single recessive nuclear gene. RSL1 was localized between two molecular markers, B7-7 and B7-9, on rice chromosome 7 by map-based cloning. PCR sequencing of the annotated genes in this interval revealed a mutation of C1683A on the eighth exon of SPL5 (LOC_Os07g10390) in rsl1, which resulted in premature termination of protein translation. Exogenous phytohormone treatments showed that rsl1 was less sensitive to salicylic acid (SA), abscisic acid (ABA), and indo-3-acetic acid (IAA) and more sensitive to methyl jasmonate (MeJA) and gibberellin acid (GA) than the wild type. In addition, the survival rate of rsl1 was lower than that of the wild type under salt, alkali, drought, and high temperature stresses, and it was higher than that of the wild type under cold stress. Quantitative real-time polymerase chain reaction (qRT-PCR) results showed that RSL1 was involved in the regulation of ABA, SA, MeJA, IAA, and GA-related genes under abiotic stresses. The present study showed that the RSL1 mutation led to the appearance of lesion mimics and affected the growth, development, and stress resistance of rsl1 under abiotic stresses. The study of the functional mechanism of this gene can provide theoretical guidance for the research on rice stress resistance.
Oryza/microbiology* ; Stress, Physiological/genetics* ; Plant Diseases/genetics* ; Cloning, Molecular ; Chromosome Mapping ; Plant Growth Regulators/metabolism* ; Plant Proteins/genetics* ; Mutation ; Cyclopentanes ; Genes, Plant ; Plant Leaves/genetics* ; Oxylipins

Rice (Oryza sativa L.), as a thermophilic crop, is highly susceptible to cold stress during its growth process. Chilling injury at the plumule stage and seedling stage often affects the morphological development and leads to yield reduction of rice. The exploration and utilization of cold tolerance genes are among the most direct and effective approaches to address cold stress in rice. To identify quantitative trait loci (QTLs) associated with cold tolerance at plumule and seedling stages, in this study, we measured the seedling rates and survived seedling rates of the indica rice cultivar 'HZ', the japonica cultivar 'Nekken2', and their 120 recombinant inbred lines (RILs) under cold stress. A previously constructed high-density genetic linkage map was used for the mapping of the QTLs conferring cold tolerance at the plumule and seedling stages. A total of 4 QTLs for plumule-stage cold tolerance and 9 QTLs for seedling-stage cold tolerance were detected, with the maximum limit of detection reaching 5.20. Notably, a genetically overlapping QTL for both plumule and seedling stages was identified on chromosome 8, spanning a physical interval of 24 432 953-25 295 129 bp. Candidate genes within the detected QTL intervals were screened, and quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to analyze the gene expression during the plumule and seedling stages. The results revealed that LOC_Os03g06570, LOC_Os03g07100, LOC_Os06g08280, LOC_Os08g38440, LOC_Os08g39100, and LOC_Os08g39540 exhibited significantly differential expression between the parental lines. These genes were either significantly downregulated or upregulated under cold stress. Among them, the first three gene (LOC_Os03g06570, LOC_Os03g07100, and LOC_Os06g08280) were hypothesized to be key candidates regulating the cold tolerance of rice seedlings, while the latter three genes (LOC_Os08g38440, LOC_Os08g39100, and LOC_Os08g39540) were identified as comprehensive regulators of cold tolerance during both plumule and seedling stages. These findings lay a foundation for the fine mapping and cloning of cold tolerance genes at the plumule and seedling stages, providing valuable insights for breeding cold-tolerant rice varieties.
Quantitative Trait Loci/genetics* ; Oryza/growth & development* ; Seedlings/growth & development* ; Cold Temperature ; Chromosome Mapping ; Gene Expression Regulation, Plant

OBJECTIVE: To analyze a patient with infertility due to complex chromosome rearrangement by optical genome mapping (OGM). METHODS: A female patient who was diagnosed with "primary infertility" at Shenzhen Longhua District Maternal and Child Health Care Hospital in April 2024 was selected as the study subject. Clinical data of the patient was collected. Chromosome G banding karyotyping analysis was carried out for the patient and her parents, in addition with OGM and copy number variation sequencing (CNV-seq). This study was approved by the Medical Ethics Committee of the Hospital (Ethics No.: 2023052504). RESULTS: The patient, a 33-year-old female, had infertility for the past 5 years. OGM revealed formation of two derivative chromosomes through rearrangement of chromosomes 5 and 18. A loss of heterozygosity on chromosome 5 was also detected by OGM and CNV-seq techniques. Both of her parents had a normal karyotype. CONCLUSION The OGM technique can refine the position of chromosomal breakpoints and determine the direction and position of insertional fragment. Combined with karyotype analysis, the OGM can accurately determine the chromosomal karyotype of the patient and facilitate genetic counseling.
Humans ; Female ; Adult ; Karyotyping ; DNA Copy Number Variations/genetics* ; Chromosome Mapping/methods* ; Chromosome Aberrations ; Infertility, Female/diagnosis*

OBJECTIVE: To apply optical genome mapping (OGM) technique for the analysis of genetic etiology in two rare families with complex chromosomal rearrangements (CCRs) and to provide precise reproductive guidance to them. METHODS: Two Chinese families diagnosed with chromosomal rearrangements by chromosomal microarray analysis (CMA) or whole-exome sequencing (WES) between June and December 2023 at the Affiliated Women and Children's Hospital of Ningbo University were selected as the study subjects. In both cases, unbalanced chromosomal translocations were suspected. Clinical data were collected, and peripheral blood from the couple, amniotic fluid sample and aborted fetal tissue was subjected to combined G-banding karyotyping and OGM for comprehensive genetic analysis. This study has been approved by the Medical Ethics Committee of the Hospital (Ethics No.: EC2023-094). RESULTS: In family 1, the fetus was signaled to have abnormal chromosome 7 by non-invasive prenatal testing (NIPT), prompting amniocentesis and CMA detection. In family 2, a pregnancy loss had occurred at 10 weeks' gestation, and trio-WES was carried out. Both fetuses were found to harbor copy number variations (CNVs) suggestive of unbalanced CCRs. Further analysis with OGM has revealed that, in family 1, an unbalanced rearrangement involving chromosomes 7, 8, and 10 was carried by the fetus and the pregnant woman, which has formed der(8) and der(10) derivative chromosomes. In family 2, a maternal CCR was found, which involved chromosomes 2 and 13 with seven breakpoints, resulting in unbalanced fetal CNVs. After genetic counseling, family 1 opted to continue with the pregnancy, considering the woman's normal appearance and inheritance of the rearrangement. For both families remained to have a risk for unbalanced rearrangements in subsequent pregnancies, preimplantation genetic testing (PGT) was recommended. CONCLUSION In both families, the OGM has precisely delineated the genetic basis of fetal CNVs and mapped the maternal CCR breakpoints, providing critical insights for genetic counseling and reproductive decision-making.
Adult ; Female ; Humans ; Male ; Pregnancy ; Chromosome Aberrations ; Chromosome Disorders/genetics* ; Chromosome Mapping/methods* ; Genetic Testing/methods* ; Pedigree ; Prenatal Diagnosis/methods* ; Translocation, Genetic

OBJECTIVE: To assess the value of Optical genome mapping (OGM) for the verification of chromosomal structural variations among patients undergoing assisting reproduction. METHODS: A retrospective analysis was carried out on the clinical data of 12 patients presented at the Reproductive Center of Ningbo University Women and Children's Hospital from October 2022 to October 2024. All patients had undergone OGM testing due to suspection of structural variants by chromosomal karyotyping or a suggestive medical history. This study was approved by the Medical Ethics Committee of the hospital (Ethics No.: EC2024-148). RESULTS: Among the 12 patients verified by OGM, one (8.3%) was in keeping with the result of chromosomal karyotyping. Revised karyotypes were confirmed in seven cases (58.3%), including four with complex chromosomal rearrangements. Structural variation was excluded in three cases (25.0%). Of note, OGM has identified a previously undetected cryptic balanced translocation, i.e., ogm[GRCh38] t(7;12)(q36.3;q24.23)(157511190_157523142;119205703_119198409). CONCLUSION OGM can serve as an auxiliary diagnostic technique to conventional karyotyping and enable validation of suspected structural variations in those with ambiguous karyotype results or a history of adverse pregnancies. This can provide more precise genetic diagnosis for patients undergoing assisted reproduction and selection of clinical intervention strategies.
Humans ; Female ; Adult ; Retrospective Studies ; Karyotyping ; Reproductive Techniques, Assisted ; Chromosome Mapping/methods* ; Chromosome Aberrations

OBJECTIVE: To explore the reasons for false negative results by Optical genome mapping (OGM) analysis of three cases and propose strategies for handling them. METHODS: Three patients presented at the Affiliated Hospital of Nantong University between July 2022 and July 2024 were selected as study subjects. The patients included a 37-year-old female with two miscarriages, a 1.5-year-old boy with delayed motor development, and a 35-year-old male whose son had intellectual disability. The patients had undergone comprehensive evaluation with chromosomal karyotyping analysis, single nucleotide polymorphism microarray (SNP array) assay, fluorescence in situ hybridization (FISH), and methylation-specific multiple ligation-dependent probe amplification (MS-MLPA). A retrospective analysis was also carried out on the results of OGM testing. This study was approved by the Medical Ethics Committee of the Hospital (Ethics No.: 2020-K004). RESULTS: The chromosomal karyotype of patient 1 was 46,XX,4qs, and no abnormality was found by SNP array, FISH, and OGM testing. Patient 2 had a normal chromosomal karyotype, and SNP array analysis did not reveal any copy number abnormalities of chromosomal fragments but the presence of a homozygous region of approximately 79.58 Mb at 15q11.2-q26.3 (chr15: 22817871_102397317). MS-MLPA detection indicated that the copy number of the 15q11.2-q13 region was 2, and the degree of methylation was relatively high (average ratio = 1.0). OGM detection confirmed the presence of approximately 67.97 Mb of homozygosity in the chr15:33814680_101787650 [hg38] region of 15q14-q26.3. Patient 3 had a chromosomal karyotype of 46,XY,t(9;14)(q13;q11.2). No abnormality was found by OGM testing for patients 1 and 3. CONCLUSION As a novel cytogenetic technique, OGM can achieve high-resolution and high-precision analysis for numerical and structural genomic abnormalities. Nevertheless, it also has certain limitations, as its false negative results are related to factors such as the type of genomic variation, the chromosomal regions involved in the variation, the type of disease, and the version of human reference genome. Currently, it cannot be used as an independent method for the diagnosis of genetic diseases.
Humans ; Male ; Female ; Adult ; Polymorphism, Single Nucleotide/genetics* ; Karyotyping ; Chromosome Mapping/methods* ; Infant ; False Negative Reactions ; In Situ Hybridization, Fluorescence

OBJECTIVE: To investigate the genetic characteristics and clinical utility of Optical genome mapping (OGM) in resolving complex genomic rearrangements in families with recurrent pregnancy loss. METHODS: A recurrent miscarriage family which presented at both the People's Hospital of Qianxinan Buyi and Miao Autonomous Prefecture and the Affiliated Women and Children's Hospital of Ningbo University in September 2024 was selected as the study subject. Relevant clinical information was collected. Peripheral blood samples of the couple were collected for G banding karyotyping analysis, and copy number variation sequencing (CNV-seq) and OGM were used for verification. This study was approved by the Medical Ethics Committee of the Affiliated Women and Children's Hospital of Ningbo University (Ethics No.: EC2024-148). RESULTS: CNV-seq in an external hospital detected a 10.67 Mb deletion in the 16q12.1q21 region, a 142.4 kb deletion in the 5p15.2 region, and a 359.55 kb duplication in the 7p22.2 region. No abnormality was found in the chromosomal karyotype of the male partner, and the initial karyotyping of the female partner suggested 46,XX,?del(16)(q12.1q22). The CNV-seq verification of her indicated only variations in the 5p15.2 and 7p22.2 fragments, and no deletion of 16q was detected. As indicated by precise OGM analysis, multiple intrachromosomal and interchromosomal translocation variations had occurred between chromosomes 10 and 16 in the female partner, with complex balanced rearrangements (including 5 transchromosomal breakpoints). CONCLUSION The complex balanced rearrangements of the female partner's chromosomes had occurred during meiosis, the resultant unbalanced gametes may be the cause of repeated miscarriage in this family. OGM can delineate complex rearrangement breakpoints and directions that are difficult to reveal by conventional karyotyping analysis and provide a basis for accurate reproductive genetic counseling.
Humans ; Abortion, Habitual/etiology* ; Female ; Pregnancy ; Male ; DNA Copy Number Variations/genetics* ; Adult ; Karyotyping ; Pedigree ; Gene Rearrangement ; Chromosome Mapping

Optical genome mapping (OGM) is an emerging technology for the detection of genetic diseases based on physical mapping, which can detect numerical chromosomal abnormalities, copy number variation (CNV) and structural variation (SV) on a genome-wide scale. In recent years, a number of studies have proved that OGM, as a new generation of cytogenomic technique, has higher resolution and stronger ability to discover genomic variants compared with conventional genetic techniques. This article has systematically reviewed the principles, characteristics, advantages and limitations of OGM technology, and its applications in the diagnosis of genetic disorders.
Humans ; DNA Copy Number Variations ; Chromosome Mapping/methods* ; Genetic Diseases, Inborn/diagnosis* ; Genome, Human

OBJECTIVE: To carry out optical genome mapping (OGM) for a Chinese pedigree with a rare paracentric reverse insertion of chromosome 17. METHODS: A high-risk pregnant woman identified at the Prenatal Diagnosis Center of Hangzhou Women's Hospital in October 2021 and her family members were selected as the study subjects. Chromosome G banding analysis, fluorescence in situ hybridization (FISH), single nucleotide polymorphism array (SNP array) and OGM were applied to verify the balanced structural abnormality of chromosome 17 in the pedigree. RESULTS: Chromosomal karyotyping analysis and SNP array assay have identified a duplication of 17q23q25 in the fetus. Karyotyping analysis of the pregnant woman showed that the structure of chromosome 17 was abnormal, whilst SNP array has detected no abnormality. OGM revealed that the woman has carried a paracentric reverse insertion, which was confirmed by FISH. The karyotype of her husband was normal. CONCLUSION The duplication of 17q23q25 in the fetus has derived from a paracentric reverse insertion of chromosome 17 in its mother. OGM has the advantage for delineating balanced chromosome structural abnormalities.
Pregnancy ; Humans ; Female ; Pedigree ; In Situ Hybridization, Fluorescence ; Chromosomes, Human, Pair 17/genetics* ; East Asian People ; Chromosome Aberrations ; Prenatal Diagnosis ; Chromosome Mapping ; Chromosome Inversion

To investigate the efficacy and value of optical genome mapping (OGM) in detecting chromosomal structural variations. In a clinical study about high-precision analysis of genomic structural variation for complex genetic diseases, a retrospective study was performed on the cases with karyotyping at the department of Obstetrics and Gynecology, and Endocrinology of Peking Union Medical College Hospital from January to December 2021. Ten cases with abnormal karyotype was detected by OGM. Partial cases were verified by fluorescence in situ hybridization (FISH), SNP array or CNV-seq. Results of ten cases, nine were detected with abnormality by OGM, including unbalanced chromosomal rearrangements (n=3), translocation (n=5) and paracentric inversion (n=1), and the results were in concordance with other standard assays. However, one case with breakpoint and reconnected at centromere has not been detected. In conclusion, ten samples were comprehensively analyzed by karyotyping, FISH, SNP array or CNV-seq, and OGM, and results demonstrated that optical genome mapping as a new technology can not only detect unbalanced rearrangements such as copy number variants as well as balanced translocations and inversions, but more importantly, it can refine breakpoints and orientation of duplicated segments or insertions. So it can contribute to the diagnosis of genetic diseases and prevent birth defect. However, the current technology is not yet capable of detecting breakpoints of balanced structural variations lying within unmapped regions.
Chromosome Mapping ; Female ; Humans ; In Situ Hybridization, Fluorescence ; Karyotyping ; Pregnancy ; Retrospective Studies ; Translocation, Genetic