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ABSTRACT The publication of several high‐quality genomes has contributed greatly to clarifying the evolution of citrus. However, due to their complex genetic backgrounds, the origins and evolution of many citrus species remain unclear. We assembled de novo the 294‐Mbp chromosome‐level genome of a more than 200‐year‐old primitive papeda (DYC002). Comparison between the two sets of homologous chromosomes of the haplotype‐resolved genome revealed 1.2% intragenomic variations, including 1.75 million SNPs, 149,471 insertions and 154,215 deletions. Using this genome as a reference, we resequenced and performed population and phylogenetic analyses of 378 representative citrus accessions. Our study confirmed that the primary origin center of core Citrus species is in South China, particularly in the Himalaya–Hengduan Mountains. Papeda species are an ancient Citrus type compared with C. ichangensis. We found that the evolution of the Citrus genus followed two radiations through two routes (to East China and Southeast Asia) along river systems. Evidence for the origin and evolution of some individual citrus species was provided. Papeda probably played an important role in the origins of Australian finger lime, citrons, Honghe papeda and pummelos; Ichang papeda originated from Yuanjiang city of Yunnan Province, China, and C. mangshanensis has a close relationship with kumquat and Ichang papeda. Moreover, the Hunan and Guangdong Provinces of China are predicted to be the origin center of mandarin, sweet orange and sour orange. Additionally, our study revealed that fruit bitterness was significantly selected against during citrus domestication. Taken together, this study provides new insight into the origin and evolution of citrus species and may serve as a valuable genomic resource for citrus breeding and improvement. [ABSTRACT FROM AUTHOR]

The article in the International Journal of Laboratory Hematology discusses a case of acute myeloid leukemia with a cryptic KMT2A::MLLT10 rearrangement, which was not initially detected by standard testing methods. The patient had an aggressive clinical course with unfavorable abnormalities. Molecular techniques, such as RT-MLPA and NGS on RNA, were crucial in identifying the rearrangement. The study emphasizes the importance of accurate genomic testing for proper disease classification and patient risk assessment in cases of AML with complex genetic abnormalities. [Extracted from the article]

SUMMARY: As a result of extensive selection, two polyploid grass weeds, Hordeum glaucum (northern barley grass; 2n = 4x = 28) and Bromus diandrus (ripgut brome; 2n = 8x = 56), have evolved resistance to glyphosate, in Australia. Previous research suggested amplification of 5‐enolpyruvylshikimate‐3‐Phosphate synthase (EPSPS) gene confers resistance in these two weed species. The objective of this research was to investigate the genomic organization of the EPSPS gene in these two species through molecular cytogenetic analyses of fluorescence in situ hybridization (FISH) to understand possible mechanism of amplification of this gene. EPSPS copy number of H. glaucum and B. diandrus plants was estimated via quantitative polymerase chain reaction. The susceptible plants of both species had one copy of EPSPS, whereas the resistant plants of H. glaucum and B. diandrus had 14–17 and 16–32 copies, respectively. FISH analysis of glyphosate‐susceptible (Hg‐RWS) H. glaucum, revealed four faint signals of the EPSPS gene in two pairs of homologous chromosomes, at the telomeric region. The glyphosate‐resistant H. glaucum (Hg‐YP1) also showed amplification of EPSPS gene at telomeric regions in two pairs of homologous chromosomes, but the signals were brighter and appeared as cluster of EPSPS genes. Similarly, the glyphosate‐susceptible B. diandrus (Bd‐S) plants showed faint signals of EPSPS gene on two homologous chromosomes, at the telomeric position. However, samples of two glyphosate‐resistant, B. diandrus, Bd‐SA988 and Bd‐Vic showed much brighter hybridization signals of EPSPS gene, located at the telomere on two homologous chromosomes, suggesting an increase in EPSPS gene copies at this position. Overall, unequal crossover during meiosis may have triggered the initial EPSPS gene duplication sparking the evolution of glyphosate resistance. [ABSTRACT FROM AUTHOR]

Summary: Two recombinases, RAD51 and DMC1, catalyze meiotic break repair to ensure crossovers (COs) between homologous chromosomes (interhomolog) rather than between sisters (intersister). FIDGETIN‐LIKE‐1 (FIGL1) downregulates both recombinases. However, the understanding of how FIGL1 functions in meiotic repair remains limited. Here, we discover new genetic interactions of Arabidopsis thaliana FIGL1 that are important in vivo determinants of meiotic repair outcome.In figl1 mutants, compromising RAD51‐dependent repair, either through the loss of RAD51 paralogs (RAD51B or XRCC2) or RAD54 or by inhibiting RAD51 catalytic activity, results in either unrepaired breaks or meiotic CO defects. Further, XRCC2 physically interacts with FIGL1 and partially counteracts FIGL1 activity for RAD51 focus formation. Our data indicate that RAD51‐mediated repair mechanisms compensate FIGL1 dysfunction.FIGL1 is not necessary for intersister repair in dmc1 but is essential for the completion of meiotic repair in mutants such as asy1 that have impaired DMC1 functions and interhomolog bias. We show that FIGL1 attenuates interhomolog repair, and ASY1 counteracts FIGL1 to promote interhomolog recombination.Altogether, this study underlines that multiple factors can counteract FIGL1 activity to promote accurate meiotic repair. [ABSTRACT FROM AUTHOR]

Summary The interaction dynamics of homologous chromosomes during meiosis, such as recognition, pairing, synapsis, recombination, and segregation are vital for species fertility and genetic diversity within populations. Meiotic crossover (CO), a prominent feature of meiosis, ensures the faithful segregation of homologous chromosomes and enriches genetic diversity within a population. Nevertheless, visually distinguishing homologous chromosomes and COs remains an intractable challenge in cytological studies, particularly in non‐model or plants with small genomes, limiting insights into meiotic dynamics. In the present study, we developed a robust and reliable enhanced haplotype oligo‐painting (EHOP) technique to image small amounts of oligos, enabling visual discrimination of homologous chromosomes. Using EHOP developed based on sequence polymorphisms and reconstructed oligonucleotides, we visually distinguished parental and most recombinant chromosomes in cucumber F1 hybrids and F2 populations. Results from EHOP revealed that meiotic CO events preferentially occur in the 30–60% intervals of chromosome arms with lower sequence polymorphisms and significant recombination bias exists between cultivated and ancestral chromosomes. Due to the occupation of extensive heterochromatin occupancy, it is not yet possible to precisely identify the meiotic COs present in the central portion of chr2 and chr4. Notably, CO accessibility was universally detected in the cytological centromere region in F2 populations, a feature rarely observed in crops with large genomes. EHOP demonstrated exceptional performance in distinguishing homologous chromosomes and holds significant potential for broad application in studying homologous chromosome interactions. [ABSTRACT FROM AUTHOR]

Background: Uniparental isodisomy (UPiD) refers to a condition, in which both homologous chromosomes are inherited from only one parental homolog, which can result in either imprinting disorders or autosomal recessive conditions. Methods: We performed chromosomal microarray analysis, exome sequencing (ES), and RNA sequencing (RNA‐seq) using the patient's urine‐derived cells on a patient with growth retardation and multiple congenital anomalies. Results: We identified a homozygous ~0.53 kb microdeletion at 5q12.1, which was transmitted from the father with paternal UPiD(5). The deletion encompassed the first exon of both the ERCC8 and NDUFAF2 genes, which are responsible for Cockayne syndrome (CS) and mitochondrial complex I deficiency, respectively. Furthermore, RNA‐seq confirmed the reduced expression of both genes. Indeed, in addition to clinical features common to both syndromes, such as growth retardation, developmental delay, and feeding difficulties, the patient exhibited blended phenotypes: the characteristic features of CS, including arthrogryposis, microcephaly, and facial dysmorphisms, and those of mitochondrial complex I deficiency, including high serum lactate levels and lethal apnea resulting in a severe clinical course. Conclusion: The results imply that ES in combination with RNA‐seq could be a powerful method for the detection of underlying factors responsible for rare genetic conditions, such as UPD. [ABSTRACT FROM AUTHOR]

Hypospadias occurs sporadically in male livestock and is characterized by a non‐fused urethra during fetal development. In this study, perineal hypospadias, a bifid scrotum, penile hypoplasia, and bilateral abdominal cryptorchidism were diagnosed in a neonatal Holstein male calf. Septicemia was also suspected due to hypothermia, blurred conjunctivae, and loss of sucking and swallowing reflexes. Gross pathology revealed that both testicles were located intraabdominally caudally to the kidneys. Histopathological examination of the hypospadias showed a urothelium‐lined mucosal fold and parts of the corpus cavernosum penis and prepuce in the subcutis. Whole genome sequencing was performed on the affected calf. Analysis of short‐read coverage depth along the chromosomes identified an entire extra copy of chromosome 26. Based on the comparison of available variant calling data from the sire, the identified trisomy 26 is due to non‐disjunction of homologous chromosomes during the generation of paternal gametes. We have shown for the first time an association between bovine hypospadias and trisomy 26, which adds to the understanding of variation in fetal male sexual development. [ABSTRACT FROM AUTHOR]

SUMMARY: The pairing and synapsis of homologous chromosomes are crucial for their correct segregation during meiosis. The LINC (Linker of Nucleoskeleton and Cytoskeleton) complex can recruit kinesin protein at the nuclear envelope, affecting telomere bouquet formation and homologous pairing. Kinesin‐1‐like protein Pollen Semi‐Sterility1 (PSS1) plays a pivotal role in male meiotic chromosomal behavior and is essential for fertility in rice. However, its exact role in meiosis, especially as kinesin involved in homologous pairing and synapsis, has not been fully elucidated. Here, we generated three pss1 mutants by genome editing technology to dissect PSS1 biological functions in meiosis. The pss1 mutants exhibit alterations in the radial microtubule organization at pachytene and manifest a deficiency in telomere clustering, which is critical for full‐length homologous pairing. We reveal that PSS1 serves as a key mediator between chromosomes and cytoskeleton, thereby regulating microtubule organization and transmitting the force to nuclei to facilitate homologous chromosome pairing and synapsis in meiosis. Significance Statement: The source of energy driving the rapid movement of chromosomes during prophase I in rice meiosis remains to be elucidated In this manuscript, we speculate a novel mechanism that PSS1 serves as a crucial mediator between chromosomes and skeleton, thereby regulating microtubule organization and transmitting the force to nuclei to facilitating homologous chromosome pairing and synapsis in meiosis. [ABSTRACT FROM AUTHOR]

Meiosis is the developmental program that generates gametes. To produce healthy gametes, meiotic recombination creates reciprocal exchanges between each pair of homologous chromosomes that facilitate faithful chromosome segregation. Using fission yeast and biochemical, genetic, and cytological approaches, we have studied the role of CDK (cyclin-dependent kinase) in the control of Swi5–Sfr1, a Rad51-recombinase auxiliary factor involved in homolog invasion during recombination. We show that Sfr1 is a CDK target, and its phosphorylation downregulates Swi5–Sfr1 function in the meiotic prophase. Expression of a phospho-mimetic sfr1-7D mutant inhibits Rad51 binding, its robust chromosome loading, and subsequently decreases interhomolog recombination. On the other hand, the non-phosphorylatable sfr1-7A mutant alters Rad51 dynamics at late prophase, and exacerbates chromatin segregation defects and Rad51 retention observed in dbl2 deletion mutants when combined with them. We propose Sfr1 phospho-inhibition as a novel cell-cycle-dependent mechanism, which ensures timely resolution of recombination intermediates and successful chromosome distribution into the gametes. Furthermore, the N-terminal disordered part of Sfr1, an evolutionarily conserved feature, serves as a regulatory platform coordinating this phospho-regulation, protein localization and stability, with several CDK sites and regulatory sequences being conserved. Synopsis: Accessory factors of Rad51 recombinase are entry points for intricate regulation of meiotic recombination. Here, fission yeast CDK is found to ensure proper chromosome distribution and faithful genome transmission into meiotic products by Swi5-Sfr1 restriction in late meiotic prophase. Sfr1 is heavily phosphorylated by CDK at the end of meiotic prophase. Sfr1 phosphorylation impairs Rad51 recombinase binding and its stable chromosome loading. Sfr1 phosphorylation contributes to dismantling Rad51-mediated homolog invasions prior to chromosome segregation. Unphosphorylated Sfr1 increases cellular propensities for retaining Rad51 and missegregating chromosomes. Swi5-Sfr1 restriction ensures homolog invasions are dismantled in a timely manner to guarantee proper chromosome distribution and faithful genome transmission into the meiotic products. [ABSTRACT FROM AUTHOR]

Cohesin is a ring‐shaped complex that is loaded on DNA in two different conformations. In one conformation, it forms loops to organize the interphase genome; in the other, it topologically encircles sibling chromosomes to facilitate homologous recombination and to establish the cohesion that is required for orderly segregation during mitosis. How, and even if, these two loading conformation are related is unclear. Here, I propose that loop binding is a required first step for topological binding. This loop‐binding‐first model integrates the known information about the two loading mechanisms, explains genetic requirements for the two and explains how topological loading evolved from loop binding. [ABSTRACT FROM AUTHOR]

Autopolyploidy is taxonomically defined as the presence of more than two copies of each genome within an organism or species, where the genomes present must all originate within the same species. Alternatively, "genetic" or "cytological" autopolyploidy is defined by polysomic inheritance: random pairing and segregation of the four (or more) homologous chromosomes present, with no preferential pairing partners. In this review, we provide an overview of methods used to categorize species as taxonomic and cytological autopolyploids, including both modern and obsolete cytological methods, marker‐segregation‐based and genomics methods. Subsequently, we also investigated how frequently polysomic inheritance has been reliably documented in autopolyploids. Pure or predominantly polysomic inheritance was documented in 39 of 43 putative autopolyploid species where inheritance data was available (91%) and in seven of eight synthetic autopolyploids, with several cases of more mixed inheritance within species. We found no clear cases of autopolyploids with disomic inheritance, which was likely a function of our search methodology. Interestingly, we found seven species with purely polysomic inheritance and another five species with partial or predominant polysomic inheritance that appear to be taxonomic allopolyploids. Our results suggest that observations of polysomic inheritance can lead to relabeling of taxonomically allopolyploid species as autopolyploid and highlight the need for further cytogenetic and genomic investigation into polyploid origins and inheritance types. [ABSTRACT FROM AUTHOR]

Fem is a W‐linked gene that encodes a piRNA precursor, and its product, Fem piRNA, is a master factor of female determination in Bombyx mori. Fem has low similarity to any known sequences, and the origin of Fem remains unclear. So far, two hypotheses have been proposed for the origin of Fem: The first hypothesis is that Fem is an allele of Masc, which assumes that the W chromosome was originally a homologous chromosome of the Z chromosome. The second hypothesis is that Fem arose by the transposition of Masc to the W chromosome. To explore the origin of Fem, we determined the W chromosome sequences of B. mori and, as a comparison, a closely relative bombycid species of Trilocha varians with a Fem‐independent sex determination system. To our surprise, although the sequences of W and Z chromosomes show no homology to each other, a few pairs of homologues are shared by W and Z chromosomes, indicating the W chromosome of both species originated from Z chromosome. In addition, the W chromosome of T. varians lacks Fem, while the W chromosome of B. mori has over 100 copies of Fem. The high‐quality assembly of the W chromosome of B. mori arose the third hypothesis about the origin of Fem: Fem is a chimeric sequence of multiple transposons. More than half of one transcriptional unit of Fem shows a significant homology to RTE‐BovB. Moreover, the Fem piRNA‐producing region could correspond to the boundary of the two transposons, gypsy and satellite DNA. [ABSTRACT FROM AUTHOR]

This article discusses a case of de novo α+‐thalassaemia, a type of thalassaemia, in a Chinese family. The study verified the presence of a ‐α3.7 deletion causing thalassaemia in the proband, which was not found in either parent, suggesting that it may have developed as a de novo occurrence. The researchers used various detection methods, including CATSA analysis, to confirm the mutation and explore its origin. The study concludes that CATSA analysis can aid in obtaining a molecular diagnosis for de novo thalassaemia in affected populations. [Extracted from the article]

SUMMARY: The sugarcane (Saccharum spp.) genome is one of the most complex of all. Modern varieties are highly polyploid and aneuploid as a result of hybridization between Saccharum officinarum and S. spontaneum. Little research has been done on meiotic control in polyploid species, with the exception of the wheat Ph1 locus harboring the ZIP4 gene (TaZIP4‐B2) which promotes pairing between homologous chromosomes while suppressing crossover between homeologs. In sugarcane, despite its interspecific origin, bivalent association is favored, and multivalents, if any, are resolved at the end of prophase I. Thus, our aim herein was to investigate the purported genetic control of meiosis in the parental species and in sugarcane itself. We investigated the ZIP4 gene and immunolocalized meiotic proteins, namely synaptonemal complex proteins Zyp1 and Asy1. The sugarcane ZIP4 gene is located on chromosome 2 and expressed more abundantly in flowers, a similar profile to that found for TaZIP4‐B2. ZIP4 expression is higher in S. spontaneum a neoautopolyploid, with lower expression in S. officinarum, a stable octoploid species. The sugarcane Zip4 protein contains a TPR domain, essential for scaffolding. Its 3D structure was also predicted, and it was found to be very similar to that of TaZIP4‐B2, reflecting their functional relatedness. Immunolocalization of the Asy1 and Zyp1 proteins revealed that S. officinarum completes synapsis. However, in S. spontaneum and SP80‐3280 (a modern variety), no nuclei with complete synapsis were observed. Importantly, our results have implications for sugarcane cytogenetics, genetic mapping, and genomics. Significance Statement: Our work provides insights into the genetic control of meiosis in sugarcane (Saccharum spp.), a man made polyploid and fertile plant of interspecific constitution. Inspired by the discoveries of the Ph1 locus, which harbors the ZIP4 gene in wheat, we identified this meiotic gene in both parental species and in two current sugarcane varieties. We analyzed both gene and protein sequence conservation, protein domains, and predicted the 3D‐protein structure. We also investigated the level of ZIP4 expression in different sugarcane tissues. Like its role in wheat, ZIP4 seems to promote pairing between homologous chromosomes while suppressing crossover between homeologs in Saccharum. Using immunocytology, we were able to determine synaptonemal complex polymerization during prophase I, using Asy1 and Zyp1 sugarcane specific antibodies, revealing synapsis defects in all genotypes except Saccharum officinarum, a parental species with regular meiotic behavior. [ABSTRACT FROM AUTHOR]

The article presents the development of an updated high-quality genome assembly of Arachis monticola, a wild peanut species. The previous genome assembly had low quality, but the use of long-read sequencing technologies allowed for a higher-quality assembly. The new assembly, called Amon2.0, has improved contiguity and completeness compared to the previous version. The genome assembly will contribute to further understanding the domestication and evolutionary histories of Arachis spp. and will be a valuable resource for functional genomics and molecular-assisted breeding in legume crops. [Extracted from the article]

Dynamic nuclear architecture and chromatin organizations are the key features of the mid‐prophase I in mammalian meiosis. The chromatin undergoes major changes, including meiosis‐specific spatiotemporal arrangements and remodeling, the establishment of chromatin loop–axis structure, pairing, and crossing over between homologous chromosomes, any deficiencies in these events may induce genome instability, subsequently leading to failure to produce gametes and infertility. Despite the significance of chromatin structure, little is known about the location of chromatin marks and the necessity of their balance during meiosis prophase I. Here, we show a thorough cytological study of the surface‐spread meiotic chromosomes of mouse spermatocytes for H3K9,14,18,23,27,36, H4K12,16 acetylation, and H3K4,9,27,36 methylation. Active acetylation and methylation marks on H3 and H4, such as H3K9ac, H3K14ac, H3K18ac, H3K36ac, H3K56ac, H4K12ac, H4K16ac, and H3K36me3 exhibited pan‐nuclear localization away from heterochromatin. In comparison, repressive marks like H3K9me3 and H3K27me3 are localized to heterochromatin. Further, taking advantage of the delivery of small‐molecule chemical inhibitors methotrexate (heterochromatin enhancer), heterochromatin inhibitor, anacardic acid (histone acetyltransferase inhibitor), trichostatin A (histone deacetylase inhibitor), IOX1 (JmjC demethylases inhibitor), and AZ505 (methyltransferase inhibitor) in seminiferous tubules through the rete testis route, revealed that alteration in histone modifications enhanced the centromere mislocalization, chromosome breakage, altered meiotic recombination and reduced sperm count. Specifically, IOX1 and AZ505 treatment shows severe meiotic phenotypes, including altering chromosome axis length and chromatin loop size via transcriptional regulation of meiosis‐specific genes. Our findings highlight the importance of balanced chromatin modifications in meiotic prophase I chromosome organization and instability. [ABSTRACT FROM AUTHOR]

Quercus section Cyclobalanopsis represents a dominant woody lineage in East Asian evergreen broadleaved forests. Regardless of its ecological and economic importance, little is known about the genomes of species in this unique oak lineage. Quercus glauca is one of the most widespread tree species in the section Cyclobalanopsis. In this study, a high‐quality haplotype‐resolved reference genome was assembled for Q. glauca from PacBio HiFi and Hi‐C reads. The genome size, contig N50, and scaffold N50 measured 902.88, 7.60, and 69.28 Mb, respectively, for haplotype1, and 913.28, 7.20, and 71.53 Mb, respectively, for haplotype2. A total of 37,457 and 38,311 protein‐coding genes were predicted in haplotype1 and haplotype2, respectively. Homologous chromosomes in the Q. glauca genome had excellent gene pair collinearity. The number of R‐genes in Q. glauca was similar to most East Asian oaks but less than oak species from Europe and America. Abundant structural variation in the Q. glauca genome could contribute to environmental stress tolerance in Q. glauca. Sections Cyclobalanopsis and Cerris diverged in the Oligocene, in agreement with fossil records for section Cyclobalanopsis, which document its presence in East Asia since the early Miocene. The demographic dynamics of closely related oak species were largely similar. The high‐quality reference genome provided here for the most widespread species in section Cyclobalanopsis will serve as an essential genomic resource for evolutionary studies of key oak lineages while also supporting studies of interspecific introgression, local adaptation, and speciation in oaks. [ABSTRACT FROM AUTHOR]

This article discusses a rare form of tumor predisposition called atypical teratoid/rhabdoid tumor (ATRT) that arises in the setting of germline ring chromosome 22. ATRT is a type of embryonal neoplasm characterized by the inactivation of the SMARCB1 gene. Germline ring chromosome 22, although not directly affecting SMARCB1, can lead to somatic mosaicism for monosomy chromosome 22, increasing the risk of ATRT. The article presents two cases of ATRT associated with germline ring chromosome 22 and provides detailed molecular characterization of the tumors. It also highlights the potential clinical manifestations and suggests considering germline karyotype and chromosomal microarray for ATRT patients with dysmorphic features, developmental delay, or disproportionate growth. Additionally, the article reports the first case of multiple meningiomas occurring in a long-term survivor of ATRT with germline ring chromosome 22, which predisposes to both SMARCB1 and NF2 deficient tumors. The authors emphasize the need for clinical monitoring in patients with germline ring chromosome 22 and suggest considering germline chromosomal microarray for all ATRT patients with loss of chromosome 22 observed in the tumor. [Extracted from the article]

Background: Recurrent miscarriage (RM) affects 1% to 5% of couples trying to conceive. Despite extensive clinical and laboratory testing, half of the RM cases remain unexplained. We report the genetic analysis of a couple with eight miscarriages and the search for their potential genetic etiology. Methods: Short tandem repeat (STR) markers, single nucleotide polymorphic (SNP) microarray, and human DNA methylation microarray were used to analyze the genotypes of two miscarriages. Exomes sequencing was performed on DNA from the two partners and identified variants were validated by Sanger sequencing. Results: STR marker genotyping demonstrated that the two available miscarriages are triploid digynic and resulted from the failure of Meiosis II. SNP microarray analysis revealed an additional Meiosis I abnormality that is the segregation of the two maternal homologous chromosomes in one triploid miscarriage. Whole‐exome sequencing on DNA from the two partners identified candidate variants only in the female partner in two genes with roles in female reproduction, a missense in EIF4ENIF1 (OMIM 607445) and a stop gain in HORMAD2 (OMIM 618842). EIF4ENIF1 is a eukaryotic translation initiation factor 4E nuclear import factor required for the oocyte germinal vesicle breakdown, and HORMAD2 is part of the synaptonemal complex that was hypothesized to act as a checkpoint mechanism to eliminate oocytes with asynapsis during meiotic prophase I in mice. Conclusion: While both genes may contribute to the phenotype, the Meiosis I abnormalities in the conceptions favor the causal role of HORMAD2 in the etiology of RM in this couple. This report illustrates the importance of comprehensively analyzing the products of conception to guide the search for the genetic causation of RM. [ABSTRACT FROM AUTHOR]

Meiosis is a specialized cell division that occurs in sexually reproducing organisms, generating haploid gametes containing half the chromosome number through two rounds of cell division. Homologous chromosomes pair and prepare for their proper segregation in subsequent divisions. How homologous chromosomes recognize each other and achieve pairing is an important question. Early studies showed that in most organisms, homologous pairing relies on homologous recombination. However, pairing mechanisms differ across species. Evidence indicates that chromosomes are dynamic and move during early meiotic stages, facilitating pairing. Recent studies in various model organisms suggest conserved mechanisms and key regulators of homologous chromosome pairing. This review summarizes these findings and compare similarities and differences in homologous chromosome pairing mechanisms across species. [ABSTRACT FROM AUTHOR]

Hardy–Weinberg proportions (HWP) are often explored to evaluate the assumption of random mating. However, in autopolyploids, organisms with more than two sets of homologous chromosomes, HWP and random mating are different hypotheses that require different statistical testing approaches. Currently, the only available methods to test for random mating in autopolyploids (i) heavily rely on asymptotic approximations and (ii) assume genotypes are known, ignoring genotype uncertainty. Furthermore, these approaches are all frequentist, and so do not carry the benefits of Bayesian analysis, including ease of interpretability, incorporation of prior information, and consistency under the null. Here, we present Bayesian approaches to test for random mating, bringing the benefits of Bayesian analysis to this problem. Our Bayesian methods also (i) do not rely on asymptotic approximations, being appropriate for small sample sizes, and (ii) optionally account for genotype uncertainty via genotype likelihoods. We validate our methods in simulations and demonstrate on two real datasets how testing for random mating is more useful for detecting genotyping errors than testing for HWP (in a natural population) and testing for Mendelian segregation (in an experimental S1 population). Our methods are implemented in Version 2.0.2 of the hwep R package on the Comprehensive R Archive Network https://cran.r‐project.org/package=hwep. [ABSTRACT FROM AUTHOR]

The article "Ancient asexuality: No scandals found with novel data" explores the concept of ancient asexual lineages and challenges the prevailing notion of their existence. Through recent experimental advances, the study suggests that organisms previously classified as ancient asexuals may retain the capacity for sexual reproduction under specific conditions. The findings highlight the importance of empirical evidence in understanding the evolutionary development of asexual organisms and indicate that truly ancient asexual lineages may not exist as previously thought. [Extracted from the article]

Meiotic crossover (CO) formation between homologous chromosomes ensures their subsequent proper segregation and generates genetic diversity among offspring. In maize, however, the mechanisms that modulate CO formation remain poorly characterized. Here, we found that both maize BREAST CANCER SUSCEPTIBILITY PROTEIN 2 (BRCA2) and AAA‐ATPase FIDGETIN‐LIKE‐1 (FIGL1) act as positive factors of CO formation by controlling the assembly or/and stability of two conserved DNA recombinases RAD51 and DMC1 filaments. Our results revealed that ZmBRCA2 is not only involved in the repair of DNA double‐stranded breaks (DSBs), but also regulates CO formation in a dosage‐dependent manner. In addition, ZmFIGL1 interacts with RAD51 and DMC1, and Zmfigl1 mutants had a significantly reduced number of RAD51/DMC1 foci and COs. Further, simultaneous loss of ZmFIGL1 and ZmBRCA2 abolished RAD51/DMC1 foci and exacerbated meiotic defects compared with the single mutant Zmbrca2 or Zmfigl1. Together, our data demonstrate that ZmBRCA2 and ZmFIGL1 act coordinately to regulate the dynamics of RAD51/DMC1‐dependent DSB repair to promote CO formation in maize. This conclusion is surprisingly different from the antagonistic roles of BRCA2 and FIGL1 in Arabidopsis, implying that, although key factors that control CO formation are evolutionarily conserved, specific characteristics have been adopted in diverse plant species. [ABSTRACT FROM AUTHOR]

CRISPR mutagenesis is an efficient way to disrupt specific target genes in many model organisms. We previously devised a targeted CRISPR recombination method to generate intragenic recombinants of alleles in Drosophila. Here, we assessed the applicability of CRISPR targeting‐induced recombination to different genetic loci. We compared the ectopic recombination rates in the male germline by CRISPR targeting at two neighboring genetic loci within the genomic region that consists of the repressed chromatin domain of the Lobe gene, and the transcriptionally active domain of PRAS40. Targeting around the transcription initiation of PRAS40 resulted in higher recombination rates of homologous chromosomes than targeting at the Lobe intron. Based on the efficient homologous recombination by CRISPR targeting observed around transcriptionally active loci, we further investigated targeted recombination between P‐elements that are inserted at different genomic locations. Male recombination by CRISPR targeting of P‐elements located proximally and distally to the ebony gene produced recombinants deficient for the intervening region of ebony transcription. Taken together, we suggest that targeted homologous recombination by CRISPR targeting may have specific genetic applications, such as generation of allelic combinations or chromosomal variations. [ABSTRACT FROM AUTHOR]

During meiosis, chromosomes with homologous partners undergo synaptonemal complex (SC)‐mediated pairing, while the remaining unpaired chromosomes are heterochromatinized through unpaired silencing. Mechanisms underlying homolog recognition during SC formation are still unclear. Here, we show that the Caenorhabditis elegans Argonaute proteins, CSR‐1 and its paralog CSR‐2, interacting with 22G‐RNAs, are required for synaptonemal complex formation with accurate homology. CSR‐1 in nuclei and meiotic cohesin, constituting the SC lateral elements, were associated with nonsimple DNA repeats, including minisatellites and transposons, and weakly associated with coding genes. CSR‐1‐associated CeRep55 minisatellites were expressing 22G‐RNAs and long noncoding (lnc) RNAs that colocalized with synaptonemal complexes on paired chromosomes and with cohesin regions of unpaired chromosomes. CeRep55 multilocus deletions reduced the efficiencies of homologous pairing and unpaired silencing, which were supported by the csr‐1 activity. Moreover, CSR‐1 and CSR‐2 were required for proper heterochromatinization of unpaired chromosomes. These findings suggest that CSR‐1 and CSR‐2 play crucial roles in homology recognition, achieving accurate SC formation between chromosome pairs and condensing unpaired chromosomes by targeting repeat‐derived lncRNAs. Synopsis: It remains unclear how the homologous sequences of meiotic chromosomes, excluding the pairing center regions, are recognized during synaptonemal complex (SC) formation. This study describes a new model where an Argonaute‐dependent small RNA system is involved in homolog recognition during SC formation in C. elegans. Argonaute protein CSR‐1 and its paralog CSR‐2 interacting with 22G‐RNAs are required for SC formation between chromosome pairs with accurate homology.CSR‐1 and CSR‐2 are also involved in the condensation of unpaired chromosomes.CSR‐1 in nuclei and meiotic cohesin containing COH‐3/4 are associated with non‐simple DNA repeats and weakly with coding genes.CSR‐1 plays pleiotropic roles in the endogenous and exogenous RNAi pathways. [ABSTRACT FROM AUTHOR]

Synteny, the ordering of sequences within homologous chromosomes, must be maintained within the genomes of sexually reproducing species for the sharing of alleles and production of viable, reproducing offspring. However, when the genomes of closely related species are compared, a loss of synteny is often observed. Unequal homologous recombination is the primary mechanism behind synteny loss, occurring more often in transposon rich regions, and resulting in the formation of chromosomal rearrangements. To examine patterns of synteny among three closely related, interbreeding, and wild Eucalyptus species, we assembled their genomes using long‐read DNA sequencing and de novo assembly. We identify syntenic and rearranged regions between these genomes and estimate that ~48% of our genomes remain syntenic while ~36% is rearranged. We observed that rearrangements highly fragment microsynteny. Our results suggest that synteny between these species is primarily lost through small‐scale rearrangements, not through sequence loss, gain, or sequence divergence. Further examination of identified rearrangements suggests that rearrangements may be altering the phenotypes of Eucalyptus species. Our study also underscores that the use of single reference genomes in genomic variation studies could lead to reference bias, especially given the scale at which we show potentially adaptive loci have highly diverged, deleted, duplicated and/or rearranged. This study provides an unbiased framework to look at potential speciation and adaptive loci among a rapidly radiating foundation species of woodland trees that are free from selective breeding seen in most crop species. [ABSTRACT FROM AUTHOR]

Summary: Increasing crop yields through plant breeding is time consuming and laborious, with the generation of novel combinations of alleles being limited by chromosomal linkage blocks and linkage‐drag. Meiotic recombination is essential to create novel genetic variation via the reshuffling of parental alleles. The exchange of genetic information between homologous chromosomes occurs at crossover (CO) sites but CO frequency is often low and unevenly distributed. This bias creates the problem of linkage‐drag in recombination 'cold' regions, where undesirable variation remains linked to useful traits. In plants, programmed meiosis‐specific DNA double‐strand breaks, catalysed by the SPO11 complex, initiate the recombination pathway, although only ~5% result in the formation of COs. To study the role of SPO11‐1 in wheat meiosis, and as a prelude to manipulation, we used CRISPR/Cas9 to generate edits in all three SPO11‐1 homoeologues of hexaploid wheat. Characterization of progeny lines shows plants deficient in all six SPO11‐1 copies fail to undergo chromosome synapsis, lack COs and are sterile. In contrast, lines carrying a single copy of any one of the three wild‐type homoeologues are phenotypically indistinguishable from unedited plants both in terms of vegetative growth and fertility. However, cytogenetic analysis of the edited plants suggests that homoeologues differ in their ability to generate COs and in the dynamics of synapsis. In addition, we show that the transformation of wheat mutants carrying six edited copies of SPO11‐1 with the TaSPO11‐1B gene, restores synapsis, CO formation, and fertility and hence opens a route to modifying recombination in this agronomically important crop. [ABSTRACT FROM AUTHOR]

Summary: During meiosis, recombination‐mediated pairing and synapsis of homologous chromosomes begin with programmed DNA double‐strand breaks (DSBs). In yeast and mice, DSBs form in a tethered loop–axis complex, in which DSB sites are located within chromatin loops and tethered to the proteinaceous axial element (AE) by DSB‐forming factors. In plants, the molecular connection between DSB sites and chromosome axes is poorly understood.By integrating genetic analysis, immunostaining technology, and protein–protein interaction studies, the putative factors linking DSB formation to chromosome axis were explored in maize meiosis.Here, we report that the AE protein ZmASY1 directly interacts with the DSB‐forming protein ZmPRD3 in maize (Zea mays) and mediates DSB formation, synaptonemal complex assembly, and homologous recombination. ZmPRD3 also interacts with ZmPRD1, which plays a central role in organizing the DSB‐forming complex. These results suggest that ZmASY1 and ZmPRD3 may work as a key module linking DSB sites to chromosome axes during DSB formation in maize.This mechanism is similar to that described in yeast and recently Arabidopsis involving the homologs Mer2/ZmPRD3 and HOP1/ZmASY1, thus indicating that the process of tethering DSBs in chromatin loops to the chromosome axes may be evolutionarily conserved in diverse taxa. [ABSTRACT FROM AUTHOR]

This document is an editorial highlights article from the journal Developmental Dynamics. It emphasizes the importance of studying various organisms to understand development, evolution, disease, and regeneration. The article highlights three specific studies: one on the role of mechanical forces in tendon development, one on the role of wnt10a in zebrafish fin development, and one on the role of ID2 in meiosis and spermatogenesis in mice. These studies provide valuable insights into the complex dynamics of developmental biology. [Extracted from the article]

Background: An impeccable female meiotic prophase is critical for producing a high‐quality oocyte and, ultimately, a healthy newborn. SYCP3 is a key component of the synaptonemal complex regulating meiotic homologous recombination. However, what regulates SYCP3 stability is unknown. Methods: Fertility assays, follicle counting, meiotic prophase stage (leptotene, zygotene, pachytene and diplotene) analysis and live imaging were employed to examine how FBXW24 knockout (KO) affect female fertility, follicle reserve, oocyte quality, meiotic prophase progression of female germ cells, and meiosis of oocytes. Western blot and immunostaining were used to examined the levels & signals (intensity, foci) of SYCP3 and multiple key DSB indicators & repair proteins (γH2AX, RPA2, p‐CHK2, RAD51, MLH1, HORMAD1, TRIP13) after FBXW24 KO. Co‐IP and immuno‐EM were used to examined the interaction between FBXW24 and SYCP3; Mass spec was used to characterize the ubiquitination sites in SYCP3; In vivo & in vitro ubiquitination assays were utilized to determine the key sites in SYCP3 & FBXW24 for ubiquitination. Results: Fbxw24‐knockout (KO) female mice were infertile due to massive oocyte death upon meiosis entry. Fbxw24‐KO oocytes were defective due to elevated DNA double‐strand breaks (DSBs) and inseparable homologous chromosomes. Fbxw24‐KO germ cells showed increased SYCP3 levels, delayed prophase progression, increased DSBs, and decreased crossover foci. Next, we found that FBXW24 directly binds and ubiquitinates SYCP3 to regulate its stability. In addition, several key residues important for SYCP3 ubiquitination and FBXW24 ubiquitinating activity were characterized. Conclusions: We proposed that FBXW24 regulates the timely degradation of SYCP3 to ensure normal crossover and DSB repair during pachytene. FBXW24‐KO delayed SYCP3 degradation and DSB repair from pachytene until metaphase II (MII), ultimately causing failure in oocyte maturation, oocyte death, and infertility. [ABSTRACT FROM AUTHOR]

Interspecies crossing and allopolyploidization increase the opportunity for generating new breeding resources for fish farming. Allotetraploid hybrid fish (4nAT) were created by crossing red crucian carp (RCC, Carassius auratus red var., ♀) with common carp (CC, Cyprinus carpio L., ♂). However, the genetic pattern of the heterogeneous genomes during gametogenesis in 4nAT is still unclear, which hinders the understanding of the mechanism of generation of new phenotypes during allopolyploidization in fish breeding. In the present study, fluorescence in situ hybridization of 5S rDNA was employed to track homologous pairing, and the characteristics of bivalents were observed using air‐drying preparation technology and electron microscopy. The results showed two strong signals of 5S rDNA localization from the RCC genome, paired in the pachytene stage and metaphase stage of meiosis I cells in 4nAT, suggesting pairing of homologous chromosomes in 4nAT occurred between identical chromosomes. Furthermore, all bivalent pairs possessed one monochiasmate and were neatly arranged in the equatorial plate during meiosis I, which ensured normal separation of homologous chromosomes in 4nAT. This study elucidated the genetic pattern of heterogeneous genomes in 4nAT, providing important evidence for the genetic stability of 4nAT. These findings are of great significance for aquatic breeding. [ABSTRACT FROM AUTHOR]

Here, we present an annotated, chromosome‐anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long‐read sequencing, paired‐end Illumina sequencing, proximity ligation (Hi‐C) sequencing, and a previously published linkage map to produce a highly contiguous assembly composed of 7378 contigs (contig N50 = 1.8 Mb) assigned to 4120 scaffolds (scaffold N50 = 44.975 Mb). Long read sequencing data were generated using DNA from a female double haploid individual. 84.7% of the genome was assigned to 42 chromosome‐sized scaffolds and 93.2% of Benchmarking Universal Single Copy Orthologues were recovered, putting this assembly on par with the best currently available salmonid genomes. Estimates of genome size based on k‐mer frequency analysis were highly similar to the total size of the finished genome, suggesting that the entirety of the genome was recovered. A mitochondrial genome assembly was also produced. Self‐versus‐self synteny analysis allowed us to identify homeologs resulting from the salmonid specific autotetraploid event (Ss4R) as well as regions exhibiting delayed rediploidization. Alignment with three other salmonid genomes and the Northern Pike (Esox lucius) genome also allowed us to identify homologous chromosomes in related taxa. We also generated multiple resources useful for future genomic research on Lake Trout, including a repeat library and a sex‐averaged recombination map. A novel RNA sequencing data set for liver tissue was also generated in order to produce a publicly available set of annotations for 49,668 genes and pseudogenes. Potential applications of these resources to population genetics and the conservation of native populations are discussed. [ABSTRACT FROM AUTHOR]

The article discusses the methods and approaches used in quantitative trait loci (QTL) mapping of autopolyploids. It challenges a previous assertion that a specific method lacks genetic linkage analysis between QTLs and surrounding markers. The article explains the concept of QTL interval mapping and the use of Hidden Markov Models (HMM) in QTL mapping methodologies. It argues that their HMM-based approach does account for genetic linkage and the complexity of tetrasomic inheritance. The article also compares their method to another approach and highlights the computational advantages of their approach. However, it notes that the practical application of the other method to realistic datasets has yet to be demonstrated. The article concludes that their approach is a more practical way to account for polysomic inheritance in QTL mapping of autopolyploids. [Extracted from the article]

Background: Uniparental disomy (UPD) is the inheritance of two homologous chromosomes from the same parent. UPD may result in clinical phenotypes when occurring on chromosomes with specific imprinting pattern, when leading to homozygosity of a deleterious recessive allele inherited from one carrier parent, or when associated with a mosaic aneuploidy. Due to the importance of UPD in genetic disease etiology, UPD analysis has started to be implemented in the context of exome sequencing (ES) or genome sequencing. Methods: We developed an in‐house algorithm TRIPS (Trio Parentage/UPD Studies) to identify UPD events in trio ES cases. This method identifies regions with uniparental inheritance by utilizing the trio genotyping data obtained from the concurrent SNP array to delineate the parental origin of the SNPs in the proband. Results: We identified 16 UPD events from 2675 ES trios. Among those, four events led to imprinting disorders, seven unmasked a pathogenic/likely pathogenic variant in a recessive disease gene, and two were consistent with a mosaic genome wide paternal UPD pattern. Twelve of these UPD events directly contributed to the molecular diagnosis of the patients. Conclusion: Our study demonstrated the contribution of UPD to the molecular diagnosis in one clinical ES cohort, thus UPD analysis should be incorporated into routine clinical ES interpretation. [ABSTRACT FROM AUTHOR]

Summary: The reciprocal exchange of genetic information between homologous chromosomes during meiotic recombination is essential to secure balanced chromosome segregation and to promote genetic diversity. The chromosomal position and frequency of reciprocal genetic exchange shapes the efficiency of breeding programmes and influences crop improvement under a changing climate. In large genome cereals, such as wheat and barley, crossovers are consistently restricted to subtelomeric chromosomal regions, thus preventing favourable allele combinations being formed within a considerable proportion of the genome, including interstitial and pericentromeric chromatin. Understanding the key elements driving crossover designation is therefore essential to broaden the regions available for crossovers. Here, we followed early meiotic chromatin dynamism in cereals through the visualisation of a homologous barley chromosome arm pair stably transferred into the wheat genetic background. By capturing the dynamics of a single chromosome arm at the same time as detecting the undergoing events of meiotic recombination and synapsis, we showed that subtelomeric chromatin of homologues synchronously transitions to an open chromatin structure during recombination initiation. By contrast, pericentromeric and interstitial regions preserved their closed chromatin organisation and become unpackaged only later, concomitant with initiation of recombinatorial repair and the initial assembly of the synaptonemal complex. Our results raise the possibility that the closed pericentromeric chromatin structure in cereals may influence the fate decision during recombination initiation, as well as the spatial development of synapsis, and may also explain the suppression of crossover events in the proximity of the centromeres. [ABSTRACT FROM AUTHOR]

Background: Wilson's disease (WD) is a rare autosomal recessive inherited disorder that is induced by defects of the ATP7B gene and characterized by damage to the liver and nervous system caused by aberrant copper metabolism. The identification of pathogenic mutations on two homologous chromosomes has become the gold standard for the diagnosis of WD. Methods: Sanger sequencing and multiplex ligation‐dependent probe amplification (MLPA) were combined to establish a genetic diagnosis for patients from 53 unrelated Chinese WD families. Results: Biallelic mutations were detected by Sanger sequencing in 50 of the probands, while single heterozygous mutations were detected in the remaining three probands. A total of 45 diverse pathogenic mutations were detected, and 6 previously unreported mutations were involved. Five asymptomatic patients were screened from 85 family members of 38 probands participating in the study. Conclusion: This study contributes to the enlargement of the mutational spectrum of the ATP7B gene among the population of China and highlights the significance of genetic testing for asymptomatic patients. [ABSTRACT FROM AUTHOR]

Genome changes, evidenced through karyotype or nuclear genome size data, can result in reproductive isolation, diversification and speciation. The aim of this study was to understand how changes in the karyotype such as chromosome number and nuclear genome size accompanied the evolution of neotropical stingless bees, and to discuss these data in a phylogenetic context focusing on the karyotype evolution of this clade. We sampled 38 species representing the three Neotropical Meliponini groups; 35 for karyotype analyses and 16 for 1C value measurement. The chromosome number varied from 2n = 16 to 2n = 34, with distinct karyotypic formulae and the presence of a few polymorphisms, such as B chromosomes in one species and arm size differences between homologous chromosomes in two species. The mean 1C value varied from 0.31 pg to 0.92 pg. We associated empirical data on chromosome number and mean 1C value to highlight the importance of Robertsonian fusion rearrangements, leading to a decrease in chromosome number during the Neotropical Meliponini evolution. These data also allowed us to infer the independent heterochromatin amplification in several genera. Although less frequent, Melipona species with 2n = 22 represent evidence of Robertsonian fissions. We also pointed out the importance of chromosomal rearrangements that did not alter chromosome number, such as inversions and heterochromatin amplification. [ABSTRACT FROM AUTHOR]

Summary: Fungi have been observed to exhibit resistance to high levels of ionizing radiation despite sharing most DNA repair mechanisms with other eukaryotes. Radioresistance, in fact, is such a common feature in fungi that it is difficult to identify species that exhibit widely different radiosensitivities, which in turn has hampered the identification of genetic elements responsible for this resistance phenotype. Due to the inherent mutagenic properties of radiation exposure, however, this can be addressed through adaptive laboratory evolution for increased ionizing radiation resistance. Here, using the black yeast Exophiala dermatitidis, we demonstrate that resistance to γ‐radiation can be greatly increased through repeated rounds of irradiation and outgrowth. Moreover, we find that the small genome size of fungi situates them as a relatively simple functional genomics platform for identification of mutations associated with ionizing radiation resistance. This enabled the identification of genetic mutations in genes encoding proteins with a broad range of functions from 10 evolved strains. Specifically, we find that greatly increased resistance to γ‐radiation is achieved in E. dermatitidis through disruption of the non‐homologous end‐joining pathway, with three individual evolutionary paths converging to abolish this DNA repair process. This result suggests that non‐homologous end‐joining, even in haploid cells where homologous chromosomes are not present during much of the cell cycle, is an impediment to repair of radiation‐induced lesions in this organism, and that the relative levels of homologous and non‐homologous repair in a given fungal species may play a major role in its radiation resistance. [ABSTRACT FROM AUTHOR]

Summary: Meiotic chromosome pairing between homoeologous chromosomes was reported in many nascent allopolyploids. Homoeologous pairing is gradually eliminated and replaced by exclusive homologous pairing in well‐established allopolyploids, an evolutionary process referred to as the diploidization of allopolyploids. A fundamental question of the diploidization of allopolyploids is whether and to what extent the DNA sequence variation among homoeologous chromosomes contribute to the establishment of exclusive homologous chromosome pairing.We developed aneuploid tetraploid maize lines that contain three copies of chromosome 10 derived from inbred lines B73 and H99. We were able to identify the parental origin of each copy of chromosome 10 in the materials using oligonucleotide‐based haplotype‐specific chromosome painting.We demonstrate that the two identical copies of chromosome 10 from H99 pair preferentially over chromosome 10 from B73 in different stages of prophase I and metaphase I during meiosis. Thus, homologous chromosome pairing is favored to partners with the most similar DNA sequences and can be discriminated based on cryptic sequence variation.We propose that innate preference of homologous chromosome pairing exists in nascent allopolyploids and serves as the first layer that would eventually block all homoeologous chromosome pairing in allopolyploids. [ABSTRACT FROM AUTHOR]

SUMMARY: A chromosome‐specific painting technique has been developed which combines the most recent approaches of the companion disciplines of molecular cytogenetics and genome research. We developed seven oligonucleotide (oligo) pools derivd from single‐copy sequences on chromosomes 1 to 7 of barley (Hordeum vulgare L.) and corresponding collinear regions of wheat (Triticum aestivum L.). The seven groups of pooled oligos comprised between 10 986 and 12 496 45‐bp monomers, and these then produced stable fluorescence in situ hybridization (FISH) signals on chromosomes of each linkage group of wheat and barley. The pooled oligo probes were applied to high‐throughput karyotyping of the chromosomes of other Triticeae species in the genera Secale, Aegilops, Thinopyrum, and Dasypyrum, and the study also extended to some wheat‐alien amphiploids and derived lines. We demonstrated that a complete set of whole‐chromosome oligo painting probes facilitated the study of inter‐species chromosome homologous relationships and visualized non‐homologous chromosomal rearrangements in Triticeae species and some wheat‐alien species derivatives. When combined with other non‐denaturing FISH procedures using tandem‐repeat oligos, the newly developed oligo painting techniques provide an efficient tool for the study of chromosome structure, organization, and evolution among any wild Triticeae species with non‐sequenced genomes. Significance Statement: We developed seven oligonucleotide pools based on single‐copy sequences on seven chromosomes of barley (Hordeum vulgare L.) and corresponding collinear regions of wheat (Triticum aestivum L.). The approach has greatly improved the resolution of chromosome identification for high‐throughput karyotyping of representative wild Triticeae species and the probes enable to characterize chromosome rearrangements for wheat‐alien transfer and evolutionary studies. [ABSTRACT FROM AUTHOR]

Summary: Meiotic recombination rates vary considerably between species, populations and individuals. The genetic exchange between homologous chromosomes plays a major role in evolution by breaking linkage between advantageous and deleterious alleles in the case of introgressions. Identifying recombination rate modifiers is thus of both fundamental and practical interest to understand and utilize variation in meiotic recombination rates.We investigated recombination rate variation in a large intraspecific hybrid population (named HEB‐25) derived from a cross between domesticated barley and 25 wild barley accessions.We observed quantitative variation in total crossover number with a maximum of a 1.4‐fold difference between subpopulations and increased recombination rates across pericentromeric regions. The meiosis‐specific α‐kleisin cohesin subunit REC8 was identified as a candidate gene influencing crossover number and patterning. Furthermore, we quantified wild barley introgression patterns and revealed how local and genome‐wide recombination rate variation shapes patterns of introgression.The identification of allelic variation in REC8 in combination with the observed changes in crossover patterning suggest a difference in how chromatin loops are tethered to the chromosome axis, resulting in reduced crossover suppression across pericentromeric regions. Local and genome‐wide recombination rate variation is shaping patterns of introgressions and thereby directly influences the consequences of linkage drag. [ABSTRACT FROM AUTHOR]

Summary: Plant breeding applications exploiting meiotic mutant phenotypes (like the increase or decrease of crossover (CO) recombination) have been proposed over the last years. As recessive meiotic mutations in breeding lines may affect fertility or have other pleiotropic effects, transient silencing techniques may be preferred. Reverse breeding is a breeding technique that would benefit from the transient downregulation of CO formation. The technique is essentially the opposite of plant hybridization: a method to extract parental lines from a hybrid. The method can also be used to efficiently generate chromosome substitution lines (CSLs). For successful reverse breeding, the two homologous chromosome sets of a heterozygous plant must be divided over two haploid complements, which can be achieved by the suppression of meiotic CO recombination and the subsequent production of doubled haploid plants. Here we show the feasibility of transiently reducing CO formation using virus‐induced gene silencing (VIGS) by targeting the meiotic gene MSH5 in a wild‐type heterozygote of Arabidopsis thaliana. The application of VIGS (rather than using lengthy stable transformation) generates transgene‐free offspring with the desired genetic composition: we obtained parental lines from a wild‐type heterozygous F1 in two generations. In addition, we obtained 20 (of the 32 possible) CSLs in one experiment. Our results demonstrate that meiosis can be modulated at will in A. thaliana to generate CSLs and parental lines rapidly for hybrid breeding. Furthermore, we illustrate how the modification of meiosis using VIGS can open routes to develop efficient plant breeding strategies. [ABSTRACT FROM AUTHOR]

Meiotic recombination is a key step in meiosis because it facilitates the pairing of homologous chromosomes and generates new combinations of genetic alleles, which results in the diversification of extant eukaryotes. Spo11, a meiosis‐specific protein, catalyses the formation of double‐strand breaks (DSBs) and initiates meiotic recombination in a wide variety of organisms, but the exact function of spo11 in the formation of gametes needs further study in fish. In this study, we knocked out the spo11 gene in zebrafish using CRISPR/Cas9 technology. Sexually dimorphic reproductive defects were found in the spo11‐mutated zebrafish. The spo11‐/‐ males were completely sterile, but spo11‐/‐ females were fertile and there was no significant difference in relative fecundity and fertilisation rates compared with WT females; however, the offspring of spo11‐/‐ females had severe developmental defects. In addition, we found that spo11 was expressed only in gonad tissue, and the level of expression in the testes was much higher than in the ovaries. Surprisingly, spo11 was also expressed in zebrafish embryos, especially at the dome stage. We compared amino acid sequences of Spo11 in ten different fish and found that Spo11 was highly conserved. Importantly, the results established zebrafish as a vertebrate model for understanding multiple roles of spo11 in meiosis. [ABSTRACT FROM AUTHOR]

During meiosis, DNA double‐strand breaks undergo interhomolog repair to yield crossovers between homologous chromosomes. To investigate how interhomolog sequence polymorphism affects crossovers, we sequenced multiple recombinant populations of the model plant Arabidopsis thaliana. Crossovers were elevated in the diverse pericentromeric regions, showing a local preference for polymorphic regions. We provide evidence that crossover association with elevated diversity is mediated via the Class I crossover formation pathway, although very high levels of diversity suppress crossovers. Interhomolog polymorphism causes mismatches in recombining molecules, which can be detected by MutS homolog (MSH) mismatch repair protein heterodimers. Therefore, we mapped crossovers in a msh2 mutant, defective in mismatch recognition, using multiple hybrid backgrounds. Although total crossover numbers were unchanged in msh2 mutants, recombination was remodelled from the diverse pericentromeres towards the less‐polymorphic sub‐telomeric regions. Juxtaposition of megabase heterozygous and homozygous regions causes crossover remodelling towards the heterozygous regions in wild type Arabidopsis, but not in msh2 mutants. Immunostaining showed that MSH2 protein accumulates on meiotic chromosomes during prophase I, consistent with MSH2 regulating meiotic recombination. Our results reveal a pro‐crossover role for MSH2 in regions of higher sequence diversity in A. thaliana. Synopsis: Meiotic DNA double‐strand breaks undergo interhomolog repair to yield crossovers between homologous chromosomes. Sequencing of polymorphisms in wild‐type and mutant plants reveals an unexpected pro‐crossover role of the mismatch repair protein MSH2 in regions of higher relative sequence diversity. Meiotic crossovers are positively associated with interhomolog polymorphism both at chromosome level and fine scales in Arabidopsis.Class I crossovers mediate association of recombination with diversity – although very high polymorphism levels suppress crossovers.Total crossover numbers are unchanged in msh2 mutants, but recombination is remodelled from the diverse pericentromeres towards the less polymorphic sub‐telomeres.Juxtaposition of megabase‐scale heterozygous and homozygous regions causes crossover remodeling towards the heterozygous regions, which is MSH2‐dependent. [ABSTRACT FROM AUTHOR]

Research over the last two decades has identified a group of meiosis‐specific proteins, consisting of budding yeast Spo13, fission yeast Moa1, mouse MEIKIN, and Drosophila Mtrm, with essential functions in meiotic chromosome segregation. These proteins, which we call meiosis I kinase regulators (MOKIRs), mediate two major adaptations to the meiotic cell cycle to allow the generation of haploid gametes from diploid mother cells. Firstly, they promote the segregation of homologous chromosomes in meiosis I (reductional division) by ensuring that sister kinetochores face towards the same pole (mono‐orientation). Secondly, they safeguard the timely separation of sister chromatids in meiosis II (equational division) by counteracting the premature removal of pericentromeric cohesin, and thus prevent the formation of aneuploid gametes. Although MOKIRs bear no obvious sequence similarity, they appear to play functionally conserved roles in regulating meiotic kinases. Here, the known functions of MOKIRs are reviewed and their possible mechanisms of action are discussed. Also see the video abstract here https://youtu.be/tLE9KL89bwk. [ABSTRACT FROM AUTHOR]

Summary: MicroRNA resources in sheep are limited compared with those in other domesticated mammalian species. By sequencing small RNAs of sheep corpus luteum and endometrium, we have generated the largest amount of miRNA‐seq data and compiled the most comprehensive list thus far of miRNAs (n = 599) in sheep. Additionally, we observed a highly conserved maternally imprinted cluster of miRNAs on chromosome 18 homologous to that found on chromosome 14 in human and several other eutherian mammals. [ABSTRACT FROM AUTHOR]

Background: Prezygotic de novo mutations may be inherited from parents with germline mosaicism and are often overlooked when the resulting phenotype affects only one child. We aimed to identify paternal germline mosaicism in an index family and provide a strategy to determine germline mosaicism.' Methods: Whole‐exome sequencing was performed on an Alport syndrome‐affected child. Variants were validated using Sanger sequencing in the pedigree analysis. An apparent de novo mutation was tested by next‐generation sequencing (NGS) following chromosome microdissection of the mutant region (MicroSeq) to clarify its homologous chromosome source. Mosaic mutation in sperm samples was detected using targeted next‐generation sequencing (TNGS). Self‐prepared mosaic DNA samples of the 3% and 0.1% mutant fractions were used to evaluate the TNGS detection sensitivity. Results: Two novel heterozygous variants, maternally inherited c.1322delT (p.Ile441Thrfs*17) and the de novo mutation c.2939T>A (p.Leu980Ter), in the COL4A3 gene were discovered in the propositus. MicroSeq identified c.2939T>A in the paternal chromosome, which was in trans with c.1322delT. The frequency of c.2937A was 2.65% in the father's sperm sample. We also showed that a 500X depth coverage may detect a mosaic mutation with an allele frequency as low as 2%–3% using TNGS. Conclusion: MicroSeq is a valuable tool to identify the allele source of de novo mutations in a single patient. TNGS can be used to assess the mosaic ratios of known sites. We provided a systematic algorithm to detect germinal mosaicism in a single patient. This algorithm may have implications for genetic and reproductive counseling on germline mosaicism. [ABSTRACT FROM AUTHOR]

SUMMARY: The manipulation of meiotic recombination in crops is essential to develop new plant varieties rapidly, helping to produce more cultivars in a sustainable manner. One option is to control the formation and repair of the meiosis‐specific DNA double‐strand breaks (DSBs) that initiate recombination between the homologous chromosomes and ultimately lead to crossovers. These DSBs are introduced by the evolutionarily conserved topoisomerase‐like protein SPO11 and associated proteins. Here, we characterized the homoeologous copies of the SPO11‐1 protein in hexaploid bread wheat (Triticum aestivum). The genome contains three SPO11‐1 gene copies that exhibit 93–95% identity at the nucleotide level, and clearly the A and D copies originated from the diploid ancestors Triticum urartu and Aegilops tauschii, respectively. Furthermore, phylogenetic analysis of 105 plant genomes revealed a clear partitioning between monocots and dicots, with the seven main motifs being almost fully conserved, even between clades. The functional similarity of the proteins among monocots was confirmed through complementation analysis of the Oryza sativa (rice) spo11‐1 mutant by the wheat TaSPO11‐1‐5D coding sequence. Also, remarkably, although the wheat and Arabidopsis SPO11‐1 proteins share only 55% identity and the partner proteins also differ, the TaSPO11‐1‐5D cDNA significantly restored the fertility of the Arabidopsis spo11‐1 mutant, indicating a robust functional conservation of the SPO11‐1 protein activity across distant plants. These successful heterologous complementation assays, using both Arabidopsis and rice hosts, are good surrogates to validate the functionality of candidate genes and cDNA, as well as variant constructs, when the transformation and mutant production in wheat is much longer and more tedious. Significance Statement: We analyzed the three homoeologous copies of the SPO11‐1 gene found in the bread wheat genome. They are very similar but not identical, revealing their parental origin from diploid wheats. These SPO11‐1 proteins contain seven essential and evolutionarily conserved motifs, now found in 105 plant species. The coding sequence of the wheat D copy significantly complemented the rice and Arabidopsis spo11‐1 mutants, indicating strong functional conservation between highly divergent species. [ABSTRACT FROM AUTHOR]

Mastitis is a common inflammatory infectious disease in dairy cows. To understand the microRNA (miRNA) expression profile changes during bovine mastitis, we undertook a genome‐wide miRNA study of normal milk and milk that tested positive on the California mastitis test for bovine mastitis (CMT+). Twenty‐five miRNAs were differentially expressed (23 miRNAs upregulated and two downregulated) during bovine mastitis relative to their expression in normal milk. Upregulated mature miR‐1246 probably derived from a U2 small nuclear RNA rather than an miR‐1246 precursor. The significantly upregulated miRNA precursors and RNU2 were significantly enriched on bovine chromosome 19, which is homologous to human chromosome 17. A gene ontology analysis of the putative mRNA targets of the significantly upregulated miRNAs showed that these miRNAs were involved in binding target mRNA transcripts and regulating target gene expression, and a Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the upregulated miRNAs were predominantly related to cancer and immune system pathways. Three novel miRNAs were associated with bovine mastitis and were relatively highly expressed in milk. We confirmed that one of the novel mastitis‐related miRNAs was significantly upregulated using a digital PCR system. The differentially expressed miRNAs were involved in human cancers, infections, and immune‐related diseases. The genome‐wide analysis of miRNA profiles in this study provides insight into bovine mastitis and inflammatory diseases. Databases: The miRNAseq generated for this study can be found in the Sequence Read Archive (SRA) under BioProject Number PRJNA421075 and SRA Study Number SRP126134 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA421075). [ABSTRACT FROM AUTHOR]

Summary: During meiosis, recombination ensures allelic exchanges through crossovers (COs) between the homologous chromosomes. Advances in our understanding of the rules of COs have come from studies of mutations including structural chromosomal rearrangements that, when heterozygous, are known to impair COs in various organisms. In this work, we investigate the effect of a large heterozygous pericentric inversion on male and female recombination in Arabidopsis. The inversion was discovered in the Atmcc1 mutant background and was characterized through genetic and next‐generation sequencing analysis. Reciprocal backcross populations, each consisting of over 400 individuals, obtained from the mutant and the wild type, both crossed with Landsberg erecta, were analyzed genome‐wide by 143 single‐nucleotide polymorphisms. The negative impact of inversion became evident in terms of CO loss in the rearranged chromosome in both male and female meiosis. No single‐CO event was detected within the inversion, consistent with a post‐meiotic selection operating against unbalanced gametes. Cytological analysis of chiasmata in F1 plants confirmed that COs were reduced in male meiosis in the chromosome with inversion. Crossover suppression on the rearranged chromosome is associated with a significant increase of COs in the other chromosomes, thereby maintaining unchanged the number of COs per cell. The CO pattern observed in our study is consistent with the interchromosomal (IC) effect as first described in Drosophila. In contrast to male meiosis, in female meiosis no IC effect is visible. This may be related to the greater strength of interference that constrains the CO number in excess of the minimum value imposed by CO assurance in Arabidopsis female meiosis. Significance Statement: This work provides further information into the poorly described phenomenon of the interchromosomal (IC) effect in plants. Indeed, the few studies on this phenomenon in maize date back to the 1960s and 1970s and have low resolution, being limited to a few specific regions and genetic markers. In this paper we underscore the significance for plant scientists of the IC effect during meiosis and provide more detailed data and analyses. [ABSTRACT FROM AUTHOR]