G3: Genes|Genomes|Genetics最新文献

Understanding the genetic basis of domestication-related traits (DRTs) is crucial for crop improvement. In this study, we developed an interspecific backcross population by crossing the elite cowpea variety Sam with a wild accession of Vigna unguiculata var. spontanea from Senegal. Using a mid-density single nucleotide polymorphism panel, we constructed a high-quality genetic linkage map consisting of 1,046 polymorphic markers spanning 1,131.6 cM across 11 chromosomes and used it as a framework for dissecting the genetic architecture of key DRTs. Over 2 consecutive years, we identified 65 quantitative trait loci (QTLs) associated with 17 key domestication traits, with 73.8% of these QTLs consistently detected across both years. Notably, we observed a significant clustering of domestication-related QTLs within 4 major genomic regions on chromosomes Vu01, Vu03, Vu08, and Vu09, particularly for organ size and phenological traits. The co-location of QTLs for traits such as pod shattering, growth habit, and flowering time suggests pleiotropy or potential co-selection of linked genes during domestication. Furthermore, our findings support the hypothesis of 2 independent domestication events in cowpea, as evidenced by similarities as well as differences in QTL regions between our study and previous reports. We hypothesized that common as well as different loci may have been selected during the 2 independent domestication events of cowpea, paralleling the dual domestication in common beans. While wild cowpea species contributed limited major-effect QTLs for yield-related traits, they remain an essential reservoir of genetic diversity, particularly for pest and disease resistance. These insights enhance our understanding of cowpea domestication and offer valuable genetic resources for breeding programs.

Phytophthora theobromicola is an emerging cacao pathogen recently identified in Brazil as an aggressive agent of black pod rot. We generated genome assemblies for two P. theobromicola isolates using long-read sequencing and five additional isolates using short reads. Comparative analysis revealed a genome size and predicted gene content comparable to P. citrophthora, a closely related species with a broad host range that includes both citrus and cacao. An intraspecies sequence-graph analysis revealed a highly dynamic genome structure with high proportion of variable effectors. Syntenic orthology analysis across 13 Phytophthora species identified orthologous gene groups conserved only in cacao pathogens and others specific to P. theobromicola. RxLR effectors and CAZymes were particularly enriched among lineage-specific syntenic groups, with RxLRs preferentially located near transposable elements and within gene-sparse, repeat-rich regions. Transcriptome analysis of infected cacao tissues showed that 88% of predicted effectors were expressed, with pods exhibiting the highest number of upregulated genes. Notably, several RxLRs classified as P. theobromicola-specific syntenic orthologs were highly expressed in infected tissues, suggesting that these lineage-specific effectors may play key roles in host-pathogen interactions unique to cacao. Together, our findings highlight the dynamic architecture and functional plasticity of the P. theobromicola genome, providing foundational insights into its virulence strategies and supporting future studies on host adaptation and effector evolution in emerging cacao pathogens.

Phakopsora pachyrhizi, the causal agent of soybean rust disease (SBR) on Glycine max (soybean), is considered one of the most globally devastating diseases of soybeans and is a particular problem in Brazil, China, Sub-Saharan Africa, and the southern United States. To better understand genetic diversity and epidemiological history of SBR in the United States, 49 P. pachyrhizi isolates collected from soybean fields in four Southeastern states (Alabama, Florida, Georgia, and Louisiana) from the 2008 to 2017 growing seasons were genotyped through restriction site-associated genotype by sequencing (GBS). Rarefaction analysis identified 54 informative SNPs among the P. pachyrhizi isolates. We found no evidence suggesting sexual or parasexual recombination, and measurements of genetic diversity were low to moderately low. Multiple different statistical approaches, including neighbor-joining trees, K-means hierarchical clustering, discriminant analysis of principal components, and principal coordinates analysis (PCoA) all identified two groups of P. pachyrhizi genotypes that associated with geographic location. One group was composed of isolates from south Georgia, and the other with isolates from Alabama, Florida, Georgia (excluding south Georgia), and Louisiana. Our results suggest that two genetically related but distinct genotypes were introduced to the continental United States in a two-phase introduction and overwinter in South Georgia and Florida. The first introduction of one genotype likely occurred in South Georgia in 2004 followed by a later introduction of a second genotype. One genotype remained in South Georgia while the other genotype became established through the Southeastern United States. Future studies are necessary to determine whether SBR in Brazil, China, or Sub-Saharan Africa shows similar patterns of genotype distribution and history or if the United States situation is unique.

By combining chromatin immunoprecipitation (ChIP) with an exonuclease digestion of protein-bound DNA fragments, ChIP-exo characterizes genome-wide protein-DNA interactions at near basepair resolution. However, the widespread adoption of ChIP-exo has been hindered by several technical challenges, including lengthy protocols, the need for multiple custom reactions, and incompatibilities with recent Illumina sequencing platforms. To address these barriers, we systematically optimized and adapted the ChIP-exo library construction protocol for the unique requirements of mammalian cells and current sequencing technologies. We introduce a mammalian-optimized ChIP-exo (MO-ChIP-exo) protocol that builds upon previous ChIP-exo protocols with systematic optimization of crosslinking, harvesting, and library construction. We validate MO-ChIP-exo by comparing it with previously published ChIP-exo protocols and demonstrate its adaptability to both suspension (K562) and adherent (HepG2, mESC) cell lines. This improved protocol provides a more robust and efficient method for generating high-quality ChIP-exo libraries from mammalian cells.

During Drosophila courtship, males chase and sing to females, while females perform abdominal behaviors to indicate their willingness to mate. The nerve cord circuits in females that produce their abdominal behaviors are poorly characterized. We recently identified an anatomically diverse population of abdominal interneurons called the dissatisfaction (dsf)- and doublesex-expressing abdominal ganglion (DDAG) neurons that influence several female mating behaviors. Here, we searched the dsf locus for cis-regulatory enhancer fragments that regulate its spatial expression in the adult and larval central nervous system. We found several enhancers, most located within 2 introns, that drove reporter expression in subsets of dsf-expressing neurons throughout the brain and nerve cord. Using one of these enhancers, we genetically isolated a single subtype of female-specific DDAG local interneurons. Optogenetic activation of these neurons triggered vaginal plate opening in both unmated and mated females, a behavior used by Drosophila females to signal receptivity to courting males. Our findings offer new reagents to target dsf-expressing cells and new insights into the neural substrates in Drosophila females that express their mating decisions during courtship.

Ansell's mole-rat (Fukomys anselli) is an African rodent known for its subterranean lifestyle and unique phenotypic traits, including extreme longevity, magnetoreception, and a cooperative breeding social structure. Efforts to dissect the genetic architecture of these traits and to decipher their phylogenetic relationships within the broader African mole-rat family would greatly benefit from a reference-grade genome. Here, we report a first genome assembly of a male Ansell's mole-rat. By combining Oxford Nanopore Technologies long reads and Illumina short reads with Hi-C data, we generated a chromosome level assembly with a total length of 2.27 Gb, 412 scaffolds, and a scaffold N50 of 72.4 Mb. We identified 99.54% of expected genes and annotated 29,094 transcripts using RNA sequencing data. This high-quality de novo genome of F. anselli lays the foundation for dissecting the genetic and evolutionary basis of its extraordinary traits and resolving African mole-rat phylogeny.

Many traditional cider apples (Malus domestica) have unique chemotypic traits that impact the sensory profile and fermentation characteristics of the final product. In particular, cider apples may have greater polyphenol, organic acid, and sugar concentration than fresh-market apples. Despite historic importance and a growing market in many parts of the world, the genetic basis underlying cider apple fruit quality remains poorly understood. Therefore, few functional genetic markers have been successfully adapted for cider apple breeding. Using a genome-wide association study on 253 cider apple accessions from the USDA Malus collection, we identified 19 significant marker-trait associations for fruit quality traits. Notably, we identified a distinct marker on chromosome 15 that was strongly associated with total polyphenols, a key determinant of bitterness and astringency. A major association on chromosome 16, near the Ma1 locus, explained a substantial proportion of the phenotypic variance for titratable acidity and pH, confirming the importance of this region. Using these 2 loci, we were able to distinguish between cider apple groups, especially for bittersweet apples. A major locus on chromosome 1 was linked to the ratio of glucose and sucrose. This locus could be targeted to select genotypes with increased glucose content, which could improve fermentation kinetics. Overall, these results provide a robust genetic analysis focusing on quality traits in a cider-specific germplasm, laying the foundation for identifying apple cultivars with desirable attributes for cider production from germplasm collections and for making marker-assisted selections within breeding programs.

Solanum microdontum Bitter is a diploid wild Andean relative of potato that has shaped the domestication and adaptation of modern cultivated potato to diverse environments. S. microdontum has the potential to provide a wealth of untapped genetic material for use in addressing current challenges in potato breeding. Here, we report a high-quality 772 Mb reference genome sequence for S. microdontum that is anchored to 12 chromosomes. The resulting genome assembly has 99.0% complete benchmarking universal single copy orthologs and an N50 scaffold length of over 57 Mb, indicating a high level of completeness. Annotation of the assembly resulted in the identification of 37,324 protein-coding genes and 65% repetitive sequence. A total of 1,187 nucleotide-binding leucine-rich repeat genes were predicted from the assembly, of which, 93.1% overlapped an annotated high-confidence gene model. A k-mer-based kinship matrix derived from a 107-member S. microdontum diversity panel revealed an underlying population structure that corresponds to geographic proximity. The S. microdontum dataset enhances publicly available potato genome resources by providing breeders with genetic, molecular, and germplasm resources for newly developed diploid potato breeding programs.

The ability of oocytes to maintain their quality is essential for successful reproduction. One critical aspect of oocyte quality and successful embryogenesis after fertilization is the proper regulation of the stores of maternal mRNA by RNA-binding proteins. Many RNA-binding proteins undergo regulated phase transitions during oogenesis, and alterations of the protein phase can disrupt its ability to regulate mRNA stability and translation. In Caenorhabditis elegans, regulators of RNA-binding protein phase transitions in maturing oocytes of young adult hermaphrodites remain poorly characterized. However, a few recently identified genes are also required for the clearance of damaged proteins during maturation, suggesting coordination between these processes. To explore this relationship and gain insight into the regulation of phase transitions, we conducted a targeted RNAi screen of genes required for removal of protein aggregates in maturing oocytes. Here, we identify 6 novel regulators of phase transitions of the KH-domain protein MEX-3. We present strong evidence that the regulation of MEX-3 phase transitions in the oocyte overlaps with, but is distinct from, the regulatory network of protein aggregate clearance.