Author: slquinlan

PLoS Genet. 2025 Jul 16;21(7):e1011742. doi: 10.1371/journal.pgen.1011742. Online ahead of print.

ABSTRACT

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used genotype-by-sequencing data to score more than 10,000 maize and teosinte lines for the presence or absence of each driver. Fewer than ~0.5% of modern inbred lines carry chromosomal drivers. In contrast, among individuals from 5331 open-pollinated landraces, 6.32% carried Ab10, 5.16% carried K10L2, and 12.28% carried at least one B chromosome. These frequencies are consistent with those reported in previous studies. Using a GWAS approach we identified unlinked loci that associate with the presence or absence of the selfish genetic elements. Many significant SNPs are positively associated with the drivers, suggesting that there may have been selection for alleles that ameliorate their negative fitness consequences. We then assessed the contributions of population structure, associated loci, and the environment on the distribution of each chromosomal driver. There was no significant relationship between any chromosomal driver and altitude, contrary to conclusions based on smaller studies. Our data suggest that the distribution of the major chromosomal drivers is primarily influenced by neutral processes and the deleterious fitness consequences of the drivers themselves. While each driver has a unique relationship to genetic background and the environment, they are largely unconstrained by either.

PMID:40668866 | DOI:10.1371/journal.pgen.1011742

Front Plant Sci. 2025 Jun 30;16:1588485. doi: 10.3389/fpls.2025.1588485. eCollection 2025.

ABSTRACT

Pearl millet [Cenchrus americanus (L.) Morrone, formerly Pennisetum glaucum (L.) R. Br.] is the sixth most important cereal globally and is used for forage and feed in the U.S. To identify genomic regions governing important physiological, agronomic and yield related traits, a recombinant inbred line population derived from the cross between Tift 99D₂B_{1 ×} Tift 454 was phenotyped in the field in 2006, 2007 and 2013. In addition, the population was phenotyped for root-knot nematode resistance in the greenhouse during 2009. Using a previously generated genetic map containing 505 single nucleotide polymorphism markers and composite interval mapping, we identified 45 QTLs for eight traits (plant height, stem diameter, days to heading, panicle diameter, panicle length, 1000 seed weight, Pyricularia leaf spot disease, and root-knot nematode egg mass) across almost all linkage groups. These QTLs explained 6.31 to 32.51% of phenotypic variance for each trait and were consistently detected over different environments. Plant height and days to heading were colocalized on LG2 and LG5 showing maturity and plant height are linked and influence each other, similarly to other cereal crops. Interestingly, 5 of 19 QTLs linked to plant height, stem diameter, panicle diameter, and panicle length colocalized to the same locations on LG3, indicating breeding for one trait could simultaneously improve the other. The markers and genes identified in the present study can be used in developing high yielding pearl millet varieties using marker-assisted selection.

PMID:40661761 | PMC:PMC12256767 | DOI:10.3389/fpls.2025.1588485

Mol Ecol. 2025 Jul 15:e70024. doi: 10.1111/mec.70024. Online ahead of print.

ABSTRACT

Understanding the impact of domestication on deleterious mutations has fascinated evolutionary biologists and breeders alike. A ‘cost of domestication’ has been reported for some organisms through accumulation of gene disruptions or radical amino acid changes. However, recent evidence paints a more complex picture of this phenomenon in different domesticated species. In this study, we used genomic sequences of 253 tomato accessions to investigate the evolution of deleterious mutations and genomic structural variants (SVs) through tomato domestication history. We apply phylogeny-based methods to identify deleterious mutations in the domesticated tomato as well as its semi-wild and wild relatives. Our results implicate a downward trend throughout domestication in the number of genetic variants, regardless of their functional impact. This suggests that demographic factors have reduced overall genetic diversity, leading to lower deleterious load and SVs as well as loss of some beneficial alleles during tomato domestication. However, we detected an increase in proportions of nonsynonymous and deleterious alleles (relative to synonymous and neutral nonsynonymous alleles, respectively) during the initial stage of tomato domestication in Ecuador. Additionally, deleterious alleles in the commonly cultivated tomato seem to be more frequent than expected under a neutral hypothesis of molecular evolution. Our analyses also revealed frequent deleterious alleles in several well-studied tomato genes, probably involved in response to biotic and abiotic stress as well as fruit development and flavour regulation. To provide a practical guide for breeding experiments, we created TomDel, a public searchable database of 21,162 potentially deleterious alleles identified in this study (hosted on the Solanaceae Genomic Network; https://solgenomics.net/).

PMID:40662302 | DOI:10.1111/mec.70024

Plants (Basel). 2025 Jun 24;14(13):1937. doi: 10.3390/plants14131937.

ABSTRACT

Advances in spinning technology have increased the demand for upland cotton (Gossypium hirsutum L.) cultivars with superior fiber quality. However, progress in breeding for traits such as fiber length is constrained by limited phenotypic and genetic diversity within upland cotton. Introgression from Gossypium barbadense, a closely related species known for its superior fiber traits, offers a promising strategy. Sealand 883 is an obsolete upland germplasm developed through G. barbadense introgression and is known for its long and fine fibers. Previous studies have identified a fiber length quantitative trait locus (QTL) on Chromosome 25, designated qFL–Chr.25, in Sealand 883, conferred by an allele introgressed from G. barbadense. This study evaluated the effect of qFL–Chr.25 in near-isogenic introgression lines (NIILs) using Advanced Fiber Information System (AFIS) measurements. Across four genetic backgrounds, NIILs carrying qFL–Chr.25 consistently exhibited longer fibers, as reflected in multiple length parameters, including UHML, L(n), L(w), UQL(w), and L5%. Newly developed TaqMan SNP diagnostic markers flanking the QTL enable automated, reproducible, and scalable screening of large populations typical in commercial breeding programs. These markers will facilitate the incorporation of qFL–Chr.25 into commercial breeding pipelines, accelerating fiber quality improvement and enhancing the competitiveness of cotton against synthetic fibers.

PMID:40647946 | PMC:PMC12251603 | DOI:10.3390/plants14131937

Plants (Basel). 2025 Jul 7;14(13):2082. doi: 10.3390/plants14132082.

ABSTRACT

Cotton is the most widely cultivated natural fiber crop worldwide, yet it is highly susceptible to various diseases and pests that significantly compromise both yield and quality. To enable rapid and accurate diagnosis of cotton diseases and pests-thus supporting the development of effective control strategies and facilitating genetic breeding research-we propose a lightweight model, the Resource-efficient Cotton Network (RF-Cott-Net), alongside an open-source image dataset, CCDPHD-11, encompassing 11 disease categories. Built upon the MobileViTv2 backbone, RF-Cott-Net integrates an early exit mechanism and quantization-aware training (QAT) to enhance deployment efficiency without sacrificing accuracy. Experimental results on CCDPHD-11 demonstrate that RF-Cott-Net achieves an accuracy of 98.4%, an F1-score of 98.4%, a precision of 98.5%, and a recall of 98.3%. With only 4.9 M parameters, 310 M FLOPs, an inference time of 3.8 ms, and a storage footprint of just 4.8 MB, RF-Cott-Net delivers outstanding accuracy and real-time performance, making it highly suitable for deployment on agricultural edge devices and providing robust support for in-field automated detection of cotton diseases and pests.

PMID:40648091 | PMC:PMC12252015 | DOI:10.3390/plants14132082

Tree Physiol. 2025 Jul 11:tpaf081. doi: 10.1093/treephys/tpaf081. Online ahead of print.

ABSTRACT

The success of CRISPR genome editing studies depends critically on the precision of guide RNA (gRNA) design. Sequence polymorphisms in outcrossing tree species pose design hazards that can render CRISPR genome editing ineffective. Despite recent advances in tree genome sequencing with haplotype resolution, sequence polymorphism information remains largely inaccessible to various functional genomics research efforts. The Populus VariantDB v3.2 addresses these challenges by providing a user-friendly search engine to query sequence polymorphisms of heterozygous genomes. The database accepts short sequences, such as gRNAs and primers, as input for searching against multiple poplar genomes, including hybrids, with customizable parameters. We provide examples to showcase the utilities of VariantDB in improving the precision of gRNA or primer design. The platform-agnostic nature of the probe search design makes Populus VariantDB v3.2 a versatile tool for the rapidly evolving CRISPR field and other sequence-sensitive functional genomics applications. The database schema is expandable and can accommodate additional tree genomes to broaden its user base.

PMID:40643191 | DOI:10.1093/treephys/tpaf081

Tree Physiol. 2025 Jul 11:tpaf080. doi: 10.1093/treephys/tpaf080. Online ahead of print.

ABSTRACT

Sulfate-proton co-transporters (SULTRs) mediate sulfate uptake, transport, storage, and assimilation in plants. The SULTR family has historically been classified into four groups (SULTR1-SULTR4), with well-characterized roles for SULTR groups 1, 2, and 4. However, the functions of the large and diverse SULTR3 group remain poorly understood. Here, we present an updated phylogenetic analysis of SULTRs across angiosperms, including multiple early-divergent lineages. Our results suggest that the enigmatic SULTR3 group comprises four distinct subfamilies that predate the emergence of angiosperms, providing a basis for reclassifying the SULTR family into seven subfamilies. This expanded classification is supported by subfamily-specific gene structures and amino acid substitutions in the substrate-binding pocket. Structural modeling identified three serine residues uniquely lining the substrate-binding pocket of SULTR3.4, enabling three hydrogen bonds with the phosphate ion. The data support the proposed neofunctionalization of this subfamily for phosphate allocation within vascular tissues. Transcriptome analysis of Populus tremula × alba revealed divergent tissue expression preferences among SULTR subfamilies and between genome duplicates. We observed partitioned expression in vascular tissues among the four SULTR3 subfamilies, with PtaSULTR3.4a and PtaSULTR3.2a preferentially expressed in primary and secondary xylem, respectively. Gene coexpression analysis revealed coordinated expression of PtaSULTR3.4a with genes involved in phosphate starvation responses and nutrient transport, consistent with a potential role in phosphate homeostasis. In contrast, PtaSULTR3.2a was strongly coexpressed with lignification and one-carbon metabolism genes and their upstream transcription regulators. PtaSULTR3.2a belongs to a eudicot-specific branch of the SULTR3.1 subfamily found only in perennial species, suggesting a specialized role in lignifying tissues. Together, our findings provide a refined phylogenetic framework for the SULTR family and suggest that the expanded SULTR3 subfamilies have undergone neofunctionalization during the evolution of vascular and perennial plants.

PMID:40643194 | DOI:10.1093/treephys/tpaf080

J Gen Virol. 2025 Jul;106(7). doi: 10.1099/jgv.0.002119.

ABSTRACT

Orthotospovirus tomatomaculae [tomato spotted wilt virus (TSWV)] is a major pathogen in horticultural and row crops worldwide including the USA. In this study, tomato spotted wilt disease incidence was monitored in Arachis hypogaea (peanut; year 1990 to 2024) and Nicotiana tabacum (tobacco; year 2000 to 2024) in commercial farmers’ fields in the Southeastern USA. Furthermore, nucleocapsid (N), nonstructural movement (NSm) and nonstructural silencing suppressor (NSs) protein gene sequences of TSWV global populations from North America, South America, Europe, Asia-Pacific, Africa and Australia were compared with local US population and analysed to understand the genetic variability in the virus genome. In our study, full-length sequences of 94 N, 111 NSm and 78 NSs genes were amplified from TSWV-infected A. hypogaea (peanut), Capsicum annuum (pepper), N. tabacum (tobacco) and Solanum lycopersicum (tomato). nt-based phylogenetic analysis of N, NSm and NSs genes correlated with the geographical location of the TSWV isolates, with notably higher substitution rates in the population of recent years. In addition, the least genetic variability was observed in the N gene of the local population upon comparison with other global TSWV population. The neutrality test of TSWV suggested a non-neutral evolution of the virus genome. Low variation among the selected genes might be attributed to strong purifying selection pressure in the populations. Furthermore, estimation of selection pressure (dN/dS) on small (S) segment-encoded N protein and nonstructural protein showed higher purifying selection than the movement protein encoded by the medium (M) segment of the TSWV isolates. Single-likelihood ancestor counting suggested an overall negative selection pressure on several codons of the selected genes, which indicated that natural selection and population bottleneck events might have influenced the evolution of TSWV. Our study also deciphered high gene flow and low genetic differentiation amid the different TSWV population sets. Additionally, BEAST analysis of TSWV N gene sequences from GA predicted the most common recent ancestor existed ~25 years ago. This data was further correlated with disease incidence data from peanut and tobacco crops obtained in the last three decades. These findings suggest the intermixing of TSWV isolates between peanut, pepper, tobacco and tomato crops, while the virus genome has undergone strong purifying selection.

PMID:40622855 | DOI:10.1099/jgv.0.002119

Plant J. 2025 Jul;123(1):e70304. doi: 10.1111/tpj.70304.

ABSTRACT

Targeted demethylation by DNA glycosylases (DNGs) results in differential methylation between parental alleles in the endosperm, which drives imprinted expression. Here, we performed RNA sequencing on endosperm derived from DNG mutant mdr1 and wild-type (WT) endosperm. Consistent with the role of DNA methylation in gene silencing, we find 108 genes and 96 TEs differentially expressed (DE) transcripts that lost expression in the hypermethylated mdr1 mutant. Compared with other endosperm transcripts, the mdr1 targets are enriched for TEs (particularly Helitrons), and DE genes are depleted for both core genes and GO term assignments, suggesting that the majority of DE transcripts are TEs and pseudo-genes. By comparing DE genes to imprinting calls from prior studies, we find that the majority of DE genes have maternally biased expression, and approximately half of all maternally expressed genes (MEGs) are DE in this study. In contrast, no paternally expressed genes (PEGs) are DE. DNG-dependent imprinted genes are distinguished by maternal demethylation and expression primarily in the endosperm, so we also performed Enzymatic Methyl-seq on hybrids to identify maternal demethylation and utilized a W22 gene expression atlas to identify genes expressed primarily in the endosperm. Overall, approximately ⅔ of all MEGs show evidence of regulation by DNGs. Taken together, this study solidifies the role of MDR1 in the regulation of maternally expressed, imprinted genes and TEs and identifies subsets of genes with DNG-independent imprinting regulation.

PMID:40587880 | DOI:10.1111/tpj.70304

BioTech (Basel). 2025 Jun 12;14(2):48. doi: 10.3390/biotech14020048.

ABSTRACT

Interspecific and intersectional crosses have introduced valuable genetic traits for blueberry (Vaccinium sect. Cyanococcus) cultivar improvement. Introgression from Vaccinium species at the diploid, tetraploid, and hexaploid levels has been found in cultivated blueberries. Continued efforts to integrate wild blueberry genetic resources into blueberry breeding are essential to broaden the genetic diversity of cultivated blueberries. However, performing heteroploid crosses among Vaccinium species is challenging. Polyploid induction through tissue culture has been useful in bridging ploidy barriers. Mixoploid or chimeric shoots often are produced, along with solid polyploid mutants. These chimeras are mostly discarded because of their genome instability and the difficulty in identifying periclinal mutants carrying germline mutations. Since induced polyploidy in blueberries often results in a low frequency of solid mutant lines, it is important to recover solid polyploids through chimera dissociation. In this study, two vegetative propagation methods, i.e., axillary and adventitious shoot induction, were evaluated for their efficiency in chimera dissociation. Significantly higher rates of chimera dissociation were found in adventitious shoot induction compared to axillary shoot induction. Approximately 89% and 82% of the adventitious shoots induced from mixoploid lines 145.11 and 169.40 were solid polyploids, respectively, whereas only 25% and 53% of solid polyploids were recovered through axillary shoot induction in these lines. Effective chimera dissociation provides useful and stable genetic materials to enhance blueberry breeding.

PMID:40558397 | DOI:10.3390/biotech14020048