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PubMed1991

The evolutionary history of D. buzzatii. XXII. Chromosomal and genic sterility in male hybrids of Drosophila buzzatii and Drosophila koepferae.

The genetic basis of sterility in F1 male hybrids of Drosophila buzzatii and D. koepferae has been investigated in two steps. (1) By successive backcrossing of hybrid females to either parental species. (2) By assessment of the effects on male fertility of selected segments of polytene chromosomes from the donor species on a background entirely derived from the recipient species. The length of introgressed segments producing sterility was progressively reduced through repeated backcrosses. This procedure sometimes led to an approximate mapping of major genes of hybrid sterility (genic sterility) on the polytene chromosome map. At other times it was found that sterility was produced only when the introgressed segment exceeded a certain threshold size (chromosomal sterility). The contribution of the autosomes to hybrid sterility seems to be mainly of the chromosomal type. The evidence concerning the X chromosome is equivocal. No fertile males were found following introgression with any of the investigated segments of this chromosome. These results are compatible both with the presence of at least six major genes of hybrid sterility (genic sterility) and with the existence of a rather small threshold size for the chromosome segments producing sterility (chromosomal sterility). The role of the Y chromosome was not investigated in this study.

Animals↗
PubMed2026

Translating functional molecular knowledge into crop-breeding success.

Historical plant breeding, which optimizes phenotypes through selective crossing guided by phenotypic evaluation and molecular markers, is limited by evolutionary constraints that hinder rapid crop improvement. A new paradigm, precision breeding, circumvents these limitations by targeting genetic variants through functional molecular knowledge. To generate this knowledge at scale, sequence-based deep learning leverages high-quality genome sequence data to predict variant effects at base-pair resolution. When linked to agronomically important traits, these predictions enable breeders to prioritize variants for precision selection or editing. Although it is still in the early stages of development, we foresee three key applications for this approach: introgressing genes from distant breeding pools, purging deleterious mutations and designing new plant ideotypes. Looking ahead, refined computational models will facilitate targeted editing and the systematic redesign of complex physiological processes to address emerging breeding goals under shifting environmental conditions.

Crops, Agricultural↗
PubMed1991

The evolutionary history of Drosophila buzzatii. XXI. Cumulative action of multiple sterility factors on spermatogenesis in hybrids of D. buzzatii and D. koepferae.

The genetic basis of sterility in male hybrids of Drosophila buzzatii and D. koepferae has been investigated by assessment of the effects on spermatogenesis of substituting separate chromosome segments of the recipient species with the homologous material from the donor species, either in heterozygous (autosomes) or hemizygous (X chromosome) condition, after successive backcrossing of hybrid females to either parental species. Introgressed segments were identified by the characteristic asynapsis of the polytene chromosomes in their heterospecific regions. Except for one case, the introgression of chromosome segments either from autosome 3, 4, or 5 brings about sterility only when the introgressed segment exceeds a minimum size (threshold size). Segments of equal size frequently produce similar abnormalities, whose severity increases with the size of the introgressed segment. Apparently, throughout these autosomes of D. buzzatii and D. koepferae there are many non-allelic, minor sterility genes, whose individual segregation cannot be recognized phenotypically, and which act cumulatively on the same characteristics of spermatogenesis, each contributing a small effect to the phenotype. Accordingly, these genes should be considered as polygenes, and the type of sterility they bring about should be properly designated polygenic sterility.

Animals↗
PubMed2026

Translating Flood-Tolerance Biology into Breeding: A 5D Framework for Next-Generation Rice Varieties.

Flooding is among the most devastating abiotic stresses limiting rice productivity. Although SUB1A introgression conferred submergence tolerance in several mega-varieties, this single-gene approach is insufficient for the diverse flood types-flash floods, stagnant floods, anaerobic germination, and deepwater inundation-progressively intensifying with climate change. Here, we review the physiological mechanisms and genetic architecture underlying tolerance to each flood type, emphasizing the dual role of reactive oxygen species (ROS) in signalling and damage, the management of elemental toxicities (Fe2+, Mn2+) under altered soil redox, and lessons from wetland species and lowland rice. We then examine why marker-assisted selection has failed for polygenic, multi-stress tolerance and identify persistent breeding bottlenecks. Building on this biological foundation, we outline an integrated 5D framework (Demand, Discovery, Design, Development, Deployment) that links gene-bank diversity, multi-omics discovery, predictive breeding and on-farm validation through continuous feedback. We discuss how connected breeding, the transition-from-trait-to-environment (TTE) strategy, and speed breeding can accelerate genetic gain, and we close with research priorities centred on the biology of multi-flood tolerance to develop climate-resilient rice.

5D breeding framework↗
PubMed2025

Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes.

The Ancestral Recombination Graph (ARG), which describes the genealogical history of a sample of genomes, is a vital tool in population genomics and biomedical research. Recent advancements have substantially increased ARG reconstruction scalability, but they rely on approximations that can reduce accuracy, especially under model misspecification. Moreover, they reconstruct only a single ARG topology and cannot quantify the considerable uncertainty associated with ARG inferences. Here, to address these challenges, we introduce SINGER (sampling and inferring of genealogies with recombination), a method that accelerates ARG sampling from the posterior distribution by two orders of magnitude, enabling accurate inference and uncertainty quantification for hundreds of whole-genome sequences. Through extensive simulations, we demonstrate SINGER's enhanced accuracy and robustness to model misspecification compared to existing methods. We demonstrate the utility of SINGER by applying it to individuals of British and African descent within the 1000 Genomes Project, identifying signals of population differentiation, archaic introgression and strong support for ancient polymorphism in the human leukocyte antigen region shared across primates.

Humans↗
PubMed2026

Population Genomics of Almond (Prunus dulcis) Reveals Region-Specific Selection and a Complex History of Domestication.

The domestication of perennial crops in the Mediterranean Basin remains unclear, particularly regarding the genomic consequences of human-mediated demographic shifts and selection. We analysed 8.1 million single nucleotide polymorphisms from 96 cultivated almond (Prunus dulcis) accessions from Europe, North America, Central Asia, and New Zealand, alongside four wild relatives. Population structure analyses revealed four geographically differentiated cultivated groups (Central Asian, North American, and two European) and three wild populations (P. spinosissima, P. orientalis, and P. fenzliana). Cultivated almonds retained high genetic diversity, consistent with weak domestication bottlenecks typical of outcrossing perennials. Elevated diversity and private allele counts in Central Asian cultivars, together with limited evidence of crop-wild gene flow, support Central Asia as an important reservoir of ancestral cultivated diversity that may have played a major role during the early stages of almond domestication. In contrast, allele sharing consistent with historical wild-to-crop introgression-especially involving P. orientalis-has contributed to the genomic composition of European and North American almonds. Genome-wide scans for selective sweeps showed most genes overlapping candidate sweep regions were population-specific, though often associated with similar biological functions, including stress responses and agronomic traits. This suggests repeated targeting of comparable pathways during and post-domestication, despite distinct selection histories. Notably, a subset of candidate genes detected in cultivated populations also occurs in wild relatives, particularly P. orientalis. This overlap is consistent with shared ancestral variation, introgression/gene flow between wild and cultivated lineages, and/or parallel adaptation. Altogether, our results support a complex domestication and diversification history for almonds, shaped by geographic expansion, gene flow with wild relatives, and recurrent selection acting in different regions. This study highlights wild relatives as important reservoirs of genetic diversity and emphasises the need for broader geographic sampling to clarify their contributions to almond domestication and adaptation.

Prunus dulcis↗
PubMedDate not supplied

Use of cellular oncogene probes to identify Morone hybrids.

We tested the ability of cellular oncogene (c-onc) probes to identify F1 hybrids and the lineage of known backcrosses within the fish genus Morone. Total DNA was isolated from five to 14 individuals per North American Morone species (striped bass, white bass, white perch, and yellow bass). The DNA was digested with two restriction enzymes, Eco RI and Hin dIII, Southern blotted, and hybridized to six different c-onc probes including v-abl, v-erb B, c-myc, c-H-ras, c-K-ras, and v-src. We found fixed genotypic differences among the four species for all six probes in single restriction enzyme digests. The heritability of these nuclear DNA genotypes was evaluated in hatchery-produced F1 Morone hybrids (striped bass x white bass and striped bass x white perch) tested with the six informative single probe/restriction enzyme combinations. All F1 individuals exhibited heterozygosity in all diagnostic nuclear DNA fragments, confirming the Mendelian inheritance of these genotypes in these fish. Furthermore, analysis of these nuclear DNA genotypes in hatchery-produced backcrosses of F1 hybrids striped bass x (white bass x striped bass) detected both recombinant and parental genotypes at all six polymorphic c-onc sequences. The lineage of suspected Morone hybrids of unknown descent collected from Lewis Smith Lake, Alabama, and from the Occoquan River, Virginia, was determined using the c-onc probes. Our results suggest that c-onc probes are suitable markers to unequivocally identify F1 hybrids and backcrosses and to quantify introgression in natural populations of fishes. The addition of RFLP analysis of mtDNA provided a complete ancestral history of individual fish.

Animals↗
PubMed1991

A novel mouse chromosome 17 hybrid sterility locus: implications for the origin of t haplotypes.

The effects of heterospecific combinations of mouse chromosome 17 on male fertility and transmission ratio were investigated through a series of breeding studies. Animals were bred to carry complete chromosome 17 homologs, or portions thereof, from three different sources-Mus domesticus, Mus spretus and t haplotypes. These chromosome 17 combinations were analyzed for fertility within the context of a M. domesticus or M. spretus genetic background. Two new forms of hybrid sterility were identified. First, the heterospecific combination of M. spretus and t haplotype homologs leads to complete male sterility on both M. spretus and M. domesticus genetic backgrounds. This is an example of symmetrical hybrid sterility. Second, the presence of a single M. domesticus chromosome 17 homolog within a M. spretus background causes sterility, however, the same combination of chromosome 17 homologs does not cause sterility within the M. domesticus background. This is a case of asymmetrical hybrid sterility. Through an analysis of recombinant chromosomes, it was possible to map the M. domesticus, M. spretus and t haplotype alleles responsible for these two hybrid sterility phenotypes to the same novel locus (Hybrid sterility-4). Previous structural studies had led to the hypothesis that the ancestral t haplotype originated through an introgression event from M. spretus or a related species. If this were true, one might expect that (1) M. spretus homologs would be transmitted at a non-Mendelian ratio within the M. domesticus background, and (2) t haplotypes would be transmitted at a ratio closer to Mendelian within the M. spretus background.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1976

Schistosomiasis at Loum, Cameroun; Schistosoma haematobium, S. intercalatum and their natural hybrid.

A survey of 500 schoolchildren in Loum in 1968 revealed an overall infection rate of 54.2% with Schistosoma intercalatum and this was the only species of schistosome encountered. In 1972 a number of children were found to be passing schistosome eggs in their urine and these eggs ranged in shape and size from the forms characteristic for S. haematobium to those of S. intercalatum. Preliminary laboratory studies demonstrated that hybridisation between the two species was occurring. Subsequent field surveys showed that the snail hosts for the two parasites (B. rohlfsi for S. haematobium and B. forskali for S. intercalatum) were both present in the river Mbette and its tributaries in Loum and the distribution of the two snail species coincided closely with the distribution of the schistosomes in the human population. Detailed study of a small group of children passing hybrid eggs in their urine revealed that few of them were passing eggs in their faeces and that those eggs which were found in faeces were not viable. Analysis of schistosome egg-shape by plotting cumulative size-frequency data on probability paper demonstrated that the graph obtained from a natural hybrid series was different from that given by a known mixture of the two separate species. The hybrid series included a number of exceptionally large eggs resembling those of S. bovis but isolation of these eggs and subsequent laboratory passage of the parasites showed that they were part of the series and were not evidence of the presence of a third species. Hybridisation experiments in the laboratory showed that the cross S. haematobium male X S. intercalatum femal is fully viable but that the reverse mating is not successful, thus accounting for the failure of the faecal eggs recovered from children with hybrid infections. Histological results from laboratory passaged hybrids suggest that the Ziehl-positive staining reaction of the egg-shells of S. intercalatum may be a recessive character. The observations reported here indicate that S. haematobium has only recently become established in Loum and that it is, through introgressive hybridisation, replacing the indigenous S. intercalatum. A suggested explanation for the change in the parasite fauna is offered and this depends upon ecological changes resulting from forest clearance and agricultural development providing improved conditions for the spread of B. rohlfsi, the snail host for S. haematobium. It is suggested that, in contrast to recent reports on the spread of S. intercalatum, this species is in fact retreating and being replaced by S. haematobium in areas where forest clearance is taking place. In conclusion it is suggested that introgressive hybridisation of this kind may have been responsible for the evolution of certain characteristic local strains of African schistosomes.

Bulinus↗
PubMed1992

An empirical test of the meiotic drive models of hybrid sterility: sex-ratio data from hybrids between Drosophila simulans and Drosophila sechellia.

Recently, there has been much discussion regarding the hypothesis that divergence of meiotic drive systems in isolated populations can generate the patterns of reproductive isolation observed in animal hybridizations. One prediction from this hypothesis is that the sex ratio of hybrids with heterospecific sex chromosomes should greatly deviate from the Mendelian expectation of 50% female. From sex-ratio data in our Drosophila hybridization studies, we find no such deviation: the sex ratio of offspring of males with introgressed heterospecific Y chromosomes with various autosomal backgrounds does not differ from that of the pure species. We also discuss other aspects of the current meiotic drive models.

Animals↗
PubMed1992

Using markers in gene introgression breeding programs.

We investigate the use of markers to hasten the recovery of the recipient genome during an introgression breeding program. The effects of time and intensity of selection, population size, number and position of selected markers are studied for chromosomes either carrying or not carrying the introgressed gene. We show that marker assisted selection may lead to a gain in time of about two generations, an efficiency below previous theoretical predictions. Markers are most useful when their map position is known. In the early generations, it is shown that increasing the number of markers over three per non-carrier chromosome is not efficient, that the segment surrounding the introgressed gene is better controlled by rather distant markers unless high selection intensity can be applied, and that selection on this segment first can reduce the selection intensity available for selection on non-carrier chromosomes. These results are used to propose an optimal strategy for selection on the whole genome, making the most of available material and conditions (e.g., population size and fertility, genetic map).

Alleles↗
PubMed2025

Genetic interactions and natural variation underlying S-RNase-independent unilateral incompatibility in Solanum.

Pistils of self-incompatible (SI) species/populations typically reject pollen of related self-compatible (SC) species/populations, but not vice versa, a pattern known as unilateral incompatibility (UI). UI is complex and includes both S-RNase-dependent and S-RNase-independent mechanisms. Pistils of Solanum pennellii LA0716 (SC, no S-RNase) reject pollen of cultivated tomato, Solanum lycopersicum (SC); UI in this system involves the expression of ornithine decarboxylase2 (ODC2) and HT-A/-B genes in the pistil, and farnesyl pyrophosphate synthase2 (FPS2), ui6.2, and ui12.2 in pollen. We show that IL12-3 (HT-A/-B) × IL3-3 (ODC2) double introgression lines reject S. lycopersicum pollen, while odc2 or ht-a mutants do not, demonstrating that ODC2 and HT-A are required for UI. Transmission ratio distortion in favor of pennellii alleles was observed in interspecific F2 S. lycopersicum × S. pennellii near ui6.2 and ui12.2, and in F2 IL12-3 × IL3-3 near ui12.2. Equivalent populations made with odc2 mutants segregate in Mendelian ratios, while ht-a mutants have little effect, indicating ui6.2 and ui12.2 interact primarily with ODC2. Pollen from fps2 mutants in S. pennellii LA0716 are incompatible on pistils of all tested S. pennellii and some Solanum habrochaites accessions, but compatible with all other tomato clade species, suggesting ODC2-dependent UI evolved in a common ancestor to S. pennellii and S. habrochaites. Within S. habrochaites, fps2 pollen rejection was observed mainly in SI or mixed mating populations, suggesting an association with outcrossing. Triple mutants of S. pennellii and S. habrochaites lacking functional ODC2, HT-A/-B, and S-RNase are cross-compatible as female parents with S. lycopersicum, allowing transfer of their cytoplasmic genomes into cultivated tomato.

Solanum↗
PubMed2025

Speed breeding: protocols, application and achievements.

One of the limiting factors in breeding and genetic research is the time required to develop pure lines. This is due, on the one hand, to the prolonged vegetative period of a single generation and, on the other hand, to the specifics of inbreeding, which typically requires 4-6 consecutive generations of self-pollination in plant material. Researchers have always sought approaches that enable the rapid development of homozygous plant lines. Consequently, methods such as greenhouse cultivation during the autumn-winter period, single-seed descent, shuttle breeding, embryo culture, and doubled haploid technology have been introduced into practice. All these methods have both advantages and limitations. One of the latest approaches facilitating a significant reduction in the vegetative period of plants is speed breeding (SB). This method is based on the application of factors that shorten the time from sowing to flowering, as well as techniques that accelerate the generative phase of development and overcome postharvest dormancy. This review provides a comprehensive list and characterization of all factors that influence the efficiency of speed breeding to varying degrees. Among the factors discussed that reduce the sowing-to-flowering period are photoperiod, light sources, spectral composition and light intensity, temperature, carbon dioxide levels, vernalization, mineral nutrition, substrate volume, mechanical shoot removal, and the use of plant growth regulators. To shorten the generative phase, the review summarizes the application of embryo culture and forced desiccation of immature seeds, along with methods to overcome postharvest dormancy. Additionally, applications of genetic approaches and genetic engineering for shortening generation time in speed breeding are described. The review also consolidates detailed protocols for approximately thirty crops. The high efficiency of speed breeding in reducing both the vegetative period per generation and the time required to develop pure lines has led to its increasing adoption in various research fields. This review highlights the application of speed breeding for hybridization and pure line development, introgression of target alleles, and genomic selection. A list of phenotypic traits exhibiting high correlation between controlled-environment and field conditions is provided.

accelerated flowering↗
PubMed2026

Genome assembly and subgenomic interactions in Brassica napus additional lines with an alien B05 chromosome from B. juncea.

Alien chromosome addition lines hold significant value for breeding and genetic research. However, the genetic interaction between the recipient genome(s) and the alien chromosomes remain largely unclear. Here, we analyzed the genomic composition and gene expression of two purple-leaved B. napus alien addition lines carrying chromosome B05 from B. juncea: the monosomic line ZYCB3 (MAAL, 2n = 39, AACC + 1B05) and the disomic line ZY52 (DAAL, 2n = 40, AACC + 2B05). We assembled a chromosome-level genome of the DAAL ZY52 disomic line and characterized its genomic variation and chromosome introgression patterns. In addition to chromosome B05, multiple introgressed fragments derived from the donor B. juncea line ZYJC were identified, revealing extensive genome remodeling during distant hybridization and backcross breeding. We then used multi-omics approaches to explore chromosomal interactions and the regulation of anthocyanin biosynthesis. Notably, the addition of chromosome B05 was associated with stronger repression of homoeologous genes on C-subgenome chromosomes than on A-subgenome chromosomes. In ZY52, homoeologous genes on chromosome C01 showed reduced expression, whereas in the ZYCB3 monosomic line reduced expression was observed on both C01 and C02. Comparative transcriptomic and metabolomic analyses further showed that highly expressed anthocyanin biosynthesis genes (ABGs) on chromosome B05contributed to anthocyanin accumulation and the purple-leaf phenotype in both addition lines. Overall, this study provides new insights into interchromosomal interactions, genome remodeling, and phenotypic variation in alien addition lines.

Journal Article↗
PubMed2025

Cytogenetics and genomics analysis of cold-hardy perennial wheatgrass: insights into agronomic performance, chromosome composition, and gene expression.

Intermedium wheatgrass (Thinopyrum intermedium), a perennial species with extensive root systems and high tolerance to cold, drought, and salinity, is a valuable genetic resource for the development of perennial crops. Over a decade-long selection process, two cold-hardy perennial wheatgrass lines were developed by crossing wheat-Thinopyrum partial amphiploids with Th. intermedium. These lines inherited key traits from Th. intermedium, including plant stature, spike morphology, and postharvest regrowth. Transcriptome-based single-nucleotide polymorphism tracing and sequential multicolor genomic in situ hybridization analyses revealed variations in the chromosome compositions of the perennial wheatgrass lines. The introgression of wheat chromosomes enhanced grain weight and size, while preserving the cold-hardy, perennial characteristics of the wheatgrass lines compared to Th. intermedium. Genome-wide gene expression was generally suppressed in the wheatgrass lines relative to Th. intermedium, particularly in conserved genes. This suppression was especially pronounced in genes involved in cell division and DNA repair pathways. In contrast, genes associated with cold tolerance and the water stress response were upregulated. We identified eight cold-tolerance genes in the Th. intermedium chromosomes and validated three of them, Thint.J05G452200, Thint.J05G452300, and Thint.V05G408900, using qRT-PCR. These genes encode proteins associated with cold tolerance and are potential candidates for further functional validation. Additionally, three chromosomes from homoeologous group 6 were introgressed, carrying six genes potentially associated with superior grain traits. Among them, TraesCS6D02G287800, which encodes a specific protein, exhibited high expression levels in both wheatgrass lines, suggesting its critical role in enhancing grain traits. Our results indicate that the suppression of grass gene expression, likely due to the introgression of wheat chromosomes and the upregulation of pathways related to cold tolerance and overwintering ability, contributes to the adaptive features of the wheatgrass lines. This study provides a genomic foundation for understanding gene expression regulation in distant hybrid progeny and offers valuable insights for designing new breeding strategies for perennial wheat or wheatgrass.

Chromosomes, Plant↗
PubMed1992

Isolation of DNA markers linked to a beet cyst nematode resistance locus in Beta patellaris and Beta procumbens.

In cultivated beet no useful level of resistance of the beet cyst nematode (BCN) Heterodera schachtii Schm. has been found, unlike the situation in wild species of the section Procumbentes. Stable introgression of resistance genes from the wild species into Beta vulgaris has not been achieved, but resistant monosomic additions (2n = 18 + 1), diploids of B. vulgaris with an extra alien chromosome carrying the resistance locus, have been obtained. Here we describe a new series of resistant monosomic fragment addition material of B. patellaris chromosome 1 (pat-1). We further describe the cloning of a single-copy DNA marker that specifically hybridizes with a monosomic addition fragment of approximately 8 Mb (AN5-90) carrying the BCN resistance locus. This marker and another fragment-specific, single-copy DNA marker probably flank the BCN locus on the addition fragment present in the AN5-203 material, which is approximately 19 Mb in size. Furthermore, several specific repetitive DNA markers have been isolated, one of which hybridizes to AN5-90 and also to DNA from a smaller DNA segment of Beta procumbens, present in line B883, carrying a BCN resistance locus introgressed into the B. vulgaris genome. This suggests that the specific repetitive marker is closely linked to the BCN locus.

Animals↗
PubMed1990

DNA fingerprints applied to gene introgression in breeding programs.

An application of DNA fingerprints (DFP) for gene introgression in breeding programs of both farm animals and plants is proposed. DFP loci, detectable by minisatellite probes, are extremely polymorphic. Individuals have unique patterns of DFP and thus can be selected for maximal genomic similarity to the recipient line, and minimal similarity to the donor line, using their DFP patterns as the criterion for similarity. This genomic selection (GS) can be performed at generations BC1, BC2 or both, and thus significantly reduce the required number of backcross generations in introgression breeding programs. The association between genomic and DFP similarity is demonstrated. Theoretical distributions and variances of the relative percentages of the donor and recipient genomes as the basis for the GS approach are presented.

Alleles↗