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PubMed2026

Chromosome-scale genome assembly and genomic prediction of essential oil compounds in Atractylodes lancea for genomics-assisted breeding.

Atractylodes lancea rhizomes are used as crude drugs. Essential oil compounds, including atractylodin, hinesol, β-eudesmol, and atractylon, are key determinants of crude drug quality. Conventional breeding of A. lancea is difficult because of its perennial growth. In this study, a chromosome-scale reference genome of A. lancea (4.79 Gb) was generated, and genome-wide association studies (GWAS) and genomic predictions of essential oil compounds were conducted to explore the potential for genome-assisted breeding. Genotyping of 480 lines using double-digest restriction-site-associated DNA-sequencing yielded 29,136 high-quality SNPs. All the compounds showed high genomic heritability (h2 = 0.758-0.915), indicating strong genetic control. Despite the high genomic heritability, GWAS detected only one weak association with atractylon and no significant loci for the three compounds. However, genomic prediction achieved moderate to high accuracy across multiple models, particularly the ridge regression, genomic best linear unbiased prediction, and Bayesian approaches. The prediction accuracy, measured as the Pearson correlation coefficient between the observed and predicted values, exceeded 0.6 for all four essential oil compounds. These results demonstrate the efficacy of genomic selection for improving essential oil compound levels in A. lancea and provide a foundation for genome-assisted breeding of medicinal plants with long breeding cycles.

Atractylodes lancea↗

PubMed2001

Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds.

We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus genotypes were used to infer genetic clusters. Individuals from each breed were inferred to belong mostly to the same cluster. The clustering success rate, measuring the fraction of individuals that were properly inferred to belong to their correct breeds, was consistently approximately 98%. When markers of highest expected heterozygosity were used, genotypes that included at least 8-10 highly variable markers from among the 27 markers genotyped also achieved >95% clustering success. When 12-15 highly variable markers and only 15-20 of the 30 individuals per breed were used, clustering success was at least 90%. We suggest that in species for which population structure is of interest, databases of multilocus genotypes at highly variable markers should be compiled. These genotypes could then be used as training samples for genetic cluster analysis and to facilitate assignments of individuals of unknown origin to populations. The clustering algorithm has potential applications in defining the within-species genetic units that are useful in problems of conservation.

Algorithms↗

PubMed2004

Effect of breeding structure on population genetic parameters in Drosophila.

The breeding structure of populations has been neglected in studies of Drosophila, even though Wright and Dobzhansky's pioneering work on the genetics of natural populations was an attempt to tackle what they regarded as an essential factor in evolution. We compared the breeding structure of sympatric populations of D. melanogaster and D. simulans, two sibling species that are widely used in evolutionary studies. We recorded changes in population density and microsatellite variation patterns for 3 years in a temperate environment of southwestern France. Results were distinctively different in the two species. Maximum population levels in summer and in autumn were similar and fluctuated greatly over years, each species being in turn the most abundant. However, genetic data showed that D. melanogaster made up a continuous breeding population in time and space of practically infinite effective size. D. simulans was fragmented into isolates with a local effective size of between 50 and 350 individuals. A consequence of this was that, while a local sample provided a reliable estimate of regional genetic variability in D. melanogaster, a sample from the same area provided an underestimate of this parameter in D. simulans. In practical terms, this means that variations in breeding structure should be accounted for in sampling schemes and in designing evolutionary genetic models. More generally, this suggests the existence of differential reactions to local environments that might contribute to several genomic differences observed between these species.

Animals↗

PubMed2026

Advances in genomics-driven genetic decoding and genomic design breeding in tomato.

Tomatoes are highly nutritious and represent one of the important vegetable fruits worldwide. Both historically and moving forward, genetic decoding and precision breeding remain fundamental to tomato improvement. Here, we summarize pivotal advances in decoding tomato genomes across domestication, improvement and evolution processes and provide a perspective on future breeding through precision design. In-depth population genetic studies have revealed how artificial selection systematically prioritized yield-related alleles at the cost of narrowing genetic diversity, especially at flavor-related loci-highlighting the urgent need to reconcile these trade-offs. Comparative genomics across species, viewed through an evolutionary lens, has uncovered critical insights into functional genes, deepening our understanding of the genetic architecture and regulatory mechanisms underlying key traits. Collectively, these advances have enabled precise identification and functional characterization of key genetic elements, paving the way for systematic redomestication of tomato through precision genomic design. Looking ahead, more efficient and precise breeding strategies will be required to accelerate genetic gains in tomato in the coming decades. The integration of recent genomic advances, coupled with genomic selection and artificial intelligence, into genomic design breeding offers a transformative framework, unlocking unprecedented opportunities for developing highly flavorful and consumer-customized tomato varieties.

Journal Article↗

PubMedDate not supplied

Frequency and inheritance of A and B blood types in feline breeds of the United States.

Using a simple hemagglutination assay to determine A and B blood types, we surveyed 1,072 domestic short- and longhair (DSH/DLH) cats and 1,100 purebred cats in the United States. Data from 234 matings with 552 offspring were consistent with the hypothesis that feline blood types A and B are due to the action of two different alleles at the same gene locus and that A is completely dominant over B. Neither an AB nor an O type cat was encountered. No type B cats were found in the Siamese and related breeds or in American Shorthair and Norwegian Forest cats. Among the breeds with type B blood, the proportion was lowest in DSH/DLH cats (0.0028) and variably higher in Abyssinian, Birman, British Shorthair, Devon Rex, Himalayan, Persian, Scottish Fold, and Somali, ranging from 0.15 to 0.59. Since all type B cats have strong, naturally occurring anti-A alloantibodies, fatal neonatal isoerythrolyses occur in type A offspring of type B mothers bred to type A males. The gene frequency of the B allele and the proportion of mating at risk of neonatal isoerythrolysis were estimated in a number of breeds. In most breeds, the frequency of the B allele was less than 0.5. Since the kittens at risk for neonatal isoerythrolysis always have the genotype AB, there is constant natural selection against heterozygotes. Heterozygote disadvantage in the cat AB system represents an unusual form of negative selection, similar to that in Rh blood group incompatibility in humans.

Alleles↗

PubMedDate not supplied

Frequency of the codon 807 mutation in the cGMP phosphodiesterase beta-subunit gene in Irish setters and other dog breeds with hereditary retinal degeneration.

Rod-cone dysplasia 1 (rcd1) in Irish setters is caused by a nonsense mutation in the cGMP phosphodiesterase beta-subunit gene (PDE6B). We examined the frequency of the mutant allele in the Irish setter population and determined if the defect is present in dogs of other breeds which are affected with other inherited photoreceptor diseases. Between 1994 and 1997, samples were obtained from 436 clinically normal Irish setters, a red wolf, and dogs from 23 different breeds. The mutation in codon 807 of PDE6B was detected in genomic DNA by heteroduplex analysis, allele-specific PCR, or restriction enzyme digestion. Of the 436 samples from clinically normal setters, 34 contained the mutation in one of the two PDE6B alleles (carrier rate = 7.8%). In contrast, the same mutation was not found in the red wolf or dogs of other breeds affected with PRA or inherited photoreceptor diseases. The high percentage of tested carriers, however, is not representative of the number of carriers in the population since some dogs tested were closely related and did not represent a random sample of the Irish setter breed.

3',5'-Cyclic-GMP Phosphodiesterases↗

PubMed1990

Larval survey of surface water-breeding mosquitoes during irrigation development in the Mahaweli Project, Sri Lanka.

A survey of ground water-breeding mosquitoes was done during 1986-1987 in an area undergoing irrigation development in the Mahaweli Project of Sri Lanka. Forty-nine species were collected during the 12-mo phase of humans settlement and infrastructure construction, and 42 species during the succeeding 12-mo period under irrigated rice culture. Development resulted in the elimination of some preexisting breeding habitats, the modification of others, and the creation of new habits. The overall change from uninhabited forest to settled irrigated rice sharply increased the prevalence of Anopheles annularis van der Wulp, An. peditaeniatus (Leicester), Aedeomyia catasticta Knab, Mimomyia hybrida (Leicester), Mansonia uniformis (Theobald), and Culex tritaeniorhynchus Giles. Equally sharp decreases occurred in the prevalence of An. barbirostris van der Wulp, An. barbumbrosus Strickland & Choudhury, Ae, jamesi (Edwards), Ae. vittatus (Bigot), Ae. pseudomediofasciatus (Theobald), Cx. halifaxii Theobald, Cx. malayi (Leicester), Cx. minutissimus (Theobald), Cx. nigropunctatus Edwards, Cx. fuscocephala Theobald, and Cx. mimulus Edwards. Other species that showed smaller positive or negative changes included An. nigerrimus Giles, An. culicifacies Giles, An. jamesii Theobald, An. subpictus Grassi, An. vagus Donitz, An. varuna Iyengar, Mi. chamberlaini (Ludlow), Ma. annulifera (Theobald), Cx. bitaeniorhynchus Giles, Cx. gelidus Theobald, and Cx. pseudovishnui Colless. Irrigation development led to reduced breeding by the majority of species; however, most species that did increase in prevalence were potential vectors of human disease. Components of the irrigation system such as reservoir and canal margins, seepages, and rice fields provided increased breeding sites for some of these species.

Animals↗

PubMed1993

Individual variation within breeds of beef cattle in resistance to horn fly (Diptera: Muscidae).

Weekly estimates of populations of horn fly, Haematobia irritans (L.), were made on individual purebred Charolais, Chianina, Hereford, Polled Hereford, and Red Poll cows in 1988, 1989, and 1990 with Angus included in 1989 and 1990. During the study period, 94 of approximately 200 individual cows were classified as either fly resistant or fly susceptible. In general, individuals retained the same classification over the 3-yr study period. The mean number of flies on individual susceptible cows in all breeds was at least twice the number of flies on resistant cows. Susceptible Chianina cows averaged > 4.5 times as many flies as resistant cows of the same breed. Individual cows within all breeds classified as fly resistant ranged in age from 2 to 12 yr, whereas fly-susceptible cows ranged in age from 2 to 14 yr; therefore, cow age did not influence the abundance of horn flies on individual cows within breeds. Two-year-old fly-resistant cows were identified accurately according to their horn fly-population density, showing the potential of host resistance in horn fly-population management.

Animals↗

PubMedDate not supplied

Comparative F statistics analysis of the genetic structure of ten Spanish dog breeds.

The genetic structure and relationships among 10 Spanish dog breeds have been studied by using F statistics. Data came from 21 structural genic loci that codify for blood-soluble proteins and enzymes detected by electrophoresis. Of the 21 loci, 11 were found to be polymorphic. The study was done at three levels of hierarchical differentiation: ancestral trunks, breeds, and subpopulations. The deficit of heterozygotes was estimated at the subpopulation, breed, and ancestral trunk levels, with values of 4.0%, 6.5%, and 11.2%, respectively. In the whole population, the deficit of heterozygotes was about 17%. The proportion of genetic variability attributable to differences between subpopulations, breeds, and ancestral trunks was estimated to be 14.2%, 9.9%, and 6.9%, respectively. The dendrogram, obtained by using values of genic differentiation (FST) as a measure of the genetic distance among populations, is topologically identical to the one obtained using Nei's index of distance, which indicates a high correlation (r = .99) between both distances. These racial groupings, however, differ from the grouping obtained from historical, archeological, and morphological data.

Animals↗

PubMed2002

Genetic diversity of Chinese native chicken breeds based on protein polymorphism, randomly amplified polymorphic DNA, and microsatellite polymorphism.

Genetic diversity of Chinese native chicken breeds was investigated using protein polymorphism, randomly amplified polymorphic DNA (RAPD), and microsatellite polymorphism. Imported broiler and layer breeds were also included in the analysis. The results from protein polymorphism did not show distinct differences between Chinese native chicken and imported broilers; however, there were small significant differences between these two types of chickens. The results from RAPD indicated that gene diversity within a population was large in Chinese native chickens, intermediate in broilers, and low in layers and that there were small differences between Chinese native chickens and both broilers and layers. A great difference between broilers and layers was observed. Microsatellite polymorphism data showed that genetic diversity was high in the Chinese native chickens and low in layers and that there was a close relationship between Chinese native chickens and broiler but a remote relationship between Chinese native chickens and layers. The wide genetic diversity of Chinese native breeds can meet different requirements of breeding for chicken quality in China.

Alkaline Phosphatase↗

PubMed1985

Immunoreactive luteinizing hormone, estradiol, progesterone, testosterone, and androstenedione levels during the breeding season and anestrus in Siberian tigers.

Seasonal analysis of 1239 captive births of Siberian tigers (Panthera tigris altaica) indicated a peak in April to June (P less than 0.001). Studies on seven animals in Minnesota indicated that behavioral heat cycles and ovarian follicular phase cycles began in late January and ceased in early June. Behavioral observation of 12 heat cycles in four tigers yielded an estrous length of 5.3 +/- 0.2 days and an interestrous interval of 25.0 +/- 1.3 days. Hormone assays on weekly blood samples (N = 180) from three female tigers indicated 16 cycles in two breeding seasons. Peak estradiol-17 beta levels were 46.7 +/- 6.0 pg/ml (N = 17) and interestrous concentrations were 8.7 +/- 0.66 pg/ml (N = 28) during the breeding season. Anestrous estradiol levels were 4.2 +/- 0.5 pg/ml (N = 70). The interestrous interval between estradiol peaks was 24.9 +/- 1.3 days (N = 9) with two outliers of 42 days. Serum progesterone concentrations from February to June were 1.2 +/- 0.15 ng/ml (N = 32), providing no evidence for ovulation or corpus luteum formation. Luteinizing hormone (LH) levels were 0.56 +/- 0.04 ng/ml (N = 180). Serum testosterone (r=0.71, P less than 0.001) and androstenedione levels (r=0.75, P less than 0.001) were correlated with estradiol during the breeding season. The duration of anestrus was 8 mo in two of these tigers. The interval was shortened in one tiger by exposure to a 16L:8D photoperiod. The Siberian tiger appears to be a polyestrous seasonal breeder and an induced ovulator whose breeding season may be synchronized by photoperiod.

Androstenedione↗

PubMed1990

Immunoreactive inhibin levels in peripheral blood during the breeding season in the female Japanese monkey.

Serum levels of immunoreactive inhibin as well as FSH, LH, estradiol-17 beta, and progesterone were measured by RIA in four mature female Japanese monkeys (Macaca fuscata fuscata) during the breeding season and subsequent transition into the nonbreeding season. During the breeding season, each monkey showed 2-6 ovulations, which were inferred from underlying endocrine events. The concentrations of serum inhibin increased during the luteal phase, but were low during the follicular phase. Such changes in serum inhibin levels correlated positively with those in serum progesterone levels. Basal levels of serum inhibin also increased during the breeding season, decreased during transition from the breeding season, and were low during the nonbreeding season. The parallel change in serum levels of inhibin and progesterone together with the increased basal levels of serum inhibin during this period suggests that both the CL and antral follicles are sources of circulating inhibin. Decreases in serum FSH levels during the luteal phase suggest that secretion of FSH is controlled by an inhibitory action of ovarian inhibin in addition to steroid hormones.

Animals↗

PubMed1999

Climate change has affected the breeding date of tree swallows throughout North America

Increasing evidence suggests that climate change has affected the breeding and distribution of wildlife. If such changes are due to global warming, then we should expect to see large-scale effects. To explore for such effects on avian reproduction, we examined 3450 nest records of tree swallows from across North America. The egg-laying date in tree swallows advanced by up to nine days during 1959-1991. This advance in phenology was associated with increasing surface air temperatures at the time of breeding. Our analysis controlled for several potentially confounding variables such as latitude, longitude, breeding density and elevation. We conclude that tree swallows across North America are breeding earlier and that the most likely cause is a long-term increase in spring temperature.

Journal Article↗

PubMed2003

Modulation of the hypothalamic-pituitary-adrenal axis of an Arctic-breeding polygynandrous songbird, the Smith's longspur, Calcarius pictus.

To successfully reproduce in the Arctic, birds must modulate their neuroendocrine and behavioural systems. These adjustments include an attenuation of the stress responsiveness of the hypothalamic-pituitary-adrenal (HPA) axis to external stimuli and a behavioural insensitivity to high corticosterone (B) levels. The HPA axis was examined in free-living territorial polygynandrous Smith's longspurs (Calcarius pictus) that migrate to breed on the Arctic tundra. Basal and stress-induced B levels were measured through the breeding season and were found to be significantly lower in females compared with males. This was not a consequence of adrenal insensitivity, because intrajugular injections of adrenocorticotrophin hormone (ACTH) enhanced B release in incubating females. In males the adrenocortical response to stress was significantly attenuated during the parental phase compared with arrival at the breeding ground. In contrast to temperate passerines, there was no significant decrease in male territorial aggressive behaviour when B was experimentally elevated, suggesting a behavioural insensitivity to glucocorticoids. This mechanism is hypothesized to increase reproductive success by preventing interruptions to parental care during transient deleterious environmental perturbations, which are often experienced in the short Arctic breeding season. Modulation of the HPA axis in this species in relation to life-history stage, lifetime reproductive success and the polygynandrous mating system is discussed.

Adrenocorticotropic Hormone↗

PubMed2004

Tropical winter habitat limits reproductive success on the temperate breeding grounds in a migratory bird.

Identifying the factors that control population dynamics in migratory animals has been constrained by our inability to track individuals throughout the annual cycle. Using stable carbon isotopes, we show that the reproductive success of a long-distance migratory bird is influenced by the quality of habitat located thousands of kilometres away on tropical wintering grounds. For male American redstarts (Setophaga ruticilla), winter habitat quality influenced arrival date on the breeding grounds, which in turn affected key variables associated with reproduction, including the number of young fledged. Based on a winter-habitat model, females occupying high-quality winter habitat were predicted to produce more than two additional young and to fledge offspring up to a month earlier compared with females wintering in poor-quality habitat. Differences of this magnitude are highly important considering redstarts are single brooded, lay clutches of only three to five eggs and spend only two-and-a-half months on the breeding grounds. Results from this study indicate the importance of understanding how periods of the annual cycle interact for migratory animals. Continued loss of tropical wintering habitat could have negative effects on migratory populations in the following breeding season, minimizing density-dependent effects on the breeding grounds and leading to further population declines. If conservation efforts are to be successful, strategies must incorporate measures to protect all the habitats used during the entire annual cycle of migratory animals.

Animal Migration↗

PubMed2004

Predation risk is an ecological constraint for helper dispersal in a cooperatively breeding cichlid.

Environmental conditions are thought to be responsible for the extent and benefits of cooperative breeding in many animal societies, but experimental tests are scarce. We manipulated predator pressure in the cooperatively breeding cichlid Neolamprologus pulcher in Lake Tanganyika, where predators have been suggested to influence helper and breeder survival, helper dispersal and group reproductive success. We varied the type and intensity of predation by releasing medium, large, or no predators inside large underwater cages enclosing two or three group territories. Helper and breeder survival, helper dispersal and group reproductive success decreased from the control, to the medium- and large-predator treatments. These effects were modified by helper body size and the number of adults protecting the group from predators, supporting the 'group augmentation hypothesis'. Predators forced helpers to stay closer to, and spend more time inside, protective shelters. The results demonstrate the importance of predators for group living in this species, and support the 'ecological constraints hypothesis' of cooperative breeding, in the sense that subordinates stay at home rather than leave and breed independently under the risk of predation.

Animals↗

PubMed2005

Environmental stochasticity in dispersal areas can explain the "mysterious" disappearance of breeding populations.

We present the results of an individual-based simulation model, showing that increasing the mortality of non-breeding dispersers within settlement areas can lead to the extinction of species and (meta)populations in a subtle way. This is because the areas where dispersers settle are generally unknown or difficult to detect. Consequently, fewer efforts are devoted to the conservation of these sites than to the conservation of breeding territories. Additionally, high mortality rates affecting the floater sector of a population become evident in the breeding sector only after several of years, when it is too difficult or too late to halt the decline. As a result, because most conservation projects on endangered species and populations mainly focus on breeding areas, many current efforts may be wasted in locations other than those in which conservation would be really necessary and effective.

Animals↗

PubMed1986

Biochemical polymorphism in Egyptian Baladi cattle and their relationship with other breeds.

Gene frequencies were estimated in a sample of Baladi cattle for milk proteins, blood proteins and blood groups. Gene frequency estimates of Bos taurus, Bos indicus and Sanga breeds were assembled from the literature. The gene frequencies were utilized for estimating the genetic distance between the breeds and breed groups. The Egyptian Baladi cattle appeared to be closer to Bos taurus breeds than to the Sanga. They are far removed from Zebus.

Alleles↗