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At least 19 recordsLinked to original sources
PubMed2026

Genomic resources to advance seed coat color and patterning genetics and breeding in common bean (Phaseolus vulgaris L.).

Seed coat color and patterning are key quality traits in common bean (Phaseolus vulgaris L.) that define market classes and strongly influence consumer preference and market value. These traits are controlled by a complex network of major genes (sometimes with epistatic interactions), which complicates the recovery of desired market class phenotypes following inter-market class hybridization. Although many of the underlying loci have been genetically mapped, diagnostic, high-throughput molecular markers for efficient allele tracking across the Middle American and Andean gene pools remain limited. In this study, we developed and validated 24 gene-specific PCR Allele Competitive Extension (PACE) markers targeting seven major seed coat color genes (G, B, V, J, Rk, T, and Z) and two patterning genes (CPi and CSt), together with a previously reported marker associated with the postharvest seed coat darkening locus (Psd). An additional PACE marker targeting the Phaseolin (Phs) locus was developed to distinguish Middle American (S-type) and Andean (T-type) gene pools, providing a complementary tool for assessing genetic background alongside seed coat-specific loci. Marker performance was evaluated across three diverse panels, revealing high diagnostic accuracy for most loci (90%-100%). However, for loci such as J, V, Rk, T, and Z, allele-specific markers or marker combinations were required to capture full allelic diversity. Haplotype analysis further revealed substantial allelic diversity across market classes and identified background-specific interactions. Collectively, these results provide a comprehensive set of high-resolution, gene-anchored PACE markers for seed coat color, patterning, and gene pool classification in common bean. These markers enable rapid and precise allele tracking in breeding populations and germplasm collections, facilitating marker-assisted selection for market class-specific seed coat traits and accelerating genetic improvement.

Phaseolus↗
PubMed1979

Alteration of the Agouti mouse coat color pattern by bromoergocryptine. Possible involvement of MSH.

In the Agouti mice C3H Avy the coat color of the dorsum changes from birth to maturity. In young animals the dorsal tegument is yellow whereas in adult mice it shifts to dark gray. The administration of bromoergocryptine, a dopamine agonist, as a single injection in a beeswax pellet prevented the color change resulting in the persistence of the immature pattern. After plucking an area of the dorsum of an adult animal, the regrown hair was dark; however, when bromoergocryptine was administered at the time of plucking the new hair was not dark but yellow. When MSH was injected in adult animals previously treated with the drug, the 'bleaching' effect of bromoergocryptine was abolished, suggesting that this substance did not act directly upon melanin synthesis. In bromoergocryptine-treated mice the MSH content of the pars intermedia was decreased and the ultrastructure of this lobe contained cells with signs of hypoactivity. These two observations suggested that the effect of the drug on the coat color might be ascribed to inhibition of the secretion of MSH. The results may indicate that in the Agouti C3H Avy mice MSH plays a physiological role in determining the coat color. On the other hand, in CH57BL mice bromoergocryptine did not elicit color changes suggesting that in this strain the normal color of the hair is not MSH-dependent.

Aging↗
PubMed2026

Museum genomics links MC1R alleles to adaptive winter coat color polymorphism in the long-tailed weasel.

Understanding the architecture of biological adaptations is a major endeavor of evolutionary biology. Using Natural History collections, we study the genetic basis and evolution of white/brown winter coat color variation in the long-tailed weasel (Neogale frenata), a crucial phenological adaptation for camouflage in habitats with seasonal snow. We produced whole-genome sequencing data for museum specimens, along two winter color morph transition areas in North America, at the West and East coasts. Genome-wide association scans identified a single genomic region linked to color variation polymorphism with approximately 300 kb and 200 kb in the West and East regions, respectively, which included the pigmentation gene MC1R. We identified three MC1R alleles, two of which with deletions of nine or eight amino acids, alternatively associated with the winter brown morphs in the West and East, respectively. These deletions affect the second transmembrane domain, and in one case also the first extracellular loop, which in silico analyses predicted to impact the protein's function. Our findings show alternative intraspecific evolutionary solutions for environmental adaptation in long-tailed weasels, building on the evidence that major genes of the melanin production pathway are hotspots for recurrent and independent evolution of winter camouflage adaptation. This adaptive variation may be crucial to anchor adaptive responses facing future environmental change.

Receptor, Melanocortin, Type 1↗
PubMed1979

In vivo somatic mutation systems in the mouse.

In an effort to meet the need for a fast and cheap in vivo prescreen for inherited mammalian point mutations, a somatic forward-mutation method, originally developed in an X-ray experiment, has more recently been tested in work with chemical mutagens. The method makes use of coat-color mutations because (a) the gene product is usually locally expressed, (b) mosaics can be detected with minimal effort, and (c) opportunities for making comparison with induction of germinal point mutations are greatest.--Following treatment of embryos that are heterozygous at specific coat-color loci, various induced genetic changes can result in expression of the recessive (RS) in clones derived from "mutant" melanocyte precursor cells. However, other events, such as decrease in the number of precursor cells, or disturbed differentiation, can also result in spots, which with careful classification can usually be distinguished from RS's on the basis of their location and color. When this is done, the relative RS frequencies for a series of compounds at least roughly parallel the relative spermatogonial mutation rates. The fact that easily measurable (though low) RS rates are obtained with compounds that have yielded negative results in spermatogonial tests is not surprising in view of the fact that RS's can be caused by several mechanisms besides point mutation.--In spite of the parallelism observed in one laboratory, the usefulness of the in vivo somatic mutation method as a prescreen could come to be doubted because of major discrepancies between results of similar experiments at different laboratories. However, it appears probable that at least some of these discrepancies are due to failure to discriminate between spots that probably resulted from melanocyte insufficiency and spots that resulted from expression of the recessive.--Reverse somatic mutation systems can potentially avoid some of the pitfalls of forward mutation systems. Such system are still in developmental stages.

Animals↗
PubMedDate not supplied

Studies on the genetic control of murine humoral response to immunization with a peptidoglycan-containing fraction extracted from Brucella melitensis.

A peptidoglycan containing fraction (fraction "5") extracted from Brucella melitensis has been injected in low infra-vaccinating doses into inbred mice. The genetic control of the resulting anti-Brucella humoral response has been studied in the C57BL/6 "good responder" X DBA2 "low responder" model. The results observed in F1, F2 and reciprocal backcrosses show that the "good responder" character, although transmitted as a dominant trait, is under polygenic control and independent of H2 haplotype, Ig allotype, sexual chromosoms or the "d" coat color gene. On the other hand, the phenotypic expression of at least one of the genes involved is sex-limited and influenced by hormonal environmental factors. Moreover the expression in females of one of these sex-dependent genes is associated with the "b" coat color gene. These results are discussed in terms of their possible relevance in spontaneous or vaccinal resistance to experimental brucellosis, of the relative role of the peptidoglycan and lipoprotein moieties in fraction "5" and of the possible importance of sex-dependent and chromosome 4-linked genetic factors for B-cell functions.

Animals↗
PubMed2026

Genome-wide SNP-based genomic diversity and population structure analysis in alpaca populations from Europe and Peru.

This study aimed to analyze the genetic diversity and population structure of alpacas in Germany, Switzerland, and Austria (German-speaking regions, GSR) and to compare with that of the country of origin of the species (Peru). A total of 179 animals from GSR and 151 from Peru were genotyped with a species-specific 76k SNP array. The observed and expected heterozygosity was 0.305 and 0.311 for GSR and 0.310 and 0.312 for Peru. The mean FROH values were 0.029 for GSR and 0.023 for Peru. In general, results show that breeders in both analyzed regions efficiently maintain genetic diversity. Principal component analysis identified the GSR and Peru populations as separate from each other, but the relative proximity of both clusters indicates the shared genetic heritage. FST and XPEHH methods identified genomic regions under selection for traits such as coat color and adaptation. Genome-wide association studies comparing black and brown with white or gray alpacas identified associated genome regions containing the ASIP and KIT genes, respectively. The association of a recently identified keratin locus on chromosome 16 with differences in fleece type in alpacas was confirmed, while the putative causality of a TRPV3 variant was rejected.

Animals↗
PubMed2026

Genome-Wide Differentiation, Inbreeding, and Candidate Selection Loci in Local Vietnamese Pig Breeds.

Vietnam harbors exceptional genetic diversity among at least 26 indigenous pig breeds. We analyzed genome-wide single-nucleotide polymorphism (SNP) data from 90 animals representing 15 local Vietnamese breeds and six Landrace pigs using principal component analysis, the windowed fixation index (FST), cross-population extended haplotype homozygosity (XP-EHH), within-population integrated haplotype score (iHS), and runs of homozygosity (ROHs). The population structure was consistent with a north-south differentiation axis, and Ba Xuyen showed elevated heterozygosity, providing suggestive evidence of a European genetic contribution; the f3 statistic was positive (f3 = +0.015), and formal evidence of admixture requires a significantly negative f3, so this criterion was not met. Integration of FST and XP-EHH identified GPC5, E2F6, NOS1, and TLR4 as top Northern candidate loci and CRYM/ZP2 as the leading Central candidate locus, and these windows were recovered at both the 90th and 95th percentile thresholds, indicating analytical robustness rather than independent biological validation. iHS was elevated at E2F6 in Northern breeds (|iHS| = 3.04) and at NOS1 across all regional groups (|iHS| = 2.66-3.36). Breed-level phenotypic XP-EHH, based on published breed descriptions and coat color rather than individual body-composition measurements, identified GALNT2 as a candidate shared across breed groups; HCAR1 and ATG10 as candidates specific to the extreme-fat/prolific breed group; and EFNA5 and HIPK2 as candidates specific to the medium-bodied breed group. ROHs identified Soc, Co, and Hung as breeds warranting particular attention in conservation planning due to elevated autozygosity. Because each breed was represented by only six individuals, and because no individual-level phenotypic measurements were available, all findings are reported as exploratory population-genomic signals requiring replication in larger cohorts. Overall, we describe genomic differentiation and candidate selection signatures among local Vietnamese pig breeds and provide a foundation for further genomic studies of these breeds.

Animals↗
PubMed1975

A mammalian spot test: induction of genetic alterations in pigment cells of mouse embryos with x-rays and chemical mutagens.

Embroys heterozygous for five recessive coat-color genes from the cross C 57 BL/6 J Han x T-stock were x-irradiated with 100/r o r treated in utero with 50 mg/3 kg methyl methanesulfonate (MMS) and ethyl methanesulfonate (EMS), respectively. Controls consisted of irradiated embryos of C 57 BL x C 57 BL matings homozygous wild-type for the genes under study, and non-treated offspring of both types of mating. The colors of the spots were observed in the adult fur were either due to expression of the recessive coat genes or were white. I. Irradiated and mutagen-treated offspring of C 57 BL x T-stock matings had almost exclusively nonwhite spots, distributed randomly over the mouse surface. 2. Irraidated offspring of C 57 BL x C 57 BL matings had only white spots which were always midventral. 3. In non-treated offspring of both types of mating no spot could be observed. After correcting for white midventral spots observed in the one type of control, the frequency of expression of one or the other of the recessive color genes is calculated to be about 11% for embryos irradiated with 100r or 101/2 days postconception, about 1% for embryos irradiated with 100r at 9 days postconception, about &% for embryos treated with 50 mg MMS/kg at 101/2 days postconception, and about 8% for embryos treated with 50 mg EMS/2 days postconception. It is discussed that the white midventral spots are preferentially the result of pigment cell killing, while the nonwhite spots are preferentially the result of gene mutations or recombinational processes like mitotic crossing over and mitotic gene conversion. Of numerical and structural chromosome aberrations only those come into question which are able to pass the filter of several mitoses. Therefore, the test system described is supposted to cover not only heitable DNA-alterations, but the whole spectrum of them.

Animals↗
PubMed1978

Chimeric mice derived from human-mouse hybrid cells.

Mouse teratocarcinoma cells from the OTT6050 ascites tumor were established in tissue culture and selected for 5-bromodeoxyuridine (BrdUrd) resistance. The embryonal carcinoma cells grew without a feeder layer, remained deficient for thymidine kinase (EC 2.7.1.75), and differentiated like the original tumor into various tissues after subcutaneous injection into 129 mice. We fused the BrdUrd-resistant mouse teratocarcinoma cells with HT1080-6TG human diploid fibrosarcoma cells deficient in hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) and selected for hybrid cells in hypoxanthine/aminopterin/thymidine medium. The resulting hybrid cells segregated human chromosomes quickly and retained one to three human chromosomes including chromosome 17 that carries the human genes for thymidine kinase and galactokinase (EC 2.7.1.6). Single hybrid cells from five independent clones containing human chromosome 17 were injected into mouse blastocysts bearing several genetic markers that affect the coat color phenotype and strain-specific enzyme variants in order to detect tissue differentiation derived from the injected cells. After the injection of single hybrid cells into a total of 103 experimental blastocysts that had been surgically transferred to pseudopregnant foster mothers, 49 mice were born and 2 of them clearly revealed coat mosaicism. In 2 of 17 mice thus far analyzed, the injected hybrid cells proved to be capable of participating substantially in development of seven different organs. However, human gene products have not yet been detected unequivocally in those tissues and weak human-specific galactokinase activity could be recovered only from two mosaic tissues. Our results demonstrate that, after in vitro culture and selection, at least some of the human-mouse hybrid cells still retain their in vivo potential to differentiate and become functionally integrated in the living organism. It now seems feasible to cycle mouse teratocarcinoma cells carrying human genetic material through mice via blastocyst injection to study human gene expression during differentiation.

Animals↗
PubMed1978

[Eye changes in the merle syndrome in the dog (author's transl)].

In 44 dachshunds of both sexes, reared and held under identical conditions in order to investigate the effects of the merle gene, ophthalmologic examinations were performed. Eleven extreme dapples with a cutaneous depigmentation beyond 50% (homozygous merle animals, MM) exhibited severe defects in variable forms: Microphthalmia and microcornea, microcoria and corectopia, cataracts and colobomas, rudimentary lenses and ectasia of episcleral vessels. In heterozygous merles with a white percentage of coat color beneath 50% (Mm), lacking tapetum lucidum, depigmented retina, papillary anomaly and ectasia of episcleral vessels were stated, as well as in MM-animals, though not in all. These findings are interpreted as obvious gene dosis effects of the incompletely dominant merle gene which is used to produce a characteric harlequin dappling in many breeds of dogs. With the exception of ectasia of episcleral vessels in a few animals, the homozygous well pigmented controls (mm) displayed none of the anomalies mentioned. The meaning of these results for comparactive medicine and animal protection is discussed.

Animals↗
PubMed2026

Genomic signatures of the Arctic-adapted North American gray wolf ecotype.

The Arctic Circle is one of Earth's most extreme environments. It features cold temperatures, resource shortages, and near-complete winter darkness. Here, we generated a chromosome-level genome assembly of a male wolf from the Arctic Archipelago (Canis lupus arctos). Our assembly and that of the related C. l. orion from Greenland was used to identify candidate genic and regulatory features of Arctic-adapted polar wolves, ranging from selection acting on standing variation and amino acid changes in genes to conserved non-exonic elements (CNEEs) that may regulate gene expression. We identified genes and nearby CNEEs associated with thermoregulation (e.g., APOB), coat color and patterning (e.g., GOLGB1), and DNA damage response (e.g., POLQ). In vitro assays supported changes in polar wolf gene (POLQ and TRPV2 amino acid substitutions) and CNEE function. Our report offers insights into the genetic mechanisms underlying polar wolf adaptations, laying a foundation for future studies on Arctic canines.

Amino acid substitutions↗
PubMed2026

Analysis of deep-resequencing data of 984 soybean accessions reveals structural variations underlying agronomic traits.

Genomic structural variants (SVs) are major sources of genetic variation and have profound impacts on phenotypic traits. However, their functional effects remain largely unexplored in soybean. Here, we resequence 940 soybean accessions. Together with 44 publicly available datasets, we identify 602,281 SVs. Using a graph-based genome, we detect an additional 58,760 presence/absence variations (PAVs) that broadly affect gene expression. Population genomic analyses reveal that SVs serve as a core driving force for soybean domestication and improvement. Integrating SVs with QTLs for oil and protein content, and performing GWAS on 27 traits, we identify key functional SVs. These include transposable element insertions altering seed coat color, multiple insertions within a cytochrome P450 gene modifying flower and hypocotyl color, and a GmMATE1 deletion enhancing seed size. Together, our study establishes a comprehensive SV map of soybean, offering a valuable resource for dissecting the genetic basis of complex traits to accelerate molecular breeding.

Glycine max↗
PubMed1977

Microsurgically produced homozygous-diploid uniparental mice.

Shortly after fertilization, either the male or the female pronucleus was microsurgically removed from 202 F(1) hybrid eggs derived from crosses of two inbred strains. Subsequent incubation of these haploid eggs in medium containing cytochalasin B, which inhibits cytokinesis but not nuclear division, enabled the remaining pronucleus to become diploid. After nuclear diploidization and transfer to regular culture medium, cleavage commenced normally, and a total of 135 successfully manipulated eggs continued in development and yielded 93 morulae and blastocysts. These embryos were surgically transferred to the uteri of pseudopregnant foster mothers who gave birth to seven live female offspring. Five of the females were derived from the maternal genome (gynogenesis) and the remaining two mice inherited only the paternal genes (androgenesis), depending on whether the female or male pronucleus had been retained in the egg, respectively. Homozygosity for a number of genetic loci positioned on different chromosomes and effecting the coat color phenotype and strain-specific allelic variants of several enzymes, urinary and plasma proteins, and hemoglobins could be demonstrated unequivocally in all instances. Chromosomal analysis revealed a normal diploid karyotype including two X chromosomes. Thus far, six of the seven homozygous-diploid (isogeneic) females have proved to be fertile and have given birth to progeny corresponding only to the pronuclear genotype of the mother.

Animals↗
PubMed2025

ODR1, the key seed dormancy and germination regulator, promotes seed Proanthocyanidin biosynthesis via interaction with TTG1 and modulation of MBW complex activity.

Seed dormancy and germination are crucial for both plant survival and reproduction and for crop sowing and harvesting. Proanthocyanidins (PAs), one of the most abundant seed metabolites, play a role in enhancing dormancy and inhibiting germination. Multiple regulatory factors involved in PAs biosynthesis can alter seed dormancy or germination capacity. However, whether the dormancy or germination factors reciprocally influence the PAs biosynthesis is unclear. Here, we report that ODR1, a seed dormancy and germination key factor and a transcriptional (co-) repressor, can regulate seed PAs biosynthesis and act as a transcriptional co-activator. The odr1 mutant shows lighter seed coat color, decreased PAs contents, and reduced expression of PAs biosynthesis genes, which are restored in the ODR1 complementary lines. ODR1 interacts with TTG1 and forms a complex with TTG1/TT2/TT8 (three MBW complex components), enhancing their activation on promoters of PAs biosynthesis genes like DFR and ANS. Overexpressing TTG1 in the odr1-2 mutant rescues or even reverses PA-related phenotypes of odr1-2, confirming that ODR1-mediated regulation of PAs biosynthesis is dependent on TTG1. Moreover, three homologous copies of ODR1 in rapeseed were identified, and simultaneous knockout of them reduces the PAs contents. These results revealed the previously uncharacterized functions of ODR1 in PAs biosynthesis, suggested its conservation between Arabidopsis and rapeseed, and provided important gene resources for rapeseed variety improvement.

Proanthocyanidins↗
PubMed1978

Host defenses in experimental scrub typhus: genetics of natural resistance to infection.

Genetic resistance to lethal infection with Rickettsia tsutsugamushi was studied in over 30 inbred strains, inbred hybrids, and outbred stocks of mice. Inbred mice infected intraperitoneally with the Gilliam strain of R. tsutsugamushi showed three patterns of response: susceptible (A/HeJ, C3H/HeDub, C3H/HeJ, C3H/HeN, C3H/St, CBA/J, DBA/1J, DBA/2J, and SJL/J), resistant (AKR/J, BALB/cDub, BALB/cJ, C57BL/6J, C57L/J, and SWR/J), and selectively resistant (A/J). The selectively resistant pattern was characterized by random deaths occurring throughout the titration range and was also observed in three of the six outbred mouse stocks surveyed. No correlation was evident between the H-2 haplotype of inbred mice and their response to Gilliam infection. The progeny from five different Gilliam-resistant by Gilliam-susceptible inbred parental crosses were all resistant. Study of F(1), F(2), and parental backcross generations of BALB/cDub (resistant) and C3H/HeDub (susceptible) hybrids indicated resistance was dominant and was controlled by a single gene or a closely linked cluster of genes that were autosomal and not linked to coat color. The resistance of BALB/cDub mice was not due to an inability of host cells to support rickettsial growth, since C3H/HeDub and BALB/cDub embryo cell cultures supported similar growth of Gilliam organisms. C3H/HeDub mice, although susceptible to intraperitoneal Gilliam infection, were capable of mounting an immune response to Gilliam antigens, since subcutaneous infection was not lethal and did protect animals against subsequent intraperitoneal challenge with either the Gilliam or Karp strains of R. tsutsugamushi.

Animals↗
PubMed1978

Resistance and susceptibility of mice to bacterial infection: genetics of listeriosis.

A survey of various strains of mice showed distinct differences in resistance or susceptibility to Listeria monocytogenes. C57B1, related sublines, NZB, and SJL were resistant to Listeria, whereas BALB/c, CBA, A, DBA/1, C3H, LP.RIII, 129, and WB were susceptible. The gene(s) responsible for resistance and susceptibility to Listeria were studied in detail. C57BL6/6, B10.D2, and B10.A mice were 100 times more resistant than were BALB/c, CBA, and A. Resistance of the (C57B1/6 X BALB/C)F1 was intermediate between the two parents, suggesting partial penetration of a dominant gene. Backcross studies in which the (C57B1/6 X BALB/c)F1 were crossed with the susceptible BALB/c parent suggested that a single gene or group of linked genes were the major determinant of resistance, although the possibility that other genes exerted a modifying influence was not excluded. By using the backcross and various congenic and recombinant mice, linkage of the genes involved to the H-1, H-2, H-3, H-4, H-7, or H-8 loci, to the immunoglobulin allotype, to the Thy-1 gene, to the Hc gene specifying C5, or to coat color genes (B, c) was excluded. There was no difference in the response of males and females. In all studies, the powerful overriding influence of the C57B1 genome was evident.

Animals↗
PubMed2017

OCA2 splice site variant in German Spitz dogs with oculocutaneous albinism.

We investigated a German Spitz family where the mating of a black male to a white female had yielded three puppies with an unexpected light brown coat color, lightly pigmented lips and noses, and blue eyes. Combined linkage and homozygosity analysis based on a fully penetrant monogenic autosomal recessive mode of inheritance identified a critical interval of 15 Mb on chromosome 3. We obtained whole genome sequence data from one affected dog, three wolves, and 188 control dogs. Filtering for private variants revealed a single variant with predicted high impact in the critical interval in LOC100855460 (XM_005618224.1:c.377+2T>G LT844587.1:c.-45+2T>G). The variant perfectly co-segregated with the phenotype in the family. We genotyped 181 control dogs with normal pigmentation from diverse breeds including 22 unrelated German Spitz dogs, which were all homozygous wildtype. Comparative sequence analyses revealed that LOC100855460 actually represents the 5'-end of the canine OCA2 gene. The CanFam 3.1 reference genome assembly is incorrect and separates the first two exons from the remaining exons of the OCA2 gene. We amplified a canine OCA2 cDNA fragment by RT-PCR and determined the correct full-length mRNA sequence (LT844587.1). Variants in the OCA2 gene cause oculocutaneous albinism type 2 (OCA2) in humans, pink-eyed dilution in mice, and similar phenotypes in corn snakes, medaka and Mexican cave tetra fish. We therefore conclude that the observed oculocutaneous albinism in German Spitz is most likely caused by the identified variant in the 5'-splice site of the first intron of the canine OCA2 gene.

Albinism, Oculocutaneous↗