Editorial Material
Multidisciplinary Sciences
Bengt Hansson, Hernan E. Morales, Cock van Oosterhout
Summary: Scott et al. bring attention to species conservation by demonstrating heterozygote superiority among translocated tortoises, but their recommended decision rule may risk setbacks in conservation genomics. Further assessment and improvement are needed to guide conservation management effectively.
Article
Biotechnology & Applied Microbiology
Motohide Nishio, Keiichi Inoue, Shinichiro Ogawa, Kasumi Ichinoseki, Aisaku Arakawa, Yo Fukuzawa, Toshihiro Okamura, Eiji Kobayashi, Masaaki Taniguchi, Mika Oe, Kazuo Ishii
Summary: The use of genomic data allows for more accurate assessment of inbreeding level and depression. Genome-based inbreeding coefficients show stronger correlations with pedigree-based inbreeding coefficients, particularly those based on runs of homozygosity (ROH) segments and heterozygosity by descent segments (HBD). Genome-based inbreeding coefficients have more significant effects on reproductive traits compared to pedigree-based inbreeding coefficients.
Article
Biology
Victoria L. Pike, Charlie K. Cornwallis, Ashleigh S. Griffin
Summary: The strength of inbreeding avoidance varies across species, with some species not avoiding related mates. Mechanisms for avoiding inbreeding are only found in species with inbreeding depression.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Agriculture, Dairy & Animal Science
Miriam Piles, Juan Pablo Sanchez, Mariam Pascual, Silvia Teresa Rodriguez-Ramilo
Summary: Inbreeding depression in closed populations has a negative impact on the growth and prolificacy traits of animals. Recent inbreeding is considered to be more damaging than ancient inbreeding, but selection can potentially reduce the frequency of unfavorable alleles over time through purging. This research aimed to quantify the effects of inbreeding depression and identify evidence of purging in two lines of rabbits. The results confirm the existence of inbreeding depression and purging of deleterious alleles in both lines, independent of the selection criteria.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2023)
Article
Genetics & Heredity
Sarah M. C. Colbert, Frank R. Wendt, Gita A. Pathak, Drew A. Helmer, Elizabeth R. Hauser, Matthew C. Keller, Renato Polimanti, Emma C. Johnson
Summary: Previous studies have suggested that autozygosity decreases over generational time. However, these studies had small samples and lacked diversity, limiting the generalizability of their findings. This study utilized large cohorts of diverse ancestries from the US and the UK to partially support the hypothesis. The results showed a decreasing trend of autozygosity over time, with differences observed between countries and the potential influence of socioeconomic factors.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Anna Wirth, Jurgen Duda, Ottmar Distl
Summary: Increasing levels of inbreeding in German brown cattle have negative effects on longevity traits, but there is no evidence of purging effects. Evaluating inbreeding levels is important to prevent further decline in longevity due to inbreeding depression.
Article
Biodiversity Conservation
Zachary L. Robinson, Donovan A. Bell, Tashi Dhendup, Gordon Luikart, Andrew R. Whiteley, Marty Kardos
Summary: Augmenting gene flow is crucial for the conservation of isolated populations, but careful evaluation and monitoring are necessary. Common assessment methods may have limitations in detecting genetic rescue effects, highlighting the need for comprehensive monitoring information to improve reliability.
CONSERVATION BIOLOGY
(2021)
Article
Biology
Emmeline W. Hill, Martin A. Stoffel, Beatrice A. McGivney, David E. MacHugh, Josephine M. Pemberton
Summary: This study used genomic data from horses to investigate the effects of inbreeding on race performance and identified a genetic haplotype associated with a reduced probability of racing and increased risk of musculoskeletal injury.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Anthony Birnie, Audrey Plat, Cemil Korkmaz, Jacques P. Bothma
Summary: In this study, the regulation of the Fushi tarazu (Ftz) gene in Drosophila melanogaster embryos was dissected using single-cell live imaging tools. It was found that the autoregulatory enhancer does not determine cell fate, but rather maintains the fate determined by the zebra enhancer. Additionally, activation of the autoregulatory enhancer is based on a timing mechanism rather than a concentration threshold. This research provides new insights into how precisely timed enhancer activity can directly regulate gene regulatory network dynamics.
Article
Cell Biology
Pablo Albertos, Kiyoshi Tatematsu, Isabel Mateos, Inmaculada Sanchez-Vicente, Alejandro Fernandez-Arbaizar, Kazumi Nakabayashi, Eiji Nambara, Marta Godoy, Jose M. Franco, Roberto Solano, Davide Gerna, Thomas Roach, Wolfgang Stoeggl, Ilse Kranner, Carlos Perea-Resa, Julio Salinas, Oscar Lorenzo
Summary: The transcription factor ANAC089 plays a crucial role in regulating redox homeostasis and nitric oxide levels during seed germination and abiotic stresses in Arabidopsis, by repressing ABA synthesis and signaling processes.
Article
Environmental Sciences
Ana Rita R. Silva, Patricia V. Silva, Ana Raquel Soares, M. Nazaret Gonzalez-Alcaraz, Cornelis A. M. van Gestel, Dick Roelofs, Gabriela Moura, Amadeu M. V. M. Soares, Susana Loureiro
Summary: The global population growth leads to increased demand for food and the use of pesticides. Persistent pesticide contamination, such as carbendazim, remains a pressing environmental concern with potential long-term impacts on aquatic ecosystems. This study exposed Daphnia magna to carbendazim and found changes in gene transcription and reproductive impairment. However, after 12 generations, the daphnids showed some level of acclimation.
Article
Horticulture
Yaqiong Wu, Tianyu Han, Lianfei Lyu, Weilin Li, Wenlong Wu
Summary: Anthocyanins are important secondary metabolites in plants, which determine the color of flowers and fruits. They have various nutritional and medicinal functions, such as antioxidant, anticancer, and cardiovascular disease prevention. This review discusses the biosynthesis pathway of plant anthocyanins, the key structural genes involved, the impact of transcription factors and microRNAs, the influence of environmental factors, and the effects of six major exogenous hormones on anthocyanin synthesis and metabolism. Future research directions and trends in anthocyanins are also considered to provide a reference for future studies and applications.
SCIENTIA HORTICULTURAE
(2023)
Review
Biochemistry & Molecular Biology
Kun Li, Ziqiang Wang
Summary: SRSF2, a splicing factor, is regulated by HSV-1 infection and can in turn modulate the levels of immune checkpoint molecules in exhausted T cells, thus playing a crucial role in disease progression.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Pattarapol Sumreddee, El Hamidi Hay, Sajjad Toghiani, Andrew Roberts, Samuel E. Aggrey, Romdhane Rekaya
Summary: This study developed a method to classify inbreeding into recent and ancient classes based on pedigree and genomic data. Recent inbreeding was found to have more detrimental effects on growth traits. Using pedigree information, recent inbreeding was identified as those generated within the last 10 to 11 generations.
Article
Biochemistry & Molecular Biology
Paula E. Adams, Anna B. Crist, Ellen M. Young, John H. Willis, Patrick C. Phillips, Janna L. Fierst
Summary: The outcrossing species C. remanei can recover from inbreeding, but the recovery is limited by the presence of a large number of segregating deleterious variants in natural populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Biodiversity Conservation
Noelia Perez-Pereira, Armando Caballero, Aurora Garcia-Dorado
Summary: Genetic rescue is viewed as a promising but underutilized conservation strategy, with limited empirical evidence to support its application. Inbreeding depression and genetic purging are key factors determining the success of rescue programs in the medium to long term. In some scenarios, hybrid vigor and purging can lead to sustained successful rescue, but in specific situations where the recipient population is too small to purge inbreeding load introduced by migrants, increased fitness inbreeding depression and extinction risk may occur.
CONSERVATION GENETICS
(2022)
Correction
Biodiversity Conservation
Noelia Perez-Pereira, Armando Caballero, Aurora Garcia-Dorado
CONSERVATION GENETICS
(2022)
Biographical-Item
Ecology
Armando Caballero, Jinliang Wang, Carlos Lopez-Fanjul
Article
Genetics & Heredity
Irene Novo, Enrique Santiago, Armando Caballero
Summary: The study explores the impact of selection and recombination rate heterogeneity on the estimation of historical Ne, indicating that NeLD mainly reflects demographic changes in population size across generations and is not affected by selection.
Article
Biodiversity Conservation
N. Perez-Pereira, E. Lopez-Cortegano, A. Garcia-Dorado, A. Caballero
Summary: The study found that the change in fitness due to deleterious recessive alleles in inbreeding can be predicted by estimating the inbreeding load and purging coefficient. These parameters can be estimated in pedigreed populations and accurately predict the change in fitness under different breeding systems. The fitness predictions can help inform conservation designs under different breeding scenarios.
ANIMAL CONSERVATION
(2023)
Article
Biodiversity Conservation
Noelia Perez-Pereira, Jinliang Wang, Humberto Quesada, Armando Caballero
Summary: This article investigates the influence of purging on the establishment of a minimum viable population (MVP) for long-term survival. Computer simulations were used to study extinction times and loss of genetic diversity for different effective population sizes. The results indicate that purging can reduce the MVP needed for a population to persist in the long term, especially for species with higher reproductive rates.
BIODIVERSITY AND CONSERVATION
(2022)
Correction
Biodiversity Conservation
Noelia Perez-Pereira, Jinliang Wang, Humberto Quesada, Armando Caballero
BIODIVERSITY AND CONSERVATION
(2023)
Article
Evolutionary Biology
Noelia Perez-Pereira, Humberto Quesada, Armando Caballero
Summary: This study evaluated the effectiveness of molecular markers in estimating inbreeding depression in fruit flies and found that genomic measures provided estimates of inbreeding depression that were comparable to those obtained from simple pedigree estimations with larger sample sizes, even under challenging scenarios.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Irene Novo, Noelia Perez-Pereira, Enrique Santiago, Humberto Quesada, Armando Caballero
Summary: The availability of high-density markers allows the estimation of historical effective population size. Recent refinement methods have been shown to be accurate with simulation data and have been applied to real data of various species. An experimental design with Drosophila melanogaster was carried out to test the method, which showed generally good performance. The limitations of the method and its application were discussed.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Enrique Santiago, Armando Caballero, Carlos Kopke, Irene Novo
Summary: A new method is developed to estimate the contemporary effective population size (Ne) based on linkage disequilibrium (LD) in non-model species. It can be applied to different mating systems and variations in family size distribution. The method uses an artificial neural network to predict confidence intervals, providing more consistent estimates.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Agriculture, Dairy & Animal Science
Armando Caballero, Almudena Fernandez, Beatriz Villanueva, Miguel A. Toro
Summary: This study investigates the accuracy of estimators of inbreeding based on molecular markers in different mating systems and artificially selected populations. The results show that when the allele frequencies of the base population are known, all estimators based on marker allele frequencies provide accurate estimates of inbreeding coefficients and inbreeding depression. When the allele frequencies are unknown, F-LH1 is the most correlated estimator with the actual values, and F-YA2 provides the most accurate estimates of inbreeding depression.
GENETICS SELECTION EVOLUTION
(2022)