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Gindri M, Ithurbide M, Pires J, Rupp R, Puillet L, Friggens NC. Responses of selected plasma metabolites to a two-day nutritional challenge of goats divergently selected for functional longevity. J Dairy Sci 2024:S0022-0302(24)00723-9. [PMID: 38608949 DOI: 10.3168/jds.2023-23908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 03/02/2024] [Indexed: 04/14/2024]
Abstract
Understanding the extent to which genetics × environment plays a role in shaping individual strategies to environmental challenges is of considerable interest for future selection of more resilient animals. Accordingly, the objective of this study was to evaluate the metabolic responses to a nutritional challenge of goats divergently selected for functional longevity based on plasma metabolites and the repeatability of these responses across 2 experimental farms and years. We carried out 6 different experimental trials from years 2018 to 2022 (4 trials on site Bourges (2018-21) and 2 trials (2021-22) on site Grignon) in which 267 first kidding goats, daughters of Alpine bucks divergently selected for functional longevity, longevity plus (n = 137), and longevity minus (n = 130), were exposed to a 2-d nutritional challenge in early lactation. The experiments consisted of a 5 or 7-d control period (pre-challenge) on a standard lactation diet followed by a 2-d nutritional challenge with straw-only feeding and then a 7 or 10-d recovery period on a standard lactation diet, for site Bourges and Grignon, respectively. During the challenge plasma metabolite composition was recorded daily. Linear mixed-effects models were used to analyze all traits, considering the individual as a random effect and the 2x2 treatments (i.e., genetic line and year nested in site) and litter size as fixed effects. The linear mixed-effects model using a piecewise arrangement was used to analyze the response/recovery profiles to the nutritional challenge. Random parameters estimated for each individual, using the mixed-effects models without the fixed effects of genetic line, were used in a Sparse Partial Least Square Discriminant Analysis (sPLS-DA) to compare the goat metabolism response to the challenge on a multivariate scale. The plasma metabolites, glucose, β-hydroxybutyrate (BHB), and nonesterified fatty acids (NEFA), and urea concentrations responded to the 2-d nutritional challenge. Selection for functional longevity did not affect plasma glucose, NEFA, BHB, and urea response/recoveries to a 2-d nutritional challenge. However, site, trial, and litter size affected these responses. Moreover, the plasma metabolites seem not to fully recover to prechallenge levels after the recovery phase. The sPLS-DA analysis did not discriminate between the 2 longevity lines. We observed meaningful between-individuals' variability in plasma BHB, especially on the prechallenge and rate of response and rate of recovery from the 2-d nutritional challenge (CV = 26.2%, 36.1%, and 41.2%, repeatability = 0.749, 0.322, and 0.741, respectively). Plasma NEFA recovery from challenge also demonstrated high between-individuals' variability (CV = 16.4%, repeatability = 0.323). Selection for functional longevity did not affect plasma metabolites responses to a 2-d nutritional challenge in dairy goats. Plasma NEFA and BHB response/recovery presented high between-individuals' variability, indicating individual adaptative characteristics to nutritional challenges not related to the environmental conditions but to inherent individual characteristics.
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Affiliation(s)
- M Gindri
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120, Palaiseau, France
| | - M Ithurbide
- GenPhySE, Université de Toulouse, INRAE, Institut National Polytechnique de Toulouse, École Nationale Vétérinaire de Toulouse, Castanet Tolosan, 31320, France
| | - J Pires
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France
| | - R Rupp
- GenPhySE, Université de Toulouse, INRAE, Institut National Polytechnique de Toulouse, École Nationale Vétérinaire de Toulouse, Castanet Tolosan, 31320, France
| | - L Puillet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120, Palaiseau, France
| | - N C Friggens
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120, Palaiseau, France.
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Campbell DR, Powers JM, Crowell M. Pollinator and habitat-mediated selection as potential contributors to ecological speciation in two closely related species. Evol Lett 2024; 8:311-321. [PMID: 38525033 PMCID: PMC10959478 DOI: 10.1093/evlett/qrad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 03/26/2024] Open
Abstract
In ecological speciation, incipient species diverge due to natural selection that is ecologically based. In flowering plants, different pollinators could mediate that selection (pollinator-mediated divergent selection) or other features of the environment that differ between habitats of 2 species could do so (environment-mediated divergent selection). Although these mechanisms are well understood, they have received little rigorous testing, as few studies of divergent selection across sites of closely related species include both floral traits that influence pollination and vegetative traits that influence survival. This study employed common gardens in sites of the 2 parental species and a hybrid site, each containing advanced generation hybrids along with the parental species, to test these forms of ecological speciation in plants of the genus Ipomopsis. A total of 3 vegetative traits (specific leaf area, leaf trichomes, and photosynthetic water-use efficiency) and 5 floral traits (corolla length and width, anther insertion, petal color, and nectar production) were analyzed for impacts on fitness components (survival to flowering and seeds per flower, respectively). These traits exhibited strong clines across the elevational gradient in the hybrid zone, with narrower clines in theory reflecting stronger selection or higher genetic variance. Plants with long corollas and inserted anthers had higher seeds per flower at the Ipomopsis tenuituba site, whereas selection favored the reverse condition at the Ipomopsis aggregata site, a signature of divergent selection. In contrast, no divergent selection due to variation in survival was detected on any vegetative trait. Selection within the hybrid zone most closely resembled selection within the I. aggregata site. Across traits, the strength of divergent selection was not significantly correlated with width of the cline, which was better predicted by evolvability (standardized genetic variance). These results support the role of pollinator-mediated divergent selection in ecological speciation and illustrate the importance of genetic variance in determining divergence across hybrid zones.
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Affiliation(s)
- Diane R Campbell
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, United States
- Rocky Mountain Biological Laboratory, Crested Butte, CO, United States
| | - John M Powers
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, United States
- Rocky Mountain Biological Laboratory, Crested Butte, CO, United States
| | - Madison Crowell
- Rocky Mountain Biological Laboratory, Crested Butte, CO, United States
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Ojeda-Marín C, Gutiérrez JP, Formoso-Rafferty N, Goyache F, Cervantes I. Differential patterns in runs of homozygosity in two mice lines under divergent selection for environmental variability for birth weight. J Anim Breed Genet 2024; 141:193-206. [PMID: 37990938 DOI: 10.1111/jbg.12835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/11/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
Runs of homozygosity (ROH) are defined as long continuous homozygous stretches in the genome which are assumed to originate from a common ancestor. It has been demonstrated that divergent selection for variability in mice is possible and that low variability in birth weight is associated with robustness. To analyse ROH patterns and ROH-based genomic inbreeding, two mouse lines that were divergently selected for birth weight variability for 26 generations were used, with: 752 individuals for the high variability line (H-Line), 766 individuals for the low variability line (L-Line) and 74 individuals as a reference population. Individuals were genotyped using the high density Affymetrix Mouse Diversity Genotyping Array. ROH were identified using both the sliding windows (SW) and the consecutive runs (CR) methods. Inbreeding coefficients were calculated based on pedigree (FPED ) information, on ROH identified using the SW method (FROHSW ) and on ROH identified using the CR method (FROHCR ). Differences in genomic inbreeding were not consistent across generations and these parameters did not show clear differences between lines. Correlations between FPED and FROH were high, particularly for FROHSW . Moreover, correlations between FROHSW and FPED were even higher when ROH were identified with no restrictions in the number of heterozygotes per ROH. The comparison of FROH estimates between either of the selected lines were based on significant differences at the chromosome level, mainly in chromosomes 3, 4, 6, 8, 11, 15 and 19. ROH-based inbreeding estimates that were computed using longer homozygous segments had a higher relationship with FPED . Differences in robustness between lines were not attributable to a higher homozygosis in the L-Line, but maybe to the different distribution of ROH at the chromosome level between lines. The analysis identified a set of genomic regions for future research to establish the genomic basis of robustness.
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Affiliation(s)
- Candela Ojeda-Marín
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Félix Goyache
- Departamento de Producción Agraria, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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Straub CS, Cuomo RG, Jimenez G. Habitat selection and refuge-use by a color polymorphic salamander reveal behavioral niche differences. Ecol Evol 2024; 14:e10978. [PMID: 38414572 PMCID: PMC10897528 DOI: 10.1002/ece3.10978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024] Open
Abstract
Color polymorphic species provide an excellent opportunity to investigate the ecology and evolution of intraspecific niche differences. The red-backed salamander, Plethodon cinereus, is a fully terrestrial lungless salamander with two common color forms, striped and unstriped. Previous research suggests the morphs may be differentially adapted to surface and subsurface microhabitats, with the unstriped morph being more fossorial. This hypothesis predicts that the unstriped morph should be more sensitive to the risks of surface activity (e.g., thermal stress, dehydration, predation), and therefore be more selective than striped morphs when choosing soil surface microhabitats. To test this hypothesis, we experimentally manipulated leaf litter mass in small forest patches (~0.45 m2). Leaf litter addition reduced soil temperatures, buffered against changes in air temperature, and likely provided physical protection from predators. Over 3 years, we found that unstriped adults responded positively to leaf litter addition, but striped adults did not. In addition, unstriped morphs spent significantly more time in protective refuges (opaque, moistened tubes) than striped morphs in laboratory assays. Taken together, the field and laboratory results support the hypothesis that the unstriped morph is more sensitive to the risks of surface activity, and therefore is more likely to be fossorial. This difference in microhabitat use, combined with spatiotemporal variation in leaf litter accumulation on the forest floor, may play an important role in the maintenance of the polymorphism.
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Affiliation(s)
- Cory S Straub
- Department of Biology Ursinus College Collegeville Pennsylvania USA
| | - Rosella G Cuomo
- Department of Biology Ursinus College Collegeville Pennsylvania USA
| | - Gabriel Jimenez
- Department of Biology Ursinus College Collegeville Pennsylvania USA
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Ojeda-Marín C, Cervantes I, Formoso-Rafferty N, Gutiérrez JP. Genomic inbreeding measures applied to a population of mice divergently selected for birth weight environmental variance. Front Genet 2023; 14:1303748. [PMID: 38155710 PMCID: PMC10752941 DOI: 10.3389/fgene.2023.1303748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023] Open
Abstract
This study aimed to compare different inbreeding measures estimated from pedigree and molecular data from two divergent mouse lines selected for environmental birth weight during 26 generations. Furthermore, the performance of different approaches and both molecular and pedigree data sources for estimating Ne were tested in this population. A total of 1,699 individuals were genotyped using a high-density genotyping array. Genomic relationship matrices were used to calculate molecular inbreeding: Nejati-Javaremi (F NEJ), Li and Horvitz (F L&H), Van Raden method 1 (F VR1) and method 2 (F VR2), and Yang (F YAN). Inbreeding based on runs of homozygosity (F ROH) and pedigree inbreeding (F PED) were also computed. F ROH, F NEJ, and F L&H were also adjusted for their average values in the first generation of selection and named F ROH0, F NEJ0, and F L&H0. ∆F was calculated from pedigrees as the individual inbreeding rate between the individual and his parents (∆F PEDt) and individual increases in inbreeding (∆F PEDi). Moreover, individual ∆F was calculated from the different molecular inbreeding coefficients (∆F NEJ0, ∆F L&H, ∆F L&H0, ∆F VR1, ∆F VR2, ∆F YAN, and ∆F ROH0). The Ne was obtained from different ∆F, such as Ne PEDt, Ne PEDi, Ne NEJ0, Ne L&H, Ne L&H0, Ne VR1, Ne VR2, Ne YAN, and Ne ROH0. Comparing with F PED , F ROH , F NEJ and F VR2 overestimated inbreeding while F NEJ0 , F L&H , F L&H0 , F VR1 and F YAN underestimated inbreeding. Correlations between inbreeding coefficients and ∆F were calculated. F ROH had the highest correlation with F PED (0.89); F YAN had correlations >0.95 with all the other molecular inbreeding coefficients. Ne PEDi was more reliable than Ne PEDt and presented similar behaviour to Ne L&H0 and Ne NEJ0. Stable trends in Ne were not observed until the 10th generation. In the 10th generation Ne PEDi was 42.20, Ne L&H0 was 45.04 and Ne NEJ0 was 45.05 and in the last generation these Ne were 35.65, 35.94 and 35.93, respectively F ROH presented the highest correlation with F PED, which addresses the identity by descent probability (IBD). The evolution of Ne L&H0 and Ne NEJ0 was the most similar to that of Ne PEDi. Data from several generations was necessary to reach a stable trend for Ne, both with pedigree and molecular data. This population was useful to test different approaches to computing inbreeding coefficients and Ne using molecular and pedigree data.
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Affiliation(s)
- Candela Ojeda-Marín
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Nora Formoso-Rafferty
- Departamento de Producción Agraria, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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EL Nagar AG, Heddi I, Sosa-Madrid BS, Blasco A, Hernández P, Ibáñez-Escriche N. Genome-Wide Association Study of Maternal Genetic Effects on Intramuscular Fat and Fatty Acid Composition in Rabbits. Animals (Basel) 2023; 13:3071. [PMID: 37835677 PMCID: PMC10571580 DOI: 10.3390/ani13193071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Maternal genetic effects (MGE) could affect meat quality traits such as intramuscular fat (IMF) and its fatty acid composition. However, it has been scarcely studied, especially in rabbits. The objectives of the present study were, first, to assess the importance of MGE on intramuscular fat and fatty acid composition by applying a Bayesian maternal animal model in two rabbit lines divergently selected for IMF. The second objective was to identify genomic regions and candidate genes of MGE that are associated with the traits of these offspring, using Bayesian methods in a Genome Wide Association Study (GWAS). Quantitative analyses were performed using data from 1982 rabbits, and 349 animals from the 9th generation and 76 dams of the 8th generation with 88,512 SNPs were used for the GWAS. The studied traits were IMF, saturated fatty acids (total SFA, C14:0; myristic acid, C16:0; palmitic acid and C18:0; stearic acid), monounsaturated fatty acids (total MUFA, C16:1n-7; palmitoleic acid and C18:1n-9; oleic acid), polyunsaturated fatty acids (total PUFA, C18:2n-6; linoleic acid, C18:3n-3; α-linolenic acid and C20:4n-6; arachidonic acid), MUFA/SFA and PUFA/SFA. The proportion of phenotypic variance explained by the maternal genetic effect ranged from 8 to 22% for IMF, depending on the model. For fatty acid composition, the proportion of phenotypic variance explained by maternal genetic effects varied from 10% (C18:0) to 46% (MUFA) in a model including both direct and additive maternal genetic effects, together with the common litter effect as a random variable. In particular, there were significant direct maternal genetic correlations for C16:0, C18:1n9, C18:2n6, SFA, MUFA, and PUFA with values ranging from -0.53 to -0.89. Relevant associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU5 and OCU19 containing some relevant candidates (TANC2, ACE, MAP3K3, TEX2, PRKCA, SH3GL2, CNTLN, RPGRIP1L and FTO) related to lipid metabolism, binding, and obesity. These regions explained about 1.2 to 13.9% of the total genomic variance of the traits studied. Our results showed an important maternal genetic effect on IMF and its fatty acid composition in rabbits and identified promising candidate genes associated with these traits.
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Affiliation(s)
- Ayman G. EL Nagar
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
- Department of Animal Production, Faculty of Agriculture at Moshtohor, Benha University, Benha 13736, Egypt
| | - Imen Heddi
- Centro Regional de Selección y Reproducción Animal (CERSYRA), Av. del Vino, 10, 13300 Valdepeñas, Spain
| | - Bolívar Samuel Sosa-Madrid
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Pilar Hernández
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
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Coves S, Soengas P, Velasco P, Fernández JC, Cartea ME. New vegetable varieties of Brassica rapa and Brassica napus with modified glucosinolate content obtained by mass selection approach. Front Nutr 2023; 10:1198121. [PMID: 37521419 PMCID: PMC10373736 DOI: 10.3389/fnut.2023.1198121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Background Glucosinolates (GSLs) constitute a characteristic group of secondary metabolites present in the Brassica genus. These compounds confer resistance to pests and diseases. Moreover, they show allelopathic and anticarcinogenic effects. All those effects are dependent on the chemical structure of the GSL. The modification of the content of specific GSLs would allow obtaining varieties with enhanced resistance and/or improved health benefits. Moreover, the attainment of varieties with the same genetic background but with divergent GSLs concentration will prompt the undertaking of studies on their biological effects. Objective and Methods The objective of this study was to evaluate the efficacy of two divergent mass selection programs to modify GSL content in the leaves of two Brassica species: nabicol (Brassica napus L.), selected by glucobrassicanapin (GBN), and nabiza (Brassica rapa L.), selected by gluconapin (GNA) through several selection cycles using cromatographic analysis. Results The response to selection fitted a linear regression model with no signs of variability depletion for GSL modification in either direction, but with higher efficiency in reducing the selected GSL than in the increasing. The selection was also effective in other parts of the plant, suggesting that there is a GSL translocation in the plant or a modification in their synthesis pathway that is not-organ specific. There was an indirect response of selection in other GSL; thus this information should be considered when designing breeding programs. Finally, populations obtained by selection have the same agronomic performance or even better than the original population. Conclusion Therefore, mass selection seems to be a good method to modify the content of specific GSL in Brassica crops.
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Irimia RE, Montesinos D, Chaturvedi A, Sanders I, Hierro JL, Sotes G, Cavieres LA, Eren Ö, Lortie CJ, French K, Brennan AC. Trait evolution during a rapid global weed invasion despite little genetic differentiation. Evol Appl 2023; 16:997-1011. [PMID: 37216028 PMCID: PMC10197227 DOI: 10.1111/eva.13548] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/12/2023] [Accepted: 03/23/2023] [Indexed: 05/24/2023] Open
Abstract
Invasive species often possess a great capacity to adapt to novel environments in the form of spatial trait variation, as a result of varying selection regimes, genetic drift, or plasticity. We explored the geographic differentiation in several phenotypic traits related to plant growth, reproduction, and defense in the highly invasive Centaurea solstitialis by measuring neutral genetic differentiation (F ST), and comparing it with phenotypic differentiation (P ST), in a common garden experiment in individuals originating from regions representing the species distribution across five continents. Native plants were more fecund than non-native plants, but the latter displayed considerably larger seed mass. We found indication of divergent selection for these two reproductive traits but little overall genetic differentiation between native and non-native ranges. The native versus invasive P ST-F ST comparisons demonstrated that, in several invasive regions, seed mass had increased proportionally more than the genetic differentiation. Traits displayed different associations with climate variables in different regions. Both capitula numbers and seed mass were associated with winter temperature and precipitation and summer aridity in some regions. Overall, our study suggests that rapid evolution has accompanied invasive success of C. solstitialis and provides new insights into traits and their genetic bases that can contribute to fitness advantages in non-native populations.
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Affiliation(s)
- Ramona E. Irimia
- Centre for Functional Ecology, Department of Life SciencesUniversity of CoimbraCoimbraPortugal
- Plant Evolutionary Ecology, Institute of Evolution and EcologyUniversity of TübingenTübingenGermany
| | - Daniel Montesinos
- Centre for Functional Ecology, Department of Life SciencesUniversity of CoimbraCoimbraPortugal
- Australian Tropical HerbariumJames Cook UniversityQueenslandCairnsAustralia
| | - Anurag Chaturvedi
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Environmental Genomics Group, School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Ian Sanders
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - José L. Hierro
- Laboratorio de Ecología, Biogeografía y Evolución Vegetal (LEByEV), Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad Nacional de La Pampa (UNLPam)Santa RosaArgentina
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, UNLPamSanta RosaArgentina
| | - Gastón Sotes
- Laboratorio de Ecología, Biogeografía y Evolución Vegetal (LEByEV), Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad Nacional de La Pampa (UNLPam)Santa RosaArgentina
| | - Lohengrin A. Cavieres
- Departamento de Botánica, Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Instituto de Ecología y Biodiversidad (IEB)SantiagoChile
| | - Özkan Eren
- Aydın Adnan Menderes Üniversitesi, Biyoloji Bölümü, Fen‐Edebiyat FakültesiAydınTurkey
| | - Christopher J. Lortie
- Department of BiologyYork UniversityOntarioTorontoCanada
- The National Center for Ecological Analysis and Synthesis (NCEAS), UCSBCaliforniaUSA
| | - Kristine French
- School of Earth, Atmospheric and Life SciencesUniversity of WollongongNew South WalesWollongongAustralia
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Li W, Jia H, Li M, Huang Y, Chen W, Yin P, Yang Z, Chen Q, Tian F, Zhang Z, Yang X, Liu L. Divergent selection of KNR6 maximizes grain production by balancing the flowering-time adaptation and ear size in maize. Plant Biotechnol J 2023. [PMID: 37061865 DOI: 10.1111/pbi.14050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/13/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Affiliation(s)
- Weiya Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Haitao Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Food Crops Institute, Hubei Academy of Agricultural Science, Hubei Hongshan Laboratory, Wuhan, China
| | - Manfei Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yiqin Huang
- Food Crops Institute, Hubei Academy of Agricultural Science, Hubei Hongshan Laboratory, Wuhan, China
| | - Wenkang Chen
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Pengfei Yin
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Zhixing Yang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Qiuyue Chen
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Feng Tian
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Ramírez-Valiente JA, Solé-Medina A, Robledo-Arnuncio JJ, Ortego J. Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks. Mol Ecol 2023; 32:983-999. [PMID: 36479963 DOI: 10.1111/mec.16816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Improving our knowledge of how past climate-driven selection has acted on present-day trait population divergence is essential to understand local adaptation processes and improve our predictions of evolutionary trajectories in the face of altered selection pressures resulting from climate change. In this study, we investigated signals of selection on traits related to drought tolerance and growth rates in two Mediterranean oak species (Quercus faginea and Q. lusitanica) with contrasting distribution ranges and climatic niches. We genotyped 182 individuals from 24 natural populations of the two species using restriction-site-associated DNA sequencing and conducted a thorough functional characterization in 1602 seedlings from 21 populations cultivated in common garden experiments under contrasting watering treatments. Our genomic data revealed that both Q. faginea and Q. lusitanica have very weak population genetic structure, probably as a result of high rates of pollen-mediated gene flow among populations and large effective population sizes. In contrast, common garden experiments showed evidence of climate-driven divergent selection among populations on traits related to leaf morphology, physiology and growth in both species. Overall, our study suggests that climate is an important selective factor for Mediterranean oaks and that ecophysiological traits have evolved in drought-prone environments even in a context of very high rates of gene flow among populations.
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Affiliation(s)
- José Alberto Ramírez-Valiente
- Ecological and Forestry Applications Research Centre, CREAF, Campus de Bellaterra (UAB), Cerdanyola del Vallès, Spain
| | - Aida Solé-Medina
- Instituto de Ciencias Forestales (ICIFOR-INIA), CSIC, Madrid, Spain
| | | | - Joaquín Ortego
- Department of Ecology and Evolution, Estación Biológica de Doñana, EBD-CSIC, Seville, Spain
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11
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Harrison SJ, Siegel PB, Honaker CF, Lewis RM. Population dynamics of a long-term selection experiment in White Plymouth Rock chickens selected for low or high body weight. Poult Sci 2023; 102:102575. [PMID: 36907125 DOI: 10.1016/j.psj.2023.102575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
The population dynamics of 2 lines of chickens from a long-term (59 generations) selection experiment were assessed based on pedigree data. These lines were propagated from phenotypic selection for low and high 8-wk BW in White Plymouth Rock chickens. Our objective was to determine whether the 2 lines maintained similar population structures over the selection horizon to allow meaningful comparisons of their performance data. A complete pedigree of 31,909 individuals, consisting of 102 founders, 1,064 from the parental generation, and 16,245 low weight (LWS) and 14,498 high weight (HWS) select chickens, was available. Inbreeding (F) and average relatedness (AR) coefficients were computed. Average F per generation and AR coefficients were 1.3 (SD 0.8) % and 0.53 (SD 0.001) for LWS, and 1.5 (SD 1.1) % and 0.66 (SD 0.001) for HWS. Mean F for the entire pedigree was 0.26 (0.16) and 0.33 (0.19), and maximum F was 0.64 and 0.63, in LWS and HWS, respectively. Based on Wright's fixation index, at generation 59, substantial genetic differences were established between lines. The effective population size was 39 in LWS and 33 in HWS. The effective number of founders was 17 and 15, effective number of ancestors were 12 and 8, and genome equivalents were 2.5 and 1.9 in LWS and HWS, respectively. About 30 founders explained the marginal contribution to both lines. By generation 59, only 7 male and 6 female founders contributed to both lines. Moderately high levels of inbreeding and low effective population sizes were inevitable, as this was a closed population. However, effects on the fitness of the population were expected to be less substantial because founders were a combination of 7 lines. The effective numbers of founders and ancestors were relatively low compared to the actual number of founders, as few ancestors contributed to descendants. Based on these evaluations, it can be inferred that LWS and HWS had similar population structures. Comparisons of selection responses in the 2 lines therefore should be reliable.
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12
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Kochish II, Titov VY, Nikonov IN, Brazhnik EA, Vorobyov NI, Korenyuga MV, Myasnikova OV, Dolgorukova AM, Griffin DK, Romanov MN. Unraveling signatures of chicken genetic diversity and divergent selection in breed-specific patterns of early myogenesis, nitric oxide metabolism and post-hatch growth. Front Genet 2023; 13:1092242. [PMID: 36712856 PMCID: PMC9874007 DOI: 10.3389/fgene.2022.1092242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction: Due to long-term domestication, breeding and divergent selection, a vast genetic diversity in poultry currently exists, with various breeds being characterized by unique phenotypic and genetic features. Assuming that differences between chicken breeds divergently selected for economically and culturally important traits manifest as early as possible in development and growth stages, we aimed to explore breed-specific patterns and interrelations of embryo myogenesis, nitric oxide (NO) metabolism and post-hatch growth rate (GR). Methods: These characteristics were explored in eight breeds of different utility types (meat-type, dual purpose, egg-type, game, and fancy) by incubating 70 fertile eggs per breed. To screen the differential expression of seven key myogenesis associated genes (MSTN, GHR, MEF2C, MYOD1, MYOG, MYH1, and MYF5), quantitative real-time PCR was used. Results: We found that myogenesis associated genes expressed in the breast and thigh muscles in a coordinated manner showing breed specificity as a genetic diversity signature among the breeds studied. Notably, coordinated ("accord") expression patterns of MSTN, GHR, and MEFC2 were observed both in the breast and thigh muscles. Also, associated expression vectors were identified for MYOG and MYOD1 in the breast muscles and for MYOG and MYF5 genes in the thigh muscles. Indices of NO oxidation and post-hatch growth were generally concordant with utility types of breeds, with meat-types breeds demonstrating higher NO oxidation levels and greater GR values as compared to egg-type, dual purpose, game and fancy breeds. Discussion: The results of this study suggest that differences in early myogenesis, NO metabolism and post-hatch growth are breed-specific; they appropriately reflect genetic diversity and accurately capture the evolutionary history of divergently selected chicken breeds.
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Affiliation(s)
- Ivan I. Kochish
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | - Vladimir Yu. Titov
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia,Federal Scientific Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Oblast, Russia
| | - Ilya N. Nikonov
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | | | - Nikolai I. Vorobyov
- All-Russia Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - Maxim V. Korenyuga
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | - Olga V. Myasnikova
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | - Anna M. Dolgorukova
- Federal Scientific Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Oblast, Russia
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Michael N. Romanov
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia,School of Biosciences, University of Kent, Canterbury, United Kingdom,*Correspondence: Michael N. Romanov,
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13
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Schuldiner‐Harpaz T, Merrill RM, Jiggins CD. Evolution of physical linkage between loci controlling ecological traits and mating preferences. J Evol Biol 2022; 35:1537-1547. [PMID: 36196988 PMCID: PMC9827829 DOI: 10.1111/jeb.14105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/26/2022] [Accepted: 08/08/2022] [Indexed: 01/12/2023]
Abstract
Coupling of multiple barriers to gene-flow, such as divergent local adaptation and reproductive isolation, facilitates speciation. However, alleles at loci that contribute to barrier effects can be dissociated by recombination. Models of linkage between diverging alleles often consider elements that reduce recombination, such as chromosomal inversions and alleles that modify recombination rate between existing loci. In contrast, here, we consider the evolution of linkage due to the close proximity of loci on the same chromosome. Examples of such physical linkage exist in several species, but in other cases, strong associations are maintained without physical linkage. We use an individual-based model to study the conditions under which the physical linkage between loci controlling ecological traits and mating preferences might be expected to evolve. We modelled a single locus controlling an ecological trait that acts also as a mating cue. Mating preferences are controlled by multiple loci, formed by mutations that are randomly placed in the "genome", within varying distances from the ecological trait locus, allowing us to examine which genomic architectures spread across the population. Our model reveals that stronger physical linkage is favoured when mating preferences and selection are weaker. Under such conditions mating among divergent phenotypes is more frequent, and matching ecological trait and mating preference alleles are more likely to become dissociated by recombination, favouring the evolution of genetic linkage. While most theoretical studies on clustering of divergent loci focus on how physical linkage influences speciation, we show how physical linkage itself can arise, establishing conditions that can favour speciation.
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14
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Zou X, Liu T, Li Y, Chen P, Yan X, Ma J, Ji J, Qu H, Cai M, He Y, He J, Xu X, Lin C, Zhou G, Shu D, Luo C. Long-term divergent selection for residual feed intake in Chinese broiler chickens. Poult Sci 2022; 102:102298. [PMID: 36638759 PMCID: PMC9843260 DOI: 10.1016/j.psj.2022.102298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 01/12/2023] Open
Abstract
This study aimed to assess the effect of inbreeding on production traits using a long-term closed-line population recorded for residual feed intake (RFI). The study first used data from a previously reported population to determine the appropriate period of divergent selection for RFI. The results showed that RFI had similar moderate heritability estimates (0.28-0.34) during the fast-growing period (7-12 wk), and RFI at 7 to 10 wk had the highest heritability (0.34). Therefore, divergent selection was performed in a Chinese broiler population for RFI at 7 to 10 wk; the total sample size from generations zero (G0) to 13 was 9050. The divergence between the 2 lines increased steadily throughout generations, resulting in G13 with average RFI values of 304.55 in high RFI (HRFI) males, -160.31 in low RFI (LRFI) males, 296.30 in HRFI females and -157.55 in LRFI females. The feed intake (FI) and feed conversion ratio were almost higher in HRFI broilers than in LRFI broilers, and the magnitude of the difference in FI increased from approximately 4% for both sexes in G1 to approximately 33% in G13. Body weight gain was irregular from G1 to G13 and higher in LRFI broilers than in HRFI broilers after G10. Indeed, the HRFI broilers consumed more food, but they were lighter than LRFI broilers. In G13, LRFI males had heavier slaughter weight, longer cecum length, more white blood cells (WBC), red blood cells (RBC) and hemoglobin (HGB), but triglycerides, lower dressed percentage, percentage of half eviscerated yield, and eviscerated yield than HRFI males. LRFI females had a higher percentage of breast muscle and gizzard yield, longer cecum length, and more WBCs, RBCs and HGB but less abdominal fat and serum total cholesterol than HRFI females. This study was the first to verify that long-term divergent selection for RFI in Chinese broiler chickens is positive and beneficial.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dingming Shu
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Key Laboratory of Animal Breeding and Nutrition & Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Key Laboratory of Animal Breeding and Nutrition & Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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15
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Dementieva NV, Shcherbakov YS, Tyshchenko VI, Terletsky VP, Vakhrameev AB, Nikolaeva OA, Ryabova AE, Azovtseva AI, Mitrofanova OV, Peglivanyan GK, Reinbah NR, Griffin DK, Romanov MN. Comparative Analysis of Molecular RFLP and SNP Markers in Assessing and Understanding the Genetic Diversity of Various Chicken Breeds. Genes (Basel) 2022; 13:genes13101876. [PMID: 36292761 PMCID: PMC9601448 DOI: 10.3390/genes13101876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 11/04/2022] Open
Abstract
Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry.
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Affiliation(s)
- Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence: (N.V.D.); (M.N.R.)
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | | | - Anatoly B. Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Anna E. Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Anastasiia I. Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Grigoriy K. Peglivanyan
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia R. Reinbah
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | | | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- Correspondence: (N.V.D.); (M.N.R.)
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16
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Cullere M, Szendrő Z, Matics Z, Gerencsér Z, Kasza R, Donkó T, Dalle Zotte A. Rabbits Divergently Selected for Total Body Fat Content: Changes in Proximate Composition and Fatty Acids of Different Meat Portions. Animals (Basel) 2022; 12. [PMID: 36139255 DOI: 10.3390/ani12182396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/23/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
The present research studied the potential of a four-generation divergent selection (Pannon maternal rabbit lines) based on the total body fat content to create two rabbit lines with different meat attributes: a Fat line to deliver greater amounts of healthy fatty acids for newborns and infants, and a Lean line intended to provide lean meat for everyday consumption. Selection was based on the fat index calculated in 10-week-old live rabbits by means of computed tomography (CT). For each generation, 60 rabbits/line were fed ad libitum with commercial pellet from weaning (5 weeks) to slaughter (11 weeks). A total of 15 rabbits/line were randomly selected for meat quality evaluations: the longissimus thoracis et lumborum muscles (LTLs), hind legs (HLs), forelegs (FLs) and abdominal wall (AW) were analyzed for their proximate composition and fatty acid (FA) profile. FA contents were also calculated. Results highlighted that it was possible to obtain leaner meat for everyday consumption in most meat portions starting from generation 4 (7.93 vs. 11.9, 5.10 vs. 5.98 and 7.26 vs. 10.9 g of lipids/100 g of meat in Lean and Fat groups for the FLs, HLs and AW, respectively). The sole exception was the LTLs, which were not affected by the divergent selection. The total PUFA amount increased in FL and AW (p < 0.05) portions of the Fat line only, attributable to a greater n-3 amount (151 vs. 216 and 73 vs. 143 mg/100 g of meat in Lean and Fat groups for the FLs and AW, respectively).
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17
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Wang Z, Cai X, Jiang X, Xia Q, Li L, Lu B. Sympatric genetic divergence between early- and late-season weedy rice populations. New Phytol 2022; 235:2066-2080. [PMID: 35637631 PMCID: PMC9544748 DOI: 10.1111/nph.18288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Sympatric genetic divergence is the most appealing and controversial pattern in the theory of ecological speciation. Examples that support sympatric genetic divergence in plant species are extremely rare. Solid evidence of sympatric genetic divergence will provide deep insights for revealing the underlying mechanisms of ecological speciation. We analysed the total genomic DNA sequences of 120 weedy rice (WR; Oryza sativa f. spontanea) plants, representing three WR population pairs separately from three early- and late-season rice fields, in comparison with those of the co-occurring rice cultivars and other rice materials. We detected substantial genetic divergence within the pairs of the sympatric early- and late-season WR populations, although genetic divergence was unevenly distributed across the genomes. Restricted gene flow was determined between the sympatric WR populations, resulting in their distinct genetic structures. We also detected relatively low genetic diversity that was likely to be associated with stronger selection in early-season WR populations. Our findings provide strong evidence for sympatric genetic divergence between the WR populations in the same fields but in different seasons. We conclude that temporal isolation plays an important role in creating genetic divergence between sympatric populations/species in plants.
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Affiliation(s)
- Zhi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Xingxing Cai
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Xiao‐Qi Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Qi‐Yu Xia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction RegionsInstitute of Tropical Bioscience and Biotechnology, CATASHaikou571101China
| | - Lin‐Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Bao‐Rong Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
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18
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Cooper HF, Best RJ, Andrews LV, Corbin JPM, Garthwaite I, Grady KC, Gehring CA, Hultine KR, Whitham TG, Allan GJ. Evidence of climate-driven selection on tree traits and trait plasticity across the climatic range of a riparian foundation species. Mol Ecol 2022; 31:5024-5040. [PMID: 35947510 DOI: 10.1111/mec.16645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022]
Abstract
Selection on quantitative traits by heterogeneous climatic conditions can lead to substantial trait variation across a species range. In the context of rapidly changing environments, however, it is equally important to understand selection on trait plasticity. To evaluate the role of selection in driving divergences in traits and their associated plasticities within a widespread species, we compared molecular and quantitative trait variation in Populus fremontii (Fremont cottonwood), a foundation riparian distributed throughout Arizona. Using SNP data and genotypes from 16 populations reciprocally planted in three common gardens, we first performed QST -FST analyses to detect selection on traits and trait plasticity. We then explored the environmental drivers of selection using trait-climate and plasticity-climate regressions. Three major findings emerged: 1) There was significant genetic variation in traits expressed in each of the common gardens and in the phenotypic plasticity of traits across gardens, both of which were heritable. 2) Based on QST -FST comparisons, there was evidence of selection in all traits measured; however, this result varied from no effect in one garden to highly significant in another, indicating that detection of past selection is environmentally dependent. We also found strong evidence of divergent selection on plasticity across environments for two traits. 3) Traits and/or their plasticity were often correlated with population source climate (R2 up to 0.77 and 0.66, respectively). These results suggest that steep climate gradients across the Southwest have played a major role in shaping the evolution of divergent phenotypic responses in populations and genotypes now experiencing climate change.
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Affiliation(s)
- Hillary F Cooper
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Rebecca J Best
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Lela V Andrews
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA
| | - Jaclyn P M Corbin
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Iris Garthwaite
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Kevin C Grady
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Catherine A Gehring
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Kevin R Hultine
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ, USA
| | - Thomas G Whitham
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Gerard J Allan
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
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19
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Leaver M, Moreno E, Kayhan M, McGaughran A, Rödelsperger C, Sommer RJ, Hyman AA. Adaptation to environmental temperature in divergent clades of the nematode Pristionchus pacificus. Evolution 2022; 76:1660-1673. [PMID: 35696526 DOI: 10.1111/evo.14520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 02/03/2022] [Accepted: 03/10/2022] [Indexed: 01/22/2023]
Abstract
Because of ongoing climate change, populations of organisms are being subjected to stressful temperatures more often. This is especially problematic for ectothermic organisms, which are likely to be more sensitive to changes in temperature. Therefore, we need to know if ectotherms have adapted to environmental temperature and, if so, what are the evolutionary mechanisms behind such adaptation. Here, we use the nematode Pristionchus pacificus as a case study to investigate thermal adaptation on the Indian Ocean island of La Réunion, which experiences a range of temperatures from coast to summit. We study the evolution of high-temperature tolerance by constructing a phylogenetic tree of strains collected from many different thermal niches. We show that populations of P. pacificus at low altitudes have higher fertility at warmer temperatures. Most likely, this phenotype has arisen recently and at least twice independently, consistent with parallel evolution. We also studied low-temperature tolerance and showed that populations from high altitudes have increased their fertility at cooler temperatures. Together, these data indicate that P. pacificus strains on La Réunion are subject to divergent selection, adapting to hot and cold niches at the coast and summit of the volcano. Precisely defining these thermal niches provides essential information for models that predict the impact of future climate change on these populations.
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Affiliation(s)
- Mark Leaver
- Biotechnologische Zentrum, Technische Universität Dresden, 01307, Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Eduardo Moreno
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Merve Kayhan
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.,Physiologisches Institut der Universität Zürich, Zürich, CH-8057, Switzerland
| | - Angela McGaughran
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.,Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, 3240, New Zealand
| | - Christian Rödelsperger
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Ralf J Sommer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Anthony A Hyman
- Biotechnologische Zentrum, Technische Universität Dresden, 01307, Dresden, Germany
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20
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de Souza AC, Donohue K, de Mattos EA. The effect of seed-dispersal timing on seedling recruitment is modulated by environmental conditions that vary across altitude in a threatened palm. Ann Bot 2022; 129:839-856. [PMID: 35325032 PMCID: PMC9292616 DOI: 10.1093/aob/mcac038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/22/2022] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS The timing of seed dispersal determines the environmental conditions that plants face during early life stages. In seasonal environments, selection is expected to favour dispersal timing that is matched to environmental conditions suitable for successful recruitment. Our aim here was to test whether the timing of seed dispersal influences seedling establishment success in two populations of Euterpe edulis that are located at contrasting altitudes, have different seed-dispersal phenologies and are subjected to distinct climatic conditions. METHODS We sowed E. edulis seeds in contrasting altitudes on different dates, and monitored seed germination, emergence and seedling establishment at each altitude over 4 years. At the high-altitude site, five seed-dispersal cohorts were established during the natural dispersal period. At the low-altitude site, three seed-dispersal cohorts were established during natural dispersal, and two were established either before or after natural dispersal. KEY RESULTS At the high-altitude site, seed-dispersal timing did not affect seed germination, seedling emergence or seedling establishment success. In contrast, at the low-altitude site, late seed dispersal near the end of the wet season resulted in a lower probability of seedling establishment, possibly due to the exposure of seeds, germinants and seedlings to unfavourable drought conditions. In addition, at the low-altitude site, the natural seed-dispersal period was poorly matched to favourable environmental conditions for seedling establishment. CONCLUSIONS The greater effect of seed-dispersal timing on seedling establishment at the low-altitude site is probably related to a more seasonal and drought-prone environment that favours a restricted period of seed dispersal. The magnitude of the effect of dispersal timing on seedling establishment success was modulated by environmental conditions that vary across altitude. Furthermore, reproductive phenology appears to be subject to more intense selection at the lower limit of the altitudinal range, due to a more restrictive window of opportunity for successful seedling establishment.
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Affiliation(s)
| | | | - Eduardo A de Mattos
- Departamento de Ecologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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21
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Rau D, Attene G, Rodriguez M, Baghino L, Pisanu AB, Sanna D, Acquadro A, Portis E, Comino C. The Population Structure of a Globe Artichoke Worldwide Collection, as Revealed by Molecular and Phenotypic Analyzes. Front Plant Sci 2022; 13:898740. [PMID: 35865281 PMCID: PMC9294547 DOI: 10.3389/fpls.2022.898740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies.
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Affiliation(s)
- Domenico Rau
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Limbo Baghino
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Anna Barbara Pisanu
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Davide Sanna
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Cinzia Comino
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
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22
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Clark JD, Benham PM, Maldonado JE, Luther DA, Lim HC. Maintenance of local adaptation despite gene flow in a coastal songbird. Evolution 2022; 76:1481-1494. [PMID: 35700208 PMCID: PMC9545442 DOI: 10.1111/evo.14538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/09/2022] [Accepted: 03/19/2022] [Indexed: 01/22/2023]
Abstract
Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist, and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment, not isolation by distance. A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.
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Affiliation(s)
- Jonathan D. Clark
- Department of Environmental Science and PolicyGeorge Mason UniversityFairfaxVirginia22030,Current Address: Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew Hampshire03824
| | - Phred M. Benham
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia94720
| | - Jesus E. Maldonado
- Department of Environmental Science and PolicyGeorge Mason UniversityFairfaxVirginia22030,Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonD.C.20013
| | - David A. Luther
- Department of BiologyGeorge Mason UniversityFairfaxVirginia22030
| | - Haw Chuan Lim
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonD.C.20013,Department of BiologyGeorge Mason UniversityFairfaxVirginia22030
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23
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Gabián M, Morán P, Saura M, Carvajal-Rodríguez A. Detecting Local Adaptation between North and South European Atlantic Salmon Populations. Biology (Basel) 2022; 11:933. [PMID: 35741456 PMCID: PMC9219887 DOI: 10.3390/biology11060933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Pollution and other anthropogenic effects have driven a decrease in Atlantic salmon (Salmo salar) in the Iberian Peninsula. The restocking effort carried out in the 1980s, with salmon from northern latitudes with the aim of mitigating the decline of native populations, failed, probably due to the deficiency in adaptation of foreign salmon from northern Europe to the warm waters of the Iberian Peninsula. This result would imply that the Iberian populations of Atlantic salmon have experienced local adaptation in their past evolutionary history, as has been described for other populations of this species and other salmonids. Local adaptation can occur by divergent selections between environments, favoring the fixation of alleles that increase the fitness of a population in the environment it inhabits relative to other alleles favored in another population. In this work, we compared the genomes of different populations from the Iberian Peninsula (Atlantic and Cantabric basins) and Scotland in order to provide tentative evidence of candidate SNPs responsible for the adaptive differences between populations, which may explain the failures of restocking carried out during the 1980s. For this purpose, the samples were genotyped with a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations. As expected, most differences concerned the comparison of the Iberian Peninsula with Scotland, although there were also differences between Atlantic and Cantabric populations. A high proportion of the genes identified are related to development and cellular metabolism, DNA transcription and anatomical structure. A particular SNP was identified within the NADP-dependent malic enzyme-2 (mMEP-2*), previously reported by independent studies as a candidate for local adaptation in salmon from the Iberian Peninsula. Interestingly, the corresponding SNP within the mMEP-2* region was consistent with a genomic pattern of divergent selection.
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Affiliation(s)
- María Gabián
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
| | - Paloma Morán
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
| | - María Saura
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain;
| | - Antonio Carvajal-Rodríguez
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
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24
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Joffard N, Olofsson C, Friberg M, Sletvold N. Extensive pollinator sharing does not promote character displacement in two orchid congeners. Evolution 2022; 76:749-764. [PMID: 35188979 DOI: 10.1111/evo.14446] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/07/2022] [Accepted: 01/18/2022] [Indexed: 01/22/2023]
Abstract
Pollinator sharing between close relatives can be costly and can promote pollination niche partitioning and floral divergence. This should be reflected by a higher species divergence in sympatry than in allopatry. We tested this hypothesis in two orchid congeners with overlapping distributions and flowering times. We characterized floral traits and pollination niches and quantified pollen limitation in 15 pure and mixed populations, and we measured phenotypic selection on floral traits and performed controlled crosses in one mixed site. Most floral traits differed between species, yet pollinator sharing was extensive. Only the timing of scent emission diverged more in mixed sites than in pure sites, and this was not mirrored by the timing of pollinator visitation. We did not detect divergent selection on floral traits. Seed production was pollen limited in most populations but not more severely in mixed sites than in pure sites. Interspecific crosses produced the same or a higher proportion of viable seeds than intraspecific crosses. The two orchid species attract the same pollinator species despite showing divergent floral traits. However, this does not promote character displacement, implying a low cost of pollinator sharing. Our results highlight the importance of characterizing both traits and ecological niches in character displacement studies.
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Affiliation(s)
- Nina Joffard
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden.,University of Lille, UMR 8198 - Evo-Eco-Paleo, Villeneuve d'Ascq, F-59655, France
| | - Caroliné Olofsson
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Magne Friberg
- Department of Biology, Lund University, Lund, SE-223 62, Sweden
| | - Nina Sletvold
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
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25
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Cheek RG, Forester BR, Salerno PE, Trumbo DR, Chen N, Sillett TS, Morrison SA, Ghalambor CK, Funk WC. Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species. Mol Ecol 2022; 31:2830-2846. [PMID: 35315161 PMCID: PMC9325526 DOI: 10.1111/mec.16438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022]
Abstract
We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km2 island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.
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Affiliation(s)
- Rebecca G Cheek
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Patricia E Salerno
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - T Scott Sillett
- Migratory Bird Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20013, USA
| | | | - Cameron K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
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26
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Formoso-Rafferty N, Gutiérrez JP, García-Álvarez A, Pérez T, Cervantes I. Impact of selection for birth weight variability on reproductive longevity: A mice model. J Anim Breed Genet 2022; 139:370-379. [PMID: 35305049 PMCID: PMC9314135 DOI: 10.1111/jbg.12676] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/24/2022] [Accepted: 03/04/2022] [Indexed: 11/29/2022]
Abstract
Uniformity, understood as a similar performance in relevant livestock traits, such as birth weight within the litter, is being included as one of the selection objectives in breeding programmes, especially for polytocous livestock species. A divergent selection experiment for birth weight within‐litter variability in mice during 23 generations showed that homogeneous animals were better for litter size, survival and feed efficiency but less heavy than heterogeneous animals. The aim of this study was to compare the reproductive longevity in both divergent lines as time to the end of the reproductive period. Two generations from both lines with an initial number of 43 females and 43 males were mated one to one and stayed together to have consecutive parturitions until the end of the reproductive life. Females were discarded when the time elapsed from the last parturition was longer than 63 days. The time to the end of the reproductive period between both lines was compared by fitting a Cox proportional hazard regression model adjusting for line, generation and its interaction. The rate of parturitions in both lines was also compared using a Prentice–Williams–Peterson model adjusted for the same effects. The low variability line was associated with a higher parturition rate, e.g., adjusted hazard ratio was 2.93 (95% CI 2.17–3.94). The Cox model showed that the low variability females also presented benefits of time to the end of the reproductive period, with an adjusted hazard ratio of 0.26 (95% CI 0.16–0.41). The median of reproductive days was 55.50 in the high variability line whilst the median was 252.50 days for the low variability females. The homogeneous line presented important reproductive advantages suggesting higher robustness and animal welfare. Further research should confirm whether the findings presented here of a better performance in the low variability line could be properly applied to some livestock species.
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Affiliation(s)
- Nora Formoso-Rafferty
- Departamento de Producción Agraria, E.T.S. Ingeniería Agronómica Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Andrés García-Álvarez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Teresa Pérez
- Departamento Estadística y Ciencia de los Datos, Facultad de Estudios Estadísticos, Universidad Complutense de Madrid, Madrid, Spain
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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27
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Maiti AK. Evolutionary Shift from Purifying Selection towards Divergent Selection of SARS-CoV2 Favors its Invasion into Multiple Human Organs. Virus Res 2022;:198712. [PMID: 35176330 DOI: 10.1016/j.virusres.2022.198712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 01/07/2023]
Abstract
SARS-CoV2 virus is believed to be originated from a closely related bat Coronavirus RaTG13 lineage and uses its key entry-point residues in S1 protein to attach with human ACE2 receptor. SARS-CoV2 could enter human from bat with its poorly developed entry-point residues much before its known appearance with slower mutation rate or recently with efficiently developed entry-point residues with higher mutation rate or through an intermediate host. Temporal analysis of SARS-CoV2 genome shows that its nucleotide substitution rate is as low as 27nt/year with an evolutionary rate of 9×10−4/site/year, which is well within the range of other RNA virus (10−4 to 10−6/site/year). TMRCA of SARS-CoV2 from bat RaTG13 lineage appears to be in between 9 and 14 years. Evolution of a critical entry-point residue Y493Q needs two substitutions with an intermediate virus carrying Y493H (Y>H>Q) but has not been identified in known twenty-nine bat CoV virus. Genetic codon analysis indicates that SARS-CoV2 evolution during propagation in human disobeys neutral evolution as nonsynonymous mutations surpass synonymous mutations with the increase of ω (dn/ds). Taken together, genetic data suggests that SARS-CoV2 is originated long time back before its appearance in human in 2019. Increase of ω signifies that SARs-CoV2 evolution is approaching towards diversifying selection from purifying selection predictably for its infection power to evade multiple human organs.
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Baker HK, Hankins DC, Shurin JB. Introgressive hybridization erodes morphological divergence between lentic and lotic habitats in an endangered minnow. Ecol Evol 2021; 11:13593-13600. [PMID: 34646492 PMCID: PMC8495819 DOI: 10.1002/ece3.8086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 11/24/2022] Open
Abstract
Introgressive hybridization may erode phenotypic divergence along environmental gradients, collapsing locally adapted populations into a hybrid swarm. Alternatively, introgression may promote phenotypic divergence by providing variation on which natural selection can act. In freshwater fishes, water flow often selects for divergent morphological traits in lake versus stream habitats. We tested the effects of introgression on lake-stream morphological divergence in the minnow Owens Tui Chub (Siphateles bicolor snyderi), which has been rendered endangered by introgession from the introduced Lahontan Tui Chub (Siphateles bicolor obesa). Using geometric morphometric analysis of 457 individual Tui Chub from thirteen populations, we found that both native and introgressing parent taxa exhibited divergent body and caudal fin shapes in lake versus stream habitats, but their trajectories of divergence were distinct. In contrast, introgressed populations exhibited intermediate body and caudal fin shapes that were not differentiated by habitat type, indicating that introgression has eroded phenotypic divergence along the lentic-lotic gradient throughout the historic range of the Owens Tui Chub. Individuals within hybrid populations were less morphologically variable than those within parent populations, suggesting hybrid adaptation to selective agents other than water flow or loss of variance by drift.
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Affiliation(s)
- Henry K. Baker
- Section of Ecology, Behavior, and EvolutionUniversity of California San DiegoLa JollaCAUSA
| | - Danielle C. Hankins
- Section of Ecology, Behavior, and EvolutionUniversity of California San DiegoLa JollaCAUSA
| | - Jonathan B. Shurin
- Section of Ecology, Behavior, and EvolutionUniversity of California San DiegoLa JollaCAUSA
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29
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White NJ, Butlin RK. Multidimensional divergent selection, local adaptation, and speciation. Evolution 2021; 75:2167-2178. [PMID: 34263939 DOI: 10.1111/evo.14312] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 12/24/2022]
Abstract
Divergent selection applied to one or more traits drives local adaptation and may lead to ecological speciation. Divergent selection on many traits might be termed "multidimensional" divergent selection. There is a commonly held view that multidimensional divergent selection is likely to promote local adaptation and speciation to a greater extent than unidimensional divergent selection. We disentangle the core concepts underlying dimensionality as a property of the environment, phenotypes, and genome. In particular, we identify a need to separate the overall strength of selection and the number of loci affected from dimensionality per se, and to distinguish divergence dimensionality from dimensionality of stabilizing selection. We then critically scrutinize this commonly held view that multidimensional selection promotes speciation, re-examining the evidence base from theory, experiments, and nature. We conclude that the evidence base is currently weak and generally suffers from confounding of possible causal effects. Finally, we propose several mechanisms by which multidimensional divergent selection and related processes might influence divergence, both as a driver and as a barrier.
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Affiliation(s)
- Nathan J White
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,Department of Marine Sciences, University of Gothenburg, Gothenburg, SE-40530, Sweden
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30
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Ghaleb W, Barre P, Teulat B, Ahmed LQ, Escobar-Gutiérrez AJ. Divergent Selection for Seed Ability to Germinate at Extreme Temperatures in Perennial Ryegrass ( Lolium perenne L.). Front Plant Sci 2021; 12:794488. [PMID: 35173750 PMCID: PMC8841656 DOI: 10.3389/fpls.2021.794488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/14/2021] [Indexed: 05/03/2023]
Abstract
Various adaptive mechanisms can ensure that seedlings are established at the most favourable time and place. These mechanisms include seed dormancy i.e., incapacity to germinate in any environment without a specific environmental trigger and inhibition i.e., incapacity to germinate in an unfavourable environment (water availability, temperature: thermoinhibition and light). The objective of this research was to study in the temperate range for germination of forage and turf grass species perennial ryegrass, if the thermal requirements for germination are under genetic controlled and could be selectively bred. Two divergent selections of three cycles were realized on a natural population: one to select for the capacity to germinate at 10°C vs. the impossibility to germinate at 10°C, and one to select for the capacity to germinate at 32°C vs. the impossibility to germinate at 32°C. Seeds of all the lots obtained from the two divergent selections were then germinated at constant temperatures from 5 to 35°C to evaluate their germination ability. Concerning the positive selection, the first cycle of positive selection at 10°C was highly efficient with a very strong increase in the germination percentage. However, afterward no selection effect was observed during the next two cycles of positive selection. By contrast, the positive selection at 32°C was efficient during all cycles with a linear increase of the percentage of germination at 32°C. Concerning the negative selection, we observed only a large positive effect of the first cycle of selection at 10°C. These findings demonstrate that seed thermoinhibition at 10 and 32°C observed in a natural population of perennial ryegrass has a genetic basis and a single recessive gene seems to be involved at 10°C.
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Affiliation(s)
- Wagdi Ghaleb
- INRAE, URP3F, F-86600 Lusignan, France
- Biotechnology Research Center (BTRC), Tripoli, Libya
| | - Philippe Barre
- INRAE, URP3F, F-86600 Lusignan, France
- *Correspondence: Philippe Barre,
| | - Béatrice Teulat
- Univ. Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France
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Galimberti M, Leuenberger C, Wolf B, Szilágyi SM, Foll M, Wegmann D. Detecting Selection from Linked Sites Using an F-Model. Genetics 2020; 216:1205-1215. [PMID: 33067324 PMCID: PMC7768260 DOI: 10.1534/genetics.120.303780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/03/2020] [Indexed: 11/18/2022] Open
Abstract
Allele frequencies vary across populations and loci, even in the presence of migration. While most differences may be due to genetic drift, divergent selection will further increase differentiation at some loci. Identifying those is key in studying local adaptation, but remains statistically challenging. A particularly elegant way to describe allele frequency differences among populations connected by migration is the F-model, which measures differences in allele frequencies by population specific FST coefficients. This model readily accounts for multiple evolutionary forces by partitioning FST coefficients into locus- and population-specific components reflecting selection and drift, respectively. Here we present an extension of this model to linked loci by means of a hidden Markov model (HMM), which characterizes the effect of selection on linked markers through correlations in the locus specific component along the genome. Using extensive simulations, we show that the statistical power of our method is up to twofold higher than that of previous implementations that assume sites to be independent. We finally evidence selection in the human genome by applying our method to data from the Human Genome Diversity Project (HGDP).
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Affiliation(s)
- Marco Galimberti
- Department of Biology, University of Fribourg, 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland
| | | | - Beat Wolf
- iCoSys, University of Applied Sciences Western Switzerland, Fribourg, 1700 Switzerland
| | - Sándor Miklós Szilágyi
- Department of Informatics, University of Medicine, Pharmacy, Science and Technology of Târgu Mureş, Târgu Mureş, 540139, Romania
| | - Matthieu Foll
- International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 69372 Lyon, France
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland
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Laghouaouta H, Sosa-Madrid BS, Zubiri-Gaitán A, Hernández P, Blasco A. Novel Genomic Regions Associated with Intramuscular Fatty Acid Composition in Rabbits. Animals (Basel) 2020; 10:ani10112090. [PMID: 33187110 PMCID: PMC7697864 DOI: 10.3390/ani10112090] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Intramuscular fat (IMF) content and its composition affect the quality of meat. Selection for IMF generated a correlated response on its fatty acid composition. The increase of IMF content is associated with an increase of its saturated (SFA) and monounsaturated (MUFA) fatty acids, and consequently a decrease of polyunsaturated fatty acids (PUFA). We carried out a genome wide association study (GWAS) for IMF composition on two rabbit lines divergently selected for IMF content, using a Bayes B procedure. Association analyses were performed using 475 individuals and 90,235 Single Nucleotide Polymorphisms (SNPs). The main objectives were to identify genomic regions associated with the IMF composition and to generate a list of candidate genes. Genomic regions associated with the intramuscular fatty acid composition were spread across different rabbit chromosomes (OCU). An important region at 34.0-37.9 Mb on OCU1 was associated with C14:0, C16:0, SFA, and C18:2n6, explaining 3.5%, 11.2%, 11.3%, and 3.2% of the genomic variance, respectively. Another relevant genomic region was found to be associated at 46.0-48.9 Mb on OCU18, explaining up to 8% of the genomic variance of MUFA/SFA. The associated regions harbor several genes related to lipid metabolism, such as SCD, PLIN2, and ERLIN1. The main genomic regions associated with the fatty acids were not previously associated with IMF content in rabbits. Nonetheless, MTMR2 is the only gene that was associated with both the IMF content and composition in rabbits. Our study highlighted the polygenic nature of the fatty acids in rabbits and elucidated its genetic background.
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Kasza R, Donkó T, Matics Z, Nagy I, Csóka Á, Kovács G, Gerencsér Z, Dalle Zotte A, Cullere M, Szendrő Z. Rabbit Lines Divergently Selected for Total Body Fat Content: Correlated Responses on Growth Performance and Carcass Traits. Animals (Basel) 2020; 10:E1815. [PMID: 33036146 PMCID: PMC7599759 DOI: 10.3390/ani10101815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 11/20/2022] Open
Abstract
The aim of this experiment was to study the effect of divergently selected rabbits for total body fat content (fat index) on growth performance and carcass traits. The fat index was determined at 10 weeks of age by computed tomography and lasted for four consecutive generations. The rabbits with the lowest fat index belonged to the lean line and those of the highest values belonged to the fat line. At generation four, 60 rabbits/line were housed in wire-mesh cages and fed with commercial pellet ad libitum from weaning (5 w of age) to slaughtering (11 w of age). Growth performance, dressing out percentage and carcass adiposity were measured. The lean line showed a better feed conversion ratio (p < 0.001) than the fat line. Furthermore, the carcass of the lean rabbits had the highest proportion of fore (p < 0.020) and hind (p < 0.006) parts. On the contrary, rabbits of the fat line had the highest carcass adiposity (p < 0.001). The divergent selection for total body fat content showed to be effective for both lean and fat lines. Selection for lower total body fat content could be useful for terminal male lines, while the selection for higher total body fat content could be an advantage for rabbit does in providing fat (energy) reserves.
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Affiliation(s)
- Rozália Kasza
- Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba S. Str. 40, H-7400 Kaposvár, Hungary; (R.K.); (Z.M.); (I.N.); (A.C.); (Z.G.); (Z.S.)
| | - Tamás Donkó
- Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba S. Str. 40, H-7400 Kaposvár, Hungary; (R.K.); (Z.M.); (I.N.); (A.C.); (Z.G.); (Z.S.)
- Medicopus Nonprofit Ltd., Guba S. Str. 40, H-7400 Kaposvár, Hungary
| | - Zsolt Matics
- Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba S. Str. 40, H-7400 Kaposvár, Hungary; (R.K.); (Z.M.); (I.N.); (A.C.); (Z.G.); (Z.S.)
| | - István Nagy
- Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba S. Str. 40, H-7400 Kaposvár, Hungary; (R.K.); (Z.M.); (I.N.); (A.C.); (Z.G.); (Z.S.)
| | - Ádám Csóka
- Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba S. Str. 40, H-7400 Kaposvár, Hungary; (R.K.); (Z.M.); (I.N.); (A.C.); (Z.G.); (Z.S.)
- Medicopus Nonprofit Ltd., Guba S. Str. 40, H-7400 Kaposvár, Hungary
| | - György Kovács
- Analytical Minds Ltd, Árpád Str. 5, H-4933 Beregsurány, Hungary;
| | - Zsolt Gerencsér
- Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba S. Str. 40, H-7400 Kaposvár, Hungary; (R.K.); (Z.M.); (I.N.); (A.C.); (Z.G.); (Z.S.)
| | - Antonella Dalle Zotte
- Department of Animal Medicine, Production and Health, University of Padova, Agripolis, Viale dell’Universitá 16, 35020 Legnaro, Italy; (A.D.Z.); (M.C.)
| | - Marco Cullere
- Department of Animal Medicine, Production and Health, University of Padova, Agripolis, Viale dell’Universitá 16, 35020 Legnaro, Italy; (A.D.Z.); (M.C.)
| | - Zsolt Szendrő
- Faculty of Agricultural and Environmental Sciences, Kaposvár University, Guba S. Str. 40, H-7400 Kaposvár, Hungary; (R.K.); (Z.M.); (I.N.); (A.C.); (Z.G.); (Z.S.)
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Abstract
AbstractEcological differentiation between lineages is widely considered to be an important driver of speciation, but support for this hypothesis is mainly derived from the detailed study of a select set of model species pairs. Mounting evidence from nonmodel taxa, meanwhile, suggests that speciation often occurs with minimal differentiation in ecology or ecomorphology, calling into question the true contribution of divergent adaptation to species richness in nature. To better understand divergent ecological adaptation and its role in speciation generally, researchers require a comparative approach that can distinguish its signature from alternative processes, such as drift and parallel selection, in data sets containing many species pairs. Here we introduce new statistical models of divergent adaptation in the continuous traits of paired lineages. In these models, ecomorphological characters diverge as two lineages adapt toward alternative phenotypic optima following their departure from a common ancestor. The absolute distance between optima measures the extent of divergent selection and provides a basis for interpretation. We encode the models in the new R package diverge and extend them to allow the distance between optima to vary across continuous and categorical variables. We test model performance using simulation and demonstrate model application using published data sets of trait divergence in birds and mammals. Our framework provides the first explicit test for signatures of divergent selection in trait divergence data sets, and it will enable empiricists from a wide range of fields to better understand the dynamics of divergent adaptation and its prevalence in nature beyond just our best-studied model systems.
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Wilder AP, Palumbi SR, Conover DO, Therkildsen NO. Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome. Evol Lett 2020; 4:430-443. [PMID: 33014419 PMCID: PMC7523562 DOI: 10.1002/evl3.189] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/09/2020] [Accepted: 07/13/2020] [Indexed: 11/09/2022] Open
Abstract
The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome‐wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity for rapid adaptation from standing genetic variation, but we know little about the patterns of genomic variation across the species range that enable this remarkable adaptability. Here, we use low‐coverage, whole‐transcriptome sequencing of Atlantic silversides sampled along an environmental cline to show marked signatures of divergent selection across a gradient of neutral differentiation. Atlantic silversides sampled across 1371 km of the southern section of its distribution have very low genome‐wide differentiation (median FST = 0.006 across 1.9 million variants), consistent with historical connectivity and observations of recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (FST > 0.95) for alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium (LD) blocks that span hundreds of genes and several megabases. Variants in these LD blocks are disproportionately nonsynonymous and concentrated in genes enriched for multiple functions related to known adaptations in silversides, including variation in lipid storage, metabolic rate, and spawning behavior. Elevated levels of absolute divergence and demographic modeling suggest selection maintaining divergence across these blocks under gene flow. These findings represent an extreme case of heterogeneity in levels of differentiation across the genome, and highlight how gene flow shapes genomic architecture in continuous populations. Locally adapted alleles may be common features of populations distributed along environmental gradients, and will likely be key to conserving variation to enable future responses to environmental change.
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Affiliation(s)
- Aryn P Wilder
- Department of Natural Resources Cornell University Ithaca New York 14853.,Current address: San Diego Zoo Institute for Conservation Research Escondido California 92027
| | - Stephen R Palumbi
- Department of Biology, Hopkins Marine Station Stanford University Pacific Grove California 93950
| | - David O Conover
- Department of Biology University of Oregon Eugene Oregon 97403
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Bisschop G, Setter D, Rafajlović M, Baird SJE, Lohse K. The impact of global selection on local adaptation and reproductive isolation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190531. [PMID: 32654652 PMCID: PMC7423272 DOI: 10.1098/rstb.2019.0531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Despite the homogenizing effect of strong gene flow between two populations, adaptation under symmetric divergent selection pressures results in partial reproductive isolation: adaptive substitutions act as local barriers to gene flow, and if divergent selection continues unimpeded, this will result in complete reproductive isolation of the two populations, i.e. speciation. However, a key issue in framing the process of speciation as a tension between local adaptation and the homogenizing force of gene flow is that the mutation process is blind to changes in the environment and therefore tends to limit adaptation. Here we investigate how globally beneficial mutations (GBMs) affect divergent local adaptation and reproductive isolation. When phenotypic divergence is finite, we show that the presence of GBMs limits local adaptation, generating a persistent genetic load at the loci that contribute to the trait under divergent selection and reducing genome-wide divergence. Furthermore, we show that while GBMs cannot prohibit the process of continuous differentiation, they induce a substantial delay in the genome-wide shutdown of gene flow. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
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Affiliation(s)
- Gertjan Bisschop
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Derek Setter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Marina Rafajlović
- Department of Marine Sciences, Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Stuart J E Baird
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Mason JG, Gilley AD, Orlowski SK, Anthony NB. Divergent selection for relative breast yield at 4 D posthatch and the effect on embryonic and early posthatch development. Poult Sci 2020; 99:2888-94. [PMID: 32475421 DOI: 10.1016/j.psj.2020.01.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/31/2019] [Accepted: 01/01/2020] [Indexed: 11/23/2022] Open
Abstract
Genetic selections for growth promotion in poultry have been highly successful in improving growth, yield, and feed conversion in the modern broiler. These selections have focused on the use of hypertrophy, the increase of muscle fiber size to improve growth. Muscle growth however is not limited solely to hypertrophy but is largely attributable to both hypertrophy and hyperplasia, the increase in muscle fiber number. As muscle fiber size has been theorized to reach an eventual physiological limit, it was determined to develop a novel method of selection focusing on hyperplasia. Divergent selection for 4-day relative breast yield (BY4) was chosen as it is believed to occur at point at which muscle cell number per gram is maximized and satellite cell activity is higher than later in life. Using a random bred control population, divergent selection was undergone for BY4. The 2 broiler lines divergently selected for BY4 are noted as the high and low BY4 lines, respectively (high 4-day breast yield and low 4-day breast yield). Heritability estimates for selection of 4-day breast percentage in the upward and downward directions were 0.63 and 0.44, respectively. Divergent selection resulted in clear divergence in BY4 and shows promise in utilizing BY4 to promote broiler growth and body composition.
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Chapurlat E, Le Roncé I, Ågren J, Sletvold N. Divergent selection on flowering phenology but not on floral morphology between two closely related orchids. Ecol Evol 2020; 10:5737-5747. [PMID: 32607187 PMCID: PMC7319237 DOI: 10.1002/ece3.6312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/09/2020] [Accepted: 03/30/2020] [Indexed: 11/08/2022] Open
Abstract
Closely related species often differ in traits that influence reproductive success, suggesting that divergent selection on such traits contribute to the maintenance of species boundaries. Gymnadenia conopsea ss. and Gymnadenia densiflora are two closely related, perennial orchid species that differ in (a) floral traits important for pollination, including flowering phenology, floral display, and spur length, and (b) dominant pollinators. If plant-pollinator interactions contribute to the maintenance of trait differences between these two taxa, we expect current divergent selection on flowering phenology and floral morphology between the two species. We quantified phenotypic selection via female fitness in one year on flowering start, three floral display traits (plant height, number of flowers, and corolla size) and spur length, in six populations of G. conopsea s.s. and in four populations of G. densiflora. There was indication of divergent selection on flowering start in the expected direction, with selection for earlier flowering in two populations of the early-flowering G. conopsea s.s. and for later flowering in one population of the late-flowering G. densiflora. No divergent selection on floral morphology was detected, and there was no significant stabilizing selection on any trait in the two species. The results suggest ongoing adaptive differentiation of flowering phenology, strengthening this premating reproductive barrier between the two species. Synthesis: This study is among the first to test whether divergent selection on floral traits contribute to the maintenance of species differences between closely related plants. Phenological isolation confers a substantial potential for reproductive isolation, and divergent selection on flowering time can thus greatly influence reproductive isolation and adaptive differentiation.
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Affiliation(s)
- Elodie Chapurlat
- Plant Ecology and EvolutionDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Iris Le Roncé
- Plant Ecology and EvolutionDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
- Master BioSciencesÉcole Normale Supérieure de LyonUniversité Claude Bernard Lyon 1Université de LyonLyonFrance
| | - Jon Ågren
- Plant Ecology and EvolutionDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Nina Sletvold
- Plant Ecology and EvolutionDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
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Lin Z, Qin P, Zhang X, Fu C, Deng H, Fu X, Huang Z, Jiang S, Li C, Tang X, Wang X, He G, Yang Y, He H, Deng XW. Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice. Proc Natl Acad Sci U S A 2020; 117:4623-31. [PMID: 32071222 DOI: 10.1073/pnas.1919086117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The successful application of heterosis in hybrid rice has dramatically improved rice productivity, but the genetic mechanism for heterosis in the hybrid rice remains unclear. In this study, we generated two populations of rice F1 hybrids with present-day commercial hybrid parents, genotyped the parents with 50k SNP chip and genome resequencing, and recorded the phenotype of ∼2,000 hybrids at three field trials. By integrating these data with the collected genotypes of ∼4,200 rice landraces and improved varieties that were reported previously, we found that the male and female parents have different levels of genome introgressions from other rice subpopulations, including indica, aus, and japonica, therefore shaping heterotic loci in the hybrids. Among the introgressed exogenous genome, we found that heterotic loci, including Ghd8/DTH8, Gn1a, and IPA1 existed in wild rice, but were significantly divergently selected among the rice subpopulations, suggesting these loci were subject to environmental adaptation. During modern rice hybrid breeding, heterotic loci were further selected by removing loci with negative effect and fixing loci with positive effect and pyramid breeding. Our results provide insight into the genetic basis underlying the heterosis of elite hybrid rice varieties, which could facilitate a better understanding of heterosis and rice hybrid breeding.
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Iffland H, Wellmann R, Schmid M, Preuß S, Tetens J, Bessei W, Bennewitz J. Genomewide Mapping of Selection Signatures and Genes for Extreme Feather Pecking in Two Divergently Selected Laying Hen Lines. Animals (Basel) 2020; 10:ani10020262. [PMID: 32041297 PMCID: PMC7070400 DOI: 10.3390/ani10020262] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/28/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Feather pecking is a behavior frequently occurring in commercial layer flocks. It often leads to skin injuries and cannibalism. Besides economic losses, severe animal welfare problems cannot be ignored. Previous research has shown that the trait is heritable. Thus breeding against feather pecking is possible, but phenotyping in a commercial environment is economically unfeasible at the moment because of the lack of proper techniques. Therefore, understanding the genetic background of the trait is mandatory to establish a genomic breeding program. This would require genotypic information of the hens, which is feasible under practical conditions. In the present study, we used different methods to identify regions in the genome that influence feather pecking and extreme feather pecking. We found one trait associated with the genomic region. The use of genotypic information from this region in terms of selection against the undesired behavior may help to improve animal welfare in layer flocks. Abstract Feather pecking (FP) is a longstanding serious problem in commercial flocks of laying hens. It is a highly polygenic trait and the genetic background is still not completely understood. In order to find genomic regions influencing FP, selection signatures between laying hen lines divergently selected for high and low feather pecking were mapped using the intra-population iHS and the inter-population FST approach. In addition, the existence of an extreme subgroup of FP hens (EFP) across both selected lines has been demonstrated by fitting a mixture of negative binomial distributions to the data and calculating the posterior probability of belonging to the extreme subgroup (pEFP) for each hen. A genomewide association study (GWAS) was performed for the traits pEFP and FP delivered (FPD) with a subsequent post GWAS analysis. Mapping of selection signatures revealed no clear regions under selection. GWAS revealed a region on Chromosome 1, where the existence of a QTL influencing FP is likely. The candidate genes found in this region are a part of the GABAergic system, which has already been linked to FP in previous studies. Despite the polygenic nature of FP, selection on these candidate genes may reduce FP.
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Affiliation(s)
- Hanna Iffland
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70593 Stuttgart, Germany; (R.W.); (M.S.); (S.P.); (W.B.); (J.B.)
- Correspondence:
| | - Robin Wellmann
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70593 Stuttgart, Germany; (R.W.); (M.S.); (S.P.); (W.B.); (J.B.)
| | - Markus Schmid
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70593 Stuttgart, Germany; (R.W.); (M.S.); (S.P.); (W.B.); (J.B.)
| | - Siegfried Preuß
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70593 Stuttgart, Germany; (R.W.); (M.S.); (S.P.); (W.B.); (J.B.)
| | - Jens Tetens
- Department of Animal Science, University of Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany;
| | - Werner Bessei
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70593 Stuttgart, Germany; (R.W.); (M.S.); (S.P.); (W.B.); (J.B.)
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70593 Stuttgart, Germany; (R.W.); (M.S.); (S.P.); (W.B.); (J.B.)
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Sosa‐Madrid BS, Hernández P, Blasco A, Haley CS, Fontanesi L, Santacreu MA, Pena RN, Navarro P, Ibáñez‐Escriche N. Genomic regions influencing intramuscular fat in divergently selected rabbit lines. Anim Genet 2020; 51:58-69. [PMID: 31696970 PMCID: PMC7004202 DOI: 10.1111/age.12873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2019] [Indexed: 12/12/2022]
Abstract
Intramuscular fat (IMF) is one of the main meat quality traits for breeding programmes in livestock species. The main objective of this study was to identify genomic regions associated with IMF content comparing two rabbit populations divergently selected for this trait, and to generate a list of putative candidate genes. Animals were genotyped using the Affymetrix Axiom OrcunSNP Array (200k). After quality control, the data involved 477 animals and 93 540 SNPs. Two methods were used in this research: single marker regressions with the data adjusted by genomic relatedness, and a Bayesian multiple marker regression. Associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU8 and OCU13. The highest value for the percentage of the genomic variance explained by a genomic region was found in two consecutive genomic windows on OCU8 (7.34%). Genes in the associated regions of OCU1 and OCU8 presented biological functions related to the control of adipose cell function, lipid binding, transportation and localisation (APOLD1, PLBD1, PDE6H, GPRC5D and GPRC5A) and lipid metabolic processes (MTMR2). The EWSR1 gene, underlying the OCU13 region, is linked to the development of brown adipocytes. The findings suggest that there is a large component of polygenic effect behind the differences in IMF content in these two lines, as the variance explained by most of the windows was low. The genomic regions of OCU1, OCU8 and OCU13 revealed novel candidate genes. Further studies would be needed to validate the associations and explore their possible application in selection programmes.
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Affiliation(s)
- Bolívar S. Sosa‐Madrid
- Institute for Animal Science and TechnologyUniversitat Politècnica de València46022 ValenciaSpain
| | - Pilar Hernández
- Institute for Animal Science and TechnologyUniversitat Politècnica de València46022 ValenciaSpain
| | - Agustín Blasco
- Institute for Animal Science and TechnologyUniversitat Politècnica de València46022 ValenciaSpain
| | - Chris S. Haley
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghCrewe Road, Edinburgh EH4 2XUUnited Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothian EH25 9RGUnited Kingdom
| | - Luca Fontanesi
- Division of Animal SciencesDepartment of Agricultural and Food SciencesUniversity of Bologna40127 BolognaItaly
| | - María A. Santacreu
- Institute for Animal Science and TechnologyUniversitat Politècnica de València46022 ValenciaSpain
| | - Romi N. Pena
- Departament de Ciència AnimalUniversitat de Lleida–Agrotecnio CentreE-25198 LleidaCatalonia, Spain
| | - Pau Navarro
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghCrewe Road, Edinburgh EH4 2XUUnited Kingdom
| | - Noelia Ibáñez‐Escriche
- Institute for Animal Science and TechnologyUniversitat Politècnica de València46022 ValenciaSpain
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Sosa-Madrid BS, Santacreu MA, Blasco A, Fontanesi L, Pena RN, Ibáñez-Escriche N. A genomewide association study in divergently selected lines in rabbits reveals novel genomic regions associated with litter size traits. J Anim Breed Genet 2019; 137:123-138. [PMID: 31657065 DOI: 10.1111/jbg.12451] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/28/2022]
Abstract
Uterine capacity (UC), defined as the total number of kits from unilaterally ovariectomized does at birth, has a high genetic correlation with litter size. The aim of our research was to identify genomic regions associated with litter size traits through a genomewide association study using rabbits from a divergent selection experiment for UC. A high-density SNP array (200K) was used to genotype 181 does from a control population, high and low UC lines. Traits included total number born (TNB), number born alive (NBA), number born dead, ovulation rate (OR), implanted embryos (IE) and embryo, foetal and prenatal survivals at second parity. We implemented the Bayes B method and the associations were tested by Bayes factors and the percentage of genomic variance (GV) explained by windows. Different genomic regions associated with TNB, NBA, IE and OR were found. These regions explained 7.36%, 1.27%, 15.87% and 3.95% of GV, respectively. Two consecutive windows on chromosome 17 were associated with TNB, NBA and IE. This genomic region accounted for 6.32% of GV of TNB. In this region, we found the BMP4, PTDGR, PTGER2, STYX and CDKN3 candidate genes which presented functional annotations linked to some reproductive processes. Our findings suggest that a genomic region on chromosome 17 has an important effect on litter size traits. However, further analyses are needed to validate this region in other maternal rabbit lines.
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Affiliation(s)
| | - María Antonia Santacreu
- Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Bologna, Italy
| | - Romi Natacha Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Center, Lleida, Spain
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain
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43
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Tortereau F, Marie-Etancelin C, Weisbecker JL, Marcon D, Bouvier F, Moreno-Romieux C, François D. Genetic parameters for feed efficiency in Romane rams and responses to single-generation selection. Animal 2020; 14:681-7. [PMID: 31640830 DOI: 10.1017/S1751731119002544] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Feeding costs represent one of the highest expenditures in animal production systems. Breeding efficient animals that express their growth potential while eating less is therefore a major objective for breeders. We estimated the genetic parameters for feed intake, feed efficiency traits (residual feed intake (RFI) and feed conversion ratio (FCR)), growth and body composition traits in the Romane meat sheep breed. In these traits, selection responses to single-generation divergent selection on RFI were evaluated. From 2009 to 2016, a total of 951 male lambs were tested for 8 weeks starting from 3 months of age. They were weighed at the beginning and at the end of the testing period. Backfat thickness and muscle depth were recorded at the end of the testing period through ultrasound measurements. Feed intake was continuously recorded over the testing period using the automatic concentrate feeders. The heritability of RFI was estimated at 0.45 ± 0.08, which was higher than the heritability of FCR (0.30 ± 0.08). No significant genetic correlations were observed between RFI and growth traits. A favourable low negative genetic correlation was estimated between RFI and muscle depth (-0.30 ± 0.15), though additional data are needed to confirm these results. The selection of low RFI sires based on their breeding values led to the production of lambs eating significantly less concentrate (3% decrease in the average daily feed intake), but with the same growth as lambs from sires selected based on high RFI breeding values. We concluded that in meat sheep, RFI is a heritable trait that is genetically independent of post-weaning growth and body composition traits. A one-generation divergent selection based on RFI breeding values highlighted that substantial gains in feeding costs can be expected in selection schemes for meat sheep breeds.
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Vera M, Pardo BG, Cao A, Vilas R, Fernández C, Blanco A, Gutierrez AP, Bean TP, Houston RD, Villalba A, Martínez P. Signatures of selection for bonamiosis resistance in European flat oyster ( Ostrea edulis): New genomic tools for breeding programs and management of natural resources. Evol Appl 2019; 12:1781-1796. [PMID: 31548857 PMCID: PMC6752124 DOI: 10.1111/eva.12832] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/18/2019] [Accepted: 06/09/2019] [Indexed: 12/18/2022] Open
Abstract
The European flat oyster (Ostrea edulis) is a highly appreciated mollusk with an important aquaculture production throughout the 20th century, in addition to playing an important role on coastal ecosystems. Overexploitation of natural beds, habitat degradation, introduction of non-native species, and epidemic outbreaks have severely affected this important resource, particularly, the protozoan parasite Bonamia ostreae, which is the main concern affecting its production and conservation. In order to identify genomic regions and markers potentially associated with bonamiosis resistance, six oyster beds distributed throughout the European Atlantic coast were sampled. Three of them have been exposed to this parasite since the early 1980s and showed some degree of innate resistance (long-term affected group, LTA), while the other three were free of B. ostreae at least until sampling date (naïve group, NV). A total of 14,065 SNPs were analyzed, including 37 markers from candidate genes and 14,028 from a medium-density SNP array. Gene diversity was similar between LTA and NV groups suggesting no genetic erosion due to long-term exposure to the parasite, and three population clusters were detected using the whole dataset. Tests for divergent selection between NV and LTA groups detected the presence of a very consistent set of 22 markers, located within a putative single genomic region, which suggests the presence of a major quantitative trait locus associated with B. ostreae resistance. Moreover, 324 outlier loci associated with factors other than bonamiosis were identified allowing fully discrimination of all the oyster beds. A practical tool which included the 84 highest discriminative markers for tracing O. edulis populations was developed and tested with empirical data. Results reported herein could assist the production of stocks with improved resistance to bonamiosis and facilitate the management of oyster beds for recovery production and ecosystem services provided by this species.
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Affiliation(s)
- Manuel Vera
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
| | - Belén G. Pardo
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
| | - Asunción Cao
- Centro de Investigacións Mariñas (CIMA)Consellería do Mar, Xunta de GaliciaPontevedraSpain
| | - Román Vilas
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
| | - Alejandro P. Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA)Consellería do Mar, Xunta de GaliciaPontevedraSpain
- Departamento de Ciencias de la VidaUniversidad de AlcaláMadridSpain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE)University of the Basque Country (UPV/EHU)Basque CountrySpain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN group, Faculty of VeterinaryUniversidade de Santiago de CompostelaLugoSpain
- Instituto de AcuiculturaUniversidade de Santiago de CompostelaLugoSpain
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Sakamoto T, Innan H. The Evolutionary Dynamics of a Genetic Barrier to Gene Flow: From the Establishment to the Emergence of a Peak of Divergence. Genetics 2019; 212:1383-1398. [PMID: 31171654 PMCID: PMC6707448 DOI: 10.1534/genetics.119.302311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 05/16/2019] [Indexed: 11/18/2022] Open
Abstract
Divergent selection works when an allele establishes in the subpopulations in which it is adaptive, but not in the ones in which it is deleterious. While such a locally adaptive allele is maintained, the target locus of selection works as a genetic barrier to gene flow or a barrier locus. The genetic divergence (or FST) around the barrier locus can be maintained, while in other regions of the genome, genetic variation can be mixed by gene flow or migration. In this work, we consider theoretically the evolutionary process of a barrier locus, from its birth to stable preservation. Under a simple two-population model, we use a diffusion approach to obtain analytical expressions for the probability of initial establishment of a locally adaptive allele, the reduction of genetic variation due to the spread of the adaptive allele, and the process to the development of a sharp peak of divergence (genomic island of divergence). Our results will be useful to understanding how genomes evolve through local adaptation and divergent selection.
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Affiliation(s)
- Takahiro Sakamoto
- SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Hideki Innan
- SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
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Cai Z, Zhou L, Ren NN, Xu X, Liu R, Huang L, Zheng XM, Meng QL, Du YS, Wang MX, Geng MF, Chen WL, Jing CY, Zou XH, Guo J, Chen CB, Zeng HZ, Liang YT, Wei XH, Guo YL, Zhou HF, Zhang FM, Ge S. Parallel Speciation of Wild Rice Associated with Habitat Shifts. Mol Biol Evol 2019; 36:875-889. [PMID: 30861529 PMCID: PMC6501882 DOI: 10.1093/molbev/msz029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a “magic” trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.
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Affiliation(s)
- Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lian Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xun Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lei Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Ming Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Su Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Li Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chun-Yan Jing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Hui Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jie Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Bin Chen
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Hua-Zhong Zeng
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Yun-Tao Liang
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Xing-Hua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hai-Fei Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Abstract
The presence and relative levels (titers) of IgM and IgG natural antibodies (NAb) binding keyhole limpet hemocyanin (KLH), and natural (auto-) antibodies (N(A)Ab) binding salmon double-stranded DNA (dsDNA), (oxidated-) phosphatidyl (phosphoryl) choline-conjugated bovine serum albumin (PC-BSA), PC-conjugated ovalbumin (PC-OVA), and OVA, respectively, were studied in adult hen plasma, egg yolk, egg albumen, plasma of their hatchlings, and in 8-day-old chick plasma. Birds and eggs were from 2 lines divergently selected for high or low NAb levels binding KLH. This study aimed to determine 1) correlated phenotypic responses of selection for NAb to KLH, 2) transfer of maternal NAb and N(A)Ab via egg compartments, 3) levels of likely maternal NAb and N(A)Ab in hatchlings and 8-day-old chicks, and 4) whether a composite trait: IgM anti-PC-BSA/IgG anti-dsDNA ratio in the compartments could be used as a parameter for health or immune status. NAb and N(A)Ab to all tested antigens were found in adult hens, but low or no levels were found for IgM in yolk and IgG in albumen. Depending on the antigen, NAb and N(A)Ab were found in hatchlings and day 8 birds. Divergent selection and breeding based on NAb binding KLH affected antibody titers of almost all antigens in almost all compartments, in a similar way. Maternal transfer of NAb and N(A)Ab from the adult hen to offspring was via specific routes for specific antigens and isotypes, especially for IgG as suggested by cluster analyses and significant correlations. There was little indication of production of new NAb and N(A)Ab to the studied antigens in either the egg compartments or the hatchlings. A composite trait of IgM PC-BSA/IgG dsDNA ratio was as yet not indicative for immune status, as no significant differences were found between the lines for all compartments. In conclusion, hens provide neonatal chickens with natural (self-) binding IgG antibodies that have been proposed to perform homeostatic functions during the period in which neonates do not produce these antibodies themselves.
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Affiliation(s)
- M Rifqi Ismiraj
- Section of Immunology, Adaptation Physiology Group, Department of Animal Sciences, Wageningen University, De Elst 1, 6708 WD Wageningen, the Netherlands
| | - Joop A J Arts
- Section of Immunology, Adaptation Physiology Group, Department of Animal Sciences, Wageningen University, De Elst 1, 6708 WD Wageningen, the Netherlands
| | - Henk K Parmentier
- Section of Immunology, Adaptation Physiology Group, Department of Animal Sciences, Wageningen University, De Elst 1, 6708 WD Wageningen, the Netherlands
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48
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Richards TJ, Ortiz‐Barrientos D, McGuigan K. Natural selection drives leaf divergence in experimental populations of Senecio lautus under natural conditions. Ecol Evol 2019; 9:6959-6967. [PMID: 31380026 PMCID: PMC6662321 DOI: 10.1002/ece3.5263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/21/2019] [Accepted: 04/23/2019] [Indexed: 11/11/2022] Open
Abstract
Leaf morphology is highly variable both within and between plant species. This study employs a combination of common garden and reciprocal transplant experiments to determine whether differences in leaf shape between Senecio lautus ecotypes has evolved as an adaptive response to divergent ecological conditions.We created a synthetic population of hybrid genotypes to segregate morphological variation between three ecotypes and performed reciprocal transplants where this hybrid population was transplanted into the three adjacent native environments. We measured nine leaf morphology traits across the experimental and natural populations at these sites.We found significant divergence in multivariate leaf morphology toward the native character in each environment, suggesting environmental conditions at each site exert selective pressure that results in a phenotypic shift toward the local phenotype of the wild populations.These associations suggest that differences in leaf morphology between S. lautus ecotypes have arisen as a result of divergent selection on leaf shape or associated traits that confer an adaptive advantage in each environment, which has led to the formation of morphologically distinct ecotypes.
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Affiliation(s)
- Thomas J. Richards
- School of Biological Sciences St LuciaUniversity of QueenslandSt LuciaQueenslandAustralia
- Department of Plant BiologySwedish University of Agricultural SciencesLinnean Center for Plant BiologyUppsalaSweden
| | | | - Katrina McGuigan
- School of Biological Sciences St LuciaUniversity of QueenslandSt LuciaQueenslandAustralia
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49
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Rifkin JL, Castillo AS, Liao IT, Rausher MD. Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea). Mol Ecol 2019; 28:1709-1729. [PMID: 30451335 DOI: 10.1111/mec.14945] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 09/03/2018] [Accepted: 11/01/2018] [Indexed: 02/03/2023]
Abstract
Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggest that sufficiently strong divergent selection can overpower gene flow, leading to loci that are highly differentiated compared to others. However, there are also alternative explanations for this pattern. Independent evidence that loci in highly differentiated regions are under divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here, we present multiple lines of evidence that many of the highly divergent SNPs in a pair of sister morning glory species, Ipomoea cordatotriloba and I. lacunosa, are the result of divergent selection in the face of gene flow. We analysed a SNP data set across the genome to assess the amount of gene flow, resistance to introgression and patterns of selection on loci resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with interspecific gene flow in sympatry. Gene flow appears to be substantially greater from I. lacunosa to I. cordatotriloba than in the reverse direction, resulting in sympatric and allopatric I. cordatotriloba being substantially more different than sympatric and allopatric I. lacunosa. Many SNPs highly differentiated in allopatry have experienced divergent selection, and, despite gene flow in sympatry, resist homogenization in sympatry. Finally, five out of eight floral and inflorescence characteristics measured exhibit asymmetric convergence in sympatry. Consistent with the pattern of gene flow, I. cordatotriloba traits become much more like those of I. lacunosa than the reverse. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.
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Affiliation(s)
- Joanna L Rifkin
- Department of Biology, Duke University, Durham, North Carolina
| | | | - Irene T Liao
- Department of Biology, Duke University, Durham, North Carolina
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, North Carolina
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50
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Rupp R, Huau C, Caillat H, Fassier T, Bouvier F, Pampouille E, Clément V, Palhière I, Larroque H, Tosser-Klopp G, Jacquiet P, Rainard P. Divergent selection on milk somatic cell count in goats improves udder health and milk quality with no effect on nematode resistance. J Dairy Sci 2019; 102:5242-5253. [PMID: 30904305 DOI: 10.3168/jds.2018-15664] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/11/2019] [Indexed: 12/30/2022]
Abstract
Milk somatic cell count (SCC) is commonly higher in goats than in cattle and sheep. Furthermore, the ability of milk SCC to predict mastitis is considered lower in goats than in cattle and sheep, and the relevance of somatic cell score (SCS)-based selection in this species has been questioned. To address this issue, we created 2 divergent lines of Alpine goats using artificially inseminated bucks with extreme estimated breeding values for SCS. A total of 287 goats, 158 in high- and 129 in low-SCS lines, were scrutinized for mastitis infections. We subjected 2,688 milk samples to conventional bacteriological analyses on agarose and bacterial counts were estimated for positive samples. The SCS, milk yield, fat content, and protein content were recorded every 3 wk. Clinical mastitis was systematically noted. A subset of 40 goats (20 from each line) was subsequently challenged with Haemonchus contortus and monitored for anemia (blood packed cell volume) and fecal egg counts to see if SCS-based selection had an indirect effect on resistance to gastrointestinal nematodes. Milk production traits, including milk quantity, fat content, and protein content, were similar in both goat lines. In contrast, the raw milk SCC almost doubled between the lines, with 1,542,000 versus 855,000 cells/mL in the high- and low-SCS lines, respectively. The difference in breeding value for SCS between lines was 1.65 genetic standard deviation equivalents. The Staphylococcus spp. most frequently isolated from milk were S. xylosus, S. caprae, S. epidermidis, and S. aureus. The frequency of positive bacteriology samples was significantly higher in the high-SCS line (49%) than in the low-SCS line (33%). The highest odds ratio was 3.49 (95% confidence interval: 11.95-6.25) for S. aureus. The distribution of bacterial species in positive samples between lines was comparable. The average quantity of bacteria in positive samples was also significantly higher in high-SCS goats (69 ± 80 growing colonies) than in low-SCS goats (38 ± 62 growing colonies). Clinical cases were rare and equally distributed between high- (n = 4; 2.5%) and low-SCS (n = 3; 2.3%) lines. Furthermore, the larger the amounts of bacteria in milk the higher the SCS level. Conversely, goats with repeatedly culture-negative udders exhibited the lowest SCC levels, with an average of below 300,000 cells/mL. We therefore confirmed that SCS is a relevant predictor of intramammary infection and hygienic quality of milk in goats and can be used for prophylactic purposes. After challenge with H. contortus, goats were anemic with high fecal egg counts but we found no difference between the genetic lines. This result provides initial evidence that resistance to mastitis or to gastrointestinal nematodes infections is under independent genetic regulation. Altogether, this monitoring of the goat lines indicated that SCS-based selection helps to improve udder health by decreasing milk cell counts and reducing the incidence of infection and related bacterial shedding in milk. Selection for low SCC should not affect a goat's ability to cope with gastrointestinal nematodes.
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Affiliation(s)
- R Rupp
- Génétique, Physiologie et Système d'Elevage (GenPhySE), Université de Toulouse, INRA, ENVT, Castanet Tolosan, F-31326, France.
| | - C Huau
- Génétique, Physiologie et Système d'Elevage (GenPhySE), Université de Toulouse, INRA, ENVT, Castanet Tolosan, F-31326, France
| | - H Caillat
- Génétique, Physiologie et Système d'Elevage (GenPhySE), Université de Toulouse, INRA, ENVT, Castanet Tolosan, F-31326, France
| | - T Fassier
- Domaine de Bourges, INRA, Osmoy, F-31326, France
| | - F Bouvier
- Domaine de Bourges, INRA, Osmoy, F-31326, France
| | - E Pampouille
- Génétique, Physiologie et Système d'Elevage (GenPhySE), Université de Toulouse, INRA, ENVT, Castanet Tolosan, F-31326, France
| | - V Clément
- Génétique, Physiologie et Système d'Elevage (GenPhySE), Université de Toulouse, INRA, ENVT, Castanet Tolosan, F-31326, France; Institut de l'Elevage, Castanet Tolosan, F-31326, France
| | - I Palhière
- Génétique, Physiologie et Système d'Elevage (GenPhySE), Université de Toulouse, INRA, ENVT, Castanet Tolosan, F-31326, France
| | - H Larroque
- Génétique, Physiologie et Système d'Elevage (GenPhySE), Université de Toulouse, INRA, ENVT, Castanet Tolosan, F-31326, France
| | - G Tosser-Klopp
- Génétique, Physiologie et Système d'Elevage (GenPhySE), Université de Toulouse, INRA, ENVT, Castanet Tolosan, F-31326, France
| | - P Jacquiet
- Interactions Hôtes-Agents Pathogènes (IHAP), Université de Toulouse, INRA, INPT, ENVT, Toulouse, F-131076, France
| | - P Rainard
- Infectiologie et santé publique (ISP), INRA, Université Tours, Nouzilly, F-37380, France
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