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inbreeding and genetic load in a pair of sibling grouse species:Tetrastes sewersowi and T.bonasia

Avian Research 2024年第2期15卷 265-270页

作者： Kai Song Tom van der Valk Bin Gao Peter Halvarsson Yun Fang Wendong Xie Siegfried Klaus Zhiming Han Yue-Hua Sun Jacob Hoglund Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing100101China Animal Ecology Department of Ecology and GeneticsUppsala UniversityNorbyvagen 18DUppsala75236Sweden Department of Cell and Molecular Biology Uppsala75273Sweden Unit of Parasitology Department of Biomedicine and Veterinary Public HealthSwedish University of Agricultural SciencesPO Box 7036Uppsala75007Sweden Lindenhohe 5 JenaD-07749Germany The State Key Laboratory of Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing100101China

Genetic load and inbreeding are recognized as important factors to be considered in conservation programs.Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals,including humans(inbreeding depression).Genomic tech-niques are increasingly used in measuring and understanding genetic load and inbreeding and their importance in evolution and conservation.We used whole genome resequencing data from two sibling grouse species in subarctic Eurasia to quantify both.We found a large range of inbreeding measured as FROH(fraction of runs of homozygosity)in individuals from different populations of Chinese Grouse(Tetrastes sewerzowi)and Hazel Grouse(T.bonasia).FROH estimated from genome-wide runs of homozygosity(ROH)ranged from 0.02 to 0.24 among Chinese Grouse populations and from 0.01 to 0.44 in Hazel Grouse.Individuals from a population of Chinese Grouse residing in the Qilian mountains and from the European populations of Hazel Grouse(including samples from Sweden,Germany and Northeast Poland)were the most inbred(FROH ranged from 0.10 to 0.23 and 0.11 to 0.44,respectively).These levels are comparable to other highly inbred populations of birds.Hazel Grouse from northern China and Chinese Grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding levels.Comparisons of the ratio between deleterious missense mutations and synonymous mutations revealed higher levels in Chinese Grouse as compared to Hazel Grouse.These results are possibly explained by higher fixation rates,mutational melt down,in the range-restricted Chinese Grouse compared to the wide-ranging Hazel Grouse.However,when we compared the relatively more severe class of loss-of-function muta-tions,Hazel Grouse had slightly higher levels than Chinese Grouse,a result which may indicate that purifying selection(purging)has been more efficient in Chinese Grouse on this class of mutations.

关键词： Genetic load inbreeding Purifying selection Qinghai-Tibetan Plateau ROH Tetrastes

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Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

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Plant Diversity 2024年第3期46卷 294-308页

作者： Zhen Yang Lisong Liang Weibo Xiang Lujun Wang Qinghua Ma Zhaoshan Wang Key Laboratory of Tree Breeding and Cultivation National Forestry and Grassland AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing 100091China National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt China Three Gorges CorporationBeijing 100083China Rare Plants Research Institute of Yangtze River China Three Gorges CorporationYichang 443133China Research Institute of Economic Forest Cultivation and Processing Anhui Academy of ForestryHefei 230031China

Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,and putative introgression.Here we generated the first chromosome-level genome of the endangered Chinese hazelnut,Corylus chinensis,and compared the genomic signatures with its sympatric widespread C.kwechowensis-C yunnanensis complex.We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation.Population genomics revealed that both C.chinensis and the C.kwechowensis-C.yunnanensis complex had diverged into two genetic lineages,forming a consistent pattern of southwestern-northern differentiation.Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene,whereas the widespread northern lineages have remained stable(C.chinensis) or have even recovered from population bottlenecks(C.kwechowensis-C.yunnanensis complex) during the Quaternary.Compared with C.kwechowensis-C. yunnanensis complex,C.chinensis showed significantly lower genomic diversity and higher inbreeding level.However,C.chinensis carried significantly fewer deleterious mutations than C.kwechowensis-C. yunnanensis complex,as more effective purging selection reduced the accumulation of homozygous variants.We also detected signals of positive selection and adaptive introgression in different lineages,which facilitated the accumulation of favorable variants and formation of local adaptation.Hence,both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C.chinensis.Overall,our study provides critical insights into lineage differentiation,local adaptation,and the potential for future recovery of endangered trees.

关键词： Conservation genomics Demographic history inbreeding Genetic load Runs of homozygosity Local adaptation

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Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement

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Journal of Animal Science and Biotechnology 2023年第4期14卷 1363-1376页

作者： Fuping Zhao Pengfei Zhang Xiaoqing Wang Deniz Akdemir Dorian Garrick Jun He Lixian Wang Key Laboratory of Animal Genetics Breeding and Reproduction(Poultry)of Ministry of Agriculture and Rural AffairsInstitute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China Center for Blood and Marrow Transplant Research MinneapolisMNUSA. AL Rae Centre for Genetics and Breeding Massey UniversityHamilton 3240New Zealand College of Animal Science and Biotechnology Hunnan Agricultural UniversityChangsha 410128China

Background Genomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values(GEBV)to accelerate the speed of genetic improvement in domestic animals.But after multi-generation selection,the rate of inbreeding and the occurrence of homozygous harmful alleles might increase,which would reduce performance and genetic diversity.To mitigate the above problems,we can utilize genomic mating(GM)based upon optimal mate allocation to construct the best genotypic combinations in the next generation.In this study,we used stochastic simulation to investigate the impact of various factors on the efficiencies of GM to optimize pairing combinations after genomic selection of candidates in a pig population.These factors included:the algorithm used to derive inbreeding coefficients;the trait heritability(0.1,0.3 or 0.5);the kind of GM scheme(focused average GEBV or inbreeding);the approach for computing the genomic relationship matrix(by SNP or runs of homozygosity(ROH)).The outcomes were compared to three traditional mating schemes(random,positive assortative or negative assortative matings).In addition,the performance of the GM approach was tested on real datasets obtained from a Large White pig breeding population.Results Genomic mating outperforms other approaches in limiting the inbreeding accumulation for the same expected genetic gain.The use of ROH-based genealogical relatedness in GM achieved faster genetic gains than using relatedness based on individual SNPs.The GROH-based GM schemes with the maximum genetic gain resulted in 0.9%-2.6%higher rates of genetic gainΔG,and 13%-83.3%lowerΔF than positive assortative mating regardless of heritability.The rates of inbreeding were always the fastest with positive assortative mating.Results from a purebred Large White pig population,confirmed that GM with ROH-based GRM was more efficient than traditional mating schemes.Conclusion Compared with traditional mating schemes,genomic mating can not only achieve sustainable genetic

关键词： Genetic gain Genomic mating Genomic selection inbreeding Pig

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Genomic patterns of homozygosity and inbreeding depression in MurcianoGranadina goats

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Journal of Animal Science and Biotechnology 2022年第3期13卷 721-734页

作者： María Gracia Luigi-Sierra Almudena Fernández Amparo Martínez Dailu Guan Juan Vicente Delgado Javier FernándezÁlvarez Vincenzo Landi Francesc Xavier Such Jordi Jordana María Saura Marcel Amills Centre for Research in Agricultural Genomics(CRAG) CSIC-IRTA-UAB-UBUniversitat Autònoma de Barcelona08193 BellaterraSpain Departamento de Mejora Genética Animal INIACarretera de la Coruña km 7528040 MadridSpain Departamento de Genética Universidad de Córdoba14071 CórdobaSpain Department of Veterinary Medicine University of Bari“Aldo Moro”62 per Casamassima km.370010 ValenzanoSPItaly Group of Research in Ruminants(G2R) Department of Animal and Food ScienceUniversitat Autònoma de Barcelona(UAB)BellaterraBarcelonaSpain Departament de Ciència Animal i dels Aliments Facultat de VeterinàriaUniversitat Autònoma de Barcelona08193 BellaterraSpain

Background:inbreeding depression can adversely affect traits related to fitness,reproduction and productive performance.Although current research suggests that inbreeding levels are generally low in most goat breeds,the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data.Results:We genotyped 1040 goats with the Goat SNP50 BeadChip.This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns.We detected38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1,2,4,6,14,16 and 17.Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes.Four regions on chromosomes 8 and 25were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count.Notably,these regions contain several genes related with immunity,such as SYK,IL27,CCL19 and CCL21.Moreover,one region on chromosome 2 was significantly associated with inbreeding depression for milk yield.Conclusions:Although genomic inbreeding levels are low in Murciano-Granadina goats,significant evidence of inbreeding depression for the logarithm of the somatic cell count,a phenotype closely associated with udder health and milk yield,have been detected in this population.Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis,which is one of the main causes of dairy goat culling.

关键词： Goat inbreeding Milk yield Murciano-Granadina Somatic cell score

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Low diversity,little genetic structure but no inbreeding in a high-density island endemic pit-viper Gloydius shedaoensis

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Current Zoology 2022年第5期68卷 526-534页

作者： Guannan Wen Long Jin Yayong Wu Xiaoping Wang Jinzhong Fu Yin Qi Chengdu Institute of Biology Chinese Academy of SciencesChengdu 610041 China Key Laboratory of Southwest China Wildlife Resources Conservation(Ministry of Education) China West Normal UniversityNanchong 637009 China College of Life Sciences and Food Engineering Yibin UniversityYibin 644007 China Nature Conservation of Snake Island and Laotieshan Mountain Dalian 116041 China Department of Integrative Biology University of GuelphGuelphOntario N1G 2W1Canada

Island species and their ecosystems play an important role in global biodiversity preservation,and many vulnerable island species are conservation priorities.Although insular habitat likely facilitates the species diversification process,it may also aggravate the fragility of these species with high risk of inbreeding.The Shedao pit-viper Gloydius shedaoensis is an island endemic species with an extremely high population density,which has been categorized as vulnerable in the IUCN(International Union for the Conservation of Nature and Natural Resources)Red List.We collected 13,148 SNP(Single Nucleotide Polymorphism)from across its genome and examined its genetic diversity and demographic history.The Shedao pit-viper has a low genetic diversity but shows no sign of inbreeding.Furthermore,population genetic structure analysis,including the neighbor-joining tree,principal coordinate analysis,clustering,and spatial autocorrelation,revealed a general lack of spatial structure.Only the isolation by distance residues suggested a weak patchiness.Overall,the population is nearly panmictic and gene flow is evenly distributed across the island.A large number of individuals,small size of the island,and the lack of population structure likely all contribute to the lack of inbreeding in this species.We also detected signs of male-biased dispersal,which likely is another inbreeding avoidance strategy.Historical demographic analysis suggested that the historical population size and distribution of the species are much larger than their current ones.The multiple transgressive–regressive events since the Late Pleistocene are likely the main cause of the population size changes.Taken together,our results provide a basic scientific foundation for the conservation of this interesting and important species.

关键词： genetic diversity and structure Gloydius shedaoensis historical demography inbreeding insular species

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inbreeding Depression on Growth and Survival of Full-Sib Family of Manila Clam(Ruditapes philippinarum)

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Journal of Ocean University of China 2017年第1期16卷 145-150页

作者： HUO Zhongming LI Na ZHANG Xuekai LI Ying YAN Xiwu YANG Feng College of Fisheries and Life Science Dalian Ocean UniversityDalian 116023P.R.China Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province Dalian Ocean UniversityDalian 116023P.R.China

In present study, the inbreeding depression(ID) of growth and survival of Manila clam(Ruditapes philippinarum) was investigated at larval and juvenile stages. Nine inbred families(A_2, B_2, C_2, D_2, E_2, F_2, G_2, H_2 and I_2) were established by mating within nine full-sib families with expected inbreeding coefficient of 0.25. Inbred families showed significant differences in shell length and hatching rate of D-larvae(straight-hinged larvae). The larvae of the nine inbred families grew slower than those of control group(CG), and their ID value ranged from 0.81% ± 6.09% to 16.10% ± 1.49%. The ID value of larval survival rate varied between 27.47% ± 9.36% and 70.50% ± 13.66%. The ID was also detected for juvenile growth in A_2, B_2, C_2, and D_2, which ranged from 4.60 ± 2.21 to 17.71 ± 7.73. The A_2 family maintained the highest juvenile survival rate, whereas the other inbred families exhibited ID values varying between 62.79% ± 4.54% and 96.14% ± 0.87%. The linear relationship of estimated ID between growth and survival was negatively correlated(R =-0.434, P inbreeding may aid to selective breeding of Manila clam.

关键词： Ruditapes philippinarum growth survival inbreeding depression

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Plant Diversity 2019年第4期41卷 250-257页

作者： Aysajan Abdusalam Qing Jun Li College of Life and Geographic Sciences Kashi UniversityKashi.Xinjiang844000PR China The Key Laboratory of Ecology and Biological Resources in Yarkand Oasis Under the Department of Education of Xinjiang Uygur Autonomous Region Kashi University.KashiXinjiang844000PR China Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical BotanicalCarden.Chinese Academy of SciencesMenglun Town666303PR China Laboratory of Ecology and Evolutionary Biology.Yunnan University KunmingYunnan650091PR China

The population characteristics of distylous species are highly sensitive to stochastic natural selection pressure.Therefore,populations growing under different environmental conditions may vary in floral morph ratios,potentially affecting female fitness and leading to inbreeding depression.However,the variation in offspring quality among populations as a result of inbreeding depression is poorly understood in distylous species.This study investigates variations in plant density,seed mass,seed viabilityfemale fitness,and post-dispersal inbreeding depression in both sexual morphs(long-styled and shortstyled plants)of the distylous Primula nivalis that were subjected to different pollination treatments along an elevational gradient from 1657 to 2704 m a.s.l.Population characteristics(morph plant density and ratio)and fruit set were significantly affected by sexual morph and elevation.Plant density and fruitset frequencies were lower for short-styled than for long-styled plants at 2704 m a.s.l.The seeds from the cross-pollinated flowers of both morphs were higher in quality than those of self-pollinated flowers.The female fitness of seeds from cross-pollinated flowers of both morphs was higher than that of seeds from open-pollinated and self-pollinated flowers.The female fitness of seeds from long-styled flowers was higher than that of seeds from short-styled flowers at all elevations.inbreeding depression increased with elevation among plants with short-styled flowers but not among those with long-styled flowers.Variation in the elevation-dependent mating system might influence female fitness and affect inbreeding depression in both floral morphs.In conclusion,the low quality of seeds from short-styled flowers at high elevations might decrease short-styled flower frequency,affecting population characteristics.

关键词： inbreeding depression Pollination treatment Seed mass Seed quality

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The Power of inbreeding： NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication

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Molecular Plant 2016年第7期9卷 975-985页

作者： Hongru Wang Xun Xu Filipe Garrett Vieira Yunhua Xiao Zhikang Li Jun Wang Rasmus Nielsen Chengcai Chu State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing) Institute of Genetics and Developmental Biology Chinese Academyof Sciences Beijing 100101 China Cotlege of Life Sciences University of Chinese Academy of Sciences Beijing 100101 China BGI-Shenzhen Shenzhen 518083 China Centre for GeoGenetics University of Copenhagen 1350 Copenhagen Denmark Institute of Crop Sciences/National Key Facilities for Crop Gene Resources and Genetic Improvement Chinese Academy of Agricultural Sciences 12 SouthZhong-Guan-Cun Street Beijing 100081 China Department of Integrative Biology University of California Berkeley CA 94720 USA These authors contributed equally to this article.

Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in hu- mans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice （Oryza sativa L.）, which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5~ and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SN Ps in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice,japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.

关键词： inbreeding GWAS rice pericarp color

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Improved genetic distance-based spatial deployment can effectively minimize inbreeding in seed orchard

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Forest Ecosystems 2020年第1期7卷 117-124,126,125,127页

作者： Boning Yang Haihong Sun Jiandong Qi Shihui Niu Yousry AEl-Kassaby Wei Li Beijing Advanced Innovation Center for Tree Breeding by Molecular Design National Engineering Laboratory for Forest Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China Liaoning Research Institute of Sandy Land Control and Utilization Xihe DistrictFuxin City 123000Liaoning ProvinceChina College of Information Science and Technology Beijing Forestry UniversityBeijing 100083China Department of Forest and Conservation Sciences Faculty of ForestryThe University of British Columbia2424 Main MallVancouverBritish Columbia V6T 1Z4Canada

Background:inbreeding in seed orchards is expected to increase with the advancement of breeding cycles,which results in the delivery of crops with suboptimal genetic gain,reduced genetic diversity,and lower seed set.Here,a genetic distance-dependent method for clonal spatial deployment in seed orchards was developed and demonstrated,which reduced the inbreeding levels.The method’s main evaluation parameter of inbreeding is the genetic distance among individuals and the deployment method used an improved adaptive parallel genetic algorithm(IAPGA)based on Python language.Using inbreeding-prone Chinese Mongolian pine breeding population material originating from a single natural population,the proposed method was compared to a traditional orchard design and a distance-based design;namely,complete randomized block(RCB)and optimum neighborhood(ONA)designs,respectively.Results:With the advancement of selective breeding cycles,group separation among orchard related individuals is expected to increase.Based on the genetic distance among individuals,the IAPGA design was superior in significantly reducing the inbreeding level as compared to the two existing designs,confirming its suitability to advanced-generation orchards where relatedness among parents is common.In the 1st,2nd,and mixed generations clonal deployment schemes,the IAPGA design produced lower inbreeding with 87.22%,81.49%,and 87.23%of RCB,and 92.78%,91.30%,and 91.67%of ONA designs,respectively.Conclusions:The IAPGA clonal deployment proposed in this study has the obvious advantage of controlling inbreeding,and it is expected to be used in clonal deployment in seed orchards on a large-scale.Further studies are needed to focus on the actual states of pollen dispersal and mating in seed orchards,and more assumptions should be taken into account for the optimized deployment method.

关键词： Seed orchard Deployment inbreeding Genetic distance Clone SSR

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Molecular mechanism of inbreeding effects based on RNA-Seq analysis of the adductor muscle of bay scallop(Argopecten irradians)

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Acta Oceanologica Sinica 2019年第2期38卷 44-51页

作者： Yu Wang Shoudu Zhang Guofan Zhang Rihao Cong Li Li CAS Key Laboratory of Experimental Marine Biology Institute of OceanologyChinese Academy of Sciences Tianjin Bohai Sea Fisheries Research Institute Tianjin Ocean Ranch Technical Engineering Center National Oceanographic Center Laboratory for Marine Biology and Biotechnology Pilot National Laboratory for Marine Science and Technology(Qingdao) Center for Ocean Mega-Science Chinese Academy of Sciences

Understanding the effects of inbreeding is critical for the long-term viability of shellfish breeding and for understanding inbreeding depression(ID) of the offspring of selfed individuals and full-sib crosses. The bay scallop(Argopecten irradians) is a simultaneous hermaphroditic marine bivalve with distinct male and female gonads and is a species with external fertilization. It is a canonical model invertebrate for analysis of the genetics of ID and evolution of outcrossing mating system. ID in bivalves is well documented with regard to the phenotype and molecular markers aspects, but little is known on how inbreeding affects genome-wide gene expression.Here, we compare the gene expression profiles of adductor muscle of A. irradians lines inbred to F=0.5 with those of its counterpart outbred lines which are originated from the same paternal individual. Inbred and outbred individuals have some differences in growth traits. The shell length and the total weight of inbred scallops are lower than the counterpart of outbred lines. We found that 1 175 genes were up-regulated while 1 390 were downregulated in inbred lines. Regarding components, differentially expressed genes(DEGs) were concentrated on sarcomeres, contractile filaments, and cell membranes. Among others, whereas regarding their function, the Gene Ontology(GO) was concentrated on transferase, phosphotransferase, peptidase, and others. The DEGsenriched metabolic pathways mainly belonged to the oxidative phosphorylation pathway and apoptosis pathway.We used another two families to verify our bioinformatic results. The selfed and the outbred family originated from different ancestors, but the selfed family showed obvious ID. By using real-time quantitative reverse transcriptase polymerase chain reaction(qRT-PCR), we verified that DEGs with inbreeding are involved in the oxidative phosphorylation and cell apoptosis pathways, suggesting that inbreeding may affect energy metabolism and homeostasis.

关键词： Argopecten irradians inbreeding depression differentially expressed genes transcriptome

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