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1.
2.
    
In line with the Gifu University''s initiative to map the Japanese quail genome, a total of 100 Japanese quail microsatellite markers isolated in our laboratory were evaluated in a population of 20 unrelated quails randomly sampled from a colony of wild quail origin. Ninety-eight markers were polymorphic with an average of 3.7 alleles per locus and a mean heterozygosity of 0.423. To determine the utility of these markers for comparative genome mapping in Phasianidae, cross-species amplification of all the markers was tested with chicken and guinea fowl DNA. Amplification products similar in size to the orthologous loci in quail were observed in 42 loci in chicken and 20 loci in guinea fowl. Of the cross-reactive markers, 57.1% in chicken and 55.0% in guinea fowl were polymorphic when tested in 20 birds from their respective populations. Five of 15 markers that could cross-amplify Japanese quail, chicken, and guinea fowl DNA were polymorphic in all three species. Amplification of orthologous loci was confirmed by sequencing 10 loci each from chicken and guinea fowl and comparing with them the corresponding quail sequence. The microsatellite markers reported would serve as a useful resource base for genetic mapping in quail and comparative mapping in Phasianidae.  相似文献   

3.
We have characterized a deletion in the MC1R gene causing the loss of one amino acid (p.Phe256del), which is perfectly associated with melanism in guinea fowl (Numida meleagris). Co‐segregation of the p.Phe256del with melanism was confirmed in 25 offspring born from a cross of two heterozygote birds; therefore we suggest that this mutation is responsible for the black phenotype. Interestingly, this is the first case of recessive melanism linked to MC1R.  相似文献   

4.
    
Structural variations (SVs) are major genetic variants that can be involved in the origin, adaptation and domestication of species. However, the identification and characterization of SVs in Spinacia species are rare due to the lack of a pan-genome. Here, we report eight chromosome-scale assemblies of cultivated spinach and its two wild species. After integration with five existing assemblies, we constructed a comprehensive Spinacia pan-genome and identified 193 661 pan-SVs, which were genotyped in 452 Spinacia accessions. Our pan-SVs enabled genome-wide association study identified signals associated with sex and clarified the evolutionary direction of spinach. Most sex-linked SVs (86%) were biased to occur on the Y chromosome during the evolution of the sex-linked region, resulting in reduced Y-linked gene expression. The frequency of pan-SVs among Spinacia accessions further illustrated the contribution of these SVs to domestication, such as bolting time and seed dormancy. Furthermore, compared with SNPs, pan-SVs act as efficient variants in genomic selection (GS) because of their ability to capture missing heritability information and higher prediction accuracy. Overall, this study provides a valuable resource for spinach genomics and highlights the potential utility of pan-SV in crop improvement and breeding programmes.  相似文献   

5.
    
Each individual has a certain number of harmful mutations in its genome. These mutations can lower the fitness of the individual carrying them, dependent on their dominance and selection coefficient. Effective population size, selection, and admixture are known to affect the occurrence of such mutations in a population. The relative roles of demography and selection are a key in understanding the process of adaptation. These are factors that are potentially influenced and confounded in domestic animals. Here, we hypothesize that the series of events of bottlenecks, introgression, and strong artificial selection associated with domestication increased mutational load in domestic species. Yet, mutational load is hard to quantify, so there are very few studies available revealing the relevance of evolutionary processes. The precise role of artificial selection, bottlenecks, and introgression in further increasing the load of deleterious variants in animals in breeding and conservation programmes remains unclear. In this paper, we review the effects of domestication and selection on mutational load in domestic species. Moreover, we test some hypotheses on higher mutational load due to domestication and selective sweeps using sequence data from commercial pig and chicken lines. Overall, we argue that domestication by itself is not a prerequisite for genetic erosion, indicating that fitness potential does not need to decline. Rather, mutational load in domestic species can be influenced by many factors, but consistent or strong trends are not yet clear. However, methods emerging from molecular genetics allow discrimination of hypotheses about the determinants of mutational load, such as effective population size, inbreeding, and selection, in domestic systems. These findings make us rethink the effect of our current breeding schemes on fitness of populations.  相似文献   

6.
    
Morphological and behavioural traits of a feral strain of the common carp Cyprinus carpio from Lake Biwa in Japan were compared with those of two domesticated strains reared in Japan (one commercial strain and one ornamental koi). To compare genetically inherited traits, all fish were reared from eggs under similar environmental conditions. Using these fish, the following five traits were compared among the three strains: body shape, consumption rate of two types of free-swimming shrimp, medaka Oryzias latipes and bottom-dwelling chironomid larvae prey items, preference for a bottom habitat, feeding skills in detecting prey and escape response to predator attack. The feral strain of fish had more streamlined bodies, higher consumption rates for free-swimming prey, a greater preference for a bottom habitat, possessed greater skill in detecting prey and were more cautious of predator attacks, compared with the fish of the two domesticated strains. These characteristics shown by the feral fish are probably adaptive to the natural environment. A genetic analysis based on five nuclear single nucleotide polymorphism markers, however, suggested that the feral strain was relatively recently derived from domesticated stocks. Considering this, the present results appear to indicate the possibility that domesticated C. carpio could re-adapt to the wild environment during a short evolutionary period, although further research using more feral strains is required.  相似文献   

7.
The chicken lysozyme gene encodes a hydrolase that has a key role in defence, especially in ovo. This gene was resequenced in global chicken populations [red, grey, Ceylon and green jungle fowl (JF)] and related bird species. Networks, summary statistics and tests of neutrality indicate that although there is extensive variation at the gene, little is present at coding sites, with the exception of one non‐synonymous site. This segregating site and a further fixed non‐synonymous change between red JF and domestic chicken populations are spatially close to the catalytic sites of the enzyme and so might affect its activity.  相似文献   

8.
    
Compared to natural selection, domestication implies a dramatic change in traits linked to fitness. A number of traits conferring fitness in the wild might be detrimental under domestication, and domesticated species typically differ from their ancestors in a set of traits known as the domestication syndrome. Specifically, trade‐offs between growth and reproduction are well established across the tree of life. According to allocation theory, selection for growth rate is expected to indirectly alter life‐history reproductive traits, diverting resources from reproduction to growth. Here we tested this hypothesis by examining the genetic change and correlated responses of reproductive traits as a result of selection for timber yield in the tree Pinus pinaster. Phenotypic selection was carried out in a natural population, and progenies from selected trees were compared with those of control trees in a common garden experiment. According to expectations, we detected a genetic change in important life‐history traits due to selection. Specifically, threshold sizes for reproduction were much higher and reproductive investment relative to size significantly lower in the selected progenies just after a single artificial selection event. Our study helps to define the domestication syndrome in exploited forest trees and shows that changes affecting developmental pathways are relevant in domestication processes of long‐lived plants.  相似文献   

9.
目的 探究抗裂荚分子机制;挖掘抗裂荚大豆种质资源;可为揭示大豆裂荚性遗传和驯化机理、加速南方大豆抗裂荚新品种的选育提供依据。 方法 结合全基因组关联分析定位和野生栽培大豆群体遗传多样性分析;探寻大豆裂荚性相关基因。使用302份大豆材料进行2年表型测定;借助95 744个单核苷酸多态性标记进行全基因组关联分析。使用包括1 308份栽培大豆和203份野生大豆的重测序数据进行QTL区段序列的遗传多样性分析。 结果 通过全基因组关联分析检测到3个表型变异解释率大于10%的QTL位点;分别为qPdh-Chr08(Gm08:3048312)、qPdh-Chr15(Gm15:312814)和qPdh-Chr16(Gm16:29951529)。其中qPdh-Chr16是已知基因pdh1(Pod dehiscence habit 1)。结合野生和栽培大豆重测序数据发现;qPdh-Chr08和qPdh-Chr15内存在人工选择导致的群体分化序列;发现2个重要候选基因Glyma.08G038600和Glyma.15G003600。根据功能注释发现;这两个基因参与生长素和木质素的代谢。 结论 使用2年数据检测到大豆裂荚性2个新的QTL位点qPdh-Chr08和qPdh-Chr15;并在QTL区域内鉴定野生栽培大豆分化基因;最终筛选到2个重要候选基因。  相似文献   

10.

Background

Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics.

Results

We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits.

Conclusion

Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1606-1) contains supplementary material, which is available to authorized users.  相似文献   

11.
    
Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety “Big Star*” and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome‐wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.  相似文献   

12.
    
Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive‐reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome‐wide approaches. Genetic divergence from the source population was minimal in an integrated line, which implemented managed gene flow by using only naturally‐born adults as captive broodstock, but significant in a segregated line, which bred only captive‐origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the latter was largely attributable to genetic drift. Three independent tests for signatures of adaptive divergence also identified temporal change within the segregated line, possibly indicating domestication selection. The results empirically demonstrate that using managed gene flow for propagating a captive‐reared population reduces genetic divergence over the short term compared to one that relies solely on captive‐origin parents. These findings complement existing studies of captive breeding, which typically focus on a single management strategy and examine the fitness of one or two generations.  相似文献   

13.
    
Captive breeding programs are increasingly being initiated to prevent the imminent extinction of endangered species and/or populations. But how well can they conserve genetic diversity and fitness, or re‐establish self‐sustaining populations in the wild? A review of these complex questions and related issues in salmonid fishes reveals several insights and uncertainties. Most programs can maintain genetic diversity within populations over several generations, but available research suggests the loss of fitness in captivity can be rapid, its magnitude probably increasing with the duration in captivity. Over the long‐term, there is likely tremendous variation between (i) programs in their capacity to maintain genetic diversity and fitness, and (ii) species or even intraspecific life‐history types in both the severity and manner of fitness‐costs accrued. Encouragingly, many new theoretical and methodological approaches now exist for current and future programs to potentially reduce these effects. Nevertheless, an unavoidable trade‐off exists between conserving genetic diversity and fitness in certain instances, such as when captive‐bred individuals are temporarily released into the wild. Owing to several confounding factors, there is also currently little evidence that captive‐bred lines of salmonids can or cannot be reintroduced as self‐sustaining populations. Most notably, the root causes of salmonid declines have not been mitigated where captive breeding programs exist. Little research has also addressed under what conditions an increase in population abundance due to captive‐rearing might offset fitness reductions induced in captivity. Finally, more empirical investigation is needed to evaluate the genetic/fitness benefits and risks associated with (i) maintaining captive broodstocks as either single or multiple populations within one or more facilities, (ii) utilizing cryopreservation or surrogate broodstock technologies, and (iii) adopting other alternatives to captive‐rearing such as translocations to new habitats. Management recommendations surrounding these issues are proposed, with the aim of facilitating meta‐analyses and more general principles or guidelines for captive‐breeding. These include the need for the following: (i) captive monitoring to involve, a priori, greater application of hypothesis testing through the use of well‐designed experiments and (ii) improved documentation of procedures adopted by specific programs for reducing the loss of genetic diversity and fitness.  相似文献   

14.
Over the past 30 years, studies of single muscles have revealed complex patterns of regional variation in muscle architecture, activation, strain and force. In addition, muscles are often functionally integrated with other muscles in parallel or in series. Understanding the extent of this complexity and the interactions between muscles will profoundly influence how we think of muscles in relation to organismal function, and will allow us to address questions regarding the functional benefits (or lack thereof) and dynamics of this complexity under in vivo conditions. This paper has two main objectives. First, we present a cohesive and integrative review of regional variation in function within muscles, and discuss the functional ramifications that can stem from this variation. This involves splitting regional variation into passive and active components. Second, we assess the functional integration of muscles between different limb segments by presenting new data involving in vivo measurements of activation and strain from the medial gastrocnemius, iliotibialis cranialis and iliotibialis lateralis pars preacetabularis of the helmeted guinea fowl (Numida meleagris) during level running on a motorized treadmill. Future research directions for both of these objectives are presented.  相似文献   

15.
We determined the complete amino acid sequences of the hemoglobin of two species, guinea fowl and California quail, in Galliformes from intact globin chain and chemical cleavage fragments in order to analyze the molecular evolution of hemoglobin for the classification of Galliformes. Galliformes have two types of hemoglobin components, HbA and HbD, which consist of identical chain and different chains. The sequences are similar to globin chains of Galliformes reported previously. These sequences were compared with those of other Galliformes (Phasianidae, Meleagrididae) using duck and goshawk as out-groups. The phylogenetic tree of major groups of Galliformes based on hemoglobin was similar to the tree model produced based on the amino acid sequence of lysozyme c.  相似文献   

16.
Captive breeding and the genetic fitness of natural populations   总被引:2,自引:0,他引:2  
Many populations of endangered species are subject to recurrent introductions of individuals from an alternative setting where selection is either relaxed or in a direction opposite to that in the natural habitat. Such population structures, which are common to captive breeding and hatchery programs, can lead to a scenario in which alleles that are deleterious (and ordinarily keptat low levels) in the wild can rise to high frequencies and, in some cases, go to fixation. We outline how these genetic responses to supplementation candevelop to a large enough extent to impose a substantial risk of extinction for natural populations on time scales of relevance to conservation biology.The genetic supplementation load can be especially severe when a captive population that is largely closed to import makes a large contribution to the breeding pool of individuals in the wild, as these conditions insure thatthe productivity of the two-population system is dominated by captive breeders. However, a substantial supplementation load can even develop when the captive breeders are always derived from the wild, and in general, a severe restriction of gene flow into the natural population is required to reduce this load to an insignificant level. Domestication selection (adaptation to the captive environment) poses a particularly serious problem because it promotes fixations of alleles that are deleterious in nature, thereby resulting in a permanent load that cannot be purged once the supplementation program is truncated. Thus, our results suggest that the apparent short-term demographic advantages of a supplementation program can be quite deceiving. Unless the selective pressures of the captive environmentare closely managed to resemble those in the wild, long-term supplementation programs are expected to result in genetic transformations that can eventually lead to natural populations that are no longer capable of sustaining themselves.  相似文献   

17.
The last 50,000-150,000 years of human history have been characterized by rapid demographic expansions and the colonization of novel environments outside of sub-Saharan Africa. Mass migrations outside the ancestral species range likely entailed many new selection pressures, suggesting that genetic adaptation to local environmental conditions may have been more prevalent in colonizing populations outside of sub-Saharan Africa. Here we report a test of this hypothesis using genome-wide patterns of DNA polymorphism. We conducted a multilocus scan of microsatellite variability to identify regions of the human genome that may have been subject to continent-specific hitchhiking events. Using published polymorphism data for a total of 624 autosomal loci in multiple populations of humans, we used coalescent simulations to identify candidate loci for geographically restricted selective sweeps. We identified a total of 13 loci that appeared as outliers in replicated population comparisons involving different reference samples for Africa. A disproportionate number of these loci exhibited reduced levels of relative variability in non-African populations alone, suggesting that recent episodes of positive selection have been more prevalent outside of sub-Saharan Africa.  相似文献   

18.
    
When long‐lasting, balancing selection can lead to “trans‐species” polymorphisms that are shared by two or more species identical by descent. In such cases, the gene genealogy at the selected site clusters by allele instead of by species, and nearby neutral sites also have unusual genealogies because of linkage. While this scenario is expected to leave discernible footprints in genetic variation data, the specific patterns remain poorly characterized. Motivated by recent findings in primates, we focus on the case of a biallelic polymorphism under ancient balancing selection and derive approximations for summaries of the polymorphism data from two species. Specifically, we characterize the length of the segment that carries most of the footprints, the expected number of shared neutral single nucleotide polymorphisms (SNPs), and the patterns of allelic associations among them. We confirm the accuracy of our approximations by coalescent simulations. We further show that for humans and chimpanzees—more generally, for pairs of species with low genetic diversity levels—these patterns are highly unlikely to be generated by neutral recurrent mutations. We discuss the implications for the design and interpretation of genome scans for ancient balanced polymorphisms in primates and other taxa.  相似文献   

19.
  总被引:1,自引:0,他引:1  
X. Xie  Y. Yang  Q. Ren  X. Ding  P. Bao  B. Yan  X. Yan  J. Han  P. Yan  Q. Qiu 《Animal genetics》2018,49(5):384-392
Deleterious mutations play an important functional role, affecting trait phenotypes in ways that decrease the fitness of organisms. Estimating the frequency of occurrence and abundance has been a topic of much interest, especially in crops and livestock. The processes of domestication and breeding allow deleterious mutations to persist at high frequency, and identifying such deleterious mutations is particularly important for breed improvement. Here, we assessed genome‐wide patterns of deleterious variation in 59 domestic and 13 wild yaks using genome resequencing data. Based on the intersection of results given by three methods (provean , polyphen 2 and sift 4g ), we identified 3187 putative deleterious mutation sites affecting 2586 genes in domestic yaks and 2067 affecting 1701 genes in wild yaks. Multiple lines of evidence indicate a significant increase in the load of deleterious mutations in domesticated yaks compared to wild yaks. Private deleterious genes were found to be associated with the perception of smell and detection of chemical stimulus. We also identified 36 genes related to Mendelian genetic diseases involved in sensory perception, skeletal development and the nervous and immune systems. This study not only adds to the understanding of the genetic basis of yak domestication but also provides a rich catalog of variants that will facilitate future breeding‐related research on the yak genome and on other bovid species.  相似文献   

20.
    
Next‐generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP‐glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well‐characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.  相似文献   

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