scholarly journals Genome-wide shifts in climate-related variation underpin responses to selective breeding in a widespread conifer

2021 ◽  
Vol 118 (10) ◽  
pp. e2016900118
Author(s):  
Ian R. MacLachlan ◽  
Tegan K. McDonald ◽  
Brandon M. Lind ◽  
Loren H. Rieseberg ◽  
Sam Yeaman ◽  
...  
Keyword(s):  
Gene Flow ◽  
Selective Breeding ◽  
Natural Populations ◽  
Cold Injury ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Differences ◽  
Climatic Regions ◽  
Breeding Populations ◽  
Trade Offs ◽  
Growth Initiation

Locally adapted temperate tree populations exhibit genetic trade-offs among climate-related traits that can be exacerbated by selective breeding and are challenging to manage under climate change. To inform climatically adaptive forest management, we investigated the genetic architecture and impacts of selective breeding on four climate-related traits in 105 natural and 20 selectively bred lodgepole pine populations from western Canada. Growth, cold injury, growth initiation, and growth cessation phenotypes were tested for associations with 18,600 single-nucleotide polymorphisms (SNPs) in natural populations to identify “positive effect alleles” (PEAs). The effects of artificial selection for faster growth on the frequency of PEAs associated with each trait were quantified in breeding populations from different climates. Substantial shifts in PEA proportions and frequencies were observed across many loci after two generations of selective breeding for height, and responses of phenology-associated PEAs differed strongly among climatic regions. Extensive genetic overlap was evident among traits. Alleles most strongly associated with greater height were often associated with greater cold injury and delayed phenology, although it is unclear whether potential trade-offs arose directly from pleiotropy or indirectly via genetic linkage. Modest variation in multilocus PEA frequencies among populations was associated with large phenotypic differences and strong climatic gradients, providing support for assisted gene flow polices. Relationships among genotypes, phenotypes, and climate in natural populations were maintained or strengthened by selective breeding. However, future adaptive phenotypes and assisted gene flow may be compromised if selective breeding further increases the PEA frequencies of SNPs involved in adaptive trade-offs among climate-related traits.

scholarly journals Genome-wide assessment of genetic diversity and population structure in Magnolia odoratissima based on SLAF-Seq

2021 ◽  
Author(s):  
Tao Zhang ◽  
Xue Li ◽  
Shuilian He
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Natural Populations ◽  
Environmental Parameters ◽  
Candidate Snps ◽  
Small Populations ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Genome Wide

Abstract Magnolia odoratissima is a highly threatened species with small populations and scattered distribution due to habitat fragmentation and human activity. The species is recognized as a Plant Species with Extremely Small Populations (PSESP) and is endemic to China. In the current study, the population structure and levels of genetic diversity of M. odoratissima in the five remaining natural populations and three cultivated populations were evaluated using single nucleotide polymorphisms (SNPs) derived from Specific-Locus Amplified Fragment Sequencing (SLAF-seq). A total of 180,650 SNP loci were found in seventy M. odoratissima individuals. The genome-wide Nei’s and Shannon’s nucleotide diversity indexes of the total M. odoratissima population were 0.3035 and 0.4695, respectively. The observed heterozygosity (Ho) and expected heterozygosity (He) were 0.1122 and 0.3011. Our results suggest that M. odoratissima has relatively high genetic diversity at the genomic level. FST and AMOVA indicated that high genetic differentiation existed among populations. A phylogenetic neighbor-joining tree, Bayesian model–based clustering and principal components analysis (PCA) all divided the studied M. odoratissima individuals into three distinct clusters. The Treemix analysis showed that there was low gene flow among the natural populations and a certain gene flow from the wild populations to the cultivated population (LS to KIB, and GN to JD). In addition, a total of 36 unique SNPs were detected as being significantly associated with environmental parameters (altitude, temperature and precipitation). These candidate SNPs were found to be involved in multiple pathways including several molecular functions and biological process, suggesting they may play key roles in environmental adaptation. Our results suggested that three distinct evolutionary significant units (ESUs) should be set up to conserve this critically endangered species.

Sex ratio and life history traits at reaching sexual maturity in the dioecious shrub Fuchsia parviflora: field and common garden experiments

2021 ◽  
pp. 1-6
Author(s):  
Jessica S. Ambriz ◽  
Clementina González ◽  
Eduardo Cuevas
Keyword(s):  
Natural Population ◽  
Sexual Maturity ◽  
Sex Ratios ◽  
Natural Populations ◽  
Common Garden ◽  
Common Garden Experiment ◽  
Trade Offs ◽  
Reproductive Biomass ◽  
Common Garden Experiments ◽  
Growth And Reproduction

Abstract Fuchsia parviflora is a dioecious shrub that depends on biotic pollination for reproduction. Previous studies suggest that the male plants produce more flowers, and male-biased sex ratios have been found in some natural populations. To assess whether the biased sex ratios found between genders in natural populations are present at the point at which plants reach sexual maturity, and to identify possible trade-offs between growth and reproduction, we performed a common garden experiment. Finally, to complement the information of the common garden experiment, we estimated the reproductive biomass allocation between genders in one natural population. Sex ratios at reaching sexual maturity in F. parviflora did not differ from 0.5, except in one population, which was the smallest seedling population. We found no differences between genders in terms of the probability of germination or flowering. When flowering began, female plants were taller than males and the tallest plants of both genders required more time to reach sexual maturity. Males produced significantly more flowers than females, and the number of flowers increased with plant height in both genders. Finally, in the natural population studied, the investment in reproductive biomass was seven-fold greater in female plants than in male plants. Our results showed no evidence of possible trade-offs between growth and reproduction. Despite the fact that female plants invest more in reproductive biomass, they were taller than the males after flowering, possibly at the expense of herbivory defence.

Shallow genetic divergence and distinct phenotypic differences between two Andean hummingbirds: Speciation with gene flow?

The Auk ◽  
2019 ◽  
Vol 136 (4) ◽  
Author(s):  
Catalina Palacios ◽  
Silvana García-R ◽  
Juan Luis Parra ◽  
Andrés M Cuervo ◽  
F Gary Stiles ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Incomplete Lineage Sorting ◽  
Lineage Sorting ◽  
Phenotypic Differences ◽  
Adaptive Mechanisms ◽  
The Face ◽  
Gloger’S Rule ◽  
Divergence With Gene Flow ◽  
Neutral Markers

Abstract Ecological speciation can proceed despite genetic interchange when selection counteracts the homogenizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, 2 parapatric Andean hummingbirds with marked plumage divergence. We sequenced putatively neutral markers (mitochondrial DNA [mtDNA] and nuclear ultraconserved elements [UCEs]) to examine genetic structure and gene flow, and a candidate gene (MC1R) to assess its role underlying divergence in coloration. We also tested the prediction of Gloger’s rule that darker forms occur in more humid environments, and examined morphological variation to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was low in both ND2 and UCEs. Coalescent estimates of migration were consistent with divergence with gene flow, but we cannot reject incomplete lineage sorting reflecting recent speciation as an explanation for patterns of genetic variation. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in morphology. Although we reject adaptation to variation in macroclimatic conditions as a cause of divergence, speciation may have occurred in the face of gene flow driven by other ecological pressures or by sexual selection. Marked phenotypic divergence with no neutral genetic differentiation is remarkable for Neotropical birds, and makes C. helianthea and C. bonapartei an appropriate system in which to search for the genetic basis of species differences employing genomics.

Breeding implications of juvenile selection in a range-wide black spruce provenance test

1984 ◽  
Vol 14 (6) ◽  
pp. 933-939 ◽  
Author(s):  
Hans Nienstaedt
Keyword(s):  
Large Range ◽  
Black Spruce ◽  
Field Tests ◽  
Simple Correlation ◽  
Growing Seasons ◽  
Breeding Populations ◽  
Provenance Test ◽  
Full Complement ◽  
Growth Initiation ◽  
Growth Differences

Using 3-year heights, the tallest 49 provenances were selected in a nursery test of 110 black spruce (Piceamariana (Mill.) B.S.P.) provenances. A field test of the selected provenances was planted in Wisconsin; two tests of 108 provenances, both in Minnesota. Characteristics evaluated in the nursery included heights after two, three, and five growing seasons, and growth initiation and cessation in the second and third growing season. Heights were measured in the field tests. Separate statistical analyses, ANOVA and simple correlation, were used for the full complement of provenances and for those that were selected. All nursery characteristics varied significantly; the correlations between latitude and height decreased with age, and were not significant after five season's growth. Differences among provenances in free growth may explain this. Selection at age 3 years was not effective; too many selection errors were evident in the test of the full complement of provenances. Early selection on the basis of heights and phenological characteristics is not an effective way of reducing large range-wide provenance tests to breeding populations.

Tales of lizard tails: effects of tail autotomy on subsequent survival and growth of free-ranging hatchling Uta stansburiana

1997 ◽  
Vol 75 (4) ◽  
pp. 542-548 ◽  
Author(s):  
P. H. Niewiarowski ◽  
J. D. Congdon ◽  
A. E. Dunham ◽  
L. J. Vitt ◽  
D. W. Tinkle
Keyword(s):  
Natural Populations ◽  
Reproductive Investment ◽  
Experimental Manipulation ◽  
Costs And Benefits ◽  
Growth And Survival ◽  
Large Sample ◽  
Uta Stansburiana ◽  
Tail Autotomy ◽  
Trade Offs ◽  
Free Ranging

Potential costs and benefits of tail autotomy in lizards have been inferred almost exclusively from experimental study in semi-natural enclosures and from indirect comparative evidence from natural populations. We present complementary evidence of the costs of tail autotomy to the lizard Uta stansburiana from detailed demographic study of a natural population. On initial capture, we broke the tails of a large sample of free-ranging hatchlings (560) and left the tails of another large sample (455) intact, and then followed subsequent hatchling growth and survival over a 3-year period. Surprisingly, in 1 out of the 3 years of study, survival of female hatchlings with broken tails exceeded that of female hatchlings with intact tails. Furthermore, no effects of tail loss on survivorship were detected for male hatchlings. However, in 2 years when recaptures were very frequent (1961, 1962), growth rates of hatchlings with broken tails were significantly slower than those of their counterparts with intact tails. We discuss our results in the broader context of estimating the relative costs and benefits of tail autotomy in natural populations, and suggest that long-term demographic studies will provide the best opportunity to assess realized fitness costs and benefits with minimum bias. We also describe how experimentally induced tail autotomy can be used as a technique to complement experimental manipulation of reproductive investment in the study of life-history trade-offs.

scholarly journals Genetic structure and gene flow of Eugenia dysenterica natural populations

2005 ◽  
Vol 40 (10) ◽  
pp. 975-980 ◽  
Author(s):  
Maria Imaculada Zucchi ◽  
José Baldin Pinheiro ◽  
Lázaro José Chaves ◽  
Alexandre Siqueira Guedes Coelho ◽  
Mansuêmia Alves Couto ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Variability ◽  
Pearson Correlation ◽  
Natural Populations ◽  
Similarity Index ◽  
Genetic Distances ◽  
Strong Positive Correlation ◽  
Randomly Amplified Polymorphic Dna ◽  
Jaccard Similarity ◽  
Eugenia Dysenterica

This study was carried out to assess the genetic variability of ten "cagaita" tree (Eugenia dysenterica) populations in Southeastern Goiás. Fifty-four randomly amplified polymorphic DNA (RAPD) loci were used to characterize the population genetic variability, using the analysis of molecular variance (AMOVA). A phiST value of 0.2703 was obtained, showing that 27.03% and 72.97% of the genetic variability is present among and within populations, respectively. The Pearson correlation coefficient (r) among the genetic distances matrix (1 - Jaccard similarity index) and the geographic distances were estimated, and a strong positive correlation was detected. Results suggest that these populations are differentiating through a stochastic process, with restricted and geographic distribution dependent gene flow.

scholarly journals Association Mapping for Improvement of Quantitative Traits in Plant Breeding Populations

1970 ◽  
Vol 2 (1) ◽  
pp. 72-89
Author(s):  
Umesh R Rosyara ◽  
Bal K Joshi
Keyword(s):  
Association Mapping ◽  
Plant Breeding ◽  
Fine Mapping ◽  
Quantitative Trait ◽  
Human Genetics ◽  
Crop Improvement ◽  
Nucleotide Polymorphisms ◽  
Breeding Populations ◽  
Validation Of Results ◽  
Mapping Populations

DNA-based molecular markers have been extensively utilized for mapping of genes and quantitative trait loci (QTL) of interest based on linkage analysis in mapping populations. This is in contrast to human genetics that use of linkage disequilibrium (LD)-based mapping for fine mapping of QTLs using single nucleotide polymorphisms. LD based association mapping (AM) has promise to be used in plants. Possible use of such approach may be for fine mapping of genes / QTLs, identifying favorable alleles for marker aided selection and cross validation of results from linkage mapping for precise location of genes / QTLs of interest. In the present review, we discuss different mapping populations, approaches, prospects and limitations of using association mapping in plant breeding populations. This is expected to create awareness in plant breeders in use of AM in crop improvement activities.Key words: Association mapping; plant breeding; DNA marker; quantitative trait lociDOI: http://dx.doi.org/10.3126/njb.v2i1.5686  Nepal Journal of Biotechnology Jan.2012, Vol.2(1): 72-89

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

scholarly journals Spatial population genomics of a recent mosquito invasion

2020 ◽  
Author(s):  
Thomas L Schmidt ◽  
T. Swan ◽  
Jessica Chung ◽  
Stephan Karl ◽  
Samuel Demok ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Nucleotide Polymorphisms ◽  
Discrete Events ◽  
Long Distance ◽  
Population Genomic ◽  
Asian Tiger ◽  
Study Designs

AbstractPopulation genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232–577. Close kin dyads revealed recent movement between islands 31–203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

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