scholarly journals From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Zachary Stansell ◽  
Thomas Björkman
Keyword(s):  
Southern Italy ◽  
Allelic Diversity ◽  
Vegetable Crops ◽  
Selective Sweeps ◽  
Horticultural Traits ◽  
Genotype By Sequencing ◽  
Genomic Regions ◽  
Landrace Accessions ◽  
Genomic Basis ◽  
Subsequent Improvement

Abstract Worldwide, broccoli (Brassica oleracea var. italica) is among the most economically important, nutritionally rich, and widely-grown vegetable crops. To explore the genomic basis of the dramatic changes in broccoli morphology in the last century, we evaluated 109 broccoli or broccoli/cauliflower intermediates for 24 horticultural traits. Genotype-by-sequencing markers were used to determine four subpopulations within italica: Calabrese broccoli landraces and hybrids, sprouting broccoli, and violet cauliflower, and to evaluate between and within group relatedness and diversity. While overall horticultural quality and harvest index of improved hybrid broccoli germplasm has increased by year of cultivar release, this improvement has been accompanied by a considerable reduction in allelic diversity when compared to the larger pool of germplasm. Two landraces are the most likely founding source of modern broccoli hybrids, and within these modern hybrids, we identified 13 reduction-in-diversity genomic regions, 53 selective sweeps, and 30 (>1 Mbp) runs of homozygosity. Landrace accessions collected in southern Italy contained 4.8-fold greater unique alleles per accessions compared to modern hybrids and provide a valuable resource in subsequent improvement efforts. This work broadens the understanding of broccoli germplasm, informs conservation efforts, and enables breeding for complex quality traits and regionally adapted cultivars.

scholarly journals Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1826
Author(s):  
Amanda R. De La Torre ◽  
Manoj K. Sekhwal ◽  
David B. Neale
Keyword(s):  
Local Adaptation ◽  
Climate Adaptation ◽  
Natural Populations ◽  
Temperature Gradients ◽  
Selective Sweeps ◽  
Coast Redwood ◽  
Giant Sequoia ◽  
Polygenic Adaptation ◽  
Genomic Regions ◽  
Genomic Basis

Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype–environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.

scholarly journals Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry

2021 ◽  
Author(s):  
Michael A Hardigan ◽  
Anne Lorant ◽  
Dominique D A Pincot ◽  
Mitchell J Feldmann ◽  
Randi A Famula ◽  
...  
Keyword(s):  
Eighteenth Century ◽  
Nucleotide Diversity ◽  
Allelic Diversity ◽  
Selective Sweeps ◽  
Fragaria Ananassa ◽  
Horticultural Traits ◽  
Genome Wide ◽  
Dna Variants ◽  
History Of ◽  
Complex Hybrid

Abstract Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (F. chiloensis and F. virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication— 59-76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that Fragaria × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis, F. virginiana, and Fragaria × ananassa (π = 0.0059-0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern Fragaria × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.

scholarly journals Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Melina Campos ◽  
Luisa D. P. Rona ◽  
Katie Willis ◽  
George K. Christophides ◽  
Robert M. MacCallum
Keyword(s):  
Population Structure ◽  
Anopheles Gambiae ◽  
Malaria Vector ◽  
Mosquito Species ◽  
Gene Clusters ◽  
Selective Sweeps ◽  
Structure Heterogeneity ◽  
Genomic Studies ◽  
Time Required ◽  
Genomic Regions

Abstract Background Whole genome re-sequencing provides powerful data for population genomic studies, allowing robust inferences of population structure, gene flow and evolutionary history. For the major malaria vector in Africa, Anopheles gambiae, other genetic aspects such as selection and adaptation are also important. In the present study, we explore population genetic variation from genome-wide sequencing of 765 An. gambiae and An. coluzzii specimens collected from across Africa. We used t-SNE, a recently popularized dimensionality reduction method, to create a 2D-map of An. gambiae and An. coluzzii genes that reflect their population structure similarities. Results The map allows intuitive navigation among genes distributed throughout the so-called “mainland” and numerous surrounding “island-like” gene clusters. These gene clusters of various sizes correspond predominantly to low recombination genomic regions such as inversions and centromeres, and also to recent selective sweeps. Because this mosquito species complex has been studied extensively, we were able to support our interpretations with previously published findings. Several novel observations and hypotheses are also made, including selective sweeps and a multi-locus selection event in Guinea-Bissau, a known intense hybridization zone between An. gambiae and An. coluzzii. Conclusions Our results present a rich dataset that could be utilized in functional investigations aiming to shed light onto An. gambiae s.l genome evolution and eventual speciation. In addition, the methodology presented here can be used to further characterize other species not so well studied as An. gambiae, shortening the time required to progress from field sampling to the identification of genes and genomic regions under unique evolutionary processes.

scholarly journals Natural variation in fecundity is correlated with species-wide levels of divergence in Caenorhabditis elegans

2021 ◽  
Author(s):  
Gaotian Zhang ◽  
Jake D Mostad ◽  
Erik C Andersen
Keyword(s):  
Life History ◽  
Caenorhabditis Elegans ◽  
Life History Traits ◽  
Life History Trait ◽  
Selective Sweeps ◽  
C Elegans ◽  
Genome Wide ◽  
Genetic Complexity ◽  
Genomic Regions ◽  
Global Population

Abstract Life history traits underlie the fitness of organisms and are under strong natural selection. A new mutation that positively impacts a life history trait will likely increase in frequency and become fixed in a population (e.g. a selective sweep). The identification of the beneficial alleles that underlie selective sweeps provides insights into the mechanisms that occurred during the evolution of a species. In the global population of Caenorhabditis elegans, we previously identified selective sweeps that have drastically reduced chromosomal-scale genetic diversity in the species. Here, we measured the fecundity of 121 wild C. elegans strains, including many recently isolated divergent strains from the Hawaiian islands and found that strains with larger swept genomic regions have significantly higher fecundity than strains without evidence of the recent selective sweeps. We used genome-wide association (GWA) mapping to identify three quantitative trait loci (QTL) underlying the fecundity variation. Additionally, we mapped previous fecundity data from wild C. elegans strains and C. elegans recombinant inbred advanced intercross lines that were grown in various conditions and detected eight QTL using GWA and linkage mappings. These QTL show the genetic complexity of fecundity across this species. Moreover, the haplotype structure in each GWA QTL region revealed correlations with recent selective sweeps in the C. elegans population. North American and European strains had significantly higher fecundity than most strains from Hawaii, a hypothesized origin of the C. elegans species, suggesting that beneficial alleles that caused increased fecundity could underlie the selective sweeps during the worldwide expansion of C. elegans.

Effects of Selection at Linked Sites on Patterns of Genetic Variability

2021 ◽  
Vol 52 (1) ◽  
pp. 177-197
Author(s):  
Brian Charlesworth ◽  
Jeffrey D. Jensen
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
Frequency Distributions ◽  
A Genome ◽  
Demographic Processes ◽  
Dna Sequence Variants ◽  
Genomic Regions ◽  
Functional Components

Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill–Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.

scholarly journals Scanning for Genomic Regions Subject to Selective Sweeps Using SNP-MaP Strategy

2010 ◽  
Vol 8 (4) ◽  
pp. 256-261
Author(s):  
Libin Deng ◽  
Xiaoli Tang ◽  
Wei Chen ◽  
Jiari Lin ◽  
Zhiqing Lai ◽  
...  
Keyword(s):  
Selective Sweeps ◽  
Snp Map ◽  
Genomic Regions

scholarly journals Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Prasun Dutta ◽  
Andrea Talenti ◽  
Rachel Young ◽  
Siddharth Jayaraman ◽  
Rebecca Callaby ◽  
...  
Keyword(s):  
Water Buffalo ◽  
Whole Genome ◽  
Selective Sweeps ◽  
Whole Genome Analysis ◽  
Genetic Studies ◽  
Cattle Breeds ◽  
Functional Variants ◽  
Species Comparisons ◽  
Disproportionate Number ◽  
Genomic Regions

Abstract More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.

Analysis of vegetative compatibility groups in nonpathogenic populations of Fusarium oxysporum isolated from symptomless tomato roots

1991 ◽  
Vol 69 (10) ◽  
pp. 2089-2094 ◽  
Author(s):  
Karol S. Elias ◽  
R. W. Schneider ◽  
M. M. Lear
Keyword(s):  
Fusarium Oxysporum ◽  
Vegetative Compatibility ◽  
Vegetable Crops ◽  
Tomato Production ◽  
Vegetative Compatibility Groups ◽  
Horticultural Traits ◽  
Tomato Roots ◽  
Constant State ◽  
Nitrate Metabolism ◽  
Tomato Cultivars

A collection of 471 isolates of Fusarium oxysporum was obtained from symptomless tomato roots of plants grown at eight locations in Louisiana. Isolates that produced nitrate metabolism mutants (317 isolates) were included in an analysis of vegetative compatibility groups. One hundred and eighty-six isolates were assigned to 48 vegetative compatibility groups (2015–2062) containing 2–15 members from one to three different collection sites. Even though each site contained sub-populations of F. oxysporum common to other sites, only about half of the vegetative compatibility groups (21 groups) contained isolates from more than one site. In addition, there were 131 isolates of F. oxysporum that formed single-member vegetative compatibility groups. This diverse population composition is probably the result of several factors, including breeding strategies for resistance to fusarium wilt and tomato production practices in Louisiana. Resistance genes and horticultural traits from several sources (Lycopersicon spp.) have been incorporated into commercial tomato cultivars currently being grown. In addition, the long growing season in Louisiana allows several tomato cultivars containing different genes for resistance to be grown consecutively in the same field in a single year. Furthermore, other vegetable crops may be alternated with the tomato crops. Thus, the selection pressures that influence the composition of the nonpathogenic populations of F. oxysporum are in a constant state of flux. Key words: Fusarium oxysporum, genetic diversity, nonpathogens, vegetative compatibility groups.

A Microsatellite-Based Multilocus Screen for the Identification of Local Selective Sweeps

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 753-763 ◽  
Author(s):  
Christian Schlötterer
Keyword(s):  
Microsatellite Loci ◽  
Selective Sweep ◽  
Demographic History ◽  
Human Populations ◽  
Selective Sweeps ◽  
Test Statistic ◽  
Data Set ◽  
History Of ◽  
Microsatellite Mutation ◽  
Genomic Regions

AbstractWith the availability of completely sequenced genomes, multilocus scans of natural variability have become a feasible approach for the identification of genomic regions subjected to natural and artificial selection. Here, I introduce a new multilocus test statistic, ln RV, which is based on the ratio of observed variances in repeat number at a set of microsatellite loci in two groups of populations. The distribution of ln RV values captures demographic history of the populations as well as variation in microsatellite mutation among loci. Given that microsatellite loci associated with a recent selective sweep differ from the remainder of the genome, they are expected to fall outside of the distribution of neutral ln RV values. The ln RV test statistic is applied to a data set of 94 loci typed in eight non-African and two African human populations.

scholarly journals The conserved PFT1 tandem repeat is crucial for proper flowering in Arabidopsis thaliana

2014 ◽  
Author(s):  
Pauline Rival ◽  
Maximilian O Press ◽  
Jacob Bale ◽  
Tanya Grancharova ◽  
Soledad F Undurraga ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transgenic Plants ◽  
Tandem Repeat ◽  
Allelic Diversity ◽  
Selective Constraint ◽  
Dependent Manner ◽  
Functional Requirements ◽  
Loss Of Function ◽  
Wild Type ◽  
Genomic Regions

It is widely appreciated that short tandem repeat (STR) variation underlies substantial phenotypic variation in organisms. Some propose that the high mutation rates of STRs in functional genomic regions facilitate evolutionary adaptation. Despite their high mutation rate, some STRs show little to no variation in populations. One such STR occurs in the Arabidopsis thaliana gene PFT1 (MED25), where it encodes an interrupted polyglutamine tract. Though the PFT1 STR is large (~270 bp), and thus expected to be extremely variable, it shows only minuscule variation across A. thaliana strains. We hypothesized that the PFT1 STR is under selective constraint, due to previously undescribed roles in PFT1 function. We investigated this hypothesis using plants expressing transgenic PFT1 constructs with either an endogenous STR or with synthetic STRs of varying length. Transgenic plants carrying the endogenous PFT1 STR generally performed best across adult PFT1-dependent traits. In stark contrast, transgenic plants carrying a PFT1 transgene lacking the STR entirely phenocopied a pft1 loss-of-function mutant for flowering time phenotypes, and were generally hypomorphic for other traits, establishing the functional importance of this domain. Transgenic plants carrying various synthetic constructs occupied the phenotypic space between wild-type and pft1-loss-of-function mutants. By varying PFT1 STR length, we discovered that PFT1 can act as either an activator or repressor of flowering in a photoperiod-dependent manner. We conclude that the PFT1 STR is constrained to its approximate wild-type length by its various functional requirements. Our study implies that there is strong selection on STRs not only to generate allelic diversity, but also to maintain certain lengths pursuant to optimal molecular function.

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