scholarly journals Patterns of genetic variation in a prairie wildflower, Silphium integrifolium, suggest a non-prairie origin and locally adaptive variation

2020 ◽  
Author(s):  
Andrew R. Raduski ◽  
Adam Herman ◽  
Cloe Pogoda ◽  
Kevin M. Dorn ◽  
David L. Van Tassel ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Population Genetic ◽  
De Novo ◽  
Agronomic Traits ◽  
Geographic Origin ◽  
Breeding Program ◽  
Oilseed Crop ◽  
Breeding Programs ◽  
Demographic Modeling

AbstractPremiseUnderstanding the relationship between genetic structure and geography provides information about a species’ evolutionary history and can be useful to breeders interested in de novo domestication. The North American prairie is especially interesting because of its relatively recent origin and subsequent dramatic fragmentation and degradation. Silphium integrifolium is an iconic perennial American prairie wildflower targeted for domestication as an oilseed crop. Germplasm in the existing breeding program is derived from accessions collected in restricted geographic regions. We present the first application of population genetic data in this species to address the following goals (1) improve breeding programs by characterizing genetic structure and (2) identify the species geographic origin and potential targets and drivers of selection during range expansion.MethodsWe developed a reference transcriptome as a genotyping reference for samples from throughout the species range. Population genetic analyses were used to describe the distribution of genetic variation and demographic modeling was used to characterize potential processes that shaped variation. Outlier scans for selection and associations with environmental variables were used to identify loci linked to putative targets and drivers of selection.Key resultsGenetic variation partitions samples into three geographic clusters. Patterns of variation and demographic modeling suggest that the species origin is in the American southeast. Breeding program accessions are from the region with lowest observed genetic variation.ConclusionsThis iconic prairie species did not originate within the modern prairie. Breeding programs can be improved by including accessions from outside of the germplasm founding region, which has relatively little variation. The geographic structuring coupled with the identified targets and drivers of adaptation can guide collecting efforts towards populations with beneficial agronomic traits.

Significant genetic differences among Heterodera schachtii populations within and among sugar beet production areas

Nematology ◽  
2020 ◽  
Vol 22 (2) ◽  
pp. 165-177 ◽  
Author(s):  
Rasha Haj Nuaima ◽  
Johannes Roeb ◽  
Johannes Hallmann ◽  
Matthias Daub ◽  
Holger Heuer
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Spatial Scales ◽  
Geographic Distance ◽  
Heterodera Schachtii ◽  
Parasitic Nematodes ◽  
Neutral Genetic Variation ◽  
Production Areas

Summary Characterising the non-neutral genetic variation within and among populations of plant-parasitic nematodes is essential to determine factors shaping the population genetic structure. This study describes the genetic variation of the parasitism gene vap1 within and among geographic populations of the beet cyst nematode Heterodera schachtii. Forty populations of H. schachtii were sampled at four spatial scales: 695 km, 49 km, 3.1 km and 0.24 km. DGGE fingerprinting showed significant differences in vap1 patterns among populations. High similarity of vap1 patterns appeared between geographically close populations, and occasionally among distant populations. Analysis of spatially sampled populations within fields revealed an effect of tillage direction on the vap1 similarity for two of four studied fields. Overall, geographic distance and similarity of vap1 patterns of H. schachtii populations were negatively correlated. In conclusion, the population genetic structure was shaped by the interplay between the genetic adaptation and the passive transport of this nematode.

scholarly journals Absence of Population Genetic Structure Among Breeding Colonies of the Waved Albatross

The Condor ◽  
2006 ◽  
Vol 108 (2) ◽  
pp. 440-445 ◽  
Author(s):  
Kathryn P. Huyvaert ◽  
Patricia G. Parker
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Breeding Population ◽  
Genetic Structuring ◽  
Galapagos Archipelago ◽  
Phoebastria Irrorata ◽  
Waved Albatrosses

Abstract We used four variable microsatellite loci to examine the distribution of genetic variation and degree of genetic structuring among three subcolonies of Waved Albatrosses (Phoebastria irrorata). The breeding population of this species is almost entirely limited to the island of Española in the Galápagos Archipelago. Such strong philopatry could lead to population genetic structure among subcolonies on the island. Pairwise values of the FST analog, θ, calculated from microsatellite genotypes, were all less than 0.012, indicating little genetic differentiation and the presence of gene flow throughout the population.

Effects of habitat fragmentation on population genetic structure in the white-footed mouse (Peromyscus leucopus)

2001 ◽  
Vol 79 (2) ◽  
pp. 285-295 ◽  
Author(s):  
Catherine A Mossman ◽  
Peter M Waser
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Habitat Fragmentation ◽  
Genetic Differentiation ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Peromyscus Leucopus ◽  
Marginal Effect ◽  
Geographic Scale ◽  
White Footed Mouse

Habitat fragmentation may have significant consequences for population genetic structure because geographic distance and physical barriers may impede gene flow. In this study, we investigated whether habitat fragmentation affects fine-scale genetic structure of populations of the white-footed mouse (Peromyscus leucopus). We studied 27 populations of P. leucopus, 17 in continuous forest and 10 in isolated woodlots. Populations were trapped in pairs that were either 500 or 2000 m apart. We estimated genetic variation at eight P. leucopus specific microsatellite DNA loci. We discovered significant genetic variation within all populations, but no significant differences in numbers of alleles or heterozygosity between populations. For given population pairs, we found significant genetic differentiation even at very short distances, based on multilocus FST estimates. The amount of genetic differentiation between population pairs was similar in the two habitats. Distance had a marginal effect on genetic differentiation when comparing paired populations separated by 2000 m with those separated by 500 m. However, at a larger geographic scale, there was no evidence of isolation by distance. This study confirms that microsatellite-based studies have the potential to detect interpopulation differentiation at an extremely local scale, and suggests that habitat fragmentation has surprisingly few effects on P. leucopus genetic structure.

Population genetic structure of the Gulf of St. Lawrence aster, Symphyotrichum laurentianum (Asteraceae), a threatened coastal endemic

Botany ◽  
2009 ◽  
Vol 87 (11) ◽  
pp. 1089-1095 ◽  
Author(s):  
Stephen B. Heard ◽  
Linley K. Jesson ◽  
Kirby Tulk
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Threatened Species ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Population Decline ◽  
Allelic Diversity ◽  
Magdalen Islands

The Gulf of St. Lawrence aster ( Symphyotrichum laurentianum (Fernald) G.L. Nesom) is an endemic annual of saline habitats in the southern Gulf of St. Lawrence. It is listed as a threatened species, and has recently experienced population declines in much of its range. We used 11 allozyme markers to assay population genetic variation in six wild populations of S. laurentianum from the Magdalen Islands, Quebec (QC), the only remaining wild population from Prince Edward Island National Park (PEI), and a greenhouse population founded in 1999 with seed collected from PEI. Symphyotrichum laurentianum harbours moderate genetic diversity (Ps = 0.36, As = 1.54), with only modest spatial genetic structure (pairwise FST < 0.15) and no significant isolation by distance. The PEI population had greatly reduced allelic diversity compared with the populations from the Magdalen Islands, which likely act as a reservoir of genetic variation in S. laurentianum. Recent loss of alleles during population decline in PEI is suggested by the retention of greater allelic diversity in the greenhouse population. Estimates of breeding structure suggest small but nonzero rates of outcross pollination (FIS = 0.73, 95% CI = 0.48–0.97; outcrossing rate ∼16%). Population genetic structure in S. laurentianum can inform those forming and carrying out conservation and recovery plans for this threatened species.

scholarly journals Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Xu ◽  
Di Wu ◽  
Tianquan Yang ◽  
Chao Sun ◽  
Zaiqing Wang ◽  
...  
Keyword(s):  
Castor Bean ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
De Novo ◽  
Agronomic Traits ◽  
Ricinus Communis ◽  
Oilseed Crop ◽  
A Genome ◽  
Trait Locus ◽  
Wild Progenitors

Abstract Background Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean. Results Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size. Conclusions This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.

scholarly journals A multi-part strategy for introgression of exotic germplasm into elite plant breeding programs using genomic selection

2022 ◽  
Author(s):  
Irene S. Breider ◽  
R. Chris Gaynor ◽  
Gregor Gorjanc ◽  
Steve Thorn ◽  
Manish K. Pandey ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Plant Breeding ◽  
Genomic Selection ◽  
Genetic Gain ◽  
Genetic Improvement ◽  
Breeding Strategy ◽  
Breeding Program ◽  
Breeding Programs ◽  
Polygenic Inheritance ◽  
Polygenic Traits

Abstract Some of the most economically important traits in plant breeding show highly polygenic inheritance. Genetic variation is a key determinant of the rates of genetic improvement in selective breeding programs. Rapid progress in genetic improvement comes at the cost of a rapid loss of genetic variation. Germplasm available through expired Plant Variety Protection (exPVP) lines is a potential resource of variation previously lost in elite breeding programs. Introgression for polygenic traits is challenging, as many genes have a small effect on the trait of interest. Here we propose a way to overcome these challenges with a multi-part pre-breeding program that has feedback pathways to optimise recurrent genomic selection. The multi-part breeding program consists of three components, namely a bridging component, population improvement, and product development. Parameters influencing the multi-part program were optimised with the use of a grid search. Haploblock effect and origin were investigated. Results showed that the introgression of exPVP germplasm using an optimised multi-part breeding strategy resulted in 1.53 times higher genetic gain compared to a two-part breeding program. Higher gain was achieved through reducing the performance gap between exPVP and elite germplasm and breaking down linkage drag. Both first and subsequent introgression events showed to be successful. In conclusion, the multi-part breeding strategy has a potential to improve long-term genetic gain for polygenic traits and therefore, potential to contribute to global food security.

Genetic Diversity and Population Genetic Structure in the Rare Chittering Grass Wattle, Acacia anomala Court

1988 ◽  
Vol 36 (3) ◽  
pp. 273 ◽  
Author(s):  
DJ Coates
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Genetic System ◽  
Small Population ◽  
Vegetative Multiplication ◽  
The Mean ◽  
Allozyme Loci

There are 10 known populations of Acacia anomala occurring in two small disjunct groups some 30 km apart. The Chittering populations reproduce sexually whereas the Kalamunda populations appear to reproduce almost exclusively by vegetative multiplication. The level and distribution of genetic variation were studied at 15 allozyme loci. Two loci were monomorphic in all populations. In the Chittering populations the mean number of alleles per locus was 2.0 and the expected panmictic heterozygosity (genetic diversity) 0.209. In the Kalamunda populations the mean number of alleles per locus was 1.15 and the expected panmictic heterozygosity 0.079, although the observed heterozygosity of 0.150 was only marginally less than the Chittering populations (0.177). These data support the contention that the Chittering populations are primarily outcrossing whereas the Kalamunda populations are clonal, with each population consisting of individuals with identical and, in three of the four populations, heterozygous, multilocus genotypes. The level of genetic diversity within the Chittering populations is high for plants in general even though most populations are relatively smsll and isolated. It is proposed that either the length of time these populations have been reduced in size and isolated is insufficient for genetic diversity to be reduced or the genetic system of this species is adapted to small population conditions. Strategies for the adequate conservation of the genetic resources of Acacia anomala are discussed.

scholarly journals Genetic Characterization of Apulian Olive Germplasm as Potential Source in New Breeding Programs

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 268 ◽  
Author(s):  
Sion ◽  
Taranto ◽  
Montemurro ◽  
Mangini ◽  
Camposeo ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Agronomic Traits ◽  
Rural Landscape ◽  
Sources Of Resistance ◽  
Breeding Programs ◽  
Potential Source ◽  
History Of ◽  
Olive Cultivation ◽  
Olive Quick Decline Syndrome

The olive is a fruit tree species with a century-old history of cultivation in theMediterranean basin. In Apulia (Southern Italy), the olive is of main social, cultural and economicimportance, and represents a hallmark of the rural landscape. However, olive cultivation in thisregion is threatened by the recent spread of the olive quick decline syndrome (OQDS) disease, thusthere is an urgent need to explore biodiversity and search for genetic sources of resistance. Herein,a genetic variation in Apulian olive germplasm was explored, as a first step to identify genotypeswith enhanced bio-agronomic traits, including resistance to OQDS. A preselected set of nuclearmicrosatellite markers allowed the acquisition of genotypic profiles, and to define geneticrelationships between Apulian germplasm and widespread cultivars. The analysis highlighted thebroad genetic variation in Apulian accessions and the presence of different unique genetic profiles.The results of this study lay a foundation for the organization of new breeding programs for olivegenetic improvement.

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