scholarly journals Exploring the Legacy of Central European Historical Winter Wheat Landraces

2021 ◽  
Author(s):  
András Cseh ◽  
Péter Poczai ◽  
Tibor Kiss ◽  
Krisztina Balla ◽  
Zita Berki ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Genetic Erosion ◽  
Effective Population ◽  
Low Frequencies ◽  
Central European ◽  
Genome Wide ◽  
Population Sizes ◽  
Wheat Landraces

Abstract Historical wheat landraces are rich sources of genetic diversity offering untapped reservoirs for broadening the genetic base of modern varieties. Using a 20K SNP array, we investigated the accessible genetic diversity in a Central European bread wheat landrace collection with great drought, heat stress tolerance and higher tillering capacity. We discovered distinct differences in the number of average polymorphisms between Central and Western European collections, and identified a set of novel rare alleles present at low frequencies in the historical collection. The detected polymorphisms were unevenly distributed along the wheat genome, and polymorphic markers co-localized with genes of great agronomic importance. The efficiency of the highly diverse population for Genome-Wide Association study was confirmed and two significant marker trait associations with seed hardness were identified on the 5DS chromosome arm. The geographical distribution of the inferred Bayesian clustering revealed six genetically homogenous ancestral groups among the collection, where the Central European core bared an admixed background originating from four ancestral groups. We evaluated the effective population sizes (Ne) of the Central European collection and assessed changes in diversity over time, which revealed a dramatic ~97% genetic erosion between 1955 and 2015.

scholarly journals Exploring the legacy of Central European historical winter wheat landraces

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
András Cseh ◽  
Péter Poczai ◽  
Tibor Kiss ◽  
Krisztina Balla ◽  
Zita Berki ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Snp Array ◽  
Genetic Erosion ◽  
Effective Population ◽  
Low Frequencies ◽  
Central European ◽  
Population Sizes ◽  
Heat Stress Tolerance ◽  
Modern Wheat ◽  
Wheat Landraces

AbstractHistorical wheat landraces are rich sources of genetic diversity offering untapped reservoirs for broadening the genetic base of modern varieties. Using a 20K SNP array, we investigated the accessible genetic diversity in a Central European bread wheat landrace collection with great drought, heat stress tolerance and higher tillering capacity. We discovered distinct differences in the number of average polymorphisms between landraces and modern wheat cultivars, and identified a set of novel rare alleles present at low frequencies in the landrace collection. The detected polymorphisms were unevenly distributed along the wheat genome, and polymorphic markers co-localized with genes of great agronomic importance. The geographical distribution of the inferred Bayesian clustering revealed six genetically homogenous ancestral groups among the collection, where the Central European core bared an admixed background originating from four ancestral groups. We evaluated the effective population sizes (Ne) of the Central European collection and assessed changes in diversity over time, which revealed a dramatic ~ 97% genetic erosion between 1955 and 2015.

scholarly journals Genome-Wide Association Study Reveals Genetic Architecture of Septoria Tritici Blotch Resistance in a Historic Landrace Collection

2021 ◽  
Author(s):  
Anik Dutta ◽  
Daniel Croll ◽  
Bruce A. McDonald ◽  
Simon G. Krattinger
Keyword(s):  
Genetic Diversity ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Phenotypic Variability ◽  
Genome Wide Association ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Genome Wide ◽  
A Genome ◽  
Wheat Landraces

Abstract Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is a major constraint in global wheat production. The lack of genetic diversity in modern elite wheat cultivars largely hinders the improvement of STB resistance. Wheat landraces are reservoirs of untapped genetic diversity, which can be exploited to find novel STB resistance genes or alleles. Here, we characterized 188 Swiss wheat landraces for resistance to STB using four Swiss Z. tritici isolates. We used a genome-wide association study (GWAS) to identify genetic variants associated with the amount of lesion and pycnidia production by the fungus. The majority of the landraces were highly resistant for both traits to the isolate 1E4, indicating a gene-for-gene relationship, while higher phenotypic variability was observed against other isolates. GWAS detected a significant SNP on chromosome 3A that was associated with both traits in the isolate 1E4. The resistance response against 1E4 was likely controlled by the Stb6 gene. Sanger sequencing revealed that the majority of these ~100-year-old landraces carry the Stb6 resistance allele. This indicates the importance of this gene in Switzerland during the early 1900s for disease control in the field. Our study demonstrates the importance of characterizing historic landrace collections for STB resistance to provide valuable information on resistance variability and contributing alleles. This will help breeders in the future to make decisions on integrating such germplasms in STB resistance breeding.

scholarly journals Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species

2019 ◽  
Vol 11 (10) ◽  
pp. 2875-2886 ◽  
Author(s):  
Venkat Talla ◽  
Lucile Soler ◽  
Takeshi Kawakami ◽  
Vlad Dincă ◽  
Roger Vila ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Nucleotide Diversity ◽  
Gene Annotation ◽  
Rate Variation ◽  
Butterfly Species ◽  
Relative Role ◽  
Effective Population ◽  
Genome Wide ◽  
Population Sizes

Abstract The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.

scholarly journals Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.)

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 2
Author(s):  
Kunyan Zou ◽  
Ki-Seung Kim ◽  
Kipoong Kim ◽  
Dongwoo Kang ◽  
Yu-Hyeon Park ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Aspect Ratio ◽  
Association Study ◽  
Arachis Hypogaea ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
The United States ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Arachis Hypogaea L

Peanut (Arachis hypogaea L.) is one of the important oil crops of the world. In this study, we aimed to evaluate the genetic diversity of 384 peanut germplasms including 100 Korean germplasms and 284 core collections from the United States Department of Agriculture (USDA) using an Axiom_Arachis array with 58K single-nucleotide polymorphisms (SNPs). We evaluated the evolutionary relationships among 384 peanut germplasms using a genome-wide association study (GWAS) of seed aspect ratio data processed by ImageJ software. In total, 14,030 filtered polymorphic SNPs were identified from the peanut 58K SNP array. We identified five SNPs with significant associations to seed aspect ratio on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09. AX-177640219 on chromosome Araip.B08 was the most significantly associated marker in GAPIT and Regularization method. Phosphoenolpyruvate carboxylase (PEPC) was found among the eleven genes within a linkage disequilibrium (LD) of the significant SNPs on Araip.B08 and could have a strong causal effect in determining seed aspect ratio. The results of the present study provide information and methods that are useful for further genetic and genomic studies as well as molecular breeding programs in peanuts.

scholarly journals Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 493
Author(s):  
Salvatore Mastrangelo ◽  
Filippo Cendron ◽  
Gianluca Sottile ◽  
Giovanni Niero ◽  
Baldassare Portolano ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Snp Array ◽  
Fixation Index ◽  
Phenotypic Traits ◽  
Plumage Color ◽  
Phenotypic Marker ◽  
Genome Wide ◽  
A Genome ◽  
The Difference ◽  
Genomic Regions

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (FST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and FST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

scholarly journals Genetic Diversity and Genome Wide Association Study of β-Glucan Content in Tetraploid Wheat Grains

PLoS ONE ◽  
2016 ◽  
Vol 11 (4) ◽  
pp. e0152590 ◽  
Author(s):  
Ilaria Marcotuli ◽  
Kelly Houston ◽  
Julian G. Schwerdt ◽  
Robbie Waugh ◽  
Geoffrey B. Fincher ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Tetraploid Wheat ◽  
Genome Wide Association ◽  
Wheat Grains ◽  
Genome Wide

scholarly journals Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

2020 ◽  
Vol 287 (1922) ◽  
pp. 20192613 ◽  
Author(s):  
Elisa G. Dierickx ◽  
Simon Yung Wa Sin ◽  
H. Pieter J. van Veelen ◽  
M. de L. Brooke ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Sex Chromosomes ◽  
Demographic History ◽  
Large Population ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Approaches To Study ◽  
Genetic Signatures

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

scholarly journals Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 361 ◽  
Author(s):  
Shuqi Diao ◽  
Shuwen Huang ◽  
Zhiting Xu ◽  
Shaopan Ye ◽  
Xiaolong Yuan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Conservation Status ◽  
Snp Array ◽  
Size Analysis ◽  
Selection Signatures ◽  
Effective Population ◽  
Low Genetic Diversity ◽  
Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

Weak genetic structuring suggests historically high genetic connectivity among recently fragmented urban populations of the scincid lizard, Ctenotus fallens

2015 ◽  
Vol 63 (4) ◽  
pp. 279 ◽  
Author(s):  
Josef Krawiec ◽  
Siegfried L. Krauss ◽  
Robert A. Davis ◽  
Peter B. S. Spencer
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Large Population ◽  
Geographic Distance ◽  
Genetic Erosion ◽  
Genetic Connectivity ◽  
Genetic Structuring ◽  
Low Genetic Diversity ◽  
Population Sizes

Populations in fragmented urban remnants may be at risk of genetic erosion as a result of reduced gene flow and elevated levels of inbreeding. This may have serious genetic implications for the long-term viability of remnant populations, in addition to the more immediate pressures caused by urbanisation. The population genetic structure of the generalist skink Ctenotus fallens was examined using nine microsatellite markers within and among natural vegetation remnants within a highly fragmented urban matrix in the Perth metropolitan area in Western Australia. These data were compared with samples from a large unfragmented site on the edge of the urban area. Overall, estimates of genetic diversity and inbreeding within all populations were similar and low. Weak genetic differentiation, and a significant association between geographic and genetic distance, suggests historically strong genetic connectivity that decreases with geographic distance. Due to recent fragmentation, and genetic inertia associated with low genetic diversity and large population sizes, it is not possible from these data to infer current genetic connectivity levels. However, the historically high levels of gene flow that our data suggest indicate that a reduction in contemporary connectivity due to fragmentation in C. fallens is likely to result in negative genetic consequences in the longer term.

scholarly journals Challenges to assessing connectivity between massive populations of the Australian plague locust

2011 ◽  
Vol 278 (1721) ◽  
pp. 3152-3160 ◽  
Author(s):  
Marie-Pierre Chapuis ◽  
Julie-Anne M. Popple ◽  
Karine Berthier ◽  
Stephen J. Simpson ◽  
Edward Deveson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Large Population ◽  
Movement Ecology ◽  
Effective Population ◽  
Continental Scale ◽  
Australian Continent ◽  
Population Structuring ◽  
Population Sizes ◽  
Approximate Bayesian ◽  
Australian Plague Locust

Linking demographic and genetic dispersal measures is of fundamental importance for movement ecology and evolution. However, such integration can be difficult, particularly for highly fecund species that are often the target of management decisions guided by an understanding of population movement. Here, we present an example of how the influence of large population sizes can preclude genetic approaches from assessing demographic population structuring, even at a continental scale. The Australian plague locust, Chortoicetes terminifera , is a significant pest, with populations on the eastern and western sides of Australia having been monitored and managed independently to date. We used microsatellites to assess genetic variation in 12 C. terminifera population samples separated by up to 3000 km. Traditional summary statistics indicated high levels of genetic diversity and a surprising lack of population structure across the entire range. An approximate Bayesian computation treatment indicated that levels of genetic diversity in C. terminifera corresponded to effective population sizes conservatively composed of tens of thousands to several million individuals. We used these estimates and computer simulations to estimate the minimum rate of dispersal, m , that could account for the observed range-wide genetic homogeneity. The rate of dispersal between both sides of the Australian continent could be several orders of magnitude lower than that typically considered as required for the demographic connectivity of populations.

Sign in / Sign up

Export Citation Format

Share Document