Genetic Diversity and Population Structure in a Legacy Collection of Spring Barley Landraces Adapted to a Wide Range of Climates

Abstract The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

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Population structure of Drosophila suzukii and signals of multiple invasions into the continental United States

10.1101/2021.03.14.435345 ◽

2021 ◽

Author(s):

Kyle M Lewald ◽

Antoine Abrieux ◽

Derek A Wilson ◽

Yoosook Lee ◽

William R Conner ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Population Structure ◽

Weather Conditions ◽

The United States ◽

Future Research ◽

Drosophila Suzukii ◽

Significant Damage ◽

Wide Range ◽

Multiple Invasions

Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. To improve on previous studies examining genetic structure of D. suzukii, we sequenced whole genomes of 237 individual flies collected across the continental U.S., as well as several representative sites in Europe, Brazil, and Asia, to identify hundreds of thousands of genetic markers for analysis. We analyzed these markers to detect population structure, to reconstruct migration events, and to estimate genetic diversity and differentiation within and among the continents. We observed strong population structure between West and East Coast populations in the U.S., but no evidence of any population structure North to South, suggesting there is no broad-scale adaptations occurring in response to the large differences in regional weather conditions. We also find evidence of repeated migration events from Asia into North America have provided increased levels of genetic diversity, which does not appear to be the case for Brazil or Europe. This large genomic dataset will spur future research into genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.

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Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species

Scientific Reports ◽

10.1038/s41598-020-75553-0 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Manosh Kumar Biswas ◽

Mita Bagchi ◽

Ujjal Kumar Nath ◽

Dhiman Biswas ◽

Sathishkumar Natarajan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Large Scale ◽

Polymorphic Information Content ◽

Pcr Amplification ◽

Efficient Manner ◽

Lilium Species ◽

Population Structure Analysis ◽

Wide Range ◽

Functional Molecular Markers

Abstract Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.

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Genetic Diversity and Population Structure of Japanese Plum-Type (Hybrids of P. salicina) Accessions Assessed by SSR Markers

Agronomy ◽

10.3390/agronomy11091748 ◽

2021 ◽

Vol 11 (9) ◽

pp. 1748

Author(s):

Brenda I. Guerrero ◽

M. Engracia Guerra ◽

Sara Herrera ◽

Patricia Irisarri ◽

Ana Pina ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Group Method ◽

Japanese Plum ◽

Pair Group ◽

Prunus Salicina ◽

Wide Range ◽

High Level ◽

Informative Content

Japanese plum (Prunus salicina Lindl.) is widely distributed in temperate zones across the world. Since its introduction to USA in the late 19th century, this species has been hybridized with up to 15 different diploid Prunus species. This high level of introgression has resulted in a wide range of traits and agronomic behaviors among currently grown cultivars. In this work, 161 Japanese plum-type accessions were genotyped using a set of eight Simple Sequence Repeats (SSR) markers to assess the current genetic diversity and population structure. A total of 104 alleles were detected, with an average of 13 alleles per locus. The overall Polymorphic Informative Content (PIC) value of SSR markers was 0.75, which indicates that these SSR markers are highly polymorphic. The Unweighted Pair Group Method with Arithmetic (UPGMA) dendrogram and the seven groups inferred by Discriminant Analysis of Principal Components (DAPC) revealed a strong correlation of the population structure to the parentage background of the accessions, supported by a moderate but highly significant genetic differentiation. The results reported herein provide useful information for breeders and for the preservation of germplasm resources.

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Multifaceted Analysis of Barley Landraces Collected during Gene Bank Expeditions in Poland at the End of the 20th Century

Agronomy ◽

10.3390/agronomy10121958 ◽

2020 ◽

Vol 10 (12) ◽

pp. 1958

Author(s):

Joanna Dziurdziak ◽

Paulina Bolc ◽

Sylwia Wlodarczyk ◽

Marta Puchta ◽

Grzegorz Gryziak ◽

...

Keyword(s):

Historical Data ◽

Agronomic Traits ◽

Spring Barley ◽

Field Evaluation ◽

Inter Simple Sequence Repeat ◽

Breeding Programs ◽

Wide Range ◽

Barley Landraces ◽

Place Of Origin ◽

Simple Sequence

The extensive genetic diversity of crop landraces deposited in gene banks is an important part of future breeding programs. However, in order to exploit this potential, it is necessary both to preserve germplasm and to collect and share a wide range of data on its characteristics and evaluation. The main objective of the presented paper was to evaluate the diversity of spring barley landraces originating from Poland. Historical data from standard field evaluation of agronomic traits, genetic data obtained from Inter Simple Sequence Repeat (ISSR) analysis and grain morphometric data were used. The analysis showed that groups of hulled and hulls barley accessions were substantially separate. Genetic and grain morphological variation did not show any relationship with eco-geographical conditions in the place of origin. There was also no clear division into forms with two- and six-row ears. The combination of the results of various types of analyzes describing this collection makes us believe that its chances of being used in research and breeding will increase.

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Genetic Diversity, Population Structure and Inter-Trait Relationships of Combined Heat and Drought Tolerant Early-Maturing Maize Inbred Lines from West and Central Africa

Agronomy ◽

10.3390/agronomy10091324 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1324

Author(s):

Alimatu Sadia Osuman ◽

Baffour Badu-Apraku ◽

Beatrice E. Ifie ◽

Pangirayi Tongoona ◽

Ebenezer Obeng-Bio ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Polymorphic Information Content ◽

Central Africa ◽

Inbred Lines ◽

Heterotic Groups ◽

Maize Inbred Lines ◽

Wide Range ◽

Early Maturing ◽

West And Central Africa

Adequate knowledge and understanding of the genetic diversity and inter-trait relationships among elite maize inbred lines are crucial for determining breeding strategies and predicting hybrid performance. The objectives of this study were to investigate the genetic diversity of 162 early maturing white and yellow tropical maize inbred lines, and to determine the population structure, heterotic groups and inter-trait relationships among the lines. Using 9684 DArT single nucleotide polymorphism (SNP) markers, a gene diversity (GD) of 0.30 was recorded for the inbred lines with polymorphic information content (PIC) ranging from 0.08 to 0.38. The genetic relatedness among the inbred lines evaluated revealed six different groups based on the history of selection, colour of endosperm and pedigree. The genotype-by-trait (GT) biplot analysis identified inbred 1 (TZEI 935) as outstanding in terms of combined heat and drought (HD) tolerance with the base index analysis identifying 15 superior inbreds in the HD environment. A wide range of genetic variability was observed among the inbred lines, indicating that they are an invaluable resource for breeding for HD tolerance in maize breeding programmes, especially in West and Central Africa.

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Genomic Analysis of Selected Maize Landraces from Sahel and Coastal West Africa Reveals Their Variability and Potential for Genetic Enhancement

Genes ◽

10.3390/genes11091054 ◽

2020 ◽

Vol 11 (9) ◽

pp. 1054

Author(s):

Charles Nelimor ◽

Baffour Badu-Apraku ◽

Ana Luísa Garcia-Oliveira ◽

Antonia Tetteh ◽

Agre Paterne ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Pool ◽

Allelic Variation ◽

Sub Saharan Africa ◽

Genetic Enhancement ◽

Gene Pools ◽

International Institute ◽

Improvement Program ◽

Wide Range

Genetic adaptation of maize to the increasingly unpredictable climatic conditions is an essential prerequisite for achievement of food security and sustainable development goals in sub-Saharan Africa. The landraces of maize; which have not served as sources of improved germplasm; are invaluable sources of novel genetic variability crucial for achieving this objective. The overall goal of this study was to assess the genetic diversity and population structure of a maize panel of 208 accessions; comprising landrace gene pools from Burkina Faso (58), Ghana (43), and Togo (89), together with reference populations (18) from the maize improvement program of the International Institute of Tropical Agriculture (IITA). Genotyping the maize panel with 5974 DArTseq-SNP markers revealed immense genetic diversity indicated by average expected heterozygosity (0.36), observed heterozygosity (0.5), and polymorphic information content (0.29). Model-based population structure; neighbor-joining tree; discriminant analysis of principal component; and principal coordinate analyses all separated the maize panel into three major sub-populations; each capable of providing a wide range of allelic variation. Analysis of molecular variance (AMOVA) showed that 86% of the variation was within individuals; while 14% was attributable to differences among gene pools. The Burkinabe gene pool was strongly differentiated from all the others (genetic differentiation values >0.20), with no gene flow (Nm) to the reference populations (Nm = 0.98). Thus; this gene pool could be a target for novel genetic variation for maize improvement. The results of the present study confirmed the potential of this maize panel as an invaluable genetic resource for future design of association mapping studies to speed-up the introgression of this novel variation into the existing breeding pipelines.

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Genetic Diversity and Population Structure of Chionanthus virginicus

Journal of the American Society for Horticultural Science ◽

10.21273/jashs05095-21 ◽

2022 ◽

Vol 147 (1) ◽

pp. 62-69

Author(s):

Phillip A. Wadl ◽

Timothy A. Rinehart ◽

Richard T. Olsen ◽

Benjamin D. Waldo ◽

Joseph H. Kirkbride

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Differentiation ◽

Isolation By Distance ◽

Germplasm Collection ◽

Eastern United States ◽

High Genetic Diversity ◽

Breeding Programs ◽

Tree Form ◽

Wide Range

The genus Chionanthus, known as fringetrees, is a member of the olive family (Oleaceae). Chionanthus virginicus is an understory tree or shrub with a wide range in forests of the eastern United States and is used as an ornamental tree that is known to be free of insects and disease in the wild. The species is tolerant of a wide range of environmental conditions, and there is interest in developing new cultivars with improved horticultural traits, such as tree form or upright growth habit and superior flowering display that are widely adapted. To identify genepools in the native range of C. virginicus for use in breeding programs, the genetic diversity and population structure were assessed for 274 individuals from 12 locations in four states (Florida, Maryland, North Carolina, and Texas) using 26 simple sequence repeats (SSRs). An average of 12.54 alleles/locus were detected, allelic richness averaged 2.80. Genetic differentiation was 0.11, indicating moderate differentiation among subpopulations. Despite the high genetic diversity and low population differentiation, Bayesian clustering analysis identified six genetic groups that match the geographic distribution of collection sites. Analysis of molecular variance indicated that most (82%) of the variation is explained within individuals, and 11% and 7% of the variation is due to differences among individuals within populations and among populations. Analysis of isolation by distance across all samples showed a weak positive relationship between geographic distance and genetic distance. The C. virginicus samples analyzed in this study indicate there is sufficient diversity for germplasm collection for use in breeding programs. Given the relatively moderate genetic differentiation, there are not likely to be unique islands of genetic diversity that may be missed when gathering parental materials for a breeding program

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AFLP-Based Analysis of Variation and Population Structure in Mutagenesis Induced Faba Bean

Diversity ◽

10.3390/d12080303 ◽

2020 ◽

Vol 12 (8) ◽

pp. 303

Author(s):

Nurmansyah ◽

Salem S. Alghamdi ◽

Hussein M. Migdadi ◽

Muhammad A. Khan ◽

Muhammad Afzal

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Faba Bean ◽

High Genetic Diversity ◽

Banding Patterns ◽

Wide Range ◽

Induced Mutagenesis ◽

Control Parent ◽

Analysis Of Variation ◽

Allele Count

Genetic diversity enrichment is urgently necessary to develop climate-resilient faba bean cultivars. The present study aimed to measure the enrichment of genetic diversity and changes in the population structure of faba bean, following induced mutagenesis. 120 samples, including 116 M2 mutant plants, generated by exposing the ILB4347 accession to four mutagen treatments (25 and 50 Gray gamma radiation and 0.01%, and 0.05% diethyl sulfate) and four reference genotypes were characterized using 11 amplified fragment length polymorphism (AFLP) primer combinations. The AFLP markers generated 1687 polymorphic alleles, including 756 alleles (45%) that were detected infrequently (f ≤ 0.1). The total allele count of the mutant plants ranged from 117 to 545. We observed a wide range of banding patterns and counts among the mutant plants, showing the high genetic diversity induced by mutation. Mutations also changed the population structure, by altering 31.78% of the total membership coefficient (Q). Although mutations changed the population structure, Nei’s genetic distance showed that the mutant population remained closely related to its control parent. This is the first report examining genetic diversity and population changes in faba bean mutant populations and, thus, could facilitate the application of induced mutagenesis during faba bean breeding.

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Genotyping-By-Sequencing Reveals Population Structure and Genetic Diversity of a Buffelgrass (Cenchrus ciliaris L.) Collection

Diversity ◽

10.3390/d12030088 ◽

2020 ◽

Vol 12 (3) ◽

pp. 88

Author(s):

Alemayehu Teressa Negawo ◽

Yilikal Assefa ◽

Jean Hanson ◽

Asebe Abdena ◽

Meki S. Muktar ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Core Collection ◽

Reference Genome ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Soil Conditions ◽

Cenchrus Ciliaris ◽

Population Structure Analysis ◽

Wide Range

Buffelgrass (Cenchrus ciliaris L.) is an important forage grass widely grown across the world with many good characteristics including high biomass yield, drought tolerance, and adaptability to a wide range of soil conditions and agro-ecologies. Two hundred and five buffelgrass accessions from diverse origins, conserved as part of the in-trust collection in the ILRI genebank, were analyzed by genotyping-by-sequencing using the DArTseq platform. The genotyping generated 234,581 single nucleotide polymorphism (SNP) markers, with polymorphic information content (PIC) values ranging from 0.005 to 0.5, and the short sequences of the markers were aligned with foxtail millet (Setaria italica) as a reference genome to generate genomic map positions of the markers. One thousand informative SNP markers, representing a broad coverage of the reference genome and with an average PIC value of 0.35, were selected for population structure and diversity analyses. The population structure analysis suggested two main groups, while the hierarchical clustering showed up to eight clusters in the collection. A representative core collection containing 20% of the accessions in the collection, with germplasm from 10 African countries and Oman, was developed. In general, the study revealed the presence of considerable genetic diversity and richness in the collection and a core collection that could be used for further analysis for specific traits of interest.

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