All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

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Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation

PLoS ONE ◽

10.1371/journal.pone.0245965 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0245965

Author(s):

Catherine Kiwuka ◽

Eva Goudsmit ◽

Rémi Tournebize ◽

Sinara Oliveira de Aquino ◽

Jacob C. Douma ◽

...

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Allelic Variation ◽

Coffea Canephora ◽

Ex Situ ◽

Negative Effects ◽

Robusta Coffee ◽

Genetic Diversity And Structure ◽

Adaptive Diversity ◽

Southern Central

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.

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Genetic diversity in common bean accessions evaluated by means of morpho-agronomical and RAPD data

Scientia Agricola ◽

10.1590/s0103-90162007000300007 ◽

2007 ◽

Vol 64 (3) ◽

pp. 256-262 ◽

Cited By ~ 12

Author(s):

Alisson Fernando Chiorato ◽

Sérgio Augusto Morais Carbonell ◽

Luciana Lasry Benchimol ◽

Marilia Barbosa Chiavegato ◽

Luiz Antonio dos Santos Dias ◽

...

Keyword(s):

Genetic Diversity ◽

Common Bean ◽

Genetic Similarity ◽

Germplasm Conservation ◽

Molecular Data ◽

Ex Situ ◽

Germplasm Bank ◽

Improvement Programs ◽

Improved Cultivars ◽

Germplasm Banks

Germplasm banks store genotype samples, improved varieties, landraces and wild species, all generically denominated accessions. The importance of characterizing germplasm banks is based on the identification and knowledge of relevant traits for genetic improvement and ex situ germplasm conservation. Thus, the present study had as aim the evaluation of the genetic diversity among 220 accessions of a Brazilian common bean germplasm bank of the "Instituto Agronômico de Campinas" (IAC) by means of 23 morpho-agronomical descriptors and 19 RAPD loci. These accessions correspond to genotypes from the Andean and Middle American gene pool as well as from cultivars derived from common bean improvement programs. The Middle American accessions and the improved cultivars were clustered into one group, distinct from the one formed by the Andean accessions. In relation to the molecular data, 47% of the genetic similarity was detected among the Middle American accessions, and similar results were observed for the improved cultivars (50%). The Andean accessions revealed 60% of genetic similarity. The cluster constituted by the improved cultivars and the Middle American genotypes differed, basically, in tegument color. Both molecular and morpho-agronomical data sets were equally effective to quantify and organize the genetic diversity of common bean accessions. This information may be useful to direct crosses and for the proper organization of the IAC germplasm bank.

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Assessment of genetic diversity and population structure of oil palm (Elaeis guineensis Jacq.) field genebank: A step towards molecular-assisted germplasm conservation

PLoS ONE ◽

10.1371/journal.pone.0255418 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0255418

Author(s):

Siou Ting Gan ◽

Chin Jit Teo ◽

Shobana Manirasa ◽

Wei Chee Wong ◽

Choo Kien Wong

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Oil Palm ◽

Core Collection ◽

Elaeis Guineensis ◽

Germplasm Conservation ◽

Ex Situ ◽

Fixation Index ◽

Core Set ◽

Genetic Diversity And Structure

Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright’s fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei’s genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.

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Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers

PeerJ ◽

10.7717/peerj.10485 ◽

2020 ◽

Vol 8 ◽

pp. e10485

Author(s):

Zhixin Wang ◽

Yalin Sun ◽

Xinfang Huang ◽

Feng Li ◽

Yuping Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Germplasm Conservation ◽

Principal Component ◽

Snp Markers ◽

Colocasia Esculenta ◽

Single Nucleotide ◽

Genome Wide ◽

Entire Collection ◽

Tuber Crop

Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.

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Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis

Animals ◽

10.3390/ani10081375 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1375

Author(s):

Hideyuki Ito ◽

Nobuyoshi Nakajima ◽

Manabu Onuma ◽

Miho Murayama

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

De Novo ◽

Draft Genome ◽

Amplicon Sequencing ◽

Snp Markers ◽

Domestic Cat ◽

Ex Situ ◽

Genetic Management ◽

Leopard Cat

The Tsushima leopard cat (Prionailurus bengalensis euptilurus) lives on Tsushima Island in Japan and is a regional population of the Amur leopard cat; it is threatened with extinction. Its genetic management is important because of the small population. We used genotyping by random amplicon sequencing-direct (GRAS-Di) to develop a draft genome and explore single-nucleotide polymorphism (SNP) markers. The SNPs were analyzed using three genotyping methods (mapping de novo, to the Tsushima leopard cat draft genome, and to the domestic cat genome). We examined the genetic diversity and genetic structure of the Tsushima leopard cat. The genome size was approximately 2.435 Gb. The number of SNPs identified was 133–158. The power of these markers was sufficient for individual and parentage identifications. These SNPs can provide useful information about the life of the Tsushima leopard cat and the pairings and for the introduction of founders to conserve genetic diversity with ex situ conservation. We identified that there are no subpopulations of the Tsushima leopard cat. The identifying units will allow for a concentration of efforts for conservation. SNPs can be applied to the analysis of the leopard cat in other regions, making them useful for comparisons among populations and conservation in other small populations.

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Genetic variability and population structure of Ethiopian chickpea (Cicer arietinum L.) germplasm

PLoS ONE ◽

10.1371/journal.pone.0260651 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0260651

Author(s):

Sintayehu Admas ◽

Kassahun Tesfaye ◽

Teklehaimanot Haileselassie ◽

Eleni Shiferaw ◽

K. Colton Flynn

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Germplasm Conservation ◽

Genetic Distances ◽

Geographic Region ◽

Ex Situ ◽

Conservation Strategies ◽

Breeding Programs

Evaluation of the genetic diversity and an understanding of the genetic structure and relationships of chickpea genotypes are valuable to design efficient germplasm conservation strategies and crop breeding programs. Information is limited, in these regards, for Ethiopian chickpea germplasms. Therefore, the present study was carried out to estimate the genetic diversity, population structure, and relationships of 152 chickpea genotypes using simple sequence repeats (SSR) markers. Twenty three SSR markers exhibited polymorphism producing a total of 133 alleles, with a mean of 5.8 alleles per locus. Analyses utilizing various genetic-based statistics included pairwise population Nei’s genetic distance, heterozygosity, Shannon’s information index, polymorphic information content, and percent polymorphism. These analyses exemplified the existence of high genetic variation within and among chickpea genotypes. The 152 genotypes were divided into two major clusters based on Nei’s genetic distances. The exotic genotypes were grouped in one cluster exclusively showing that these genotypes are distinct to Ethiopian genotypes, while the patterns of clustering of Ethiopian chickpea genotypes based on their geographic region were not consistent because of the seed exchange across regions. Model-based population structure clustering identified two discrete populations. These finding provides useful insight for chickpea collections and ex-situ conservation and national breeding programs for widening the genetic base of chickpea.

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Genetic Diversity and Population Structure of Sorghum [Sorghum Bicolor (L.) Moench] Accessions as Revealed by Single Nucleotide Polymorphism Markers

Frontiers in Plant Science ◽

10.3389/fpls.2021.799482 ◽

2022 ◽

Vol 12 ◽

Author(s):

Muluken Enyew ◽

Tileye Feyissa ◽

Anders S. Carlsson ◽

Kassahun Tesfaye ◽

Cecilia Hammenhag ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Sorghum Bicolor ◽

Conservation Status ◽

Snp Markers ◽

Ex Situ ◽

Eastern Region ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Landrace Accessions

Ethiopia is the center of origin for sorghum [Sorghum bicolor (L.) Moench], where the distinct agro-ecological zones significantly contributed to the genetic diversity of the crops. A large number of sorghum landrace accessions have been conserved ex situ. Molecular characterization of this diverse germplasm can contribute to its efficient conservation and utilization in the breeding programs. This study aimed to investigate the genetic diversity of Ethiopian sorghum using gene-based single nucleotide polymorphism (SNP) markers. In total, 359 individuals representing 24 landrace accessions were genotyped using 3,001 SNP markers. The SNP markers had moderately high polymorphism information content (PIC = 0.24) and gene diversity (H = 0.29), on average. This study revealed 48 SNP loci that were significantly deviated from Hardy–Weinberg equilibrium with excess heterozygosity and 13 loci presumed to be under selection (P < 0.01). The analysis of molecular variance (AMOVA) determined that 35.5% of the total variation occurred within and 64.5% among the accessions. Similarly, significant differentiations were observed among geographic regions and peduncle shape-based groups. In the latter case, accessions with bent peduncles had higher genetic variation than those with erect peduncles. More alleles that are private were found in the eastern region than in the other regions of the country, suggesting a good in situ conservation status in the east. Cluster, principal coordinates (PCoA), and STRUCTURE analyses revealed distinct accession clusters. Hence, crossbreeding genotypes from different clusters and evaluating their progenies for desirable traits is advantageous. The exceptionally high heterozygosity observed in accession SB4 and SB21 from the western geographic region is an intriguing finding of this study, which merits further investigation.

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Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction

Diversity ◽

10.3390/d12080299 ◽

2020 ◽

Vol 12 (8) ◽

pp. 299

Author(s):

Colette Blyth ◽

Matthew J. Christmas ◽

Doug C. Bickerton ◽

Renate Faast ◽

Jasmin G. Packer ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

South Australia ◽

Genomic Analysis ◽

Unknown Origin ◽

Genetic Connectivity ◽

Conservation Genomics ◽

Low Genetic Diversity ◽

Pollinator Community ◽

Management Recommendations

In this paper we apply a conservation genomics approach to make evidence-based management recommendations for Acacia whibleyana, an endangered shrub endemic to Eyre Peninsula, South Australia. We used population genomic analysis to assess genetic connectivity, diversity, and historical inbreeding across all known stands of the species sampling remnant stands, revegetated stands of unknown origin, and a post-fire seedling cohort. Our results indicate a degree of historical connectivity across the landscape, but habitat loss and/or pollinator community disruption are potential causes of strong genetic structure across the remnant stands. Remnant stands had low genetic diversity and showed evidence of historical inbreeding, but only low levels of intra-stand relatedness indicating that risks of contemporary inbreeding are low. Analysis of a post-fire first generation cohort of seedlings showed they likely resulted from intra-stand matings, resulting in reduced genetic diversity compared to the parents. However, admixed seedlings in this cohort showed an increase in heterozygosity relative to likely sources and the non-admixed seedlings of the same stand. Assisted inter-stand gene flow may prove an effective management strategy to boost heterozygosity and corresponding increases in adapting capacity in this endangered species.

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EST–SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives

Genes ◽

10.3390/genes11080916 ◽

2020 ◽

Vol 11 (8) ◽

pp. 916

Author(s):

Roberto Mariotti ◽

Angjelina Belaj ◽

Raul De La Rosa ◽

Lorenzo Leòn ◽

Federico Brizioli ◽

...

Keyword(s):

Olea Europaea ◽

Expressed Sequence Tag ◽

Germplasm Conservation ◽

Snp Markers ◽

Genomic Diversity ◽

Wild Plants ◽

Species Differentiation ◽

Snp Analysis ◽

Functional Polymorphisms ◽

Olea Europaéa

Background: The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers. Methods: In the present work, more than 1000 transcript-specific SNP markers obtained by the genotyping of 260 individuals were studied. These genotypes included cultivated, oleasters, and samples of subspecies guanchica, and were analyzed in silico, in order to identify polymorphisms on key genes distinguishing different Olea europaea forms. Results: Phylogeny inference and principal coordinate analysis allowed to detect two distinct clusters, clearly separating wilds and guanchica samples from cultivated olives, meanwhile the structure analysis made possible to differentiate these three groups. Sequences carrying the polymorphisms that distinguished wild and cultivated olives were analyzed and annotated, allowing to identify 124 candidate genes that have a functional role in flower development, stress response, or involvement in important metabolic pathways. Signatures of selection that occurred during olive domestication, were detected and reported. Conclusion: This deep EST–SNP analysis provided important information on the genetic and genomic diversity of the olive complex, opening new opportunities to detect gene polymorphisms with potential functional and evolutionary roles, and to apply them in genomics-assisted breeding, highlighting the importance of olive germplasm conservation.

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