Simulating the impact of genetic diversity of Medicago truncatula on germination and emergence using a crop emergence model for ideotype breeding

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

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Impact of cyclones on hard coral and metapopulation structure, connectivity and genetic diversity of coral reef fish

Coral Reefs ◽

10.1007/s00338-021-02096-9 ◽

2021 ◽

Author(s):

Gabriele Gerlach ◽

Philipp Kraemer ◽

Peggy Weist ◽

Laura Eickelmann ◽

Michael J. Kingsford

Keyword(s):

Genetic Diversity ◽

Coral Reef ◽

Genetic Structure ◽

Reef Fish ◽

Coral Reef Fish ◽

Population Genetic Study ◽

Hard Coral ◽

Great Loss ◽

Metapopulation Structure ◽

The Impact

AbstractCyclones have one of the greatest effects on the biodiversity of coral reefs and the associated species. But it is unknown how stochastic alterations in habitat structure influence metapopulation structure, connectivity and genetic diversity. From 1993 to 2018, the reefs of the Capricorn Bunker Reef group in the southern part of the Great Barrier Reef were impacted by three tropical cyclones including cyclone Hamish (2009, category 5). This resulted in substantial loss of live habitat-forming coral and coral reef fish communities. Within 6–8 years after cyclones had devastated, live hard corals recovered by 50–60%. We show the relationship between hard coral cover and the abundance of the neon damselfish (Pomacentrus coelestis), the first fish colonizing destroyed reefs. We present the first long-term (2008–2015 years corresponding to 16–24 generations of P. coelestis) population genetic study to understand the impact of cyclones on the meta-population structure, connectivity and genetic diversity of the neon damselfish. After the cyclone, we observed the largest change in the genetic structure at reef populations compared to other years. Simultaneously, allelic richness of genetic microsatellite markers dropped indicating a great loss of genetic diversity, which increased again in subsequent years. Over years, metapopulation dynamics were characterized by high connectivity among fish populations associated with the Capricorn Bunker reefs (2200 km2); however, despite high exchange, genetic patchiness was observed with annual strong genetic divergence between populations among reefs. Some broad similarities in the genetic structure in 2015 could be explained by dispersal from a source reef and the related expansion of local populations. This study has shown that alternating cyclone-driven changes and subsequent recovery phases of coral habitat can greatly influence patterns of reef fish connectivity. The frequency of disturbances determines abundance of fish and genetic diversity within species.

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Genetic Diversity of Wild Oat (Avena fatua)Populations from China and the United States

Weed Science ◽

10.1614/ws-06-108.1 ◽

2007 ◽

Vol 55 (2) ◽

pp. 95-101 ◽

Cited By ~ 21

Author(s):

Runzhi Li ◽

Shiwen Wang ◽

Liusheng Duan ◽

Zhaohu Li ◽

Michael J. Christoffers ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Gene Diversity ◽

Genetic Relationships ◽

The United States ◽

Mantel Test ◽

Wild Oat ◽

Chinese Populations ◽

Nei's Distance ◽

The Impact

Weed genetic diversity is important for understanding the ability of weeds to adapt to different environments and the impact of herbicide selection on weed populations. Genetic diversity within and among six wild oat populations in China varying in herbicide selection pressure and one population in North Dakota were surveyed using 64 polymorphic alleles resulting from 25 microsatellite loci. Mean Nei's gene diversity (h) for six wild oat populations from China was between 0.17 and 0.21, and total diversity (HT) was 0.23. A greater proportion of this diversity, however, was within (Hs= 0.19) rather than among (Gst= 0.15) populations. For the wild oat population from the United States,h= 0.24 andHT= 0.24 were comparable to the values for the six populations from China. Cluster analysis divided the seven populations into two groups, where one group was the United States population and the other group included the six Chinese populations. The genetic relationships among six populations from China were weakly correlated with their geographic distribution (r= 0.22) using the Mantel test. Minimal difference in gene diversity and small genetic distance (Nei's distance 0.07 or less) among six populations from China are consistent with wide dispersal of wild oat in the 1980s. Our results indicate that the wild oat populations in China are genetically diverse at a level similar to North America, and the genetic diversity of wild oat in the broad spatial scale is not substantially changed by environment, agronomic practices, or herbicide usage.

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Scanning SNPs from a large set of expressed genes to assess the impact of artificial selection on the undomesticated genetic diversity of white spruce

Evolutionary Applications ◽

10.1111/j.1752-4571.2012.00242.x ◽

2012 ◽

Vol 5 (6) ◽

pp. 641-656 ◽

Cited By ~ 13

Author(s):

Marie-Claire Namroud ◽

Jean Bousquet ◽

Trevor Doerksen ◽

Jean Beaulieu

Keyword(s):

Genetic Diversity ◽

Artificial Selection ◽

White Spruce ◽

Large Set ◽

The Impact

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Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in Northwest China

10.7287/peerj.preprints.26837 ◽

2018 ◽

Author(s):

Yanfen Zhao ◽

Hongxiang Zhang ◽

Borong Pan ◽

Mingli Zhang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Population Genetic ◽

Divergence Time ◽

Northwest China ◽

Northwestern China ◽

Intraspecific Diversity ◽

Early Pleistocene ◽

Helan Mountains ◽

The Impact

Climactic fluctuations during the Quaternary played a crucial role in genetic diversity and population genetic structure of many plant species in northwestern China. In order to understand the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Two chloroplast DNA intergenic spacers (trnH-psbA and rpoB-trnC) were used to sequence 269 individuals from 27 populations and seven haplotypes were identified. Genetic structure and demographic characteristics were estimated using AMOVA, neutrality tests, and mismatch distribution analyses. The divergence times between the seven haplotypes were estimated using Beast. Our results revealed high levels of total genetic diversity (HT = 0.673±0.0869) and low levels of average within-population genetic diversity (HS = 0.033±0.0214). The analysis of molecular variance indicated major genetic differentiation among the three groups: northern, central, and eastern group. The species distribution modeling and demographic analysis indicated that P. lanata has not experience a recent range expansion. The divergence time within P. lanata occurred between the early Pleistocene and the late Pleistocene, which coincides with aridification and the expansion of the deserts in northwestern China that resulted in species diversification and habitat fragmentation. In addition, we speculate that the deserts and the Helan Mountains acted as effective geographic barriers that led to intraspecific diversity.

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Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad

10.22541/au.161374091.18087680/v1 ◽

2021 ◽

Author(s):

Binia De Cahsan ◽

Katrin Kiemel ◽

Michael Westbury ◽

Maike Lauritsen ◽

Marijke Autenrieth ◽

...

Keyword(s):

Genetic Diversity ◽

Local Adaptation ◽

Agricultural Land ◽

Introgressive Hybridization ◽

Mitochondrial Control Region ◽

The Body ◽

Immune Gene ◽

Range Margin ◽

Adaptive Immune ◽

The Impact

Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden, this decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after presumed illegal release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (as a proxy for fitness) of introgressed and non-introgressed populations, and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition. We observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency towards higher body weight, relative to regional non-introgressed populations. These differences were not observed among introgressed and non-introgressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than southern populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of struggling range margin populations without distortion of local adaptation.

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Human Genetic Diversity Alters Therapeutic Gene Editing Off-Target Outcomes

Blood ◽

10.1182/blood-2021-152429 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 3993-3993

Author(s):

Linda Yingqi Lin ◽

Samuele Cancellieri ◽

Jing Zeng ◽

Francesco Masillo ◽

My Anh Nguyen ◽

...

Keyword(s):

Genetic Diversity ◽

Clinical Trials ◽

Genome Editing ◽

Gene Editing ◽

Conflicts Of Interest ◽

African Ancestry ◽

Great Promise ◽

Personal Genome ◽

Hematopoietic Stem ◽

The Impact

Abstract CRISPR gene editing holds great promise to modify somatic genomes to ameliorate disease. In silico prediction of homologous sites coupled with biochemical evaluation of possible genomic off-targets may predict genotoxicity risk of individual gene editing reagents. However, standard computational and biochemical methods focus on reference genomes and do not consider the impact of genetic diversity on off-target potential. Here we developed a web application called CRISPRme that explicitly and efficiently integrates human genetic variant datasets with orthogonal genomic annotations to predict and prioritize off-target sites at scale. The method considers both single-nucleotide variants (SNVs) and indels, accounts for bona fide haplotypes, accepts spacer:protospacer mismatches and bulges, and is suitable for personal genome analyses. We tested the tool with a guide RNA (gRNA) targeting the BCL11A erythroid enhancer that has shown therapeutic promise in clinical trials for sickle cell disease (SCD) and β-thalassemia (Frangoul et al. NEJM 2021). We find that the top predicted off-target site is produced by a non-reference allele common in African-ancestry populations (rs114518452, minor allele frequency (MAF) = 4.5%) that introduces a protospacer adjacent motif (PAM) for SpCas9. We validate that SpCas9 generates indels (~9.6% frequency) and chr2 pericentric inversions in a strictly allele-specific manner in edited CD34+ hematopoietic stem/progenitor cells (HSPCs), although a high-fidelity Cas9 variant mitigates this off-target. This report illustrates how population and private genetic variants should be considered as modifiers of genome editing outcomes. We expect that variant-aware off-target assessment will be required for therapeutic genome editing efforts going forward, including both ongoing and future clinical trials, and we provide a powerful approach for comprehensive off-target prediction. CRISPRme is available at crisprme.di.univr.it. Disclosures No relevant conflicts of interest to declare.

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Alive and kicking, or, living on borrowed time? – Microsatellite diversity in natural populations of the endangered Ulmus minor Mill. sensu latissimo from Croatia

Acta Botanica Croatica ◽

10.1515/botcro-2016-0007 ◽

2016 ◽

Vol 75 (1) ◽

pp. 53-59 ◽

Cited By ~ 2

Author(s):

Marko Zebec ◽

Marilena Idžojtić ◽

Zlatko Šatović ◽

Igor Poljak ◽

Zlatko Liber

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Genetic Bottleneck ◽

Dutch Elm Disease ◽

Significant Excess ◽

Mediterranean Populations ◽

Ulmus Minor ◽

Study Results ◽

The Impact ◽

Microsatellite Diversity

AbstractThe main objective of this research was to assess the genetic diversity of 5 natural field elm populations in Croatia. The study results suggest that the observed populations are characterized by a satisfactory amount of heterozygosity, and that the impact of the Dutch elm disease on the amount of genetic diversity in the sampled populations is currently negligible. However, one population displayed a significant excess of heterozygosity, implying a genetic bottleneck. The existence of a very clear genetic differentiation between the continental and the Mediterranean populations of Ulmus minor in Croatia was noticed.

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Heterologous Expression of Rhizobial CelC2 Cellulase Impairs Symbiotic Signaling and Nodulation in Medicago truncatula

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-11-17-0265-r ◽

2018 ◽

Vol 31 (5) ◽

pp. 568-575 ◽

Cited By ~ 5

Author(s):

Marta Robledo ◽

Esther Menéndez ◽

Jose Ignacio Jiménez-Zurdo ◽

Raúl Rivas ◽

Encarna Velázquez ◽

...

Keyword(s):

Medicago Truncatula ◽

Cell Walls ◽

Rhizobium Leguminosarum ◽

Root Nodules ◽

Root Hairs ◽

Nod Factors ◽

Model Legume ◽

Ensifer Meliloti ◽

Early Nodulin ◽

The Impact

The infection of legume plants by rhizobia is tightly regulated to ensure accurate bacterial penetration, infection, and development of functionally efficient nitrogen-fixing root nodules. Rhizobial Nod factors (NF) have key roles in the elicitation of nodulation signaling. Infection of white clover roots also involves the tightly regulated specific breakdown of the noncrystalline apex of cell walls in growing root hairs, which is mediated by Rhizobium leguminosarum bv. trifolii cellulase CelC2. Here, we have analyzed the impact of this endoglucanase on symbiotic signaling in the model legume Medicago truncatula. Ensifer meliloti constitutively expressing celC gene exhibited delayed nodulation and elicited aberrant ineffective nodules, hampering plant growth in the absence of nitrogen. Cotreatment of roots with NF and CelC2 altered Ca2+ spiking in root hairs and induction of the early nodulin gene ENOD11. Our data suggest that CelC2 alters early signaling between partners in the rhizobia-legume interaction.

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No Evidence of Low Genetic Diversity Despite High Levels of Inbreeding and Poor Genetic Connectivity Among Tetrastigma loheri (Vitaceae) Populations in Remaining Forest Areas in Cebu, Philippines

Systematic Botany ◽

10.1600/036364421x16370109698614 ◽

2021 ◽

Vol 46 (4) ◽

pp. 951-961

Author(s):

Jasper John A. Obico ◽

Hemres Alburo ◽

Julie F. Barcelona ◽

Marie Hale ◽

Lisa Paguntalan ◽

...

Keyword(s):

Genetic Diversity ◽

Habitat Fragmentation ◽

Tropical Forests ◽

Forest Cover ◽

Genetic Connectivity ◽

Philippine Island ◽

Low Genetic Diversity ◽

History Of ◽

Gap Data ◽

The Impact

Abstract— Little is known about the effects of habitat fragmentation on the patterns of genetic diversity and genetic connectivity of species in the remaining tropical forests of Southeast Asia. This is particularly evident in Cebu, a Philippine island that has a long history of deforestation and has lost nearly all of its forest cover. To begin filling this gap, data from 13 microsatellite loci developed for Tetrastigma loheri (Vitaceae), a common vine species in Philippine forests, were used to study patterns of genetic diversity and genetic connectivity for the four largest of the remaining forest areas in Cebu. Evidence of relatively high levels of inbreeding was found in all four areas, despite no evidence of low genetic diversity. The four areas are genetically differentiated, suggesting low genetic connectivity. The presence of inbreeding and low genetic connectivity in a commonly encountered species such as T. loheri in Cebu suggests that the impact of habitat fragmentation is likely greater on rare plant species with more restricted distributions in Cebu. Conservation recommendations for the remaining forest areas in Cebu include the establishment of steppingstone corridors between nearby areas to improve the movement of pollinators and seed dispersers among them.

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