Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces

Maize landraces are well adapted to their local environments and present valuable sources of genetic diversity for breeding and conservation. But the maintenance of open-pollinated landraces in ex-situ programs is challenging, as regeneration of seed can often lead to inbreeding depression and the loss of diversity due to genetic drift. Recent reports suggest that the production of doubled-haploid (DH) lines from landraces may serve as a convenient means to preserve genetic diversity in a homozygous form that is immediately useful for modern breeding. The production of doubled-haploid (DH) lines presents an extreme case of inbreeding which results in instantaneous homozygosity genome-wide. Here, we analyzed the effect of DH production on genetic diversity, using genome-wide SNP data from hundreds of individuals of five European landraces and their related DH lines. In contrast to previous findings, we observe a dramatic loss of diversity at both the haplotype level and that of individual SNPs. We identify thousands of SNPs that exhibit allele frequency differences larger than expected under models of neutral genetic drift and document losses of shared haplotypes. We find evidence consistent with selection at functional sites that are potentially involved in the diversity differences between landrace and DH populations. Although we were unable to uncover more details about the mode of selection, we conclude that landrace DH lines may be a valuable tool for the introduction of variation into maize breeding programs but come at the cost of decreased genetic diversity.

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Selective loss of diversity in doubled-haploid lines from European maize landraces

10.1101/817791 ◽

2019 ◽

Cited By ~ 1

Author(s):

Leo Zeitler ◽

Jeffrey Ross-Ibarra ◽

Markus G Stetter

Keyword(s):

Genetic Diversity ◽

Genetic Drift ◽

Doubled Haploid ◽

Ex Situ ◽

Functional Sites ◽

Genome Wide ◽

Individual Snps ◽

Maize Landraces ◽

Loss Of Diversity ◽

Dh Lines

ABSTRACTMaize landraces are well adapted to their local environments and present valuable sources of genetic diversity for breeding and conservation. But the maintenance of open-pollinated landraces in ex-situ programs is challenging, as regeneration of seed can often lead to inbreeding depression and the loss of diversity due to genetic drift. Recent reports suggest that the production of doubled-haploid (DH) lines from landraces may serve as a convenient means to preserve genetic diversity in a homozygous form that is immediately useful for modern breeding. The production of doubled-haploid (DH) lines presents an extreme case of inbreeding which results in instantaneous homozygosity genome-wide. Here, we analyzed the effect of DH production on genetic diversity, using genome-wide SNP data from hundreds of individuals of five European landraces and their related DH lines. In contrast to previous findings, we observe a dramatic loss of diversity at both the haplotype level and that of individual SNPs. We identify thousands of SNPs that exhibit allele frequency differences larger than expected under models of neutral genetic drift and document losses of shared haplotypes. We find evidence consistent with selection at functional sites that are potentially involved in the diversity differences between landrace and DH populations. Although we were unable to uncover more details about the mode of selection, we conclude that landrace DH lines may be a valuable tool for the introduction of variation into maize breeding programs but come at the cost of decreased genetic diversity and increased genetic load.

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Conservation genetics of the threatened plant species Physaria filiformis (Missouri bladderpod) reveals strong genetic structure and a possible cryptic species

PLoS ONE ◽

10.1371/journal.pone.0247586 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0247586

Author(s):

Christine E. Edwards ◽

Brooke C. Tessier ◽

Joel F. Swift ◽

Burgund Bassüner ◽

Alexander G. Linan ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Plant Species ◽

Genetic Drift ◽

Rare Species ◽

Ex Situ ◽

Ouachita Mountains ◽

Genetic Diversity And Structure ◽

Genetic Clusters

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species.

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Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

10.1101/094540 ◽

2016 ◽

Cited By ~ 2

Author(s):

Stephen R. Doyle ◽

Catherine Bourguinat ◽

Hugues C. Nana-Djeunga ◽

Jonas A. Kengne-Ouafo ◽

Sébastien D.S. Pion ◽

...

Keyword(s):

Genetic Diversity ◽

Next Generation Sequencing ◽

Genetic Drift ◽

Onchocerca Volvulus ◽

Molecular Pathways ◽

Ivermectin Treatment ◽

Genetic Changes ◽

Genome Wide ◽

Parasite Populations ◽

Generation Sequencing

ABSTRACTBackgroundTreatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana - exposed to more than a decade of regular ivermectin treatment - have raised concern that sub-optimal responses to ivermectin’s anti-fecundity effect are becoming more frequent and may spread.Methodology/Principal FindingsPooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR.Conclusions/SignificanceThis study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait in which identical or related molecular pathways but not necessarily individual genes likely determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic drift rather than genetic selection of SOR is the underlying driver of population differentiation, which has significant implications for the emergence and potential spread of SOR within and between these parasite populations.Author summaryOnchocerciasis is a human parasitic disease endemic across large areas of Sub-Saharan Africa, where more that 99% of the estimated 100 million people globally at-risk live. The microfilarial stage of Onchocerca volvulus causes pathologies ranging from mild itching to visual impairment and ultimately, irreversible blindness. Mass administration of ivermectin kills microfilariae and has an anti-fecundity effect on adult worms by temporarily inhibiting the development in utero and/or release into the skin of new microfilariae, thereby reducing morbidity and transmission. Phenotypic and genetic changes in some parasite populations that have undergone multiple ivermectin treatments in Cameroon and Ghana have raised concern that sub-optimal response to ivermectin’s anti-fecundity effect may increase in frequency, reducing the impact of ivermectin-based control measures. We used next generation sequencing of small pools of parasites to define genome-wide genetic differences between phenotypically characterised good and sub-optimal responder parasites from Cameroon and Ghana, and identified multiple genomic regions differentiating the response types. These regions were largely different between parasites from both countries but revealed common molecular pathways that might be involved in determining the extent of response to ivermectin’s anti-fecundity effect. These data reveal a more complex than previously described pattern of genetic diversity among O. volvulus populations that differ in their geography and response to ivermectin treatment.

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Associative Overdominance and Negative Epistasis Shape Genome-Wide Ancestry Landscape in Supplemented Fish Populations

Genes ◽

10.3390/genes12040524 ◽

2021 ◽

Vol 12 (4) ◽

pp. 524

Author(s):

Maeva Leitwein ◽

Hugo Cayuela ◽

Louis Bernatchez

Keyword(s):

Genetic Diversity ◽

Genetic Drift ◽

Recombination Rate ◽

Management Strategies ◽

Population Level ◽

Negative Effects ◽

Isolated Populations ◽

Positive Effects ◽

Genome Wide ◽

Negative Epistasis

The interplay between recombination rate, genetic drift and selection modulates variation in genome-wide ancestry. Understanding the selective processes at play is of prime importance toward predicting potential beneficial or negative effects of supplementation with domestic strains (i.e., human-introduced strains). In a system of lacustrine populations supplemented with a single domestic strain, we documented how population genetic diversity and stocking intensity produced lake-specific patterns of domestic ancestry by taking the species’ local recombination rate into consideration. We used 552 Brook Charr (Salvelinus fontinalis) from 22 small lacustrine populations, genotyped at ~32,400 mapped SNPs. We observed highly variable patterns of domestic ancestry between each of the 22 populations without any consistency in introgression patterns of the domestic ancestry. Our results suggest that such lake-specific ancestry patterns were mainly due to variable associative overdominance (AOD) effects among populations (i.e., potential positive effects due to the masking of possible deleterious alleles in low recombining regions). Signatures of AOD effects were also emphasized by highly variable patterns of genetic diversity among and within lakes, potentially driven by predominant genetic drift in those small isolated populations. Local negative effects such as negative epistasis (i.e., potential genetic incompatibilities between the native and the introduced population) potentially reflecting precursory signs of outbreeding depression were also observed at a chromosomal scale. Consequently, in order to improve conservation practices and management strategies, it became necessary to assess the consequences of supplementation at the population level by taking into account both genetic diversity and stocking intensity when available.

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Genetic diversity and selection signatures in maize landraces compared across 50 years of in situ and ex situ conservation

Heredity ◽

10.1038/s41437-021-00423-y ◽

2021 ◽

Author(s):

Francis Denisse McLean-Rodríguez ◽

Denise Elston Costich ◽

Tania Carolina Camacho-Villa ◽

Mario Enrico Pè ◽

Matteo Dell’Acqua

Keyword(s):

Genetic Diversity ◽

Selection Criteria ◽

Sampling Site ◽

In Situ Conservation ◽

Genetic Distances ◽

Ex Situ ◽

Conservation Strategies ◽

Genome Wide ◽

Agrobiodiversity Conservation

AbstractGenomics-based, longitudinal comparisons between ex situ and in situ agrobiodiversity conservation strategies can contribute to a better understanding of their underlying effects. However, landrace designations, ambiguous common names, and gaps in sampling information complicate the identification of matching ex situ and in situ seed lots. Here we report a 50-year longitudinal comparison of the genetic diversity of a set of 13 accessions from the state of Morelos, Mexico, conserved ex situ since 1967 and retrieved in situ from the same donor families in 2017. We interviewed farmer families who donated in situ landraces to understand their germplasm selection criteria. Samples were genotyped by sequencing, producing 74,739 SNPs. Comparing the two sample groups, we show that ex situ and in situ genome-wide diversity was similar. In situ samples had 3.1% fewer SNPs and lower pairwise genetic distances (Fst 0.008–0.113) than ex situ samples (Fst 0.031–0.128), but displayed the same heterozygosity. Despite genome-wide similarities across samples, we could identify several loci under selection when comparing in situ and ex situ seed lots, suggesting ongoing evolution in farmer fields. Eight loci in chromosomes 3, 5, 6, and 10 showed evidence of selection in situ that could be related with farmers’ selection criteria surveyed with focus groups and interviews at the sampling site in 2017, including wider kernels and larger ear size. Our results have implications for ex situ collection resampling strategies and the in situ conservation of threatened landraces.

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Study of Androgenic Plant Families of Alloplasmic Introgression Lines (H. vulgare) –T. aestivum and the Use of Sister DH Lines in Breeding

Plants ◽

10.3390/plants9060764 ◽

2020 ◽

Vol 9 (6) ◽

pp. 764

Author(s):

Lidiya Pershina ◽

Nataliya Trubacheeva ◽

Ekaterina Badaeva ◽

Igor Belan ◽

Ludmila Rosseeva

Keyword(s):

Genetic Diversity ◽

Disease Resistance ◽

Anther Culture ◽

Doubled Haploid ◽

Grain Quality ◽

High Fertility ◽

Fertility Level ◽

Fungal Disease Resistance ◽

Plant Families ◽

Dh Lines

One of the limitations in obtaining the genetic diversity of doubled haploid (DH) lines via anther culture is the development of families of regenerants, and each family represents a clone. This work examines the results of studying this phenomenon in anther culture of alloplasmic (H. vulgare)–T. aestivum and euplasmic lines with 1RS.1BL and 7DL-7Ai translocations and hybrids between them. Parameters of androgenesis such as the number of embryo-like structures, the total number of regenerants, and the number of green regenerants per 100 anthers varied depending on the genotype. In all genotypes from embryo-like structures, predominant development of families of plantlets rather than single plantlets was found. The source of family plantlets was polyembryos. About 75% of families consisted of regenerants at the same fertility level. On average, 37.74%4% of the R0 plants were fertile. The sister DH lines of three hybrid combinations were formed from seeds of R1 plants (2n = 42) with high fertility and in the presence of wheat–alien translocations. After four years of breeding trials, the sister DH lines of three families with fungal disease resistance increased yield, and some parameters of grain quality exceeding the controls were identified as promising for breeding.

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Genome-wide SNP genotyping of DNA pools identifies untapped landraces and genomic regions that could enrich the maize breeding pool

10.1101/2020.09.30.321018 ◽

2020 ◽

Cited By ~ 2

Author(s):

Mariangela Arca ◽

Brigitte Gouesnard ◽

Tristan Mary-Huard ◽

Marie-Christine Le Paslier ◽

Cyril Bauland ◽

...

Keyword(s):

Genetic Diversity ◽

Geographic Origin ◽

Haplotype Diversity ◽

Inbred Lines ◽

Genomic Diversity ◽

Breeding Programs ◽

Genome Wide ◽

Dna Pools ◽

Maize Landraces ◽

Modern Breeding

ABSTRACTMaize landraces preserved in genebanks have a large genetic diversity that is still poorly characterized and underexploited in modern breeding programs. Here, we genotyped DNA pools from 156 American and European landraces with a 50K SNP Illumina array to study the effect of both human selection and environmental adaptation on the genome-wide diversity of maize landraces. Genomic diversity of landraces varied strongly in different parts of the genome and with geographic origin. We detected selective footprints between landraces of different geographic origin in genes involved in the starch pathway (Su1, Waxy1), flowering time (Zcn8, Vgt3, ZmCCT9) and tolerance to abiotic and biotic stress (ZmASR, NAC and dkg genes). Landrace diversity was compared to that of (i) 327 inbred lines representing American and European diversity (“CK lines) and (ii) 103 new lines derived directly from landraces (“DH-SSD lines”). We observed limited diversity loss or selective sweep between landraces and CK lines, except in peri-centromeric regions. However, analysis of modified Roger’s distance between landraces and the CK lines showed that most landraces were not closely related to CK lines. Assignment of CK lines to landraces using supervised analysis showed that only a few landraces, such as Reid’s Yellow Dent, Lancaster Surecrop and Lacaune, strongly contributed to modern European and American breeding pools. Haplotype diversity of CK lines was more enriched by DH-SSD lines that derived from the landraces with no related lines and the lowest contribution to CK lines. Our approach opens an avenue for the identification of promising landraces for pre-breeding.SIGNIFICANCE STATEMENTSMaize landraces are a valuable source of genetic diversity for addressing the challenges of climate change and the requirements of low input agriculture as they have been long selected to be well adapted to local agro-climatic conditions and human uses. However, they are underutilized in modern breeding programs because they are poorly characterized, genetically heterogeneous and exhibit poor agronomic performance compared to elite hybrid material. In this study, we developed a high-throughput approach to identify landraces that could potentially enlarge the genetic diversity of modern breeding pools. We genotyped DNA pools from landraces using 50K array technology, which is widely used by breeders to characterize the genetic diversity of inbred lines. To identify landraces that could enrich the modern maize germplasm, we estimated their contribution to inbred lines using supervised analysis and a new measurement of genetic distance.

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Genetic diversity of maize landraces from the South-West of France

10.1101/2020.08.17.253690 ◽

2020 ◽

Cited By ~ 2

Author(s):

Yacine Diaw ◽

Christine Tollon-Cordet ◽

Alain Charcosset ◽

Stéphane Nicolas ◽

Delphine Madur ◽

...

Keyword(s):

Genetic Diversity ◽

Snp Array ◽

Ex Situ ◽

The South ◽

Genetic Groups ◽

South West ◽

Tropical Germplasm ◽

Maize Genetic ◽

Maize Landraces ◽

Genetic Drifts

AbstractFrom the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France, a traditional region for maize cultivation. A set of landraces were collected in this region between the 1950s and 1980s and were then conserved ex situ in a germplam collection. Previous studies using molecular markers on approx. twenty landraces fo this region showed that they belonged to a Pyrenees-Galicia Flint genetic group and originated from hybridization between Caribbean and Northern Flint germplasms introduced in Europe. In this study, we assessed the structure and genetic diversity of 194 SWF maize landraces to elucidate their origin, using a 50K SNP array and a bulk DNA approach. We identified two weakly differentiated genetic groups, one in the Western part and the other in the Eastern part. We highlighted the existence of a longitudinal gradient along the SWF area that was probably maintained through the interplay between genetic drifts and restricted gene flows, rather than through differential climatic adaptation. The contact zone between the two groups observed near the Garonne valley may be the result of these evolutionnary forces. We found only few significant cases of hybridization between Caribbean and Northern Flint germplasms in the region. We also found gene flows from various maize genetic groups to SWF landraces. Thus, we assumed that SWF landraces had a multiple origin with a slightly higher influence of Tropical germplasm in the West and preponderance of Northern Flint germplasm in the East.

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European maize landraces made accessible for plant breeding and genome-based studies

Theoretical and Applied Genetics ◽

10.1007/s00122-019-03428-8 ◽

2019 ◽

Vol 132 (12) ◽

pp. 3333-3345 ◽

Cited By ~ 14

Author(s):

Armin C. Hölker ◽

Manfred Mayer ◽

Thomas Presterl ◽

Therese Bolduan ◽

Eva Bauer ◽

...

Keyword(s):

Genetic Variation ◽

Early Development ◽

Doubled Haploid ◽

Agronomic Traits ◽

Allelic Diversity ◽

Growth Stages ◽

Total Biomass ◽

Phenotypic Data ◽

Maize Landraces ◽

Dh Lines

Key message Doubled-haploid libraries from landraces capture native genetic diversity for a multitude of quantitative traits and make it accessible for breeding and genome-based studies. Abstract Maize landraces comprise large allelic diversity. We created doubled-haploid (DH) libraries from three European flint maize landraces and characterized them with respect to their molecular diversity, population structure, trait means, variances, and trait correlations. In total, 899 DH lines were evaluated using high-quality genotypic and multi-environment phenotypic data from up to 11 environments. The DH lines covered 95% of the molecular variation present in 35 landraces of an earlier study and represent the original three landrace populations in an unbiased manner. A comprehensive analysis of the target trait plant development at early growth stages as well as other important agronomic traits revealed large genetic variation for line per se and testcross performance. The majority of the 378 DH lines evaluated as testcrosses outperformed the commercial hybrids for early development. For total biomass yield, we observed a yield gap of 15% between mean testcross yield of the commercial hybrids and mean testcross yield of the DH lines. The DH lines also exhibited genetic variation for undesirable traits like root lodging and tillering, but correlations with target traits early development and yield were low or nonsignificant. The presented diversity atlas is a valuable, publicly available resource for genome-based studies to identify novel trait variation and evaluate the prospects of genomic prediction in landrace-derived material.

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Genetic diversity of maize landraces from the South-West of France

PLoS ONE ◽

10.1371/journal.pone.0238334 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0238334

Author(s):

Yacine Diaw ◽

Christine Tollon-Cordet ◽

Alain Charcosset ◽

Stéphane D. Nicolas ◽

Delphine Madur ◽

...

Keyword(s):

Genetic Diversity ◽

Snp Array ◽

Ex Situ ◽

The South ◽

East Part ◽

Genetic Groups ◽

South West ◽

Maize Cultivation ◽

Maize Landraces ◽

Genetic Drifts

From the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France (SWF), a traditional region for maize cultivation. A set of landraces were collected in this area between the 1950s and 1980s and were then conserved ex situ in a germplam collection. Previous studies using molecular markers on approx. twenty landraces from this region suggested that they belonged to a Pyrenees-Galicia Flint genetic group and originated from hybridizations between Caribbean and Northern Flint germplasms introduced to Europe. In this study, we assessed the structure and genetic diversity of 194 SWF maize landraces to better elucidate their origin, using a 50K SNP array and a bulk DNA approach. We identified two weakly differentiated genetic groups, one in the Western part and the other in the Eastern part of the studied region. We highlighted the existence of a longitudinal gradient along the SWF area that was probably maintained through the interplay between genetic drifts and restricted gene flows. The contact zone between the two groups observed near the Garonne valley may be the result of these evolutionnary forces. We found in landraces from the East part of the region significant cases of admixture between landraces from the Northern Flint group and landraces from either the Caribbean, Andean or Italian groups. We then assumed that SWF landraces had a multiple origin with a predonderance of Northern Flint germplasm for the two SWF groups, notably for the East part.

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