Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species--Capsella rubella, Arabidopsis lyrata subsp. petraea, and A. thaliana

Abstract High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2,326 and 2,454 SNP markers that spanned a total genetic distance of 2,133 cM across 16 linkage groups and 2,169 cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1,123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.

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Smooth Descent: a Ploidy-Aware Algorithm To Improve Linkage Mapping In The Presence of Genotyping Errors

10.21203/rs.3.rs-1165750/v1 ◽

2022 ◽

Author(s):

Alejandro Thérèse Navarro ◽

Peter M. Bourke ◽

Eric van de Weg ◽

Paul Arens ◽

Richard Finkers ◽

...

Keyword(s):

Error Detection ◽

Linkage Mapping ◽

Diploid Species ◽

Simulated Data ◽

R Package ◽

Error Rates ◽

Genetic Maps ◽

Genotyping Errors ◽

Identity By Descent ◽

Mapping Algorithms

Abstract Linkage mapping is an approach to order markers based on recombination events. Mapping algorithms cannot easily handle genotyping errors, which are common in high-throughput genotyping data. To solve this issue, strategies have been developed, aimed mostly at identifying and eliminating these errors. One such strategy is SMOOTH (van Os et al. 2005), an iterative algorithm to detect genotyping errors. Unlike other approaches, SMOOTH can also be used to impute the most probable alternative genotypes, but its application is limited to diploid species and to markers heterozygous in only one of the parents. In this study we adapted SMOOTH to expand its use to any marker type and to autopolyploids with the use of identity-by-descent probabilities, naming the updated algorithm Smooth Descent (SD). We applied SD to real and simulated data, showing that in the presence of genotyping errors this method produces better genetic maps in terms of marker order and map length. SD is particularly useful for error rates between 5% and 20% and when error rates are not homogeneous among markers or individuals. Moreover, the simplicity of the algorithm allows thousands of markers to be efficiently processed, thus being particularly useful for error detection in high-density datasets. We have implemented this algorithm in the R package SmoothDescent.

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Endosperm-based hybridization barriers explain the pattern of gene flow between Arabidopsis lyrata and Arabidopsis arenosa in Central Europe

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1615123114 ◽

2017 ◽

Vol 114 (6) ◽

pp. E1027-E1035 ◽

Cited By ~ 43

Author(s):

Clément Lafon-Placette ◽

Ida M. Johannessen ◽

Karina S. Hornslien ◽

Mohammad F. Ali ◽

Katrine N. Bjerkan ◽

...

Keyword(s):

Gene Flow ◽

Central Europe ◽

Diploid Species ◽

Biological Species ◽

Biological Species Concept ◽

Interspecific Gene Flow ◽

Seed Formation ◽

Arabidopsis Lyrata ◽

Hybrid Seeds ◽

Arabidopsis Arenosa

Based on the biological species concept, two species are considered distinct if reproductive barriers prevent gene flow between them. In Central Europe, the diploid species Arabidopsis lyrata and Arabidopsis arenosa are genetically isolated, thus fitting this concept as “good species.” Nonetheless, interspecific gene flow involving their tetraploid forms has been described. The reasons for this ploidy-dependent reproductive isolation remain unknown. Here, we show that hybridization between diploid A. lyrata and A. arenosa causes mainly inviable seed formation, revealing a strong postzygotic reproductive barrier separating these two species. Although viability of hybrid seeds was impaired in both directions of hybridization, the cause for seed arrest differed. Hybridization of A. lyrata seed parents with A. arenosa pollen donors resulted in failure of endosperm cellularization, whereas the endosperm of reciprocal hybrids cellularized precociously. Endosperm cellularization failure in both hybridization directions is likely causal for the embryo arrest. Importantly, natural tetraploid A. lyrata was able to form viable hybrid seeds with diploid and tetraploid A. arenosa, associated with the reestablishment of normal endosperm cellularization. Conversely, the defects of hybrid seeds between tetraploid A. arenosa and diploid A. lyrata were aggravated. According to these results, we hypothesize that a tetraploidization event in A. lyrata allowed the production of viable hybrid seeds with A. arenosa, enabling gene flow between the two species.

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Differential transferability of EST-SSR primers developed from the diploid species Pseudoroegneria spicata, Thinopyrum bessarabicum, and Thinopyrum elongatum

Genome ◽

10.1139/gen-2016-0157 ◽

2017 ◽

Vol 60 (6) ◽

pp. 530-536 ◽

Cited By ~ 7

Author(s):

Richard R.-C. Wang ◽

Steve R. Larson ◽

Kevin B. Jensen

Keyword(s):

Expressed Sequence Tag ◽

Genome Mapping ◽

Diploid Species ◽

Genetic Maps ◽

Pseudoroegneria Spicata ◽

Ssr Primers ◽

Polymorphic Species ◽

Thinopyrum Bessarabicum ◽

Species Specific ◽

Thinopyrum Elongatum

Simple sequence repeat technology based on expressed sequence tag (EST-SSR) is a useful genomic tool for genome mapping, characterizing plant species relationships, elucidating genome evolution, and tracing genes on alien chromosome segments. EST-SSR primers developed from three perennial diploid species of Triticeae, Pseudoroegneria spicata (Pursh) Á. Löve (having St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (Jb = Eb = J), and Thinopyrum elongatum (Host) D.R. Dewey (Je = Ee = E), were used to produce amplicons in these three species to (i) assess relative transferability, (ii) identify polymorphic species-specific markers, and (iii) determine genome relationships among the three species. Because of the close relationship between Jb and Je genomes, EST-SSR primers derived from Th. bessarabicum and Th. elongatum had greater transferability to each other than those derived from the St-genome P. spicata. A large number of polymorphic species- and genome-specific EST-SSR amplicons were identified that will be used for construction of genetic maps of these diploid species, and tracing economically useful genes in breeding or gene transfer programs in various species of Triticeae.

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Accounting for Errors in Low Coverage High-Throughput Sequencing Data when Constructing Genetic Maps using Biparental Outcrossed Populations

10.1101/249722 ◽

2018 ◽

Author(s):

Timothy P. Bilton ◽

Matthew R. Schofield ◽

Michael A. Black ◽

David Chagné ◽

Phillip L. Wilcox ◽

...

Keyword(s):

High Throughput ◽

Genetic Linkage ◽

High Throughput Sequencing ◽

Diploid Species ◽

Genotyping By Sequencing ◽

Genetic Maps ◽

Linkage Maps ◽

Sequencing Data ◽

Genetic Linkage Maps ◽

Low Coverage

ABSTRACTNext generation sequencing is an efficient method that allows for substantially more markers than previous technologies, providing opportunities for building high density genetic linkage maps, which facilitate the development of non-model species’ genomic assemblies and the investigation of their genes. However, constructing genetic maps using data generated via high-throughput sequencing technology (e.g., genotyping-by-sequencing) is complicated by the presence of sequencing errors and genotyping errors resulting from missing parental alleles due to low sequencing depth. If unaccounted for, these errors lead to inflated genetic maps. In addition, map construction in many species is performed using full-sib family populations derived from the outcrossing of two individuals, where unknown parental phase and varying segregation types further complicate construction. We present a new methodology for modeling low coverage sequencing data in the construction of genetic linkage maps using full-sib populations of diploid species, implemented in a package called GUSMap. Our model is based on an extension of the Lander-Green hidden Markov model that accounts for errors present in sequencing data. Results show that GUSMap was able to give accurate estimates of the recombination fractions and overall map distance, while most existing mapping packages produced inflated genetic maps in the presence of errors. Our results demonstrate the feasibility of using low coverage sequencing data to produce genetic maps without requiring extensive filtering of potentially erroneous genotypes, provided that the associated errors are correctly accounted for in the model.

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Construction of a High-Density Genetic Map of Acca sellowiana (Berg.) Burret, an Outcrossing Species, Based on Two Connected Mapping Populations

Frontiers in Plant Science ◽

10.3389/fpls.2021.626811 ◽

2021 ◽

Vol 12 ◽

Author(s):

Marianella Quezada ◽

Rodrigo Rampazo Amadeu ◽

Beatriz Vignale ◽

Danilo Cabrera ◽

Clara Pritsch ◽

...

Keyword(s):

De Novo ◽

Genetic Research ◽

Diploid Species ◽

Eucalyptus Grandis ◽

Snp Markers ◽

High Density ◽

Genetic Maps ◽

Acca Sellowiana ◽

Marker Distance ◽

Connected Populations

Acca sellowiana, known as feijoa or pineapple guava, is a diploid, (2n = 2x = 22) outcrossing fruit tree species native to Uruguay and Brazil. The species stands out for its highly aromatic fruits, with nutraceutical and therapeutic value. Despite its promising agronomical value, genetic studies on this species are limited. Linkage genetic maps are valuable tools for genetic and genomic studies, and constitute essential tools in breeding programs to support the development of molecular breeding strategies. A high-density composite genetic linkage map of A. sellowiana was constructed using two genetically connected populations: H5 (TCO × BR, N = 160) and H6 (TCO × DP, N = 184). Genotyping by sequencing (GBS) approach was successfully applied for developing single nucleotide polymorphism (SNP) markers. A total of 4,921 SNP markers were identified using the reference genome of the closely related species Eucalyptus grandis, whereas other 4,656 SNPs were discovered using a de novo pipeline. The individual H5 and H6 maps comprised 1,236 and 1,302 markers distributed over the expected 11 linkage groups, respectively. These two maps spanned a map length of 1,593 and 1,572 cM, with an average inter-marker distance of 1.29 and 1.21 cM, respectively. A large proportion of markers were common to both maps and showed a high degree of collinearity. The composite map consisted of 1,897 SNPs markers with a total map length of 1,314 cM and an average inter-marker distance of 0.69. A novel approach for the construction of composite maps where the meiosis information of individuals of two connected populations is captured in a single estimator is described. A high-density, accurate composite map based on a consensus ordering of markers provides a valuable contribution for future genetic research and breeding efforts in A. sellowiana. A novel mapping approach based on an estimation of multipopulation recombination fraction described here may be applied in the construction of dense composite genetic maps for any other outcrossing diploid species.

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The story of promiscuous crucifers: origin and genome evolution of an invasive species, Cardamine occulta (Brassicaceae), and its relatives

Annals of Botany ◽

10.1093/aob/mcz019 ◽

2019 ◽

Vol 124 (2) ◽

pp. 209-220 ◽

Cited By ~ 6

Author(s):

Terezie Mandáková ◽

Judita Zozomová-Lihová ◽

Hiroshi Kudoh ◽

Yunpeng Zhao ◽

Martin A Lysak ◽

...

Keyword(s):

Invasive Species ◽

Genome Evolution ◽

Large Scale ◽

Genome Structure ◽

Diploid Species ◽

Wide Distribution ◽

Ecological Niches ◽

Polyploid Evolution ◽

Weedy Species ◽

Species Specific

Abstract Background and Aims Cardamine occulta (Brassicaceae) is an octoploid weedy species (2n = 8x = 64) originated in Eastern Asia. It has been introduced to other continents including Europe and considered to be an invasive species. Despite its wide distribution, the polyploid origin of C. occulta remained unexplored. The feasibility of comparative chromosome painting (CCP) in crucifers allowed us to elucidate the origin and genome evolution in Cardamine species. We aimed to investigate the genome structure of C. occulta in comparison with its tetraploid (2n = 4x = 32, C. kokaiensis and C. scutata) and octoploid (2n = 8x = 64, C. dentipetala) relatives. Methods Genomic in situ hybridization (GISH) and large-scale CCP were applied to uncover the parental genomes and chromosome composition of the investigated Cardamine species. Key Results All investigated species descended from a common ancestral Cardamine genome (n = 8), structurally resembling the Ancestral Crucifer Karyotype (n = 8), but differentiated by a translocation between chromosomes AK6 and AK8. Allotetraploid C. scutata originated by hybridization between two diploid species, C. parviflora and C. amara (2n = 2x = 16). By contrast, C. kokaiensis has an autotetraploid origin from a parental genome related to C. parviflora. Interestingly, octoploid C. occulta probably originated through hybridization between the tetraploids C. scutata and C. kokaiensis. The octoploid genome of C. dentipetala probably originated from C. scutata via autopolyploidization. Except for five species-specific centromere repositionings and one pericentric inversion post-dating the polyploidization events, the parental subgenomes remained stable in the tetra- and octoploids. Conclusions Comparative genome structure, origin and evolutionary history was reconstructed in C. occulta and related species. For the first time, whole-genome cytogenomic maps were established for octoploid plants. Post-polyploid evolution in Asian Cardamine polyploids has not been associated with descending dysploidy and intergenomic rearrangements. The combination of different parental (sub)genomes adapted to distinct habitats provides an evolutionary advantage to newly formed polyploids by occupying new ecological niches.

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Sequence-tagged high-density genetic maps ofZoysia japonicaprovide insights into genome evolution in Chloridoideae

The Plant Journal ◽

10.1111/tpj.12842 ◽

2015 ◽

Vol 82 (5) ◽

pp. 744-757 ◽

Cited By ~ 14

Author(s):

Fangfang Wang ◽

Ratnesh Singh ◽

Anthony D. Genovesi ◽

Ching Man Wai ◽

Xiaoen Huang ◽

...

Keyword(s):

Genome Evolution ◽

High Density ◽

Genetic Maps

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Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species

BMC Biology ◽

10.1186/s12915-019-0712-y ◽

2019 ◽

Vol 17 (1) ◽

Cited By ~ 7

Author(s):

Peter J. Maughan ◽

Rebekah Lee ◽

Rachel Walstead ◽

Robert J. Vickerstaff ◽

Melissa C. Fogarty ◽

...

Keyword(s):

Diploid Species ◽

Genetic Maps ◽

Human Consumption ◽

Past Century ◽

Genome Wide ◽

Species Analysis ◽

Homoeologous Relationships ◽

Species Specific ◽

Nutritional Benefits ◽

Genome Assemblies

Abstract Background Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat’s adaptive and food quality characteristics. Results The A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species—including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species. Conclusions The genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.

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Chromosome structural changes in diploid and tetraploid A genomes of Gossypium

Genome ◽

10.1139/g05-116 ◽

2006 ◽

Vol 49 (4) ◽

pp. 336-345 ◽

Cited By ~ 44

Author(s):

Aparna Desai ◽

Peng W Chee ◽

Junkang Rong ◽

O Lloyd May ◽

Andrew H Paterson

Keyword(s):

Genome Evolution ◽

Linkage Mapping ◽

Structural Variation ◽

Structural Changes ◽

Diploid Species ◽

Gossypium Arboreum ◽

Linkage Groups ◽

Recombination Rates ◽

A Genome ◽

Polyploid Genome

The genus Gossypium, which comprises a divergent group of diploid species and several recently formed allotetraploids, offers an excellent opportunity to study polyploid genome evolution. In this study, chromosome structural variation among the A, At, and D genomes of Gossypium was evaluated by comparative genetic linkage mapping. We constructed a fully resolved RFLP linkage map for the diploid A genome consisting of 275 loci using an F2 interspecific Gossypium arboreum × Gossypium herbaceum family. The 13 chromosomes of the A genome are represented by 12 large linkage groups in our map, reflecting an expected interchromosomal translocation between G. arboreum and G. herbaceum. The A-genome chromosomes are largely collinear with the D genomes, save for a few small inversions. Although the 2 diploid mapping parents represent the closest living relatives of the allotetraploid At-genome progenitor, 2 translocations and 7 inversions were observed between the A and At genomes. The recombination rates are similar between the 2 diploid genomes; however, the At genome shows a 93% increase in recombination relative to its diploid progenitors. Elevated recombination in the Dt genome was reported previously. These data on the At genome thus indicate that elevated recombination was a general property of allotetraploidy in cotton.Key words: comparative mapping, polyploidy, genome evolution, inversions, translocations, RFLP.

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