Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in <i>Salix viminalis</i>

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Abstract

Background

Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and Salix indicating flexible sex determination systems, ideal for studies of processes involved in sex chromosome evolution. We have performed genome-wide association studies of sex and analysed sex chromosomes in a population of 265 wild collected Salix viminalis accessions and studied the sex determining locus.

Results

A total of 19,592 markers were used in association analyses using both Fisher’s exact tests and a single-marker mixed linear model, which resulted in 48 and 41 sex-associated (SA) markers respectively. Across all 48 SA markers, females were much more often heterozygous than males, which is expected if females were the heterogametic sex. The majority of the SA markers were, based on positions in the S. purpurea genome, located on chromosome 15, previously demonstrated to be the sex chromosome. Interestingly, when mapping the genotyping-by-sequencing sequence tag harbouring the two SA markers with the highest significance to the S. viminalis genomic scaffolds, five regions of very high similarity were found: three on a scaffold that represents a part of chromosome 15, one on a scaffold that represents a part of chromosome 9 and one on a scaffold not anchored to the genome. Based on segregation differences of the alleles at the two marker positions and on differences in PCR amplification between females and males we conclude that females had multiple copies of this DNA fragment (chromosome 9 and 15), whereas males only had one (chromosome 9). We therefore postulate that the female specific sequences have been copied from chromosome 9 and inserted on chromosome 15, subsequently developing into a hemizygous W chromosome linked region.

Conclusions

Our results support that sex determination in S. viminalis is controlled by one locus on chromosome 15. The segregation patterns observed at the SA markers furthermore confirm that S. viminalis females are the heterogametic sex. We also identified a translocation from chromosome 9 to the W chromosome.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08021-2.

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Most cited references 53

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Inference of Population Structure Using Multilocus Genotype Data

Jonathan Pritchard, Matthew Stephens, Peter Donnelly … (2001)

We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.

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TASSEL: software for association mapping of complex traits in diverse samples.

P J Bradbury, Z. Zhang, D. E. Kroon … (2007)

Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend with the confounding effects of both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically. Database browsing and data importation is facilitated by integrated middleware. Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components.

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A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

Robert Elshire, Jeffrey C. Glaubitz, Qi-ying Sun … (2011)

Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM) and barley (Oregon Wolfe Barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

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Author and article information

Contributors

Ann Christin Rönnberg-Wästljung: anki.wastljung@slu.se

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 2 October 2021

Publication date PMC-release: 2 October 2021

Publication date Collection: 2021

Volume: 22

Electronic Location Identifier: 710

Affiliations

[1 ]GRID grid.6341.0, ISNI 0000 0000 8578 2742, Department of Plant Biology, Uppsala BioCenter, , Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, ; Box 7080, SE-750 07 Uppsala, Sweden

[2 ]GRID grid.425967.b, ISNI 0000 0001 0442 6365, Present Address: Skogforsk (The Forestry Research Institute of Sweden), ; Uppsala Science Park, SE-751 83 Uppsala, Sweden

Article

Publisher ID: 8021

DOI: 10.1186/s12864-021-08021-2

PMC ID: 8487499

PubMed ID: 34600471

SO-VID: 6353d596-9bdd-4f6e-bd6f-4d802eafea57

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 18 March 2021

Date accepted : 14 September 2021

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100004527, Energimyndigheten;

Award ID: 30599-2

Funded by: Swedish Research Council

Award ID: 2011-3544

Funded by: Swedish University of Agricultural Sciences

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: sex determination,salix viminalis,female heterogamety,association mapping,gwas,paralogous loci,copy number variation,sex specific markers

Data availability:

ScienceOpen disciplines: Genetics

Keywords: sex determination, salix viminalis, female heterogamety, association mapping, gwas, paralogous loci, copy number variation, sex specific markers

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Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis

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Abstract

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Supplementary Information

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Genome Integrity

Most cited references 53

Inference of Population Structure Using Multilocus Genotype Data

TASSEL: software for association mapping of complex traits in diverse samples.

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

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