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Extent and overlap of segregation distortion regions in 12 barley crosses determined via a Pool-GBS approach

Theoretical and Applied Genetics volume 129, pages 1393–1404 (2016)Cite this article

Abstract

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Extent and overlap of segregation distortion regions in 12 barley crosses determined via a Pool-GBS approach.

Abstract

Segregation distortion is undesirable as it alters the frequency of alleles and can reduce the chances of obtaining a particular combination of alleles. In this work, we have used a pooled genotyping-by-sequencing (Pool-GBS) approach to estimate allelic frequencies and used it to examine segregation distortion in 12 segregating populations of barley derived from androgenesis. Thanks to the extensive genome-wide SNP coverage achieved (between 674 and 1744 markers), we determined that the proportion of distorted markers averaged 28.9 % while 25.3 % of the genetic map fell within segregation distortion regions (SDRs). These SDRs were characterized and identified based on the position of the marker showing the largest distortion and the span of each SDR. Summed across all 12 crosses, 36 different SDR peaks could be distinguished from a total of 50 SDRs and a majority of these SDRs (27 of 36) were observed in only one population. While most shared SDRs were common to only two crosses, two SDRs (SDR3.1 and SDR4.2) were exceptionally recurrent (seen in five and four crosses, respectively). Because of the broad span of most SDRs, an average of 30 % of crosses showed segregation distortion in any given chromosomal segment. In reciprocal crosses, although some SDRs were clearly shared, others were unique to a single direction. In summary, segregation distortion is highly variable in its extent and the number of loci underpinning these distortions seems to be quite large even in a narrow germplasm such as six-row spring barley.

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Acknowledgments

S. Bélanger gratefully acknowledges graduate studentships from the Fonds de recherche nature et technologies of Quebec (FRQNT). This work was also supported by a research grant from the Natural Sciences and Engineering Research Council (NSERC) of Canada to F. Belzile.

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  1. Département de phytologie and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, QC, Canada

    Sébastien Bélanger, Isabelle Clermont, Patricio Esteves & François Belzile

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  1. Sébastien Bélanger
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  2. Isabelle Clermont
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  3. Patricio Esteves
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  4. François Belzile
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Correspondence to François Belzile.

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The authors declare that they have no conflict of interest.

Additional information

Communicated by D. E. Mather.

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122_2016_2711_MOESM1_ESM.docx

Supplementary Fig. 1 Distribution of SNP markers and their allelic frequency across all chromosomes and populations. The genetic map position of the markers on the barley consensus map (x-axis, in cM) and the estimated allelic frequency at each locus (y-axis) are plotted. Each dot shows the actual allelic frequency estimated based on the read counts supporting each allele. The solid curved lines show the regression that best fits the variation in allelic frequency. Red and green are used to identify the parental origin of the alleles while the dotted red lines indicate the values above or below which segregation distortion was significant (q value < 0.01)

122_2016_2711_MOESM2_ESM.docx

Supplementary Fig. 2 Distribution and overlap of segregation distortion regions (SDRs) observed across DH barley populations of this study and previous studies. The line to the left of the schematized chromosome (grey bar) indicates the genetic position (in cM). Colored bars illustrate the location and span of segregation distortion regions while a black oval indicates the position of the marker showing the largest distortion (SDR peak) observed in 12 barley population of this work. Markers exhibiting a significant segregation distortion in three previously studied populations (Igri x Franka in Graner et al. 1991; TX9425 x Franklin and Yerong x Franklin in Li et al. 2010) were positioned (when possible) on the same genetic map and show the location of previously reported SDRs (dotted lines)

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Bélanger, S., Clermont, I., Esteves, P. et al. Extent and overlap of segregation distortion regions in 12 barley crosses determined via a Pool-GBS approach. Theor Appl Genet 129, 1393–1404 (2016). https://doi.org/10.1007/s00122-016-2711-5

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  • DOI: https://doi.org/10.1007/s00122-016-2711-5

Keywords

  • Double Haploid
  • Segregation Distortion
  • Reciprocal Cross
  • Distorted Marker
  • Isolate Microspore Culture