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Paternity testing in an autotetraploid alfalfa breeding polycross

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Abstract

Determining unknown parentage in autotetraploid alfalfa (Medicago sativa L.) (2n = 4x = 32) can improve breeding gains. An exclusion analysis-based paternity testing SAS code, amenable to genotyping errors, is presented for autotetraploid species utilizing co-dominant molecular markers with ambiguous dosage. To demonstrate the paternity testing SAS code, 19 SSR loci were genotyped and analyzed on 1,107 progeny from a commercial, isolated, clonally replicated, 16-parent alfalfa breeding polycross which was pollinated by leafcutter bees (Megachile rotundata F.). Paternal assignment success rate was over 90 %. Among typed progeny, 45 % were the result of self-fertilization. Significant differences were detected between the 15 parents that produced seed and were observed as fathers for (1) total fertilizing pollen contribution (% deviation from expectation), (2) self-fertilization rates (%), and (3) outcrossing fertilizing pollen contribution (% deviation from expectation). Physical within-cage distance between parental plants was correlated with outcrossing fertilizing pollen frequency (negative power function). Parental seed yield was positively correlated with total fertilizing pollen contribution, particularly with self-fertilization rates (42 % self-fertilization and 17 % outcrossing). These correlations suggest that selecting for increased seed yield may result in indirect selection for increased self-fertilization rates. Parental total fertilizing pollen contribution was 62 % determined by outcrossing and 35 % by self-fertilization. This study cautions alfalfa breeders that heretofore unconsidered sources of inbreeding could be present in some breeding materials. This study also provides cost effective and easy to use molecular genetic tools for detecting, managing, and/or selecting against (through breeding) those sources of inbreeding.

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Authors and Affiliations

  1. US Dairy Forage Research Center, USDA-ARS, Madison, WI, 53706, USA

    Heathcliffe Riday & John A. Raasch

  2. Cal/West Seeds, West Salem, WI, 54669, USA

    David W. Johnson, Mark E. Darling & Jay M. Sandman

  3. Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA

    Karolina Heyduk

Authors
  1. Heathcliffe Riday
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  2. David W. Johnson
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  3. Karolina Heyduk
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  4. John A. Raasch
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  5. Mark E. Darling
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  6. Jay M. Sandman
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Correspondence to Heathcliffe Riday.

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Riday, H., Johnson, D.W., Heyduk, K. et al. Paternity testing in an autotetraploid alfalfa breeding polycross. Euphytica 194, 335–349 (2013). https://doi.org/10.1007/s10681-013-0938-7

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  • DOI: https://doi.org/10.1007/s10681-013-0938-7

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