Mapping Autotetraploid Alfalfa

1
Mapping Autotetraploid Alfalfa

• Joseph G. Robins and
• E. Charles Brummer

2
Objective

• Determine the genetic basis of forage yield in
  alfalfa.
• Develop a genetic linkage map of tetraploid
  alfalfa.
• Map quantitative trait loci (QTL) associated with
  forage yield.
• Implement a marker-assisted selection (MAS)
  program for alfalfa improvement.

Robins and Brummer. CAIC. 2003.
3
Problem
 

• Lack of gain in alfalfa forage yield since the
  early 1980s.

Courtesy Riday and Brummer, 2002.
Robins and Brummer. CAIC. 2003.
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Autopolyploid Genetics

• Forage yield gain is complicated by the
  complexities of alfalfa genetics.
• Complementary gene action (Bingham et al. 1994).
• Irregular meiosis, when compared to diploids,
  with non-conventional segregation patterns.
• Potential multivalent pairing.
• Potential double reduction.

Robins and Brummer. CAIC. 2003.
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Our Approach

• A potential solution is to identify genomic
  regions associated with forage yield.
• Create genetic map of a segregating population
  using molecular markers.
• Combine marker and phenotype data to identify
  associations between markers and phenotype (QTL)
• Utilize QTL in a marker-assisted breeding program
  to increase forage yield.

Robins and Brummer. CAIC. 2003.
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Experiment

• Created F1 mapping population
• by crossing
• WISFAL-6 (M. sativa subsp. falcata) x ABI-408 (M.
  sativa subsp. sativa).
• Placed at Ames, IA, Nashua, IA Ithaca, NY for
  forage yield analysis from 1999 - 2001.
• Measurements were also taken for a variety of
  other traits.
• Lsmeans across years and locations.

Robins and Brummer. CAIC. 2003.
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Forage Yield Results

• Population exhibits large amount of genetic
  variation for forage yield.
• Broad-sense heritability 0.57 0.06.
• H2 s2G / s2P.
• Where s2G s2A s2D s2F s2T s2I.
• Based on entry means across years and locations.
• Identified high and low transgressive segregants.

Robins and Brummer. CAIC. 2003.
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Genetic Mapping

• Developed a genetic map of the population using
  RFLPs, AFLPs, and SSRs.

• Autopolyploid genetics complicate mapping.
• Used RFLPs, AFLPs, and SSRs.
• Single and double dose alleles.
• Developed maps of both parents.

Robins and Brummer. CAIC. 2003.
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Mapping Summary

• Both parental maps are preliminary and currently
  composed of fourteen consensus linkage groups.
• ABI-408 120 RFLPs, 201 AFLPs, 7 SSRs
• 179 single-dose, 32 double-dose, 120 distorted.
• WISFAL-6 106 RFLPs, 139 AFLPs, 4 SSRs
• 115 single-dose, 50 double-dose, 84 distorted.

Robins and Brummer. CAIC. 2003.
10
QTL Analysis

• Utilized single-marker analysis (ANOVA) to
  identify molecular markers significantly
  associated with forage yield.
• ABI-408 Identification of three potential forage
  yield QTL.
• WISFAL-6 Identification of two potential forage
  yield QTL.

Robins and Brummer. CAIC. 2003.
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Possible QTL
Associations based on average forage yield
(g plant-1) across locations and
years. Parent Marker Yield (marker
present/absent) P-value ABI-408 UGA189a 175 /
189 0.004 Vg2D11a 174 / 187 0.007 AGC/CAC216
177 / 195 0.0007 WISFAL-6 Vg2D11 186 /
169 0.005 UGA83 185 / 168 0.007
Robins and Brummer. CAIC. 2003.
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ABI-408 QTL Mapping

• Markers (highlighted in red) associated with
  forage yield in the sativa parent.

Only three of fourteen consensus linkage groups
shown.
Robins and Brummer. CAIC. 2003.
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WISFAL-6 QTL Mapping

• Markers (highlighted in red) associated with
  forage yield in the falcata parent.

Only two of fourteen consensus linkage groups
shown.
Robins and Brummer. CAIC. 2003.
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QTL x Environment

• Our next step will be to analyze QTL as they
  change over the different locations and years.
• The extent of our phenotypic data will allow us
  to identify QTL that are specific to individual
  locations, years, or location/year combinations.
• This should allow us to identify QTL that are
  important in the developmental process of alfalfa
  (as the plant ages, it is possible that QTL may
  change) and QTL that are or are not influenced by
  environmental factors.
• We hope to have results from these analyses
  shortly.

Robins and Brummer. CAIC. 2003.
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Summary

• We have
• Developed preliminary linkage maps of ABI-408
  and WISFAL-6.
• We are continuing to add SSRs.
• Used single-marker analysis to identify potential
  QTL associated with forage yield in both parents.
• Associations will be further verified with
  permutation testing.
• We then hope to incorporate the results for
  alfalfa forage yield improvement.

Robins and Brummer. CAIC. 2003.
16
Acknowledgements
Dr. Charlie Brummer Dr. Diane Luth Dr.
Heathcliffe Riday Meenakshi Santra Baldomero
Alarcón-Zúñiga ISU-Forage Breeding Group
Iowa State University Plant Science
Institute USDA-NRI Competitive Grants Program

Robins and Brummer. CAIC. 2003.