Fine Mapping of Leaf Trichome Density Revealed a 747-kb Region on Chromosome 1 in Cold-Hardy Hybrid Wine Grape Populations

Lu Yin, Avinash Karn, Lance Cadle-Davidson, Cheng Zou, Anna Underhill, Paul Atkins, Erin Treiber, Daniel Voytas, Matthew Clark

Research output: Contribution to journalArticlepeer-review

Abstract

Segregation for leaf trichome density was observed in a cold-hardy hybrid grape population GE1025 (N = ∼125, MN1264 × MN1246) that was previously used to detect a quantitative trait locus (QTL) underlying foliar phylloxera resistance on chromosome 14. Our hypothesis was that high trichome density was associated with resistance to phylloxera. Existing literature found trichome density QTL on chromosomes 1 and 15 using a hybrid grape population of “Horizon” × Illinois 547-1 and suggested a few candidate genes. To validate the reported QTL and our hypothesis, interval mapping was conducted in GE1025 with previous genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) genotype data and phenotypic scores collected using a 0–6 trichome density scale at several leaf positions. Evaluations were done on replicated forced dormant cuttings in 2 years and on field-grown leaves in 1 year. There was no strong relationship between trichome density and phylloxera resistance except for a Pearson’s correlation (r) of about -0.2 between a few trichome density traits and phylloxera severity traits at 2 and 3 weeks after infestation. Two genetic regions were repeatedly detected for multiple trichome density traits: from 10 to 20.7 Mbp (∼10 Mbp) on chromosome 1 for ribbon and simple density traits and from 2.4 to 8.9 Mbp on chromosome 10 for ribbon density traits, explaining 12.1–48.2 and 12.6–27.5% of phenotypic variation, respectively. To fine map, we genotyped a larger population, GE1783 (N = ∼1,023, MN1264 × MN1246), with conserved rhAmpSeq haplotype markers across multiple Vitis species and phenotyped 233 selected potential recombinants. Evaluations were conducted on field-grown leaves in a single year. The QTL for ribbon trichome density on adaxial vein and adaxial leaf and simple density on abaxial vein was fine mapped to 12.63–13.38 Mbp (747 kb) on chromosome 1. We found variations of MN1264 and MN1246 at candidate genes NAC transcription factor 29, EF-hand protein, and MYB140 in this region and three other surrounding candidate genes proposed previously. Even though no strong relationship between foliar phylloxera resistance and trichome density was found, this study validated and fine mapped a major QTL for trichome density using a cold-hardy hybrid grape population and shed light on a few candidate genes that have implications for different breeding programs.

Original languageEnglish (US)
Article number587640
JournalFrontiers in Plant Science
Volume12
DOIs
StatePublished - Mar 3 2021

Bibliographical note

Funding Information:
We would like to thank Soon Li Teh and Jonathan Fresnedo Ramirez for their previous work on the GE1025 GBS SNP data. Jason Londo and Qi Sun for their work on the GE1783 rhAmpSeq genotype data. The Watkins lab, particularly Dominic Petrella, for their allowance and assistance to use the Epson V550 scanner. Killian Harnish for his efforts in taking GE1025 microscopic images even though this study did not end up using them. John Thull, Jack Olson, and Eliana Wilson for their assistance in collecting the stem cuttings, leaf samples, leaf images, and trichome scores. John Thull, Jennifer Thull, and Colin Zumwalde for maintenance of the field plantings of the populations. Jack Olson and Nelson Garcia for information on the long-range PCR. Yinjie Qiu and Minnesota Supercomputing Institute particularly Adam Herman for their assistance in sequence alignment and obtaining trichome candidate genes. Laise Moreira for her encouragement in starting this project. Funding. USDA-NIFA Specialty Crop Research Initiative Award No. 2017-51181-26829 provided funding for rhAmpSeq genotyping. The Minnesota Department of Agriculture Specialty Crop Grant provided funding for the LY?s salary and phenotyping work. The University of Minnesota Grant-in-Aid Program provided funding for the planting of GE1025 and GE1783 in the vineyard.

Funding Information:
USDA-NIFA Specialty Crop Research Initiative Award No. 2017-51181-26829 provided funding for rhAmpSeq genotyping. The Minnesota Department of Agriculture Specialty Crop Grant provided funding for the LY’s salary and phenotyping work. The University of Minnesota Grant-in-Aid Program provided funding for the planting of GE1025 and GE1783 in the vineyard.

Publisher Copyright:
© Copyright © 2021 Yin, Karn, Cadle-Davidson, Zou, Underhill, Atkins, Treiber, Voytas and Clark.

Keywords

  • QTL mapping
  • candidate gene
  • fine mapping
  • hybrid grape
  • phylloxera resistance
  • trichome density

PubMed: MeSH publication types

  • Journal Article

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