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

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.

Candidate resistance genes to foliar phylloxera identified at Rdv3 of hybrid grape

“…Sequence variations could be compared at the candidate genes between MN1264 and MN1246 and their parents to provide further insights of inheritance of resistance. The selective phenotyping approach, using the fine mapping population we developed, will be a useful resource for identifying candidate genes for other traits previously mapped in GE1025, including color [ 41 ], trichome density [ 42 ], cluster compactness [ 43 ], and powdery mildew resistance [ 27 ].…”

“…Genotyping was conducted on GE1783 seedlings and parents using RNase H2 dependent amplicon sequencing (rhAmpSeq) marker platform [ 31 ]. The same rhAmpSeq genotyping data/protocol was used previously to fine map leaf trichome density in this population [ 42 ]. Briefly, collected leaf tissues were oven dried at 50°C overnight and sent to Intertek AgriTech (Sweden), where DNA was extracted using an automated magnetic bead method using the sbeadex kit by LGC (Teddington, U.K.).…”

“…Because multiple SNPs, insertions, and/or deletions can occur in each amplicon, these markers represent up to 4 alleles per locus in this F 1 population of two heterozygous parents [ 31 ]. A sex-averaged consensus genetic map was constructed from 1387 quality-controlled rhAmpSeq markers in Lep-MAP3 v 0.2 [ 45 ] as previously described [ 31 , 42 ]. For details on how we identified haplotype variants and constructed the genetic map to obtain the 4-way phased genotype data, see Zou et al (2020) [ 31 ].…”

Genome-Wide Association Study Reveals a Genomic Region Associated with Mite-Recruitment Phenotypes in the Domesticated Grapevine (Vitis vinifera)

“…Given the considerable economic toll of powdery mildew and spider mites in grape and wine production worldwide [ 23 , 24 ], this study presents an exciting step in understanding the genetic underpinnings of phenotypes that provide defense in grapevines without the use of harmful pesticides or fungicides. Furthermore, mite domatia have evolved repeatedly many times across plants, occurring in over 2000 plant species from over 20 plant families, including in other important forestry and crop plants such as oak, maple, beech, cherry, and coffee [ 4 , 59 ]. Thus, this study demonstrates its importance as one of the first to examine the genetic associations of these widespread indirect defensive traits.…”

The Genetic Basis of Anthocyanin Acylation in North American Grapes (Vitis spp.)

“…DNA from individuals was extracted using modified Qiagen DNeasy columns with 2.7% PVP-40 added to the extraction buffer, as previously described [ 18 ]. rhAmpSeq local haplotype sequencing targeting the core Vitis genome was conducted as described in the work of [ 19 , 20 ]. rhAmpSeq markers targeted 250 bp regions evenly distributed across the genome; because there could be multiple polymorphisms (SNPs and indels) per region, each marker represented up to four alleles in the F1 populations studied here.…”