Genetic mapping and fine mapping of leaf trichome density in cold-hardy hybrid wine grape populations

Authors: YIN, LU - University Of Minnesota; KARN, AVINASH - Cornell University; ZOU, CHENG - Cornell University; Cadle-Davidson, Lance; Underhill, Anna; ATKINS, PAUL - University Of Minnesota; VOYTAS, DAN - University Of Minnesota; TREIBER, ERIN - University Of Minnesota; CLARK, MATT - University Of Minnesota

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/21/2021
Publication Date: 3/3/2021
Citation: Yin, L., Karn, A., Zou, C., Cadle Davidson, L.E., Underhill, A.N., Atkins, P., Voytas, D., Treiber, E., Clark, M. 2021. Genetic mapping and fine mapping of leaf trichome density in cold-hardy hybrid wine grape populations. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2021.587640.
DOI: https://doi.org/10.3389/fpls.2021.587640

Interpretive Summary: To test the hypothesis that hairy grape leaves have increased severity of leaf galls caused by phylloxera aphids, we studied the genetics of both traits in 125 seedlings of a cold-hardy hybrid grape family, MN1264 × MN1246. This family was previously used to detect a genetic region on chromosome 14 predicting leaf phylloxera resistance. In the current study, evaluations were done on shoots emerging from dormant wood in two years and on field-grown leaves in one year. There was no strong relationship between trichome hair density and phylloxera resistance, but there was a trend that some types of leaf hairs were associated with lower phylloxera severity traits at 2 and 3 weeks after infestation. Two genetic regions were repeatedly detected for multiple trichome density traits: chromosome 1 for ribbon-shaped and thorn-shaped hair density on different positions of the leaf, and chromosome 10 for ribbon density, explaining 12.1-48.2% and 12.6-27.5% of observed variation, respectively. A deeper analysis of 1023 seedlings from the same parents identified several candidate genes on chromosome 1 controlling leaf hair density. Even though no strong relationship between leaf phylloxera resistance and trichome density was found, the genetic knowledge and markers for these traits can be used for grape breeding.

Technical Abstract: (N=~125, MN1264 × MN1246) which was previously used to detect a 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 GBS 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 two years and on field-grown leaves in one 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. We refined these two regions using a larger population, GE1783 (N=~1023, 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 were fine mapped to 12.75 - 12.89 Mbp (140 kb) on chromosome 1. We found insertion/deletion variations of MN1264 and MN1246 in one candidate pseudogene in this region and three other 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 on chromosome 1 using a cold-hardy hybrid grape population and shed light on a few candidate genes which has implications for different breeding programs.