Single and multiple phenotype QTL analyses of downy mildew resistance in interspecific grapevines

Abstract

Key messageDowny mildew resistance across days post-inoculation, experiments, and years in two interspecific grapevine F1 families was investigated using linear mixed models and Bayesian networks, and five new QTL were identified.AbstractBreeding grapevines for downy mildew disease resistance has traditionally relied on qualitative gene resistance, which can be overcome by pathogen evolution. Analyzing two interspecific F1 families, both having ancestry derived from Vitis vinifera and wild North American Vitis species, across 2 years and multiple experiments, we found multiple loci associated with downy mildew sporulation and hypersensitive response in both families using a single phenotype model. The loci explained between 7 and 17% of the variance for either phenotype, suggesting a complex genetic architecture for these traits in the two families studied. For two loci, we used RNA-Seq to detect differentially transcribed genes and found that the candidate genes at these loci were likely not NBS-LRR genes. Additionally, using a multiple phenotype Bayesian network analysis, we found effects between the leaf trichome density, hypersensitive response, and sporulation phenotypes. Moderate–high heritabilities were found for all three phenotypes, suggesting that selection for downy mildew resistance is an achievable goal by breeding for either physical- or non-physical-based resistance mechanisms, with the combination of the two possibly providing durable resistance.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-018-3065-y) contains supplementary material, which is available to authorized users.

Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on Whole-Genome Resequencing

“…In the past ten years, a number of grape genetic maps have been constructed based on different mapping populations [20,[22][23][24][25][26][27][28][29][30][31][32][33]. Numerous QTLs for important economic traits, including resistance to downy mildew [10,16,22,[34][35][36][37][38], powdery mildew [34,36,[39][40][41], anthracnose [24], root-knot nematodes [42], and grape phylloxera [43,44], as well as flower sex [45,46], berry color [46,47], seedlessness [48], berry weight [18,32], soluble solid content [32], acidity [20], and muscat flavor [49], have been identified.…”

TheRpv3-3haplotype and stilbenoid induction mediate downy mildew resistance in a grapevine interspecific population

“…A total of 27 Quantitative Trait Loci (QTLs) associated with DM resistance in different genetic backgrounds are known and described (VIVC, 2018). In particular, the major Rpv loci originated from Muscadinia rotundifolia (Merdinoglu et al, 2003), Vitis riparia (Marguerit et al, 2009;Moreira et al, 2011), V. amurensis (Blasi et al, 2011;Schwander et al, 2012;Venuti et al, 2013), V. cinerea (Ochssner et al, 2016), and V. rupestris (Divilov et al, 2018). To close the list, the Rpv3 locus is a major determinant of grapevine DM resistance.…”

Rpv29, Rpv30 and Rpv31: Three Novel Genomic Loci Associated With Resistance to Plasmopara viticola in Vitis vinifera

“…Among the 27 QTL already identified, three ( Rpv8 , 12, and 19) map on chromosome 14, while no QTL were found to map on chromosomes 3 and 16. Rpv8 and Rpv12 both mapped on the upper arm of chromosome 14 ( Blasi et al, 2011 ; Venuti et al, 2013 ), while Rpv19 mapped on the lower arm, at around position 24 Mb ( Divilov et al, 2018 ). Because the SNPs identified in this work do not physically co-locate to the QTL already identified, it is possible to conclude that the three loci are novel associations.…”

“…), exhibit varying levels of resistance, ranging from moderate to high, due to co-evolution with the pathogen ( Jürges et al, 2009 ). Several QTL (Quantitative Trait Loci), conferring downy mildew resistance, at different levels ranging from weak to total, were discovered in Vitis species background: Rpv1 and Rpv2 in Muscadinia rotundifolia Michaux ( Merdinoglu et al, 2003 ; Wiedemann-Merdinoglu et al, 2006 ); Rpv3 and Rpv19 in Vitis rupestris Scheele ( Welter et al, 2007 ; Bellin et al, 2009 ; Divilov et al, 2018 ; Vezzulli et al, 2019 ; Foria et al, 2020 ); Rpv4 , Rpv7 , Rpv11 , Rpv17 , Rpv18 , Rpv20 , and Rpv21 , in unspecified American species ( Fischer et al, 2004 ; Welter et al, 2007 ; Bellin et al, 2009 ; Divilov et al, 2018 ); Rpv5 , Rpv6 , Rpv9 , and Rpv13 in V. riparia ( Marguerit et al, 2009 ; Moreira et al, 2011 ); Rpv8 , Rpv10 , Rpv12 , Rpv22 , Rpv23 , Rpv24 , Rpv25 , and Rpv26 in V . amurensis ( Blasi et al, 2011 ; Schwander et al, 2012 ; Venuti et al, 2013 ; Song et al, 2018 ; Lin et al, 2019 ); Rpv14 in V. cinerea ( Ochssner et al, 2016 ); Rpv15 and Rpv16 in Vitis piasezkii Maxim.…”