Wines & Vines

142 WINES&VINES Collector's Edition GRAPEGROWING WINE EAST B efore inexpensive DNA sequencing was available, grape breeders had to rely solely on traits observed in the field (phenotypes) to decide which new seedlings produced through crosses to keep and which to discard. For disease resistance, this meant tossing out any plants that showed powdery mildew or downy mildew infections at the seedling stage during the first year of growth. Although they kept those that didn't show any symptoms, this method of field phenotyping didn't help them much in determining which and how many genes were involved and whether or not the trait would sur- vive a subsequent round of breeding intact. DNA mark- ers and more extensive use of mapping populations have changed all that. Since about 2000, genetics researchers have been busy linking DNA sequences (called markers) to specific locations on grape chromosomes (loci) that are associated with ob- served traits of grapevines in the field (phenotypes). To date, they have identified markers for at least 13 loci for powdery mildew resistance and 27 for downy mildew re- sistance (Figure 1). Now that they have these markers, grape breeders can test seedlings for the presence of specific genes or loci and know what and how many loci for disease resistance they have in their new seedlings (see "Grape breeders no longer flying blind," Wines & Vines, March 2018,). This is a powerful new approach that gives breeders the means to reliably incorporate desirable traits into breeding lines. For example, having DNA markers for a strong locus for Pierce's disease resistance (named Pdr1 for Pierce's disease resistance 1) allowed University of California, Davis professor Andy Walker to pass through five successive "backcross cycles" confidently and quickly, to incorporate Pdr1 (from wild Vitis arizonica) in a 98% Vitis vinifera background, resulting in new varieties that are resistant to Pierce's disease. Mapping populations and markers How do breeders and geneticists find these DNA markers among the approximately 500 million DNA base pairs and 19 chromosomes in the grapevine genome? The answer is that they have to make special crosses between two existing varieties or wild accessions and place the resulting seedlings into a special planting called a "mapping population." Mapping populations (there are 12 in the VitisGen2 project) typically consist of 200-300 full-sibling progeny of these crosses, grown in the field. These siblings share half of each parent's DNA, and each vine carries a unique set of traits. The next step is to use DNA sequencing techniques to identify snippets of DNA sequences (markers) that vary among the two parents. Using a technique called genotyping by sequencing (GBS), VitisGen researchers were able to identify roughly 2,000 DNA markers (~100 for each of the 19 chromosomes) at a cost of $15 for each individual vine tested. Obtaining a detailed genetic map of 200 unique individuals, each with 2,000 markers, used to be very ex- The Phenotyping Bottleneck How grape breeders link desired traits to DNA markers By Tim Martinson and Lance Cadle-Davidson Disease resistance loci identified since 2000 for powdery mildew and downy mildew. Black loci denote those that have been identified by scientists in the VitisGen projects. 2000 2002 2004 2006 2008 2010 2012 2014 2016 2018 Rpv1 Rpv11 Rpv2 Rpv3 Rpv4 Rpv5 Rpv6 Rpv7 Rpv8 Rpv9 Rpv13 Rpv15 Rpv16 Rpv17 Rpv18 Rpv19 Rpv20 Rpv21 Rpv22 Rpv23 Rpv24 Rpv25 Rpv26 Rpv27 Rpv14 Rpv12 Rpv10 V V V V V V V V V V DOWNY MILDEW 2000 2002 2004 2006 2008 2010 2012 2014 2016 2018 Ren2 Ren1 Run1 Run2 Ren4 Ren5 Ren8 Reb9 Ren10 Ren 6 Ren7 Sen1 V V V V V V V FIGURE 1: POWDERY MILDEW Ren3 V

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