Issue link: http://winesandvines.uberflip.com/i/946131
March 2018 WINES&VINES 65 WINE EAST GRAPEGROWING GARRIS, A.; L. CLARK; C. OWENS; S. MCKAY; J. LUBY; K. MATHIASON AND A. FENNELL. 2009. "MAPPING OF PHOTOPERIOD-INDUCED GROWTH CESSATION IN THE WILD GRAPE, VITIS RIPARIA." J. AMER. SOC. HORTIC. SCI. 134:2, 261-272. quire wire and trellis as they grow. That trans- lates to much more expense for each cross and progeny evaluated. Wheat and corn breeders have histori- cally been able to map the chromosomes and determine how traits are inherited much more easily—simply because they can crank out large families of progeny and evaluate them in one cropping cycle. Even before modern DNA sequencing, they were able to develop specialized genetic stocks (mutant collections, chromosome-deletion lines, near-isogenic lines) that provided tools for mapping genes. Grape geneticists, by contrast, faced a more complex task in determining how desirable traits were inherited and mapping these traits to specific locations on each chromosome. Finding even a few molecular markers for simple traits required years of effort. The first grape genetics maps were developed at Cornell University 25 years ago. At that time, it took five years to map a few traits, including genes for flower sex determination and "REN2" pow- dery mildew resistance. Phenotypic selection Because of this, grape breeding programs relied on observed phenotypes (vine charac- teristics), most often without much idea of their genetic basis. For example, some seed- lings in Cornell's "no-spray" block show re- markably few powdery mildew colonies on their leaves, but only now are we learning what gene or genes are associated with the observed resistance. The cost of maintaining experimental vine- yards and the time it takes to evaluate phe- notypes set an upper limit on how much genetic knowledge grape breeders could ob- tain. Compared to corn and wheat breeders, grape breeders have had fewer tools and a much more rudimentary genetic map in their toolbox. They have been flying blind. The genetic revolution and genetic markers Sequencing technology has changed the equation. The cost of obtaining DNA sequenc- ing information has fallen dramatically. For example, according to the National Institutes of Health (2017), the cost of obtaining a com- plete human genome sequence has dropped in the past 10 years from $10 million to just above $1,000, a 10,000-fold reduction in cost. The cost of sequencing each mega-base (1 million base pairs) now stands at a little more than a penny (1.2 cents), down from $500 in 2007. This dramatic drop in cost exceeds the historical doubling in computer chip circuitry every two years that "Moore's law" famously predicted. DNA sequence in- formation is now very inexpensive. For grape breeders and geneticists, the previous trickle of scarce genetic knowledge has turned into a flood of DNA sequence in- formation. For the first time, there is enough sequence information to allow geneticists to make a detailed map of the 19 pairs of chro- mosomes and 500 million base pairs in the grape genome. This map enables them to lo- cate genetic markers (short DNA sequences) associated with single gene loci, or what they call Quantitative Trait Loci (QTLs). Using inexpensive tests of the DNA from each seedling to detect these genetic mark- ers, they can identify which seedlings result- ing from their crosses are carrying the genes of interest. Instead of waiting years to iden- tify which vines have the desired traits, they can find out almost overnight which seed- lings carry the desired genes by snipping out a small leaf sample, extracting DNA and car- rying out inexpensive lab-based analyses. To date, the USDA-funded VitisGen proj- ect has identified more than 70 marker-trait associations for disease resistance (powdery mildew, downy mildew, phomopsis, black rot), fruit quality traits (anthocyanins, skin color, sugar and acid content) and more. These markers are being put to use in select- ing or discarding seedlings before planting them out in the field. Since 2014, more than 16,000 seedlings have been screened using marker-assisted selection. Moreover, DNA markers now give grape breeders the tools to stack multiple genes for disease resistance into the same variety. Field observations of phenotypes could only tell you whether a seedling was resistant or sus- ceptible—but not which gene was respon- sible. Now DNA markers can tell you whether one, two, three or more resistance genes are present in one seedling. This should allow breeders to develop stable, long-lasting re- sistance with multiple modes of action. Before automated DNA sequencing, ex- tracting genetic information was like turning on a faucet and watching it drip slowly. Now that the cost of DNA sequencing is trivial, the flow of information is more like a torrent from a firehose. The challenge for breeders and geneticists is to correctly interpret and use this flood of information. From now on, grape breeders won't be flying blind. Dr. Tim Martinson, a senior extension associate in the Cornell University School of Integrative Plant Science, works with regional extension educators and industry groups to provide growers and wineries with educa- tional programs, workshops, newsletters and applied on-farm research that supports profitable production of grapes, grape products and wine. This research was supported by the USDA-NIFA Spe- cialty Crop Research Initiative (Award No. 2017- 51181- 26829). The references for this article are available online at winesandvines.com/features. New DNA sequencing techniques have allowed more detailed maps of grape chromosomes. At left are 12 simple sequence repeat (SSR) markers on chromosomes 1 and 2, identified by Garris et al. (2009). By 2014 (right), with the use of genotyping by sequencing (GBS), researchers had increased that number by a factor of 10 to more than 120 GBS markers on the same chromosomes (Yang et al., 2016). PROGRESS IN GENE MAPPING SINCE 2009 SSR Markers 2009 GBS Markers 2014 Chr01 Chr02