Staff Spotlight with Robert Richter

Robert Richter

Robert Richter started working with VitisGen2 as a postdoctoral associate in September 2021 after completing his PhD at the Julius-Kühn Institute for Grapevine Breeding Geilweilerhof (JKI). His PhD thesis focused on the determination of key drivers of grapevine cluster architecture and the detection of genetic regions and candidate genes involved in cluster architecture.

Learn more about Robert’s work with VitisGen2 at VitisGen2 Staff Spotlight – Robert Richter.

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Comparing short-read sequence aligners to determine the best tool for your research needs

Figure 1 An FM index of the work "knickknack".Researchers Ryan Musich, Lance Cadle-Davidson, and Michael V. Osier reviewed seven different short-read sequence aligners utilizd in genomic and transcriptomic analysis in this April, 2021 article in Frontiers in Plant Science.

Researchers used Powdery Mildew (PM) Erysiphe necator isolates to test the various packages. Most performed well, with the exception of TopHat2, which was outperformed by HISAT2. BWA had the overall best performance,  for longer transcripts HISAT2 and STAR were also good performers. The results of this study could help biologists determine strengths and weaknesses of the different tools for their particular area of research.

Read more at Comparison of Short-Read Sequence Aligners Indicates Strengths and Weaknesses for Biologists to Consider.

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Exploring the genetics behind flower sex in grapevines

A close-up photo of grape flowers.Team members Tim Martinson, Cheng Zou, Qi Sun, Jason Londo, Mélanie Massonnet and Dario Cantu have a new article featured in October’s edition of Wine Business Monthly.  The article explores the complex origins of flower sex in grapevines.

Grapevine sex genes are located in the sex-determining region (SDR) of chromosome 2. The identification of the specific DNA variations for flower formation types allows grapevine sex in plants to be determined using high-throughput DNA sequencing. This improves the selection of  breeding canidates by allowing grape breeders to identify desirable hermaphrodite haplotype seedlings before plants are old enough to flower. These seedlings are able to self-pollinate. The ability to cull less desirable seedlings early lowers the amount of nursery and vineyard space required.

Read the full article: How Genetics Determine Flower Sex in Grapevines

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Researchers discover new QTLs for grape berry acid and tannins in V. aestivalis ‘Norton’ and V. vinifera ‘Cabernet Sauvignon’ hybrid population

A photo of Surya Sapkota in a vineyard and holding a ziplock bag full of grapes

Vitis aestivalis-derived ‘Norton’ grapes are a popular cultivar with vineyards in midwestern and eastern United States due to high disease resistance and cold temperature hardiness.

VitisGen2 researcher Chin-Feng Hwang and his team from Missouri State University recently published a new article in Fruit Research on fruit chemistry in Vitis aestivalis-derived ‘Norton’ grapes.

The article describes how acidity and tannin concentrations of this popular grape variety vary from commercial and consumer expectations of V. vinifera, and explore the genetic determinants of these components. The research team describes the identification of several new QTLs for these traits which may assist with improved hybrid cultivar breeding through marker-assisted selection.

Learn more by reading ‘Identification of QTLs for berry acid and tannin in a Vitis aestimvalis-derived ‘Norton’-based population‘.

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New publication by VitisGen2 team describes Ren-11 powdery mildew resistance location

Vines with and without powdery mildew

Grapevines with (left) and without (right) powdery mildew. Powdery mildew can cause slowed growth, reduced fruit quality, lower yield and poor winter hardiness in grapevines.

Researchers Avinash Karn, Cheng Zou, Siraprapa Brooks, Jonathan Fresnedo-Ramírez, Franka Gabler, Qi Sun, David Ramming, Rachel Naegele, Craig Ledbetter and Lance Cadle-Davidson from the VitisGen2 project have announced the discovery of a new, stable qualitative resistance locus in Vitis aestivalis named REN 11, located on chromosome 15, that was found to be effective in reducing powdery mildew in nearly all vineyard environments on leaves, rachis, berries and most of the time in stems.

The paper describes 15 years of work with one of the three original mapping families that established the foundation for VitisGen. Over those years, 5 postdocs and 3 USDA grape breeders have provided support. Learn more about this discovery of the REN 11 locus in ‘Discovery of the REN11 Locus from Vitis aestivalis for Stable Resistance to Grapevine Powdery Mildew in a Family Segregating for Several Unstable and Tissue-Specific Quantitative Resistance Loci‘ in the September 3, 2021 edition of Frontiers in Plant Science.

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Breeding Insight brings bioinformatics to specialty crop breeding. VitisGen2 brings technology to the table

VItisGen2 LogoBreeding Insight Logo


By Tim Martinson and Michelle Podolec.

Public and private breeders of commodity crops such as maize and soybeans have long used sophisticated bioinformatics, statistical tools, and ‘big data’ to guide their breeding programs. These tools increasingly leverage detailed DNA sequence information to predict the performance of each crop’s breeding lines – and ultimately help breeders release improved varieties more quickly.

But these sophisticated breeding tools have not been available to breeders of smaller-scale specialty crops. With their limited resources, obtaining even rudimentary genetic maps has been time-consuming and expensive. So specialty crop breeding has relied heavily upon field observations (phenotyping), and the breeder’s individual knowledge and experience in making crosses and selecting (or discarding) progeny. Specialty crop breeding has been as much of an ‘art’ as a ‘science’.

Dramatic drops in the cost of DNA sequencing and genome assembly have, for the first time, made genetic data abundant and financially accessible to specialty crop breeders. In grapes, for example, obtaining high quality whole-genome sequences of the ~500 million DNA base pairs on 19 chromosomes has dropped in cost from millions of dollars in the early 2000s to about $3000 per accession today.

Now specialty crop breeders have access to a torrent of new DNA sequence data. But they still lack the infrastructure and access to bioinformatics that commodity crop breeders have enjoyed for decades.

Read more…

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VitisGen2 researchers describe improved deep learning method for quantification of Grape PM at ASABE Meeting

Powdery white sheen on top of grape leaf.Deep learning-based saliency maps for the quantification of grape powdery mildew at the microscopic level
VitisGen2 team members Tian Qiu, Anna Underhill, Surya Datta Sapkota, Lance Cadle-Davidson, and Yu Jiang recently presented a paper at the 2021 American Society of Agricultural and Biological Engineers (ASABE) International Virtual Meeting that urges the breeding of Powdery Mildew (PM) resistant crops and how to overcome the bottleneck in image analysis at the microscopic level.  The researchers described a new method developed using high-throughput phenotyping to more rapidly quantify disease. The method uses the Blackbird phenotyping robot to automate and improve the speed of processing samples, and could lower costs.

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How researchers are seeking DNA sequence variations that affect micronutrient uptake in Vitis vinifera

Researchers Rachel Naegele, Jason Londo, Cheng Zou and Peter Cousins recently published a paper in Peer J where they explore the results of seeking DNA sequence variations that affect micronutrient uptake in Vitis vinifera.

Nutrient accumulation impacts all stages of plant growth and development, and heritability for micro and macro nutrients is complex in perennial crops like grapes.  Learning more about the genes responsible for balanced leaf nutrient levels will be important to better understand how to identify the specific genes that affect leaf traits in grapes.

Identification of SNPs associated with magnesium and sodium uptake and the effect of their accumulation on micro and macro nutrient levels in Vitis vinifera

Authors: Rachel P. Naegele, Jason P. Londo, Cheng Zou, Peter Cousins

PeerJ 9:e10773 https://doi.org/10.7717/peerj.10773

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“Research in Plain English” article on how fine mapping of leaf trichome density revealed trait location in a cold-hardy hybrid wine grape populations now available

Grape Vine Leaves

The new “Research In Plain English” on how fine mapping of leaf trichome density revealed the trait’s location in a cold-hardy wine grape population is available now. VitisGen2 team members Matt Clark and Lu Yin describe their team’s work fine mapping how grape leaf hair density in grape varies by genetic background (species). Analysis confirmed genetic control for leaf hairs in maturing leaves on chromosome 1. Fine-mapping using a large population narrowed the region to several candidate genes in a diverse genetic background.

Fine mapping of leaf trichome density revealed a 747-kb region on chromosome 1 in cold-hardy hybrid wine grape populations
Authors: Lu Yin, Avinash Karn, Lance Cadle-Davidson, Cheng Zou, Anna Underhill, Paul Atkins, Erin Treiber, Daniel Voytas, Matthew Clark
Frontiers in Plant Science 12 (2021):150 DOI: 10.3389/fpls.2021.587640

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Central Role of Mapping Populations in Marker-Assisted Grape Breeding

An image of the parent vines, siblings and half-siblings showing leaves and fruit.

Parents and selected progeny from three mapping populations. Illinois 547-1 is the offspring of V. rupestrix x V. cinerea and originated in the early 1960’s at the University of Illinois. Horizon is a commercial cultivar released by Cornell University’s grape breeding program in 1982. Illinois 547-1 and V. cinerea B9 are both male vines that do not produce fruit. The V. rupestris B38 parent is a female vine.

VitisGen2 is excited to announce a new article from team members Tim Martinson and Bruce Reisch of Cornell Agritech, and Rebecca Weipz of University of Wisconsin-Madison’s Peninsular Agricultural Research Station. Continue reading

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