Phenotyping at the World Vegetable Center


 

Speaker:  

Dr. Roland Schafleitner (World Vegetable Center, Taiwan))

Title: Phenotyping at the World Vegetable Center

Date:  Septmeber 4th  2020 / Time: 14:00   (Berlin Time) /  7.00 AM (CDT)

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Abstract:

The World Vegetable Center holds the world’s largest public sector vegetable germplasm collection with more than 60,000 accessions of around 450 species. Screening of this collection for new traits to breed improved stress tolerant vegetable varieties is one of the key tasks of the Center. Trait capture in large collections is laborious and logistically challenging. Specialized populations such as core collections comprising 5-20 % of the accessions of the whole collection, but representing a large proportion of the available diversity of a species facilitate germplasm screening. Nevertheless, it is still laborious to reliably measure traits in core collections comprising several hundreds of genotypes. Automatized phenotyping methods can be very helpful in collecting high quality data from many entries. The World Vegetable Center uses an automatized phenotyping system based on Phenospex PlantEye F500 multispectral 3D scanners to quantify growth performance and other traits of vegetable germplasm in the field. Up to present, eggplant, amaranth, okra and pepper germplasm panels have been studied and genotypic differences in plant development and growth have been recorded. Exposure of okra to flooding and pepper to heat stress and determining growth parameters over time led to the identification of stress tolerant genotypes. Accurate phenotyping in large genotyped germplasm panels has opened the path to genome-wide association studies to detect genetic loci associated with variation of plant performance. Vegetable breeding programs start to benefit of the newly available phenotypic information and from the genotype-trait associations.

 

Short Bio:

Education: MSc Molecular Microbiology (Vienna University), PhD Biochemical Technology (Technical University Vienna, Austria).

Experience: Worked for nine years as Biotechnology Research Associate at the Austrian Research Centers Seibersdorf (now AIT), one year as PostDoc in Tree Pathology at INRA Bordeaux (France), almost seven years at the International Potato Center (CIP) in Lima, Peru, and the last ten years at the World Vegetable Center in Taiwan, first as Head of Molecular Genetics, and since 2018 also as Flagship Program Leader “Vegetable Diversity & Improvement”. Besides: teaching a few biotechnology classes at the National Cheng Kung University in Tainan, Taiwan.

Realized the importance of accurate phenotyping when working on drought and heat tolerance of potato and developed screening methods to identify tolerant materials. Current activities: apply high throughput genotyping and phenotyping to identify and map stress tolerance in vegetables to breed more resilient tomato, pepper, eggplant, mungbean, okra, amaranth and cucurbit varieties.

 

Publications (past 3 years):

Shaw P, Raubach S, Kilian B, Dreher K, Amri A, Bassi Filippo M, Boukar O; Cook D; Cruickshank AW, Fatokun CA.; El Haddad N; Humphries A; Jordan D; Kehel Z; Kumar S; Nguyen LH; Mace E; McCouch S; McNally K; Marshall DF; Mikwa EO; Milne I; Odeny, DA; Plazas M; Prohens J; Rieseberg L; Schafleitner R; Sharma S; Stephen G; Tin HQ; Togol, A; Warschefsky E; Werner  (2020). From bits to bites: Advancement of the germinate platform to support genetic resources collections and pre-breeding informatics for crop wild relatives. Crop Science, accepted

Matsumura H, Hsiao MC, Lin YP, Toyoda A, Taniai N, Tarora K, Urasaki N , Anand S, Dhillon NPS, Schafleitner R, Lee CL (2020) Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of non-classic domestication. PNAS, https://doi.org/10.1073/pnas.1921016117

Shin IS, Hsu JC, Huang SM, Chen JR, Wang JF, Hanson P, Schafleitner R (2020) Construction of a Single Nucleotide Polymorphism Marker based QTL map and validation of resistance loci to Bacterial Wilt caused by Ralstonia solanacearum species complex in tomato. Euphytica, in press.

van Zonneveld M, Rakha M, Tan SY, Chou YY, Chang CH, Yen JY, Schafleitner R, Nair R, Naito K, Solberg SØ (2020) Mapping patterns of abiotic and biotic stress resilience uncovers conservation gaps and breeding potential of Vigna wild relatives. Scientific Reports 10:1-1.

Schafleitner R. (2020) Molecular marker resources and their application. In: The Mungbean Genome, pp. 107-124, Springer, Cham.

Schafleitner R, Nair RM (2020) Future prospects and challenges in mungbean breeding. In: The Mungbean Genome, pp. 181-191. Springer, Cham.

Nair RM, Pandey AK, War AR, Hanumantharao B, Shwe T, Alam AK, Pratap A, Malik SR, Karimi R, Mbeyagala EK, Douglas CA, Rane J, Schafleitner R (2019) Biotic and abiotic constraints in mungbean production—progress in genetic improvement. Frontiers in Plant Science 10.

Lin CP, Schafleitner R, Chen CY, Lo HF, Chen LF (2019) The complete mitochondrial genome of wild mung bean (Vigna radiata var. sublobata TC1966). Mitochondrial DNA Part B. 4:3016-7.

Dhillon NP, Sanguansil S, Srimat S, Laenoi S, Schafleitner R, Pitrat M, McCreight JD (2019) Inheritance of Resistance to Cucurbit Powdery Mildew in Bitter Gourd. HortScience 54:1013-6.

Breria CM, Hsieh CH, Yen JY, Nair R, Lin CY, Huang SM, Noble TJ, Schafleitner R (2019) Population structure of the World Vegetable Center mungbean mini core collection and genome-wide association mapping of loci associated with variation of seed coat luster. Tropical Plant Biology 1-2.

Malini P, Ramasamy S, Schafleitner R, Muthukalingan K (2019) Pheromone‐binding proteins based phylogenetics and phylogeography of Maruca spp. from Asia, Africa, Oceania, and South America. Ecology and Evolution https://doi.org/10.1002/ece3.5471.

Pratap A, Gupta S, Nair RM, Gupta SK, Schafleitner R, Basu PS, Singh CM, Prajapati U, Gupta AK, Nayyar H, Mishra AK (2019). Using plant phenomics to exploit the gains of genomics. Agronomy 9:126.

Taher D, Rakha M, Ramasamy S, Solberg S, Schafleitner R (2019) Sources of resistance for two-spotted spider mite (Tetranychus urticae) in scarlet (Solanum aethiopicum L.) and gboma (S. macrocarpon L.) eggplant germplasms. HortScience 54:240-5.

Sokolkova AB, Vishnyakova MA, Schafleitner R, von Wettberg EB, Samsonova MG, Nuzhdin SV (2019) Population genomics and analysis of agronomic traits of green gram (Vigna radiata) and black gram (Vigna mungo). Plant Genetics, Genomics, Bioinformatics, and Biotechnology (PlantGen2019) pp. 199.

Burlyaeva M, Vishnyakova M, Gurkina M, Kozlov K, Lee CR, Ting CT, Schafleitner R, Nuzhdin S, Samsonova M, von Wettberg E (2019). Collections of mungbean [Vigna radiata)(L.) R. Wilczek] and urdbean [V. mungo (L.) Hepper] in Vavilov Institute (VIR): traits diversity and trends in the breeding process over the last 100 years. Genetic Resources and Crop Evolution 66:767-81.

Ahmad M, Pataczek L, Hilger TH, Zahir ZA, Hussain A, Rasche F, Schafleitner R, Solberg SØ (2018) Perspectives of microbial inoculation for sustainable development and environmental management. Frontiers in Microbiology 9:2992.

Naresh P, Lin SW, Lin CY, Wang YW, Schafleitner R, Kilian A, Kumar S (2018) Molecular markers associated to two non-allelic genic male sterility genes in peppers (Capsicum annuum L.). Frontiers in Plant Science 9.

Dhillon NP, Sanguansil S, Srimat S, Schafleitner R, Manjunath B, Agarwal P, Xiang Q, Masud MA, Myint T, Hanh NT, Cuong TK (2018) Cucurbit powdery mildew-resistant bitter gourd breeding lines reveal four races of Podosphaera xanthii in Asia. HortScience 1;53(3):337-41.