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Title: Using genotyping-by-sequencing to identify SNPs linked to the Zucchini yellow mosaic virus resistance trait in bottle gourd and development of CAPS markers useful for marker assisted selection

Author
item WILDER, ALAN
item FEI, ZHANGJUN - BOYCE THOMPSON INSTITUTE
item Levi, Amnon
item Ling, Kai-Shu

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/4/2014
Publication Date: 10/12/2014
Citation: Wilder, A.J., Fei, Z., Levi, A., Ling, K. 2014. Using genotyping-by-sequencing to identify SNPs linked to the Zucchini yellow mosaic virus resistance trait in bottle gourd and development of CAPS markers useful for marker assisted selection. Cucurbitaceae 2014 Proceedings. p 94-97.

Interpretive Summary: N/A

Technical Abstract: Bottle gourd [Lagenaria siceraria L.] is an important root stock for watermelon as well as a nutritious vegetable. Previously, we identified several sources of resistance in bottle gourd to Zucchini yellow mosaic virus (ZYMV). Breeding populations were generated from two resistant lines (USVL1VR-Ls and USVL5VR-Ls) in order to elucidate the genetic basis of inheritance to ZYMV resistance. Results showed that inheritance of resistance to ZYMV in bottle gourd was controlled by a single dominant gene. To facilitate molecular marker identification, we employed the newly developed Genotyping-By-Sequencing (GBS) technology. In two experiments, GBS generated 2.1 to 2.5 million reads per run. Since the bottle gourd genome sequence was not available, alignments to the reference sequence was conducted against the closely related watermelon and cucumber genomes. After filtration, 171 and 95 single nucleotide polymorphisms (SNPs) were shown to be polymorphic in the tested bottle gourd F2 population. Two SNPs with close linkage to the Zym locus were located at 26.6 Mbp and 28.8 Mbp in the chromosome 1 of watermelon genome. Based on these SNPs, cleaved amplified polymorphic sequence (CAPS) markers were designed and shown to have a close association to the Zym locus, indicating their usefulness for marker-assisted selection. This work demonstrates the powerfulness of the GBS technology in translational genomic application to a plant species whose genome sequence is yet available.