Highly differentiated genomic regions among different populations harbor many genes related to disease resistance and stress tolerance, potentially contributing to their local adaptations.
CucCAP Genomics & Bioinformatics Team
Genomics & BioinformaticsTeam contributions to the CucCAP grant including captioned images of research activities, publications available online, and articles about the team’s research efforts and accomplishments.
Genomics and Bioinformatics Team | 2024 Progress Report
View the Genomics Team progress report including all tables and figures in pages 12 – 19 of the pdf version of this report.
Genomics and Bioinformatics Team members:
Zhangjun Fei (Boyce Thompson Institute)
Shan Wu (Boyce Thompson Institute)
Amnon Levi (USDA, ARS)
Yiqun Weng (USDA, ARS)
Michael Mazourek (Cornell University)
Jim McCreight (USDA, ARS)
Rebecca Grumet (Michigan State University)
Early Career Scientist Spotlight | Xuebo Zhao
Xuebo Zhao is a postdoctoral researcher in the Fei Lab at Boyce Thompson Institute. The focus of Xuebo’s work is genomics. Her research is to unravel the evolution of Cucurbits using pan-genome.
Sequencing watermelon reveals disease-resistance genes bred out generations ago
Researchers at the Boyce Thompson Institute in Ithaca, New York, have analyzed genomes of watermelon and its ancestors, revealing traits that early breeders may have inadvertently removed in their quest to maximize the red, sweet, watery flesh of the fruit. Their report appears in Plant Biotechnology Journal.
Super-pangenome for watermelon and its wild relatives
“The super-pangenome provides a valuable genetic toolkit for breeders and researchers to improve cultivated watermelon,” said Fei. “By understanding the genetic makeup and evolutionary patterns of watermelons, we can develop varieties with enhanced yield, increased disease resistance, and improved adaptability.”
The “super-pangenome” for watermelon and its wild relatives, the researchers hope, will uncover beneficial genes lost during domestication. Traits of interest affect seeds; rind thickness; fruit size, shape, texture, and sweetness; and improving disease resistance, which might lessen reliance on agrochemicals.
Genomics and Bioinformatics Team | 2023 Progress Report
The CucCAP Genomics and Bioinformatics Team reported on project progress and ongoing research in April 2023.
CucCAP researchers assemble genomic tools to study the development of giant pumpkin fruit
Cucurbit fruits come in different shapes and sizes, controlled by genes underlying cell size and number. In a recent study, a team at West Virginia State University (WVSU) identified genetic factors underlying the giant fruit size of the mammoth group of Cucurbita maxima. The study elucidated genome diversity and identified single nucleotide polymorphism (SNP) markers associated with genes controlling fruit size. In addition to the genomic toolkit useful for breeding programs aiming at pumpkin fruit traits, this study provides insight into population differentiation and evolutionary origins of rare variants contributing to the giant fruit size of certain pumpkin varieties.
Cucurbit Genomics Database version 2
Version 2 of the Cucurbit Genomics database (CuGenDBv2) was released in April 2022. Database users will notice improved speed and performance.The updated database includes 33 reference genomes from 26 cucurbit species/subspecies belonging to 10 different genera; novel functions for mining and analysis of large-scale variant data; and a comprehensive cucurbit expression atlas.
