36th International Carrot Conference Abstract

Utilizing Genotyping by Sequencing to identify candidate genes underlying domestication traits in carrot (Daucus carota L.)

Shelby Ellison¹, Massimo Iorizzo¹, Phil Simon², Doug Senalik²

¹University of Wisconsin-Madison Department of Horticulture; ²USDA Vegetable Crops Research Unit

Domestication of carrots as a root crop (Daucus carota L.) began in Central Asia over 1,000 years ago. Several traits associated with the domestication syndrome of carrot include increased pigment (carotenoid and anthocyanin) and sugar accumulation, decreased lateral root formation and reduced bolting. With the exception of the Rs locus controlling sugar accumulation and type, very little is known about the genetic loci controlling these aforementioned traits. The focus of this work was to use a Genotyping by Sequencing (GBS) approach to identify the location of candidate genes underlying two domestication traits: 1) carotenoid accumulation and 2) reduced lateral root formation. Previously an advanced inbred (F₄) population, segregating for both traits, was developed from a cross between a white-branched wild carrot (Queen Anne’s lace - QAL) and a smooth-orange USDA inbred line (B493). The population, comprising 174 carrot roots, was grown in Hancock, WI over the summer of 2012 and later phenotyped for carotenoid content using visual assessment and High Performance Liquid Chromatography (HPLC). Additionally, a novel scale and procedure was developed for scoring lateral root prominence. DNA from the carrot roots was extracted and used to genotype the population using the GBS platform. 2688 non-overlapping SNPs were aligned to the draft carrot genome assembly and used to identify genome-wide associations for the traits of interest. A 450 kb region of the genome, containing the Y₂ locus, was flanked by two of the most significant markers for carotenoid accumulation whereas two regions of the genome were identified to contain significant marker associations for lateral root development. We are currently analyzing the data of an RNA-Sequencing experiment to identify genes that are differentially expressed within these regions as well as throughout the genome. Together these experiments will be used to locate candidate genes for two agronomically important domestication traits. Further, the molecular markers developed in this project will facilitate rapid genotypic screening for carrot population improvement within the breeding program.

Last updated Thursday, 25-Jul-2013 12:24:25 CDT