Location: Plant Genetic Resources
2012 Annual Report
One hundred and twenty one SSR markers will be used to screen accessions at the seedling stage. These SSR markers have amplified at least one band when screening the parents of our F2:3 broccoli population. An initial screening set of 16 accessions will be utilized to detect amplification and polymorphisms on agarose gels using unlabeled primers. A set of 25 to 30 markers will be chosen on the basis of this initial screen for analysis of the 400 accessions.
Primers (25-30) displaying the greatest degree of polymorphisms during initial screening will be used to genotype all 400 lines. A similarity matrix will be generated with Jaccards coefficient, (Sij) using the software package NTsys. A dendogram will be generated from the similarity matrix using the average unweighted group mean (UGMA) and principle component analysis (PCA) estimates will also be generated from the same program. Population genetic substructure will be estimated using the program STUCTURE 2.1 that utilizes a Bayesian algorithm to assign accessions to putative sub-populations (k) in Hardy-Weinberg equilibrium and can provide an estimate of the degree of admixture of the accessions that can be utilized as a matrix of co-factors in structured association programs.
In addition to genotyping cabbage accessions using SSR markers, we had the opportunity to transplant a subset of the accessions (100 accessions) in the field of Piedmont Research Station located at Salisbury, NC. This allowed us to take some phenotypic observations on the plant growth and head formation and color. Some of the accessions showed to flower with no head formation (PI 176440). With accessions that formed heads, head size varied from 2661g ( PI 214148) to 238g (PI 343520). The head shape and compactness also varied ranging from very loose (PI 1518837) to mostly compact (most of the accessions tested). Some of the accessions had formed good flat head (1800g) such as PI 419104, while others had cone-shaped heads (290g) such as PI 343610. Most of other tested accessions showed a normal cabbage head shape. Though this was not included in the agreement, samples were collected from cabbage heads and lyophilized for further analyses including phytochemical contents such as glucosinolates, carotenoids, and flavonoids. This phenotypic evaluation will be conducted after all SSR genotyping is complete, and will provide the USDA with this data to aid in selection for certain genotypes with specific phytonutrient profile later. We are glad to have the opportunity to genotype and evaluate such large number of cabbage accessions provided by the USDA at Geneva, NY, and hope information generated from this project will aid in selecting accessions with the potential to be used successfully in a breeding program that can result in improved cabbage lines.