Genotyping Brassica Accessions Using SNP Array

Genomic DNA was extracted from the bulked young leaves of 24 plants of each genotype using the TIANGEN^® plant genomic extraction kit (DP305-03) (Beijing, China). Accessions were genotyped using the Brassica 60K Illumina Infinium^® SNP array (Edwards et al., 2013 (link)), according to the Infinium^® HD Assay Ultra Protocol Guide. Using a local BLASTn search, the SNPs of the array were aligned to the B. napus reference genome assembly v4.1 (Chalhoub et al., 2014 (link)). Only the top BLAST hits against the reference genome were considered, allowing no less than 50 bp overlap, 90% sequence identity, and no gaps (Clarke et al., 2016 (link)).

Free full text: Click here

Wei D., Cui Y., He Y., Xiong Q., Qian L., Tong C., Lu G., Ding Y., Li J., Jung C, & Qian W. (2017). A genome-wide survey with different rapeseed ecotypes uncovers footprints of domestication and breeding. Journal of Experimental Botany, 68(17), 4791-4801.

Publication 2017

Brassica 60K Illumina Infinium® SNP array

Assay Brassica Genome No bp Plant Snps

Corresponding Organization : Southwest University

Other organizations : University of Giessen, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Kiel University

Top 5 similar protocols

Variable analysis

independent variables

Genotype

dependent variables

Genotype

control variables

Genomic DNA extraction method (TIANGEN® plant genomic extraction kit (DP305-03))
Genotyping method (Brassica 60K Illumina Infinium® SNP array)
Sequence alignment parameters (top BLAST hits against the reference genome with at least 50 bp overlap, 90% sequence identity, and no gaps)

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!