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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Sunflower and Plant Biology Research » Research » Publications at this Location » Publication #368539

Research Project: Novel Weed Management Solutions: Understanding Weed-Crop Interactions in Northern Climates

Location: Sunflower and Plant Biology Research

Title: A new diversity panel for winter rapeseed (Brassica napus, L.) genome wide association studies

item Horvath, David
item STAMM, MICHAEL - Kansas State University
item TALUKDER, ZAHIRUL - North Dakota State University
item Fiedler, Jason
item HORVATH, AIDAN - University Of Michigan
item HORVATH, GREGOR - Purdue University
item Chao, Wun
item Anderson, James

Submitted to: Agronomy Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/14/2020
Publication Date: 12/20/2020
Citation: Horvath, D.P., Stamm, M., Talukder, Z., Fiedler, J.D., Horvath, A., Horvath, G., Chao, W.S., Anderson, J.V. 2020. A new diversity panel for winter rapeseed (Brassica napus, L.) genome wide association studies. Agronomy Journal. 10(12):2006.

Interpretive Summary: Statistically associating genetic differences with how a plant looks or changes after a treatment is powerful way to identify genes that control plant growth and stress responses. Once plant and genetic database resources are developed for such association studies, they can easily be used by others for many different research projects. ARS scientists in Fargo, ND, successfully developed resources for a set of 429 varieties of winter canola– an important oil seed crop in the midwestern US and around the world. The resource was validated by identifying genes that control the speed of flowering in winter canola. Both the seedstock and the genetic database from this set of plants are now available to researchers studying agronomically important traits of winter canola.

Technical Abstract: A diverse population (429 member) of canola (Brassica napus, L.) consisting primarily of winter biotypes was assembled and used in genome-wide association studies. Genotyping-by-sequencing analysis of the population identified and mapped 290,972 high quality markers ranging from 18.5-82.4% missing markers per line and an average of 36.8%. After interpolation, 251,575 high quality markers remained. The average distance between these markers is 3,377 bases with a median of 53 and a range from 1 to 198358 bases. The heterozygosity among the interpolated population ranges from 0.9-11.0% with an average of 5.4%. This information was used to determine population structure and kinship, which indicated a fairly unstructured population with the best K value of 6. These results indicate the majority of the population have substantial sequence from a single genotype with sub-clusters of, and admixtures with several other populations. A phylogenetic relationship based on kinship indicated a relatively diverse phylogeny with many equally distant sub-clusters. Linkage disequilibrium decay was estimated to occur over a very short distance within a range from 1 to ~300K bases. Analysis of chromosomal linkage disequilibrium decay ranged from ~2.5 Kb for Chrm A01 to ~30 Kb for Chrm C01. This population was used to identify loci associated with flowering time that revealed 14 different associated loci with numerous potential candidate genes with known or suspected roles in floral regulation.