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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #314741

Title: Population genetics related to adaptation in elite oat germplasm

item Esvelt Klos, Kathy
item HUANG, YUNG-FEN - National Taiwan University
item Babiker, Ebrahiem
item BEATTIE, AARON - University Of Saskatchewan
item BEKELE, WUBISHET - Agriculture And Agri-Food Canada
item BJORNSTAD, ASMUND - Norwegian University Of Life Sciences
item Bonman, John
item CARSON, MARTIN - Retired ARS Employee
item Chao, Shiaoman
item GNANESH, BELAGHIHALLI - Agriculture And Agri-Food Canada
item HARRISON, STEVE - Louisiana State University
item HOWARTH, CATHERINE - Aberystwyth University
item Hu, Gongshe
item IBRAHIM, AMIR - Texas A&M University
item ISLAMOVIC, EMIR - Basf Corporation North America
item JACKSON, ERIC - General Mills, Inc
item Jannink, Jean-Luc
item KOLB, FREDERIC - University Of Illinois
item MCMULLEN, MICHAEL - North Dakota State University
item FETCH, JENNIFER - Agriculture And Agri-Food Canada
item MURPHY, J. PAUL - North Carolina State University
item OBERT, DON - Limagrain Cereal Seeds
item OHM, HERBERT - Purdue University
item RINES, HOWARD - University Of Minnesota
item ROSSNAGEL, BRIAN - University Of Saskatchewan
item SCHULETER, JESSICA - University Of North Carolina
item WIGHT, CHARLENE - Agriculture And Agri-Food Canada
item YAN, WEIKAI - Agriculture And Agri-Food Canada
item TINKER, NICHOLAS - Agriculture And Agri-Food Canada

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/7/2016
Publication Date: 7/7/2016
Citation: Esvelt Klos, K.L., Huang, Y., Babiker, E.M., Beattie, A., Bekele, W.A., Bjornstad, A., Bonman, J.M., Carson, M.L., Chao, S., Gnanesh, B.N., Harrison, S.A., Howarth, C.J., Hu, G., Ibrahim, A., Islamovic, E., Jackson, E.W., Jannink, J., Kolb, F.L., Mcmullen, M.S., Fetch, J.M., Murphy, J., Obert, D.E., Ohm, H.W., Rines, H.W., Rossnagel, B., Schuleter, J.A., Wight, C.P., Yan, W., Tinker, N.A. 2016. Population genetics related to adaptation in elite oat germplasm. The Plant Genome. 9(2):1-12. doi: 10.3835/plantgenome2015.10.0103.

Interpretive Summary: The use of advanced genomic technologies is critical to meeting the needs of oat producers for high-yielding, high-quality oat varieties. Molecular genetic markers are one such technology, tools for which have been developed in this study. Characteristics of the genetic diversity, population structure and linkage disequilibrium of elite oat lines are described and evaluated. Genome-wide association analysis was used to find several regions of the genome containing genes that contribute to the regional adaptation of oat varieties. The genomics tools developed here will be used to speed up the development of new oat varieties.

Technical Abstract: Six hundred thirty five oat lines and 2,635 SNP loci were used to evaluate population structure, linkage disequilibrium (LD) and genotype-phenotype association with heading date. The first five principal components (PC) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PC nor the cross-validation errors from K=1 to 20 model-based analyses suggested a structured population. However, the PC and K=2 model-based analyses supported clustering of lines on spring oat vs. southern U.S. origin, accounting for 16% of genetic variation (p<0.0001). Single-locus FST in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of r2=0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring sub-population. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location/years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24