Population genetics related to adaptation in elite oat germplasm

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