Genome–wide association mapping for heading date in oats under subtropical environments

Zimmer, Cristiano Mathias; Oliveira, Guilherme; Arruda, Klever Márcio Antunes; Pacheco, Marcelo Teixeira; Federizzi, Luiz Carlos

doi:10.1590/1678-992X-2020-0355

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Genetics and Plant Breeding • Sci. agric. (Piracicaba, Braz.) 79 (3) • 2022 • https://doi.org/10.1590/1678-992X-2020-0355 copy

Genome–wide association mapping for heading date in oats under subtropical environments

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT:

Selection for heading date has been a decisive factor to increase areas cropped with oats in Brazil. Although important to oat breeders, genomic regions controlling heading date have not been completely identified. The objective of this study was to identify genomic regions controlling oat heading date in subtropical environments. A set of 412 oat genotypes, developed from 1974 to 2015, was assessed for heading date in contrasting environments and genotyped using genotyping–by–sequencing (GBS). Phenotypic and genotypic data were used in single and multi–environment association models. Quantitative trait loci (QTL) associated to heading date were identified on oat consensus groups Mrg02, Mrg05, Mrg06, Mrg12, and Mrg21. Some of the findings confirmed the association of genomic regions with heading date, while others emerge as new candidate regions associated to the trait. The genomic regions identified on Mrg02 and Mrg12 were associated to Vernalization 3 (Vrn3), while the genomic region identified on Mrg21 is associated with Vernalization 1 (Vrn1). The Vrn1 region was detected in Londrina, an environment with reduced vernalization condition, and in the multi–environment model. The results reveal that some genotypes of the panel are responsive to vernalization, increasing the days to heading without this environmental stimulus. Our results provide important contribution for a better understanding of heading date in subtropical environments and a strong basis for marker–assisted selection in oats.

Keywords:
Avena sativa L; flowering time; marker–assisted selection; quantitative trait loci

Marker	Consensus LG^‡ ‡ Based on Bekele et al. (2018).	Position^‡ ‡ Based on Bekele et al. (2018).	LON –log₁₀ (p)	ELD –log₁₀ (p)	Multi–e –log₁₀ (p)	PVE	Candidate gene	Reference
		cM				%
avgbs2_82665.2.9	Mrg02	26.8	–	–	4.81	4.17
avgbs_95303.1.18	Mrg02	33.6	5.84	–	–	5.24	Vrn3	Esvelt Klos et al. (2016)Esvelt Klos, K.; Huang, Y.F.; Bekele, W.A.; Obert, D.E.; Babiker, E.; Beattie, A.D.; Bjørnstad, Å.; Bonman, J.M.; Carson, M.L.; Chao, S.; Gnanesh, B.N.; Griffiths, I.; Harrison, S.A.; Howarth, C.J.; Hu, G.; Ibrahim, A.; Islamovic, E.; Jackson, E.W.; Jannink, J.L.; Kolb, F.L.; McMullen, M.S.; Fetch, J.M.; Murphy, J.P.; Ohm, H.W.; Rines, H.W.; Rossnagel, B.G.; Schlueter, J.A.; Sorrels, M.E.; Wight, C.P.; Yan, W.; Tinker, N.A. 2016. Population genomics related to adaptation in elite oat germplasm. Plant Genome 9: 103.
avgbs_95272.1.27	Mrg02	34.1	12.25	8.65	13.82	13.22	Vrn3	Esvelt Klos et al. (2016)Esvelt Klos, K.; Huang, Y.F.; Bekele, W.A.; Obert, D.E.; Babiker, E.; Beattie, A.D.; Bjørnstad, Å.; Bonman, J.M.; Carson, M.L.; Chao, S.; Gnanesh, B.N.; Griffiths, I.; Harrison, S.A.; Howarth, C.J.; Hu, G.; Ibrahim, A.; Islamovic, E.; Jackson, E.W.; Jannink, J.L.; Kolb, F.L.; McMullen, M.S.; Fetch, J.M.; Murphy, J.P.; Ohm, H.W.; Rines, H.W.; Rossnagel, B.G.; Schlueter, J.A.; Sorrels, M.E.; Wight, C.P.; Yan, W.; Tinker, N.A. 2016. Population genomics related to adaptation in elite oat germplasm. Plant Genome 9: 103.
avgbs2_89121.1.55	Mrg02	34.1	6.33	–	7.09	6.52	Vrn3	Esvelt Klos et al. (2016)Esvelt Klos, K.; Huang, Y.F.; Bekele, W.A.; Obert, D.E.; Babiker, E.; Beattie, A.D.; Bjørnstad, Å.; Bonman, J.M.; Carson, M.L.; Chao, S.; Gnanesh, B.N.; Griffiths, I.; Harrison, S.A.; Howarth, C.J.; Hu, G.; Ibrahim, A.; Islamovic, E.; Jackson, E.W.; Jannink, J.L.; Kolb, F.L.; McMullen, M.S.; Fetch, J.M.; Murphy, J.P.; Ohm, H.W.; Rines, H.W.; Rossnagel, B.G.; Schlueter, J.A.; Sorrels, M.E.; Wight, C.P.; Yan, W.; Tinker, N.A. 2016. Population genomics related to adaptation in elite oat germplasm. Plant Genome 9: 103.
avgbs2_17557.1.22	Mrg02	87.3	–	6.02	5.86	5.42
avgbs2_67891.1.49	Mrg02	87.3	–	–	4.82	4.19
avgbs_110804.1.56	Mrg05	56.5	5.80	6.77	6.44	6.19
avgbs_220423.1.53	Mrg06	14.5	–	–	4.54	3.90
avgbs_cluster_42139.1.55	Mrg06	63.2	–	–	4.31	3.66
avgbs2_169922.1.31	Mrg12	44.5	–	4.84	4.37	4.21	Vrn3	Nava et al. (2012)Nava, I.C.; Wight, C.P.; Pacheco, M.T.; Federizzi, L.C.; Tinker, N.A. 2012. Tagging and mapping candidate loci for vernalization and flower initiation in hexaploid oat. Molecular Breeding 30: 1295-1312.
avgbs2_71505.1.33	Mrg21	113.2	–	–	4.73	4.09	Vrn1	Maloney et al. (2011)Maloney, P.V.; Lyerly, J.H.; Wooten, D.R.; Anderson, J.M.; Livingston III, D.P.; Brown–Guedira, G.; Marshall, D.; Murphy, J.P. 2011. Marker development and quantitative trait loci in a fall-sown oat recombinant inbred population. Crop Science 51: 490-502.
avgbs_cluster_16378.1.28	Mrg21	122.8	6.01	–	4.78	5.41
avgbs2_188948.1.42	Mrg21	122.8	5.94	–	–	5.34
avgbs_119304.1.27	Mrg21	122.8	5.56	–	4.69	4.95
avgbs2_165679.1.58	Mrg21	122.8	4.46	–	–	3.81
avgbs_93789.1.22	Mrg21	122.8	4.44	–	–	3.79

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[1] *Corresponding author <federizi@ufrgs.br>