Genome-wide association analysis for lodging tolerance and plant height in a diverse European hexaploid oat collection

Sensitivity to lodging of oat varieties has been reduced in the last decades through the introduction of dwarfing genes. However, lodging may still cause significant yield loss, underscoring the need for new oat varieties with higher levels of lodging tolerance. In the present study, we analysed lodging and plant height in a collection of European oat accessions including landraces, old and modern varieties, in order to perform a genome-wide association study (GWAS) for identifying markers associated to lodging tolerance. This collection has been recently genotyped by the Infinium 6K SNP array for oat and SNP data were analysed as continuous intensity ratios, rather than as discrete genotypes (Tumino et al. 2016, Theor Appl Genet 129, pp. 1711–1724). Phenotypes for lodging severity, plant height and growth habit were collected under natural conditions in eight European countries. Plant height correlated to lodging severity as previously observed in many studies, explaining about 30% of lodging variation. GWAS analyses detected six significant associations for lodging and two for plant height. These results indicate that GWAS can successfully be used for identifying markers associated to lodging in oat, even though lodging is a quantitative trait influenced by several plant characteristics.

[1]  H. Marshall,et al.  Effects of Nitrogen Fertilizer Rate, Seeding Rate, and Row Spacing on Semidwarf and Conventional Height Spring Oat 1 , 1987 .

[2]  A. M. Stanca,et al.  Varietal Responses in Spring Barley to Natural and Artificial Lodging and to a Growth Regulator , 1979, The Journal of Agricultural Science.

[3]  J. Li,et al.  Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix , 2005, Heredity.

[4]  S. Chao,et al.  Population Structure and Genotype–Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars , 2016, Front. Plant Sci..

[5]  Steven G. Blanchard,et al.  A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement , 2016, The plant genome.

[6]  J. Holland,et al.  Quantitative Trait Loci and Epistasis for Oat Winter-Hardiness Component Traits , 2009 .

[7]  G. Scoles,et al.  An updated doubled haploid oat linkage map and QTL mapping of agronomic and grain quality traits from Canadian field trials. , 2012, Genome.

[8]  T. Langdon,et al.  High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat , 2016, Theoretical and Applied Genetics.

[9]  P. Berry,et al.  Understanding the genetic control of lodging-associated plant characters in winter wheat (Triticum aestivum L.) , 2015, Euphytica.

[10]  H. Marshall,et al.  Inheritance of Dwarfness in Three Oat Crosses and Relationship of Height to Panicle and Culm Length 1 , 1981 .

[11]  N. Tinker,et al.  A molecular linkage map with associated QTLs from a hulless × covered spring oat population , 2004, Theoretical and Applied Genetics.

[12]  A. Börner,et al.  Optimizing wheat grain yield: effects of Rht (gibberellin-insensitive) dwarfing genes , 1997, The Journal of Agricultural Science.

[13]  O. Folkerts,et al.  Gene expression profiling of two related maize inbred lines with contrasting root-lodging traits. , 2001, Journal of experimental botany.

[14]  S. Kuriyama,et al.  Transfer of new dwarfing genes from the weed species Avena fatua into cultivated oat A. byzantina , 2007 .

[15]  M. Smulders,et al.  Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios , 2016, Theoretical and Applied Genetics.

[16]  S. Salvi,et al.  Root-ABA1 QTL affects root lodging, grain yield, and other agronomic traits in maize grown under well-watered and water-stressed conditions. , 2006, Journal of experimental botany.

[17]  Tadashi Hirasawa,et al.  New approach for rice improvement using a pleiotropic QTL gene for lodging resistance and yield , 2010, Nature communications.

[18]  J. W. Pendleton.  The Effect of Lodging on Spring Oat Yields and Test Weight 1 , 1954 .

[19]  Michael Lee,et al.  QTLs and epistasis associated with vernalization responses in oat , 1997 .

[20]  Morten Lillemo,et al.  Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array , 2014, Plant biotechnology journal.

[21]  A. R. Ennos,et al.  Understanding and Reducing Lodging in Cereals , 2004 .

[22]  Weikai Yan,et al.  Population Genomics Related to Adaptation in Elite Oat Germplasm , 2016, The plant genome.

[23]  R. Phillips,et al.  Molecular genetic mapping of dwarfing genes in oat , 1997, Theoretical and Applied Genetics.

[24]  Bjarni J. Vilhjálmsson,et al.  Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines , 2010 .

[25]  M. Sorrells,et al.  Chromosomal regions associated with quantitative traits in oat , 1996 .

[26]  S. Myles,et al.  Genetic mapping in grapevine using SNP microarray intensity values , 2015, Molecular Breeding.

[27]  J. Poland,et al.  A SNP Genotyping Array for Hexaploid Oat , 2014 .

[28]  J. Valentine,et al.  Morphological and biochemical characterization of spikelet development in naked oats (Avena sativa) , 1996 .

[29]  P. Berry,et al.  Historical analysis of the effects of breeding on the height of winter wheat (Triticum aestivum) and consequences for lodging , 2014, Euphytica.

[30]  E. V. Laureles,et al.  Lodging reduces yield of rice by self-shading and reductions in canopy photosynthesis , 1997 .

[31]  S. Salvi,et al.  Characterization of root-yield-1.06, a major constitutive QTL for root and agronomic traits in maize across water regimes. , 2010, Journal of experimental botany.