Association of markers with straighthead phenotype using two recombined inbred line (RIL) F₉ populations and a global germplasm collection including 72 accessions (some germplasm accessions had no parental alleles for a certain marker).

a<p>The accessions or RILs selected for marker verification were either resistant with straighthead rating 4 or below or susceptible with rating 6 or above in global germplasm collection and two F₉ populations.</p>b<p>A total of 34 accessions were selected for verification of AP3858-1 because remaining 38 had either no alleles of or different from parental Zhe733, R312, Cocodrie and Jing185, and for the same reason, 42 accessions were applied for verification of InDell 11. Hybrid genotypes were included as the resistance group since resistance was dominant over susceptibility.</p

Polymorphic SSR markers designed for fine mapping straighthead resistance QTL <i>qSH-8</i> on chromosome (chr) 8 using two recombined inbred line (RIL) F₉ populations.

<p>Polymorphic SSR markers designed for fine mapping straighthead resistance QTL <i>qSH-8</i> on chromosome (chr) 8 using two recombined inbred line (RIL) F₉ populations.</p

The structure analysis divided our population into five groups, which was validated by the principal components analysis (PCA) and cluster analysis.

<p>(A) Population structure analysis of 217 sub-core entries showing five sub-groups, the estimated membership probability listed on the y-axis and each entry represented by a thin vertical line in different color: red = ARO, <i>aromatic</i>; blue = AUS, <i>aus</i>; pink = IND, <i>indica</i>; green = TEJ, <i>temperate japonica</i> and yellow = TRJ, <i>tropical japonica</i>. (B) The spatial distribution of the entries with two dimensions in the principal components analysis (PCA). (C) The unweighted pair-group method with arithmetic mean (UPGMA) tree based on Nei's genetic distance using five sub-group partitioning.</p

QTLs identified in two recombined inbred line (RIL) F₉ populations using Qgene 4.3.8.

a<p>According to permutation function in Qgene, LOD≥2.8 was used to claim QTL associated with straighthead in Zhe733/R312 and LOD≥3.8 in Cocodrie/Jing185 using a probability level of 0.05.</p

The physical position of marker loci significantly associated with sheath blight in our study (with underlines) in comparison with previous studies.

<p>The black bars show the estimated location according to their flanking markers. The positions of marker loci were cited from the Annotated Nipponbare Sequence 2009 on Gramene (<a href="http://www.gramene.org/" target="_blank">http://www.gramene.org/</a>).</p

Recombinants identified in the target region from population Zhe733/R312 between RM6838 and RM72.

a<p>‘a’ for resistant genotype of Zhe733, ‘b’ for susceptible genotype of R312.</p>b<p>Straighthead rating using a 1–9 scale was averaged over 3 replications per year and 2 years for which the SD was estimated. Straighthead rating of 4 or below was resistant and 6 or above was susceptible.</p

Recombinants identified in the target region from population Cocodrie/Jing185 between RM22559 and RM72.

a<p>‘a’ for resistant genotype of Jing185, ‘b’ for susceptible genotype of Cocodrie.</p>b<p>Straighthead rating using a 1–9 scale was averaged over 3 replications per year and 2 years for which the SD was estimated. Straighthead rating of 4 or below was resistant and 6 or above was susceptible.</p

Fine mapping of <i>qSH-8</i> on chromosome 8 using Zhe733/R312 (A-C) and Cocodrie/Jing185 (D-F) F₉ RIL populations.

<p>Genetic distance cM is the number between markers and physical distance is placed below markers, <i>qSH-8</i> in a 1.2 cM region between RM6838 and RM72 (A), a 340 kb region between RM22573 and RM22589 (B) and a 290 kb region between RM22573 and InDel 27 (C) in Zhe733/R312; and a 2.8 cM between RM22559 and RM72 (D), a 710 kb region between AP3858-1 and RM22613 (E), and a 690 kb region between InDel 11 and RM22613 (F) in Cocodrie/Jing185.</p

Comparative analysis of different subgroups using structure (Q model) and different dimensions in principal components analysis (PCA) for association mapping of sheath blight resistance using 217 entries genotyped with 155 molecular markers.

<p>BIC: Bayesian Information Criterion (the smaller, the better); Deviance: −2log likelihood.</p

The cumulative distributions of observed -Log10(P) values before and after genomic control (GC) in PCA5 model.

<p>The genomic controlled PCA5 (PCA5+GC) model had a more uniform distribution and closer to the expected -Log10(P) values, thus greater power to control the Type I errors than PCA5.</p