Statistical analysis of 14 traits generated at Stuttgart, Arkansas and Beaumont, Texas in 2009 in the USDA rice mini-core collection.

<p>Statistical analysis of 14 traits generated at Stuttgart, Arkansas and Beaumont, Texas in 2009 in the USDA rice mini-core collection.</p

Geographic distribution of 203 accessions based on their latitude and longitude.

<p>ARO: <i>Aromatic</i>; AUS: <i>aus</i>; IND: <i>Indica</i>; TRJ: <i>Tropical japonica</i>; TEJ: <i>Temperate japonica</i>; ARO-TEJ-TRJ: admixture of ARO with TEJ and TRJ; AUS-IND: admixture of AUS with IND; AUS-TRJ-IND: admixture of AUS with TRJ and IND; TEJ-TRJ: admixture of TEJ with TRJ and TRJ-IND: admixture of TRJ with IND. ★: Stuttgart AR, ☆: Beaumont TX.</p

Structure analysis of USDA rice mini-core collection using A: <i>STRUCTURE</i>, B: Unrooted UPMGA and C: PCA.

<p>ARO: <i>aromatic</i> in red; AUS: <i>aus</i> in green; IND: <i>Indica</i> in purple; TRJ: <i>Tropical japonica</i> in yellow; TEJ: <i>Temperate japonica</i> in blue; ARO-TEJ-TRJ: admixture of ARO with TEJ and TRJ; AUS-IND: admixture of AUS with IND; AUS-TRJ-IND: admixture of AUS with TRJ and IND; TEJ-TRJ: admixture of TRJ with TEJ; TRJ-IND: admixture of TRJ with IND.</p

Relationship map constructed by PCA for 14 traits at A: Stuttgart, AR and B: Beaumont, TX.

<p>The distance between traits is inversely proportional to the size of the correlation coefficients. <i>Solid</i> and <i>dashed lines</i> indicate positive and negative correlations, respectively. Trait names are T1:Heading; T2:Plant height; T3:Plant weight; T4:Tillers; T5:Grain yield; T6:Harvest index; T7:Panicle length; T8:Panicle branches; T9:Kernels/panicle; T10:Seed set; T11:1000 Seed weight; T12:Kernels/cm panicle; T13:Kernels/branch panicle; T14: weight/panicle. The variation explained by the principal components is showed in the brackets.</p

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

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

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

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

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