Additional file 2 of Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture
Creators: name: Adam, Hélène
name: Gutiérrez, Andrés
name: Couderc, Marie
name: Sabot, François
name: Ntakirutimana, Fabrice
name: Serret, Julien
name: Orjuela, Julie
name: Tregear, James
name: Jouannic, Stefan
name: Lorieux, Mathias
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. CSSL Finder screenshots showing graphical representations of the genotypes of the 60 BC3DH lines along with corresponding data for each evaluated panicle trait across the two repetitions together and for each repetition separated (rep1 and rep2). (a) RL, Rachis Length; (b) SBN/PBN, Secondary Branch Number per Primary Branch; (c) SpN. Spikelet Number; (d) PBN, Primary Branch Number; (e) PBL, Primary Branch Length; (f) TBN, Tertiary Branch Number.. The 12 chromosomes are displayed vertically. They are covered by 200 evenly dispersed SSR markers. The genotypes of the individual lines are displayed horizontally. Shading indicates the allelic composition of chromosomes. Light gray areas represent the Os_Caiapó genetic background, black areas represent the Og_MG12 chromosome segments, dark gray areas represent the heterozygous segments and blue areas correspond to missing data. On the right, solid color bars indicate the values of the panicle traits tested for each line. At the bottom of each graph, the dotted line indicates the statistical threshold of the F-test for the evaluated panicle trait. Figure S2. Graphic representation of the genotypes of the 60 BC3DH CSSLs, showing line x trait significant associations and QTL positions. The 12 chromosomes are covered by 200 evenly dispersed SSR markers. Genotypes are displayed horizontally. Black areas represent the O. glaberrima MG12 target chromosome segments, the set of segments broadly covering the entire O. glaberrima MG12 genome. White areas represent the O. sativa Caiapó genetic background and grey areas represent O. glaberrima additional chromosomal segments. Phenotypic effects of CSSL lines are represented in relative terms as circles on the right of the figure. The area of each circle is proportional to its relative effect. Horizontal bars at the bottom of the figure indicate QTL positions deduced from analyses performed using CSSL finder software. The colors of the circles and bars represent the effect as follows: red, increasing effect compared to the recurrent parent Os_Caiapó; green; decreasing effect. Figure S3. Genetic and phenotypic description of CSSLs showing the extreme significant differences for the panicle trait analyzed (A) SBN/PBN, (B) SpN, (C) PBN, (D) PBL and (E) TBN. Upper subpanel: Chromosome graphical representation of Og_MG12 introgression positions in the CSSL. Position of the SSR markers is indicated in Mbp. Lower subpanel: boxplots of the phenotypic variation observed in Year 1 and Year 2 in these lines. Each point represents the phenotypic value for one panicle. Statistical significance (t-test p-values) between Os_Caiapó and each line for the panicle morphological trait is indicated as follows: NS if the test is non-significant; *p-values &lt; 0.05; **&lt;0.01; ***&lt;0.001. Abbreviations: PBN, primary branch number; PBL, primary branch length; TBN, tertiary branch number; SBN/PBN, ratio between secondary branch and primary branch numbers; SpN, Spikelet number. Figure S4. Phenotypic description of BC4 lines to dissect the effects of QTLs on panicle traits. Boxplot of the phenotypic variation observed in Os_Caiapó (yellow), Og_MG12 (green), and BC4 (blue) lines in greenhouse (2021). Each point represents the phenotypic value for one panicle. Statistical significance (t-test p-values) between Os_Caiapó and each line for the panicle morphological traits is indicated as follows: ** p-values &lt;0.01; ***&lt;0.001. Abbreviations: PBN, primary branch number; PBL, primary branch length; TBN, tertiary branch number; SBN/PBN, ratio between secondary branch and primary branch numbers; SpN, spikelet number. Figure S5. Dotplots of the minimap2 alignment (implemented in D-GENIES web facilities) of panicle trait-related QTLs detected between the Os_Caiapó and Og_MG12 genomes and between each of the latter aligned against O. sativa cv. Nipponbare as a reference genome. QTL coordinates in each genome are indicated on axis X and Y. Dot colors are relative to the identity value (I) which is a BLAST-like alignment identity (I=Number of bases, including gaps per number of matching bases in the bases). Figure S6. Physical map positions of detected QTLs and colocalizations with known genes related to branching and flowering.