Additional file 1 of Uncovering the genetic mechanisms regulating panicle architecture in rice with GPWAS and GWAS
Creators: name: Zhong, Hua
name: Liu, Shuai
name: Meng, Xiaoxi
name: Sun, Tong
name: Deng, Yujuan
name: Kong, Weilong
name: Peng, Zhaohua
name: Li, Yangsheng
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. The kinship plot of 406 accessions from RDP1. Figure S2. The distribution of SNP numbers in genes. Figure S3. Genome-wide association analysis for total spikelets number per panicle (TSNP) with general linear model (GLM), mixed linear models (MLM), Fixed and random model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) methods (left). Quantile-quantile plot of each model (right). Red texts indicate reported genes, blue texts indicate candidate genes. The horizontal solid red line indicates the Bonferroni-corrected significance threshold at -log10(P) = 6.91. Figure S4. Genome-wide association analysis for grain number per panicle (GNP) with general linear model (GLM), mixed linear models (MLM), Fixed and random model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) methods (left). Red texts indicate reported genes. The horizontal solid red line indicates the Bonferroni-corrected significance threshold and -log10(P) = 6.91. Figure S5. Genome-wide association analysis for EGNP with general linear model (GLM), mixed linear models (MLM), Fixed and random model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) methods (left). Quantile-quantile plot of each model (right). Red texts indicate reported genes. The horizontal solid red line indicates the Bonferroni-corrected significance threshold at -log10(P) = 6.91. Figure S6. Genome-wide association analysis for PBN with general linear model (GLM), mixed linear models (MLM), Fixed and random model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) methods (left). Quantile-quantile plot of each model (right). Red texts indicate reported genes. The horizontal solid red line indicates the Bonferroni-corrected significance threshold at -log10(P) = 6.91. Figure S7. Genome-wide association analysis for PL with general linear model (GLM), mixed linear models (MLM), Fixed and random model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) methods (left). Quantile-quantile plot of each model (right). Red texts indicate reported genes. The horizontal solid red line indicates the Bonferroni-corrected significance threshold at -log10(P) = 6.91. Figure S8. Genome-wide association analysis for PN with general linear model (GLM), mixed linear models (MLM), Fixed and random model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) methods (left). Quantile-quantile plot of each model (right). Red texts indicate reported genes. The horizontal solid red line indicates the Bonferroni-corrected significance threshold at -log10(P) = 6.91. Figure S9. Expression pattern of Os01g0140100 in different tissues. Anther: Anther; Embryo-25 DAP: Embryo 25 Days After Pollination; Endosperm-25 DAP: Endosperm 25 Days After Pollination; Leaves-20 days: 20 Day Leaves; Pistil: Pistil; Pre-emergence inflorescence: Early Inflorescence; Post-emergence inflorescence: Emerging Inflorescence; Seed-5 DAP: Seed 5 Days After Pollination; Seed-10 DAP: Seed 10 Days After Pollination.