Additional file 1 of Characterization of the ‘Oat-Like Rice’ Caused by a Novel Allele OsMADS1Olr Reveals Vital Importance of OsMADS1 in Regulating Grain Shape in Oryza sativa L.
Creators: name: Li, Penghui
name: Li, Hui
name: Liu, Zhijian
name: Zhuang, Yong
name: Wei, Ming
name: Gu, Yuanyang
name: Liu, Yangxuan
name: Sun, Xiuqiang
name: Tang, Yuying
name: Yue, Lu
name: Lu, Longxiang
name: Luo, Dagang
name: Huang, Weizao
name: Tu, Shengbin
name: Wang, Songhu
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Morphologies of NIP and Oat-like rice at maturation stage. Figure S2. Grain shape (a) and grain length (b) of 23 representative rice varieties or accessions from 15 countries in the world in comparison with that of Oat-like rice. Bar: (a) 5 mm. Figure S3. Variation in floral organ numbers, morphologies and structures of Oat-like rice. Figure S4. Sequence alignment of exon 1 of the OsMADS1Olr or OsMADS1 gene among Oat-like rice and representatively normal rice varieties. Figure S5. Protein sequence alignment of the MADS domain among OsMADS1Olr or OsMADS1 and other MADS-Box family members in rice. Figure S6. Abnormal spikelet phenotypes of OsMADS1Olr-overexpressing plants in comparison with the wild-type plants. Figure S7. Abnormal spikelet phenotypes of OsMADS1-RNAi plants in comparison with the wild-type plants. Figure S8. Tissue-specific expression pattern of OsMADS1 (a and c) and OsTip3 (b and d), respectively. a and b Expression pattern of OsMADS1 (a) and OsTip3 (b) in various vegetative, reproductive tissues &amp; organs, and seeds according to the microarray data released in the ePlant Rice database ( http://bar.utoronto.ca/eplant_rice/ ). Color scale represents microarray signal level. P1: 0–3 cm inflorescence, floral transition and floral organ development; P2 and P3: 3–10 cm inflorescence, meiotic stage; P4: 10–15 cm inflorescence, young microspore stage; P5: 15–22 cm inflorescence, vacuolated pollen stage; P6: 22–30 cm inflorescence, mature pollen stage; Seed S1: 0–2 DAP, early globular embryo; Seed S2: 3–4 DAP, middle and late globular embryo; Seed S3: 5–10 DAP, embryo morphogenesis; Seed S4: 11–20 DAP, embryo maturation; Seed S5: 21–29 DAP, dormancy and desiccation tolerance; DAP: Days After Pollination; SAM: Shoot Apical Meristems. c and d Expression pattern of OsMADS1 (c) and OsTip3 (d) in various vegetative, reproductive tissues &amp; organs, in addition to ovary, embryo and endosperm of seeds during different developmental stages according to the microarray data released in the Rice Expression Profile Database (RiceXPro) ( https://ricexpro.dna.affrc.go.jp/category-select.php ). The numbers 10,301 (c) and 02686 (d) indicate feature numbers of expression pattern of OsMADS1 and OsTip3 by using the corresponding probe, S-8726 (c) and S-2143 (d), respectively; DAF: Days After Fertilization. OsMADS1 is expressed in inflorescences, spikelets, floral organs and seeds (a and c), and OsTip3 is specifically expressed in seeds (b and d). Figure S9. Normal spikelet phenotypes of T0 pOsTip3::OsMADS1-RNAi plants (T3-Ri-6 (T0), T3-Ri-3 (T0), T3-Ri-4 (T0) and T3-Ri-7 (T0)) in comparison with wild-type (NIP). a-o Phenotypic analysis of spikelets and floral organs of NIP (a-c) and pOsTip3::OsMADS1-RNAi plants (d-o) by stereomicroscope. a, d, g, j and m A normal spikelet of NIP (a), T3-Ri-6 (T0) (d), T3-Ri-3 (T0) (g), T3-Ri-4 (T0) (j) and T3-Ri-7 (T0) (m). b, e, h, k and n A normal and dissected spikelet of NIP (b), T3-Ri-6 (T0) (e), T3-Ri-3 (T0) (h), T3-Ri-4 (T0) (k) and T3-Ri-7 (T0) (n) in which a lemma and a palea were ripped off, consisting of a pair of empty glumes, a pair of lodicules, six stamens and a pistil. c, f, i, l and o A normal pistil from a spikelet of NIP (c), T3-Ri-6 (T0) (f), T3-Ri-3 (T0) (i), T3-Ri-4 (T0) (l) and T3-Ri-7 (T0) (o) consists of an ovary and a pair of stigmas. eg, empty glume; le, lemma; pa, palea; lo, lodicule; st, stamen; pi, pistil; sti, stigma; ov, ovary. Bars: (a-o) 1 mm. Figure S10. Grain shape and relative expression of OsMADS1 in 12 DAF grains of T0 pOsTip3::OsMADS1-RNAi plants (T3-Ri-6 (T0), T3-Ri-3 (T0), T3-Ri-4 (T0) and T3-Ri-7 (T0)) in comparison with wild-type (NIP). a-d Grain shape and phenotypes of T0 pOsTip3::OsMADS1-RNAi plants (T3-Ri-6 (T0) (a), T3-Ri-3 (T0) (b), T3-Ri-4 (T0) (c) and T3-Ri-7 (T0) (d)) in comparison with NIP. e Relative expression of OsMADS1 in 12 DAF grains of wild-type and T0 pOsTip3::OsMADS1-RNAi plants (T3-Ri-6 (T0), T3-Ri-3 (T0), T3-Ri-4 (T0) and T3-Ri-7 (T0)). The value of OsActin mRNA was used as an internal control for data normalization, and the expression level of OsMADS1 in (NIP) were set as 1.0. DAF, Days After Fertilization. Values are means ± SDs of three replicates. Student’s t-test: *p &lt; 0.05; ***p &lt; 0.001. Bars: (a-d) 5 mm. Figure S11. Grain shape and phenotypes of T2 pOsTip3::OsMADS1-RNAi lines (T3-Ri-5, T3-Ri-9 and T3-Ri-12) in comparison with grains of the negative control (NC) line, which shows the backside view of the grains shown in Fig. 11a. Figure S12. Schematic diagrams of the transgenic vectors. Table S1. Major agronomic traits of NIP and Oat-like rice. Table S2. Statistical analysis of variation in floral organ numbers of Oat-like rice. Table S3. Segregation analysis of F2 population derived from a cross combination between Oat-like rice and NIP. Table S4. PCR-based SSR and InDel molecular makers used and developed for fine mapping of the OsMADS1Olr gene in rice. Table S5. Primers used for RT-PCR amplification and cDNA sequencing analysis of OsMADS1 and OsMADS1Olr. Table S6. Primers used for qRT-PCR analysis. Table S7. Primers developed for vector construction.