Rice Science ›› 2024, Vol. 31 ›› Issue (5): 556-571.DOI: 10.1016/j.rsci.2024.06.001
收稿日期:2024-02-16
接受日期:2024-04-18
出版日期:2024-09-28
发布日期:2024-10-11
. [J]. Rice Science, 2024, 31(5): 556-571.
Fig. 1. Rice plants with high (HS) and low seed-setting rates (LS) in F5 population, as well as their parents Nipponbare and KDML105. Data are Mean ± SD (n = 48), and different lowercase letters above the bars show significant differences at P < 0.05.
Fig. 2. Microscopic analysis of anther morphology in high (HS) and low seed- setting rate (LS) lines at anthesis in F5 generation. A and B, Morphology of six mature anthers from HS (A) and LS (B) lines. Scale bars are 1 mm, and the field diameters are 6.7×. C and D, Light microscope images of an anther from HS (C) and LS (D) lines. Scale bars are 1 mm, and the field diameters are 30×. E and F, Scanning electron microscope images of an anther from HS (E) and LS (F) lines. Scale bar are 500 µm, and the field diameters are 50×. G and H, Morphology of dehisced anthers from HS (G) and LS (H) lines. Scale bars are 500 µm, and the field diameters are 50×. I and J, Dehiscence for pollen dispersal at the apical of anthers from HS (I) and LS (J) lines. Scale bars are 100 µm, and the field diameters are 300×.
Fig. 3. Filled grains and pollen fertility in high (HS) and low seed-setting rate (LS) rice lines. A and B, Filled grains in a plant (A) and a panicle (B) in HS and LS rice lines. Scale bars are 1 cm. The red arrows represent a zoom from the red square. C, Pollen stained with I2-KI solution in HS and LS rice lines. Scale bars are 200 μm. D, Pollen fertility rate of HS and LS rice lines.
Fig. 4. Pollen-stigma adhesion, pollen grain germination, and pollen tube growth of high (HS) and low seed- setting rate (LS) rice lines in vivo. A and B, Aniline blue staining of HS (A) and LS (B) pistils at 1‒2 h before flowering (BF). C and D, Aniline blue staining of HS (C) and LS (D) pistils at 1‒2 h after flowering with the pollinated state. E and F, Aniline blue staining of HS (E) and LS (F) pistils at 4‒5 h after pollination. Scale bars are 100 μm. The white arrows indicate pollen-stigma adhesion, and the red arrows indicate pollen tubes.
Fig. 5. Co-expression, hierarchical cluster analysis, and significant differentially expressed genes (DEGs) specific to high (HS) and low seed-setting rate (LS) rice lines. A, Venn diagram presenting the number of genes uniquely expressed in each sample, with overlapping regions indicating the number of genes expressed in both samples, based on a 0.5 FPKM (fragments per kilobase of transcript per million reads) threshold. B, Hierarchical clustering of genes specifically expressed in HS and LS samples based on FPKM values. Green indicates lower expression, while red indicates higher expression. Columns represent individual experiments, and rows represent genes. C, The number of up-regulated and down-regulated genes specific to HS and LS rice lines. Green and red represent up-regulated and down-regulated DEGs, respectively, and the numbers on the columns indicate the count of DEGs.
| Gene ID | Gene | Gene annotation | KEGG orthology accession | Log2(Fold change) |
|---|---|---|---|---|
| Os06g0133000 | Wx | Granule-bound starch synthase, synthesis of amylose in endosperm | K13679 | 2.32 |
| Os09g0457400 | Amy3A | Alpha-amylase isozyme 3A precursor (1,4-alpha-d-glucan glucanohydrolase) | K01176 | 2.07 |
| Os06g0185100 | Similar to estradiol 17-beta dehydrogenase 8 | K00059 | 1.94 | |
| Os11g0701100 | Similar to class III chitinase homologue | K01183 | 1.83 | |
| Os02g0467600 | Similar to cinnamate 4-hydroxylase CYP73 | K00487 | 1.82 | |
| Os03g0382100 | Thiolase-like, subgroup domain containing protein | K15397 | 1.45 | |
| Os02g0134400 | Fumarate reductase/succinate dehydrogenase flavoprotein, C-terminal domain containing protein | K00278 | -1.07 | |
| Os03g0670200 | Similar to YJR013Wp (Fragment) | K05284 | -1.20 | |
| Os03g0368900 | Haem peroxidase family protein | K00430 | -1.20 | |
| Os04g0573100 | HTH1 | Putative glucose-methanol-choline oxidoreductase, cutin biosynthesis, anther development, and pollen fertility | K07729 | -1.25 |
| Os03g0321800 | Similar to transcription factor WRKY55 | K23735 | -1.46 |
Table 1. Eleven high seed-setting rate (HS)-specific differentially expressed genes assigned to metabolic pathways using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database.
| Gene ID | Gene | Gene annotation | KEGG orthology accession | Log2(Fold change) |
|---|---|---|---|---|
| Os06g0133000 | Wx | Granule-bound starch synthase, synthesis of amylose in endosperm | K13679 | 2.32 |
| Os09g0457400 | Amy3A | Alpha-amylase isozyme 3A precursor (1,4-alpha-d-glucan glucanohydrolase) | K01176 | 2.07 |
| Os06g0185100 | Similar to estradiol 17-beta dehydrogenase 8 | K00059 | 1.94 | |
| Os11g0701100 | Similar to class III chitinase homologue | K01183 | 1.83 | |
| Os02g0467600 | Similar to cinnamate 4-hydroxylase CYP73 | K00487 | 1.82 | |
| Os03g0382100 | Thiolase-like, subgroup domain containing protein | K15397 | 1.45 | |
| Os02g0134400 | Fumarate reductase/succinate dehydrogenase flavoprotein, C-terminal domain containing protein | K00278 | -1.07 | |
| Os03g0670200 | Similar to YJR013Wp (Fragment) | K05284 | -1.20 | |
| Os03g0368900 | Haem peroxidase family protein | K00430 | -1.20 | |
| Os04g0573100 | HTH1 | Putative glucose-methanol-choline oxidoreductase, cutin biosynthesis, anther development, and pollen fertility | K07729 | -1.25 |
| Os03g0321800 | Similar to transcription factor WRKY55 | K23735 | -1.46 |
Fig. 6. Expression analysis of high (HS)- and low seed-setting rate (LS)-specific differentially expressed genes (DEGs) before and after pollination by qRT-PCR. A‒C, Relative expression levels of Os02g0467600 (A), Os12g0563700 (B), and Os06g0583900 (C). The relative expression values were normalized to the rice UBQ5 gene (OsUBQ5). The results were obtained from two biological replicates. Error bars indicate standard deviation.
| Gene ID | Gene | Gene annotation | KEGG orthology accession | Log2(Fold change) |
|---|---|---|---|---|
| Pentose and glucuronate interconversion pathway | ||||
| Os03g0300500 | OsPME10 | Pectin methylesterase 10 | K01051 | 1.43 |
| Os12g0563700 | OsPME35 | Pectin lyase fold domain-containing protein | K01051 | 1.13 |
| Os02g0214400 | OsPLL3 | Pectate lyase-like protein | K01728 | 1.21 |
| Os06g0583900 | OsPLL9 | Pectate lyase | K01728 | 1.30 |
| Flavonoid biosynthesis pathway | ||||
| Os02g0767300 | Flavonol synthase/flavanone 3-hydroxylase | K05278 | -1.34 | |
| Os04g0101400 | Flavone synthase II, biosynthesis of tricin O-linked conjugate | K23180 | -1.73 | |
Table 2. Highest fold enrichment of low seed-setting rate (LS)-specific differentially expressed genes (DEGs) in pentose and glucuronate interconversion and flavonoid biosynthesis pathways.
| Gene ID | Gene | Gene annotation | KEGG orthology accession | Log2(Fold change) |
|---|---|---|---|---|
| Pentose and glucuronate interconversion pathway | ||||
| Os03g0300500 | OsPME10 | Pectin methylesterase 10 | K01051 | 1.43 |
| Os12g0563700 | OsPME35 | Pectin lyase fold domain-containing protein | K01051 | 1.13 |
| Os02g0214400 | OsPLL3 | Pectate lyase-like protein | K01728 | 1.21 |
| Os06g0583900 | OsPLL9 | Pectate lyase | K01728 | 1.30 |
| Flavonoid biosynthesis pathway | ||||
| Os02g0767300 | Flavonol synthase/flavanone 3-hydroxylase | K05278 | -1.34 | |
| Os04g0101400 | Flavone synthase II, biosynthesis of tricin O-linked conjugate | K23180 | -1.73 | |
Fig. 7. Physical maps showing co-localization of dominant enrichment genes specific to high (HS) and low seed-setting rates (LS) with previously identified QTLs/genes involved in spikelet fertility. The previously identified QTLs and functional genes involved in spikelet fertility, pollen growth, and yield components are labeled in blue, and the dominant enrichment differentially expressed genes specific to HS and LS are labeled in black and red, respectively.
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