Scientia Agricultura Sinica ›› 2025, Vol. 58 ›› Issue (11): 2062-2080.doi: 10.3864/j.issn.0578-1752.2025.11.002

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Map-Based Cloning and Functional Verification of A Novel Split Glume Gene OsSG2 in Rice (Oryza sativa L.)

ZENG YueHui1,2(), ZOU WenGuang2,3(), ZHAO FuMing1,2, XIAO ChangChun1,2, HUANG JianHong1,2, MA BinLin2,3, YANG WangXing2,3, WEI XinYu1,2(), XU XuMing2,3()   

  1. 1 Biotechnology Research Institute, Sanming Academy of Agricultural Sciences, Sanming 365500, Fujian
    2 Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountainous Areas, Sanming 365500, Fujian
    3 Rice Research Institute, Sanming Academy of Agricultural Sciences, Sanming 365500, Fujian
  • Received:2024-11-20 Accepted:2024-12-19 Online:2025-06-01 Published:2025-06-09
  • Contact: WEI XinYu, XU XuMing

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Abstract:

【Objective】 The sg2 (split glume 2) is a naturally occurring rice mutant derived from an advanced-generation breeding population of the restorer line GK1327 originating from the Sanming Academy of Agricultural Sciences (SAAS). In this work, the OsSG2 (Oryza sativa Split Glume 2) gene in the mutant was performed to conduct genetic analysis, map-based cloning and functional verification, which will provide a theoretical basis and an important germplasm resource for further study on the function of OsSG2 in the development of rice floral organs.【Method】 The morphological characteristics of the sg2 mutant florets were anatomically observed to analyze the features of floral organ development. By investigating the phenotypic and agronomic characteristics of wild-type GK1327 and sg2 mutant, and observing the pollen staining in I2-KI, the effects of the mutant phenotype on yield-related traits and pollen fertility were analyzed. The F2 populations developed by crossing sg2 mutant with wild-type GK1327 and 9311, respectively, were used to perform genetic analysis and physical mapping of the OsSG2. Bulked segregant analysis (BSA) combined with next-generation sequencing (NGS) technology (BSA-seq) was used to screen the candidate genes of OsSG2, and a combination of RT-PCR (reverse-transcription PCR) and qRT-PCR (quantitative real-time PCR) was performed to analyze their expression patterns. The OsSG2 candidate genes were cloned and sequenced by PCR amplification and sequencing approaches, and the functional verification was conducted by knockout using CRISPR-cas9 and a complementation test.【Result】 The sg2 mutant exhibited an abnormal spikelet phenotype at the reproductive stage, the palea and lemma of florets were weak, distorted, and dehiscent, and with the proportion of abnormal florets in the panicles were 100%. Compared with the wild-type GK1327, the seed setting rate, the 1000-grain weight, and the seed germination rate of sg2 mutant were markedly lower, whereas the pollen fertility was normal. Genetic analysis demonstrated that a recessive nuclear gene was responsible for the mutant phenotype of sg2. A map-based cloning strategy delimited OsSG2 to a 919.85 kb physical interval on the short arm of chromosome 3, flanked by two InDel (insertion/deletion) markers, InDel-12083 and InDel-17610, that included 75 putative ORFs (open read frames). Moreover, a BSA-seq technology identified a potential candidate gene LOC_Os03g11614 as the OsSG2 gene, which encodes an OsMADS1 transcription factor localized to the nucleus. Expression and sequence analyses revealed that the transcript levels of LOC_Os03g11614 were markedly lower in young panicles of the sg2 mutant compared with those in the wild-type GK1327 during the flowering stage, and a SNP (single nucleotide polymorphism) mutation (G-A) was identified at the third nucleotide position of exon 1 in the LOC_Os03g11614, resulting in the change of the start codon from ATG to ATA, which caused a transcriptional suppression of LOC_Os03g11614 and a functional loss of the OsMADS1 protein. These results further supported the tentative identification of LOC_Os03g11614 as the candidate OsSG2 gene, which was confirmed by knockout using CRISPR-cas9 and a functional complementation test.【Conclusion】 The split glume gene OsSG2, which was successfully isolated from sg2 mutant in this work, was identified as a new allele of OsMADS1 in rice.

Key words: rice (Oryza sativa L.), floral organ, OsSG2, map-based cloning, gene editing, OsMADS1

Fig. 1

Phenotypic and agronomic characteristics of wild-type and sg2 mutant plants A: Phenotype of WT and sg2 individual plant during the filling stage, Bar=10 cm; B and C: Phenotype of WT and sg2 mutant panicle during the filling stage, Bar=5 cm, where Figure C is the magnified map of the area of sg2 mutant panicle in Fig.B, Bar=2 cm; D: Phenotype of floral organs of sg2 mutant during flowering stage, Bar=1 cm; E: Anatomic structure of sg2 floral organs, Bar=1 cm; F and G: Phenotype of WT and sg2 mutant grains during the filling stage (F, Bar=1 cm) and the mature stage (G, Bar=1 cm), respectively; H-J: Seed-setting rate (H), 1000-grain weight (I), and Germination rate of seeds (J) of WT and sg2 mutant; K: I2-KI staining identification of pollen fertility of WT and sg2 mutant, Bar=1mm. le:Lemma; pa: Palea; st: Stamen; pi: Pistil; sl: Sterile lemma; WT: Wild-type GK1327.**: P<0.01. The same as below"

Table 1

Segregation analysis of sg2 crosses"

杂交组合
Cross combinations		 F2表型F2 phenotype χ2 χ20.05 P
分离群体 Segregation population 野生型 WT 突变型 Mutant type
sg2×WT 1136 863 273 0.565 3.84 0.8513
sg2×9311 1448 1091 357 0.092 3.84 0.9741
9311×sg2 1040 798 243 1.661 3.84 0.7175

Table 2

Sequences of primers used in this study"

引物名称
Primer name		 正向引物
Forward primer (5′-3′)		 反向引物
Reverse primer (5′-3′)		 用途
Usage
Rm14462 TCTGTATTCAAGGAGGGCTAGATGC GCTGGAGAGATGCATTGACTGG OsSG2初步定位
Preliminary mapping for OsSG2
Rm3392 AGCAACCAACCCAGTAGTTAGCC GCTCATTTGCATGCTGTGTTAGC
Rm14722 ACACACCACATTGTTGGCATTGG TGGTGGGAGGAAGATTTCAGTGG
Rm14728 CTCAGCGGACTAGAATGCAAGC AAACGGATACATCTTCGCAGAACG
Rm7 TTCGCCATGAAGTCTCTCG CCTCCCATCATTTCGTTGTT
InDel-2923 GCCTAAATTTGCAGTGATGTG TACCAGTGCCCAATAATCGT OsSG2精细定位
Fine mapping for OsSG2
InDel-12083 GCAATCAGGTCGCGTATCAG GGTTGGGTGTTCGACGTATC
InDel-17610 ACGAATGTAACTTTGGCATGTCA ATGCTCTGAGGTGATTACTTTT
InDel-31068 AAGCCCCGTTTGACTTAGGT AAGCCCCGTTTGACTTAGGT
InDel-31355 TTAGGCCCAGTTTTGCTCTC CTCCCTCCGTCCCGAAAA
OsMADS1-Q TTGGAGAGGTACCGCAGC TCTGGTTCTCAAGCTGCTCC OsMADS1的qRT-PCR检测
qRT-PCR detection for OsMADS1
OsMADS1-Seq01 CGACGTGACAGCAGTTTGAT AGCACTAAAAGCACGCGAAA OsMADS1的测序
Sequencing for OsMADS1
OsMADS1-Seq02 TGCGCAAATCAAAACTGTACAG ATTGCGGCCCATCTAAACTG
OsMADS1-Seq03 TAGGGCGCATTGTGACTTTG GCCTGTGTTAAAAGCCATGC
OsMADS1-Seq04 AGCAAGCACTTCACACCATG AGAACAGTGCTAGAACCGCT
OsMADS1-Seq05 AGCCATCGATCACCCTGAAA GTCTGCTGCTTCATTGCTCA
OsMADS1-Seq06 CCATCAGGGTCTTCTCCACC TGAGATAACAGCTGCCGTCT
OsActin-F/R ACCTTCAACACCCCTGCTAT CACCATCACCAGAGTCCAAC OsActin的qRT-PCR检测
qRT-PCR detection for OsActin (as internal standard)
FMHPT-F/R ATTTGTGTACGCCCGACAGT GTGCTTGACATTGGGGAGTT PCR鉴定HPT PCR detection for HPT
FMCas9-F/R AGAACCTCTCCGATGCTATCC AGCAAGAGGACCAACGTAG PCR鉴定Cas9 PCR detection for Cas9

Fig. 2

Fine mapping of OsSG2 A: OsSG2 was preliminarily mapped to a region on chromosome 3 between SSR molecular markers Rm3392 and Rm14722; B: Fine mapping of OsSG2 using 600 F2 mutant individuals from the crosses 9311×sg2 and sg2×9311, and the OsSG2 locus was narrowed down to a 919.85 kb genomic DNA region between InDel markers InDel-12083 and InDel-17610; C: A BAC contig spanning the OsSG2 locus; D: Seventy-five predicted open reading frames (ORFs) identified as candidate OsSG2 genes according to genomic information of the japonica rice cultivar Nipponbare. The numbers in parentheses beneath each of the molecular markers linked to the OsSG2 represent the number of recombinants among the 600 F2 mutant individuals. The numbers below the chromosome indicate the actual physical location of the corresponding linkage molecular markers on rice chromosome 3 based on the Gramene database"

Table 3

The quality of sequencing data"

样本
Samples		 原始数据量
Raw base (Gb)		 有效数据量
Clean base (Gb)		 有效数据占比
Clean base percent (%)		 >Q20
(%)		 >Q30
(%)		 GC含量
GC content (%)
9311 26.84 26.28 97.93 97.67 93.43 42.80
sg2 27.78 27.20 97.92 97.65 93.39 42.92
WT-Pool 29.36 28.68 97.71 97.84 93.86 42.81
MT-Pool 30.73 30.03 97.73 97.81 93.79 42.82

Table 4

Sequencing depth and coverage"

样本
Samples		 有效序列数
Total reads		 比对序列数
Mapped reads		 比对率
Mapped rate (%)		 平均覆盖深度
Average coverage (×)		 1×覆盖度
1×coverage (%)		 10×覆盖度
10×coverage (%)
9311 176181050 136126271 98.23 52.7028 93.72 88.85
sg2 182366852 140044150 98.16 54.2271 93.16 88.38
WT-Pool 192599862 145760573 98.13 56.2530 94.71 90.18
MT-Pool 201645008 152345579 98.11 58.7479 94.74 90.45

Fig. 3

ΔSNP-index/ΔInDel-index correlation analysis chart based on InDel and SNP of BSA-seq A and B: ΔSNP-index/ΔInDel-index association analysis chart based on InDel (A) and SNP (B) of BSA-seq, the black arrow points to the associated chromosome region, and the confidence intervals represented by yellow and purple lines are 95% and 99%, respectively; C: Functional annotation results of candidate genes in linkage region"

Fig. 4

Expression analysis of candidate gene LOC_Os03g11614 A: Expression analysis of candidate gene LOC_Os03g11614 in various tissues of WT during the flowering stage, determined by RT-PCR; B: Expression analysis of candidate gene LOC_Os03g11614 in various tissues of WT and sg2 mutant during the flowering stage, determined by qRT-PCR. R: Root; S: Stem; FL: Flag leaf; YP: Young panicle; M: 2000 bp DNA Marker; WT: Wild-type GK1327"

Fig. 5

Sequence analysis of candidate gene LOC_Os03g11614 A: Comparison analysis of CDS of candidate gene LOC_Os03g11614 in 9311, Nipponbare, Minghui82, Minghui86, Minghui63, Minghui2155, Minhui3301, R498, Zhonghua11, WT, and sg2; B: Structure of candidate gene LOC_Os03g11614 and its encoded protein OsMADS1; C: The location of transcription start site ATG in LOC_Os03g11614; D: Comparison analysis of amino acid sequences between PP-02, PP-04, PP-06, PP-09, PP-11 and OsMADS1. PP: Polypeptide; aa: Amino acid; WT: Wild-type GK1327"

Fig. 6

CRISPR-Cas9 verification of OsSG2 candidate gene LOC_Os03g11614 A: Two positive transgenic lines of T0 generation, OsMADS1-Cas9-1# and OsMADS1-Cas9-3#, generated using the CRISPR-Cas9 system, Bar=3 cm; B and C: PCR identification of the positive transgenic plants in the gene-editing lines of T0 generation with the functional markers FMCas9-F/R (B) and FMHPT-F/R (C), where + and - indicate the positive control and negative control, respectively, and M represent 2000 bp DNA Marker; D: Mutation analysis at the Target 1 of LOC_Os03g11614 in the OsMADS1-Cas9-1# and OsMADS1-Cas9-3#, respectively. The nucleotides with red font and boxed in the black rectangle represent Target and PAM sequence, respectively, and - represent base deletions; E: The relative expression level of LOC_Os03g11614 in the young panicles of WT, OsMADS1-Cas9-1#, and OsMADS1-Cas9-3# during the flowering stage, respectively, determined by qRT-PCR; F: The phenotype of young panicles of OsMADS1-Cas9-1# and OsMADS1-Cas9-3# during the flowering stage, respectively. Bars=2 cm (left), 6 cm (middle), and 2 cm (right). WT: Wild-type GK1327"

Fig. 7

Functional verification of OsSG2 candidate gene LOC_Os03g11614 by using a complementation test A: Three positive transgenic lines of T0 generation, OsMADS1-OE1#, OsMADS1-OE2#, and OsMADS1-OE5#, generated using a complementation test, Bar=3 cm; B: PCR identification of the positive transgenic plants in the overexpressed lines of T0 generation with the functional marker FMHPT-F/R, where + and - indicate the positive control and negative control, respectively, and M represent 2000 bp DNA Marker; C: The relative expression level of LOC_Os03g11614 in the young panicles of WT, sg2, OsMADS1-OE1#, OsMADS1-OE2#, and OsMADS1-OE5# during the flowering stage, respectively, determined by qRT-PCR; D: The phenotype of young panicles of WT, OsMADS1-OE1#, OsMADS1-OE2#, and OsMADS1-OE5# during the flowering stage, respectively. Bar=6 cm. WT: Wild-type GK1327"

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