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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (6): 1467-1479.doi: 10.3724/SP.J.1006.2025.42052

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

Identification of an adaxially-curled-leaf mutant acl3 and function analysis of the regulated gene in rice (Oryza sativa L.)

LEI Song-Han(), FAN Jun-Yang, CHE Yan-Yi, DAI Yong-Dong, ZHENG Yu-Meng, TIAN Wei-Jiang, SANG Xian-Chun(), WANG Xiao-Wen()   

  1. College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
  • Received:2024-12-02 Accepted:2025-03-26 Online:2025-06-12 Published:2025-04-09
  • Contact: *E-mail: xwwang78@126.com;E-mail: sangxianchun@163.com
  • Supported by:
    the Chongqing Modern Agricultural Industry Technology System(CQMAITS202401);the National Key Research and Development Program of China(2022YFD1201600);the College Students’ Innovation and Entrepreneurship Training Scientific Research Project(202410635004)

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Abstract:

Moderate leaf curling is beneficial for cross-pollination, fruit set, and enhancing the photosynthetic efficiency of crop canopies, making it highly valuable for hybrid rice seed production and cultivation. To elucidate the molecular mechanisms underlying leaf rolling in rice, we identified a stably inherited adaxial leaf-rolling mutant, acl3 (adaxially curled leaf 3), from an ethyl methanesulfonate (EMS)-mutagenized population. In addition to leaf curling, acl3 exhibits reduced plant height and seed-setting rate, along with a highly significant increase in 1000-grain weight. Histological analysis using paraffin sections revealed that the extreme curling in acl3 primarily results from a reduction in both the number and area of bulliform cells between vascular bundles in the adaxial epidermis. Genetic analysis indicated that the acl3 mutant phenotype is controlled by a single recessive nuclear gene, which was preliminarily mapped to a 409 kb physical region between Indel markers 07g89 and 07g498 on chromosome 7. Whole-genome sequencing of acl3 and the wild-type Xida 1B was performed, and sequence variations within the acl3 mapping interval were identified using IGV software. A G-to-A base substitution was detected in the sixth exon of the annotated gene LOC_Os07g01240/SRL1/CLD1, leading to a structural change in the encoded protein. This gene was preliminarily identified as the candidate gene for ACL3. Complementary vector construction and transformation of the acl3 mutant restored the mutant traits—leaf curling, plant height, and grain size to wild-type levels, confirming that ACL3 is a new allele of SRL1 with pleiotropic effects. Quantitative real-time PCR (qRT-PCR) analysis revealed highly significant upregulation of leaf-rolling-related genes REL2 and NAL7. Further investigation of auxin IAA pathway-related genes showed that auxin synthesis gene YUCCA2, auxin response genes ARF1 and ARF7, and primary auxin response genes IAA10, IAA21, and IAA22 were all upregulated to varying degrees, suggesting that ACL3 may regulate rice plant architecture development through the auxin signaling pathway.

Key words: rice (Oryza sativa L.), bulliform cells, curled leaf, SRL1, auxin

Table 1

Primer sequences used for gene mapping and qRT-PCR analysis"

引物名称
Primer name		 正向引物
Forward primer (5′-3′)		 反向引物
Reverse primer (5′-3′)
07g20 GCCACTTATCCAAATGCCCTT GCTGGGCCAAAGGAGAGAGG
07g89 GCTGCTACTCGATGATGATGATC TCTTCTTCCAGGACCAGCTTGC
07g498 CGGATTGAAACCCATCCACC ATGTTGGGTGGACGTGGATG
07g798 TGATGTCCGAAGTCAAGGTGC GCTTAACCGCAAACGTGGATT
ACTIN GACCCAGATCATGTTTGAGACCT CAGTGTGGCTGACACCATCAC
ADL1 AATGGAATGGTCCGTGGTCAG CACCTGCACTATAACCACGCCA
ACL1 TCTAGGGGCATCGACCTGAA GCATGACGTAGATGAAGCAGCGA
ROC5 AGGTGGAAATGTGAAGTGTAGG AGGCGAGACCAGACCGAAG
RL14 CTATCCACCGTGCTTGAA AGAACCATTTGCCATCCT
REL2 CTTGCTATCGTCGCTGTCGT GCTCTTCCCTTCCATTGACT
NAL7 CAGGAGGACGGTGAGTTGTTC GCAGTAGAGCCCGTTTGGAC
SLL1 CGGCGACATGGACCAGTCGT GCTCGATCTGCACGGTTCCAA
AVB CACAGTCTTCTCCGGGCAGCAA CATTACCACCACCTAAGCCAGCTCT

Fig. 1

Phenotypic identification of the wild type (WT) and mutant (acl3) A-C: plant phenotypes of Xida 1B (WT) and acl3 mutant at the 3-leaf and 1-tiller stage, jointing stage, and maturity stage. A, scale bar: 5 cm; B and C, scale bar: 10 cm. D: flag leaf phenotype of WT and acl3 mutant at the maturity stage, with scale bar of 1 cm. E: leaf rolling index (LRI) of WT and acl3 mutant. F: phenotype of panicle and internode in WT (left) and acl3 mutant (right), with scale bar of 5 cm. G: statistics of panicle and internode length in WT and acl3 mutant. * and ** indicate significant differences at P < 0.05 and P < 0.01, respectively."

Fig. 2

Statistical analysis of yield traits in wild type (WT) and mutant (acl3) A: panicle structure of WT and acl3 mutant, the red arrow indicates unfertilized empty spikelets (Scale bar = 3.5 cm); B: comparison of primary and secondary branch numbers in WT and acl3 mutant; C: flower structure of WT and acl3 mutant, ① and ② represent pollen grains stained with 1% KI-I2 solution (Scale bar = 2 mm); D: seed setting rates of WT and acl3 mutant; E: seed morphological characteristics of WT and acl3 mutant, with scale bars of 6 mm; F: 1000-grain weight comparison of WT and acl3 mutant; G: grain length comparison of WT and acl3 mutant; H: grains width comparison of WT and acl3 mutant; I: grains thickness comparison of WT and acl3 mutant; J: effective panicle comparison of WT and acl3 mutant; ** indicates significant differences at P < 0.01."

Table 2

Comparison of major agronomic traits between WT and acl3 mutant"

性状Trait 野生型Wild type 突变体Mutant
株高 Plant height (cm) 89.00±1.41 71.00±1.22**
穗长 Panicle length (cm) 25.80±0.45 24.00±1.00*
有效穗数 Panicles per plant 5.80±0.84 6.80±0.45
结实率 Seed-setting rate (%) 92.71±2.40 40.33±7.11**
粒长 Grain length (mm) 9.10±0.10 8.78±0.08**
粒宽 Grain width (mm) 2.76±0.05 2.82±0.04
粒厚 Grain thickness (mm) 1.92±0.04 2.13±0.04**
千粒重 1000-grain weight (g) 23.25±0.28 3.13±0.62**

Fig. 3

Cytological observations and photosynthetic efficiency in wild type (WT) and mutant (acl3) A and B: cross-section of the flag leaf between WT and acl3 mutant at the heading stage, with scale bars of 500 μm; a and b: enlarged views of the red-boxed regions in Fig. A and B, with scale bars of 100 μm; C: comparison of bulliform cell numbers between two minor vascular bundles; D: total area of bulliform cells; E: net photosynthetic rate; F: stomatal conductance; G: transpiration rate; H: intercellular CO2 concentration. BC: bulliform cells. * and ** indicate significant differences at P < 0.05 and P < 0.01, respectively."

Table 3

Genetic analysis of rolling leaf acl3 mutant"

组合名称
Combination		 F2群体株数
Total number		 野生型株数
Wild type number		 突变株数
Mutant number		 理论值
Theory value		 χ2 0.05=3.84
acl3/缙恢10 acl3/Jinhui 10 636 463 173 3:1 1.64

Fig. 4

Map-based cloning of ACL3 A: gene mapping of ACL3; B: different locus in gene-mapped region identified by IGV, the red arrow indicates the sites of base difference; C: mutational sequence of wild type (WT) and acl3 mutant, the red box indicates the mutant base; D: gene structure of candidate gene LOC_Os07g01240, the white and black boxes indicate 5′UTR and exons respectively, the white arrow indicates 3′UTR and the black lines indicate introns, the mutation site was marked by red line; E: phenotypes of WT, acl3 and complementary transgenic plants (COM), with scale bar of 20 cm; F: flag leaf shape of WT, acl3 and COM, with scale bar of 1 cm."

Fig. 5

Protein structure and phylogenetic analysis of ACL3 A: ACL3 structure in WT and acl3 mutant. The arrow indicates the variant region. B: phylogenetic analysis of ACL3; C: conserved domain of ACL3 (red box) and the amino acid mutation site (red asterisk)."

Fig. 6

qRT-PCR analysis of genes involved in leaf curling and auxin pathway A: qRT-PCR analysis of genes regulating curled leaves; B: qRT-PCR analysis of genes regulating auxin pathway. * and ** indicate significant differences at P < 0.05 and P < 0.01, respectively."

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