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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (6): 1569-1581.doi: 10.3724/SP.J.1006.2025.43056

• TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY • Previous Articles     Next Articles

Genetic analysis and molecular identification of a small kernel mutant mn-like1 in maize

YUAN Xin1(), ZHAO Zhuo-Fan2, ZHAO Rui-Qing1, LIU Xiao-Wei1, ZHENG Ming-Min3, LIU Yu-Sheng4, DONG Hao-Sheng4, DENG Li-Juan4, CAO Mo-Ju1,*(), HUANG Qiang4,*()   

  1. 1Maize Research Institute, Sichuan Agricultural University / Key Laboratory of Biology and Genetic of Maize in Southwest Region, Ministry of Agriculture and Rural Affairs, Chengdu 611130, Sichuan, China
    2Chengdu University of Technology, Chengdu 610051, Sichuan, China
    3College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu 611130, Sichuan, China
    4Sichuan Institute of Atomic Energy / Irradiation Preservation and Effect Key Laboratory of Sichuan Province, Chengdu 610101, Sichuan, China
  • Received:2024-12-10 Accepted:2025-03-26 Online:2025-06-12 Published:2025-04-08
  • Contact: *E-mail: qianghuang2804@163.com;E-mail: caomj@sicau.edu.cn
  • Supported by:
    the Sichuan Science and Technology Program(2022NSFSC0018);the Sichuan Science and Technology Program(2021YFYZ0011);the Sichuan Science and Technology Program(2024NSFSC1210);the Sichuan Science and Technology Program(2023YFH0020)

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Abstract:

The kernel serves as the primary storage organ in maize, and its proper development requires on an adequate carbohydrate supply and efficient nutrient transport channels. In this study, we identified a natural mutant, small kernel 18 (smk18), exhibiting defects in kernel development. After multi-year and multi-location field trials, the smk18 mutant trait remained genetically stable. Segregation analysis of the (B73 × smk18) F2 population revealed that the mutant phenotype was controlled by a single recessive gene. The smk18 mutant was backcrossed to the inbred line RP125 for five generations to construct the near-isogenic mn-like1 (RP125smk18 smk18). Phenotypic evaluation showed that mn-like1 exhibited increased plant height and ear height compared to RP125, whereas hundred-kernel weight, kernel length, and kernel width were significantly reduced. Through molecular mapping, we localized the causal gene between Indel 4 and Indel 5 on chromosome 2. Within this interval, the Miniature1 (Mn1) gene had been previously reported to encode a cell wall invertase (INCW2) essential for carbohydrate transport during early kernel development. Sequencing of the Mn1 coding sequence (CDS) in mn-like1 revealed a 9-bp deletion in exon 5, leading to the loss of three amino acids (positions 409-411) in the Mn1 protein and alterations in its structure. Expression analysis showed that Mn1 transcript levels were significantly reduced in mn-like1 kernels at 13 days after pollination (DAP). An allelism test between mn-like1 and the transposon insertion mutant mn1-mu confirmed that mn-like1 is a novel allelic variant of Mn1. Further subcellular localization studies, carbohydrate quantification, and glycogen staining indicated that Mn1 is specifically expressed in the basal transfer layer of the endosperm. Mutation of Mn1 disrupted carbohydrate transport, leading to a significant reduction in sucrose and starch content in mn-like1 kernels, ultimately resulting in kernel developmental defects. In conclusion, this study expands the repertoire of Mn1 mutants in diverse genetic backgrounds and provides valuable genetic resources for elucidating the regulatory mechanisms of Mn1 in kernel development and the catalytic function of Mn1 protein.

Key words: maize, gene mapping, nutrient transport, cell wall invertase, kernel development

Table 1

Primers related to gene mapping"

引物名称
Primer name		 正向引物物理位置
Physical location of the forward sequences in Chr. 2		 正向引物
Forward sequence (5'-3')		 反向引物
Reverse sequence (5'-3')
Indel 1 5,565,500 TTGCTGCCGTTTCTTAGGTC GGGAGTGCAAAAATATCCGA
bnlg125 14,147,507 GGGACAAAAGAAGAAGCAGAG GAAATGGGACAGAGACAGACAAT
Indel 2 28,305,440 CAAACATGCCCAAATGTCAA CGGTACAGGGGATACATTCCT
Indel 3 48,135,660 ACCTCCGTTTGCCCGAGT CCCCCGTTTTGTTCTCTCTC
Indel 4 48,740,600 CGGTTTGGAACGCAATTC AATCGCGTTTAGGAAGAGCA
Indel 5 60,131,793 GCACACGTTTCATATCTCCG CCAGGTTGAGGTTGATAAGC
Indel 6 64,261,020 TCCCCTCAGCTCAGTAGTCA CGTGGTGCTTTTGGGTAGAT
umc1635 86,060,326 GCTGAGCAGATCTTTCCTTGTTTC AAGGAGCAGAACTCGGAGACG

Table 2

Primers for gene cloning and identification of Mu mutants"

引物名称
Primer name		 正向引物
Forward sequence (5'-3')		 反向引物
Reverse sequence (5'-3')		 用途
Usage
Mn1-CDSF1/R1 CTCTGTATGTGAGTGAGGCCA ATTCCTCAGGCGCCACTATG CDS扩增CDS amplification
Mn1-qpcrF1/R1 TCTTCAGGGTGTTCAAGCCC TCGATCAGGCTTCTCAGGGA qRT-PCR
ZmActin-F1/R1 TCACCCTGTGCTGCTGACCG GAACCGTGTGGCTCACACCA qRT-PCR
mu-F/R CCACCCGGACATCAACTACC AGAACGTCTTGGACGCGTAG Mu突变体鉴定
Identification of Mu mutants

Fig. 1

Comparison of agronomic traits between RP125 and mn-like1 A: mn-like1 and RP125 plants after pollen dispersal; B, C: RP125 and mn-like1 ear and ear nodes 16 days after pollination; D: internode number of mn-like1 and RP125; E: mn-like1 and RP125 seedling plants; F, G and H: mn-like1 and RP125 kernel length, kernel width and budding potential. Scale in Fig. A is 10 cm; Scale in Figs. B, C and E is 2 cm; Scale in Fig. D is 2.5 cm; Scale in Figs. F, G and H is 1 cm."

Table 3

Comparison of agronomic traits between RP125 and mn-like1"

农艺性状
Agronomic trait		 mn-like1 RP125 相比RP125
Compare with RP125 (%)
株高 Plant height (cm) 183.54±14.65 167.40±14.47 +8.79**
穗位高 Ear height (cm) 81.48±8.12 75.40±8.12 +7.46**
节间数 Internode number 13.59±0.78 11.78±0.97 +15.36**
茎粗(第1节) Stem size (section 1) (mm) 18.70±3.18 15.99±3.00 +14.49**
百粒重 Hundred-grain weight (g) 5.62±0.78 27.39±0.03 -79.48**
粒长 Kernel length (mm) 6.35±0.64 9.45±0.42 -32.80**
粒宽 Kernel width (mm) 5.80±0.42 8.42±0.05 -31.11**

Fig. 2

Comparison of kernel development between RP125 and mn-like1 A: observation on dynamic kernel development of RP125; B: dynamic development observation of mn-like1 seed development. Scale in Figs. A and B is 2 mm. DAP: days after pollination."

Table 4

Genetic analysis of (B73 × smk18) F2 population"

群体
Population		 果穗
Ear		 总粒数
Total number of kernel		 正常籽粒
Normal kernel		 突变籽粒
Mutant kernel		 实际比例
Actual ratio		 理论比例
Theoretical ratio		 χ2
chi-square test
(B73×smk18) F2 1 635 475 160 2.97 3∶1 0.004
2 545 415 130 3.19 3∶1 0.006
3 542 404 138 2.93 3∶1 0.009

Fig. 3

Physical map of gene mapping Initial mapping of candidate genes. n: population size; Recombinants: number of individual plants of recombination."

Fig. 4

Analysis of ZmMn1 CDS sequence variation, expression, protein structure, and function A: comparison of ZmMn1 CDS between RP125 and mn-like1; B: comparison of ZmMn1 expression in RP125 and mn-like1; C: phylogenetic tree of Mn1 protein in different species; D: three-dimensional structure of Mn1 protein(On the left is the three-dimensional structure of Mn1 protein in RP125, and on the right is the three-dimensional structure of Mn1 protein in mn-like1; the red box shows the three-dimensional structure difference area of Mn1 protein); E and F: analysis of conserved sites of Mn1 protein in different species. ** means signifant difference at the 0.01 probability level."

Fig. 5

Subcellular localization of ZmMn1 A: ZmMn1-eGFP fusion protein colocates with cell membrane marker (mCherry); B: ZmMn1-eGFP fusion protein colocates with cell wall marker (CFW). C: ZmMn-like1-eGFP fusion protein colocates with cell membrane marker (mCherry); D: ZmMn-like1-eGFP fusion protein colocates with cell wall marker (CFW)."

Fig. 6

Allelic test of mn-like1 and mn1-mu A: diagram of Mu transposon insertion into Zm00001d003776 gene; B: molecular identification of Mu transposon insertion mutants; C: kernel phenotypes of mn-like1, mn1-mu and (mn-like1×mn1-mu) F1 generation; D: ear phenotypes of mn-like1, mn1-mu and (mn-like1×mn1-mu) F1 generation. M: DL2000; Scale in Fig. C is 1 cm; Scale in Fig. D is 2.5 cm."

Fig. 7

Comparison of sucrose and starch contents between RP125 and mn-like1 A: comparison of sucrose content between RP125 and mn-like1. B: comparison of I-IK staining and starch content of RP125 and mn-like1 grains."

Fig. 8

Comparison of periodic acid-schiff (PAS) histological staining in longitudinal sections of RP125 and mn-like1 kernels at 13 days after pollination A: PAS staining of longitudinal sections in RP125 kernels. BETL: basal endosperm transfer layer. PED: pedicle. ENDO: endosperm. B: glycogen accumulation in endosperm of RP125. The red circle represents the amount of glycogen accumulated in a single starch endosperm cell. C: PAS staining of longitudinal sections in mn-like1 kernels. D: mn-like1 glycogen accumulation in endosperm. The red circle represents the amount of glycogen accumulated in a single cell."

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