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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (10): 1903-1912.doi: 10.3724/SP.J.1006.2021.03060

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Fine mapping and candidate gene analysis of maize defective kernel mutant dek54

ZHOU Lian(), LIU Chao-Xian, CHEN Qiu-Lan, WANG Wen-Qin, YAO Shun, ZHAO Zi-Kun, ZHU Si-Ying, HONG Xiang-De, XIONG Yu-Han, CAI Yi-Lin*()   

  1. Maize Research Institute / Academy of Agricultural Sciences / State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing 400715, China
  • Received:2020-10-15 Accepted:2021-01-13 Online:2021-10-12 Published:2021-03-02
  • Contact: CAI Yi-Lin E-mail:zhoulianjojo@swu.edu.cn;caiyilin1789@163.com
  • Supported by:
    National Natural Science Foundation of China(31601312)

Abstract:

Maize kernel is closely related to yield and nutritive quality. Study on the function of maize kernel development relative genes provides important basis for the molecular mechanism analysis, yield increasing and nutritive quality improving. B73 pollen was treated with ethyl methylmethanesulfonate (EMS) and a defective maize kernel defective kernel 54 (dek54) was screened. dek54 had small mature kernel, wrinkled and whitened seed coat phenotype. Genetic analysis indicated that dek54 is a recessive mutant controlled by a single gene. Paraffin sections showed starchy endosperm cells of dek54 had irregular shape and dense arrangement at developmental stage. Scanning electron microscopy observation indicated that protein bodies around starch granules in the central region of the dek54 mature kernel endosperm were fewer and arranged more loosely compare to wild type. Total protein, zein, amino acids components contents and total nitrogen content of dek54 mature kernel were significantly lowered compared with the wild type. dek54 was located on chromosome 7 within the interval of the physical distance of about 290 kb between markers SSR6 and SSR7. Sequencing revealed that the 351th base G on the 2nd exon of Zm00001d019294 gene changed into A, which led to the premature termination of the protein translation. Zm00001d019294 gene was specifically expressed in immature maize kernel, and has the highest expression in 12 DAP (days after pollination) immature kernel. Targeted mutation was performed using CRISPR/Cas9 system to identify that mutant phenotype was caused by candidate gene Zm00001d019294. Dek54 encoded an MFS (major facilitator superfamily) protein and had high homology with ZmNRT1.5 (nitrate transporter). Besides, Dek54 protein was localized in the plasma membrane of maize protoplasts. The study of dek54 laid the foundation for the molecular mechanism analysis of maize kernel development.

Key words: maize (Zea mays L.), defective kernel 54, kernel development, fine mapping

Fig. 1

Phenotypic characterization of dek54 mutant A: F2 segregating population of mature ear; B: phenotypes of kernels; C: cross section of kernels; D: longitudinally section of kernels; E: 100-kernel weight, ten-kernel length, and ten-kernel width of WT and dek54 mutant kernels from F2 segregating population. Bar: 0.5 cm. Em: embryo; En: endosperm; SE: starchy endosperm; VE: vitreous endosperm."

Fig. S1

Germination test of wildtype and dek54 mature kernels (5 days after germination) Bar: 1 cm."

Fig. 2

Histological observatin of dek54 mutant A: longitudinal paraffin sections observation of developing WT and dek54 mutant kernels at 16 DAP. Bar: 100 µm. AL: aleurone layer; SG: starch endosperm. B: scanning electron microscopy observation of the central regions of WT and dek54 mutant mature kernel endosperm. Bar: 50 µm. SG: starch granule; PB: protein body."

Fig. 3

Biochemical component analysis of dek54 mutant Protein (A), starch (B), amino acid components (C), and total nitrogen contents (D) of WT and dek54 mutant kernels."

Table 1

Sequences of SSR markers for dek54 mapping"

标记类型
Type
标记名称
Name
正向引物序列
Forward sequence (5′-3′)
反向引物序列
Reverse sequence (5′-3′)
SSR SSR23403 ACTAGTATGTGGATTGCTCGTCG GCTGCTGAGCTGTATGTACCA
SSR SSR1 CCCTGACGAAAGCATGAATGAG ACAGATGACTCTGCACCTCAAG
SSR SSR2 TGCCCATAAGAGCTTCGAGGATA AGCCTTAGTTGTCAGTCCATCG
SSR SSR3 TGCCCATAAGAGCTTCGAGGATA AGCCTTAGTTGTCAGTCCATCG
SSR SSR4 CCATCTGTACTAATGGCACCTGA GCCAGCAAAGCTTTTCAAGAGT
SSR SSR5 GGCTACATAAGATGCAAAGCGG TACCCTTTGACAGAGCCTACCT
SSR SSR6 GGTGCCAAAAACATCTCCCAAC TAGCGTGGGGTCATAGCAACA
SSR SSR7 CATGGCCAAAATATCGCACGAG TGACGTACATGAACACCTCGG
SSR SSR8 GCTAGGTGCAGTGTCTCTGCTT CCTTGAACGTGGGGTAGGCT
SSR SSR10308 GCAAATGTTCTGTGCAAGGCTA GCCCCACAAGAACTCCATCTAT

Table 2

Gene annotation in the mapping region of dek54 "

编号
No.
基因ID
Gene ID
功能注释
Function annotation
1 Zm00001d019292 无注释 No annotation
2 Zm00001d019293 异柠檬酸/异丙基苹果酸脱氢酶 Isocitric acid/isopropyl malate dehydrogenase
3 Zm00001d019294 MFS家族 Major facilitator superfamily

Fig. 4

Linkage SSR marker screening and fine mapping of dek54 A: the polymorphic PCR products amplified by umc2160 between WP and MP; B: confirmation of linkage SSR marker umc2160 by genotyping 33 dek54 mutant plants; C: fine mapping of dek54 using F2 population including 1566 individuals. dek54 was mapped to an interval about 290 kb flanked by SSR6 and SSR7. The symbols above and below the black vertical solid lines represent the molecular marker and the number of recombinants, respectively."

Fig. 5

Mutation site and spatio-temporal expression analysis of Zm00001d019294 A: gene structure diagram of Zm00001d019294. The red arrow indicates mutation sites. B: the relative expression level of Zm00001d019294 in different tissues and developing immature kernel."

Fig. 6

Phenotypic characterization of CRISPR/Cas9 targeted mutation of Zm00001d019294 A: the sequence in the Zm00001d019294 locus targeted using CRISPR/Cas9. The sgRNA target sequence is green. Protospacer-adjacent motif (PAM) is blue. Red letters and dashes represent insertions and deletions, respectively. B: mature F2 ear of dek54-cas9-1xMo17. C: mature WT and dek54-cas9-1 kernels. D: longitudinal paraffin sections of mature WT and dek54-cas9-1 kernels. Em: embryo; En: endosperm. Bars: 0.5 cm."

Fig. 7

Conserved domain (A) and phylogenetic (B) analysis of Dek54 protein"

Fig. 8

Observation of subcellular localization of Dek54 in maize protoplasts Dek54-GFP was co-localized with a mCherry-labeled plasma membrane marker (mCherry-PM; CD3-1007). Bar: 20 μm."

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