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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (3): 586-5897.doi: 10.3724/SP.J.1006.2025.44112

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

Genome-wide identification and expression analysis of SHMT gene family in foxtail millet (Setaria italica L.)

GUO Bing1(), QIN Jia-Fan3, LI Na1, SONG Meng-Yao1, WANG Li-Ming1, LI Jun-Xia2,*(), MA Xiao-Qian1,*()   

  1. 1College of Agriculture, Henan University of Science and Technology, Luoyang 471023, Henan, China
    2Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China
    3Luoyang Academy of Agricultural and Forestry Sciences, Luoyang 471023, Henan, China
  • Received:2024-07-09 Accepted:2024-10-25 Online:2025-03-12 Published:2024-10-30
  • Contact: *E-mail: lijunxia@126.com; E-mail: maxq20210812@163.com
  • Supported by:
    Henan Provincial Key Research and Development Project(231111110300);National Natural Science Foundation of China(32301841);National Natural Science Foundation of Henan Province(242300421320);Category A PhD Research Startup Foundation of Henan University of Science and Technology(13480103)

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Abstract:

Serine hydroxymethyltransferase (SHMT) is involved in carbon metabolism and photorespiration, and is widely present in crops, playing a critical role in growth, development, and stress resistance. However, the SHMT genes in foxtail millet are largely unexplored. In this study, we identified the members of the SiSHMT gene family at the whole-genome level and systematically analyzed their gene structures, evolutionary relationships, chromosomal localizations, interspecies collinearity, cis-acting elements, expression patterns, and dominant haplotypes. Our results revealed five SiSHMT members in foxtail millet, with molecular weights ranging from 51.70 to 64.37 kD, and similar spatial structures. Phylogenetic analysis classified these genes into three groups, with members distributed across different chromosomes. The analysis of cis-acting elements in the gene promoters indicated the presence of numerous photo-responsive elements, anaerobic response elements, hormone response elements, and other cis-acting elements. Interspecies collinearity analysis showed that SiSHMT3 and SiSHMT4 exhibited collinearity with their orthologous genes in monocot crops such as rice, wheat, sorghum, and maize, with SiSHMT3 displaying multiple collinear pairs with rice, wheat, and maize. The expression levels of SiSHMT family members varied across different developmental stages and tissues of foxtail millet. Notably, SiSHMT4 was highly expressed in developing panicles and was significantly induced by drought, salt, and ABA treatments. Haplotype analysis of SiSHMT4 revealed that Hap1 was the dominant haplotype, significantly outperforming other haplotypes in panicle length, width, and weight. These findings provide valuable gene resources for improving drought and salt tolerance in foxtail millet and lay a theoretical foundation for the breeding of high-yield, stress-resistant foxtail millet varieties in the future.

Key words: foxtail millet, SHMTs, gene family, growth and development, abiotic stress

Table 1

qRT-PCR primers"

基因名称
Gene name		 正向引物
Forward primer (5′-3′)		 反向引物
Reverse primer (5′-3′)
SiSHMT1 TGCGACATGGCTCATATCAGT TGTGGGTGGTAGTGGTAATCAC
SiSHMT2 GGCCCTCACAATCACCAGAT GCATTCGCCTTCACTTGCTTT
SiSHMT3 TGGCGCATATCAGTGGTCTTG CCCTGAGGTTCTTGTGAGTAGTTG
SiSHMT4 CTGAGGGTGCTGTGTATGACTA GGTTGTGAGGACCACCTTGTAG
SiSHMT5 AGGCGGGCCTCATAACCATAC GCTCTTGATAAGCTCGGTACTCT
SiActin7 AACATTGTGCTCAGCGGTGG TGGAAGGTGCTAAGGGAGGC

Table 2

Main characteristics of SiSHMT gene family members"

基因名称
Gene name		 基因号
Gene ID		 蛋白长度
Protein length		 分子量Molecular weight (kD) 等电点
pI		 不稳定指数Instability index 亲水性系数Hydropathicity 亚细胞定位Subcellular
localization
SiSHMT1 SETIT_021684mg 543 58.64 7.65 41.21 -0.160 线粒体
Mitochondrion
SiSHMT2 SETIT_001011mg 523 57.27 8.52 46.02 -0.231 线粒体
Mitochondrion
SiSHMT3 SETIT_000781mg 591 64.37 6.61 44.03 -0.391 细胞质
Cytoplasmic
SiSHMT4 SETIT_026132mg 471 51.70 7.15 40.61 -0.274 细胞质
Cytoplasmic
SiSHMT5 SETIT_035240mg 513 56.52 8.58 39.75 -0.245 线粒体
Mitochondrion

Fig. 1

Phylogenetic tree of SHMT gene family members in foxtail millet, Arabidopsis, rice, and wheat SiSHMT: foxtail millet SHMT (red five-pointed star); AtSHMT: Arabidopsis SHMT (blue quadrilateral); OsSHMT: rice SHMT (yellow triangular star); TaSHMT: wheat SHMT (purple circle)."

Fig. 2

Phylogeny tree, gene structure, domain, and Motif analysis of SiSHMT gene family members A: SiSHMT phylogenetic tree; B: gene structure; C: structural domain; D: conservative motif."

Table 3

Secondary structure and tertiary structure of SiSHMT gene family members"

基因名称
Gene name		 α-螺旋
Alpha helix
(%)		 延长链Extended strand (%) 不规则卷曲
Random coil (%)		 二级结构要素的分布
Distribution of secondary structure elements		 三维结构
Three-dimensional structure
SiSHMT1 45.30 9.76 44.94
SiSHMT2 40.15 9.75 50.10
SiSHMT3 39.93 11.17 48.90
SiSHMT4 46.50 11.89 41.61
SiSHMT5 45.03 12.09 42.88

Fig. 3

Chromosome localization of SiSHMT gene family members Genes of the same color belong to the same group in evolutionary relationships."

Fig. 4

Collinearity between foxtail millet and rice, wheat, sorghum, and maize Gray line: collinearity of other genes in the genome; blue line: collinearity of SHMT genes."

Table S1

Analysis of selection pressure for homologous genes between species"

同源基因对
Homologous gene pairs		 非同义替换率
Ka		 同义替换率
Ks		 非同义替换/同义替换
Ka/Ks		 有效长度
Effective length		 平均S位点
Average S-sites
SiSHMT3-Os01t0874900-01 0.0622 0.6008 0.1036 1758 424.1667
SiSHMT3-Os05t0429000-01 0.1357 0.8855 0.1533 1677 406.5000
SiSHMT4-Os11t0455800-01 0.0285 0.4216 0.0677 1413 341.0833
SSiSHMT3-EES01843 0.0359 0.3310 0.1085 1770 429.7500
SiSHMT4-EES08452 0.0132 0.2161 0.0609 1413 340.8333
SiSHMT3-TraesCS3A02G385600.1 0.0581 0.5998 0.0969 1749 423.4167
SiSHMT3-TraesCS3B02G417800.1 0.0508 0.6013 0.0845 1545 370.7500
SiSHMT3-TraesCS3D02G378700.1 0.0567 0.5694 0.0995 1743 423.5833
SiSHMT4-Zm00001eb170020_T001 0.0113 0.2477 0.0456 1413 341.3333
SiSHMT3-Zm00001eb146170_T002 0.0392 0.3823 0.1024 1764 427.3333
SiSHMT3-Zm00001eb366470_T002 0.0511 0.3953 0.1293 1749 425.0000

Fig. 5

Cis-acting elements of the upstream 2000 bp sequence of initiation codons of SiSHMT gene family members"

Fig. 6

Number of hormone elements contained of the SiSHMT gene family members ABA: abscisic acid; IAA: auxin; GA: gibberellin; MeJA: methyl jasmonate; SA: salicylic acid."

Fig. 7

Analysis of expression patterns of SiSHMT gene family members S: seedling stage; B: booting stage; H: heading period; SAM: shoot apical meristem; bf: before flowering; daf: days after flowering."

Fig. 8

Relative expression of abiotic stress in SiSHMT gene family members I: simulating drought stress; II: salt stress; III: abscisic acid stress; Abscissa: processing time; Ordinate: relative expression."

Fig. 9

SiSHMT4 gene dominant haplotype A: haplotype of the SiSHMT4 gene; B: different haplotype sites, the haplotype on the right side contains the number of samples."

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