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作物学报 ›› 2025, Vol. 51 ›› Issue (3): 586-5897.doi: 10.3724/SP.J.1006.2025.44112

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

谷子SHMT基因家族全基因组鉴定与表达分析

郭冰1(), 秦家范3, 李娜1, 宋梦瑶1, 王黎明1, 李君霞2,*(), 马小倩1,*()   

  1. 1河南科技大学农学院, 河南洛阳 471023
    2河南省农业科学院粮食作物研究所, 河南郑州 450002
    3洛阳市农林科学院, 河南洛阳 471023
  • 收稿日期:2024-07-09 接受日期:2024-10-25 出版日期:2025-03-12 网络出版日期:2024-10-30
  • 通讯作者: *李君霞, E-mail: lijunxia@126.com; 马小倩, E-mail: maxq20210812@163.com
  • 作者简介:E-mail: 18317373922@163.com
  • 基金资助:
    河南省重点研发专项(231111110300);国家自然科学基金项目(32301841);河南省自然科学基金项目(242300421320);河南科技大学A类博士人才项目(13480103)

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 Published:2025-03-12 Published online: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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摘要：

丝氨酸羟甲基转移酶(SHMT)在作物中广泛存在, 参与作物碳代谢、光呼吸等途径, 在作物生长发育及抗逆胁迫中发挥重要作用, 但是目前关于谷子SHMT基因的研究较少。本研究在全基因组水平鉴定了谷子SHMT基因家族成员, 系统分析了SiSHMTs的基因结构、进化关系、染色体定位、物种间共线性、顺式作用元件、表达模式、优势单倍型等。结果表明, 谷子中共有5个SiSHMTs, 分子量在51.70~64.37 kD之间, 空间结构相近, 进化关系将其分为3组, 每组成员散落在各条染色体上。启动子顺式作用元件分析发现, 在启动子中包含多个光反应响应元件、厌氧响应元件、激素响应元件等作用元件。物种间共线性分析结果表明, SiSHMT3和SiSHMT4与单子叶作物水稻、小麦、高粱、玉米存在共线性, SiSHMT3与水稻、小麦、玉米存在多个共线对。SiSHMT成员在谷子不同发育时期、不同组织中表达量不同, SiSHMT4表达量较高, 在穗发育过程持续高表达, 并受到干旱、盐和ABA的显著诱导。SiSHMT4单倍型分析显示, Hap1为优势单倍型, 在穗长、穗宽、穗重各表型中都显著优于其他单倍型。研究结果为挖掘谷子抗旱、耐盐新功能基因提供基因源, 为今后选择培育高产抗逆谷子新品种奠定理论基础。

关键词: 谷子, SHMTs, 基因家族, 生长发育, 非生物胁迫

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

表1

qRT-PCR引物"

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

表2

SiSHMT基因家族成员的主要特征"

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

图1

谷子、拟南芥、水稻、小麦中SHMT基因家族成员系统发育进化树 SiSHMT: 谷子SHMT (红色五角星); AtSHMT: 拟南芥SHMT (蓝色四边形); OsSHMT: 水稻SHMT (黄色三角星); TaSHMT: 小麦SHMT (紫色圆形)。"

图2

SiSHMT基因家族成员的系统进化树、基因结构、结构域及Motif分析 A: SiSHMT系统发育树; B: 基因结构; C: 结构域; D: 保守基序。"

表3

SiSHMT基因家族成员的二级结构、三级结构"

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

图3

SiSHMT基因家族成员染色体定位 同一颜色的基因在进化关系中属于同一组。"

图4

谷子与水稻、小麦、高粱、玉米之间的共线性 灰色线: 全基因组内其他基因的共线性; 蓝色线: SHMT基因的共线性。"

附表1

物种间同源基因对选择压力分析"

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

图5

SiSHMT基因家族成员启始密码子上游2000 bp序列顺式作用元件"

图6

SiSHMT基因家族成员包含激素元件数量 ABA: 脱落酸; IAA: 生长素; GA: 赤霉素; MeJA: 茉莉酸甲酯; SA: 水杨酸。"

图7

SiSHMT基因家族成员表达模式分析 S: 苗期; B: 孕穗期; H: 抽穗期; SAM: 芽顶端分生组织; bf: 开花前; daf: 开花后天数。"

图8

SiSHMT基因家族成员非生物胁迫相对表达量 I: 干旱胁迫; II: 盐胁迫; III: 脱落酸胁迫; 横坐标: 处理时间; 纵坐标: 相对表达量。"

图9

SiSHMT4基因优势单倍型 A: SiSHMT4基因的单倍型; B: 不同单倍型位点, 右侧是单倍型包含样本数量。"

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