谷子黄绿叶突变体<i>ygl7</i>的精细定位及候选基因分析

doi:10.7668/hbnxb.20194486

摘要/Abstract

摘要：

叶色突变体是研究C4光合途径及叶绿素代谢机制的理想材料。为了研究谷子黄绿叶突变的分子机制,为黄绿叶基因的功能研究及叶绿素代谢的分子机制解析奠定基础,在长农35号甲基磺酸乙酯(EMS)突变体库中鉴定到1份可稳定遗传的谷子黄绿叶突变体ygl7,并对突变体及野生型进行农艺性状调查、光合色素含量及光合参数测定、叶绿体超微结构观察;同时对突变体叶色进行遗传分析,采用BSA法进行基因初定位,利用F₂群体进行精细定位,并根据功能注释结合RNA-Seq预测候选基因。采用qRT-PCR进行表达模式分析,采用酵母双杂交试验进行蛋白互作验证。结果表明,与野生型相比,ygl7苗期、拔节期叶片呈明显黄绿色,抽穗期逐步转为浅绿色,ygl7整个生育期叶绿素含量及光合速率都显著低于野生型,且叶绿体结构出现异常。遗传分析表明,ygl7黄绿叶表型由1对隐性单基因控制,基因精细定位将黄绿叶基因定位于第Ⅶ染色体434.9 kb区间内,候选基因分析预测编码原卟啉Ⅸ镁鳌合酶Ⅰ亚基的Seita.7G290300为调控黄绿叶的候选基因。qRT-PCR结果显示,Seita.7G290300在叶片中高表达,且在突变体中的表达量低于野生型;叶绿素合成途径(CHLD、CHLI)和光系统(LHCB1、LHCB6)相关基因在突变体中均下调表达。酵母双杂交试验表明,SiYGL7与MORF2存在互作。

关键词: 谷子, 黄绿叶突变体, 精细定位, 镁鳌合酶Ⅰ亚基

Abstract:

Leaf color mutant is an ideal material for studying C4 photosynthesis pathway and chlorophyll metabolism mechanism.In order to study the molecular mechanism of yellow-green leaf mutation in millet,and lay a foundation for the functional study of yellow-green leaf genes and the molecular mechanism analysis of chlorophyll metabolism,a stable hereditary yellow-green leaf mutant ygl7 was identified in the ethyl methacrylate(EMS)mutant library of Changnong 35.Agronomic traits,photosynthetic pigment content and photosynthetic parameters,and chloroplast ultrastructure observation were carried out on the mutant and wild type.At the same time,genetic analysis of mutant leaf color was performed,primary mapping was performed by BSA method,fine mapping was performed by an F₂ population,and candidate genes were predicted according to functional annotation combined with RNA-Seq.The expression pattern was analyzed by qRT-PCR,and the protein interaction was verified by yeast two-hybrid experiment.The results showed that the leaves of ygl7 were obviously yellow-green at seedling stage and elongation stage,and gradually turned to light green at heading stage compared with the wild type.The chlorophyll content and photosynthetic rate of ygl7 during the whole growth stage were significantly lower than that of the wild type,and the chloroplast structure was abnormal.Genetic analysis showed that ygl7 yellow-green leaf phenotype was controlled by a pair of recessive single genes.Yellow-green leaf gene was located in the 434.9 kb region of chromosome Ⅶ.Candidate gene analysis predicted that Seita.7G290300 encoding protoporphyrin Ⅸ magnesium chelatase Ⅰ was the candidate gene for regulating yellow-green leaf.The results of qRT-PCR showed that Seita.7G290300 was highly expressed in leaves,and the expression of Seita.7G290300 in mutant was lower than that of wild type.The expression levels of genes related to chlorophyll synthesis pathway(CHLD,CHLI)and photosystem(LHCB1,LHCB6)were down-regulated in the mutants.The experiment of yeast two-hybrid showed that SiYGL7 interacted with MORF2.

Key words: Foxtail millet, Yellow-green leaf mutant, Fine mapping, Magnesium chelatase Ⅰ subunit

连世超, 韩康妮, 杜晓芬, 王智兰, 李禹欣, 李颜方, 成锴, 张林义, 王军. 谷子黄绿叶突变体ygl7的精细定位及候选基因分析[J]. 华北农学报, 2024, 39(2): 27-38. doi: 10.7668/hbnxb.20194486.

LIAN Shichao, HAN Kangni, DU Xiaofen, WANG Zhilan, LI Yuxin, LI Yanfang, CHENG Kai, ZHANG Linyi, WANG Jun. Fine Mapping and Candidate Gene Analysis of Yellow-Green Leaf Mutant ygl7 in Foxtail Millet[J]. Acta Agriculturae Boreali-Sinica, 2024, 39(2): 27-38. doi: 10.7668/hbnxb.20194486.

http://www.hbnxb.net/CN/Y2024/V39/I2/27

图/表 13

图1 突变体(ygl7)和野生型(长农35号)植株在不同生长期的表型 A.苗期野生型(长农35号,WT)与ygl7叶片;B.拔节期植株;C.抽穗期植株。

Fig.1 Phenotypes of the ygl7 mutant and wild-type Changnong 35 plants at different growth stages A.Leaves of ygl7 and Changnong 35 plants at the seedling stage; B.Plants at the elongation stage;C.Plants at the heading stage.

表1 长农35与ygl7农艺性状

Tab.1 Agronomic traits of Changnong 35 and ygl7

品种 Variety	株高/cm Plant height	茎节数 Stem nodes number	穗下节长/cm Peduncle length	穗长/cm Panicle length	穗粗/cm Panicle diameter	千粒质量/ g Thousand-grain weight
长农35 Changnong 35	178.20±1.74Aa	14.30±0.67Aa	31.84±3.64Aa	18.30±1.42Bb	3.15±0.36Aa	3.20±0.13Aa
ygl7	116.63±3.17Bb	12.70±0.48Bb	21.91±1.93Bb	31.61±2.35Aa	2.86±0.23Bb	2.37±0.13Bb

图2 野生型(长农35)和突变体ygl7光合特性不同大写字母表示差异极显著(P<0.01);不同小写字母表示差异显著(P<0.05)。图8—9同。

Fig.2 Photosynthetic characteristics of wild type(Changnong 35)and mutant ygl7 The different uppercase letter indicated extremely significant difference (P<0.01); the different lowercase letters indicate significant difference (P<0.05).The same as Fig.8—9.

图3 突变体与野生型叶绿体超微结构 A、C.野生型植株叶肉细胞及叶绿体;B、D.突变体ygl7植株叶肉细胞及叶绿体;Cp.叶绿体;sg.淀粉粒;gl.基粒片层。

Fig.3 Ultrastructure of mutant and wild type chloroplast A,C.Mesophyll cells and chloroplasts of wild type plants;B,D.Mesophyll cells and chloroplasts of mutant ygl7 plants; Cp.Chloroplast; sg.Starch granules; gl.Grana lamella.

表2 本研究用到的分子标记

Tab.2 Molecular markers used in this study

引物名称 Primer name	正向引物(5'—3') Forward primer(5'—3')	反向引物(5'—3') Reverse primer(5'—3')	用途 Purpose	文献 Literature
SIsv0356b1	GGAGCATGGACTTGTTCAGAG	AATCAGCGGTGAAAACAGCT	基因初定位	[34]
SIsv0682b1	TGCAACGAAGGGATTAGGTT	CTGTAGTACGCTATGGTAGC
SIsv0690b1	CAATTACACTCTAGTCTTGCC	TGCACAAAGACCCTTACGTT
SIsv0987	TTGCATGGTAGCCCTTTACC	GTACGGCTGCCACTCACATT
SIsv1208b1	ACCAGAACAACCAAGTCCTG	GTTAGCTCACATGCCGTAGT
M14	CAAGCCGTGGAGTAGTGATG	TACTTTGTATGCAGCGTGGC	基因精细定位
M16	ATTGGAGCATGTACCGGAGT	CCACTCCACTCAATCATGCG
M18	GAAGCGTTGAGGGTCTTGAA	CCAACTACATCCTCCCTGTCA
M34	CTTGCTGGCATGTGTTAAGC	TCCAGTCCAGTCCATGCTTT
M26	GGTTGAGAATGCACACCAAAAG	GGGGTCTTCAACACTTAACTCA
M20	TAATACCAGGGGCGGATCTG	GGCCCTCTTGTAGTTGAGCT
M32	TGCAAAACAGACCCTAACATTTT	TGCATTCTCCGACTCTTGCT
M31	CTCCAAAACCCTCGCTCTTG	GCATCCACTCCTCTCCACAA
YL001	CCCACAAGTAGCTGATCAAGTG	CGTGAATTATAGGCATTTTCCGG
M3	CAAGTGTCCGGCTGATTTGG	TGCAGCACTGGAGTTAGGAA
G300-CDS	ATACCCTTCCACACAGCCTC	TGCTGCCAGAATTTGTGACT	基因CDS扩增
G300-RT(CHLI)	GCTGAGGGTGAAAATCGTGG	ACACGGAGGTCATGGTCAAT	候选基因表达
Si-actin	TTGCGTCGACTTACTTCAGC	CATGCTCCTCACATCGGTTG
CHLD-RT	CAAATGCGGACCCTAA	ATGCCATCATCCAACAGA	叶绿素合成相关基因表达	[27]
CHLH-RT	CCGCTCGTGTTCCAGAC	AACAGTGATTGCCAGTTTCTT
hemA-RT	CTATCGCTGAGATCGCCAACTG	TCAGCAGTCTGAATACGAGGCTA
PPOX-RT	ACCTCCCGTTCTTCGATCTCAT	ACCTTCCCAAATGCAGCTTTCA
CAO1-RT	GTGCTTCTCCAGAAAGGTGGTT	ATGTACTTGGAGCCAGGGAAGT
RbcL-RT	TGAAAAAGATCGTTCTCGCGGT	TTACCTTCACGAGCAAGATCGC	光合作用相关基因表达
PsaD-2-RT	GGCAAGAACACCTTCGACATCT	CGAGCTAGATCGCAAGAAGAGT
PsbP-RT	GTAGCATTCAGAGATGCACGGT	ACGGTTGTTTCGCAGTTGTTTC
LHCB1-RT	GGCAAGTCGAGATGATGAGTCG	GTCTCGCGAATTAGCCTCCAT
LHCB6-RT	GAGGCTAAAGAAGAGCGCGTAG	GAGGCTAAAGAAGAGCGCGTAG

表2 本研究用到的分子标记

Tab.2 Molecular markers used in this study

引物名称 Primer name	正向引物(5'—3') Forward primer(5'—3')	反向引物(5'—3') Reverse primer(5'—3')	用途 Purpose	文献 Literature
SIsv0356b1	GGAGCATGGACTTGTTCAGAG	AATCAGCGGTGAAAACAGCT	基因初定位	[34]
SIsv0682b1	TGCAACGAAGGGATTAGGTT	CTGTAGTACGCTATGGTAGC
SIsv0690b1	CAATTACACTCTAGTCTTGCC	TGCACAAAGACCCTTACGTT
SIsv0987	TTGCATGGTAGCCCTTTACC	GTACGGCTGCCACTCACATT
SIsv1208b1	ACCAGAACAACCAAGTCCTG	GTTAGCTCACATGCCGTAGT
M14	CAAGCCGTGGAGTAGTGATG	TACTTTGTATGCAGCGTGGC	基因精细定位
M16	ATTGGAGCATGTACCGGAGT	CCACTCCACTCAATCATGCG
M18	GAAGCGTTGAGGGTCTTGAA	CCAACTACATCCTCCCTGTCA
M34	CTTGCTGGCATGTGTTAAGC	TCCAGTCCAGTCCATGCTTT
M26	GGTTGAGAATGCACACCAAAAG	GGGGTCTTCAACACTTAACTCA
M20	TAATACCAGGGGCGGATCTG	GGCCCTCTTGTAGTTGAGCT
M32	TGCAAAACAGACCCTAACATTTT	TGCATTCTCCGACTCTTGCT
M31	CTCCAAAACCCTCGCTCTTG	GCATCCACTCCTCTCCACAA
YL001	CCCACAAGTAGCTGATCAAGTG	CGTGAATTATAGGCATTTTCCGG
M3	CAAGTGTCCGGCTGATTTGG	TGCAGCACTGGAGTTAGGAA
G300-CDS	ATACCCTTCCACACAGCCTC	TGCTGCCAGAATTTGTGACT	基因CDS扩增
G300-RT(CHLI)	GCTGAGGGTGAAAATCGTGG	ACACGGAGGTCATGGTCAAT	候选基因表达
Si-actin	TTGCGTCGACTTACTTCAGC	CATGCTCCTCACATCGGTTG
CHLD-RT	CAAATGCGGACCCTAA	ATGCCATCATCCAACAGA	叶绿素合成相关基因表达	[27]
CHLH-RT	CCGCTCGTGTTCCAGAC	AACAGTGATTGCCAGTTTCTT
hemA-RT	CTATCGCTGAGATCGCCAACTG	TCAGCAGTCTGAATACGAGGCTA
PPOX-RT	ACCTCCCGTTCTTCGATCTCAT	ACCTTCCCAAATGCAGCTTTCA
CAO1-RT	GTGCTTCTCCAGAAAGGTGGTT	ATGTACTTGGAGCCAGGGAAGT
RbcL-RT	TGAAAAAGATCGTTCTCGCGGT	TTACCTTCACGAGCAAGATCGC	光合作用相关基因表达
PsaD-2-RT	GGCAAGAACACCTTCGACATCT	CGAGCTAGATCGCAAGAAGAGT
PsbP-RT	GTAGCATTCAGAGATGCACGGT	ACGGTTGTTTCGCAGTTGTTTC
LHCB1-RT	GGCAAGTCGAGATGATGAGTCG	GTCTCGCGAATTAGCCTCCAT
LHCB6-RT	GAGGCTAAAGAAGAGCGCGTAG	GAGGCTAAAGAAGAGCGCGTAG

图4 ygl7精细定位

Fig.4 Fine mapping of ygl7

图5 RNA-Seq差异表达基因分析 A—B.差异表达基因(ygl7 VS长农35号);C.定位区间内差异表达基因表达图谱。

Fig.5 Analysis of RNA-Seq differentially expressed genes A—B.Differentially expressed gene(ygl7 VS Changnong 35);C.Heat map of differentially expressed genes in the localization interval.

图6 ygl7与长农35号之间DEGs的 GO富集分析 GO:0008150.生物过程;GO:0006952.防御响应;GO:0006355.转录调控,DNA模板化;GO:0006468.蛋白质磷酸化;GO:0006351转录,DNA模板化;GO:0055114.过时的氧化还原过程;GO:0009813.类黄酮生物合成过程;GO:0044550.次生代谢物的生物合成过程;GO:0007165.信号转导;GO:0051603.参与细胞蛋白质分解代谢过程的蛋白质水解;GO:0052696.类黄酮葡萄糖醛酸化;GO:0009737.脱落酸响应;GO:0009409.冷响应;GO:0046686.镉离子响应;GO:0007166.细胞表面受体信号通路;GO:0009651.盐胁迫响应;GO:0055085.跨膜运输;GO:0009414.失水响应;GO:0043161.蛋白酶体介导泛素依赖性蛋白分解代谢;GO:0050832.真菌防御响应;GO:0006508.蛋白质水解;GO:0009416.光刺激响应;GO:0009611.损伤响应;GO:0042742.细菌防御响应;GO:0007275.多细胞生物的发育;GO:0005634.细胞核;GO:0005886.质膜;GO:0005737.细胞质;GO:0016021.膜的整体成分;GO:0009507.叶绿体;GO:0005576.胞外区;GO:0005829.细胞溶质;GO:0005739.线粒体;GO:0016020.膜;GO:0009506.胞间连丝;GO:0005794.高尔基体;GO:0005783.内质网;GO:0043231.胞内膜;GO:0005618.细胞壁;GO:0009570.叶绿体基质;GO:0005515.蛋白结合;GO:0003674.分子功能;GO:0005524.ATP结合;GO:0004674.蛋白丝氨酸/苏氨酸激酶活性;GO:0003700.DNA-结合转录因子的活性;GO:0003677.DNA结合;GO:0046872.金属离子结合;GO:0016301.激酶活性;GO:0043565.特异性DNA结合序列;GO:0008270.锌离子结合。

Fig.6 GO enrichment analysis of DEGs between ygl7 and Changnong 35 GO:0008150.Biological-process; GO:0006952.Defense response; GO:0006355.Regulation of transcription, DNA-templated; GO:0006468.Protein phosphorylation; GO:0006351.Transcription,DNA-templated; GO:0055114.Obsolete oxidation-reduction process; GO:0009813.Flavonoid biosynthetic process; GO:0044550.Secondary metabolite biosynthetic process; GO:0007165.Signal transduction; GO:0051603.Proteolysis involved in cellular protein catabolic process; GO:0052696.Flavonoid glucuronidation; GO:0009737.Response to abscisic acid; GO:0009409.Response to cold; GO:0046686.Response to cadmium ion; GO:0007166.Cell surface receptor signaling pathway; GO:0009651.Response to salt stress; GO:0055085.Transmembrane transport; GO:0009414.Response to water deprivation; GO:0043161.Proteasome-mediated ubiquitin-dependent protein catabolic process; GO:0050832.Defense response to fungus; GO:0006508.Proteolysis; GO:0009416.Response to light stimulus; GO:0009611.Response to wounding; GO:0042742.Defense response to bacterium; GO:0007275.Protein ubiquitination; GO:0005634. Nucleus; GO:0005886. Plasma membrane; GO:0005737. Cytoplasm; GO:0016021.Integral component of membrane; GO:0009507. Chloroplast; GO:0005576.Extracellular region; GO:0005829.Cytosol; GO:0005739.Mitochondrionn; GO:0016020.Membrane; GO:0009506.Plasmodesma; GO:0005794. Golgi apparatus; GO:0005783. Endoplasmic reticulum; GO:0043231. Intracellular membrane; GO:0005618.Cell wall; GO:0009570. Chloroplast stroma; GO:0005515.Protein binding; GO:0003674.Molecular function; GO:0005524.ATP binding; GO:0004674.Protein serine/threonine kinase activity; GO:0003700. DNA-binding transcription factor activity; GO:0003677.DNA binding; GO:0046872.Metal ion binding;GO:0016301.Kinase activity;GO:0043565. Sequence-specific DNA binding; GO:0008270.Zinc ion binding.

图7 ygl7与长农35号之间DEGs的 KEGG途径富集分析 sita04626.植物-病原体互作;sita00940.苯丙素的生物合成;sita00941.黄酮类生物合成;sita00904.二萜类生物合成;sita00196.光合作用的-天线蛋白; sita00073.角质、软碱和蜡的生物合成;sita00500.淀粉和蔗糖代谢淀粉和蔗糖代谢;sita00945.类二苯/芳基的生物合成;sita00942.花青素生物合成;sita00592.α-亚麻酸代谢;sita00360.苯丙氨酸代谢;sita00900.萜类主干生物合;sita00480.谷胱甘肽代谢;sita00062.脂肪酸延伸;sita00333.原胞苷生物合成;sita00944.黄酮和黄酮醇的生物合成;sita00052.半乳糖代谢;sita01053.铁载体基非核糖体肽的生物合成;sita00901.惰性生物碱生物合成;sita00903.柠檬烯和针烯降解。

Fig.7 KEGG pathway enrichment analysis of DEGs between ygl7 and Changnong 35 sita04626.Plant-pathogen interaction; sita00940.Phenylpropanoid biosynthesis; sita00941.Flavonoid biosynthesis; sita00904.Diterpenoid biosynthesis; sita00196.Photosynthesis-antenna proteins; sita00073.Cutin, suberine and wax biosynthesis; sita00500.Starch and sucrose metabolism; sita00945.Stilbenoid, diarylheptanoid biosynthesis; sita00942.Anthocyanin biosynthesis; sita00592.Alpha-Linolenic acid metabolism; sita00360.Phenylalanine metabolism; sita00900.Terpenoid backbone biosynthesis; sita00480.Glutathione metabolism; sita00062.Fatty acid elongation; sita00333.Prodigiosin biosynthesis; sita00944.Flavone and flavonol biosynthesis; sita00052.Galactose metabolism; sita01053.Biosynthesis of siderophore group nonribosomal peptides; sita00901.Indole alkaloid biosynthesis; sita00903.Limonene and pinene degradation.

表3 定位区间内差异表达基因及预测功能

Tab.3 DEGs and predictive functions within the localization interval

基因 Gene	预测功能 Putative functions
Seita.7G290300	镁螯合酶Ⅰ亚基
Seita.7G289400	未知功能蛋白
Seita.7G286500	CBS结构域蛋白
Seita.7G285700	假定蛋白
Seita.7G289200	假定蛋白
Seita.7G289900	DNAJ GFA2伴侣蛋白
Seita.7G288400	推测的抗病rpp13样蛋白3亚型X1
Seita.7G289300	假定蛋白
Seita.7G286000	未知功能蛋白
Seita.7G287300	未知功能蛋白
Seita.7G291100	mRNA前体剪接因子cwc22
Seita.7G288800	天冬氨酸蛋白酶保护细胞
Seita.7G285600	未知功能蛋白
Seita.7G286100	未知功能蛋白

图8 SiYGL7突变位点及表达 A.SiYGL7基因结构及突变位点;B.Seita.7G290300在长农35号和ygl7不同时期叶片中的相对表达。

Fig.8 Mutation sites and expression of SiYGL7 A.SiYGL7 gene structure and mutation sites;B.Relative expression levels of Seita.7G290300 in leaves of Changnong 35 and ygl7 at different stages.

图9 qRT-PCR分析 A.SiYGL7基因在长农35号不同组织中的表达;B.野生型和突变体ygl7中叶绿素合成及光合作用相关基因的qRT-PCR分析。

Fig.9 qRT-PCR analysis A. Expression of SiYGL7 gene in different tissues of Changnong 35;B.qRT-PCR analysis of genes related to chlorophyll synthesis and photosynthesis in wild type and mutant ygl7 at seedling stage.

图10 SiYGL7与MORF2在酵母中互作

Fig.10 The interaction between SiYGL7 and MORF2 in yeast

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谷子黄绿叶突变体ygl7的精细定位及候选基因分析

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