Fine Mapping and Candidate Gene Analysis of Yellow-Green Leaf Mutant ygl7 in Foxtail Millet

doi:10.7668/hbnxb.20194486

Abstract

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

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.

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Figures/Tables 13

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.

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

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.

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.

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

Fig.4 Fine mapping of ygl7

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.

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.

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.

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

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.

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.

Fig.10 The interaction between SiYGL7 and MORF2 in yeast

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