基于转录组分析花生单粒精播与多粒穴播植株荚果产量差异的分子机制

doi:10.3864/j.issn.0578-1752.2023.22.003

Abstract

Abstract:

【Objective】In China, in order to ensure the emergence rate and quality of seedlings, the field often adopts multiple seed seeding. However, inter-plant competition in multi-seeds sowing often limits the growth and eventual yield of subsequent plants. In order to solve this contradiction, the team studied and established the high-yield cultivation technology of single-seed precision seeding. The combination of seed saving and yield increase effect of single-seed precision seeding technology can bring greater benefits and realize cost savings and increased efficiency. The differentially expressed genes in peanut leaves, roots and pods under different planting methods were used to explore the regulatory mechanism of single-seeding precision sowing to improve peanut pod yield, providing theoretical basis and technical support for further promoting peanut high yield and high efficiency. 【Method】Peanut variety Huayu 25 was used as the test material, while the yield related indexes of single-seed sowing and multi-seeds sowing were determined. Inverted three leaves, taproot and lateral root of peanut at 30 days after flowering and peanut pod at young fruit stage of chicken head were selected for transcriptome sequencing, and the yield differences of peanut under different sowing methods were revealed on the molecular level. 【Result】Compared with multi-seeds sowing, the pod number per plant, full fruit number per plant, fruit weight per plant and economic coefficient of single-seed sowing were significantly increased. After the transcriptome data is assembled, each library contains an average of 44.3 million readings. Through the analysis of differentially expressed genes, GO and KEGG pathways in different combinations, it was found that the expression levels of transcription factors, photosystem Ⅱ oxygen-releasing complex, chloroplast membrane, oxidation-reduction reaction and other genes involved in the processes of GA signal and light signal transduction were increased in the leaves of plants under single-seed sowing compared with multi-grain cave seeding. Genes related to phenylpropyl metabolism pathway induced by biological and abiotic stress were significantly enriched in roots, including cytochrome P450 gene, oxidation-reduction gene, stress response transcription factor and signal regulatory protein. The accumulation of starch and sucrose metabolism genes was more conducive to seed kernel enrichment during pod development. 【Conclusion】The up-regulated expression of photosynthetic related genes in peanut leaves at seedling stage could promote the increase of photosynthetic efficiency, which was closely related to the increase of yield. Single-seed sowing improved the ability of root system to resist biological and abiotic stress, and combined with the up-regulation of energy and material related genes in the early stage of pod development, it was beneficial for the development of underground peanut pod and increased peanut yield.

Key words: peanut, single seed precision sowing, yield, RNA-Seq, photosynthesis, phenylpropanoid pathway

YANG Sha, LIU KeKe, LIU Ying, GUO Feng, WANG JianGuo, GAO HuaXin, MENG JingJing, ZHANG JiaLei, WAN ShuBo. The Molecular Mechanism of Pod Yield Difference Between Single- Seeding Precision Sowing and Multi-Seeds Sowing of Peanut Based on Transcriptome Analysis[J].Scientia Agricultura Sinica, 2023, 56(22): 4386-4402.

Figures/Tables 11

Fig. 1

Table 1

Table 2

Fig. 2

Table 3

GO and KEGG enrichment analysis of DEGs in peanut leaves, roots and pods under different sowing methods"

说明 Description	上调 Up	下调 Down
GO
SL vs FL	序列特异性DNA结合Sequence-specific DNA binding	核小体组装、染色质组装、核小体组织、DNA包装 Nucleosome assembly, chromatin assembly, nucleosome organization, DNA packaging
SL vs TL	光系统Ⅱ放氧复合体、膜外成分、类囊体膜、氧化还原复合体、光系统Ⅱ Photosystem Ⅱoxygen evolving complex, extrinsic component of membrane, thylakoid membrane, oxidoreductase complex, photosystem Ⅱ	核小体组装、染色质组装、核小体组织、DNA包装、染色质组装或卸载 Nucleosome assembly, chromatin assembly, nucleosome organization, DNA packaging, chromatin assembly or disassembly
KEGG
SL vs FL	植物-病原体互作、甘油脂代谢类胡萝卜素、生物合成、甘油磷脂代谢 Plant-pathogen interaction, glycerolipid metabolism, carotenoid biosynthesis, glycerophospholipid metabolism	硫胺素代谢、2-氧代羧酸代谢 Thiamine metabolism, 2-Oxocarboxylic acid metabolism
SL vs TL	甘油脂代谢、卟啉和叶绿素代谢 Glycerolipid metabolism, porphyrin and chlorophyll metabolism	柠檬酸循环、氨基酸生物合成、精氨酸和脯氨酸代谢、半胱氨酸和蛋氨酸代谢 Citrate cycle, biosynthesis of amino acids, arginine and proline metabolism, cysteine and methionine metabolism
GO
SR vs FR	对生物刺激的响应、对氧化胁迫的响应、过氧化物酶活性、氧化还原酶活性、抗氧化剂活性 Response to biotic stimulus, response to oxidative stress, peroxidase activity, oxidoreductase activity, antioxidant activity	二糖代谢过程、低聚糖生物合成过程、丝氨酸水解酶活性 Disaccharide metabolic process, oligosaccharide biosynthetic process, serine hydrolase activity
SR vs TR	过氧化物酶活性、氧化还原酶活性、细胞壁、对氧化胁迫响应、多种有机体过程 Peroxidase activity, oxidoreductase activity, cell wall, response to oxidative stress, multi-organism process	生长素响应、糖脂运输、糖脂转运蛋白活性、磺基转移酶活性 Response to auxin, glycolipid transport, glycolipid transporter activity, sulfotransferase activity
KEGG
SR vs FR	苯丙素生物合成、MAPK信号途径、植物-病原体互作、谷胱甘肽代谢 Phenylpropanoid biosynthesis, MAPK signaling pathway, plant- pathogen interaction, glutathione metabolism	淀粉和蔗糖代谢、ABC转运蛋白 Starch and sucrose metabolism, ABC transporters
SR vs TR	植物-病原体互作、苯丙素生物合成、MAPK信号途径、类黄酮生物合成 Plant-pathogen interaction, phenylpropanoid biosynthesis, MAPK signaling pathway, flavonoid biosynthesis	剪接体、嘌呤代谢、内质网中的蛋白质加工、内吞作用 Spliceosome, purine metabolism, protein processing in endoplasmic reticulum, endocytosis
GO
SP vs FP	细胞外区域、聚半乳糖醛酸酶活性、内肽酶活性 Extracellular region, polygalacturonase activity, endopeptidase activity	金属离子运输、细胞葡聚糖代谢过程、质外体、序列特异性DNA结合 Metal ion transport, cellular glucan metabolic process, apoplast, sequence-specific DNA binding
SP vs TP	对生物刺激的反应、多糖代谢过程、防御反应、纤维素合酶活性、聚半乳糖醛酸酶活性 Response to biotic stimulus, polysaccharide metabolic process, defense response, cellulose synthase activity, polygalacturonase activity	DNA复制、DNA代谢过程、染色体、DNA包装复合体、微管结合 DNA replication, DNA metabolic process, chromosome, DNA packaging complex, microtubule binding
KEGG
SP vs FP	苯丙素生物合成、淀粉和蔗糖代谢 Phenylpropanoid biosynthesis, starch and sucrose metabolism	植物-病原体互作、脂肪酸降解 Plant-pathogen interaction, fatty acid degradation
SP vs TP	苯丙素生物合成、卟啉与叶绿素代谢、生长素响应、淀粉和蔗糖代谢 Phenylpropanoid biosynthesis, porphyrin and chlorophyll metabolism, auxin response, starch and sucrose metabolism	DNA复制、类黄酮生物合成、错配修复、色氨酸代谢、糖酵解/糖异生 DNA replication, flavonoid biosynthesis, mismatch repair, tryptophan metabolism, glycolysis/gluconeogenesis

Table 3

Table 4

List of differentially expressed genes related to high yield in leaf, root and pod under single-seed sowing"

基因ID Gene_ID	基因说明 Gene description	比较组 Comparison group
转录因子Transcription factor			SL vs FL
arahy.Tifrunner.gnm1.ann1.DV7QWZ	MYB类DNA结合域MYB-like DNA-binding domain	2.62
arahy.Tifrunner.gnm1.ann1.HAG9AR	MYB类DNA结合域MYB-like DNA-binding domain	1.86
arahy.Tifrunner.gnm1.ann1.C9M3KU	MYB类DNA结合域MYB-like DNA-binding domain	1.78
arahy.Tifrunner.gnm1.ann1.F9DTFM	GRAS结构域家族GRAS domain family	2.19
arahy.Tifrunner.gnm1.ann1.CF7XAP	GRAS结构域家族GRAS domain family	1.67
arahy.Tifrunner.gnm1.ann1.8X00QX	GRAS结构域家族GRAS domain family	1.68
arahy.Tifrunner.gnm1.ann1.52HH2Q	DnaJ结构域DnaJ domain	2.74
arahy.Tifrunner.gnm1.ann1.BDT6Z1	DnaJ结构域DnaJ domain	2.87
arahy.Tifrunner.gnm1.ann1.206U1W	WRKY DNA结合域WRKY DNA-binding domain	2.81
arahy.Tifrunner.gnm1.ann1.KK3V44	WRKY DNA结合域WRKY DNA-binding domain	2.01
arahy.Tifrunner.gnm1.ann1.EXJ5K8	WRKY DNA结合域WRKY DNA-binding domain	1.98
arahy.Tifrunner.gnm1.ann1.TC7Y0P	WRKY DNA结合域WRKY DNA-binding domain	2.48
arahy.Tifrunner.gnm1.ann1.N4K2VQ	HSP70蛋白HSP70 protein	2.05
arahy.Tifrunner.gnm1.ann1.LTRJ1V	HSP70蛋白HSP70 protein	1.82
arahy.Tifrunner.gnm1.ann1.ECZ3V7	HSP70蛋白HSP70 protein	1.95
		SL vs TL
arahy.Tifrunner.gnm1.ann1.ZTD7SX	WRKY DNA结合域WRKY DNA-binding domain	3.48
arahy.Tifrunner.gnm1.ann1.13YX47	WRKY DNA结合域WRKY DNA-binding domain	2.62
arahy.Tifrunner.gnm1.ann1.EXJ5K8	WRKY DNA结合域WRKY DNA-binding domain	2.36
arahy.Tifrunner.gnm1.ann1.WH6N3S	WRKY DNA结合域WRKY DNA-binding domain	3.51
arahy.Tifrunner.gnm1.ann1.TC7Y0P	WRKY DNA结合域WRKY DNA-binding domain	1.69
arahy.Tifrunner.gnm1.ann1.LTRJ1V	HSP70蛋白Hsp70 protein	1.88
arahy.Tifrunner.gnm1.ann1.N4K2VQ	HSP70蛋白Hsp70 protein	1.91
arahy.Tifrunner.gnm1.ann1.PR7AYB	MYB类DNA结合域Myb-like DNA-binding domain	1.74
arahy.Tifrunner.gnm1.ann1.UW10HH	DnaJ结构域DnaJ domain	1.29
arahy.Tifrunner.gnm1.ann1.BDT6Z1	DnaJ结构域DnaJ domain	2.44
arahy.Tifrunner.gnm1.ann1.6YZ37K	DnaJ结构域DnaJ domain	1.55
arahy.Tifrunner.gnm1.ann1.FPX6WQ	GRAS结构域家族GRAS domain family	1.38
arahy.Tifrunner.gnm1.ann1.F9DTFM	GRAS结构域家族GRAS domain family	2.17
arahy.Tifrunner.gnm1.ann1.3U6Z4I	GRAS结构域家族GRAS domain family	1.52
MAPK信号途径MAPK signal pathway		SR vs FR
arahy.Tifrunner.gnm1.ann1.VQ5KVR	聚酮环化酶Polyketide cyclase	1.18
arahy.Tifrunner.gnm1.ann1.UY7VYK	氨基转移酶Ⅰ类和Ⅱ类Aminotransferase classⅠandⅡ	2.33
arahy.Tifrunner.gnm1.ann1.744VXT	半胱氨酸富集分泌蛋白家族Cysteine-rich secretory protein family	5.92
arahy.Tifrunner.gnm1.ann1.WP6DIZ	半胱氨酸富集分泌蛋白家族Cysteine-rich secretory protein family	10.14
arahy.Tifrunner.gnm1.ann1.SLKX21	半胱氨酸富集分泌蛋白家族Cysteine-rich secretory protein family	8.91
arahy.Tifrunner.gnm1.ann1.T12YHH	半胱氨酸富集分泌蛋白家族Cysteine-rich secretory protein family	10.98
arahy.Tifrunner.gnm1.ann1.WFS9KG	NADPH 氧化酶NADPH oxidase	3.56
		SR vs TR
arahy.Tifrunner.gnm1.ann1.XA421G	蛋白激酶结构域Protein kinase domain	1.61
arahy.Tifrunner.gnm1.ann1.RQ7QZ9	蛋白激酶结构域Protein kinase domain	1.27
arahy.Tifrunner.gnm1.ann1.CD5B6Y	蛋白磷酸酶2C Protein phosphatase 2C	1.39
arahy.Tifrunner.gnm1.ann1.GYA3XJ	蛋白激酶结构域Protein kinase domain	2.02
arahy.Tifrunner.gnm1.ann1.SQ16A9	蛋白激酶结构域Protein kinase domain	1.65
arahy.Tifrunner.gnm1.ann1.UY7VYK	氨基转移酶Ⅰ类和Ⅱ类Aminotransferase classⅠandⅡ	2.64
arahy.Tifrunner.gnm1.ann1.S2Q0RR	氨基转移酶Ⅰ类和Ⅱ类Aminotransferase classⅠandⅡ	4.41

Table 4

Table 5

Significant GO terms for DEGs in SP vs TP"

分类 Category	GO ID	描述 Description	基因占比 Gene ratio	Bg比例 Bg ratio	<BOLD>P</BOLD>	padj	基因号 <BOLD>G</BOLD>ene ID	基因 Gene	数量 Count
生物过程 Biological processes	GO:0009733	生长素响应 Response to auxin	4/1852	56/15502	0.914927	1	arahy.Tifrunner.gnm1.ann1.T2QDAL/arahy.Tifrunner.gnm1.ann1.DWH8JW/arahy.Tifrunner.gnm1.ann1.SE3NL1/arahy.Tifrunner.gnm1.ann1.3U3G48	arahy.T2QDAL/arahy.DWH8JW/arahy.SE3NL1/arahy.3U3G48	4
	GO:0016567	蛋白泛素化 Protein ubiquitination	7/1852	93/15502	0.938425	1	arahy.Tifrunner.gnm1.ann1.VNN39M/arahy.Tifrunner.gnm1.ann1.AS1G8G/arahy.Tifrunner.gnm1.ann1.2EPV6W/novel.3009/arahy.Tifrunner.gnm1.ann1.U5RGLT/arahy.Tifrunner.gnm1.ann1.SWIT4Z/arahy.Tifrunner.gnm1.ann1.3VLA0M	arahy.VNN39M/arahy.AS1G8G/arahy.2EPV6W/-/arahy.U5RGLT/arahy.SWIT4Z/arahy.3VLA0M	7
	GO:0032446	蛋白修饰 Protein modification by small protein conjugation	7/1852	95/15502	0.946406	1	arahy.Tifrunner.gnm1.ann1.VNN39M/arahy.Tifrunner.gnm1.ann1.AS1G8G/arahy.Tifrunner.gnm1.ann1.2EPV6W/novel.3009/arahy.Tifrunner.gnm1.ann1.U5RGLT/arahy.Tifrunner.gnm1.ann1.SWIT4Z/arahy.Tifrunner.gnm1.ann1.3VLA0M	arahy.VNN39M/arahy.AS1G8G/arahy.2EPV6W/-/arahy.U5RGLT/arahy.SWIT4Z/arahy.3VLA0M	7
	GO:0070647	蛋白修饰 Protein modification by small protein conjugation	9/1852	156/15502	0.996949	1	arahy.Tifrunner.gnm1.ann1.VNN39M/arahy.Tifrunner.gnm1.ann1.AS1G8G/arahy.Tifrunner.gnm1.ann1.2EPV6W/novel.3009/arahy.Tifrunner.gnm1.ann1.U5RGLT/arahy.Tifrunner.gnm1.ann1.SWIT4Z/arahy.Tifrunner.gnm1.ann1.IA0PF7/arahy.Tifrunner.gnm1.ann1.3VLA0M/novel.4376	arahy.VNN39M/arahy.AS1G8G/arahy.2EPV6W/-/arahy.U5RGLT/arahy.SWIT4Z/arahy.IA0PF7/arahy.3VLA0M/-	9
细胞组成 Cell composition	GO:0009507	叶绿体 Chloroplast	4/629	18/5537	0.139551	0.853529	arahy.Tifrunner.gnm1.ann1.L27P26/arahy.Tifrunner.gnm1.ann1.ZGZX3T/arahy.Tifrunner.gnm1.ann1.RCVM4C/arahy.Tifrunner.gnm1.ann1.L0KK3Q	arahy.L27P26/arahy.ZGZX3T/arahy.RCVM4C/arahy.L0KK3Q	4
分子功能 Molecular function	GO:0004842	泛素蛋白转移酶活性 Ubiquitin-protein transferase activity	7/2629	125/23997	0.987201	1	arahy.Tifrunner.gnm1.ann1.VNN39M/arahy.Tifrunner.gnm1.ann1.AS1G8G/arahy.Tifrunner.gnm1.ann1.2EPV6W/novel.3009/arahy.Tifrunner.gnm1.ann1.U5RGLT/arahy.Tifrunner.gnm1.ann1.SWIT4Z/arahy.Tifrunner.gnm1.ann1.3VLA0M	arahy.VNN39M/arahy.AS1G8G/arahy.2EPV6W/-/arahy.U5RGLT/arahy.SWIT4Z/arahy.3VLA0M	7
分子功能 Molecular function	GO:0019787	泛素类蛋白转移酶活性 Ubiquitin-like protein transferase activity	7/2629	125/23997	0.987201	1	arahy.Tifrunner.gnm1.ann1.VNN39M/arahy.Tifrunner.gnm1.ann1.AS1G8G/arahy.Tifrunner.gnm1.ann1.2EPV6W/novel.3009/arahy.Tifrunner.gnm1.ann1.U5RGLT/arahy.Tifrunner.gnm1.ann1.SWIT4Z/arahy.Tifrunner.gnm1.ann1.3VLA0M	arahy.VNN39M/arahy.AS1G8G/arahy.2EPV6W/-/arahy.U5RGLT/arahy.SWIT4Z/arahy.3VLA0M	7

Table 5

Fig. 3

Fig. 4

Fig. 5

Fig. 6

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处理 Treatment	单株荚果数 Pods number per plant	单株饱果数 Full pods number per plant	单株果重 Pod weight per plant (g)	经济系数 Economic coefficient
单粒精播Single-seeding sowing	36.65a	24.53a	49.76a	0.50a
三粒穴播Three-seeds sowing	25.36b	15.28b	30.08b	0.47b
五粒穴播Five-seeds sowing	18.32c	11.57c	21.61c	0.44c

样品名称 Sample	总Reads数 Total Reads	比对Reads数（比例，%） Mapped Reads (rate, %)	唯一比对Reads数（比例，%） Unique mapped Reads (rate, %)	GC (%)	Q30 (%)
SL1	44772228	38582620(86.18)	33161778(74.07)	44.66	92.74
SL2	46785506	32233417(68.90)	27751126(59.32)	43.93	93.31
SL3	44432256	32447247(73.03)	28195266(63.46)	43.72	92.98
TL1	45116924	34153847(75.70)	29418012(65.20)	43.99	92.73
TL2	43591552	31397226(72.03)	27154180(62.29)	43.86	92.28
TL3	42632812	26466552(62.08)	22807469(53.50)	43.4	92.07
FL1	44072996	35858508(81.36)	31020506(70.38)	44.3	92.71
FL2	45559666	43974477(96.52)	38094612(83.61)	44.79	92.81
FL3	46187310	31797098(68.84)	27572825(59.70)	43.88	93.07
SR1	47377928	43355223(91.51)	37493509(79.14)	44.5	92.19
SR2	45195968	41281627(91.34)	36025392(79.71)	43.88	92.36
SR3	45334094	41321686(91.15)	35598328(78.52)	44.39	95.29
TR1	41574892	37787724(90.89)	32604339(78.42)	44.05	92.44
TR2	41568054	38387877(92.35)	33053700(79.52)	44.18	92.58
TR3	42011010	37666147(89.66)	32554905(77.49)	44.1	92.28
FR1	44329820	40528849(91.43)	35108182(79.20)	44.04	92.27
FR2	45598270	40336991(88.46)	34921268(76.58)	43.95	92.45
FR3	43519726	39373659(90.47)	34031257(78.20)	44.14	92.91
SP1	49413724	47483883(96.09)	41146339(83.27)	43.03	93
SP2	45104370	42742170(94.76)	36636507(81.23)	44.65	92.98
SP3	43696522	41148585(94.17)	35223387(80.61)	44.6	93.11
TP1	44665792	43185909(96.69)	37602935(84.19)	44.34	92.98
TP2	42940308	40711465(94.81)	34920983(81.32)	44.29	93.2
TP3	40846304	38967000(95.40)	33445775(81.88)	43.97	93.65
FP1	41393174	38868585(93.90)	33223381(80.26)	44.02	93.27
FP2	44726794	42588347(95.22)	36499220(81.60)	43.88	93.13
FP3	43701578	41660050(95.33)	35997345(82.37)	43.46	93.61

The Molecular Mechanism of Pod Yield Difference Between Single- Seeding Precision Sowing and Multi-Seeds Sowing of Peanut Based on Transcriptome Analysis

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