Screening of candidate genes for plant height in forage oat （Avena sativa） through combined transcriptome and proteome analysis

doi:10.11686/cyxb2024418

Abstract

Abstract:

Forage oat （Avena sativa） is a high-yielding， high-quality， and stress-resistant forage that plays a significant role in China’s forage industry. In this study， high-throughput transcriptome sequencing （RNA-Seq） and quantitative proteomic analysis were performed on stem nodes and internode tissues from high-stalk （No.972） and low-stalk （No.1289） forage oat varieties. The aim was to identify differentially expressed genes （DEGs） and differentially expressed proteins （DEPs） between these two varieties to discover plant height-related genes in A. sativa. We identified 22762 DEGs and 3934 DEPs between the two germplasm lines. Further integrated analyses revealed 1147 overlapping DEGs/DEPs in the transcriptome and proteome datasets. Gene Ontology （GO） enrichment and KEGG pathway analysis indicated that these 1147 overlapping genes/proteins were significantly enriched in pathways associated with cell growth， metabolism， and cell wall formation. Among these DEGs/DEPs， 10 candidate transcription factors were identified through transcription factor analysis， and their transcription profiles were validated using quantitative real-time polymerase chain reaction （qRT-PCR） analyses. The transcription patterns of the ten candidate genes were highly consistent with those predicted from the transcriptomic and proteomic data， confirming the reliability of the sequencing results. Tissue-specific analyses of their transcriptional profiles showed that these ten candidate genes exhibited higher transcript levels in stems and nodes but lower levels in other tissues， suggesting that they play roles in regulating plant height in forage oat. In summary， through integrated transcriptomic and proteomic analyses， along with differential gene function annotation and transcription factor analyses， we identified ten candidate genes related to plant height in forage oat. These candidate genes primarily regulate processes such as cell growth， metabolism， and cell wall development， contributing to plant height formation in forage oat. These findings provide a foundation for further exploration of the molecular mechanisms underlying plant height and offer key candidate genes for forage oat breeding programs.

Key words: forage oat, plant height, transcriptome, proteome, combined analysis

Zhi-peng ZHANG, Qing-xue JIANG, Xin-yue ZHOU, Tong MIAO, Jun TANG, Deng-xia YI, Xue-min WANG, Lin MA. Screening of candidate genes for plant height in forage oat （Avena sativa） through combined transcriptome and proteome analysis[J]. Acta Prataculturae Sinica, 2025, 34(9): 147-161.

Figures/Tables 15

References 31

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基因ID Gene ID	正向引物Forward primer （5′-3′）	反向引物Reverse primer （5′-3′）
AVESA.00010b.r1.2CG3384710	CATCACCGCCAACATCACC	GCAGCCTCCACGATCTCC
AVESA.00010b.r1.3CG0669440	AAGAAGTTGGTGGTTATTGG	CTGCTTCCTTACCTCTCC
AVESA.00010b.r1.4AG2537620	CGGACCTACAACCAGAACC	CAGCCCAAAGTGCCTCTC
AVESA.00010b.r1.5DG0437330	CGGTCTTCTTGCGAATGG	CGATGTACTCCACGAAACC
AVESA.00010b.r1.3CG2847600	ATGCTCTTCACCGTCTCC	CTGGTTGATGTAGTCCTTGG
AVESA.00010b.r1.4AG1741330	GCATAGCGAGCAGTGAAGAG	ACACGGAGATCAGCAGAGC
AVESA.00010b.r1.2CG1087750	CTCCTCCTCCTGCTCGTC	GTGCCCTTGAACCTGTGG
AVESA.00010b.r1.2DG0384520	TGTGCTACGGGAGAAACG	AACTTGATGCCGCTATTCG
AVESA.00010b.r1.2CG0426050	ACCTTCACGCTCAACTTCTCC	GCTCTCCACGCAGTTCTCC
AVESA.00010b.r1.4AG0885780	AACTTCCCGTGCTCTGATCC	GTCGTCTCGTCGGCTTCC

基因ID Gene ID	正向引物Forward primer （5′-3′）	反向引物Reverse primer （5′-3′）
AVESA.00010b.r1.2CG3384710	CATCACCGCCAACATCACC	GCAGCCTCCACGATCTCC
AVESA.00010b.r1.3CG0669440	AAGAAGTTGGTGGTTATTGG	CTGCTTCCTTACCTCTCC
AVESA.00010b.r1.4AG2537620	CGGACCTACAACCAGAACC	CAGCCCAAAGTGCCTCTC
AVESA.00010b.r1.5DG0437330	CGGTCTTCTTGCGAATGG	CGATGTACTCCACGAAACC
AVESA.00010b.r1.3CG2847600	ATGCTCTTCACCGTCTCC	CTGGTTGATGTAGTCCTTGG
AVESA.00010b.r1.4AG1741330	GCATAGCGAGCAGTGAAGAG	ACACGGAGATCAGCAGAGC
AVESA.00010b.r1.2CG1087750	CTCCTCCTCCTGCTCGTC	GTGCCCTTGAACCTGTGG
AVESA.00010b.r1.2DG0384520	TGTGCTACGGGAGAAACG	AACTTGATGCCGCTATTCG
AVESA.00010b.r1.2CG0426050	ACCTTCACGCTCAACTTCTCC	GCTCTCCACGCAGTTCTCC
AVESA.00010b.r1.4AG0885780	AACTTCCCGTGCTCTGATCC	GTCGTCTCGTCGGCTTCC

样品名称 Sample	过滤后数据 Clean reads （M）	过滤后序列 Clean bases （G）	碱基质量>30的占比Q₃₀ （%）	GC含量 GC content （%）	唯一比对（对比率） Uniquely mapped （mapping ratio， %）	多方比对（对比率） Multiple mapped （mapping ratio， %）
H-1	43.09	6.11	94.99	53.21	83.39	14.16
H-2	43.05	6.13	95.07	52.98	83.80	14.22
H-3	43.08	6.13	94.84	53.08	83.92	14.09
L-1	43.13	6.33	94.06	51.53	85.83	11.67
L-2	44.62	6.57	94.58	51.38	85.79	11.62
L-3	42.36	6.23	93.99	51.16	85.83	11.60

样品名称 Sample	过滤后数据 Clean reads （M）	过滤后序列 Clean bases （G）	碱基质量>30的占比Q₃₀ （%）	GC含量 GC content （%）	唯一比对（对比率） Uniquely mapped （mapping ratio， %）	多方比对（对比率） Multiple mapped （mapping ratio， %）
H-1	43.09	6.11	94.99	53.21	83.39	14.16
H-2	43.05	6.13	95.07	52.98	83.80	14.22
H-3	43.08	6.13	94.84	53.08	83.92	14.09
L-1	43.13	6.33	94.06	51.53	85.83	11.67
L-2	44.62	6.57	94.58	51.38	85.79	11.62
L-3	42.36	6.23	93.99	51.16	85.83	11.60

变化趋势 Change trend	转录因子家族 Transcription factor family	数量 Number
转录本与蛋白共同上调Transcripts and proteins jointly up-regulated	Nin-like	1
转录本与蛋白共同下调Transcripts and proteins jointly down-regulated	Trihelix	3
	FAR1	1
	ERF	1
转录本下调、蛋白上调Transcript down-regulation and protein up-regulation	TCP	1
	bHLH	1
	NF	1
转录本上调、蛋白下调Transcript up-regulation and protein down-regulation	Whirly	1
	NAC	1
	B3	1