Preliminary screening of Northern Salix (Salix psammophila) architecture related genes based on RNA-Seq analysis and quantitative PCR technique

doi:10.3969/j.issn.1004-1524.20221404

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (10): 2332-2345.DOI: 10.3969/j.issn.1004-1524.20221404

• Horticultural Science • Previous Articles Next Articles

Preliminary screening of Northern Salix (Salix psammophila) architecture related genes based on RNA-Seq analysis and quantitative PCR technique

HE Rong¹(), ZHAO Kai¹, HE Yujiao¹, ALATENG Suhe², WANG Aijun³, NING Jing³, HAN Ruoshuang⁴, SUN Guirong², ZHANG Guosheng¹^,^*()

1. College of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, China
2. Forest General Site of Erdos, Erdos 014300, Inner Mongolia, China
3. Inner Mongolia Forestry Scientific Research Institute, Hohhot 010013, China
4. Inner Mongolia Autonomous Region Forestry and Grassland Seedling General Station, Hohhot 010010, China

Received:2022-09-27 Online:2023-10-25 Published:2023-10-31

Abstract

Abstract:

In order to construct a molecularly assisted breeding system for efficient targeted breeding of Salix psammophila architectures, a combination of transcriptome sequencing in the hydroponic population and quantitative PCR analysis in the field training population was used to explore candidate gene mining techniques related to Salix psammophila architectures, using the correlation coefficient between gene expression (FPKM value) and ratio of crown and height in RNA-Seq analysis as predictive values. The results showed that there was a correlation between ratio of crown and height (plant architecture characteristic value) and FPKM value in Salix psammophila, and the trend remained largely consistent in the hydroponic prediction population and field training population. The predicted values of plant architecture (or branching)-related genes (TAC2, LAZY1b, ZFP4, TB1, SPA2, ABF2 and PYL1) reported in the literature ranged from 0 to 0.6, and the predicted values of ATX1, RFK1 and FHY1 genes (not reported to be plant architecture-related) were higher (0.6 to 1.0). The two-gene combination (ATX1+FHY1) was selected as the gene for the identification of Salix psammophila architectures according to the principle of “the least number of genes and the highest correlation coefficient”. Morphology and transcriptomics as a whole are the characteristics of this study, and the results can also provide a theoretical basis for molecularly assisted breeding of other plants and other traits.

Key words: ratio of crown and height, correlation coefficient, transcriptome sequencing technology, quantitative real-time PCR, gene mining, Salix psammophila

CLC Number:

S793

HE Rong, ZHAO Kai, HE Yujiao, ALATENG Suhe, WANG Aijun, NING Jing, HAN Ruoshuang, SUN Guirong, ZHANG Guosheng. Preliminary screening of Northern Salix (Salix psammophila) architecture related genes based on RNA-Seq analysis and quantitative PCR technique[J]. Acta Agriculturae Zhejiangensis, 2023, 35(10): 2332-2345.

Figures/Tables 8

References 27

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组别 Group	无性系号 Asexual line number	冠高比 Ratio of crown and height	组别 Group	无性系号 Asexual line number	冠高比 Ratio of crown and height	组别 Group	无性系号 Asexual line number	冠高比 Ratio of crown and height
第一组	17-13	0.26	第二组	17-17	0.66	第三组	11-44	0.81
Group 1	10-15	0.45	Group 2	8-38	0.66	Group 3	2-15	0.81
	14-32	0.46		11-32	0.66		4-30	0.81
	8-36	0.46		12-34	0.67		14-26	0.82
	11-30	0.51		5-36	0.67		8-14	0.82
	7-6	0.51		8-15	0.67		5-18	0.83
	6-34	0.52		5-4	0.68		14-44	0.85
	16-29	0.56		6-46	0.68		10-16	0.86
	5-30	0.60		5-16	0.69		11-42	0.87
	4-28	0.61		3-17	0.71		12-14	0.88
	11-16	0.62		20-13	0.72		7-22	0.88
	7-18	0.62		5-17	0.72		5-18	0.88
	5-2	0.64		3-36	0.73		8-16	0.89
	9-21	0.65		4-6	0.74		19-25	0.92
				4-24	0.75		4-16	0.92
				3-6	0.76		11-36	0.93
				8-22	0.78		5-42	0.93
				8-14	0.79		14-50	0.94
第四组	4-26	0.97	第五组	13-30	1.10	第六组	2-50	1.24
Group 4	15-28	0.97	Group 5	10-24	1.11	Group 6	4-40	1.27
	19-23	0.97		19-13	1.13		1-19	1.29
	6-4	0.97		8-18	1.14		1-2	1.30
	6-2	0.98		2-4	1.14		6-24	1.32
	10-8	0.98		1-28	1.15		7-50	1.33
	11-18	0.98		4-22	1.15		15-16	1.33
	12-2	0.99		11-21	1.15		7-21	1.35
	15-40	0.99		10-50	1.16		11-19	1.37
	3-20	1.00		6-12	1.19		2-24	1.37
	12-22	1.01		13-15	1.20		6-42	1.37
	11-20	1.01		6-30	1.21		6-8	1.45
	7-42	1.05		6-40	1.22		1-44	1.46
	21-13	1.05		7-38	1.23		8-40	1.51
	4-14	1.07					7-2	1.53
	21-17	1.08					9-14	1.54
							11-22	1.65

组别 Group	无性系号 Asexual line number	冠高比 Ratio of crown and height	组别 Group	无性系号 Asexual line number	冠高比 Ratio of crown and height	组别 Group	无性系号 Asexual line number	冠高比 Ratio of crown and height
第一组	17-13	0.26	第二组	17-17	0.66	第三组	11-44	0.81
Group 1	10-15	0.45	Group 2	8-38	0.66	Group 3	2-15	0.81
	14-32	0.46		11-32	0.66		4-30	0.81
	8-36	0.46		12-34	0.67		14-26	0.82
	11-30	0.51		5-36	0.67		8-14	0.82
	7-6	0.51		8-15	0.67		5-18	0.83
	6-34	0.52		5-4	0.68		14-44	0.85
	16-29	0.56		6-46	0.68		10-16	0.86
	5-30	0.60		5-16	0.69		11-42	0.87
	4-28	0.61		3-17	0.71		12-14	0.88
	11-16	0.62		20-13	0.72		7-22	0.88
	7-18	0.62		5-17	0.72		5-18	0.88
	5-2	0.64		3-36	0.73		8-16	0.89
	9-21	0.65		4-6	0.74		19-25	0.92
				4-24	0.75		4-16	0.92
				3-6	0.76		11-36	0.93
				8-22	0.78		5-42	0.93
				8-14	0.79		14-50	0.94
第四组	4-26	0.97	第五组	13-30	1.10	第六组	2-50	1.24
Group 4	15-28	0.97	Group 5	10-24	1.11	Group 6	4-40	1.27
	19-23	0.97		19-13	1.13		1-19	1.29
	6-4	0.97		8-18	1.14		1-2	1.30
	6-2	0.98		2-4	1.14		6-24	1.32
	10-8	0.98		1-28	1.15		7-50	1.33
	11-18	0.98		4-22	1.15		15-16	1.33
	12-2	0.99		11-21	1.15		7-21	1.35
	15-40	0.99		10-50	1.16		11-19	1.37
	3-20	1.00		6-12	1.19		2-24	1.37
	12-22	1.01		13-15	1.20		6-42	1.37
	11-20	1.01		6-30	1.21		6-8	1.45
	7-42	1.05		6-40	1.22		1-44	1.46
	21-13	1.05		7-38	1.23		8-40	1.51
	4-14	1.07					7-2	1.53
	21-17	1.08					9-14	1.54
							11-22	1.65

极强相关Highly related		中相关Moderate related		极弱相关Low related
基因序列号 Gene identifier	相关系数 Correlation coefficient	基因序列号 Gene identifier	相关系数 Correlation coefficient	基因序列号 Gene identifier	相关系数 Correlation coefficient
SapurV1A.0256s0170	0.907 8	SapurV1A.1836s0090	0.500 0	SapurV1A.1426s0040	0.001 1
SapurV1A.0223s0180	0.903 3	SapurV1A.0577s0020	0.499 9	SapurV1A.0163s0360	0.001 1
SapurV1A.0210s0130	0.903 2	SapurV1A.1223s0010	0.499 8	SapurV1A.1086s0060	0.001 1
SapurV1A.0374s0080	0.899 7	SapurV1A.3131s0030	0.499 4	SapurV1A.0621s0040	0.001 1
SapurV1A.1401s0040	0.894 3	SapurV1A.1712s0040	0.499 2	SapurV1A.0038s0420	0.001 1
SapurV1A.0744s0030	0.893 8	SapurV1A.1352s0010	0.498 9	SapurV1A.1001s0080	0.001 1
SapurV1A.0878s0060	0.892 7	MSTRG.2962	0.498 7	SapurV1A.2098s0020	0.001 1
SapurV1A.0222s0270	0.889 9	SapurV1A.0470s0220	0.498 5	SapurV1A.0052s0830	0.001 1
MSTRG.12920	0.878 7	SapurV1A.0307s0230	0.498 1	SapurV1A.1878s0050	0.001 1
SapurV1A.5044s0020	0.870 8	SapurV1A.0006s1570	0.498 1	MSTRG.22590	0.001 1

极强相关Highly related		中相关Moderate related		极弱相关Low related
基因序列号 Gene identifier	相关系数 Correlation coefficient	基因序列号 Gene identifier	相关系数 Correlation coefficient	基因序列号 Gene identifier	相关系数 Correlation coefficient
SapurV1A.0256s0170	0.907 8	SapurV1A.1836s0090	0.500 0	SapurV1A.1426s0040	0.001 1
SapurV1A.0223s0180	0.903 3	SapurV1A.0577s0020	0.499 9	SapurV1A.0163s0360	0.001 1
SapurV1A.0210s0130	0.903 2	SapurV1A.1223s0010	0.499 8	SapurV1A.1086s0060	0.001 1
SapurV1A.0374s0080	0.899 7	SapurV1A.3131s0030	0.499 4	SapurV1A.0621s0040	0.001 1
SapurV1A.1401s0040	0.894 3	SapurV1A.1712s0040	0.499 2	SapurV1A.0038s0420	0.001 1
SapurV1A.0744s0030	0.893 8	SapurV1A.1352s0010	0.498 9	SapurV1A.1001s0080	0.001 1
SapurV1A.0878s0060	0.892 7	MSTRG.2962	0.498 7	SapurV1A.2098s0020	0.001 1
SapurV1A.0222s0270	0.889 9	SapurV1A.0470s0220	0.498 5	SapurV1A.0052s0830	0.001 1
MSTRG.12920	0.878 7	SapurV1A.0307s0230	0.498 1	SapurV1A.1878s0050	0.001 1
SapurV1A.5044s0020	0.870 8	SapurV1A.0006s1570	0.498 1	MSTRG.22590	0.001 1

引物名称 Primer name	引物序列 Primer sequence(5'-3')	引物名称 Primer name	引物序列 Primer sequence(5'-3')
ZFP4-F	AACCTGCATCACGTACCACA	SPA2-F	CTTAGCCATTGTTGGTACATCG
ZFP4-R	AATGAGGATCCATGCAGAGG	SPA2-R	AAGGTATGACTACGGGAAATCC
TB1-F	AAGCAAGCAAAACTATCGAGTG	FHY1-F	TGGGGATTTTTATGGTGAGGAA
TB1-R	GAAGAAACACTCTTGCTGTCAG	FHY1-R	AAGTTTATGGATGCTTGCAGTG
TAC2-F	AAAGATGGGCTCGCTGGAAA	RFK1-F	AAGGACAGACCAGCATCCAG
TAC2-R	GTGAATCCTCTACAGCGCGA	RFK1-R	GGAAGACGTGGAGGTGGATA
LAZY1b-F	CACTGAAGGATTTTGCTATCGG	ABF2-F	CAAGAACTTCTCAAATGACCCG
LAZY1b-R	CAGAAAACCATGGAATAGCTCG	ABF2-R	TGAAGCTCGTCAAAAGTTAACG
ATX1-F	AAGCAAGCAAAACTATCGAGTG	PYL1-F	GCAGGTCACGGGGTTTAGTA
ATX1-R	GAAGAAACACTCTTGCTGTCAG	PYL1-R	CCGTGTGTCTTCCTCGGTAT
UBQ-F	AAGCCCAAGAAGATCAAGCA
UBQ-R	ACCACCAGCCTTCTGGTAAA

Preliminary screening of Northern Salix (Salix psammophila) architecture related genes based on RNA-Seq analysis and quantitative PCR technique

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基因名称 Gene name	采样部位 Sampling position	平均值 Mean	标准偏差 Standard deviation	P值 P value	最小值 Minimum	最大值 Maximum
ATX1	茎尖Shoot tip	0.654	0.315	0.012	0.140	1.420
	腋芽Axillary bud	0.726	0.309	0.000	0.130	1.410
LAZY1b	茎尖Shoot tip	1.224	1.283	0.054	0.030	5.960
	腋芽Axillary bud	0.302	0.182	0.061	0.040	1.160
TAC2	茎尖Shoot tip	0.381	0.291	0.002	0.010	1.260
	腋芽Axillary bud	2.345	1.847	0.207	0.340	8.810
TB1	茎尖Shoot tip	3.192	1.949	0.326	0.600	9.900
	腋芽Axillary bud	0.730	0.579	0.000	0.200	5.190
ZFP4	茎尖Shoot tip	8.771	5.257	0.001	0.120	28.980
	腋芽Axillary bud	19.732	23.706	0.099	0.110	109.230
ABF2	茎尖Shoot tip	2.107	2.094	0.233	0.210	16.700
	腋芽Axillary bud	1.315	0.765	0.044	0.240	4.730
FHY1	茎尖Shoot tip	10.564	9.017	0.121	1.000	61.210
	腋芽Axillary bud	2.631	1.596	<0.001	0.170	8.090
RFK1	茎尖Shoot tip	2.129	1.262	0.483	0.030	6.640
	腋芽Axillary bud	0.657	0.505	<0.001	0.020	2.790
SPA2	茎尖Shoot tip	0.420	0.398	0.002	0.030	1.930
	腋芽Axillary bud	0.794	0.760	0.078	0.070	4.520
PYL1	茎尖Shoot tip	0.963	0.876	0.073	0.050	4.980
	腋芽Axillary bud	1.684	1.407	0.038	0.060	7.630

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