Genome-wide association analysis of stomatal characters of cultivated local tea plants in Guizhou, China

doi:10.3969/j.issn.1004-1524.20230261

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (7): 1550-1563.DOI: 10.3969/j.issn.1004-1524.20230261

• Crop Science • Previous Articles Next Articles

Genome-wide association analysis of stomatal characters of cultivated local tea plants in Guizhou, China

BAI Dingchen¹(), ZHAO Zhifei², GONG Xue³, LIU Yuan³, NIU Suzhen¹^,⁴^,^*(), CHEN Zhengwu⁵

1. College of Tea, Guizhou University, Guiyang 550025, China
2. College of Cultural Tourism and Regional Development, Guiyang College of Humanities and Technology, Guiyang 550025, China
3. Guiyang Agricultural Technology Extension Station, Guiyang 550081,China
4. Institute of Agricultural Bioengineering, Guizhou University, Guiyang 550025, China
5. Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China

Received:2023-03-03 Online:2023-07-25 Published:2023-08-17
Contact: NIU Suzhen

Abstract

Abstract:

In order to provide a basis for the development and utilization of cultivated local tea trees in Guizhou. Through Genome-Wide Association Study (GWAS) on the stomatal traits of cultivated local tea trees in Guizhou, the genes related to stomatal development were identified.This study utilized Simplified Genotyping-by-Sequencing (GBS) technology to conduct GWAS analysis on 253 cultivated local tea tree germplasm resources in Guizhou. The results showed that a total of 45 SNP loci were associated with 5 stomatal phenotypic traits, and a total of 20 genes were detected within the 45 SNPS loci range of 50 kb downstream. Among them, 6 genes are related to stomatal length (SL), 1 gene is related to stomatal width (SW), 7 genes are related to stomatal area (SA), 2 genes are related to stomatal density (SD), and 4 genes are related to stomatal perimeter (SP). This research achievement is beneficial for the development and utilization of cultivated tea tree resources with complex genetic backgrounds and rich ecological types, and for screening excellent tea tree varieties with strong adaptability and promoting the adjustment of the tea industry variety structure in Guizhou.

Key words: germplasm resources, cultivated tea tree, genome-wide association analysis

CLC Number:

S571.1

BAI Dingchen, ZHAO Zhifei, GONG Xue, LIU Yuan, NIU Suzhen, CHEN Zhengwu. Genome-wide association analysis of stomatal characters of cultivated local tea plants in Guizhou, China[J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1550-1563.

Figures/Tables 11

References 55

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	SL/μm	SW/μm	SD/mm^-2	SA/μm²	SP/μm
最大值Max value	44.80	39.60	633.33	1 169.37	124.85
最小值Min value	25.49	15.69	202.78	292.96	67.45
平均值Average value	35.15	27.65	418.06	731.17	96.15

	SL/μm	SW/μm	SD/mm^-2	SA/μm²	SP/μm
最大值Max value	44.80	39.60	633.33	1 169.37	124.85
最小值Min value	25.49	15.69	202.78	292.96	67.45
平均值Average value	35.15	27.65	418.06	731.17	96.15

性状 Traits	变异系数 CV	偏度 Skewness	偏度标准差 Deviation standard deviation	峰度 Kurtosis	峰度标准差 Kurtosis standard deviation
SL	0.73	-0.19	0.16	-0.15	0.32
SW	1.13	-0.12	0.16	-0.51	0.32
SD	1.47	0.15	0.16	-0.48	0.32
SA	1.64	0.10	0.16	-0.48	0.32
SP	0.82	-0.25	0.16	-0.25	0.33

性状 Traits	变异系数 CV	偏度 Skewness	偏度标准差 Deviation standard deviation	峰度 Kurtosis	峰度标准差 Kurtosis standard deviation
SL	0.73	-0.19	0.16	-0.15	0.32
SW	1.13	-0.12	0.16	-0.51	0.32
SD	1.47	0.15	0.16	-0.48	0.32
SA	1.64	0.10	0.16	-0.48	0.32
SP	0.82	-0.25	0.16	-0.25	0.33

基因ID Gene ID	基因位点 Genetic locus	关联位点 SNP locus	功能注释 Function comment
CSS0006464.1	S3_4364269	S3_4364392 S3_4364468	与异亮氨酸tRNA合成酶、锌指FYVE结构域蛋白、形成具有光学活性的木质素有关 It is related to Isoleucine tRNA synthetase, zinc finger FYVE domain protein, and the formation of lignin with optical activity
CSS0014538.1	S3_4404126	S3_4364392 S3_4364468	1)膜整体组分;2)电子载流子活性; 3)铁离子结合。该基因与At1g13570同源,F-box/FBD/LRR-repeat蛋白有关;也可能与CYT1同源,细胞色素C1,血红素蛋白,线粒体蛋白有关 1) Overall membrane composition; 2) Electron carrier activity; 3) Iron ion binding. This gene is homologous to At1g13570 and is associated with the F-box/FBD/LRR repeat protein; It may also be related to CYT1 homology, cytochrome C1, heme protein, and mitochondrial protein
CSS0049436.1	S6_93764367	S6_93745614	编码蛋白和四肽重复序列(TPR)结构域有关,这种多肽存在于多种蛋白质(包括与伴侣、细胞周期、转录和蛋白质转运复合体有关的蛋白质)中 The coding protein is related to the tetrapeptide repeat sequence (TPR) domain, which is present in various proteins, including proteins related to chaperones, cell cycle, transcription, and protein transport complexes
CSS0014397.1	S7_45292716	S7_45292798	该基因与COL16基因同源,编码蛋白与B-box锌指蛋白有关 This gene is homologous to the COL16 gene and encodes a protein related to the B-box zinc finger protein
CSS0006487.1	S13_4398763	S13_4399128	该基因与HSL1同源,参与蛋白磷酸化 This gene is homologous to HSL1 and participates in protein phosphorylation
CSS0038141.1	S13_93296595	S13_93263501	谷胱甘肽氧化还原酶活性Glutathione oxidoreductase activity

Genome-wide association analysis of stomatal characters of cultivated local tea plants in Guizhou, China

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基因编号 Gene ID	基因位点 Genetic locus	关联位点 SNP locus	功能注释 Function comment
CSS0006464.1	S3_4364269	S3_4364468	异亮氨酸tRNA合成酶、锌指FYVE结构域蛋白、形成具有光学活性的木质素有关 Isoleucine tRNA synthase, zinc finger FYVE domain protein, and the formation of lignin with optical activity
CSS0032323.1	S4_94940525	S4_94978574 S4_94978635	1)参与蛋白磷酸化、含磷复合代谢等生物过程;2)蛋白丝氨酸/苏氨酸激酶活性、ATP结合、腺嘌呤核糖核苷酸结合、蛋白激酶活性等分子过程 1) Participate in biological processes such as protein phosphorylation and phosphorus containing compound metabolism; 2) Molecular processes such as protein serine/Threonine kinase activity, ATP binding, Adenine ribonucleotide binding, protein kinase activity, etc
CSS0018568.1	S4_94940525	S4_94978574 S4_94978635	1)在细胞组成上作为膜整体组分,与生长素激活信号通路、防御反应有关; 2)可能PAM16同源,调节ATP依赖的蛋白易位到线粒体基质;3)也可能与MWL1和2家族同源,参与次生细胞壁形成学,特别是木质素的生物合成 1) As an integral component of membrane in cell composition, it is related to auxin activated signal pathway and defense response; 2) It may be that PAM16 is homologous, regulating ATP dependent protein translocation to Mitochondrial matrix; 3) It may also be homologous to the MWL1 and 2 families and participate in secondary cell wall formation, especially in lignin biosynthesis
CSS0008651.1	S6_48047596	S6_48077984	衰老相关蛋白,可能与P85基因同源,参与冷胁迫、盐胁迫响应 Aging related proteins, possibly homologous to the P85 gene, participate in cold stress and salt stress responses
CSS0003026.1	S6_48077858	S6_48077984	负载-tRNA氨基酸修饰,糖基转移酶活性,TRNA A64-2'-O-核糖磷酸转移酶活性 Load tRNA amino acid modification, glycosyltransferase activity, TRNA A64-2'-O-ribose phosphotransferase activity
CSS0049436.1	S6_93764367	S6_93745614	编码蛋白和四肽重复序列(TPR)结构域有关,这种多肽存在于多种蛋白质(包括与伴侣、细胞周期、转录和蛋白质转运复合体有关的蛋白质)中 The coding protein is related to the tetrapeptide repeat sequence (TPR) domain, which is present in various proteins, including proteins related to chaperones, cell cycle, transcription, and protein transport complexes
CSS0004296.1	S6_124832429	S6_124873652 S6_124873657 S6_124873688 S6_124873718 S6_124873720	编码蛋白与Vps62蛋白家族功能相似,可能同时参与了羧肽酶Y和碱性磷酸酶途径 The function of the encoded protein is similar to that of the Vps62 protein family, which may be involved in the carboxypeptidase Y and alkaline phosphatase pathways at the same time

基因ID Gene ID	基因位点 Genetic locus	关联位点 SNP locus	功能注释 Function comment
CSS0004296.1	S6_124832429	S6_124873720	编码蛋白与Vps62蛋白家族功能相似,可能同时参与了羧肽酶Y和碱性磷酸酶途径 The function of the encoded protein is similar to that of the Vps62 protein family, which may be involved in the Carboxypeptidase Y and Alkaline phosphatase pathways at the same time
CSS0049436.1	S6_93764367	S6_93745614	编码蛋白和四肽重复序列(TPR)结构域有关,这种多肽存在于多种蛋白质(包括与伴侣、细胞周期、转录和蛋白质转运复合体有关的蛋白质)中 The coding protein is related to the tetrapeptide repeat sequence (TPR) domain, which is present in various proteins, including proteins related to chaperones, cell cycle, transcription, and protein transport complexes
CSS0014397.1	S7_45292716	S7_45292797	该基因与COL16基因同源,编码蛋白与B-box锌指蛋白有关 This gene is homologous to the COL16 gene and encodes a protein related to the B-box zinc finger protein
CSS0030051.1	S15_43099708	S15_43052771	磷脂酰肌醇转移活性Phosphatidylinositol transfer activity

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