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Qiu Z, Guo W, Yu Q, Li D, Zhao M, Lv H, Hua X, Wang Y, Ma Q, Ding Z. Gibberellin 2-oxidase 1(CsGA2ox1) involved gibberellin biosynthesis regulates sprouting time in camellia sinensis. BMC PLANT BIOLOGY 2024; 24:869. [PMID: 39289599 PMCID: PMC11406726 DOI: 10.1186/s12870-024-05589-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 09/12/2024] [Indexed: 09/19/2024]
Abstract
BACKGROUND Tea is an important cash crop and buds are its main product. To elucidate the molecular mechanism of the sprouting time of tea plants, 'Yuchunzao', which was an early sprouting tea cultivar, was studied. 'Echa 1', sprout one week later than 'Yuchunzao' in spring, was used as the control. RESULTS A total of 26 hormonal compounds and its derivatives in tea plants were qualified by using Ultra Performance Liquid Chromatography-Tandem mass spectrometry (UPLC-MS/MS). The result showed that GA20, GA3 and ICA were significantly different in 'Yuchunzao' than in 'Echa 1', with GA20 and GA3 up-regulated and ICA down-regulated. Based on the Illumina platform, transcriptome analysis revealed a total of 5,395 differentially expressed genes (DEGs). A diterpenoid biosynthesis related gene, gibberellin 2-oxidase 1 (CsGA2ox1), was downregulated in 'Yuchunzao' compared to 'Echa 1'. CsGA2ox1 regulate the transformation of GA different forms in plants. The relative expression of CsGA2ox1 showed an adverse trend with the content of GA20 and GA3. Our results suggest that down regulation of CsGA2ox1 resulted in the accumulation of GA3 and GA20, and then promoted sprout of 'Yuchunzao'. CONCLUSION This study provides theoretical basis of tea plants sprout and guides the tea breeding in practice.
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Affiliation(s)
- Ziyuan Qiu
- College of Agronomy, Liaocheng University, Liaocheng, 252000, China
| | - Wenhui Guo
- College of Agronomy, Liaocheng University, Liaocheng, 252000, China
| | - Qian Yu
- College of Agronomy, Liaocheng University, Liaocheng, 252000, China
| | - Dongxue Li
- College of Agronomy, Liaocheng University, Liaocheng, 252000, China
| | - Mengjie Zhao
- College of Agronomy, Liaocheng University, Liaocheng, 252000, China
| | - Han Lv
- College of Agronomy, Liaocheng University, Liaocheng, 252000, China
| | - Xuewen Hua
- College of Agronomy, Liaocheng University, Liaocheng, 252000, China
| | - Yu Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qingping Ma
- College of Agronomy, Liaocheng University, Liaocheng, 252000, China.
| | - Zhaotang Ding
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
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Hu G, Li X, Yang J, Yuan Q, Yang S, Fu W, Zhang X, Li Y, Shen Z, Jiang J. Effects of Photoperiod and Light Quality on Germination and Growth of Camellia sinensis 'HuangKui'. PLANTS (BASEL, SWITZERLAND) 2024; 13:1782. [PMID: 38999624 PMCID: PMC11244327 DOI: 10.3390/plants13131782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024]
Abstract
Light, as a critical environmental factor, plays a pivotal role in photosynthesis, ultimately influencing the timing of bud flush in tea plants. However, the synergistic effects of different photoperiods and light qualities on the timing of bud flush in the albino tea cultivar 'HuangKui' (later germination variety) remain unknown. Thus, the objective of this study was to investigate the effects of different photoperiods (12L/12D, 14L/10D, 16L/8D, and 18L/6D, where L = the number of daylight hours and D = the number of hours of darkness) and ratios of red (R) to blue (B) light (R/B 1:1, R/B 1:2, R/B 1:3, and R/B 2:1) on the germination and growth of the albino tea variety 'HuangKui'. In our study, we examined how different photoperiods and red light and blue light affected tea germination and growth by investigating the timing of bud flush, photosynthesis, chlorophyll content, and growth indicators. First, our study showed that 'HuangKui' germinated 4 days, 2 days, and 1 day earlier under the 16L/8D photoperiod at the one bud and one leaf period compared with plants cultivated under the 12L/12D, 14L/10D, and 18L/6D photoperiods under light simulating the solar spectrum. Also, the growth of 'HuangKui' was maximumly promoted under the 16L/8D photoperiod treatment. Additionally, the earliest germination of 'HuangKui' was observed for the 16L/8D photoperiod under the R/B 2:1 (red/blue) treatment compared with the other treatments. Moreover, the greatest plant height, length of the new shoots, and new leaf areas were detected in the albino tea variety 'HuangKui' under R/B 2:1. Moreover, the contents of auxin (indole acetic acid, IAA) and trans-zeatin (tZ) under R/B 2:1 were significantly higher than those under the R/B 1:1 and control treatments with the 16L/8D photoperiod. Additionally, the auxin-related expression levels of CsIAA13, CsGH3.1, CsAUX1, and CsARF2 under the R/B 2:1 treatment were significantly higher than those in the control. The expression of CsARR-B, a positive regulator of cytokinin-related genes, was significantly higher under the R/B 2:1 treatment than under the control treatment, while the opposite result was found for the expression of the negative regulator CsARR-A. Therefore, the R/B 2:1 treatment with the 16L/8D photoperiod was an appropriate means of timing the bud flush for the albino tea variety 'HuangKui', which may be related to IAA or tZ signal transduction. In conclusion, our research offers a novel lighting strategy that promotes the germination and growth of albino tea cultivars.
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Affiliation(s)
- Gan Hu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Xingchen Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Junlong Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Qingqing Yuan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Shijun Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Wenjun Fu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Xianchen Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yeyun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Zhougao Shen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Jiayue Jiang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
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Wang H, Wang X, Yang Y, Zhu Y, Wang S, Chen Q, Yan D, Dong X, Li M, Lu S. Genome-wide identification of quantitative trait loci and candidate genes for seven carcass traits in a four-way intercross porcine population. BMC Genomics 2024; 25:582. [PMID: 38858624 PMCID: PMC11165779 DOI: 10.1186/s12864-024-10484-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Carcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs, including dressing percentage (DP), number of ribs (RIB), skin thinkness (ST), carcass straight length (CSL), carcass diagonal length (CDL), loin eye width (LEW), and loin eye thickness (LET). RESULTS A total of 227,921 high-quality single nucleotide polymorphisms (SNPs) were detected to perform GWAS. A total of 30 SNPs were identified for seven carcass traits using the mixed linear model (MLM) (p < 1.0 × 10- 5), of which 9 SNPs were located in previously reported quantitative trait loci (QTL) regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43 to 16.32%. Furthermore, 11 candidate genes (LYPLAL1, EPC1, MATN2, ZFAT, ZBTB10, ZNF704, INHBA, SMYD3, PAK1, SPTBN2, and ACTN3) were found for carcass traits in pigs. CONCLUSIONS The GWAS results will improve our understanding of the genetic basis of carcass traits. We hypothesized that the candidate genes associated with these discovered SNPs would offer a biological basis for enhancing the carcass quality of pigs in swine breeding.
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Affiliation(s)
- Huiyu Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Faculty of Animal Science, Xichang University, Xichang, Sichuan, 615000, China
| | - Xiaoyi Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yongli Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yixuan Zhu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Shuyan Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Dawei Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xinxing Dong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Mingli Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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Wang L, Qian Y, Wu L, Wei K, Wang L. The MADS-box transcription factor CsAGL9 plays essential roles in seed setting in Camellia sinensis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108301. [PMID: 38232497 DOI: 10.1016/j.plaphy.2023.108301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
The number of seed setting (NSS) is an important biological trait that affects tea propagation and yield. In this study, the NSS of an F1 tea population (n = 324) generated via a cross between 'Longjing 43' and 'Baihaozao' was investigated at two locations in two consecutive years. Quantitative trait locus (QTL) mapping of the NSS was performed, and 10 major QTLs were identified. In total, 318 genes were found in these 10 QTLs intervals, and 11 key candidate genes were preliminarily identified. Among them, the MADS-box transcription factor AGAMOUS LIKE 9 (CsAGL9, CSS0037962) located in the most stable QTL (qNSS2) was identified as a key gene affecting the NSS. CsAGL9 overexpression in Arabidopsis promoted early flowering and significantly decreased the length and number of pods and number of seeds per pod. Transcriptome analysis demonstrated that the auxin pathway, a key hormone pathway regulating plant reproduction, was highly affected in the transgenic lines. The auxin pathway was likewise the most prominent in the gene co-expression network study of CsAGL9 in tea plants. In summary, we identified CsAGL9 is essential for seed setting using QTL mapping integrated with RNA-seq, which shed a new light on the mechanism NSS of seed setting in tea plants.
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Affiliation(s)
- Liubin Wang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yinhong Qian
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liyun Wu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China
| | - Kang Wei
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China.
| | - Liyuan Wang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China.
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Wang Y, Niu S, Deng X, Bai D, Chen Z, Deng X, Huang D. Genome-wide association study, population structure, and genetic diversity of the tea plant in Guizhou Plateau. BMC PLANT BIOLOGY 2024; 24:79. [PMID: 38287242 PMCID: PMC10826100 DOI: 10.1186/s12870-024-04761-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/23/2024] [Indexed: 01/31/2024]
Abstract
BACKGROUND Guizhou Plateau, as one of the original centers of tea plant, has a profound multi-ethnic cultural heritage and abundant tea germplasm resources. However, the impact of indigenous community factors on the genetic diversity, population structure and geographical distribution of tea plant is still unclear. RESULTS Using the genotyping-by-sequencing (GBS) approach, we collected 415 tea plant accessions from the study sites, estimated genetic diversity, developed a core collection, and conducted a genome-wide association study (GWAS) based on 99,363 high-quality single-nucleotide polymorphisms (SNPs). A total of 415 tea accessions were clustered into six populations (GP01, GP02, GP03, GP04, GP05 and GP06), and the results showed that GP04 and GP05 had the highest and lowest genetic diversity (Pi = 0.214 and Pi = 0.145, respectively). Moreover, 136 tea accessions (33%) were selected to construct the core set that can represent the genetic diversity of the whole collection. By analyzing seven significant SNP markers associated with the traits such as the germination period of one bud and two leaves (OTL) and the germination period of one bud and three leaves (OtL), four candidate genes possibly related to OTL and OtL were identified. CONCLUSIONS This study revealed the impact of indigenous communities on the population structure of 415 tea accessions, indicating the importance of cultural practices for protection and utilization of tea plant genetic resources. Four potential candidate genes associated with the OTL and OtL of tea plant were also identified, which will facilitate genetic research, germplasm conservation, and breeding.
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Affiliation(s)
- Yihan Wang
- College of Tea Science, Guizhou University, Guiyang, Guizhou Province, 550025, China
| | - Suzhen Niu
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, China.
| | - Xinyue Deng
- School of Architecture, Guizhou university, Guiyang, Guizhou Province, 550025, China
| | - Dingchen Bai
- College of Tea Science, Guizhou University, Guiyang, Guizhou Province, 550025, China
| | - Zhengwu Chen
- lnstitute of Tea, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou Province, 550006, China.
| | - Xiuling Deng
- College of Tea Science, Guizhou University, Guiyang, Guizhou Province, 550025, China
| | - Dejun Huang
- College of Tea Science, Guizhou University, Guiyang, Guizhou Province, 550025, China
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Jiang L, Xie S, Zhou C, Tian C, Zhu C, You X, Chen C, Lai Z, Guo Y. Analysis of the Genetic Diversity in Tea Plant Germplasm in Fujian Province Based on Restriction Site-Associated DNA Sequencing. PLANTS (BASEL, SWITZERLAND) 2023; 13:100. [PMID: 38202408 PMCID: PMC10780744 DOI: 10.3390/plants13010100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024]
Abstract
Fujian province, an important tea-producing area in China, has abundant tea cultivars. To investigate the genetic relationships of tea plant cultivars in Fujian province and the characteristics of the tea plant varieties, a total of 70 tea cultivars from Fujian and other 12 provinces in China were subjected to restriction site-associated DNA sequencing (RAD-seq). A total of 60,258,975 single nucleotide polymorphism (SNP) sites were obtained. These 70 tea plant cultivars were divided into three groups based on analyzing the phylogenetic tree, principal component, and population structure. Selection pressure analysis indicated that nucleotide diversity was high in Southern China and genetically distinct from cultivars of Fujian tea plant cultivars, according to selection pressure analysis. The selected genes have significant enrichment in pathways associated with metabolism, photosynthesis, and respiration. There were ten characteristic volatiles screened by gas chromatography-mass spectrometry (GC-MS) coupled with multivariate statistical methods, among which the differences in the contents of methyl salicylate, 3-carene, cis-3-hexen-1-ol, (E)-4-hexen-1-ol, and 3-methylbutyraldehyde can be used as reference indicators of the geographical distribution of tea plants. Furthermore, a metabolome genome-wide association study (mGWAS) revealed that 438 candidate genes were related to the aroma metabolic pathway. Further analysis showed that 31 genes of all the selected genes were screened and revealed the reasons for the genetic differences in aroma among tea plant cultivars in Fujian and Southern China. These results reveal the genetic diversity in the Fujian tea plants as well as a theoretical basis for the conservation, development, and utilization of the Fujian highly aromatic tea plant cultivars.
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Affiliation(s)
- Lele Jiang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.J.); (C.Z.); (C.T.); (Z.L.)
| | - Siyi Xie
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China;
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.J.); (C.Z.); (C.T.); (Z.L.)
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Caiyun Tian
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.J.); (C.Z.); (C.T.); (Z.L.)
| | - Chen Zhu
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China;
| | - Xiaomei You
- Tea Research Institute, Fujian Academy of Agricultural Sciences, No. 104 Pudang Road, Xindian Town, Jin’an District, Fuzhou 350012, China; (X.Y.); (C.C.)
| | - Changsong Chen
- Tea Research Institute, Fujian Academy of Agricultural Sciences, No. 104 Pudang Road, Xindian Town, Jin’an District, Fuzhou 350012, China; (X.Y.); (C.C.)
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.J.); (C.Z.); (C.T.); (Z.L.)
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.J.); (C.Z.); (C.T.); (Z.L.)
- Anxi College of Tea Science (College of Digital Economy), Fujian Agriculture and Forestry University, Quanzhou 362400, China
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Lei X, Li H, Li P, Zhang H, Han Z, Yang B, Duan Y, Njeri NS, Yang D, Zheng J, Ma Y, Zhu X, Fang W. Genome-Wide Association Studies of Biluochun Tea Plant Populations in Dongting Mountain and Comprehensive Identification of Candidate Genes Associated with Core Agronomic Traits by Four Analysis Models. PLANTS (BASEL, SWITZERLAND) 2023; 12:3719. [PMID: 37960075 PMCID: PMC10650078 DOI: 10.3390/plants12213719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
The elite germplasm resources are key to the beautiful appearance and pleasant flavor of Biluochun tea. We collected and measured the agronomic traits of 95 tea plants to reveal the trait diversity and breeding value of Biluochun tea plant populations. The results revealed that the agronomic traits of Biluochun tea plant populations were diverse and had high breeding value. Additionally, we resequenced these tea plant populations to reveal genetic diversity, population structure, and selection pressure. The Biluochun tea plant populations contained two groups and were least affected by natural selection based on the results of population structure and selection pressure. More importantly, four non-synonymous single nucleotide polymorphisms (nsSNPs) and candidate genes associated with (-)-gallocatechin gallate (GCG), (-)-gallocatechin (GC), and caffeine (CAF) were detected using at least two GWAS models. The results will promote the development and application of molecular markers and the utilization of elite germplasm from Biluochun populations.
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Affiliation(s)
- Xiaogang Lei
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Haoyu Li
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Pingping Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Huan Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Zhaolan Han
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Bin Yang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Yu Duan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Ndombi Salome Njeri
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Daqiang Yang
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Junhua Zheng
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
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Li JW, Li H, Liu ZW, Wang YX, Chen Y, Yang N, Hu ZH, Li T, Zhuang J. Molecular markers in tea plant (Camellia sinensis): Applications to evolution, genetic identification, and molecular breeding. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107704. [PMID: 37086694 DOI: 10.1016/j.plaphy.2023.107704] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Tea plants have a long cultivation history in the world, and the beverage (tea) made from its leaves is well known in the world. Due to the characteristics of self-incompatibility, long-term natural and artificial hybridization, tea plants have a very complex genetic background, which make the classification of tea plants unclear. Molecular marker, one type of genetic markers, has the advantages of stable inheritance, large amount of information, and high reliability. The development of molecular marker has facilitated the understanding of complex tea germplasm resources. So far, molecular markers had played important roles in the study of the origin and evolution, the preservation and identification of tea germplasms, and the excellent cultivars breeding of tea plants. However, the information is scattered, making it difficult to understand the advance of molecular markers in tea plants. In this paper, we summarized the development process and types of molecular markers in tea plants. In addition, the application advance of these molecular markers in tea plants was reviewed. Perspectives of molecular markers in tea plants were also systematically provided and discussed. The elaboration of molecular markers in this paper should help us to renew understanding of its application in tea plants.
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Affiliation(s)
- Jing-Wen Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Wei Liu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yi Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ni Yang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Hang Hu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tong Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
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Chen Y, Niu S, Deng X, Song Q, He L, Bai D, He Y. Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing. BMC PLANT BIOLOGY 2023; 23:196. [PMID: 37046207 PMCID: PMC10091845 DOI: 10.1186/s12870-023-04192-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Studying the genetic characteristics of tea plant (Camellia spp.) leaf traits is essential for improving yield and quality through breeding and selection. Guizhou Plateau, an important part of the original center of tea plants, has rich genetic resources. However, few studies have explored the associations between tea plant leaf traits and single nucleotide polymorphism (SNP) markers in Guizhou. RESULTS In this study, we used the genotyping-by-sequencing (GBS) method to identify 100,829 SNP markers from 338 accessions of tea germplasm in Guizhou Plateau, a region with rich genetic resources. We assessed population structure based on high-quality SNPs, constructed phylogenetic relationships, and performed genome-wide association studies (GWASs). Four inferred pure groups (G-I, G-II, G-III, and G-IV) and one inferred admixture group (G-V), were identified by a population structure analysis, and verified by principal component analyses and phylogenetic analyses. Through GWAS, we identified six candidate genes associated with four leaf traits, including mature leaf size, texture, color and shape. Specifically, two candidate genes, located on chromosomes 1 and 9, were significantly associated with mature leaf size, while two genes, located on chromosomes 8 and 11, were significantly associated with mature leaf texture. Additionally, two candidate genes, located on chromosomes 1 and 2 were identified as being associated with mature leaf color and mature leaf shape, respectively. We verified the expression level of two candidate genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and designed a derived cleaved amplified polymorphism (dCAPS) marker that co-segregated with mature leaf size, which could be used for marker-assisted selection (MAS) breeding in Camellia sinensis. CONCLUSIONS In the present study, by using GWAS approaches with the 338 tea accessions population in Guizhou, we revealed a list of SNPs markers and candidate genes that were significantly associated with four leaf traits. This work provides theoretical and practical basis for the genetic breeding of related traits in tea plant leaves.
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Affiliation(s)
- Yanjun Chen
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Suzhen Niu
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Xinyue Deng
- School of Architecture, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Qinfei Song
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Limin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Dingchen Bai
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Yingqin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
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Chen C, Hu X, Ahmad MJ, Niu K, Ye T, Liang A, Yang L. Novel Insight into the Role of Squalene Epoxidase ( SQLE) Gene in Determining Milk Production Traits in Buffalo. Int J Mol Sci 2023; 24:ijms24032436. [PMID: 36768756 PMCID: PMC9916492 DOI: 10.3390/ijms24032436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
Understanding the genetic mechanisms underlying milk production traits contribute to improving the production potential of dairy animals. Squalene epoxidase (SQLE) is one of the rate-limiting enzymes for cholesterol biosynthesis and was highly expressed in the buffalo mammary. The objectives of the present study were to detect the polymorphisms within SQLE in buffalo, the genetic effects of these mutations on milk production traits, and to understand the gene regulatory effects on buffalo mammary epithelial cells (BuMECs). A total of five SNPs were identified by sequencing, g.18858G > A loci were significantly associated with fat yield, and g.22834C > T loci were significantly associated with peak milk yield, milk yield, fat yield, and protein yield. Notably, linkage disequilibrium analysis indicated that 2 SNPs (g.18858G > A and g.22834C > T) formed one haplotype block, which was found to be significantly associated with milk fat yield, fat percentage, and protein yield. Furthermore, expression of SQLE was measured in different tissues of buffalo and was found to be higher in the mammary. Knockdown of SQLE gene expression significantly affected the growth of BuMECs, including proliferation, cell cycle, and apoptosis, and significantly downregulated the expression of related genes MYC, PCNA, and P21. In addition, knockdown of the SQLE gene significantly reduces triglyceride concentrations and the signal intensity of oil red O staining. In addition, silencing of SQLE was also found to regulate the synthesis and secretion of β-casein and κ-casein negatively. Furthermore, SQLE knockdown is accompanied by the downregulation of critical genes (RPS6KB1, JAK2, eIF4E, and SREBP1) related to milk fat and protein synthesis. The current study showed the potential of the SQLE gene as a candidate for buffalo milk production traits. It provides a new understanding of the physiological mechanisms underlying buffalo milk production regulation.
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Affiliation(s)
- Chao Chen
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangwei Hu
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammad Jamil Ahmad
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kaifeng Niu
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingzhu Ye
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aixin Liang
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan 430070, China
| | - Liguo Yang
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan 430070, China
- Correspondence:
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11
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Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits in Brassica napus L. Int J Mol Sci 2022; 23:ijms232415892. [PMID: 36555533 PMCID: PMC9785822 DOI: 10.3390/ijms232415892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Salt stress severely affects crop growth and development and reduces the yield of Brassica napus. Exploring natural genetic variations for high salt tolerance in B. napus seedlings is an effective approach to improve productivity under salt stress. Using 10,658 high-quality single nucleotide polymorphic (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, genome-wide association studies (GWAS) were performed to investigate the genetic basis of salt tolerance and yield-related traits of B. napus. The results revealed that 77 and 497 SNPs were significantly associated with salt tolerance and yield-related traits, of which 40 and 58 SNPs were located in previously reported QTLs/SNPs, respectively. We identified nineteen candidate genes orthologous with Arabidopsis genes known to be associated with salt tolerance and seven potential candidates controlling both salt tolerance and yield. Our study provides a novel genetic resource for the breeding of high-yield cultivars resistant to salt stress.
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12
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Liu G, Li Y, Sun X, Guo X, Jiang N, Fang Y, Chen J, Bao Z, Ma F. Association study of SNP locus for color related traits in herbaceous peony ( Paeonia lactiflora Pall.) using SLAF-seq. FRONTIERS IN PLANT SCIENCE 2022; 13:1032449. [PMID: 36544869 PMCID: PMC9760751 DOI: 10.3389/fpls.2022.1032449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Paeonia lactiflora Pall. (P. lactiflora) is a famous ornamental plant with showy and colorful flowers that has been domesticated in China for 4,000 years. However, the genetic basis of phenotypic variation and genealogical relationships in P. lactiflora population is poorly understood due to limited genetic information, which brings about bottlenecks in the application of effective and efficient breeding strategies. Understanding the genetic basis of color-related traits is essential for improving flower color by marker-assisted selection (MAS). In this study, a high throughput sequencing of 99 diploid P. lactiflora accessions via specific-locus amplified fragment sequencing (SLAF-seq) technology was performed. In total, 4,383,645 SLAF tags were developed from 99 P. lactiflora accessions with an average sequencing depth of 20.81 for each SLAF tag. A total of 2,954,574 single nucleotide polymorphisms (SNPs) were identified from all SLAF tags. The population structure and phylogenetic analysis showed that P. lactiflora population used in this study could be divided into six divergent groups. Through association study using Mixed linear model (MLM), we further identified 40 SNPs that were significantly positively associated with petal color. Moreover, a derived cleaved amplified polymorphism (dCAPS) marker that was designed based on the SLAF tag 270512F co-segregated with flower colors in P. lactiflora population. Taken together, our results provide valuable insights into the application of MAS in P. lactiflora breeding programs.
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Affiliation(s)
- Genzhong Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Ying Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Xia Sun
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Xianfeng Guo
- College of Forestry, Shandong Agricultural University, Tai-An, Shandong, China
| | - Nannan Jiang
- Institute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, China
| | - Yifu Fang
- Institute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, China
| | - Junqiang Chen
- Institute of ornamental plants, Shandong Academy of Forestry, Jinan, Shandong, China
| | - Zhilong Bao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
| | - Fangfang Ma
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China
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Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population. Genes (Basel) 2022; 13:genes13111990. [DOI: 10.3390/genes13111990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/04/2022] Open
Abstract
Growth traits are crucial economic traits in the commercial pig industry and have a substantial impact on pig production. However, the genetic mechanism of growth traits is not very clear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to analyze ten growth traits on 223 four-way intercross pigs. A total of 227,921 highly consistent single nucleotide polymorphisms (SNPs) uniformly dispersed throughout the entire genome were used to conduct GWAS. A total of 53 SNPs were identified for ten growth traits using the mixed linear model (MLM), of which 18 SNPs were located in previously reported quantitative trait loci (QTL) regions. Two novel QTLs on SSC4 and SSC7 were related to average daily gain from 30 to 60 kg (ADG30–60) and body length (BL), respectively. Furthermore, 13 candidate genes (ATP5O, GHRHR, TRIM55, EIF2AK1, PLEKHA1, BRAP, COL11A2, HMGA1, NHLRC1, SGSM1, NFATC2, MAML1, and PSD3) were found to be associated with growth traits in pigs. The GWAS findings will enhance our comprehension of the genetic architecture of growth traits. We suggested that these detected SNPs and corresponding candidate genes might provide a biological foundation for improving the growth and production performance of pigs in swine breeding.
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D’Auria JC, Cohen SP, Leung J, Glockzin K, Glockzin KM, Gervay-Hague J, Zhang D, Meinhardt LW. United States tea: A synopsis of ongoing tea research and solutions to United States tea production issues. FRONTIERS IN PLANT SCIENCE 2022; 13:934651. [PMID: 36212324 PMCID: PMC9538180 DOI: 10.3389/fpls.2022.934651] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/25/2022] [Indexed: 06/01/2023]
Abstract
Tea is a steeped beverage made from the leaves of Camellia sinensis. Globally, this healthy, caffeine-containing drink is one of the most widely consumed beverages. At least 50 countries produce tea and most of the production information and tea research is derived from international sources. Here, we discuss information related to tea production, genetics, and chemistry as well as production issues that affect or are likely to affect emerging tea production and research in the United States. With this review, we relay current knowledge on tea production, threats to tea production, and solutions to production problems to inform this emerging market in the United States.
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Affiliation(s)
- John C. D’Auria
- Metabolic Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Stephen P. Cohen
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Jason Leung
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Kayla Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Kyle Mark Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Jacquelyn Gervay-Hague
- Department of Chemistry, University of California, University of California, Davis, Davis, CA, United States
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
| | - Lyndel W. Meinhardt
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
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15
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An Y, Xia X, Jing T, Zhang F. Identification of gene family members and a key structural variation reveal important roles of OVATE genes in regulating tea ( Camellia sinensis) leaf development. FRONTIERS IN PLANT SCIENCE 2022; 13:1008408. [PMID: 36212328 PMCID: PMC9539550 DOI: 10.3389/fpls.2022.1008408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
OVATE genes are a new class of transcriptional repressors with important regulatory roles in plant growth and development. Through genome-wide analysis of the OVATE gene family of tea plants, 26 and 13 family members were identified in cultivated and ancient tea plants, respectively. Syntenic results showed that OVATE gene family in cultivated tea plants may have experienced a special expansion event. Based on phylogenetic tree analysis, all OVATE genes were divided into four groups, and the third group had the largest number, reaching 16. Transcriptome data from different organs and populations indicated that many OVATE family members were highly expressed in young shoots and leaves, and their expression levels gradually decreased as tea leaves developed. Finally, the expression trends of the six key candidate genes were verified by RT-qPCR, which were consistent with the transcriptome results, indicating that the ovate gene family plays an important role in regulating the process of tea leaf development. In addition, we identified a key structural variation with a length of 184 bp, and the population genotyping showed that it was closely related to the area of tea leaves. Our research provides an important clue for further exploring the function of ovate gene family in tea plants and the development mechanism of tea leaves.
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Affiliation(s)
- Yanlin An
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Xiaobo Xia
- CIMMYT-JAAS Joint Center for Wheat Diseases/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River (Nanjing) Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Feng Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
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16
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Wang H, Wang X, Yan D, Sun H, Chen Q, Li M, Dong X, Pan Y, Lu S. Genome-wide association study identifying genetic variants associated with carcass backfat thickness, lean percentage and fat percentage in a four-way crossbred pig population using SLAF-seq technology. BMC Genomics 2022; 23:594. [PMID: 35971078 PMCID: PMC9380336 DOI: 10.1186/s12864-022-08827-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/05/2022] [Indexed: 12/12/2022] Open
Abstract
Background Carcass backfat thickness (BFT), carcass lean percentage (CLP) and carcass fat percentage (CFP) are important to the commercial pig industry. Nevertheless, the genetic architecture of BFT, CLP and CFP is still elusive. Here, we performed a genome-wide association study (GWAS) based on specific-locus amplified fragment sequencing (SLAF-seq) to analyze seven fatness-related traits, including five BFTs, CLP, and CFP on 223 four-way crossbred pigs. Results A total of 227, 921 highly consistent single nucleotide polymorphisms (SNPs) evenly distributed throughout the genome were used to perform GWAS. Using the mixed linear model (MLM), a total of 20 SNP loci significantly related to these traits were identified on ten Sus scrofa chromosomes (SSC), of which 10 SNPs were located in previously reported quantitative trait loci (QTL) regions. On SSC7, two SNPs (SSC7:29,503,670 and rs1112937671) for average backfat thickness (ABFT) exceeded 1% and 10% Bonferroni genome-wide significance levels, respectively. These two SNP loci were located within an intron region of the COL21A1 gene, which was a protein-coding gene that played an important role in the porcine backfat deposition by affecting extracellular matrix (ECM) remodeling. In addition, based on the other three significant SNPs on SSC7, five candidate genes, ZNF184, ZNF391, HMGA1, GRM4 and NUDT3 were proposed to influence BFT. On SSC9, two SNPs for backfat thickness at 6–7 ribs (67RBFT) and one SNP for CLP were in the same locus region (19 kb interval). These three SNPs were located in the PGM2L1 gene, which encoded a protein that played an indispensable role in glycogen metabolism, glycolysis and gluconeogenesis as a key enzyme. Finally, one significant SNP on SSC14 for CLP was located within the PLBD2 gene, which participated in the lipid catabolic process. Conclusions A total of two regions on SSC7 and SSC9 and eight potential candidate genes were found for fatness-related traits in pigs. The results of this GWAS based on SLAF-seq will greatly advance our understanding of the genetic architecture of BFT, CLP, and CFP traits. These identified SNP loci and candidate genes might serve as a biological basis for improving the important fatness-related traits of pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08827-8.
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Affiliation(s)
- Huiyu Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, No. 95 of Jinhei Road, Kunming, 650201, Yunnan, China.,Faculty of Animal Science, Xichang University, Xichang, 615000, Sichuan, China
| | - Xiaoyi Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, No. 95 of Jinhei Road, Kunming, 650201, Yunnan, China
| | - Dawei Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, No. 95 of Jinhei Road, Kunming, 650201, Yunnan, China
| | - Hao Sun
- Faculty of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, No. 95 of Jinhei Road, Kunming, 650201, Yunnan, China
| | - Mingli Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, No. 95 of Jinhei Road, Kunming, 650201, Yunnan, China
| | - Xinxing Dong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, No. 95 of Jinhei Road, Kunming, 650201, Yunnan, China
| | - Yuchun Pan
- Faculty of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, No. 95 of Jinhei Road, Kunming, 650201, Yunnan, China.
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17
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Lin Y, Sun H, Shaukat A, Deng T, Abdel-Shafy H, Che Z, Zhou Y, Hu C, Li H, Wu Q, Yang L, Hua G. Novel Insight Into the Role of ACSL1 Gene in Milk Production Traits in Buffalo. Front Genet 2022; 13:896910. [PMID: 35734439 PMCID: PMC9207818 DOI: 10.3389/fgene.2022.896910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding the genetic mechanisms underlying milk production traits contribute to improving the production potential of dairy animals. Long-chain acyl-CoA synthetase 1 (ACSL1) plays a key role in fatty acid metabolism and was highly expressed in the lactating mammary gland epithelial cells (MGECs). The objectives of the present study were to detect the polymorphisms within ACSL1 in Mediterranean buffalo, the genetic effects of these mutations on milk production traits, and understand the gene regulatory effects on MGECs. A total of twelve SNPs were identified by sequencing, including nine SNPs in the intronic region and three in the exonic region. Association analysis showed that nine SNPs were associated with one or more traits. Two haplotype blocks were identified, and among these haplotypes, the individuals carrying the H2H2 haplotype in block 1 and H5H1 in block 2 were superior to those of other haplotypes in milk production traits. Immunohistological staining of ACSL1 in buffalo mammary gland tissue indicated its expression and localization in MGECs. Knockdown of ACSL1 inhibited cell growth, diminished MGEC lipid synthesis and triglyceride secretion, and downregulated CCND1, PPARγ, and FABP3 expression. The overexpression of ACSL1 promoted cell growth, enhanced the triglyceride secretion, and upregulated CCND1, PPARγ, SREBP1, and FABP3. ACSL1 was also involved in milk protein regulation as indicated by the decreased or increased β-casein concentration and CSN3 expression in the knockdown or overexpression group, respectively. In summary, our present study depicted that ACSL1 mutations were associated with buffalo milk production performance. This may be related to its positive regulation roles on MGEC growth, milk fat, and milk protein synthesis. The current study showed the potential of the ACSL1 gene as a candidate for milk production traits and provides a new understanding of the physiological mechanisms underlying milk production regulation.
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Affiliation(s)
- Yuxin Lin
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hui Sun
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Aftab Shaukat
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tingxian Deng
- Guangxi Key Laboratory of Buffalo Genetice, Breeding and Reproduxtion, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Guangxi, China
| | - Hamdy Abdel-Shafy
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Zhaoxuan Che
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Zhou
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huazhao Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qipeng Wu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liguo Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR); Frontiers Science Center for Animal Breeding and Sustainable Production; Key Laboratory of Smart Farming for Agricultural Animals, Huazhong Agricultural University, Wuhan, China
| | - Guohua Hua
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR); Frontiers Science Center for Animal Breeding and Sustainable Production; Key Laboratory of Smart Farming for Agricultural Animals, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Guohua Hua,
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Tan L, Cui D, Wang L, Liu Q, Zhang D, Hu X, Fu Y, Chen S, Zou Y, Chen W, Wen W, Yang X, Yang Y, Li P, Tang Q. Genetic analysis of the early bud flush trait of tea plants ( Camellia sinensis) in the cultivar 'Emei Wenchun' and its open-pollinated offspring. HORTICULTURE RESEARCH 2022; 9:uhac086. [PMID: 35694722 PMCID: PMC9178331 DOI: 10.1093/hr/uhac086] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/25/2022] [Indexed: 05/19/2023]
Abstract
The timing of bud flush (TBF) in the spring is one of the most important agronomic traits of tea plants (Camellia sinensis). In this study, we designed an open-pollination breeding program using 'Emei Wenchun' (EW, a clonal tea cultivar with extra-early TBF) as a female parent. A half-sib population (n = 388) was selected for genotyping using specific-locus amplified fragment sequencing. The results enabled the identification of paternity for 294 (75.8%) of the offspring, including 11 (2.8%) from EW selfing and 217 (55.9%) assigned to a common father, 'Chuanmu 217' (CM). The putative EW × CM full-sib population was used to construct a linkage map. The map has 4244 markers distributed in 15 linkage groups, with an average marker distance of 0.34 cM. A high degree of collinearity between the linkage map and physical map was observed. Sprouting index, a trait closely related to TBF, was recorded for the offspring population in 2020 and 2021. The trait had moderate variation, with coefficients of variation of 18.5 and 17.6% in 2020 and 2021, respectively. Quantitative trait locus (QTL) mapping that was performed using the linkage map identified two major QTLs and three minor QTLs related to the sprouting index. These QTLs are distributed on Chr3, Chr4, Chr5, Chr9, and Chr14 of the reference genome. A total of 1960 predicted genes were found within the confidence intervals of QTLs, and 22 key candidate genes that underlie these QTLs were preliminarily screened. These results are important for breeding and understanding the genetic base of the TBF trait of tea plants.
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Affiliation(s)
- Liqiang Tan
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, Sichuan, China
- Corresponding authors. E-mail: ;
| | - Dong Cui
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Liubin Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Qinling Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Dongyang Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiaoli Hu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yidan Fu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Shengxiang Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Yao Zou
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Wei Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Weiqi Wen
- Mingshan Tea Plant Breeding and Reproduce Farm of Sichuan Province, Yaan 625101, Sichuan, China
| | - Xuemei Yang
- Mingshan Tea Plant Breeding and Reproduce Farm of Sichuan Province, Yaan 625101, Sichuan, China
| | - Yang Yang
- Sichuan Yizhichun Tea Industry Co., Ltd,, Leshan 614503, Sichuan, China
| | - Pinwu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Qian Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Tea Refining and Innovation Key Laboratory of Sichuan Province, Chengdu 611130, Sichuan, China
- Corresponding authors. E-mail: ;
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Fang K, Xia Z, Li H, Jiang X, Qin D, Wang Q, Wang Q, Pan C, Li B, Wu H. Genome-wide association analysis identified molecular markers associated with important tea flavor-related metabolites. HORTICULTURE RESEARCH 2021; 8:42. [PMID: 33642595 PMCID: PMC7917101 DOI: 10.1038/s41438-021-00477-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 05/02/2023]
Abstract
The characteristic secondary metabolites in tea (theanine, caffeine, and catechins) are important factors contributing to unique tea flavors. However, there has been relatively little research on molecular markers related to these metabolites. Thus, we conducted a genome-wide association analysis of the levels of these tea flavor-related metabolites in three seasons. The theanine, caffeine, and catechin levels in Population 1 comprising 191 tea plant germplasms were examined, which revealed that their heritability exceeded 0.5 in the analyzed seasons, with the following rank order (highest to lowest heritabilities): (+)-catechin > (-)-gallocatechin gallate > caffeine = (-)-epicatechin > (-)-epigallocatechin-3-gallate > theanine > (-)-epigallocatechin > (-)-epicatechin-3-gallate > catechin gallate > (+)-gallocatechin. The SNPs detected by amplified-fragment SNP and methylation sequencing divided Population 1 into three groups and seven subgroups. An association analysis yielded 307 SNP markers related to theanine, caffeine, and catechins that were common to all three seasons. Some of the markers were pleiotropic. The functional annotation of 180 key genes at the SNP loci revealed that FLS, UGT, MYB, and WD40 domain-containing proteins, as well as ATP-binding cassette transporters, may be important for catechin synthesis. KEGG and GO analyses indicated that these genes are associated with metabolic pathways and secondary metabolite biosynthesis. Moreover, in Population 2 (98 tea plant germplasm resources), 30 candidate SNPs were verified, including 17 SNPs that were significantly or extremely significantly associated with specific metabolite levels. These results will provide a foundation for future research on important flavor-related metabolites and may help accelerate the breeding of new tea varieties.
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Affiliation(s)
- Kaixing Fang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Zhiqiang Xia
- Institute of Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570100, China
- Hainan University, Haikou, 570228, China
| | - Hongjian Li
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Xiaohui Jiang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Dandan Qin
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Qiushuang Wang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Qing Wang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Chendong Pan
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Bo Li
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Hualing Wu
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China.
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Tan LQ, Yang CJ, Zhou B, Wang LB, Zou Y, Chen W, Xia T, Tang Q. Inheritance and quantitative trait loci analyses of the anthocyanins and catechins of Camellia sinensis cultivar 'Ziyan' with dark-purple leaves. PHYSIOLOGIA PLANTARUM 2020; 170:109-119. [PMID: 32333383 DOI: 10.1111/ppl.13114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/12/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Owing to the potential health benefits, anthocyanin-rich teas (Camellia sinensis) have attracted interest over the past decade. Previously, we developed the cultivar 'Ziyan,' which has dark-purple leaves because of the accumulation of a high amount of anthocyanins. In this study, we performed a genetic analysis of this anthocyanin-rich tea cultivar and 176 of its naturally pollinated offspring. For two consecutive years, we quantified the anthocyanins and catechins of 'Ziyan' and the offspring population. While >60% of the offspring accumulated less than half of the amount of anthocyanins of 'Ziyan,' 17 (2018) and 15 (2019) individuals exceeded 'Ziyan' in anthocyanin content. A negative correlation between anthocyanin and total catechin content (r = -0.59, P < 0.001) was observed. The population was genotyped with 131 SSR markers spanning all linkage groups of the C. sinensis genome. Kruskal-Wallis tests identified 10 markers significantly associated with anthocyanins, catechins and their ratios in both years. Quantitative trait locus (QTL) analyses using the interval mapping method detected 13 QTLs, suggesting the dark-purple trait of 'Ziyan' is because of the pyramiding of anthocyanin-promoting alleles on at least five linkage groups. Two genetic loci reversely related to anthocyanin and total catechin contents were identified. This study provides valuable information for genetic improvement of purple tea cultivars and for fine-mapping related genes.
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Affiliation(s)
- Li-Qiang Tan
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chun-Jing Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bin Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liu-Bin Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yao Zou
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qian Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
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