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Ramirez-Ramirez AR, Mirzaei K, Menéndez-Grenot M, Clapé-Borges P, Espinosa-Lopéz G, Bidot-Martínez I, Bertin P. Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes. FRONTIERS IN PLANT SCIENCE 2024; 15:1367632. [PMID: 38504901 PMCID: PMC10948478 DOI: 10.3389/fpls.2024.1367632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/12/2024] [Indexed: 03/21/2024]
Abstract
The Baracoa region, eastern Cuba, hosts around 80 % of the country cacao (Theobroma cacao L.) plantations. Cacao plants in farms are diverse in origin and propagation, with grafted and hybrid plants being the more common ones. Less frequent are plants from cuttings, TSH progeny, and traditional Cuban cacao. A national cacao gene bank is also present in Baracoa, with 282 accessions either prospected in Cuba or introduced from other countries. A breeding program associated with the gene bank started in the 1990s based on agro-morphological descriptors. The genetic diversity of cacao resources in Baracoa has been poorly described, except for traditional Cuban cacao, affecting the proper development of the breeding program and the cacao planting policies in the region. To assess the population structure and genetic diversity of cacao resources in Baracoa region, we genotyped plants from both cacao gene bank (CG) and cacao farms (CF) applying a new ddRADseq protocol for cacao. After data processing, two SNPs datasets containing 11,425 and 6,481 high-quality SNPs were generated with 238 CG and 135 CF plants, respectively. SNPs were unevenly distributed along the 10 cacao chromosomes and laid mainly in noncoding regions of the genome. Population structure analysis with these SNP datasets identified seven and four genetic groups in CG and CF samples, respectively. Clustering using UPGMA and principal component analysis mostly agree with population structure results. Amelonado was the predominant cacao ancestry, accounting for 49.22 % (CG) and 57.73 % (CF) of the total. Criollo, Contamana, Iquitos, and Nanay ancestries were detected in both CG and CF samples, while Nacional and Marañon backgrounds were only identified in CG. Genetic differentiation among CG (FST ranging from 0.071 to 0.407) was higher than among CF genetic groups (FST: 0.093-0.282). Genetic diversity parameters showed similar values for CG and CF samples. The CG and CF genetic groups with the lowest genetic diversity parameters had the highest proportion of Amelonado ancestry. These results should contribute to reinforcing the ongoing breeding program and updating the planting policies on cacao farms, with an impact on the social and economic life of the region.
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Affiliation(s)
- Angel Rafael Ramirez-Ramirez
- Faculty of Agroforestry, University of Guantánamo, Guantánamo, Cuba
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-neuve, Belgium
| | - Khaled Mirzaei
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-neuve, Belgium
| | - Miguel Menéndez-Grenot
- Unidad de Ciencia y Técnica de Base-Baracoa / Instituto de Investigaciones Agroforestales (UCTBBaracoa / INAF), Baracoa, Cuba
| | - Pablo Clapé-Borges
- Unidad de Ciencia y Técnica de Base-Baracoa / Instituto de Investigaciones Agroforestales (UCTBBaracoa / INAF), Baracoa, Cuba
| | | | | | - Pierre Bertin
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-neuve, Belgium
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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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Shu G, Wang A, Wang X, Ding J, Chen R, Gao F, Wang A, Li T, Wang Y. Identification of southern corn rust resistance QTNs in Chinese summer maize germplasm via multi-locus GWAS and post-GWAS analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1221395. [PMID: 37810381 PMCID: PMC10552154 DOI: 10.3389/fpls.2023.1221395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 10/10/2023]
Abstract
Southern corn rust (SCR) caused by Puccinia polysora Underw is a major disease leading to severe yield losses in China Summer Corn Belt. Using six multi-locus GWAS methods, we identified a set of SCR resistance QTNs from a diversity panel of 140 inbred lines collected from China Summer Corn Belt. Thirteen QTNs on chromosomes 1, 2, 4, 5, 6, and 8 were grouped into three types of allele effects and their associations with SCR phenotypes were verified by post-GWAS case-control sampling, allele/haplotype effect analysis. Relative resistance (RRR) and relative susceptibility (RRs) catering to its inbred carrier were estimated from single QTN and QTN-QTN combos and epistatitic effects were estimated for QTN-QTN combos. By transcriptomic annotation, a set of candidate genes were predicted to be involved in transcriptional regulation (S5_145, Zm00001d01613, transcription factor GTE4), phosphorylation (S8_123, Zm00001d010672, Pgk2- phosphoglycerate kinase 2), and temperature stress response (S6_164a/S6_164b, Zm00001d038806, hsp101, and S5_211, Zm00001d017978, cellulase25). The breeding implications of the above findings were discussed.
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Affiliation(s)
- Guoping Shu
- Center of Biotechnology, Beijing Lantron Seed, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Aifang Wang
- Center of Biotechnology, Beijing Lantron Seed, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Xingchuan Wang
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruijie Chen
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Fei Gao
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Aifen Wang
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Ting Li
- Center of Biotechnology, Beijing Lantron Seed, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Yibo Wang
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, LongPing High-tech Corp., Zhengzhou, Henan, China
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Gu L, Mu X, Qi J, Tang B, Zhen W, Xia L. Nitrogen reduction combined with ET c irrigation maintained summer maize yield and increased water and nitrogen use efficiency. FRONTIERS IN PLANT SCIENCE 2023; 14:1180734. [PMID: 37426974 PMCID: PMC10324978 DOI: 10.3389/fpls.2023.1180734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/06/2023] [Indexed: 07/11/2023]
Abstract
Introduction High rainfall and excessive urea application are counterproductive to summer maize growth requirements and lower grain yield and water/nitrogen (N) use efficiency. The objective of this study was to determine whether ETc irrigation based on summer maize demand and reduced nitrogen rate in the Huang Huai Hai Plain increased water and nitrogen use efficiency without sacrificing yield. Methods To achieve this, we conducted an experiment with four irrigation levels [ambient rainfall (I0) and 50% (I1), 75% (I2), and 100% (I3) of actual crop evapotranspiration (ETc)] and four nitrogen rates [no nitrogen fertilizer (N0), recommended nitrogen rate of urea (NU), recommended nitrogen rate of blending controlled-release urea with conventional urea fertilizer (BCRF) (NC), and reduced nitrogen rate of BCRF (NR)] in 2016-2018. Results The results show that reduced irrigation and nitrogen rate reduced Fv/Fm, 13C-photosynthate, and nitrogen accumulation both in the kernel and plant. I3NC and I3NU accumulated higher 13C-photosynthate, nitrogen, and dry matter. However, 13C-photosynthate and nitrogen distribution to the kernel was decreased from I2 to I3 and was higher in BCRF than in urea. I2NC and I2NR promoted their distribution to the kernel, resulting in a higher harvest index. Compared with I3NU, I2NR increased root length density by 32.8% on average, maintaining considerable leaf Fv/Fm and obtaining similar kernel number and kernel weight. The higher root length density of I2NR of 40-60 cm promoted 13C-photosynthate and nitrogen distribution to the kernel and increased the harvest index. As a result, the water use efficiency (WUE) and nitrogen agronomic use efficiency (NAUE) in I2NR increased by 20.5%-31.9% and 11.0%-38.0% than that in I3NU, respectively. Discussion Therefore, 75%ETc deficit irrigation and BCRF fertilizer with 80% nitrogen rate improved root length density, maintained leaf Fv/Fm in the milking stage, promoted 13C-photosynthate, and distributed nitrogen to the kernel, ultimately providing a higher WUE and NAUE without significantly reducing grain yield.
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Affiliation(s)
- Limin Gu
- Cereal Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinyuan Mu
- Cereal Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jianshuang Qi
- Cereal Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Baojun Tang
- Cereal Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenchao Zhen
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
- Key Laboratory of North China Water-saving Agriculture, Ministry of Agriculture and Rural Affairs, Baoding, Hebei, China
| | - Laikun Xia
- Cereal Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
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He L, Luo J, Niu S, Bai D, Chen Y. Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau. BMC PLANT BIOLOGY 2023; 23:255. [PMID: 37189087 DOI: 10.1186/s12870-023-04239-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Tea, the second largest consumer beverage in the world after water, is widely cultivated in tropical and subtropical areas. However, the effect of environmental factors on the distribution of wild tea plants is unclear. RESULTS A total of 159 wild tea plants were collected from different altitudes and geological types of the Guizhou Plateau. Using the genotyping-by-sequencing method, 98,241 high-quality single nucleotide polymorphisms were identified. Genetic diversity, population structure analysis, principal component analysis, phylogenetic analysis, and linkage disequilibrium were performed. The genetic diversity of the wild tea plant population from the Silicate Rock Classes of Camellia gymnogyna was higher than that from the Carbonate Rock Classes of Camellia tachangensis. In addition, the genetic diversity of wild tea plants from the second altitude gradient was significantly higher than that of wild tea plants from the third and first altitude gradients. Two inferred pure groups (GP01 and GP02) and one inferred admixture group (GP03) were identified by population structure analysis and were verified by principal component and phylogenetic analyses. The highest differentiation coefficients were determined for GP01 vs. GP02, while the lowest differentiation coefficients were determined for GP01 vs. GP03. CONCLUSIONS This study revealed the genetic diversity and geographical distribution characteristics of wild tea plants in the Guizhou Plateau. There are significant differences in genetic diversity and evolutionary direction between Camellia tachangensis with Carbonate Rock Classes at the first altitude gradient and Camellia gymnogyna with Silicate Rock Classes at the third altitude gradient. Geological environment, soil mineral element content, soil pH, and altitude markedly contributed to the genetic differentiation between Camellia tachangensis and Camellia gymnogyna.
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Affiliation(s)
- Limin He
- College of Tea Science / Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Jing Luo
- College of Tea Science / Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Suzhen Niu
- College of Tea Science / Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, People's Republic of China.
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Guizhou University, Ministry of Education, Institute of Agro-Bioengineering, Guiyang, 550025, Guizhou Province, People's Republic of China.
| | - Dingchen Bai
- College of Tea Science / Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Yanjun Chen
- College of Tea Science / Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, People's Republic of China
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Fu R, Wang X. Modeling the influence of phenotypic plasticity on maize hybrid performance. PLANT COMMUNICATIONS 2023; 4:100548. [PMID: 36635964 DOI: 10.1016/j.xplc.2023.100548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/31/2022] [Accepted: 01/10/2023] [Indexed: 05/11/2023]
Abstract
Phenotypic plasticity, the ability of an individual to alter its phenotype in response to changes in the environment, has been proposed as a target for breeding crop varieties with high environmental fitness. Here, we used phenotypic and genotypic data from multiple maize (Zea mays L.) populations to mathematically model phenotypic plasticity in response to the environment (PPRE) in inbred and hybrid lines. PPRE can be simply described by a linear model in which the two main parameters, intercept a and slope b, reflect two classes of genes responsive to endogenous (class A) and exogenous (class B) signals that coordinate plant development. Together, class A and class B genes contribute to the phenotypic plasticity of an individual in response to the environment. We also made connections between phenotypic plasticity and hybrid performance or general combining ability (GCA) of yield using 30 F1 hybrid populations generated by crossing the same maternal line with 30 paternal lines from different maize heterotic groups. We show that the parameters a and b from two given parental lines must be concordant to reach an ideal GCA of F1 yield. We hypothesize that coordinated regulation of the two classes of genes in the F1 hybrid genome is the basis for high GCA. Based on this theory, we built a series of predictive models to evaluate GCA in silico between parental lines of different heterotic groups.
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Affiliation(s)
- Ran Fu
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China; Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Xiangfeng Wang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China; Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China.
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Skovbjerg CK, Angra D, Robertson-Shersby-Harvie T, Kreplak J, Keeble-Gagnère G, Kaur S, Ecke W, Windhorst A, Nielsen LK, Schiemann A, Knudsen J, Gutierrez N, Tagkouli V, Fechete LI, Janss L, Stougaard J, Warsame A, Alves S, Khazaei H, Link W, Torres AM, O'Sullivan DM, Andersen SU. Genetic analysis of global faba bean diversity, agronomic traits and selection signatures. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:114. [PMID: 37074596 PMCID: PMC10115707 DOI: 10.1007/s00122-023-04360-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/31/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE We identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection. Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for sustainable protein production. However, little is known about the genetics underlying trait diversity. In this study, we used 21,345 high-quality SNP markers to genetically characterize 2678 faba bean genotypes. We performed genome-wide association studies of key agronomic traits using a seven-parent-MAGIC population and detected 238 significant marker-trait associations linked to 12 traits of agronomic importance. Sixty-five of these were stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identified three subpopulations differentiated by geographical origin and 33 genomic regions subjected to strong diversifying selection between subpopulations. We found that SNP markers associated with the differentiation of northern and southern accessions explained a significant proportion of agronomic trait variance in the seven-parent-MAGIC population, suggesting that some of these traits were targets of selection during breeding. Our findings point to genomic regions associated with important agronomic traits and selection, facilitating faba bean genomics-based breeding.
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Affiliation(s)
- Cathrine Kiel Skovbjerg
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark.
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Deepti Angra
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | | | - Jonathan Kreplak
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Wolfgang Ecke
- Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Alex Windhorst
- Georg-August-Universität Göttingen, DNPW, Carl-Sprengel 1, Germany
| | | | | | | | - Natalia Gutierrez
- Área de Mejora Vegetal y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo 3092, 14080, Córdoba, Spain
| | - Vasiliki Tagkouli
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Lavinia Ioana Fechete
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Luc Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Ahmed Warsame
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Sheila Alves
- Crops Research, Teagasc, Oak Park, Carlow, Ireland
| | - Hamid Khazaei
- Production Systems, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Wolfgang Link
- Georg-August-Universität Göttingen, DNPW, Carl-Sprengel 1, Germany
| | - Ana Maria Torres
- Área de Mejora Vegetal y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo 3092, 14080, Córdoba, Spain
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Zhao M, Shu G, Hu Y, Cao G, Wang Y. Pattern and variation in simple sequence repeat (SSR) at different genomic regions and its implications to maize evolution and breeding. BMC Genomics 2023; 24:136. [PMID: 36944913 PMCID: PMC10029318 DOI: 10.1186/s12864-023-09156-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 01/30/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Repetitive DNA sequences accounts for over 80% of maize genome. Although simple sequence repeats (SSRs) account for only 0.03% of the genome, they have been widely used in maize genetic research and breeding as highly informative codominant DNA markers. The genome-wide distribution and polymorphism of SSRs are not well studied due to the lack of high-quality genome DNA sequence data. RESULTS In this study, using data from high-quality de novo-sequenced maize genomes of five representative maize inbred lines, we revealed that SSRs were more densely present in telomeric region than centromeric region, and were more abundant in genic sequences than intergenic sequences. On genic sequences, tri- and hexanucleotide motifs were more abundant in CDS sequence and some mono- and dinucleotide motifs were more abundant in UTR sequences. Median length and chromosomal density of SSRs were both narrowly range-bound, with median length of 14-18 bp and genome-wide average density of 3355.77 bp/Mbp. LTR-RTs of < 0.4 Mya had higher SSR density (4498-4992 bp/Mbp). The genome-specific and motif-specific SSR polymorphism were studied. Their potential breeding applications were discussed. CONCLUSIONS We found that the median length of SSR sequences of different SSR motifs was nearly constant. SSR density in genic regions was much higher than intergenic regions. In addition, SSR density at LTR-RTs of different evolutionary ages varied in a narrow range. The SSRs and their LTR-RT carriers evolved at an equal rate. All these observations indicated that SSR length and density were under control of yet unknown evolutionary forces. The chromosome region-specific and motif-specific SSR polymorphisms we observed supported the notion that SSR polymorphism was invaluable genome resource for developing highly informative genome and gene markers in maize genetic research and molecular breeding.
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Affiliation(s)
- Meiqi Zhao
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Guoping Shu
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001, China
| | - Yanhong Hu
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001, China
| | - Gangqiang Cao
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yibo Wang
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China.
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001, China.
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, 450001, China.
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Guo J, Qu L, Wei Q, Lu D. Effects of post-silking low temperature on the starch and protein metabolism, endogenous hormone contents, and quality of grains in waxy maize. FRONTIERS IN PLANT SCIENCE 2022; 13:988172. [PMID: 36407592 PMCID: PMC9673756 DOI: 10.3389/fpls.2022.988172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Waxy maize has many excellent characteristics in food and nonfood industries. However, post-silking low temperature (LT) has severe limitations on its grain yield and quality. In this study, field and pot trials were conducted to investigate the effects of post-silking LT on the physiological, biochemical, and functional characteristics of two waxy maize grains. The field and pot trials were performed with sowing date and artificial climate chamber, respectively, for LT treatment from silking stage to maturity. Results in pot trial were used to explain and validate the findings in field trial. Compared with the ambient treatment, the LT treatment significantly reduced kernel weight during the grain filling stage (P < 0.05). LT treatment in both environments resulted in an average decrease in dry weight of SYN5 and YN7 at maturity by 36.6% and 42.8%, respectively. Enzymatic activities related to starch and protein biosynthesis decreased under the LT treatment during the filling stage, accompanied by a decrease in the accumulation amounts and contents of soluble sugar and starch, and a decrease in protein accumulation amount. Meanwhile, the contents of abscisic acid, indole-3-acetic acid, and gibberellin 3 in grains decreased under the LT treatment during the filling stage. Peak, trough, breakdown, final, and setback viscosities of grains decreased by LT. LT treatment decreased the gelatinization enthalpy of grains and increased the retrogradation percentage. In conclusion, post-silking LT stress altered the content of grain components by inhibiting the production of phytohormones and down-regulating the enzymatic activities involved in starch and protein metabolism, which resulted in the deterioration of grain pasting and thermal properties.
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Affiliation(s)
- Jian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Lingling Qu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College, Yangzhou University, Yangzhou, China
| | - Qi Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College, Yangzhou University, Yangzhou, China
| | - Dalei Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
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Guo J, Wang Z, Qu L, Hu Y, Lu D. Transcriptomic and alternative splicing analyses provide insights into the roles of exogenous salicylic acid ameliorating waxy maize seedling growth under heat stress. BMC PLANT BIOLOGY 2022; 22:432. [PMID: 36076169 PMCID: PMC9461148 DOI: 10.1186/s12870-022-03822-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Salicylic acid (SA) is a phytohormone which works to regulate the abiotic stress response of plants. However, the molecular mechanism by which SA mediates heat tolerance in waxy maize (Zea mays L. sinsensis Kulesh) remains unknown. RESULTS Two varieties of waxy maize seedlings, heat-tolerant 'Yunuo7' (Y7) and heat-sensitive 'Suyunuo5' (S5), were pretreated with SA prior to heat stress (HTS). After treatment, physiological and transcriptomic changes were analyzed. Compared with HTS, the exogenous application of SA enhanced the shoot dry weight, the activities of antioxidant enzymes (e.g., SOD, POD, CAT and APX), and the concentration of endogenous phytohormones (e.g., SA, ABA, IAA, GA3), while decreased the MDA content. Transcriptome analysis showed that the number of differentially expressed genes (DEGs) identified in the control (CK) vs HTS and HTS vs HTS + SA comparisons were more in S5 than in Y7. HTS induced the downregulation of genes involved in photosynthesis and the upregulation of genes encoding heat shock transcription factors (HSFs) and heat shock proteins (HSPs). Compared with HTS, SA pretreatment reversed the expression of 5 photosynthesis-related genes, 26 phytohormone-related genes, and all genes encoding HSFs and HSPs in S5. Furthermore, the number of alternative splicing (AS) events increased under HTS treatment for both varieties, while decreased under SA pretreatment of S5. Differentially spliced genes (DSGs) showed little overlap with DEGs, and DEGs and DSGs differed significantly in functional enrichment. CONCLUSIONS Physiological and transcriptional together indicated that HTS and SA pretreatment had a greater effect on S5 than Y7. Additionally, it appears that transcriptional regulation and AS work synergistically to enhance thermotolerance in heat-sensitive waxy maize. Our study revealed the regulatory effects and underlying molecular mechanisms of SA on waxy maize seedling under HTS.
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Affiliation(s)
- Jian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, People's Republic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Zitao Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Lingling Qu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Yifan Hu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Dalei Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, People's Republic of China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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Population Structure Analysis and Association Mapping for Turcicum Leaf Blight Resistance in Tropical Maize Using SSR Markers. Genes (Basel) 2022; 13:genes13040618. [PMID: 35456424 PMCID: PMC9030036 DOI: 10.3390/genes13040618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 12/04/2022] Open
Abstract
Maize is an important cereal crop in the world for feed, food, fodder, and raw materials of industries. Turcicum leaf blight (TLB) is a major foliar disease that can cause more than 50% yield losses in maize. Considering this, the molecular diversity, population structure, and genome-wide association study (GWAS) for TLB resistance were studied in 288 diverse inbred lines genotyped using 89 polymorphic simple sequence repeats (SSR) markers. These lines werescreened for TLB disease at two hot-spot locations under artificially inoculated conditions. The average percent disease incidence (PDI) calculated for each genotype ranged from 17 (UMI 1201) to 78% (IML 12-22) with an overall mean of 40%. The numbers of alleles detected at a locus ranged from twoto nine, with a total of 388 alleles. The polymorphic information content (PIC) of each marker ranged between 0.04 and 0.86. Out of 89 markers, 47 markers were highly polymorphic (PIC ≥ 0.60). This indicated that the SSR markers used were very informative and suitable for genetic diversity, population structure, and marker-trait association studies.The overall observed homozygosity for highly polymorphic markers was 0.98, which indicated that lines used were genetically pure. Neighbor-joining clustering, factorial analysis, and population structure studies clustered the 288 lines into 3–5 groups. The patterns of grouping were in agreement with the origin and pedigree records of the genotypesto a greater extent.A total of 94.10% lines were successfully assigned to one or another group at a membership probability of ≥0.60. An analysis of molecular variance (AMOVA) revealed highly significant differences among populations and within individuals. Linkage disequilibrium for r2 and D′ between loci ranged from 0 to 0.77 and 0 to 1, respectively. A marker trait association analysis carried out using a general linear model (GLM) and mixed linear model (MLM), identified 15 SSRs markers significantly associated with TLB resistance.These 15 markers were located on almost all chromosomes (Chr) except 7, 8, and 9. The phenotypic variation explained by these loci ranged from 6% (umc1367) to 26% (nc130, phi085). Maximum 7 associated markers were located together on Chr 2 and 5. The selected regions identified on Chr 2 and 5 corroborated the previous studies carried out in the Indian maize germplasm. Further, 11 candidate genes were identified to be associated with significant markers. The identified sources for TLB resistance and associated markers may be utilized in molecular breeding for the development of suitable genotypes.
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Kumar B, Rakshit S, Kumar S, Singh BK, Lahkar C, Jha AK, Kumar K, Kumar P, Choudhary M, Singh SB, Amalraj JJ, Prakash B, Khulbe R, Kamboj MC, Chirravuri NN, Hossain F. Genetic Diversity, Population Structure and Linkage Disequilibrium Analyses in Tropical Maize Using Genotyping by Sequencing. PLANTS (BASEL, SWITZERLAND) 2022; 11:799. [PMID: 35336681 PMCID: PMC8955159 DOI: 10.3390/plants11060799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Several maize breeding programs in India have developed numerous inbred lines but the lines have not been characterized using high-density molecular markers. Here, we studied the molecular diversity, population structure, and linkage disequilibrium (LD) patterns in a panel of 314 tropical normal corn, two sweet corn, and six popcorn inbred lines developed by 17 research centers in India, and 62 normal corn from the International Maize and Wheat Improvement Center (CIMMYT). The 384 inbred lines were genotyped with 60,227 polymorphic single nucleotide polymorphisms (SNPs). Most of the pair-wise relative kinship coefficients (58.5%) were equal or close to 0, which suggests the lack of redundancy in the genomic composition in the majority of inbred lines. Genetic distance among most pairs of lines (98.3%) varied from 0.20 to 0.34 as compared with just 1.7% of the pairs of lines that differed by <0.20, which suggests greater genetic variation even among sister lines. The overall average of 17% heterogeneity was observed in the panel indicated the need for further inbreeding in the high heterogeneous genotypes. The mean nucleotide diversity and frequency of polymorphic sites observed in the panel were 0.28 and 0.02, respectively. The model-based population structure, principal component analysis, and phylogenetic analysis revealed three to six groups with no clear patterns of clustering by centers-wise breeding lines, types of corn, kernel characteristics, maturity, plant height, and ear placement. However, genotypes were grouped partially based on their source germplasm from where they derived.
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Affiliation(s)
- Bhupender Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Sonu Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Brijesh Kumar Singh
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Chayanika Lahkar
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Abhishek Kumar Jha
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Krishan Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Pardeep Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Shyam Bir Singh
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - John J. Amalraj
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India;
| | - Bhukya Prakash
- ICAR-Directorate of Poultry Research, Hyderabad 500030, India;
| | - Rajesh Khulbe
- Department of Crop Imrovement, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora 263601, India;
| | - Mehar Chand Kamboj
- Department of Plant Breeding, CCS-Haryana Agricultural University, Regional Research Station, Uchani 132001, India;
| | - Neeraja N. Chirravuri
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India;
| | - Firoz Hossain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
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Zhao Z, Song Q, Bai D, Niu S, He Y, Qiao D, Chen Z, Li C, Luo J, Li F. Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau. BMC PLANT BIOLOGY 2022; 22:55. [PMID: 35086484 PMCID: PMC8793275 DOI: 10.1186/s12870-022-03438-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/12/2022] [Indexed: 05/17/2023]
Abstract
BACKGROUND Tea plants originated in southwestern China. Guizhou Plateau is an original center of tea plants, and is rich in germplasm resources. However, the genetic diversity, population structure and distribution characteristics of cultivated-type tea plants in the region are unknown. In this study, we explored the genetic diversity and geographical distribution of cultivated-type tea accessions in Guizhou Plateau. RESULTS We used 112,072 high-quality genotyping-by-sequencing to analyze the genetic diversity, principal components, phylogeny, population structure, and linkage disequilibrium, and develop a core collection of 253 cultivated-type tea plant accessions from Guizhou Plateau. The results showed Genetic diversity of the cultivated-type tea accessions of the Pearl River Basin was significantly higher than that of the cultivated-type tea accessions of the Yangtze River Basin. Three inferred pure groups (CG-1, CG-2 and CG-3) and one inferred admixture group (CG-4), were identified by a population structure analysis, and verified by principal component and phylogenetic analyses. The highest genetic distance and differentiation coefficients were determined for CG-2 vs CG-3. The lower genetic distance and differentiation coefficients were determined for CG-4 vs CG-2 and CG-4 vs CG-3, respectively. We developed a core set and a primary set. The primary and core sets contained 77.0 and 33.6% of all individuals in the initial set, respectively. The primary set may serve as the primary population in genome-wide association studies, while the core collection may serve as the core population in multiple treatment setting studies. CONCLUSIONS The present study demonstrated the genetic diversity and geographical distribution characteristics of cultivated-type tea plants in Guizhou Plateau. Significant differences in genetic diversity and evolutionary direction were detected between the ancient landraces of the Pearl River Basin and the those of the Yangtze River Basin. Major rivers and ancient hubs were largely responsible for the genetic exchange between the Pearl River Basin and the Yangtze River Basin ancient landraces as well as the formation of the ancient hubs evolutionary group. Genetic diversity, population structure and core collection elucidated by this study will facilitate further genetic studies, germplasm protection, and breeding of tea plants.
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Affiliation(s)
- Zhifei Zhao
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Qinfei Song
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Dingchen Bai
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Suzhen Niu
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Yingqin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Dahe Qiao
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Zhengwu Chen
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Caiyun Li
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Jing Luo
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Fang Li
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
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