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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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Vallarino JG, Jun H, Wang S, Wang X, Sade N, Orf I, Zhang D, Shi J, Shen S, Cuadros-Inostroza Á, Xu Q, Luo J, Fernie AR, Brotman Y. Limitations and advantages of using metabolite-based genome-wide association studies: focus on fruit quality traits. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 333:111748. [PMID: 37230189 DOI: 10.1016/j.plantsci.2023.111748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 05/27/2023]
Abstract
In the last decades, linkage mapping has help in the location of metabolite quantitative trait loci (QTL) in many species; however, this approach shows some limitations. Recently, thanks to the most recent advanced in high-throughput genotyping technologies like next-generation sequencing, metabolite genome-wide association study (mGWAS) has been proposed a powerful tool to identify the genetic variants in polygenic agrinomic traits. Fruit flavor is a complex interaction of aroma volatiles and taste being sugar and acid ratio key parameter for flavor acceptance. Here, we review recent progress of mGWAS in pinpoint gene polymorphisms related to flavor-related metabolites in fruits. Despite clear successes in discovering novel genes or regions associated with metabolite accumulation affecting sensory attributes in fruits, GWAS incurs in several limitations summarized in this review. In addition, in our own work, we performed mGWAS on 194 Citrus grandis accessions to investigate the genetic control of individual primary and lipid metabolites in ripe fruit. We have identified a total of 667 associations for 14 primary metabolites including amino acids, sugars, and organic acids, and 768 associations corresponding to 47 lipids. Furthermore, candidate genes related to important metabolites related to fruit quality such as sugars, organic acids and lipids were discovered.
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Affiliation(s)
- José G Vallarino
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, 29071 Málaga, Spain
| | - Hong Jun
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | | | - Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Isabel Orf
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Dabing Zhang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Jianxin Shi
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | | | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Alisdair R Fernie
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany; Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria.
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel.
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Yang Y, Wang W, Hu Q, Raman H, Liu J. Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed ( Brassica napus). FRONTIERS IN PLANT SCIENCE 2023; 13:1097534. [PMID: 36714779 PMCID: PMC9880488 DOI: 10.3389/fpls.2022.1097534] [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: 11/14/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
Spatial distribution and orientation of pods on the main raceme (stem) and branches could affect rapeseed yield. However, genomic regions underlying the pod orientation were not described in Brassica species. Here, we determined the extent of genetic variation in pod orientation, described as the angles of pedicel on raceme (APR) and angles of the pod on pedicel (APP) among 136 rapeseed accessions grown across three environments of the upper, middle and lower Yangtze River in China. The APR ranged from 59° to 109°, while the APP varied from 142° to 178°. Statistical analysis showed that phenotypic variation was due to genotypic (G) and environmental (E) effects. Using the genome-wide association analysis (GWAS) approach, two QTLs for APR (qBnAPR.A02 and qBnAPR.C02) and two for APP (qBnAPP.A05 and qBnAPP.C05), having minor to moderate allelic effects (4.30% to 19.47%) were identified. RNA-seq analysis revealed 606 differentially expressed genes (DEGs) in two rapeseed accessions representing the extreme phenotypes for pod orientation and different alleles at the QTLs of APR. Three DEGs (BnLAZY4.A02, BnSAUR32.A02, and BnSAUR32.C02) were identified as the most likely candidates responsible for variation in pod orientation (APR). This study elucidates the genomic regions and putative candidate genes underlying pod orientation in B. napus.
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Affiliation(s)
- Yuting Yang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Shenzhen Graduate School, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Wenxiang Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiong Hu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Harsh Raman
- New South Wales (NSW) Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Jia Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
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