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Zhang Y, Zhang W, Liu Y, Zheng Y, Nie X, Wu Q, Yu W, Wang Y, Wang X, Fang K, Qin L, Xing Y. GWAS identifies two important genes involved in Chinese chestnut weight and leaf length regulation. PLANT PHYSIOLOGY 2024; 194:2387-2399. [PMID: 38114094 DOI: 10.1093/plphys/kiad674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023]
Abstract
There are many factors that affect the yield of Chinese chestnut (Castanea mollissima), with single nut weight (SNW) being one of the most important. Leaf length is also related to Chinese chestnut yield. However, the genetic architecture and gene function associated with Chinese chestnut nut yield have not been fully explored. In this study, we performed genotyping by sequencing 151 Chinese chestnut cultivars, followed by a genome-wide association study (GWAS) on six horticultural traits. First, we analyzed the phylogeny of the Chinese chestnut and found that the Chinese chestnut cultivars divided into two ecotypes, a northern and southern cultivar group. Differences between the cultivated populations were found in the pathways of plant growth and adaptation to the environment. In the selected regions, we also found interesting tandemly arrayed genes that may influence Chinese chestnut traits and environmental adaptability. To further investigate which horticultural traits were selected, we performed a GWAS using six horticultural traits from 151 cultivars. Forty-five loci that strongly associated with horticultural traits were identified, and six genes highly associated with these traits were screened. In addition, a candidate gene associated with SNW, APETALA2 (CmAP2), and another candidate gene associated with leaf length (LL), CRYPTOCHROME INTERACTING BASIC HELIX-LOOP-HELIX 1 (CmCIB1), were verified in Chinese chestnut and Arabidopsis (Arabidopsis thaliana). Our results showed that CmAP2 affected SNW by negatively regulating cell size. CmCIB1 regulated the elongation of new shoots and leaves by inducing cell elongation, potentially affecting photosynthesis. This study provided valuable information and insights for Chinese chestnut breeding research.
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Affiliation(s)
- Yu Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Weiwei Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yang Liu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Xinghua Nie
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Qinyi Wu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Wenjie Yu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yafeng Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Xuefeng Wang
- Longtan Forestry Station, Liyang Bureau of Natural Resources and Planning, Liyang, Jiangsu 213300, China
| | - Kefeng Fang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Ling Qin
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yu Xing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
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Zhou Z, Liu F, Xu Y, Hu W. Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu. PLANTS (BASEL, SWITZERLAND) 2024; 13:618. [PMID: 38475465 DOI: 10.3390/plants13050618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/14/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024]
Abstract
Rubus chingii Hu is the only species that is used for both edible and medicinal purposes among the 194 species of the genus Rubus in China. It is well known for its sweet and sour fresh fruits that are rich in vitamins and for its dried immature fruits that are used to treat kidney-related ailments. This study aims to evaluate genetic diversity and population structure and build a core germplasm repository of 132 R. chingii accessions from the provinces of Jiangxi and Fujian, using Hyper-seq-derived single-nucleotide polymorphism (SNP) markers. This is the first genetic study of R. chingii based on SNP molecular markers, and a total of 1,303,850 SNPs and 433,159 insertions/deletions (InDels) were identified. Low values for observed heterozygosity, nucleotide diversity (Pi) and fixation indexes (Fis) indicated low genetic diversity within populations, and an analysis of molecular variance (AMOVA) showed that 37.4% and 62.6% of the variations were found between populations and within samples, respectively. Four main clusters were identified by means of neighbor-joining (NJ) trees, the ADMIXTURE program and principal component analysis (PCA). Based on the genetic diversity, we finally constructed 38 representative core collections, representing 50% of the total core germplasm samples and 95.3% of the genotypes. In summary, the results of our study can provide valuable information on the genetic structure of R. chingii germplasm resources, which is helpful for further explorations of potential high-quality genes and for formulating future breeding and conservation strategies.
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Affiliation(s)
- Ziwei Zhou
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332900, China
| | - Fen Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332900, China
| | - Yanqin Xu
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Weiming Hu
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang 330004, 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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Orhan E, Kara D. Use of retrotransposon based iPBS markers for determination of genetic relationship among some Chestnut Cultivars (Castanea sativa Mill.) in Türkiye. Mol Biol Rep 2023; 50:8397-8405. [PMID: 37615924 DOI: 10.1007/s11033-023-08697-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/18/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND The aim of this study was to reveal the genetic relationships among some economically important chestnut cultivars for Türkiye by using retrotransposon-based inter primer binding site (iPBS) markers. METHODS AND RESULTS In this study, a total of 19 iPBS markers were used to determine the genetic relationships among 11 chestnut cultivars (Castanea sativa Mill.). In the study, chestnut cultivars named Hacıömer, Osmanoğlu, Sarıaşlama, Erfelek, Kemer, Işıklar, Şekerci, Siyah Bursa, Tülü, Bouche De Betizac and Marigoule were the preferred cultivars utilised. Using the online marker efficiency calculator (iMEC), some indices of polymorphism, such as the mean heterozygosity, polymorphism information content, marker index and discriminating power, were determined. In addition, the size ranges of alleles, number of average alleles, number of total alleles, number of polymorphic alleles, and polymorphism rate were determined at a successful level. The chestnut cultivars of Hacıömer and Şekerci were determined to be the most similar cultivars with a similarity coefficient value of 0.924, and they formed a subgroup together with the chestnut cultivars Osmanoğlu and Erfelek, showing close similarity with these two cultivars. CONCLUSIONS The use of iPBS markers in chestnuts in Türkiye was carried out for the first time in this study. The power of iPBS markers to evaluate the genetic relationship for our preferred chestnut cultivars was revealed. For this reason, it has emerged that it will be useful in the molecular characterization of both genotypes in natural chestnut populations and chestnut breeding materials such as varieties and cultivars in chestnut breeding programs.
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Affiliation(s)
- Emine Orhan
- Faculty of Agriculture, Department of Agricultural Biotechnology, Atatürk University, Erzurum, Türkiye, 25240, Turkey.
| | - Didem Kara
- Graduate School of Natural and Applied Sciences, Department of Agricultural Biotechnology, Graduate-Agricultural Engineer, Atatürk University, Erzurum, Türkiye, 25240, Turkey
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