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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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Jin Y, Luo X, Li Y, Peng X, Wu L, Yang G, Xu X, Pei Y, Li W, Zhang W. Fine mapping and analysis of candidate genes for qBT2 and qBT7.2 locus controlling bolting time in radish (Raphanus sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:4. [PMID: 38085292 DOI: 10.1007/s00122-023-04503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE Two major QTLs for bolting time in radish were mapped to chromosome 02 and 07 in a 0.37 Mb and 0. 52 Mb interval, RsFLC1 and RsFLC2 is the critical genes. Radish (Raphanus sativus L.) is an important vegetable crop of Cruciferae. The premature bolting and flowering reduces the yield and quality of the fleshy root of radish. However, the molecular mechanism underlying bolting and flowering in radish remains unknown. In YZH (early bolting) × XHT (late bolting) F2 population, a high-density genetic linkage map was constructed with genetic distance of 2497.74 cM and an average interval of 2.31 cM. A total of nine QTLs for bolting time and two QTLs for flowering time were detected. Three QTLs associated with bolting time in radish were identified by QTL-seq using radish GDE (early bolting) × GDL (late bolting) F2 population. Fine mapping narrowed down qBT2 and qBT7.2 to an 0.37 Mb and 0.52 Mb region on chromosome 02 and 07, respectively. RNA-seq and qRT-PCR analysis showed that RsFLC1 and RsFLC2 were the candidate gene for qBT7.2 and qBT2 locus, respectively. Subcellular localization exhibited that RsFLC1 and RsFLC2 were mainly expressed in the nucleus. A 1856-bp insertion in the first intron of RsFLC1 was responsible for bolting time. Overexpression of RsFLC2 in Arabidopsis was significantly delayed flowering. These findings will provide new insights into the exploring the molecular mechanism of late bolting and promote the marker-assisted selection for breeding late-bolting varieties in radish.
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Affiliation(s)
- Yueyue Jin
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Xiaobo Luo
- Guizhou Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, 550003, Guizhou, China
| | - Yadong Li
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Xiao Peng
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Linjun Wu
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Guangqian Yang
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Xiuhong Xu
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Yun Pei
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Wei Li
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China
- Guizhou Higher Education Facility Vegetable Engineering Reseach Centre, Guizhou University, Guiyang, 550003, Guizhou, China
| | - Wanping Zhang
- College of Agriculture, Guizhou University, Guiyang, 550003, Guizhou, China.
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003, Guizhou, China.
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