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Zhang M, Zheng C, Li J, Wang X, Liu C, Li X, Xu Z, Du K. Genetic diversity, population structure, and DNA fingerprinting of Ailanthus altissima var. erythrocarpa based on EST-SSR markers. Sci Rep 2023; 13:19315. [PMID: 37935877 PMCID: PMC10630516 DOI: 10.1038/s41598-023-46798-2] [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: 06/23/2023] [Accepted: 11/05/2023] [Indexed: 11/09/2023] Open
Abstract
Ailanthus altissima var. erythrocarpa is an A. altissima variety with high economic, ecological and ornamental value, but there have been no reports on the development of SSR primers for it. According to the SSR primer information provided by the transcriptome of A. altissima var. erythrocarpa, 120 individuals with different redness levels were used to screen polymorphic primers. Transcriptomic analysis revealed 10,681 SSR loci, of which mononucleotide repeats were dominant (58.3%), followed by dinucleotide and trinucleotide repeats (16.6%, 15.1%) and pentanucleotide repeats (0.2%). Among 140 pairs of randomly selected primers, nineteen pairs of core primers with high polymorphism were obtained. The average number of alleles (Na), average number of effective alleles (Ne), average Shannon's diversity index (I), average observed heterozygosity (Ho), average expected heterozygosity (He), fixation index (F) and polymorphic information content (PIC) were 11.623, 4.098, 1.626, 0.516, 0.696, 0.232 and 0.671, respectively. Nineteen EST-SSR markers were used to study the genetic diversity and population structure of A. altissima var. erythrocarpa. The phylogenetic tree, PCoA, and structure analysis all divided the tested resources into two categories, clearly showing the genetic variation between individuals. The population showed high genetic diversity, mainly derived from intraspecific variation. Among nineteen pairs of primers, 4 pairs (p33, p15, p46, p92) could effectively distinguish and be used for fingerprinting of the tested materials. This study is of great significance for genetic diversity analysis and molecular-assisted breeding of A. altissima var. erythrocarpa.
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Affiliation(s)
- Manman Zhang
- Hebei Agricultural University, Baoding, 071000, Hebei, China
- Hebei Technical Innovation Center for Forest Improved Variety, Shijiazhuang, 050061, Hebei, China
| | - Conghui Zheng
- Hebei Technical Innovation Center for Forest Improved Variety, Shijiazhuang, 050061, Hebei, China
- Hebei Academy of Forestry and Grassland Sciences, Shijiazhuang, 050061, Hebei, China
| | - Jida Li
- Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Xueyong Wang
- Hebei Technical Innovation Center for Forest Improved Variety, Shijiazhuang, 050061, Hebei, China
- Hebei Academy of Forestry and Grassland Sciences, Shijiazhuang, 050061, Hebei, China
| | - Chunpeng Liu
- Hebei Technical Innovation Center for Forest Improved Variety, Shijiazhuang, 050061, Hebei, China
- Hebei Academy of Forestry and Grassland Sciences, Shijiazhuang, 050061, Hebei, China
| | - Xiangjun Li
- Hebei Technical Innovation Center for Forest Improved Variety, Shijiazhuang, 050061, Hebei, China
- Hebei Academy of Forestry and Grassland Sciences, Shijiazhuang, 050061, Hebei, China
| | - Zhenhua Xu
- Hebei Technical Innovation Center for Forest Improved Variety, Shijiazhuang, 050061, Hebei, China.
- Hebei Academy of Forestry and Grassland Sciences, Shijiazhuang, 050061, Hebei, China.
| | - Kejiu Du
- Hebei Agricultural University, Baoding, 071000, Hebei, China.
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Li L, Li X, Liu F, Zhao J, Zhang Y, Zheng W, Fan L. Preliminary Investigation of Essentially Derived Variety of Tea Tree and Development of SNP Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:1643. [PMID: 37111866 PMCID: PMC10145075 DOI: 10.3390/plants12081643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/02/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
The continuous emergence of Essentially Derived Varieties (EDVs) in the process of tea tree breeding will endanger and affect the innovation ability and development potential of tea tree breeding. In this study, genotyping by sequencing (GBS) technology was used to screen high-quality genomic SNPs for the first time to investigate the derived relationships of 349 tea trees from 12 provinces in China. A total of 973 SNPs uniformly covering 15 tea tree chromosomes with high discrimination capacity were screened as the core SNP set. A genetic similarity analysis showed that 136 pairs of tea trees had a genetic similarity coefficient (GS) > 90%, among which 60 varieties/strains were identified as EDVs, including 22 registered varieties (19 were indisputably EDVs). Furthermore, 21 SNPs with 100% identification of 349 tea trees were selected as rapid identification markers, of which 14 SNP markers could be used for 100% identification of non-EDV. These results provide the basis for the analysis of the genetic background of tea trees in molecular-assisted breeding.
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Affiliation(s)
- Li Li
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan 354300, China; (X.L.); (F.L.); (J.Z.); (Y.Z.); (W.Z.)
| | - Xiangru Li
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan 354300, China; (X.L.); (F.L.); (J.Z.); (Y.Z.); (W.Z.)
- College of Horticulture, Fujian Agriculture and Forestry University, 15# Shangxiadian Road, Fuzhou 350002, China
| | - Fei Liu
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan 354300, China; (X.L.); (F.L.); (J.Z.); (Y.Z.); (W.Z.)
| | - Jialin Zhao
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan 354300, China; (X.L.); (F.L.); (J.Z.); (Y.Z.); (W.Z.)
| | - Yan Zhang
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan 354300, China; (X.L.); (F.L.); (J.Z.); (Y.Z.); (W.Z.)
| | - Weiming Zheng
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan 354300, China; (X.L.); (F.L.); (J.Z.); (Y.Z.); (W.Z.)
| | - Li Fan
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan 354300, China; (X.L.); (F.L.); (J.Z.); (Y.Z.); (W.Z.)
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Zhang J, Yang J, Lv Y, Zhang X, Xia C, Zhao H, Wen C. Genetic diversity analysis and variety identification using SSR and SNP markers in melon. BMC PLANT BIOLOGY 2023; 23:39. [PMID: 36650465 PMCID: PMC9847184 DOI: 10.1186/s12870-023-04056-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Melon is an important horticultural crop with a pleasant aromatic flavor and abundance of health-promoting substances. Numerous melon varieties have been cultivated worldwide in recent years, but the high number of varieties and the high similarity between them poses a major challenge for variety evaluation, discrimination, as well as innovation in breeding. Recently, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), two robust molecular markers, have been utilized as a rapid and reliable method for variety identification. To elucidate the genetic structure and diversity of melon varieties, we screened out 136 perfect SSRs and 164 perfect SNPs from the resequencing data of 149 accessions, including the most representative lines worldwide. This study established the DNA fingerprint of 259 widely-cultivated melon varieties in China using Target-seq technology. All melon varieties were classified into five subgruops, including ssp. agrestis, ssp. melo, muskmelon and two subgroups of foreign individuals. Compared with ssp. melo, the ssp. agrestis varieties might be exposed to a high risk of genetic erosion due to their extremely narrow genetic background. Increasing the gene exchange between ssp. melo and ssp. agrestis is therefore necessary in the breeding procedure. In addition, analysis of the DNA fingerprints of the 259 melon varieties showed a good linear correlation (R2 = 0.9722) between the SSR genotyping and SNP genotyping methods in variety identification. The pedigree analysis based on the DNA fingerprint of 'Jingyu' and 'Jingmi' series melon varieties was consistent with their breeding history. Based on the SNP index analysis, ssp. agrestis had low gene exchange with ssp. melo in chromosome 4, 7, 10, 11and 12, two specific SNP loci were verified to distinguish ssp. agrestis and ssp. melon varieties. Finally, 23 SSRs and 40 SNPs were selected as the core sets of markers for application in variety identification, which could be efficiently applied to variety authentication, variety monitoring, as well as the protection of intellectual property rights in melon.
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Affiliation(s)
- Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Yanling Lv
- Institute of Vegetable, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Xiaofei Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Changxuan Xia
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Hong Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
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Wang Y, Wu X, Li Y, Feng Z, Mu Z, Wang J, Wu X, Wang B, Lu Z, Li G. Identification and Validation of a Core Single-Nucleotide Polymorphism Marker Set for Genetic Diversity Assessment, Fingerprinting Identification, and Core Collection Development in Bottle Gourd. FRONTIERS IN PLANT SCIENCE 2021; 12:747940. [PMID: 34868131 PMCID: PMC8636714 DOI: 10.3389/fpls.2021.747940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Germplasm collections are indispensable resources for the mining of important genes and variety improvement. To preserve and utilize germplasm collections in bottle gourd, we identified and validated a highly informative core single-nucleotide polymorphism (SNP) marker set from 1,100 SNPs. This marker set consisted of 22 uniformly distributed core SNPs with abundant polymorphisms, which were established to have strong representativeness and discriminatory power based on analyses of 206 bottle gourd germplasm collections and a multiparent advanced generation inter-cross (MAGIC) population. The core SNP markers were used to assess genetic diversity and population structure, and to fingerprint important accessions, which could provide an optimized procedure for seed authentication. Furthermore, using the core SNP marker set, we developed an accessible core population of 150 accessions that represents 100% of the genetic variation in bottle gourds. This core population will make an important contribution to the preservation and utilization of bottle gourd germplasm collections, cultivar identification, and marker-assisted breeding.
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Affiliation(s)
- Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yanwei Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zishan Feng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zihan Mu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiang Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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A novel barcode system for rapid identification of rice (Oryza sativa L.) varieties using agro-morphological descriptors and molecular markers. Mol Biol Rep 2021; 48:2209-2221. [PMID: 33675464 DOI: 10.1007/s11033-021-06230-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
Rice varietal identification is a crucial aspect in breeding, seed production and trade in order to protect the interests of the farmers and consumers. As the number of varieties released is rising every year, the need to identify them unambiguously also increases. Here, we developed a novel barcode system to identify 62 rice genotypes using agro-morphological descriptors and molecular markers. In all, 62 rice genotypes, for 22 agro-morphological traits were recorded. In addition, 19 molecular markers were used for developing genotype-specific DNA fingerprints. The descriptor notes of 10 essential agro-morphological traits and allele codes of the polymorphic markers were used to generate two-dimensional (2-D) barcodes for the rice genotypes. Using agro-morphological traits, 31 rice genotypes were unambiguously distinguished while, with the polymorphic markers we were able to distinguish all rice genotypes except BPT2295 and Jaya. However, using both agro-morphological descriptors and molecular markers in combination, it was possible to distinguish all the rice genotypes used in the present study. These agro-morphological notes and allele codes from the molecular marker data together were used to develop QR (Quick Response) codes for rapid identification of rice genotypes as they facilitate storage of more data. In the present investigation, we have demonstrated the potentiality of agro-morphological traits and molecular markers in distinguishing rice genotypes. The novel QR code system proposed in the present study can also be extended to other crops not only for varietal identification but also for germplasm management and trade.
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Singh D, Leskovar DI, Sharma SP, Sarao NK, Vashisht VK. Genetic diversity and interrelationship among Indian and exotic melons based on fruit morphology, quality components and microsatellite markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:985-1002. [PMID: 32377048 PMCID: PMC7196569 DOI: 10.1007/s12298-020-00814-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/16/2020] [Accepted: 04/07/2020] [Indexed: 05/19/2023]
Abstract
Seventy melon (Cucumis melo L.) accessions comprising of landraces, inbred lines, cultivars, wild relatives and exotic populations were characterized using fifteen fruit traits and 30 SSR markers. Overall, aim of this study was to investigate the genetic relatedness across origins, horticultural groups and accession categories. Significant differences were observed for days to first fruit maturity, fruit weight, fruits per vine, yield per plant, flesh thickness, fruit shape index, total soluble solids, β-carotene, ascorbic acid and titrable acidity. Twenty-four polymorphic SSRs detected 67 distinct alleles with moderate polymorphic information content (0.43) and genetic diversity (0.44). Observed heterozygosity (0.53) was higher than expected heterozygosity (0.48) which can be attributed to out-cross nature of melons. Neighbor joining tree based on SSRs diverged 70 accessions into six clusters independent of geographic sites of collections. Momordica and inodorus accessions formed distinct clusters, with some exceptions. Intermixing of landraces, modern cultivars and exotic accessions belonging to different taxa and geographic regions indicated genetic resemblance with each other. Hybridization among exotic and indigenous genetic resources can be utilized for genetic enhancement and introgression of new traits in modern melon cultivars.
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Affiliation(s)
- Dildar Singh
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Daniel I. Leskovar
- Texas A&M AgriLife Research Center, Texas A&M University, Uvalde, TX 78801 USA
| | - Sat Pal Sharma
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Navraj Kaur Sarao
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - V. K. Vashisht
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab 141004 India
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Du H, Yang J, Chen B, Zhang X, Zhang J, Yang K, Geng S, Wen C. Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties. BMC PLANT BIOLOGY 2019; 19:578. [PMID: 31870303 PMCID: PMC6929450 DOI: 10.1186/s12870-019-2122-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/07/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties. RESULTS The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index (p < 0.0001). CONCLUSIONS Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.
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Affiliation(s)
- Heshan Du
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Bin Chen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Xiaofen Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Kun Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sansheng Geng
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China.
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China.
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Microsatellite Markers Reveal Genetic Diversity and Relationships within a Melon Collection Mainly Comprising Asian Cultivated and Wild Germplasms. BIOMED RESEARCH INTERNATIONAL 2019; 2019:7495609. [PMID: 30886863 PMCID: PMC6388322 DOI: 10.1155/2019/7495609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/29/2018] [Accepted: 12/12/2018] [Indexed: 11/30/2022]
Abstract
Melon, Cucumis melo L., is an important horticultural crop with abundant morphological variability, but the genetic diversity and relationships within wild and cultivated melons remain unclear to date. In this study, thick-skinned (TC) (cultivated subspecies melo), thin-skinned (TN) (cultivated subspecies agrestis), and wild accessions were analyzed for genetic diversity and relationships using 36 microsatellite markers. A total of 314 alleles were detected with a mean allelic number of 8.72 and polymorphism information content of 0.67. Cluster analysis of the accessions resulted in four distinct clusters (I, II, III, and IV) broadly matching with the TC, TN, and wild groups. Cluster I contained only two Indian wild accessions. Cluster II was consisted of 49 South Asian accessions, 34 wild accessions, and 15 TN accessions. Cluster III was a typical TC group including 51 multiorigin TC accessions and one wild accession. The remaining 88 accessions, including 75 TN accessions, 6 wild accessions, and 7 TC accessions, formed the cluster IV, and all the TN and wild accessions in this cluster were from China. These findings were also confirmed by Principal component analysis and STRUCTURE analysis. The South Asian subspecies agrestis accessions, wild and cultivated, had close genetic relationships with a distinctive genetic background. Chinese wild melons showed closeness to cultivated subspecies agrestis landraces and could be a return from the indigenous cultivated melons. The AMOVA and pairwise F statistics (FST) presented genetic differentiation among the three groups, with the strongest differentiation (FST = 0.380) between TC and TN melons. These results offer overall information on genetic diversity and affiliations within a variety of melon germplasms and favor efficient organization and utilization of these resources for the current breeding purpose.
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Yang J, Zhang J, Han R, Zhang F, Mao A, Luo J, Dong B, Liu H, Tang H, Zhang J, Wen C. Target SSR-Seq: A Novel SSR Genotyping Technology Associate With Perfect SSRs in Genetic Analysis of Cucumber Varieties. FRONTIERS IN PLANT SCIENCE 2019; 10:531. [PMID: 31105728 PMCID: PMC6492046 DOI: 10.3389/fpls.2019.00531] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/05/2019] [Indexed: 05/03/2023]
Abstract
Simple sequence repeats (SSR) - also known as microsatellites - have been used extensively in genetic analysis, fine mapping, quantitative trait locus (QTL) mapping, as well as marker-assisted selection (MAS) breeding and other techniques. Despite a plethora of studies reporting that perfect SSRs with stable motifs and flanking sequences are more efficient for genetic research, the lack of a high throughput technology for SSR genotyping has limited their use as genetic targets in many crops. In this study, we developed a technology called Target SSR-seq that combined the multiplexed amplification of perfect SSRs with high throughput sequencing. This method can genotype plenty of SSR loci in hundreds of samples with highly accurate results, due to the substantial coverage afforded by high throughput sequencing. We also detected 844 perfect SSRs based on 182 resequencing datasets in cucumber, of which 91 SSRs were selected for Target SSR-seq. Finally, 122 SSRs, including 31 SSRs for varieties identification, were used to genotype 382 key cucumber varieties readily available in Chinese markets using our Target SSR-seq method. Libraries of PCR products were constructed and then sequenced on the Illumina HiSeq X Ten platform. Bioinformatics analysis revealed that 111 filtered SSRs were accurately genotyped with an average coverage of 1289× at an extremely low cost; furthermore, 398 alleles were observed in 382 cucumber cultivars. Genetic analysis identified four populations: northern China type, southern China type, European type, and Xishuangbanna type. Moreover, we acquired a set of 16 core SSRs for the identification of 382 cucumber varieties, of which 42 were isolated as backbone cucumber varieties. This study demonstrated that Target SSR-seq is a novel and efficient method for genetic research.
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Affiliation(s)
- Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Ruixi Han
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Beijing, China
| | - Feng Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Aijun Mao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Jiang Luo
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Bobo Dong
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Hui Liu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Hao Tang
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Beijing, China
| | - Jianan Zhang
- Molbreeding Biotechnology Company, Shijiazhuang, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- *Correspondence: Changlong Wen,
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Zhu Q, Gao P, Liu S, Amanullah S, Luan F. Comparative analysis of single nucleotide polymorphisms in the nuclear, chloroplast, and mitochondrial genomes in identification of phylogenetic association among seven melon ( Cucumis melo L.) cultivars. BREEDING SCIENCE 2016; 66:711-719. [PMID: 28163587 PMCID: PMC5282756 DOI: 10.1270/jsbbs.16066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/17/2016] [Indexed: 05/09/2023]
Abstract
A variety of melons are cultivated worldwide, and their specific biological properties make them an attractive model for molecular studies. This study aimed to investigate the single nucleotide polymorphisms (SNPs) from the mitochondrial, chloroplast, and nuclear genomes of seven melon accessions (Cucumis melo L.) to identify the phylogenetic relationships among melon cultivars with the Illumina HiSeq 2000 platform and bioinformatical analyses. The data showed that there were a total of 658 mitochondrial SNPs (207-295 in each), while there were 0-60 chloroplast SNPs among these seven melon cultivars, compared to the reference genome. Bioinformatical analysis showed that the mitochondrial tree topology was unable to separate the melon features, whereas the maximum parsimony/neighbor joining (MP/NJ) tree of the chloroplast SNPs could define melon features such as seed length, width, thickness, 100-seed weight, and type. SNPs of the nuclear genome were better than the mitochondrial and chloroplast SNPs in the identification of melon features. The data demonstrated the usefulness of mitochondrial, chloroplast, and nuclear SNPs in identification of phylogenetic associations among these seven melon cultivars.
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Affiliation(s)
- Qianglong Zhu
- Horticulture College, Northeast Agricultural University,
Harbin, Heilongjiang 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture,
Harbin, Heilongjiang 150030,
China
| | - Peng Gao
- Horticulture College, Northeast Agricultural University,
Harbin, Heilongjiang 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture,
Harbin, Heilongjiang 150030,
China
| | - Shi Liu
- Horticulture College, Northeast Agricultural University,
Harbin, Heilongjiang 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture,
Harbin, Heilongjiang 150030,
China
| | - Sikandar Amanullah
- Horticulture College, Northeast Agricultural University,
Harbin, Heilongjiang 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture,
Harbin, Heilongjiang 150030,
China
| | - Feishi Luan
- Horticulture College, Northeast Agricultural University,
Harbin, Heilongjiang 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture,
Harbin, Heilongjiang 150030,
China
- Corresponding author (e-mail: )
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Hu J, Wang P, Li Q, Su Y. Microsatellite analysis of genetic relationships between wild and cultivated melons in Northwest and Central China. Mol Biol Rep 2014; 41:7723-8. [PMID: 25109253 DOI: 10.1007/s11033-014-3668-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 07/27/2014] [Indexed: 11/29/2022]
Abstract
The genetic relationships between the wild and cultivated melon accessions from Northwest and Central China were dissected using 22 microsatellite markers. A total of 153 alleles, a high level of expected heterozygosity (0.669), and a low observed heterozygosity (0.156) were detected in the total panel. Differences on the allelic composition and heterozygosity levels were found between the two accession types and the wild accessions revealed a higher level of genetic diversity. The UPGMA analysis of the total panel showed that (a) most wild accessions from Northwest China were clustered independently from the cultivated accessions, and (b) the wild and cultivated accessions from Central China presented a high genetic closeness and showed a divergence from those of Northwest China. Similar positioning of the most accessions was observed with the principal coordinate analysis and STRUCTURE analysis. Pairwise FST and Nei's genetic distance quantified the genetic differentiation among the different accession types and further verified our findings. We concluded that the wild melons from Northwest China have a distinctive genetic background and could be the true wild forms, while the wild melons from Central China showed a close relationship to the local cultivars and could be a return from the cultivated melons in the same region. Our results offer an insight into the genetic resources of the main melon producing regions in China, which is essential for maximizing utilization of the traits of interest in wild melons.
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Affiliation(s)
- Jianbin Hu
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, People's Republic of China,
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