Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Yang, Yuyao; Lv, Mingjie; Li, Jun; Wu, Jianjin; Wang, Qian; Xie, Tianyu; Li, Haichao; Chen, Rui; DeLing, Sun; Yang, Yujiu; Yao, Xingwei

doi:10.1186/s12870-022-03920-2

Cited by 9 publications

(6 citation statements)

References 50 publications

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“…To effectively utilize germplasm resources and safeguard variety rights, access to genetic relationships and population structure at the genomic level is required [ 74 ]. There is some evidence of significant genetic differentiation in wild R. chingii populations in the current investigation.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu

Zhou,

Liu,

et al. 2024

Plants

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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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Section: Discussionmentioning

confidence: 99%

Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu

Zhou,

Liu,

et al. 2024

Plants

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“…the development of high-throughput sequencing, SNP markers due to their high number, wide distribution and good stability, are considered ideal for genetic studies of germplasm resources. With the application of KASP technology, SNP markers have been widely used in cruciferous vegetable crops such as cabbage (Li et al, 2019), kale (Li et al, 2020, cauliflower (Yang et al, 2022) and broccoli (Shen et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…Further studies on the genetic diversity, genetic relationships and population structure of 372 broccoli materials showed that the broccoli population had a limited genetic background. In cauliflower, Yang et al (2022) identified 41 highly polymorphic SNPs and constructed 329 cauliflower DNA fingerprints. However, thus far, no SNP-based fingerprint database for radish has been reported.…”

Section: Introductionmentioning

confidence: 99%

Construction of SNP fingerprints and genetic diversity analysis of radish (Raphanus sativus L.)

Xing,

Hu,

Wang

et al. 2024

Front. Plant Sci.

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Radish (Raphanus sativus L.) is a vegetable crop with economic value and ecological significance in the genus Radish, family Brassicaceae. In recent years, developed countries have attached great importance to the collection and conservation of radish germplasm resources and their research and utilization, but the lack of population genetic information and molecular markers has hindered the development of the genetic breeding of radish. In this study, we integrated the radish genomic data published in databases for the development of single-nucleotide polymorphism (SNP) markers, and obtained a dataset of 308 high-quality SNPs under strict selection criteria. With the support of Kompetitive Allele-Specific PCR (KASP) technology, we screened a set of 32 candidate core SNP marker sets to analyse the genetic diversity of the collected 356 radish varieties. The results showed that the mean values of polymorphism information content (PIC), minor allele frequency (MAF), gene diversity and heterozygosity of the 32 candidate core SNP markers were 0.32, 0.30, 0.40 and 0.25, respectively. Population structural analysis, principal component analysis and genetic evolutionary tree analysis indicated that the 356 radish materials were best classified into two taxa, and that the two taxa of the material were closely genetically exchanged. Finally, on the basis of 32 candidate core SNP markers we calculated 15 core markers using a computer algorithm to construct a fingerprint map of 356 radish varieties. Furthermore, we constructed a core germplasm population consisting of 71 radish materials using 32 candidate core markers. In this study, we developed SNP markers for radish cultivar identification and genetic diversity analysis, and constructed DNA fingerprints, providing a basis for the identification of radish germplasm resources and molecular marker-assisted breeding as well as genetic research.

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“…pi and pj are the i th and j th allele frequencies, respectively, and n is the number of alleles; (7) heterozygosity rate<0.25 [8,9,30,40,41]. The core SNPs were obtained after the screening of the above steps.…”

Section: Core Snp Selection and Functional Annotationmentioning

confidence: 99%

Construction of a SNP fingerprinting of exotic pine germplasm resources in China based on 51K liquid- phased probes

Wu,

Diao,

Ding

et al. 2024

Preprint

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【Background】Slash pine (Pinus elliottii), loblolly pine (P. taeda), caribbean pine (P. caribaea) and their hybrid pine are the major timber species in China, which have been introduced from North America for 100 years. Distinguishing them is challenging due to the nutritional organs similarity and the combined characteristics inherited from their parent species in hybrid pines. 【Results】In this study, we aimed at constructing a set of DNA fingerprint of 38 pine varieties including four kinds of pines species for accurately identifying them. The genotypes of 38 pines were captured by 51K liquid-phased probes developed by our team and 5,60,567 SNPs were genotyped by the following next-generation sequencing. A total of 344 core SNPs were obtained through the screening of the minor allele frequency, miss rate, heterozygosity rate and other parameter conditions. Additionally, employing the Random Forest model in conjunction with PCA led to the retention of 28 SNPs demonstrating identification capabilities for the pine varieties. 【Conclusions】The DNA fingerprint of the 38 pine varieties was successfully established using the set of 28 SNPs, which serve as a valuable reference for identifying the exotic pine varieties, managing germplasm , and conducting genetic diversity analysis.

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Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Cited by 9 publications

References 50 publications

Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu

Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu

Construction of SNP fingerprints and genetic diversity analysis of radish (Raphanus sativus L.)

Construction of a SNP fingerprinting of exotic pine germplasm resources in China based on 51K liquid- phased probes

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