Genetic diversity evaluation and core collection construction of pomegranate (Punica granatum L.) using genomic SSR markers

Wang, R.X.; Zhong, Yuhang; Hong, Wenjuan; Luo, Haiwei; Li, Daili; Zhao, Liang; Zhang, Hengyue; Wang, Jun

doi:10.1016/j.scienta.2023.112192

Cited by 4 publications

(1 citation statement)

References 49 publications

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“…Research has shifted from enzyme-based to various DNA-based molecular markers. SSR molecular markers are considered ideal due to their co-dominance, wide distribution, high mutation rate, and high polymorphism [ 14 ]. In addition, SSR molecular markers have been widely used in Cucurbitaceae plants, such as melon [ 15 ], bitter gourd [ 16 ], cucumber [ 17 ] and bottle gourd [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote

Cheng,

Su,

Guo

et al. 2024

BMC Plant Biol

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Background Chayote is a high economic crop in the Cucurbitaceae family, playing an important role in food production, disease treatment and the production of degradable materials in industries. Due to the harsh environment, such as high temperature, drought and frost, some chayote resources are gradually disappearing. It is crucial to collect, characterize, and conserve chayote resources. However, the genetic diversity of chayote resources in China has not been studied so far. Results In this study, we collected 35 individuals of chayote from 14 provinces in China. Subsequently, we found 363,156 SSR motifs from the chayote genome and designed 57 pairs of SSR primers for validation. Out of these, 48 primer pairs successfully amplified bands, with 42 of them showing polymorphism. These 42 primer pairs detected a total of 153 alleles, averaging 3.64 alleles per locus. The polymorphic information content ranged from 0.03 to 0.78, with an average value of 0.41, indicating a high level of polymorphism. Based on the analysis using STRUCTURE, PCoA, and UPGMA methods, the 35 chayote individuals were divided into two major clusters. Through further association analysis, 7 significantly associated SSR markers were identified, including four related to peel color and three related to spine. Conclusions These molecular markers will contribute to the analysis of genetic diversity and genetic breeding improvement of chayote in the future.

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Section: Introductionmentioning

confidence: 99%

Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote

Cheng,

Su,

Guo

et al. 2024

BMC Plant Biol

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Establishment of novel SSR markers from transcriptome data of Chimonanthus praecox and application in the variety identification

Liu,

Wu,

Cao

et al. 2024

Preprint

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Background Chimonanthus praecox, belongs to the Calycanthaceae, is a unique traditional famous flower and special economic tree species in China. There are numerous varieties but only a few cultivars were named. At present, EST-SSR markers are widely used to identify different species and varieties, as researchers can identify a large number of microsatellites from transcriptome databases. Result A total of 162,638 unigenes were assembled by using RNA-seq, and 82,778 unigenes was annotated by Nr, Nt, Swiss-Prot, Pfam, GO, KOG and KEGG databases. A total of 13,556 SSR loci were detected from 11,691 unigenes, with trinucleotide repeat motifs being the most abundant among the six types of repeat motifs. In order to develop markers, 64,440 pairs of SSR primers with polymorphism potential were designed, and 75 pairs of primers were randomly selected for amplification. Among them, seven pairs amplified fragments of the expected size with high polymorphism, and twelve C.praecoxvarieties were clustered into two monophyletic clades by the seven EST-SSR markers. Conclusion The microsatellites in the transcriptome of C.preacox have the advantages of rich types, strong specificity, and great polymorphism potential. These EST-SSR markers can provide molecular technical methods for identifying different varieties of C.preacox, and can also explore a large number of candidate genes associated to traits.

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Construction and Evaluation of Pepper Core Collection Based on Phenotypic Traits and SSR Markers

Deng,

Zhao,

Guan

et al. 2024

Applied Sciences

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To streamline germplasm preservation, enhance resource utilization, and improve breeding efficiency, a core germplasm bank was established using 24 phenotypic traits and DNP markers from 155 pepper resources across various regions. Selection of the optimal core germplasm was based on intra-group retention ratio, overall retention scale, and intra-group stepwise clustering retention. Evaluation of phenotypic trait data for the core germplasm utilized mean, variance, range, and coefficient of variation, with principal component analysis confirming the selection. For molecular evaluation, the core germplasm pre-selection plan was based on SSR clustering, allele retention ratio, and Shannon-Weaver diversity index. This approach resulted in a core germplasm of 41 resources, including 6 var. fasciculatum, 7 var. grossum, 3 var. cerasiorme, 6 var. conoides, and 19 var. longum, representing the maximum phenotypic retention and genetic diversity of the 155 pepper resources. Additionally, a core germplasm of 32 resources was generated based on SSR markers, retaining all 54 polymorphic loci. By integrating phenotypic and molecular core collections, a combined core collection of 57 varieties was developed. This collection achieved a 92.55% phenotype retention ratio and a 100% polymorphism site retention ratio. With a 90% compression ratio, it encapsulates the broad genetic diversity of the original germplasm, serving as a comprehensive resource for further research and breeding applications.

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Genetic diversity evaluation and core collection construction of pomegranate (Punica granatum L.) using genomic SSR markers

Cited by 4 publications

References 49 publications

Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote

Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote

Establishment of novel SSR markers from transcriptome data of Chimonanthus praecox and application in the variety identification

Construction and Evaluation of Pepper Core Collection Based on Phenotypic Traits and SSR Markers

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