Development of novel genome‑wide simple sequence repeats (SSR) markers in Bunium persicum

Bansal, Sangita; Kumar, Amit; Lone, Ajaz A.; Khan, M. N.; Malhotra, Era Vaidya; Singh, Rakesh

doi:10.1016/j.indcrop.2022.114625

Cited by 8 publications

(2 citation statements)

References 36 publications

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“…Swingle [28], Bunium persicum (Boiss.) Fedtsch [29], Punica granatum L. [30,31], Oryza sativa [32], and Populus trichocarpa (Torr. & Gray) [33], which might be explained by easier strand separation for poly(A) and poly(T) structures than poly(C) and poly(G) [34].…”

Section: Discussionmentioning

confidence: 99%

Development of Novel Genomewide Simple Sequence Repeat Markers for Acer truncatum Bunge and Assessment of Their Transferability to Other Closely Related Species

Long,

Bao,

Jin

et al. 2024

Forests

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Acer truncatum Bunge is a versatile woody tree species with high economic and medicinal value in the production of bioactive substances and unsaturated fatty acids (especially nervonic acid). However, the exploitation and evaluation of A. truncatum germplasm resources are limited owing to a lack of sound molecular marker systems. In this study, a large set of genomewide simple sequence repeat (SSR) markers of A. truncatum was developed based on its whole-genome sequences. A total of 462,331 SSR loci were identified in the genome sequences, 99.3% (459,193) of which were located on 13 chromosomes. The chromosome length was significantly positively correlated with the number of SSR loci on the chromosome (r = 0.977, p < 0.001). The (A/T)n, (AT/TA)n, and (AAT/ATT/TAA/TTA/TAT/ATA)n were the most frequent motifs for mono-, di-, and trinucleotide repeat motifs, respectively, showing A/T-base bias. After BLASTN and electronic polymerase chain reaction (PCR) analyses, 199,990 loci with specific physical positions were screened. Most of the SSR loci were located in the intergenic regions and fewest in the coding sequences (CDSs). The frequency of loci with tri- and hexanucleotide repeat motifs was the highest in the CDSs, potentially serving to maintain the stability of gene function and structure. In randomly selected 105 SSR markers, 82 (78.1%) showed allelic polymorphism, with polymorphism information content (PIC) values of 0.032–0.926 (0.481 on average). The SSRs in the noncoding regions exhibited significantly higher PIC values than those in the CDSs. The transferability of the 105 markers was 48.6%–59.0% to seven other Acer species. The large set of valid SSR markers provides a powerful tool for studies on population genetics, conservation genetics, linkage mapping, comparative genomics, and marker-assisted breeding of the genus Acer.

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Section: Discussionmentioning

confidence: 99%

Development of Novel Genomewide Simple Sequence Repeat Markers for Acer truncatum Bunge and Assessment of Their Transferability to Other Closely Related Species

Long,

Bao,

Jin

et al. 2024

Forests

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“…The parameters set by SSR of these Cucurbitaceae species are that trinucleotide (Tri-), tetranucleotide (Tetra-), pentanucleotide (Penta-) and hexanucleotide (Hexa-) are repeated four times, while the standard set in this study is at least 5 times. Previous studies have shown that the more repetitions, the higher the polymorphism [ 23 ]. We identified 124,177, 221,986, 260,094, and 163,710 SSR motifs in the genomes of cucumber, melon, pumpkin, and watermelon, respectively, using the same parameters.…”

Section: Discussionmentioning

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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Polyphenolics, antioxidant characterization and DNA barcoding of Kala zeera [Bunium persicum (Boiss.) Fedtsch] through multiple barcode analysis to unravel best barcode combination

et al. 2022

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Development of novel genome‑wide simple sequence repeats (SSR) markers in Bunium persicum

Cited by 8 publications

References 36 publications

Development of Novel Genomewide Simple Sequence Repeat Markers for Acer truncatum Bunge and Assessment of Their Transferability to Other Closely Related Species

Development of Novel Genomewide Simple Sequence Repeat Markers for Acer truncatum Bunge and Assessment of Their Transferability to Other Closely Related Species

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

Polyphenolics, antioxidant characterization and DNA barcoding of Kala zeera [Bunium persicum (Boiss.) Fedtsch] through multiple barcode analysis to unravel best barcode combination

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