Development and application of SSR markers derived from <i>Bauhinia Strychnifolia</i> a semi-endemic plant in Thailand

Sraphet, Supajit; Chantravisut, Pattra; Srisawad, Nattaya; Suksee, Nawarat; Smith, Duncan R.; Triwitayakorn, Kanokporn

doi:10.1080/10496475.2018.1520775

Cited by 4 publications

(2 citation statements)

References 19 publications

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“…The development of enriched genomic libraries reduces the cost of the microsatellite markers and enhances the efficiency of marker development [ 35 , 36 ]. Thus, the microsatellite library enrichment techniques have been used for the development of microsatellite markers in various crop species including the fruit species, date palm [ 40 ], peach [ 52 – 54 ], lychee [ 55 ], mango [ 56 ], Chinese jujube [ 57 ], and recently in Bauhinia strychnifolia [ 58 ]. In the present investigation, genomic libraries were constructed using the genomic DNA of guava cv.…”

Section: Discussionmentioning

confidence: 99%

Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies

Kumar

Singh

et al. 2020

PLoS ONE

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Dearth of genomic resources particularly, microsatellite markers in nutritionally and commercially important fruit crop, guava necessitate the development of the novel genomic SSR markers through the library enrichment techniques. Three types of 3’ -biotinylated oligonucleotide probes [(CT) 14 , (GT) 12 , and (AAC) 8 ] were used to develop microsatellite enriched libraries. A total of 153 transformed colonies were screened of which 111 positive colonies were subjected for Sanger sequencing. The clones having more than five motif repeats were selected for primer designing and a total of 38 novel genomic simple sequence repeats could be identified. The g-SSRs had the motif groups ranging from monomer to pentamer out of which dimer group occurred the most (89.47%). Out of 38 g-SSRs markers developed, 26 were found polymorphic, which showed substantial genetic diversity among the guava genotypes including wild species. The average number of alleles per locus, major allele frequency, gene diversity, expected heterozygosity and polymorphic information content of 26 SSRs were 3.46, 0.56, 0.53, 0.29 and 0.46, respectively. The rate of cross-species transferability of the developed g-SSR loci varied from 38.46 to 80.77% among the studied wild Psidium species. Generation of N-J tree based on 26 SSRs grouped the 40 guava genotypes into six clades with two out-groups, the wild guava species showed genetic distinctness from cultivated genotypes. Furthermore, population structure analysis grouped the guava genotypes into three genetic groups, which were partly supported by PCoA and N-J tree. Further, AMOVA and PCoA deciphered high genetic diversity among the present set of guava genotypes including wild species. Thus, the developed novel g-SSRs were found efficient and informative for diversity and population structure analyses of the guava genotypes. These developed novel g-SSR loci would add to the new genomic resource in guava, which may be utilized in genomic-assisted guava breeding.

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Section: Discussionmentioning

confidence: 99%

Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies

Kumar

Singh

et al. 2020

PLoS ONE

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“…Several methods have been employed to develop SSR markers in different plant species, and the microsatellite enrichment method is considered one of the most robust, reproducible, and cost-effective techniques [ 20 ]. This technique has been exploited for the development of SSR markers in several plant species including medicinal crops viz ., Paeonia lactiflora [ 21 ], Centella asiatica [ 22 ], Tinospora cordifolia [ 23 ], and Bauhinia strychnifolia [ 24 ]. Therefore, the development of novel SSR markers was undertaken in A. paniculata using the microsatellite enrichment technique.…”

Section: Introductionmentioning

confidence: 99%

Development of Novel Genomic Simple Sequence Repeat (g-SSR) Markers and Their Validation for Genetic Diversity Analyses in Kalmegh [Andrographis paniculata (Burm. F.) Nees]

Kumar

Paliwal

et al. 2020

Plants

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Kalmegh (Andrographis paniculata (Burm. F.) Nees) is one of the most important medicinal plants and has been widely explored as traditional medicine. To exploit its natural genetic diversity and initiations of molecular breeding to develop novel cultivars or varieties, developments of genomic resources are essential. Four microsatellite-enriched genomic libraries—(CT)14, (GT)12, (AG)15 and (AAC)8—were constructed using the genomic DNA of A. paniculata. Initially, 183 recombinant colonies were screened for the presence of CT, GT, AG, and AAC microsatellite repeats, out of which 47 clones found positive for the desired simple sequence repeats (SSRs). It was found that few colonies had more than one desirable SSR. Thus, a sum of 67 SSRs were designed and synthesized for their validation among 42 A. paniculata accessions. Out of the 67 SSRs used for genotyping, only 41 were found to be polymorphic. The developed set of g-SSR markers showed substantial genetic variability among the selected A. paniculata accessions, with an average polymorphic information content (PIC) value of 0.32. Neighbor-joining tree analysis, population structure analysis, analysis of molecular variance (AMOVA), and principal coordinate analysis (PCoA) illustrated the considerable genetic diversity among them. The novel g-SSR markers developed in the present study could be important genomic resources for future applications in A. paniculata.

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

Bansal

Kumar

Lone

et al. 2022

Industrial Crops and Products

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Development and application of SSR markers derived from Bauhinia Strychnifolia a semi-endemic plant in Thailand

Cited by 4 publications

References 19 publications

Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies

Development of novel g-SSR markers in guava (Psidium guajava L.) cv. Allahabad Safeda and their application in genetic diversity, population structure and cross species transferability studies

Development of Novel Genomic Simple Sequence Repeat (g-SSR) Markers and Their Validation for Genetic Diversity Analyses in Kalmegh [Andrographis paniculata (Burm. F.) Nees]

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

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