Polymorphism levels of some SSR markers (Simple Sequence Repeat) for parental line identification on low temperature tolerance

Dalimunthe, Sri Romaito; Siregar, Luthfi Aziz Mahmud; Putri, Lollie Agustina P.; Chairunnisa, Tengku; Hairmansis, Aris

doi:10.1088/1755-1315/454/1/012165

Cited by 4 publications

(3 citation statements)

References 12 publications

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“…The level of polymorphism can also be determined by the number of alleles generated by each marker. Markers that produce fewer alleles have a lower ability to distinguish the tested samples [76].…”

Section: Molecular Analysismentioning

confidence: 99%

Diversity Analysis of 53 Soybean Accessions Introduced from China Based on Morphological Characteristics and SSR Markers

Dyah,

Wibisono,

Terryana

et al. 2024

Curr. Appl. Sci. Technol.

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Indonesia still faces challenges in meeting its national soybean demand. Genetic diversity can provide new resources to improve soybean production and quality. Genetic diversity of 53 soybean accessions introduced from China, based on morphological characteristics and 17 SSR markers, was analyzed in this study. Principal component analysis (PCA) conducted on morphological characters produced a total diversity value of 64.67% and identified four main components. Based on phylogenetic analysis and principal coordinate analysis (PCoA) two accessions showed low genetic similarity of 78% (China cult-55 and Mi yang niu mao huang), which indicated that they could be selected as parents for plant breeding programs. In addition, 772 SSR alleles at an average of 45 alleles per locus were detected. The average heterozygosity was 0.83, and the average polymorphic information content (PIC) value was 0.96. All SSR markers showed a PIC value > 0.8, indicating their informativeness in analyzing genetic diversity of soybean. The phylogenetic analysis indicated a genetic similarity of 82% and the accessions were grouped into two main clusters. The phylogenetic analysis depicted that several accessions could be grouped based on the growth type and origin. The results of morphological characterization and molecular markers in the analysis of genetic diversity are beneficial for selecting parental crosses when developing new varieties.

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Section: Molecular Analysismentioning

confidence: 99%

Diversity Analysis of 53 Soybean Accessions Introduced from China Based on Morphological Characteristics and SSR Markers

Dyah,

Wibisono,

Terryana

et al. 2024

Curr. Appl. Sci. Technol.

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“…Primers with the highest PIC value provide the most informative DNA band patterns and are hence the most useful molecular markers. According to Dalimunthe et al (2020), the PIC were classified into three categories: highly informative (PIC > 0.5), moderate (0.25 > PIC > 0.5), and low informative (PIC < 0.25). The PIC values of FMbadh2-E7 and Badex7-5 was 0.44 and 0.46, respectively.…”

Section: Aroma Detection Using Simple Sequence Repeats (Ssrs)mentioning

confidence: 99%

Evaluation of Aroma in Malaysian Rice Landraces Through Sensory Test and Molecular Approach

Noorzuraini,

Rosimah,

Faridah

et al. 2024

THE JAPS

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Aroma is one of the primary rice grain quality traits that play a vital role in consumer preferences. In Malaysia, consumers have shown a marked preference for high-quality rice. Therefore, it is essential to identify rice landraces with considerable aroma for promotion as potential donors for the development of high-quality rice in future breeding programs to meet consumer demand and reduce dependency on imported high-quality rice types. Thirty-three rice genotypes comprising thirty Malaysian rice landraces and three modern rice cultivars were evaluated for aroma using sensory tests and molecular markers. The presence of aroma in cooked rice was determined through nose sensory evaluation by five panellists. Molecular analysis was performed using two aroma-specific SSR primers i.e., FMbadh2-E7 and Badex7-5. The sensory test revealed that only five rice landraces had a strong aroma; whereas eleven had a slight aroma. FMbadh2-E7 was found to have most of the alleles with a major allele frequency of 0.53. Whereas, Badex7-5, has a major allele frequency of 0.51, with five alleles at the locus. The dendrogram was generated by UPGMA cluster analysis using two aroma-specific primers, which characterized the rice genotypes into two distinct clusters; Cluster 1 consisted of fifteen rice landraces with non-aroma standards, while Cluster 2 consisted of fifteen rice landraces with aroma standards. Based on the sensory test and molecular approach, the identified rice landraces with aroma were i.e.

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“…The PIC value is information to detect primers that are capable of producing polymorphic bands in a population [38], [42]. The high level of genetic diversity is influenced by the level of polymorphism of genetic markers used.…”

Section: A Rapd Analysismentioning

confidence: 99%

Application of RAPD Molecular Technique to Study the Genetic Variations of Citrus in South Sulawesi, Indonesia

Tuwo¹,

Kuswinanti²,

Nasruddin³

et al. 2022

Int. J. Adv. Sci. Eng. Inf. Technol.

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Indonesia is a tropical country with superior local citrus species and varieties. Citrus fruits were very useful for cultivation, especially to meet the nutritional needs of the wider community. A province in Indonesia, namely South Sulawesi is one of the centers for citrus development. A preliminary study showed various cultivated citrus in South Sulawesi namely Mandarin Orange cultivar Selayar, Mandarin Orange cultivar Batu, JC lime, Pummelo Pangkep, tangerine, Santang Madu, Dekopon, lime, and Kaffir lime. This study aims to evaluate genetic diversity at several citrus plantation centers in South Sulawesi using the RAPD technique. The analysis was carried out using five primers. In this study, RAPD primers could be used to characterize the genetic diversity and similarity of thirteen citrus cultivars in South Sulawesi. One informative RAPD primer based on its PIC value was OPC-09. The results of the genetic similarity analysis are presented in the form of a dendrogram. The first cluster consisted of Mandarin Orange cultivar Selayar (Seeded Selayar, Selayar-Selayar, JC-Selayar), JC lime, Mandarin Orange cultivar Batu, Santang Madu, and Pummelo Pangkep (cultivar Pangkep Merah, Pangkep Putih, Pangkep Golla-golla). The second cluster consisted of Mandarin Orange cultivar Selayar (selayar-selayar, JCselayar), Santang Madu, tangerine, Mandarin Orange cultivar Batu, Dekopon, lime, and Kaffir lime. The clusters with the most distant genetic relationship are cluster A with cluster B, with a genetic similarity of 62%. Meanwhile, clusters with the closest genetic relationship are clusters I and II, with 79% genetic similarity.

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Polymorphism levels of some SSR markers (Simple Sequence Repeat) for parental line identification on low temperature tolerance

Cited by 4 publications

References 12 publications

Diversity Analysis of 53 Soybean Accessions Introduced from China Based on Morphological Characteristics and SSR Markers

Diversity Analysis of 53 Soybean Accessions Introduced from China Based on Morphological Characteristics and SSR Markers

Evaluation of Aroma in Malaysian Rice Landraces Through Sensory Test and Molecular Approach

Application of RAPD Molecular Technique to Study the Genetic Variations of Citrus in South Sulawesi, Indonesia

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