Genetic Variation, Population Structure and the Possibility of Association Mapping of Biochemical and Agronomic Traits Using Dominant Molecular Markers in Iranian Tea Accessions

Rahimi, Mehdi; Kordrostami, Mojtaba; Sanam, SafaeiChaeikar

doi:10.1007/s40995-019-00784-4

Cited by 5 publications

(3 citation statements)

References 40 publications

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“…In many cases, the results obtained from molecular markers do not align perfectly with phenotypic traits. This discrepancy can be attributed to the polygenic control of agronomic traits and their susceptibility to environmental influences 33 , 36 , 37 , 66 . Morphological markers, which are based on agronomic data, may not accurately reflect the genetic differentiation of individuals based on their geographic environment.…”

Section: Discussionmentioning

confidence: 99%

“…Validating these associated markers and converting them into specific SCAR markers or specific DNA sequences for targeted breeding is a practical and applicable solution. These markers can be utilized for important traits identified in this study 36 , 37 . The use of association analysis to identify markers linked to morphological traits in Sickleweed populations was documented for the first time in this study.…”

Section: Discussionmentioning

confidence: 99%

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Genetic diversity in Sickleweed (Falcaria vulgaris) and using stepwise regression to identify marker associated with traits

Rahimi

Ahmadi-Afzadi

Kordrostami

2023

Sci Rep

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One of the well-known medicinal plants in the Falcaria genus is Sickleweed. Falcaria species exhibit a high degree of genetic variability, posing challenges in the examination of genetic diversity due to the significant potential for hybridization and introgression among them. Utilizing morphological traits and molecular markers may prove to be a valuable approach in evaluating and harnessing germplasm, considering the current obstacles faced in breeding this medicinal herb. In 2021, fifteen Sickleweed populations were cultivated in pots under field conditions, employing a randomized complete block design with three replications. This aimed to assess genetic diversity and conduct marker-trait association analyses utilizing morpho-physiological characteristics and SSR markers. The Sickleweed populations displayed considerable genetic diversity across all traits. Through cluster analysis of traits and the utilization of the UPGMA method based on the Gower distance matrix, the population was classified into three distinct clusters. Upon examining all genotypes, 52 polymorphic bands were detected, with an average of 8.68 bands per primer. The average expected heterozygosity across all loci was 0.864, while the average PIC was 0.855. Molecular data analysis employing the Jaccard similarity index and UPGMA method revealed the division of Sickleweed populations into two major groups. Furthermore, the results of molecular variance analysis indicated that variation within the population exceeded that between populations. Thirty-two SSR fragments were found to be significantly associated with genomic regions controlling the studied traits, determined through the application of stepwise regression. Selection based on molecular markers offers a rapid method for breeding programs, with the genetic information obtained from these markers playing a crucial role. Therefore, alongside traits, selecting superior genotypes and populations of high value in breeding programs becomes feasible. The findings highlight that certain markers are linked to multiple traits, emphasizing the critical importance of this characteristic in plant breeding for the simultaneous improvement of numerous traits. The study’s insights regarding markers hold potential for application in Sickleweed breeding programs.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genetic diversity in Sickleweed (Falcaria vulgaris) and using stepwise regression to identify marker associated with traits

Rahimi

Ahmadi-Afzadi

Kordrostami

2023

Sci Rep

Self Cite

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“…Primers are based on a repeat sequence, often with a degenerate 3′anchor, and amplify plenty number of amplicons, providing high reproducibility at a low cost. ISSRs have been used for a wide range of organisms in DNA fingerprinting, diversity analysis, and genome mapping (Rahimi et al, 2019). ISSR technique has demonstrated as a powerful, rapid, simple, reproducible, and inexpensive way, especially ISSR markers are more reproducible than RAPD for the same purpose (Verma et al, 2017).…”

Section: Inter-simple Sequence Repeats (Issrs)mentioning

confidence: 99%

Molecular markers for analysis of plant genetic diversity

Nam¹,

Hang²,

Linh³

et al. 2021

Vietnam J. Biotechnol.

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Genetic diversity plays an important role in diversity conservation at multiple levels and supports to monitor and assess genetic variation. In plants, genetic diversity provides the ability to adapt and respond to environmental conditions that helps plants to survive through changing environments. Genetic diversity analyses based on molecular genetic markers are effective tools for conservation and reintroduction of rare and endangered species. In recent years, the development of various chemical and molecular techniques for studying genetic diversity has received great attention. While biochemical markers are primarily used in the diagnosis of pathogens, DNA markers have been developed and widely applied for identification of species and population based on the genotype of an organism that is more stable and not easily affected by the environmental factors. PCR-based molecular marker tools, such as restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPD), simple sequence repeats (SSRs) are used for analysing the difference in the targeted DNA sequences. With the rapid and robust development of genomic sequencing technology it is now possible to obtain and analyse DNA sequences of the whole genome of studied organisms. However, each type of DNA markers has different principles, as well as the pros and cons of specificity. In this article, we review methods and point out DNA markers, which are considered as reliable and widely used tools for the detection of genetic variation. In addition, we present the application of DNA marker in analysing genetic diversity of wild, domestic and medicinal plants, as well as some perspectives on the future of DNA marker’s application in the analysis of genetic diversity.

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Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects

Manoj

2023

Planta

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Genetic Variation, Population Structure and the Possibility of Association Mapping of Biochemical and Agronomic Traits Using Dominant Molecular Markers in Iranian Tea Accessions

Cited by 5 publications

References 40 publications

Genetic diversity in Sickleweed (Falcaria vulgaris) and using stepwise regression to identify marker associated with traits

Genetic diversity in Sickleweed (Falcaria vulgaris) and using stepwise regression to identify marker associated with traits

Molecular markers for analysis of plant genetic diversity

Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects

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