Comprehensive functional analysis and mapping of SSR markers in the chickpea genome (Cicer arietinum L.)

Asadi, AliAkbar; Ebrahimi, Asa; Rashidi-Monfared, Sajad; Basiri, Mohammad M.; Akbari-Afjani, Javad

doi:10.1016/j.compbiolchem.2019.107169

Cited by 7 publications

(3 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Cirsimaritin could take another route with F8OMT enzyme which leads to formation of xanthomicrol, with known anticancer and antioxidant properties 43 . Although, xanthomicrol formation is occurred by methoxlyation of carbon atomic number 8 of cirsimaritin 19 , no transcripts belong to the F8H enzyme were found in D. kotschyi transcriptome dataset. This may be due to the loss of this transcript during assembly or the presence of a similar and unknown enzyme for this function; and finally, it may be catalyzed by one of the known hydroxylase enzymes which could have several substrates also reported in flavone biosynthesis pathways 44 .…”

Section: Discussionmentioning

confidence: 97%

Toward understanding of the methoxylated flavonoid biosynthesis pathway in Dracocephalum kotschyi Boiss

Poursalavati

Rashidi-Monfared

Ebrahimi

2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

Nowadays, with the development and advancement of next-generation sequencing technologies, a new path has been provided for transcriptomic studies. In this study, the transcriptome of Dracocephalum kotschyi Boiss., as an endemic and endangered plant which is contained a large amount of valuable secondary metabolites with antioxidant and anticancer properties, was sequenced. Then functional annotation and gene ontology analysis for 165,597 assembled transcripts were performed, most were associated with the metabolic pathways. This might be because there are various active biochemical pathways in this plant. Furthermore, after comprehensive transcript annotation, the putative genes involved in the main metabolic pathways of D. kotschyi were identified. Then, the biosynthetic pathway of its valuable methoxylated flavones was proposed. Finally, the accumulations of important methoxylated-flavone metabolites in three different tissues were quantified by HPLC. The relative expression of the genes involved in the proposed pathway was investigated by qRT-PCR, which indicated high expression levels in the bud tissue. The present results may lead to the design strategies to preserve the genetic diversity of endangered D. kotschyi plants and apply the new methods for engineering its valuable methoxylated-flavones pathway.

show abstract

Section: Discussionmentioning

confidence: 97%

Toward understanding of the methoxylated flavonoid biosynthesis pathway in Dracocephalum kotschyi Boiss

Poursalavati

Rashidi-Monfared

Ebrahimi

2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…Amplification of the Simple Sequence Repeat (SSR) is a common molecular method because of its benefits including hypervariability, broad genomic distribution, co-dominant inheritance, polymorphism, and chromosome-specific locations (Osorio-Guarín et al, 2020). In addition to being more practical to use in comparison to other DNA typification assays, PCR-based SSRs are regarded as being the most promising markers to comprehend population genetics (Asadi et al, 2019) and identifying probable parental genotypes in the oil palm. Using molecular markers, only some attempts have been done in India to increase the genetic diversity of local germplasm (Satish and Mohankumar, 2007).…”

Section: P R E S Smentioning

confidence: 99%

MOLECULAR CHARACTERISATION OF OIL PALM (Elaeis guineensis Jacq.) HYBRIDS

2024

JOPR

View full text Add to dashboard Cite

“…SSRs obtained from transcriptome sequences have great significance for the development of molecular markers in genic regions (Kaur et al 2011;He et al 2020). SSRs located in the coding regions are vital tools for analyzing the genetic diversity, population structure, and for markerassisted breeding (Ashkani et al 2012;Zong et al 2015;Girichev et al 2017;Li et al 2018;Asadi et al 2019). Moreover, EST-SSR markers are best candidates for identifying favorable trait-associated loci, essential for breeding experiments.…”

Section: Introductionmentioning

confidence: 99%

Development of SSR markers based on transcriptome data and association mapping analysis for fruit shell thickness associated traits in oil palm (Elaeis guineensis Jacq.)

et al. 2020

View full text Add to dashboard Cite

Present study mainly aimed to ascertain the distribution characteristics of gene-based microsatellite loci and to develop polymorphic SSR markers from the already available transcriptome data of Elaeis guineensis Jacq, an important oil crop. From this study, we identified the sum of 5791 SSRs across 51,425 unigenes from the transcripts of oil palm. We were able to evaluate 331primer pairs and characterized 183 polymorphic gene-based SSR markers. We identified a total of 506 alleles from the 183 polymorphic SSR loci, with an average of 2.77 alleles per locus. The characterized gene-based SSR markers from the transcriptome data of oil palm exhibited moderate levels of polymorphism with a significant level of heterozygosity ranges from 0.096 to 0.594 (mean = 0.336 ± 0.11). Among the identified SSR markers, sixty polymorphic markers were used to analyze genotypes of 55 oil palm accessions selected from three different provinces of China. Association mapping analysis provided the information of four markers that are associated with fruit shell thickness trait of oil palm. Among the four markers identified from association analysis, one SSR marker obtained from Unigene17150 is strictly associated with the oil palm fruit shell thickness trait.

show abstract

Comprehensive functional analysis and mapping of SSR markers in the chickpea genome (Cicer arietinum L.)

Cited by 7 publications

References 43 publications

Toward understanding of the methoxylated flavonoid biosynthesis pathway in Dracocephalum kotschyi Boiss

Toward understanding of the methoxylated flavonoid biosynthesis pathway in Dracocephalum kotschyi Boiss

MOLECULAR CHARACTERISATION OF OIL PALM (Elaeis guineensis Jacq.) HYBRIDS

Development of SSR markers based on transcriptome data and association mapping analysis for fruit shell thickness associated traits in oil palm (Elaeis guineensis Jacq.)

Contact Info

Product

Resources

About