SSR-based genetic linkage map construction in pistachio using an interspecific F1 population and QTL analysis for leaf and shoot traits

Motalebipour, Elmira Ziya; Gözel, H.; Khodaeiaminjan, Mortaza; Kafkas, Salih

doi:10.1007/s11032-018-0893-z

Cited by 5 publications

(5 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, we obtained some small linkage groups, the same as in Juglans regia [31]. These phenomena have been found in many species [16,18,31,33,40,41] and indicate that some gaps prevent connection between linkage groups belonging to the same chromosome, which needs to be optimised in the future by expanding mapping population, increasing parental combinations and adopting new markers. By contrast with the variety of mapping populations in crops [42,43], the growth cycle of trees was long, and the genetic offspring was difficult to be obtained.…”

Section: Genetic Linkage Mapmentioning

confidence: 52%

“…The QTLs identified for each trait were distributed in different linkage groups, suggesting that the trait may be regulated by multiple genes with large effect. Three traits (tree height, ground diameter and crown diameter) had a complex genetic background, which was also confirmed for Pistacia vera (pistachio) [40], J. regia [31], P. tremula (European aspen) [44], H. brasiliensis [16] and Camellia sinensis (tea tree) [45]. The phenotypic variation explained by each QTL had a wide range, and the sum of the phenotypic variation for one trait was more than 100%.…”

Section: Qtl Analysismentioning

confidence: 53%

See 1 more Smart Citation

Update of Genetic Linkage Map and QTL Analysis for Growth Traits in Eucommia ulmoides Oliver

Jin

et al. 2020

Forests

View full text Add to dashboard Cite

Eucommia ulmoides (Tu-chung) is an economically and ecologically important tree species which has attracted worldwide attention due to its application in pharmacology, landscaping, wind sheltering and sand fixation. Molecular marker technologies can elucidate the genetic mechanism and substantially improve the breeding efficiency of E. ulmoides. The current research updated the original linkage map, and quantitative trait loci (QTL) analysis was performed on tree growth traits measured over 10 consecutive years in an E. ulmoides F1 population (“Xiaoye” × “Qinzhong No.1”). In total, 452 polymorphic markers were scored from 365 simple sequence repeat (SSR) primers, with an average of 1.24 polymorphic markers per primer combination. The integrated map was 1913.29 cM (centimorgan) long, covering 94.10% of the estimated genome and with an average marker density of 2.20 cM. A total of 869 markers were mapped into 19 major independent linkage groups. Growth-related traits measured over 10 consecutive years showed a significant correlation, and 89 hypothetical QTLs were forecasted and divided into 27 distinct loci. Three traits for tree height, ground diameter and crown diameter detected 25 QTLs (13 loci), 32 QTLs (17 loci) and 15 QTLs (10 loci), respectively. Based on BLASTX search results in the NCBI database, six candidate genes were obtained. It is important to explore the growth-related genetic mechanism and lay the foundation for the genetic improvement of E. ulmoides at the molecular level.

show abstract

Section: Genetic Linkage Mapmentioning

confidence: 52%

Section: Qtl Analysismentioning

confidence: 53%

Update of Genetic Linkage Map and QTL Analysis for Growth Traits in Eucommia ulmoides Oliver

Jin

et al. 2020

Forests

View full text Add to dashboard Cite

show abstract

“…Forty-five in silico novel SSR markers developed by Khodaeiaminjan et al [35] were used to construct in silico polymorphic SSR-based genetic linkage maps in pistachio and five SSR markers developed by Motalebipour et al [36] in pistachio were used for testing the amplification and polymorphism in eight terebinth genotypes. The 38 of 45 in silico polymorphic novel SSR markers have been used for the first time in the characterization study of Pistacia wild species.…”

Section: In Silico Polymorphic Ssr-pcr Reactionsmentioning

confidence: 99%

Genetic Diversity and Relationships of Terebinth (Pistacia terebinthus L.) Genotypes Growing Wild in Turkey

et al. 2021

Self Cite

View full text Add to dashboard Cite

Genetic diversity and relationships of 54 wild-grown terebinths (Pistacia terebinthus L.) were determined using 40 SSR (simple sequence repeat) markers (38 in silico polymorphic SSR markers and 2 SSR markers). In silico polymorphic SSR analysis, 430 alleles were identified. The number of alleles per locus ranged from 3 to 25 with a mean value of 11 alleles per locus. The values of polymorphism information content (PIC) ranged from 0.34 (CUPOhBa4344) to 0.91 (CUPSiBa4072) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), the Structure, and Principal Coordinates (PCoA) based clustering. The structure analysis and UPGMA clustering of the genotypes depicted two major clusters. PCoA results supported cluster analysis results. The dendrogram revealed two major clusters. Forty-two samples were obtained from the Kazankaya canyon and 12 samples from the Karanlıkdere region. The two regions are 130 km apart from each other but in a dendrogram, we did not find geographical isolation. The results proved the efficiency of SSRs for genetic diversity analysis in the terebinth. Based on the results, SSRs can be applied as a trustworthy tool for the evaluation of genetic diversity in terebinth genotypes. Molecular analysis on the terebinth genotypes in this study will promote the germplasm collection and the selection of the populations in future studies on terebinths for genetic mapping, genetic diversity, germplasm characterization, and rootstock breeding.

show abstract

“…A total of 385 SSR markers was mapped along with 15 chromosomes, and the consensus map had 1511.3 cM length with an average of 25.6 SSR markers per LG, and the average distance between the markers was 3.9 cM with a 0.25 marker density. The first QTL study in pistachio was performed by Motalebipour et al [35] who constructed a genetic linkage map of pistachio using an inter-specific F1 population and SSR markers. The authors mapped a total of 388 SSR markers along with 15 linkage groups.…”

Section: Use Of Ssr Markers In the Genus Pistaciamentioning

confidence: 99%

“…Recently, Khodaeiaminjan et al [28] constructed the first complete SSR-based linkage map of pistachio using an intraspecific F1 population. More recently, Motalebipour et al [35] constructed a genetic linkage map and performed the first QTL analysis in pistachio by using an interspecific F1 population.…”

Section: Introductionmentioning

confidence: 99%

SSR Markers in the Genus Pistacia

Kafkas¹

2020

Sustainable Crop Production

Self Cite

View full text Add to dashboard Cite

Simple sequence repeats (SSRs) are one of the most powerful molecular marker systems due to abundance in the genomes, its codominant nature, and high repeatability. P. vera L. is cultivated species in the genus Pistacia due to commercial value of its edible nuts. Other species in the genus are in the wild and are important especially for rootstock sources as well as for ornamental and forest trees. There were a very limited number of SSR markers for Pistacia species until several years ago; however, next-generation sequencing (NGS) technology has allowed to develop plenty of SSRs since 2016 in the genus. There are currently about 1500 published SSR markers developed from cultivated P. vera. There are also several studies generating SSR loci from wild Pistacia species. In a conclusion, there are currently an adequate number of SSR markers for cultivated pistachio and that can be used in wild Pistacia species due to their high level of transferability rate between Pistacia species. These SSRs can be used for assaying diversity in natural populations, marker discovery, germplasm characterization, parental identification, genetic linkage mapping, and evolutionary studies in the genus Pistacia.

show abstract

SSR-based genetic linkage map construction in pistachio using an interspecific F1 population and QTL analysis for leaf and shoot traits

Cited by 5 publications

References 64 publications

Update of Genetic Linkage Map and QTL Analysis for Growth Traits in Eucommia ulmoides Oliver

Update of Genetic Linkage Map and QTL Analysis for Growth Traits in Eucommia ulmoides Oliver

Genetic Diversity and Relationships of Terebinth (Pistacia terebinthus L.) Genotypes Growing Wild in Turkey

SSR Markers in the Genus Pistacia

Contact Info

Product

Resources

About