In silico polymorphic novel SSR marker development and the first SSR-based genetic linkage map in pistachio

Khodaeiaminjan, Mortaza; Kafkas, Salih; Motalebipour, Elmira Ziya; Çoban, Nergiz

doi:10.1007/s11295-018-1259-8

Cited by 28 publications

(28 citation statements)

References 67 publications

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“…Khodaeiaminjan et al [28] calculated the number of repeats in 4 genotypes, and 4 and 11 repeated motifs were the most abundant followed by 12, 8, 5, and 13 times repeated motifs (Figure 4).…”

Section: Ssr Distribution In P V E Ramentioning

confidence: 99%

“…Khodaeiaminjan et al [28] had about 10x Illumina data of three P. vera (Siirt, Ohadi, and Bağyolu) cultivars and one P. atlantica genotype (Pa-18) to find pairwise polymorphic SSR loci in silico. The authors detected a total of 3821, 3833, 2024, and 4597 SSRs in Siirt, Ohadi, and Bağyolu P. vera cultivars and in P. atlantica genotype, respectively.…”

Section: Ssr Distribution In P V E Ramentioning

confidence: 99%

“…Khodaeiaminjan et al [28] used in silico approach to develop polymorphic SSR markers in pistachio. The authors compared 10× Illumina sequencing data of three P. vera (Siirt, Ohadi, and Bağyolu) cultivars and one P. atlantica genotype (Pa-18) to find pairwise polymorphic SSR loci in silico, and 750 loci were detected.…”

Section: Development Of Ssrs From P V E Ramentioning

confidence: 99%

“…They are also very valuable markers especially for genetic linkage mapping and evolutionary studies [26] and have a high level of transferability between closely related species. The development of SSR markers from P. vera [14,16,17,[27][28][29] and from wild Pistacia species was performed in several studies [30][31][32][33].…”

Section: Introductionmentioning

confidence: 99%

“…SSR Markers in the Genus Pistacia DOI: http://dx.doi.org /10.5772/intechopen.89966 The first complete genetic linkage map was constructed in pistachio by [34] who used SRAP, ISSR, and AFLP markers in an inter-specific F1 population derived from a cross between P. vera and P. atlantica. 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%

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SSR Markers in the Genus Pistacia

Kafkas¹

2020

Sustainable Crop Production

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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.

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Section: Ssr Distribution In P V E Ramentioning

confidence: 99%

Section: Ssr Distribution In P V E Ramentioning

confidence: 99%

Section: Development Of Ssrs From P V E Ramentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

SSR Markers in the Genus Pistacia

Kafkas¹

2020

Sustainable Crop Production

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SSR‐based DNA fingerprinting of fruit crops

et al. 2023

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The DNA fingerprinting of fruit crops, based on DNA microsatellite markers that are considered to be the key markers for the molecular analysis of germplasm collections, is reviewed. Simple sequence repeats (SSRs) remain the markers of choice for fingerprinting in humans, animals, plants, and other living organisms. This review, that considers 44 fruit species, provides a set of markers that are suitable for profiling accessions and that should make the databases produced in different laboratories more comparable. Every effort has been made to select SSR markers that are robust and easily scorable considering that such analyses are sometimes used in legal cases. The review first describes the basic protocols, procedures, and methods of data analyses; it then describes the fingerprinting of individual species or groups of species, providing a set of SSR markers and appropriate guidance based on the revised literature and on the authors' experience.

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