Exploring the genetic diversity and population structure of upland cotton germplasm by iPBS-retrotransposons markers

Baran, Nurettin; Shimira, Flavien; Nadeem, Muhammad Azhar; Altaf, Muhammad Tanveer; Andirman, Mehtap; Baloch, Faheem Shehzad; Temiz, Mefhar Gültekin

doi:10.1007/s11033-023-08399-0

Cited by 10 publications

(11 citation statements)

References 41 publications

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“…Regarding investigated diversity indices like the number of effective alleles, gene diversity, and Shanon information index, we found higher values compared to those reported by Baran et al (2023). These results confirmed the existence of higher genetic variation in the studied germplasm compared to those evaluated by Baran et al (2023). Rana et al (2004) obtained a mean PIC value of 0.312 using AFLP and 0.206 using RAPD markers to analyze 16 diploid cotton cultivars for genetic diversity evaluation.…”

Section: Discussionsupporting

confidence: 71%

“…However, we reported a higher mean PIC value (0.395) compared to reported by Baran et al (2023). Regarding investigated diversity indices like the number of effective alleles, gene diversity, and Shanon information index, we found higher values compared to those reported by Baran et al (2023). These results confirmed the existence of higher genetic variation in the studied germplasm compared to those evaluated by Baran et al (2023).…”

Section: Discussionsupporting

confidence: 67%

Section: Discussionmentioning

confidence: 40%

“…Recently, Baran et al (2023) screened upland cotton germplasm and reported a higher number of total and polymorphic bands compared to our study. However, we reported a higher mean PIC value (0.395) compared to reported by Baran et al (2023). Regarding investigated diversity indices like the number of effective alleles, gene diversity, and Shanon information index, we found higher values compared to those reported by Baran et al (2023).…”

Section: Discussionmentioning

confidence: 40%

“…Previously, different molecular markers have been used for the molecular characterization of cotton germplasm (Baran et al 2023;Kumlay et al 2021). But it is predicted that studies with bigger germplasm will be more qualified in genetic diversity and population analysis.…”

Section: Introductionmentioning

confidence: 99%

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Elucidating the genetic diversity and population structure of international Cotton germplasm using iPBS Retrotransposon Marker System

Bayrıl,

Bakhsh,

Nadeem

et al. 2023

Preprint

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Cotton (Gossypium hirsutum L.) is an important crop throughout the world and is one of the most important industrial raw materials. It is very important to characterize the available cotton germplasm aiming to identify novel genetic and genomic resources that can be used for future cotton breeding. Keeping this in view, a total of 179 cotton genotypes were characterized with the interPrimer Binding Site (iPBS). Seven iPBS-retrotransposons primers yielded a total of 134 scoreable bands and among these totals of 134, 128 bands were polymorphic. The mean polymorphic bands per primer were 18.28, with values between 16 and 21. The mean polymorphism rate of 7 iPBS retrotransposon primers was calculated as 96.28%. The polymorphism information content (PIC) value varies between 0.31 and 0.46 with an average of 0.395. Genetic similarity was calculated using the POPGENE software and values ranged between 0.320 and 0.955. Population structure and neighbor-joining analysis divided the evaluated germplasm into two populations. The analysis of molecular variance revealed that maximum variations (96%) are due to differences within the populations. The information presented here has comprehensively demonstrated the potential of iPBS-retrotransposon markers in detecting genetic diversity and phylogenetic association analyses of cotton and resulted information will be helpful for future cotton breeding.

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Section: Discussionsupporting

confidence: 71%

Section: Discussionsupporting

confidence: 67%

Section: Discussionmentioning

confidence: 40%

Section: Discussionmentioning

confidence: 40%

Section: Introductionmentioning

confidence: 99%

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Elucidating the genetic diversity and population structure of international Cotton germplasm using iPBS Retrotransposon Marker System

Bayrıl,

Bakhsh,

Nadeem

et al. 2023

Preprint

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Mutagenesis: Exploring Genetic Diversity of Industrial Crop Plants

Mir,

Faheem,

Sial

et al. 2024

Interdisciplinary Biotechnological Advances

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Investigation of genetic diversity among autochthonous grape cultivars grown in Türkiye using molecular primers

Sümbül,

Yildiz,

Sabir

et al. 2024

Genet Resour Crop Evol

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Grape is a type of fruit widely grown globally and in Türkiye thanks to its importance in human nutrition and diversity of usage areas. Türkiye has a long history of grape cultivation, and the genetic diversity of local grapes grown in some regions has still not been revealed. This study showed the genetic diversity between 60 local grape genotypes selected from north Central Anatolia and nine reference grape cultivars;10 inter simple sequence repeats (ISSR) and 7 inter-primer binding site (IPBS) retrotransposon primers were used. The mean values of genetic diversity indices in ISSR and IPBS retrotransposon primers were calculated as expected allelic frequency (p) 0.476/0.195, observed allelic frequency (q) 0.524/0.805, number of effective alleles (Ne) 1.326/1.378, Shannon’s information index (I) 0.308/0.367, expected heterozygosity (He) 0.199/0.232 and unbiased expected heterozygosity (uHe) 0.201/0.234, respectively. Unweighted pair group method with arithmetic mean (UPGMA) and model-based STRUCTURE analysis divided the studied germplasm into two groups. However, local genotypes were not grouped per the regions where they grew. As a result of the analysis of molecular variance (AMOVA) analysis, the inter-population variation was determined to be 11%, and the intra-population variation was determined to be 89%. The mean genetic differentiation value (Fst) between populations was 0.303. The results showed that ISSR and IPBS retrotransposon primers effectively explained the genetic diversity.

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Exploring the genetic diversity and population structure of upland cotton germplasm by iPBS-retrotransposons markers

Cited by 10 publications

References 41 publications

Elucidating the genetic diversity and population structure of international Cotton germplasm using iPBS Retrotransposon Marker System

Elucidating the genetic diversity and population structure of international Cotton germplasm using iPBS Retrotransposon Marker System

Mutagenesis: Exploring Genetic Diversity of Industrial Crop Plants

Investigation of genetic diversity among autochthonous grape cultivars grown in Türkiye using molecular primers

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