Molecular characterization of popcorn inbreds using 25k SNP array
Authors
Mladenović Drinić, SnežanaSrdić, Jelena
Anđelković, Violeta
Grčić, Nikola
Kravić, Natalija
Filipović, Milomir
Nikolić, Ana
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Popcorn is a type of specialty maize and plays important role in the history and the spread of
this species. This type of maize historicaly received little atention in genetic diversity studies
while the fact is that information on genetic variability and population structure is of crucial
importance for improvement of breeding programs. The genetic variation of popcorn maize
was mainly analysed using SSR markers, but there are not many studies applying high-density
SNP markers with lower genotyping errors. The aim of this study was the assesment of genetic
diversity and population structure of popcorn germplasm which represents the genetic
resources currently used in breeding programs in Maize Research Institute „Zemun Polje“.
Molecular characterization of 44 popcorn genotypes was done using 25k SNP Illumina Infinum
Array for maize. After quality control filtering, 12335 SNPs were selected for downstream
analyses. Genetic distance detected ranged from 0.001 to 0.51 with an a...verage of 0.33. The
majority of genetic distances (70.6%) fell between 0.30 and 0.51 revealing significant genetic
variability in a set of maize genotypes under study. SNP markes were moderatly informative
with an average PIC value of 0.26. Also, for more than 50% of SNPs, PIC value was greater
than 0.30. The average observed heterozygosity was 0.04 ranging from 0 to 0.11. The
clustering, principal component and model-based STRUCTURE analyses showed similar
grouping of popcorn lines, generally in accordance with their genetic background. The results
of this research gave valuable information for initiation of future breeding strategies.
Keywords:
popcorn maize / SNPs / genetic diversity / population structureSource:
25. EUCARPIA Maize and sorghum conference:"Current challenges and new methods for maize and sorghum breeding", 30.05-02.06.2022., Belgrade - Book of abstracts, 2022Publisher:
- Belgrade : Maize Research Institute, Zemun Polje
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MRIZPTY - CONF AU - Mladenović Drinić, Snežana AU - Srdić, Jelena AU - Anđelković, Violeta AU - Grčić, Nikola AU - Kravić, Natalija AU - Filipović, Milomir AU - Nikolić, Ana PY - 2022 UR - http://rik.mrizp.rs/handle/123456789/958 AB - Popcorn is a type of specialty maize and plays important role in the history and the spread of this species. This type of maize historicaly received little atention in genetic diversity studies while the fact is that information on genetic variability and population structure is of crucial importance for improvement of breeding programs. The genetic variation of popcorn maize was mainly analysed using SSR markers, but there are not many studies applying high-density SNP markers with lower genotyping errors. The aim of this study was the assesment of genetic diversity and population structure of popcorn germplasm which represents the genetic resources currently used in breeding programs in Maize Research Institute „Zemun Polje“. Molecular characterization of 44 popcorn genotypes was done using 25k SNP Illumina Infinum Array for maize. After quality control filtering, 12335 SNPs were selected for downstream analyses. Genetic distance detected ranged from 0.001 to 0.51 with an average of 0.33. The majority of genetic distances (70.6%) fell between 0.30 and 0.51 revealing significant genetic variability in a set of maize genotypes under study. SNP markes were moderatly informative with an average PIC value of 0.26. Also, for more than 50% of SNPs, PIC value was greater than 0.30. The average observed heterozygosity was 0.04 ranging from 0 to 0.11. The clustering, principal component and model-based STRUCTURE analyses showed similar grouping of popcorn lines, generally in accordance with their genetic background. The results of this research gave valuable information for initiation of future breeding strategies. PB - Belgrade : Maize Research Institute, Zemun Polje C3 - 25. EUCARPIA Maize and sorghum conference:"Current challenges and new methods for maize and sorghum breeding", 30.05-02.06.2022., Belgrade - Book of abstracts T1 - Molecular characterization of popcorn inbreds using 25k SNP array UR - https://hdl.handle.net/21.15107/rcub_rik_958 ER -
@conference{ author = "Mladenović Drinić, Snežana and Srdić, Jelena and Anđelković, Violeta and Grčić, Nikola and Kravić, Natalija and Filipović, Milomir and Nikolić, Ana", year = "2022", abstract = "Popcorn is a type of specialty maize and plays important role in the history and the spread of this species. This type of maize historicaly received little atention in genetic diversity studies while the fact is that information on genetic variability and population structure is of crucial importance for improvement of breeding programs. The genetic variation of popcorn maize was mainly analysed using SSR markers, but there are not many studies applying high-density SNP markers with lower genotyping errors. The aim of this study was the assesment of genetic diversity and population structure of popcorn germplasm which represents the genetic resources currently used in breeding programs in Maize Research Institute „Zemun Polje“. Molecular characterization of 44 popcorn genotypes was done using 25k SNP Illumina Infinum Array for maize. After quality control filtering, 12335 SNPs were selected for downstream analyses. Genetic distance detected ranged from 0.001 to 0.51 with an average of 0.33. The majority of genetic distances (70.6%) fell between 0.30 and 0.51 revealing significant genetic variability in a set of maize genotypes under study. SNP markes were moderatly informative with an average PIC value of 0.26. Also, for more than 50% of SNPs, PIC value was greater than 0.30. The average observed heterozygosity was 0.04 ranging from 0 to 0.11. The clustering, principal component and model-based STRUCTURE analyses showed similar grouping of popcorn lines, generally in accordance with their genetic background. The results of this research gave valuable information for initiation of future breeding strategies.", publisher = "Belgrade : Maize Research Institute, Zemun Polje", journal = "25. EUCARPIA Maize and sorghum conference:"Current challenges and new methods for maize and sorghum breeding", 30.05-02.06.2022., Belgrade - Book of abstracts", title = "Molecular characterization of popcorn inbreds using 25k SNP array", url = "https://hdl.handle.net/21.15107/rcub_rik_958" }
Mladenović Drinić, S., Srdić, J., Anđelković, V., Grčić, N., Kravić, N., Filipović, M.,& Nikolić, A.. (2022). Molecular characterization of popcorn inbreds using 25k SNP array. in 25. EUCARPIA Maize and sorghum conference:"Current challenges and new methods for maize and sorghum breeding", 30.05-02.06.2022., Belgrade - Book of abstracts Belgrade : Maize Research Institute, Zemun Polje.. https://hdl.handle.net/21.15107/rcub_rik_958
Mladenović Drinić S, Srdić J, Anđelković V, Grčić N, Kravić N, Filipović M, Nikolić A. Molecular characterization of popcorn inbreds using 25k SNP array. in 25. EUCARPIA Maize and sorghum conference:"Current challenges and new methods for maize and sorghum breeding", 30.05-02.06.2022., Belgrade - Book of abstracts. 2022;. https://hdl.handle.net/21.15107/rcub_rik_958 .
Mladenović Drinić, Snežana, Srdić, Jelena, Anđelković, Violeta, Grčić, Nikola, Kravić, Natalija, Filipović, Milomir, Nikolić, Ana, "Molecular characterization of popcorn inbreds using 25k SNP array" in 25. EUCARPIA Maize and sorghum conference:"Current challenges and new methods for maize and sorghum breeding", 30.05-02.06.2022., Belgrade - Book of abstracts (2022), https://hdl.handle.net/21.15107/rcub_rik_958 .