TY  - JOUR
AU  - Galić, Vlatko
AU  - Anđelković, Violeta
AU  - Kravić, Natalija
AU  - Grčić, Nikola
AU  - Ledenčan, Tatjana
AU  - Jambrović, Antun
AU  - Zdunić, Zvonimir
AU  - Nicolas, Stephane
AU  - Charcosset, Alain
AU  - Šatović, Zlatko
AU  - Šimić, Domagoj
PY  - 2023
UR  - http://rik.mrizp.rs/handle/123456789/1148
AB  - Southeast Europe (SEE) is a very important maize-growing region, comparable to the Corn belt region of the United
States, with similar dent germplasm (dent by dent hybrids). Historically, this region has undergone several genetic
material swaps, following the trends in the US, with one of the most signifcant swaps related to US aid programs
after WWII. The imported accessions used to make double-cross hybrids were also mixed with previously adapted
germplasm originating from several more distant OPVs, supporting the transition to single cross-breeding. Many of
these materials were deposited at the Maize Gene Bank of the Maize Research Institute Zemun Polje (MRIZP) between
the 1960s and 1980s. A part of this Gene Bank (572 inbreds) was genotyped with Afymetrix Axiom Maize Genotyping Array with 616,201 polymorphic variants. Data were merged with two other genotyping datasets with mostly
European fint (TUM dataset) and dent (DROPS dataset) germplasm. The fnal pan-European dataset consisted of 974
inbreds and 460,243 markers. Admixture analysis showed seven ancestral populations representing European fint,
B73/B14, Lancaster, B37, Wf9/Oh07, A374, and Iodent pools. Subpanel of inbreds with SEE origin showed a lack of
Iodent germplasm, marking its historical context. Several signatures of selection were identifed at chromosomes 1, 3,
6, 7, 8, 9, and 10. The regions under selection were mined for protein-coding genes and were used for gene ontology (GO) analysis, showing a highly signifcant overrepresentation of genes involved in response to stress. Our results
suggest the accumulation of favorable allelic diversity, especially in the context of changing climate in the genetic
resources of SEE.
PB  - Springer Nature
T2  - BMC Plant biology
T1  - Genetic diversity and selection signatures in a gene bank panel of maize inbred lines from Southeast Europe compared with two West European panels
VL  - 23
SP  - 315
DO  - 10.1186/s12870-023-04336-2
ER  - 

@article{
author = "Galić, Vlatko and Anđelković, Violeta and Kravić, Natalija and Grčić, Nikola and Ledenčan, Tatjana and Jambrović, Antun and Zdunić, Zvonimir and Nicolas, Stephane and Charcosset, Alain and Šatović, Zlatko and Šimić, Domagoj",
year = "2023",
abstract = "Southeast Europe (SEE) is a very important maize-growing region, comparable to the Corn belt region of the United
States, with similar dent germplasm (dent by dent hybrids). Historically, this region has undergone several genetic
material swaps, following the trends in the US, with one of the most signifcant swaps related to US aid programs
after WWII. The imported accessions used to make double-cross hybrids were also mixed with previously adapted
germplasm originating from several more distant OPVs, supporting the transition to single cross-breeding. Many of
these materials were deposited at the Maize Gene Bank of the Maize Research Institute Zemun Polje (MRIZP) between
the 1960s and 1980s. A part of this Gene Bank (572 inbreds) was genotyped with Afymetrix Axiom Maize Genotyping Array with 616,201 polymorphic variants. Data were merged with two other genotyping datasets with mostly
European fint (TUM dataset) and dent (DROPS dataset) germplasm. The fnal pan-European dataset consisted of 974
inbreds and 460,243 markers. Admixture analysis showed seven ancestral populations representing European fint,
B73/B14, Lancaster, B37, Wf9/Oh07, A374, and Iodent pools. Subpanel of inbreds with SEE origin showed a lack of
Iodent germplasm, marking its historical context. Several signatures of selection were identifed at chromosomes 1, 3,
6, 7, 8, 9, and 10. The regions under selection were mined for protein-coding genes and were used for gene ontology (GO) analysis, showing a highly signifcant overrepresentation of genes involved in response to stress. Our results
suggest the accumulation of favorable allelic diversity, especially in the context of changing climate in the genetic
resources of SEE.",
publisher = "Springer Nature",
journal = "BMC Plant biology",
title = "Genetic diversity and selection signatures in a gene bank panel of maize inbred lines from Southeast Europe compared with two West European panels",
volume = "23",
pages = "315",
doi = "10.1186/s12870-023-04336-2"
}

Galić, V., Anđelković, V., Kravić, N., Grčić, N., Ledenčan, T., Jambrović, A., Zdunić, Z., Nicolas, S., Charcosset, A., Šatović, Z.,& Šimić, D.. (2023). Genetic diversity and selection signatures in a gene bank panel of maize inbred lines from Southeast Europe compared with two West European panels. in BMC Plant biology
Springer Nature., 23, 315.
https://doi.org/10.1186/s12870-023-04336-2

Galić V, Anđelković V, Kravić N, Grčić N, Ledenčan T, Jambrović A, Zdunić Z, Nicolas S, Charcosset A, Šatović Z, Šimić D. Genetic diversity and selection signatures in a gene bank panel of maize inbred lines from Southeast Europe compared with two West European panels. in BMC Plant biology. 2023;23:315.
doi:10.1186/s12870-023-04336-2 .

Galić, Vlatko, Anđelković, Violeta, Kravić, Natalija, Grčić, Nikola, Ledenčan, Tatjana, Jambrović, Antun, Zdunić, Zvonimir, Nicolas, Stephane, Charcosset, Alain, Šatović, Zlatko, Šimić, Domagoj, "Genetic diversity and selection signatures in a gene bank panel of maize inbred lines from Southeast Europe compared with two West European panels" in BMC Plant biology, 23 (2023):315,
https://doi.org/10.1186/s12870-023-04336-2 . .

TY  - JOUR
AU  - Simić, Domagoj
AU  - Zdunić, Zvonimir
AU  - Jambrović, Antun
AU  - Ledencan, Tatjana
AU  - Brkić, Josip
AU  - Brkić, Andrija
AU  - Brkić, Ivan
AU  - Mladenović Drinić, Snežana
PY  - 2012
UR  - http://rik.mrizp.rs/handle/123456789/422
AB  - Detecting genes that influence biofortification traits in cereal grain could help increase the concentrations of bioavailable mineral elements in crops to solve the global mineral malnutrition problem. The aims of this study were to detect the quantitative trait loci (QTLs) for phosphorus (P), iron (Fe), zinc (Zn), and magnesium (Mg) concentrations in maize grain in a mapping population, as well as QTLs for bioavailable Fe, Zn, and Mg, by precalculating their respective ratios with P. Elemental analysis of grain samples was done by coupled plasma-optical emission spectrometry in 294 F(4) lines of a biparental population taken from field trials of over 3 years. The population was mapped using sets of 121 polymorphic markers. QTL analysis revealed 32 significant QTLs detected for 7 traits, of which some were colocalized. The Additive-dominant model revealed highly significant additive effects, suggesting that biofortification traits in maize are generally controlled by numerous small-effect QTLs. Three QTLs for Fe/P, Zn/P, and Mg/P were colocalized on chromosome 3, coinciding with simple sequence repeats marker bnlg1456, which resides in close proximity to previously identified phytase genes (ZM phys1 and phys2). Thus, we recommend the ratios as bioavailability traits in biofortification research.
PB  - Oxford Univ Press Inc, Cary
T2  - Journal of Heredity
T1  - Quantitative Trait Loci for Biofortification Traits in Maize Grain
VL  - 103
IS  - 1
SP  - 47
EP  - 54
DO  - 10.1093/jhered/esr122
ER  - 

@article{
author = "Simić, Domagoj and Zdunić, Zvonimir and Jambrović, Antun and Ledencan, Tatjana and Brkić, Josip and Brkić, Andrija and Brkić, Ivan and Mladenović Drinić, Snežana",
year = "2012",
abstract = "Detecting genes that influence biofortification traits in cereal grain could help increase the concentrations of bioavailable mineral elements in crops to solve the global mineral malnutrition problem. The aims of this study were to detect the quantitative trait loci (QTLs) for phosphorus (P), iron (Fe), zinc (Zn), and magnesium (Mg) concentrations in maize grain in a mapping population, as well as QTLs for bioavailable Fe, Zn, and Mg, by precalculating their respective ratios with P. Elemental analysis of grain samples was done by coupled plasma-optical emission spectrometry in 294 F(4) lines of a biparental population taken from field trials of over 3 years. The population was mapped using sets of 121 polymorphic markers. QTL analysis revealed 32 significant QTLs detected for 7 traits, of which some were colocalized. The Additive-dominant model revealed highly significant additive effects, suggesting that biofortification traits in maize are generally controlled by numerous small-effect QTLs. Three QTLs for Fe/P, Zn/P, and Mg/P were colocalized on chromosome 3, coinciding with simple sequence repeats marker bnlg1456, which resides in close proximity to previously identified phytase genes (ZM phys1 and phys2). Thus, we recommend the ratios as bioavailability traits in biofortification research.",
publisher = "Oxford Univ Press Inc, Cary",
journal = "Journal of Heredity",
title = "Quantitative Trait Loci for Biofortification Traits in Maize Grain",
volume = "103",
number = "1",
pages = "47-54",
doi = "10.1093/jhered/esr122"
}

Simić, D., Zdunić, Z., Jambrović, A., Ledencan, T., Brkić, J., Brkić, A., Brkić, I.,& Mladenović Drinić, S.. (2012). Quantitative Trait Loci for Biofortification Traits in Maize Grain. in Journal of Heredity
Oxford Univ Press Inc, Cary., 103(1), 47-54.
https://doi.org/10.1093/jhered/esr122

Simić D, Zdunić Z, Jambrović A, Ledencan T, Brkić J, Brkić A, Brkić I, Mladenović Drinić S. Quantitative Trait Loci for Biofortification Traits in Maize Grain. in Journal of Heredity. 2012;103(1):47-54.
doi:10.1093/jhered/esr122 .

Simić, Domagoj, Zdunić, Zvonimir, Jambrović, Antun, Ledencan, Tatjana, Brkić, Josip, Brkić, Andrija, Brkić, Ivan, Mladenović Drinić, Snežana, "Quantitative Trait Loci for Biofortification Traits in Maize Grain" in Journal of Heredity, 103, no. 1 (2012):47-54,
https://doi.org/10.1093/jhered/esr122 . .

TY  - JOUR
AU  - Šimić, Domagoj
AU  - Ledenčan, Tatjana
AU  - Jambrović, Antun
AU  - Zdunić, Zvonimir
AU  - Brkić, Josip
AU  - Brkić, Andrija
AU  - Mladenović Drinić, Snežana
AU  - Brkić, Ivan
PY  - 2009
UR  - http://rik.mrizp.rs/handle/123456789/250
AB  - Although highly polymorphic SSRs are currently the marker of choice worldwide in maize breeding, single nucleotide polymorphisms (SNPs) as a newer marker system are recently used more extensively. The objective of this study was investigate the utility of SSR and SNP markers for mapping of a maize population adapted to conditions of Southeast Europe. Total of 294 F2:3 lines derived from a biparental mapping population were genotyped using 121 polymorphic SNP and SSR markers. The SNP markers were analyzed using the SNPlex technology. 56 of the 142 tested SNPs (39%) were polymorphic between the parents of the mapping population and were successfully mapped. The remaining markers were either not functional (5 = 3.5%) or not polymorphic (81 = 57%). No mapped SNP marker showed more than 10% missing data. On average, the level of missing data for SNPs (1.5%) was considerably lower than that for SSRs (3.4%). For the mapping procedure, the SNP data were combined SSR data. A comparison of the mapping data with the publicly available mapping data on SSR markers and the proprietary mapping data indicates that the map is of good quality and that the map position of almost all markers agrees with their published map position. Thus, information obtained from both marker systems is utilizable for further QTL analysis.
AB  - Iako su trenutno visoko polimorfni SSR markeri izbora, novi markeri SNP se od nedavno koriste veoma intenzivno u programima oplemenjivanja kukuruza u svetu. Cilj ovog istraživanja je ispitivanje primene SSR i SNP markera za mapiranje populacije kukuruza koje su prilagođene uslovima Jugoistočne Evrope. Ukupno 294 F2:3 linija dobijeno iz biparentalne mapirajuće populacije je analizirano sa 121 polimorfnim SNP i SSR markerom. SNP markeri su analizirani primenom SNPlex tehnologije. Pedeset šest od 142 ispitanih SNP markera (39%) je bilo polimorfno između roditelja mapirajuće populacije i uspešno je mapirano. Preostali markeri su bili ili nefunkcionalni (5=3,5%) ili nisu bili polimorfni (81=57%). Nemapirani SNP markeri su imali više od 10% podataka koji su nedostajali. U proseku, nivo podataka koji su nedostajali za SNP (1,5%) je bio značajno niži nego za SSR (3,4%). Za mapiranje kombinovani su SNP i SSR podaci. Poređenje mapirajućih podataka sa javno dostupnim mapirajućim podacima za SSR i zaštićenim mapirajućim podacima ukazuje da je mapa dobrog kvaliteta i da se pozicije na mapi skoro svih markera slažu sa njihovim prethodno objavljenim pozicijama. Otuda, informacije dobijene primenom oba marker sistema se mogu koristiti za buduće QTL analize.
PB  - Društvo genetičara Srbije, Beograd
T2  - Genetika
T1  - SNP and SSR marker analysis and mapping of a maize population
T1  - Analiza i mapiranje SNP i SSR markera u populaciji kukuruza
VL  - 41
IS  - 3
SP  - 237
EP  - 246
DO  - 10.2298/GENSR0903237S
ER  - 

@article{
author = "Šimić, Domagoj and Ledenčan, Tatjana and Jambrović, Antun and Zdunić, Zvonimir and Brkić, Josip and Brkić, Andrija and Mladenović Drinić, Snežana and Brkić, Ivan",
year = "2009",
abstract = "Although highly polymorphic SSRs are currently the marker of choice worldwide in maize breeding, single nucleotide polymorphisms (SNPs) as a newer marker system are recently used more extensively. The objective of this study was investigate the utility of SSR and SNP markers for mapping of a maize population adapted to conditions of Southeast Europe. Total of 294 F2:3 lines derived from a biparental mapping population were genotyped using 121 polymorphic SNP and SSR markers. The SNP markers were analyzed using the SNPlex technology. 56 of the 142 tested SNPs (39%) were polymorphic between the parents of the mapping population and were successfully mapped. The remaining markers were either not functional (5 = 3.5%) or not polymorphic (81 = 57%). No mapped SNP marker showed more than 10% missing data. On average, the level of missing data for SNPs (1.5%) was considerably lower than that for SSRs (3.4%). For the mapping procedure, the SNP data were combined SSR data. A comparison of the mapping data with the publicly available mapping data on SSR markers and the proprietary mapping data indicates that the map is of good quality and that the map position of almost all markers agrees with their published map position. Thus, information obtained from both marker systems is utilizable for further QTL analysis., Iako su trenutno visoko polimorfni SSR markeri izbora, novi markeri SNP se od nedavno koriste veoma intenzivno u programima oplemenjivanja kukuruza u svetu. Cilj ovog istraživanja je ispitivanje primene SSR i SNP markera za mapiranje populacije kukuruza koje su prilagođene uslovima Jugoistočne Evrope. Ukupno 294 F2:3 linija dobijeno iz biparentalne mapirajuće populacije je analizirano sa 121 polimorfnim SNP i SSR markerom. SNP markeri su analizirani primenom SNPlex tehnologije. Pedeset šest od 142 ispitanih SNP markera (39%) je bilo polimorfno između roditelja mapirajuće populacije i uspešno je mapirano. Preostali markeri su bili ili nefunkcionalni (5=3,5%) ili nisu bili polimorfni (81=57%). Nemapirani SNP markeri su imali više od 10% podataka koji su nedostajali. U proseku, nivo podataka koji su nedostajali za SNP (1,5%) je bio značajno niži nego za SSR (3,4%). Za mapiranje kombinovani su SNP i SSR podaci. Poređenje mapirajućih podataka sa javno dostupnim mapirajućim podacima za SSR i zaštićenim mapirajućim podacima ukazuje da je mapa dobrog kvaliteta i da se pozicije na mapi skoro svih markera slažu sa njihovim prethodno objavljenim pozicijama. Otuda, informacije dobijene primenom oba marker sistema se mogu koristiti za buduće QTL analize.",
publisher = "Društvo genetičara Srbije, Beograd",
journal = "Genetika",
title = "SNP and SSR marker analysis and mapping of a maize population, Analiza i mapiranje SNP i SSR markera u populaciji kukuruza",
volume = "41",
number = "3",
pages = "237-246",
doi = "10.2298/GENSR0903237S"
}

Šimić, D., Ledenčan, T., Jambrović, A., Zdunić, Z., Brkić, J., Brkić, A., Mladenović Drinić, S.,& Brkić, I.. (2009). SNP and SSR marker analysis and mapping of a maize population. in Genetika
Društvo genetičara Srbije, Beograd., 41(3), 237-246.
https://doi.org/10.2298/GENSR0903237S

Šimić D, Ledenčan T, Jambrović A, Zdunić Z, Brkić J, Brkić A, Mladenović Drinić S, Brkić I. SNP and SSR marker analysis and mapping of a maize population. in Genetika. 2009;41(3):237-246.
doi:10.2298/GENSR0903237S .

Šimić, Domagoj, Ledenčan, Tatjana, Jambrović, Antun, Zdunić, Zvonimir, Brkić, Josip, Brkić, Andrija, Mladenović Drinić, Snežana, Brkić, Ivan, "SNP and SSR marker analysis and mapping of a maize population" in Genetika, 41, no. 3 (2009):237-246,
https://doi.org/10.2298/GENSR0903237S . .