Effects of Recurrent Selection on Population Structure and Allele Frequencies in the M3S Maize Population

Miroslav Bukan (), Ana Mandić, Vinko Kozumplik, Ramsey S. Lewis, Domagoj Šimić and Hrvoje Šarčević
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Miroslav Bukan: Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
Ana Mandić: Department of Plant Breeding, Genetics, Seed Production and Biometrics, Faculty of Agriculture and Food Technology, University of Mostar, Biskupa Čule bb, 88000 Mostar, Bosnia and Herzegovina
Vinko Kozumplik: Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
Ramsey S. Lewis: Department of Crop and Soil Science, North Carolina State University, Campus Box 7620, Raleigh, NC 27695, USA
Domagoj Šimić: Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia
Hrvoje Šarčević: Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia

Agriculture, 2023, vol. 14, issue 1, 1-17

Abstract: The effects of four cycles of recurrent selection on the allele frequencies of simple sequence repeat (SSR) markers and population structure were examined in the Maksimir 3 Synthetic (M3S) maize population ( Zea mays L.). Genotyping of 32 plants from each selection cycle at 38 SSR loci revealed that the mean number of alleles per locus and the mean expected heterozygosity were preserved across selection cycles, indicating the maintenance of sufficient genetic variability in the population required for future genetic gain. The Waples test of selective neutrality revealed that genetic drift was the main force in changing allele frequencies in the population. The proportion of selectively non-neutral loci in single cycles of selection varied between 16% and 37%. Some non-neutral loci shared the same genomic locations with previously published QTLs controlling important agronomic traits. An analysis of molecular variance revealed that 5.6% of the genetic variation occurred among and 94.4% within cycle populations. Between 5% and 29% of loci were found to be in a significant Hardy–Weinberg (HW) disequilibrium, with the majority showing an excess of homozygosity. The excess of homozygosity at several loci was highly consistent across cycle populations, suggesting positive assortative mating as a possible cause of the observed HW disequilibrium. Linkage disequilibrium (LD) tests revealed that the M3S population was essentially in linkage equilibrium. The proportion of pairs of loci in significant LD varied from 0.1% to 1.8% across selection cycles, probably due to the effects of genetic drift and epistatic selection.

Keywords: maize; recurrent selection; grain yield; allele frequency; population structure; SSR markers (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2023
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