Molecular characterization of doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic (BSSS) maize population

Abstract

Molecular characterization of a given set of maize germplasm could be useful for understanding the use of the assembled germplasm for further improvement in a breeding program, such as analyzing genetic diversity, selecting a parental line, assigning heterotic groups, creating a core set of germplasm and/or performing association analysis for traits of interest. In this study, we used single nucleotide polymorphism (SNP) markers to assess the genetic variability in a set of doubled haploid (DH) lines derived from the unselected Iowa Stiff Stalk Synthetic (BSSS) maize population, denoted as C0 (BSSS(R)C0), the seventeenth cycle of reciprocal recurrent selection in BSSS (BSSS(R)C17), denoted as C17 and the cross between BSSS(R)C0 and BSSS(R)C17 denoted as C0/C17. With the aim to explore if we have potentially lost diversity from C0 to C17 derived DH lines and observe whether useful genetic variation in C0 was left behind during the selection process since C0 could be a reservoir of genetic diversity that could be untapped using DH technology. Additionally, we quantify the contribution of the BSSS progenitors in each set of DH lines. The molecular characterization analysis confirmed the apparent separation and the loss of genetic variability from C0 to C17 through the recurrent selection process. Which was observed by the degree of differentiation between the C0_DHL versus C17_DHL groups by Wright’s F-statistics (FST). Similarly for the population structure based on principal component analysis (PCA) revealed a clear separation among groups of DH lines. Some of the progenitors had a higher genetic contribution in C0 compared with C0/C17 and C17 derived DH lines. Although genetic drift can explain most of the genetic structure genome-wide, phenotypic data provide evidence that selection has altered favorable allele frequencies in the BSSS maize population through the reciprocal recurrent selection program.

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

“…In contrast, Labate et al [18] and Hinze et al [19] observed a significant decrease in the mean number of alleles per locus and expected heterozygosity in the BSSS and BSCB1 populations after 12 and 15 cycles of reciprocal RS, respectively. A decrease in marker diversity (in terms of the number of polymorphic loci, mean number of alleles per locus, expected heterozygosity, or observed heterozygosity) within maize populations that underwent various numbers of RS cycles has also been reported in several previous studies [7,14,[20][21][22][42][43][44][45][46][47].…”

Genome-wide association analysis of plant architecture traits using doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic maize population

“…Additionally, inbreeding from landraces results in a high load of recessive alleles, mutations, and deleterious alleles that need to be selected against by conventional breeding methods ( Strigens et al., 2013 ). According to Ledesma et al. (2023) , the 17 cycles of reciprocal recurrent selection program have left behind useful genetic variation present in the C0_DHL during the selection process.…”

“…Thus, selected DH lines could be introgressed into current germplasm to improve the adaptation to high plant density. The large genetic distances of the C0_DHL compared to the C17_DHL ( Ledesma et al., 2023 ) demonstrated the potential of the C0_DHL group to broaden the genetic base of the Stiff Stalk (SS) germplasm. However, more studies need to be conducted at the testcross level to know the hybrid combinations’ performance.…”

“…Also, the C0/C17_DH lines group was scattered over a broader range, similar to the C0_DHL group. PCA results and molecular characterization of the DH lines within and among the cycles of selection are presented in Ledesma et al. (2023) .…”

“…Also, the C0/C17_DH lines group was scattered over a broader range, similar to the C0_DHL group. PCA results and molecular characterization of the DH lines within and among the cycles of selection are presented in Ledesma et al (2023). The incorporation of population structure through PCA as a covariate in the fixed effect model increases the power to detect associations, and it has the advantage of eliminating false positives due to non-genetic effects associated with the population structure.…”