Abstract
Homologous recombination (HR), the most significant event in meiosis, has important implications for genetic diversity and evolution in organisms. Heteroduplex DNA (hDNA), the product of HR, can be captured by artificially induced chromosome doubling during the development of the embryo sac to inhibit postmeiotic segregation, subsequently, and hDNAs are directly detected using codominant simple sequence repeat (SSR) markers. In the present study, two hybrid triploid populations derived from doubling the chromosomes of the embryo sac induced by high temperature in Populus tomentosa served as starting materials. Eighty-seven, 62, and 79 SSR markers on chromosomes 01, 04, and 19, respectively, that were heterozygous in the maternal parent and different from the paternal parent were screened to detect and characterize the hDNA in P. tomentosa. The results showed that the hDNA frequency patterns on chromosomes changed slightly when the number of SSR primers increased. The highest hDNA frequency occurred at the adjacent terminal on chromosomes, which was slightly higher than those at the terminals in the two genotypic individuals, and the hDNA frequency gradually decreased as the locus-centromere distance decreased. With the increase in the number of SSR markers employed for detection, the number of recombination events (REs) detected significantly increased. In regions with high methylation or long terminal repeat (LTR) retrotransposon enrichment, the frequency of hDNA was low, and high frequencies were observed in regions with low sequence complexity and high gene density. High-frequency recombination occurring at high gene density regions strongly affected the association between molecular markers and quantitative trait loci (QTLs), which was an important factor contributing to the difficulty encountered by MAS in achieving the expected breeding results.
Highlights
The basic principle of molecular marker-assisted selection (MAS) is to use molecular markers closely linked to target genes to screen the selected population to realize the direct selection of genotypes during the juvenile phase and improve breeding efficiency (Collard et al, 2005; Ben-Ari and Lavi, 2012)
The correlation results between the Heteroduplex DNA (hDNA) frequency and the locus-centromere distance were significantly positive under the five marker combinations (P < 0.05), indicating that the hDNA frequency increased as the locus-centromere distance increased (Figure 1)
The correlation results between the hDNA frequency and the locus-centromere distance (Figure 5) were significantly positive on chromosome 01 (Chr01) and 04 (P < 0.05), indicating that the hDNA frequency increased as the locus-centromere distance increased (Figure 5)
Summary
The basic principle of molecular marker-assisted selection (MAS) is to use molecular markers closely linked to target genes to screen the selected population to realize the direct selection of genotypes during the juvenile phase and improve breeding efficiency (Collard et al, 2005; Ben-Ari and Lavi, 2012). For the selection of qualitative traits (inherited traits with Mendelian or near-Mendelian inheritance), examples of MAS have been reported for berry color, seedlessness, and flower sex in grape and disease resistance in apples and grapes (Myles, 2013), as well as major quantitative trait loci (QTL) selections, such as fruit acidity (Boudehri et al, 2009), fruit size (De Franceschi et al, 2013), rice yield (Spindel et al, 2013), and rice drought tolerance (Dixit et al, 2017) The occurrence of HR has a direct impact on short-term selection efficiency (McClosky and Tanksley, 2013)
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