Comparative QTL analysis in peach ‘Earlygold’ F2 and backcross progenies

Construction of a collection of introgression lines of “Texas” almond DNA fragments in the “Earlygold” peach genetic background

“…Segregation in the “Earlygold” background was also studied with the SNP chip. Results ( Figures 4 and 5 ) show that there were large regions without segregating markers, covering approximately half of the genome (50.5%) as previously observed [ 19 , 23 ]. The rest of the genome of each IL segregated in large blocks for the two alleles of “Earlygold”.…”

“…[ 24 ]), was studied in the spring/summer of 2021. This trait has sometimes been scored as qualitative and sometimes as quantitative, depending on the alleles present [ 20 , 23 , 24 ]. In the case of the T × E, T1E and E × E populations ( Supplementary Table 6 ) there are three alleles, one inherited from “Texas” to the MB1.37 hybrid ( T ), and the other two ( E1 and E2 ) from Earlygold, where the T allele produces the latest maturity date, while it is intermediate with E1 and early with E2 , with gene action predominantly additive.…”

“…A third reason is that we expected that the variability detected by the almond genome would often be of a sufficiently different nature and genome position compared to that of peach, as shown in previous results based on the analysis of “Texas” × “Earlygold” progenies [ 19 , 20 ], making interferences between almond/peach vs. peach/peach easily detectable and interpretable. Additionally, “Earlygold” is heterozygous in less than half of its genome [ 20 , 23 ], because of the existence of large DNA fragments identical by descent, as in many other modern peach varieties [ 27 ], due to the recent history of co-ancestry of modern peach breeding programs [ 28 ], so we were only expecting a relatively narrow window of segregation to occur in its offspring. The inheritance analysis of a large set of characters of the F2 of “Earlygold” is available [ 23 ], and relevant for this work as it identified a limited number of QTLs.…”

“…Additionally, “Earlygold” is heterozygous in less than half of its genome [ 20 , 23 ], because of the existence of large DNA fragments identical by descent, as in many other modern peach varieties [ 27 ], due to the recent history of co-ancestry of modern peach breeding programs [ 28 ], so we were only expecting a relatively narrow window of segregation to occur in its offspring. The inheritance analysis of a large set of characters of the F2 of “Earlygold” is available [ 23 ], and relevant for this work as it identified a limited number of QTLs. Only one of these, a major QTL located on G4 in the region of MD that, in addition to maturity date, partially affects other fruit characters such as fruit weight, soluble solid contents and leaf color at senescence, appears to be of concern when studying fruit or color-related traits.…”

“…Other lines having this fragment in homozygosity, along with additional introgressed fragments, were too young to produce fruit. The case of one IL (PAILE4-0226a) with an intermediate maturity date phenotype while it was expected to mature late as it had the almond introgression, can be explained by the interaction of the almond allele with an allele of “Earlygold” that confers early maturity [ 20 , 23 ], as opposed to other ILs that had the late allele of “Earlygold”. This would be a clear case of segregation in the “Earlygold” background that would result in an unexpected phenotype in an IL.…”