Genetic Dissection Of Specific Genomic Regions For Maize Foundation Parents Ye478 And 08-641

Maize with the biggest planted area and the highest total yield plays a crucial role in China.Stress tolerance,the utilization of heterosis,and genetic improvement had key impacts on the improvement of maize varieties during the breeding process.“Local inbreds×Imported inbreds”is one of the preferred heterotic patterns in southwest China as one of the main maize production zones with low planting densities,and several elite founders are frequently used,such as 08-641,18-599,and S37.Therefore,elucidating the genetics of high-density tolerance and mid-parent heterosis for the agronomic traits,as well as focusing on genetic improvement of the most important founders will allow us to have a better understanding of genetic architecture of those traits for maize breeding.Here,we measured 31 plant architecture and yield-related traits in a mapping population that consisted of 301 recombinant inbred lines（RILs）released by single seed descendance from the cross between 08-641 and Ye478.The RILs were evaluated under low and high planting density across four environments.An immortalized F₂（IF₂）with 298 F₁ hybrids that was built from the RIL population,along with the RILs and the parental lines were planted at the low density across three environments.Similarly,30 agronomic traits were measured in the inbred and hybrid mapping populations at adjacent blocks with a randomized complete block design with two replications.Stable QTLs were obtained from the RIL and IF₂ populations.Then,we observed the transmission of these QTLs from foundation parents to 64 RILs,19 08-641 descendants,and 5 Ye478 related lines.These lines as males were crossed with 5 testers according to the North Carolina Design II in2015.Then,three testcross populations consisted of 435 F₁ hybrids along with their parental lines were evaluated in adjacent and separate blocks at two locations.Similar field management and phenotyping were performed for all the inbreds and hybrids.Finally,we analyzed the significance level of the presence of these QTLs on general combining ability（GCA）of those derivatives and discussed the formation and genetic improvement of Ye478 and 08-641.A BC₄F₂ population was produced by backcrossing the residual heterozygous line RIL111 to Ye478 four times and self-pollinating once,to validate the environmentally stable QTL q TL2-3 for tassel length within specific genomic region 2.07.The main results were listed as follows:1.A total of 683 SNPs selected for their uniform distribution throughout the 10 maize chromosomes were used to construct the linkage map with a total genetic length of 1786.1 c M.Joint analysis across all environments found 92 QTLs were simultaneously detected across both low-and high-densities,while 70 QTLs were specific for high planting density,revealing different genetic regulation of agronomic traits under low and high densities.Approximately70%QTLs with phenotypic contribution≤5%indicate that these agronomic traits were greatly affected by many alleles with small phenotypic effects.Besides,the analyses of epistatic interactions（EPI）and the interaction between QTL and environments（QEI）found 50 pairs of loci exhibiting significant EPI and 16 loci showing significant QEI under low planting density.A total of 16 pairs of loci showed significant EPI and 22 loci significantly interacted with environments under high planting density.These loci exhibiting EPI and QEI with minor effects were of less importance in phenotypic variation than those single-locus QTLs that were greatly influenced by environments and densities.The current work also addressed the pleiotropic effects of loci for the correlated traits.Though plant height-related traits,leaf widths,and leaf angles at different positions could be partially affected by several common QTLs,there are still different genetic mechanisms of those sharing regions response to plant density.2.Similar patterns of correlations among agronomic traits were observed in the RIL and IF₂ populations.Significant genetic variances and moderate-to-high heritability for the main agronomic traits indicate these traits were greatly affected by genotype.QTL mapping via joint analysis across all environments identified 525 QTLs for 30 agronomic traits and mid-parent heterosis（MPH）for those traits.A large proportion of alleles showed minor effects.Besides,85 QTLs were found in at least two of the datasets（RIL,IF₂,and MPH dataset）.These results reveal that QTL detection was affected by different genetic mapping populations.The analyses of the ratio of dominance to additive effects via genome-wide markers,single-marker analysis,and QTL mapping indicate that over half of the loci exhibited overdominance for kernel weight per ear（KWPE）,EWPE,and kernel number per row（KNPR）,while the loci for the remaining traits mainly showed a quite low degree of the ratio of dominance to additive effects.The total phenotypic variation explained by the single-locus QTLs and EPI togetherly approached up to90%,thus indicating the genetic mechanisms of agronomic traits and mid-parent heterosis for these traits could be explained by the cumulative effects of the genetic effects mentioned above.Overdominance is more important than other genetic effects for the heterosis for EWPE,KWPE,and KNPR.We also found that QTL pleiotropy may be involved in regulating the genetic basis of heterosis for those traits.Among them,specific chromosomal regions 3.07-3.09 and 10.04-10.07 associated with different agronomic traits and the heterosis for those traits were repeatedly reported in former studies.3.The current study found 153 stable QTLs in the inbred and hybrid mapping populations.The QTL information combining with GCA analyses in three testcross populations indicate that 75 out of these QTLs had significant effects on the GCA effects for their corresponding traits,revealing different genetic mechanisms underlying these traits per se,hybrids performance,and GCA effects.Considering those 75 QTLs with≥40%of elite founders’relatives transmitted from foundation parents,twelve genomic regions were identified.Bins2.07-2.08 and 5.04-5.05 being particularly interesting are mainly responsible for genetic improvement of plant architecture for Ye478 and repeatedly presented in former studies.Also,different rate of QTL transmission and similar agronomic traits across both foundation parents and their corresponding derivatives emphasized large discrepancies in genetic improvement of elite inbreds Ye478 and 08-641,and the accumulation of new favorable alleles from other donors and the fixed alleles across generations play a crucial role in the process of genetic improvement for both elite founders and maintenance of high-density tolerance and heterosis between Ye478 and 08-641-derived inbreds.Additionally,moderate-to-high heritability in those populations along with a predominant GCA over SCA effects for most traits implied that GCA information could be greatly useful to predict the performance for most traits in the inbred and hybrid populations.The present work sheds new light on understanding the genetic basis of heterosis underlying different heterotic patterns,genetic improvement of foundation parents,and breeding of new elite lines.