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This study aimed to map quantitative trait loci （QTL） for resistance to southern corn rust using a highly resistant maize inbred line，providing basis for elucidating molecular marker-assisted breeding and genetic regulation mechanisms of disease resistance of maize.
The F2 population derived from a cross between the highly resistant inbred line S311 and the highly susceptible inbred line HY813，comprising 186 individuals，were genotyped using a 10K SNP chip to construct a high-density genetic linkage map. By integrating the genetic linkage map with phenotypic data，the composite interval mapping （CIM） and genome-wide composite interval mapping （GCIM） were employed to determine the positions and effects of QTLs.
The resistance to southern corn rust in the F2 population tended to resemble that of the paternal parent S311. The disease severity was rated from 1 to 9，with skewness and kurtosis both between -1.00 and 1.00，which was consistent with the distribution characteristics of quantitative traits. A total of 3103 single nucleotide polymorphism （SNP） markers were used to construct a genetic linkage map whose total length was 3607.39 cM，and average genetic distance between markers was 1.16 cM. A total of 4 QTLs were detected using CIM，located on chromosomes 1 and 3，among which the QTL loci qSCR3-1 and qSCR3-2 on chromosome 3 had higher （logarithm of odds LOD） values，explaining 25.6% and 10.0% of phenotypic variation respectively. A total of two QTL loci，namely qSCR3-1 and qSCR3-2 on chromosome 3，were detected using GCIM，explaining 64.4% and 16.5% of phenotypic variation respectively. A total of four candidate genes associated with disease resistance，namely Zm00001d042214，Zm00001d041994，Zm00001d042013，and Zm00001d042051，were identified within the QTL loci commonly detected by both methods. After pathogen inoculation，the relative expression of Zm00001d042214，Zm00001d041994，Zm00001d042013，and Zm00001d042051 in leaves of S311 was all extremely significantly increased compared with those before inoculation （CK） （P<0.0001）. In HY813 after pathogen inoculation，however，the relative expression of Zm00001d042214 showed no significant change （P>0.05），while Zm00001d042013 was extremely significantly up-regulated compared with CK （P<0.01），and both Zm00001d041994 and Zm00001d042051 were extremely significantly up-regulated compared with CK （P<0.0001）.
In the inbred line S311，two major QTL loci （qSCR3-1 and qSCR3-2） for resistance to southern corn rust are mapped，and four candidate genes related to resistance to southern corn rust are screened within the QTL intervals，namely Zm00001d042214，Zm00001d041994，Zm00001d042013，and Zm00001d042051.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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