Scientia Agricultura Sinica ›› 2019, Vol. 52 ›› Issue (12): 2033-2041.doi: 10.3864/j.issn.0578-1752.2019.12.002

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

QTL Mapping and Genetic Analysis of a Gene with High Resistance to Southern Corn Rust

WANG BingWei,QIN JiaMing(),SHI ChengQiao,ZHENG JiaXing,QIN YongAi,HUANG AnXia   

  1. Maize Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007
  • Received:2019-02-03 Accepted:2019-04-21 Online:2019-06-16 Published:2019-06-22
  • Contact: JiaMing QIN E-mail:savage131@163.com

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Abstract:

【Objective】This study aimed at constructing regional genetic map and positioning the resistant gene to Southern Corn Rust by using one of the 8 F2 populations, deriving from crosses of the highly resistant tropical maize line S313 with 4 highly susceptible inbred lines to Southern Corn Rust, in 3 seasons of two years. In addition, a major QTL for Southern Corn Rust resistance was fine-mapped by applying new-developed molecular markers to a larger mapping population.【Method】Total 8 F2 populations were planted in 3 consecutive seasons of 2016 and 2017, all of which received triple inoculation. Individual F2 plants grown in the field were scored for resistance to southern rust using a nine-point relative scale at late growth stage. Finally, the segregation ratio of resistant to susceptible plants for each F2 population was investigated by phenotypic identification. A 56K-SNP chip was used for screening polymorphisms between the two parents, among which 192 SNP markers were picked for genotyping the 30 high resistant and 30 susceptible plants in an F2 population of S313×PHW52. Nineteen newly developed SNP markers on the short arm of chromosome 10 were used for genotyping the whole F2 population and constructing a regional genetic map. The resistant QTL mapping was proceeded by the combination of genetic map and phenotypic identification. The genotyping to second population with 10 newly developed SNP markers within the initial mapping region was performed, and the interval was delimited according to the number of exchanged plants. According to the information of maize B73 genome, all genes in corresponding interval were listed. By the gene functional annotation information, the candidate genes were determined.【Result】 By Chi-square test, the ratio of resistant plants to susceptible plants in these 8 F2 populations was all statistically a 3:1 ratio, which indicated that the resistance to Southern Corn Rust of S313 was controlled by a main effect QTL. A total of 16426 polymorphic markers between the two parents were screened out from the 56K-SNP chip. A resistance-linked marker Affx-90241059 was identified by the linkage analysis of 30 resistant and 30 susceptible plants with 192 markers of uniform distribution across chromosomes. A regional genetic map with total distance of 31.8cM and average distance 1.77 cM was constructed by using 19 SNPs. By the composite interval mapping method, the main effect QTL was located within the interval between marker Affx-91298359 and marker Affx-91182449, which size was 2M approximately. Furtherly, the interval was delimited to the size of 474K by using a larger F2 population and 10 SNP markers. There are 63 genes in the 474k interval of B73 reference genome, among which, gene LOC103640657, LOC100191493 and LOC103640673 encode plant disease resistance-related proteins. Thus, these three genes were listed as candidate genes resistant to Southern Corn Rust of tropical maize inbred line S313. 【Conclusion】 By field phenotypic identification, the ratio of resistant plants to susceptible plants in all F2 populations was determined as 3:1, which indicated that the resistance to Southern Corn Rust of S313 was under controlled by a main effect QTL. By the methods of population construction and molecular marker, the main effect QTL of S313 was located in the interval of about 0.47M size on the short arm of maize chromosome 10. There are 3 candidate genes related to Southern Corn Rust in this region.

Key words: maize, southern corn rust, disease resistance, QTL mapping

Table 1

The statistical table of the segregation ratios of resistant and susceptible plants in F2 population of S313 and Qi319× susceptible parents"

年份
Year		 群体
Population		 总株数
Total plants		 抗病株数
Resistant plants		 感病株数
Susceptible plants		 卡方值
χ2 value		 χ2测验
Chi-square test		 实际抗﹕感值
Actual R﹕S value
2016秋 2016 Autumn S313×ZD415 356 271 85 0.18 3﹕1 3.19
2016秋 2016 Autumn ZD415×S313 284 209 75 0.23 3﹕1 2.79
2016秋 2016 Autumn S313×PHW52 313 232 81 0.09 3﹕1 2.86
2016秋 2016 Autumn PHW52×S313 260 189 71 0.62 3﹕1 2.66
2016秋 2016 Autumn S313×368M 277 217 60 1.47 3﹕1 3.62
2016秋 2016 Autumn 368M×S313 300 222 78 0.11 3﹕1 2.85
2016秋 2016 Autumn S313×TS647 288 214 74 0.04 3﹕1 2.89
2016秋 2016 Autumn TS647×S313 385 285 100 0.15 3﹕1 2.85
2016秋 2016 Autumn TS647×齐319 314 103 211 295.95 非3﹕1 Non 3﹕1 0.49
2016秋 2016 Autumn S313×齐319 266 244 22 38.82 非3﹕1 Non 3﹕1 11.09
2017春 2017 Spring S313×TS647 747 539 208 3.07 3﹕1 2.59
2017春 2017 Spring S313×PHW52 275 201 74 0.44 3﹕1 2.72
2017春 2017 Spring S313×ZD415 631 457 174 2.10 3﹕1 2.63
2017秋 2017 Spring S313×PHW52 6705 4984 1721 1.56 3﹕1 2.90
2017秋 2017 Spring S313×TS647 4206 3182 1024 0.92 3﹕1 3.11

Table 2

The field statistical table of the segregation ratios of resistant and susceptible plants in 100 F2:3 families"

F2病级
F2 disease grade		 家系数
Family number		 F2:3抗病鉴定
F2:3 resistant identification
1 20 6个家系全表现1—3级抗病,14个家系抗感分离
6 families exhibiting resistant of 1-3 grade,14 families exhibiting separation of resistance and susceptible
3 20 4个家系全表现1—3级抗病,16个家系抗感分离
4 families exhibiting resistant of 1-3 grade,16 families exhibiting separation of resistance and susceptible
5 20 全感5—9级 All exhibiting susceptible of 5-9 grade
7 20 全感7—9级 All exhibiting susceptible of 7-9 grade
9 20 全感7—9级 All exhibiting susceptible of 7-9 grade

Fig. 1

The partial genetic linkage map of a F2 population with 182 plants"

Fig. 2

The positioning map of a major QTL of Southern Corn Rust"

Fig. 3

The physical position of 10 SNP markers and corresponding number of exchanged plants"

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