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Euphytica

, 214:120 | Cite as

Fine mapping of major QTLs for alkaline tolerance at the seedling stage in maize (Zea mays L.) through genetic linkage analysis combined with high-throughput DNA sequencing

  • Chunxiao Zhang
  • Fengxue Jin
  • Shufang Li
  • Wenping Liu
  • Xiaojun Ma
  • Shan Yang
  • Deguang Yang
  • Xiaohui Li
Review
  • 136 Downloads

Abstract

Exploiting genes and quantitative trait loci (QTLs) related to maize (Zea mays L.) alkaline tolerance is helpful for improving alkaline resistance. To explore the inheritance of maize alkaline tolerance at the seedling stage, a mapping population comprising 151 F2:3 lines derived from the maize cross between Zheng58, tolerant to alkaline, and Chang7-2, sensitive to alkaline, was used to establish a genetic linkage map with 200 SSR loci across the 10 maize linkage groups, with an average interval of 6.5 cM between adjacent markers. QTLs for alkaline resistant traits of alkaline tolerance rating (ATR), germination rate (GR), relative conductivity (RC), weight per plant (WPP) and proline content (PC) were detected. The obtained results were as follows: Five QTLs on chromosomes 2, 5 and 6 (GR and WPP: chr. 2; PC and ATR: chr. 5; and RC: chr. 6) were mapped. For precise mapping of the QTLs related to alkaline resistance, two bulked deoxyribonucleic acid (DNA) pools were constructed using individual DNAs from the most tolerant 30 F2 individuals and the most sensitive 30 F2 individuals according to the ATR and used to establish a high density map of SLAF markers strongly associated with the ATR by specific locus amplified fragment sequencing (SLAF-Seq) combined with super bulked segregant analysis (superBSA). One marker-intensive region involved three SLAFs at 296,000–6,203,000 bp on chromosome 5 that were closely related to the ATR. Combined with preliminary QTL mapping with superBSA, two major QTLs on chromosome 5 associated with alkaline tolerance at the maize seedling stage were mapped to marker intervals of dCap-SLAF31521 and dCap-SLAF31535 and phi024 and dCap-SLAF31521, respectively. These QTL regions involved 9 and 75 annotated genes, respectively. These results will be helpful for improving maize alkaline tolerance at the seedling stage by marker-assisted selection programs and will be useful for fine mapping QTLs for maize breeding.

Keywords

Maize (Zea mays L.) Alkaline tolerance Super bulked segregant analysis (superBSA) Specific locus amplified fragment sequencing (SLAF-Seq) 

Notes

Compliance of ethical standards

Funding

The research was supported by the Agricultural Science and Technology Innovation Program of Jilin Province “Discovery of excellent germplasms and cultivation of inbred lines suitable for mechanized harvesting in maize” and the Program for Chinese Outstanding Talents in Agricultural Scientific Research, 2016.

Supplementary material

10681_2018_2190_MOESM1_ESM.xlsx (181 kb)
Supplementary Table 1 The genetic linkage map constructed using SSR markers in this study (XLSX 180 kb)
10681_2018_2190_MOESM2_ESM.xlsx (10 kb)
Supplementary Table 2 Sequencing data for each sample (XLSX 9 kb)
10681_2018_2190_MOESM3_ESM.xlsx (11 kb)
Supplementary Table 3 Number distribution of SLAF tag, marker, and Diff_marker on each chromosome (XLSX 10 kb)
10681_2018_2190_MOESM4_ESM.xlsx (10 kb)
Supplementary Table 4 dCAPs markers used for the construction of a genetic linkage map (XLSX 10 kb)
10681_2018_2190_MOESM5_ESM.xlsx (20 kb)
Supplementary Table 5 Reported salt-alkali tolerance QTL in the study (XLSX 19 kb)

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Chunxiao Zhang
    • 1
  • Fengxue Jin
    • 1
  • Shufang Li
    • 1
  • Wenping Liu
    • 1
  • Xiaojun Ma
    • 2
  • Shan Yang
    • 2
  • Deguang Yang
    • 2
  • Xiaohui Li
    • 1
  1. 1.Crop Germplasm Resources Institute, Jilin Academy of Agricultural SciencesGongzhulingChina
  2. 2.College of Agronomy Northeast Agricultural UniversityHarbinChina

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