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Related Experiment Video

Updated: Mar 29, 2026

Scalable Transfection of Maize Mesophyll Protoplasts
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QTL-Seq Identifies Extra QTLs and Candidate Genes Controlling High Haploid Induction Rate in Maize.

Kanogporn Khammona1, Abil Dermail2, Yu-Ru Chen3

  • 1Rice Science Center, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand.

Plants (Basel, Switzerland)
|March 28, 2026
PubMed
Summary

New maize loci were identified to improve haploid induction rate (HIR) stability. These findings offer valuable markers for enhancing haploid inducer breeding programs, boosting efficiency in developing inbred lines.

Keywords:
QTL-seq analysisdoubled haploid techniquehaploid induction ratemaize haploid inducersmaternal haploid induction

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Area of Science:

  • Plant Breeding
  • Genetics
  • Genomics

Background:

  • Double-haploid (DH) technology accelerates maize inbred line development.
  • Existing loci (qhir1, qhir8) improve haploid induction rate (HIR), but HIR stability remains a challenge.
  • Novel genetic loci are needed to enhance HIR consistency in breeding programs.

Purpose of the Study:

  • Identify novel quantitative trait loci (QTLs) associated with haploid induction rate (HIR) in maize.
  • Characterize genetic variations influencing HIR stability.
  • Develop molecular markers for marker-assisted selection (MAS) to improve maize breeding.

Main Methods:

  • QTL-seq analysis was performed on 337 S2 haploid inducers derived from a K8 x BHI306 cross.
  • DNA from extreme high-HIR and low-HIR bulks was sequenced to identify candidate intervals.
  • High-confidence SNPs/InDels and missense mutations in candidate genes were analyzed for association with HIR.

Main Results:

  • Candidate QTLs (qHI2, qHI3, qHI6, qHI8) were identified on chromosomes 2, 3, 6, and 8.
  • Fifteen missense mutation SNPs were identified in three genes (GRMZM2G359746, AC198725.4, GRMZM2G091276) associated with HIR.
  • SNPs in GRMZM2G359746 (qHI2) and GRMZM2G091276 (qHI8) showed strong associations (R2 range 0.27-0.72).
  • Lines with favorable alleles at novel loci and existing qhir1/qhir8 showed significantly higher HIR (12.77%) compared to those with unfavorable alleles (6.66%).

Conclusions:

  • Novel QTLs, particularly qHI2 and qHI8, significantly contribute to HIR stability in maize.
  • Identified SNPs provide valuable molecular markers for marker-assisted selection in haploid inducer breeding.
  • These findings enhance the efficiency and stability of DH technology application in maize breeding programs.