Genetic architecture of embryogenic callus induction in maize from the perspective of population genomics

• Published in: Plant cell, tissue and organ culture Vol. 150; no. 2; pp. 345 - 359
• Main Authors: Dai, Liqiang, Han, Siping, Zhang, Yan, Hao, Dongyun
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-08-2022; Springer Nature B.V
• Subjects: Alleles; Biomedical and Life Sciences; Biotechnology; Callus; Cell culture; Corn; Embryos; Genes; Genome-wide association studies; Genomes; Genomics; Heritability; Inbreeding; Life Sciences; Linkage disequilibrium; Mutation; Nucleotides; Original Article; Plant breeding; Plant Genetics and Genomics; Plant Pathology; Plant Physiology; Plant Sciences; Population; Population genetics; Population studies; Single-nucleotide polymorphism; Zea mays; Genome-wide association study (GWAS); Allelic variation; Maize inbred lines; Candidate genes; Embryogenic callus
• ISSN: 0167-6857; 1573-5044
• DOI: 10.1007/s11240-022-02284-7

Embryogenic callus induction (ECI) is an initial step in plant cell totipotency that is essential for somatic cell regeneration. Identifying genes associated with embryogenic callus (EC) formation is critical to understand the molecular mechanism of totipotency and crop biotechnology breeding. In this study, we used a population of 177 maize (
Zea mays
L.) inbred lines as an association panel to investigate the percentage of embryogenic callus induction (%ECI) from their immature embryos in two independent seasons. Whole-genome resequencing of this population produced 3,786,431 high-quality single nucleotide polymorphisms (SNPs), after which a genome-wide association study (GWAS) was performed for the ECI trait. The results showed that %ECIs varied greatly from 0.00 to 98.15% among the tested inbred lines, with a broad-sense heritability of 0.71. Using the FarmCPU method, we detected 104 candidate genes within the linkage disequilibrium (LD) blocks of 57 significant SNPs (
P
 < 0.000001). Among these genes,
ZmCLE4B
and
Ereb83
harbored significant sense mutations, and inbred lines with different alleles of these genes showed significant differences in ECI (
P
 < 0.00001). Expression analyses of these two genes in five EC-induction stages in two ECI-contradictory inbred lines revealed that different alleles of the genes behave divergently in response to callus induction culture. Additionally, using an intermate population, we noted that
ZmCLE4B
plants with different homozygous alleles were phenotypically different (
P
 < 0.01). Taken together, the current results suggest that
ZmCLE4B
is likely a major factor in ECI.
Key message
A total of 104 candidate genes for embryogenic callus induction (ECI) were identified, and molecular evidence showed that the
ZmCLE4B
gene is likely a major factor in ECI.