The Ga1 locus of the genus Zea is associated with novel genome structures derived from multiple, independent nonhomologous recombination events

Abstract

The Ga1 locus controls cross-incompatibility between field corn and popcorn. The Ga1-S haplotype contains 2 types of pectin methylesterase (PME) genes, ZmPme3 and several copies of ZmGa1P that are expressed in silk and pollen, respectively. The ga1 haplotype contains nonfunctional tandem repeat sequences related to ZmPme3 and ZmGa1P. This haplotype can cross-pollinate freely and is widely present in field corn. The primary objective of this study is to characterize the repeat sequences from a diverse collection of maize and teosinte lines and use this information to understand the evolution of the Ga1 locus. First, we characterized the complexity of the Ga1 genome region in high-quality maize genome assemblies that led to their categorization into 5 groups based on the number and type of PME-like sequences found at this region. Second, we studied duplication events that led to the ga1 and Ga1-S repeats using maximum likelihood phylogenetic reconstruction. Divergence estimates of the ga1 haplotype suggest that the duplication events occurred more than 600 KYA whereas those in Ga1-S occurred at 3 time points, i.e. >600, ∼260, and ∼100 KYA. These estimates suggest that the ga1 and Ga1-S tandem duplication events occurred independently. Finally, analysis of ZmPme3 and ZmGa1P homologs in Zea and Tripsacum genomes suggests that ga1 and Ga1-S repeats originated from an ancestral pair of PME genes that duplicated and diverged through 2 evolutionary branches prior to the domestication of maize.

Keywords: Plant Genetics and Genomics; evolution; pectin methylesterase; pseudogenes; repeated sequences.

Fig. 1.

Position of Ga1 PME genes, and PME pseudogene and gene fragments in 5 representative inbred lines. The haplotype of the Ga1 locus is shown in parentheses below the name of each line. Genome positions are adjusted to align with the first base of the cluster in each genotype for ease of comparison. Group letters on the secondary axis are from Table 1.

Fig. 2.

Analysis of ZmPme3-like sequences of the ga1 haplotype. a) Phylogenetic analysis of ZmPme3-like sequences in B73. The tree has been rooted using Tripsacum ZmPme3 homologs. Sequences are numbered according to their relative positions in the genome. Sequences B73-Pme3-S(1,4,6,8,11//12,14,17//18,20//21,24,26,33,34,36,42,48//49,52) are part of the repeat motif ZmPme3-N-ZmGa1P and are shown in colored text. The symbol (//) indicates sequences with transposon insertions. Tcb1-f is a PME gene similar in sequence to ZmPme3 but at the Tcb1 locus. b) Stop codons in sequences of the ZmPme3 phylogeny. The tree topology shows 2 groups of sequences. In group I, stop codons 774 and 549 are shared by the majority of its members. Group II sequences have more unshared stop codons. c) Genome positions of ZmPme3 pseudogene sequences in B73 (colored by group).

Fig. 3.

Analysis of ZmGa1P-gene and pseudogene sequences in Hp301. a) Phylogenetic tree for ZmGa1P homologs in Hp301. Sequences Hp301-Ga1P-S(10,11,14,15,16,18,21,23) do not contain any disablements and are shown in colored text. The tree has been rooted using Tripsacum homologs of ZmGa1P. The tree shows 2 groups of sequences that duplicated at 2 different time points. b) Stop codons in the duplicated sequences. c) Genomic positions of ZmGa1P repeat sequence array in Hp301 (colored by group).

Fig. 4.

ZmPme3 and ZmGa1P genes and pseudogene arrays on chromosome 4 in the Zea genus. Partial chromosomes (0–70 Mb) are shown for all Zea genomes except Zea luxurians. For Zea luxurians, the genomic region between 290 and 360 Mb has been shown. The figure has been generated using CVit (Cannon and Cannon 2011). Zl, Z. luxurians; Zn, Zea nicaraguensis; Zd, Z. diploperennis; Zh, Z. mays huehuetenangensis; Zx, Z. mays mexicana; Zv, Z. mays parviglumis; Zm, Z. mays mays.

Fig. 5.

Phylogenetic tree of ZmPme3 BLAST hits in all Zea genomes with Tripsacum homologs as outgroup. Highlighted sequences are full length.

Fig. 6.

Relative genomic positions of pseudogenes in B73 (field corn) and TIL11 and Momo accessions (teosintes).

Fig. 7.

ZmPme3 and ZmGa1P from BLAST search results in 4 grass species and maize (Supplementary Table 6). Accessions XM_002454758.2, XM_015761261.2 and XM_006663606.3 in sorghum and rice chromosomes have sequence similarity to both ZmGa1P and QRT1 and were more like QRT1. The dashed segment of maize chromosome 4 is syntenic with rice chromosome 11. Overall length of chromosomes is not represented; instead, the regions between 0 and 80 Mb are depicted.

Fig. 8.

Model of Ga1 evolution leading to ga1 and Ga1-S haplotypes.