Rearrangement with the nkd2 promoter contributed to allelic diversity of the r1 gene in maize (Zea mays)

SUMMARY The maize red1 (r1) locus regulates anthocyanin accumulation and is a classic model for allelic diversity; changes in regulatory regions are responsible for most of the variation in gene expression patterns. Here, an intrachromosomal rearrangement between the distal upstream region of r1 and the region of naked endosperm 2 (nkd2) upstream to the third exon generated a nkd2 null allele lacking the first three exons, and the R1‐st (stippled) allele with a novel r1 5′ promoter region homologous to 5′ regions from nkd2‐B73. R1‐sc:124 (an R1‐st derivative) shows increased and earlier expression than a standard R1‐g allele, as well as ectopic expression in the starchy endosperm compartment. Laser capture microdissection and RNA sequencing indicated that ectopic R1‐sc:124 expression impacted expression of genes associated with RNA modification. The expression of R1‐sc:124 resembled nkd2‐W22 expression, suggesting that nkd2 regulatory sequences may influence the expression of R1‐sc:124. The r1‐sc:m3 allele is derived from R1‐sc:124 by an insertion of a Ds6 transposon in intron 4. This insertion blocks anthocyanin regulation by causing mis‐splicing that eliminates exon 5 from the mRNA. This allele serves as an important launch site for Ac/Ds mutagenesis studies, and two Ds6 insertions believed to be associated with nkd2 mutant alleles were actually located in the r1 5′ region. Among annotated genomes of teosinte and maize varieties, the nkd2 and r1 loci showed conserved overall gene structures, similar to the B73 reference genome, suggesting that the nkd2‐r1 rearrangement may be a recent event. Significance Statement The iconic maize R1 gene encodes a HLH transcription factor that conditions anthocyanin pigmentation in aleurone, and has been instrumental in studies of gene expression and transposons. The R1‐sc124 allele is foundational to important genome mutagenesis projects and was created by an intrachromosomal rearrangement that brought regulatory sequences from the nkd2 gene, 1 Mb away, to produce elevated and ectopic R1 expression, resulting in ectopic downstream gene regulation in starchy endosperm tissue.