Molecular dissection and functional characterization of the liguleless1 gene for manipulation of leaf angle in maize

Recessive liguleless1 (lg1) gene significantly reduces leaf angle in maize and has become the choice in breeding for high plant density. Here, we sequenced the entire lg1 gene (5560 bp) among seven wild-type (Lg1) and one mutant (lg1) inbreds. The analysis revealed a total of 229 SNPs and 155 InDels within the Lg1 gene. The study also revealed the existence of three exons, with lg1-mutant having two exons. The lg1-mutant harboured an insertion of 130 bp Tourist MITE transposable element in exon-2 at 1663^rd base, which deleted 157 amino acids of C-terminal region of the mutant LG1 protein. The mutant LG1 protein was 247 amino acids in length, in contrast to 399-404 amino acids in wild-type protein. The analysis with 26 paralogues and 66 orthologues of Lg1 revealed conservation of the squamosa promoter-binding (SBP) domain. A PCR-based co-dominant InDel marker (MGU-lg1-Tourist) specific to insertion of 130 bp was developed that differentiated the mutant allele (lg1) from the wild-type allele (Lg1). The marker was validated in two F₂ populations, which showed a 1:2:1 ratio. F₂ plants showed a 3 (wide angle: 41.58^°) :1 (narrow angle: 5.88^°) segregation for leaf angle. A set of 11 gene-based InDel markers (MGU-InDel1 to MGU-InDel11) specific to Lg1 was also developed, and along with MGU-lg1-Tourist, they classified a diverse set of 48 inbreds into 35 distinct haplotypes (hap1 to hap35) with lg1-based inbreds possessing hap1. This is the first report of the development and validation of a co-dominant gene-based marker specific to lg1, and information generated assumes great significance in maize breeding aimed to tailor the plant architecture suitable for high plant density..