Identification of glutinous maize landraces and inbred lines with altered transcription of waxy gene

Waxy maize has little or very low content of amylose (< 5 %) in grain starch and carries null mutations of the waxy (Wx) gene. With important uses as fresh maize or as an ingredient in food, textile, adhesive, and paper industries, two types of wx allele, wx-D7 and wx-D10, had been identified. In the present study, 10 accessions carrying neither wx-D7 nor wx-D10 allele were identified from a collection of 325 waxy maize accessions. The Wx locus of these 10 accessions was sequenced, but no potential causative mutation was detected. Further sequencing of the full-length complementary DNAs revealed that 6 of the 10 accessions had alternative splicing patterns while the other 4 had wild-type Wx transcripts. Among the six accessions, one generated transcripts identical to the wx-D7 allele, two had the same transcripts as the wx-D10 allele, another two generated transcripts with deletion of the 10th and the 11th exon, yet the other one produced transcripts of various lengths due to deletions from part of the 2nd exon to part of the 12th exon. The wx alleles with the above alternative splicing modes are referred to as wx-tD7, wx-tD10, wx-tD10-11, and wx-tD2-12, respectively. Real-time quantitative reverse-transcription polymerase chain reaction analysis of two waxy accessions that produced Wx transcripts showed significantly decreased expression, having only 47.3 and 3.6 % transcription level compared with B73. Sequence analysis of deletions in the transcripts with comparison with wild one showed short direct repeats at deletion endpoints, similar to reported signatures of DNA deletions. The waxy accessions present unique wx alleles for waxy maize breeding as well as for transcriptional regulation studies in plants.