INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow‐leafed lupin (Lupinus angustifolius L.)

• Published in: Plant, cell and environment cell and environment, 2019-01, Vol.42 (1), p.174-187
• Main Authors: Taylor, Candy M., Kamphuis, Lars G., Zhang, Weilu, Garg, Gagan, Berger, Jens D., Mousavi‐Derazmahalleh, Mahsa, Bayer, Philipp E., Edwards, David, Singh, Karam B., Cowling, Wallace A., Nelson, Matthew N.
• Format: Article
• Language: English
• Subjects: Adaptation; Agronomy; cis‐regulation; Cultivation; Flowering; FLOWERING LOCUS T (FT); Flowers - genetics; Flowers - growth & development; Gene deletion; Gene expression; Gene Expression Regulation, Plant - genetics; Gene Expression Regulation, Plant - physiology; Genes, Plant - genetics; Genes, Plant - physiology; Genetic diversity; Genetic Variation - genetics; Germplasm; Homology; INDEL Mutation - genetics; INDEL Mutation - physiology; Insertion; insertion/deletion (INDEL); Legumes; Linkage Disequilibrium - genetics; Loci; Lupinus - genetics; Lupinus - growth & development; Lupinus angustifolius; Original; Phenotypes; Phenotyping; Polymorphism, Single Nucleotide - genetics; Promoter Regions, Genetic - genetics; Seasons; variant series; Vernalization
• ISSN: 0140-7791; 1365-3040
• DOI: 10.1111/pce.13320

Narrow‐leafed lupin (Lupinus angustifolius L.) cultivation was transformed by 2 dominant vernalization‐insensitive, early flowering time loci known as Ku and Julius (Jul), which allowed expansion into shorter season environments. However, reliance on these loci has limited genetic and phenotypic diversity for environmental adaptation in cultivated lupin. We recently predicted that a 1,423‐bp deletion in the cis‐regulatory region of LanFTc1, a FLOWERING LOCUS T (FT) homologue, derepressed expression of LanFTc1 and was the underlying cause of the Ku phenotype. Here, we surveyed diverse germplasm for LanFTc1 cis‐regulatory variation and identified 2 further deletions of 1,208 and 5,162 bp in the 5' regulatory region, which overlap the 1,423‐bp deletion. Additionally, we confirmed that no other polymorphisms were perfectly associated with vernalization responsiveness. Phenotyping and gene expression analyses revealed that Jul accessions possessed the 5,162‐bp deletion and that the Jul and Ku deletions were equally capable of removing vernalization requirement and up‐regulating gene expression. The 1,208‐bp deletion was associated with intermediate phenology, vernalization responsiveness, and gene expression and therefore may be useful for expanding agronomic adaptation of lupin. This insertion/deletion series may also help resolve how the vernalization response is mediated at the molecular level in legumes. “Greater genetic and phenotypic diversity for flowering time would enhance the adaptation of narrow‐leafed lupin to Australian and northern European agricultural environments. We studied the major floral integrator gene in narrow‐leafed lupin, LanFTc1, and found a series of three overlapping independent deletions within the promoter region that reduce vernalization responsiveness, shorten flowering time, and heighten expression of LanFTc1. The smallest deletion results in a unique intermediate phenotype, which may be valuable for breeding purposes and expanding the agronomic adaptation of lupin to new and existing production regions. Additionally, the insertion/deletion series may also help to increase knowledge of how signalling within the vernalization pathway is mediated at a molecular level in legumes.”