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.)

Abstract

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.

Genomic Analysis of Sugar Transporter Gene Family in Cultivated Peanut (Arachis Hypogaea): Evolution, Expression Profiles and Gene Variation

“…[45], and gene variation is probably to be the most direct cause for altering gene expression pattern. The expansion or contraction of SSR, the transition or transversion of SNP and the insertion or deletion of InDel in gene sequence or promoter region, all can lead to changes in gene expression pattern and function via mutation in CDS, UTR, intron or promoter region [46][47][48]. Gene sequence of AhSTP19 was found conservation in the two subspecies, but SNP and InDel in the promoter region caused altering of CREs.…”

Legumes—The art and science of environmentally sustainable agriculture

“…Thedeletions are associated with altered responsiveness to vernalization, flowering time, and expression of LanFTc1 in the absence of vernalization. A third smaller deletion, reported in Taylor et al, 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 (INDEL) variant series may also help to increase knowledge of how signalling within the vernalization pathway is mediated at a molecular level in legumes.…”

“…In Europe and Australia, breeders independently found mutations which eliminated vernalization response in narrow‐leafed lupin, and these mutations predominate in breeding programmes in Europe and Australia to this day. Researchers in Australia have shown that these two mutations were caused by similar deletions in the promotor region of LanFTc1, a major flowering time gene in narrow‐leafed lupin (Taylor et al, ). Thedeletions are associated with altered responsiveness to vernalization, flowering time, and expression of LanFTc1 in the absence of vernalization.…”

Functional characterization of mungbean CONSTANS-LIKE genes reveals a key role for CONSTANS-LIKE 2 in the control of flowering time in A. thaliana under short-day conditions

“…Several functional pathways have been identi ed that regulate the switch from vegetative to reproductive development. These include the photoperiodic, vernalization, ambient temperature, plant hormone, and autonomous owering pathways [1,[4][5][6][7][8][9][10]. Within these pathways, a number of genes have been identi ed as involved in owering time regulation, including CONSTANS-LIKE (COL) genes, phosphatidyl ethanolamine-binding protein (PEBP) genes and several members of MADS-Box gene family [1][2][11][12][13][14][15][16][17][18][19].…”