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.).

Candy M Taylor,Weilu Zhang,Matthew N Nelson,Jens D Berger,Lars G Kamphuis,Wallace A Cowling,Philipp E Bayer,David Edwards,Mahsa Mousavi‐Derazmahalleh,Karam B Singh,Gagan Garg

doi:10.1111/pce.13320

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.

Highlights

Narrow-leafed lupin (Lupinus angustifolius L.) is one of three fully domesticated Old World Lupinus species originating from the Mediterranean and northern Africa (Gladstones, 1974)
A 1,423 bp deletion between 4,248 and 2,826 bp upstream of the ATG start codon of LanFTc1 was previously hypothesised as the causal sequence variant modifying vernalisation responsiveness in the breeding line, 83A:476 (Ku), compared to the wild-type LanFTc1 sequence represented by P27255, and no polymorphisms were observed between accessions in the coding sequence (Nelson et al, 2017)
A 1,423 bp deletion in the 5’ regulatory region of LanFTc1, an FLOWERING LOCUS T (FT) homologue, was recently hypothesised as the causal mutation behind the Ku locus that has been significant in establishing narrow-leafed lupin as a viable pulse crop in Australia and northern Europe (Nelson et al, 2017)

Summary

Introduction

Narrow-leafed lupin (Lupinus angustifolius L.) is one of three fully domesticated Old World Lupinus species originating from the Mediterranean and northern Africa (Gladstones, 1974). It is predominantly grown in Australia and several northern European countries, including Poland, Russia, Germany, Ukraine and Belarus, as a winter and summer annual pulse crop, respectively (FAO, 2014; Gladstones, 1970). In light of the nutritional and metabolomics properties of narrow-leafed lupin seed (Lima-Cabello et al, 2017) and the associated benefits to human health and disease prevention (Foyer et al, 2016; Kouris-Blazos & Belski, 2016), it is being promoted in the human food market. In addition to high-protein grain production, narrow-leafed lupin has great agricultural value as a superior break crop. Lupin crops mobilise soil-bound phosphorus through carboxylate exudation (Lambers et al, 2013) and improve soil nitrogen through symbiosis, which, together with disease and weed control, is beneficial to the performance of subsequent crop rotations (Seymour et al, 2012)

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