Alternative splicing of flowering time gene FT is associated with halving of time to flowering in coconut

Abstract

Coconut palm has two distinct types-"tall" and "dwarf"-which differ morphologically. Tall coconut varieties need 8-10 years to start flowering, while dwarf coconut varieties only require 3-5 years. We compared seedling and reproductive stage transcriptomes for both coconut types to determine potential molecular mechanisms underlying control of flowering time in coconut. Several key genes in the photoperiod pathway were differentially expressed between seedling and reproductive leaf samples in both tall and dwarf coconut. These genes included suppressor of overexpression of constans (SOC1), flowering locus T (FT), and Apetala 1 (AP1). Alternative splicing analysis of genes in the photoperiod pathway further revealed that the FT gene produces different transcripts in tall compared to dwarf coconut. The shorter alternative splice variant of FT [which included a 6 bp deletion, alternative 3′ splicing sites (A3SS)] was found to be exclusively present in dwarf coconut varieties but absent in most tall coconut varieties. Our results provide a valuable information resource as well as suggesting a probable mechanism for differentiation of flowering time onset in coconut, providing a target for future breeding work in accelerating time to flowering in this crop species. Coconut palm (Cocos nucifera L., 2n = 32) belongs to the monocotyledonous family Arecaceae (Palmaceae) and is an important tropical oil and fruit crop. Presently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific island, where it accounts for over 12 million hectares 1. Coconut palm is divided into "tall" and "dwarf " types based on distinct morphological and breeding features between the two groups. Tall coconuts take 8-10 years to complete the vegetative to reproductive transition, can grow to a height of about 20-30 m, and have medium-to-large nuts. Tall coconuts are hardy and can adapt to a wide range of environmental conditions. Dwarf coconuts are early-flowering (4-6 years after planting), can grow to a height of about 10-15 m, and can produce a number of small nuts 2. The large difference in flowering time between these two types is of particular interest for breeding and production: flowering time limits not only generation speed but also time to first harvest after planting, such that shorter flowering times are almost always desirable. However, to date little is known about regulation of flowering time in coconut. In the last several decades, a great deal of work has been done in elucidating the molecular mechanisms underlying the transformation from vegetative growth to reproductive growth in plants. Four flowering regulation pathways have been described in model plant Arabidopsis thaliana: the photoperiod pathway 3 , the vernalization pathway 4 , the gibberellin pathway 5 and the autonomous pathway 6. Time to flowering in Arabidopsis thaliana is predominantly determined by expression of the Flowering Locus T (FT) gene 7. In Arabidopsis thaliana FT is negatively r...

Morphological, phenological, and transcriptional analyses provide insight into the diverse flowering traits of a mutant of the relic woody plant Liriodendron chinense

“…In Brachypodium , alternative splicing of FT2 generates two splice variants, FT2α and FT2β , and the latter cannot interact with FD but can form heterodimers with the former and FT1 to prevent floral initiation 53 . In coconut, a shorter alternative splice variant of FT was extensively present in the dwarf varieties, which need fewer years to begin blooming than the tall varieties in which no shorter variant of FT has been found 54 .…”

“…Cases of alternative splicing of FT have been reported in Brachypodium 53 and coconut 54 . In Brachypodium , alternative splicing of FT2 generates two splice variants, FT2α and FT2β , and the latter cannot interact with FD but can form heterodimers with the former and FT1 to prevent floral initiation 53 .…”

The vascular targeted citrus FLOWERING LOCUS T3 gene promotes non-inductive early flowering in transgenic Carrizo rootstocks and grafted juvenile scions

“…AP1 accumulation in the meristem is necessary for flowering induction 52 confirmed by earlier results, which indicated that FT can act as a redundancy gene of LFY to activate AP1 53 . A recent transcriptomic study failed to detect an upregulation of LFY in an early flowering coconut genotype 54 . However, it is possible that the signaling cascade may differ from the classical Arabidopsis flowering induction.…”

Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice

“…Apart from unique variants and SVs identified in the flowering genes such as Hd3a, RFT1, OsMADS14, OsMADS15, and OsMADS56 (Tables S8 and S9), there were changes in the splicing events (Tables 2 and S7), which could have contributed to the differential expression pattern between PSRR-1 and Cypress. Differential AS events in rice were reported as coping mechanisms under adverse environments [41][42][43], and specifically, the flowering time in coconut was influenced by AS of the FT gene [44].…”