Divergence of Flowering‐Related Genes in Three Legume Species

Abstract

We used a set of approximately 200 Arabidopsis thaliana (L.) Heynh. genes that are involved in the control of flowering time as a reference to identify orthologous (or homologous) counterparts of these genes in three legume species, that is, Lotus corniculatus L. var. (FPIs), and floral meristem identity. Many key genes, including the FPI genes FT, SOC1, and LFY, are conserved in the legumes while CO, FRI, FLC, and FD were not. Eighteen genes were conserved as single copy genes in all three legume species, including GI, VRN2, COP1, and TSF. The chromosomal distribution of paralog-rich genes revealed differences in the major evolutionary processes affecting flowering genes in legumes, including whole genome duplication in soybean, tandem duplication in M. truncatula, and ectopic duplication in L. corniculatus var. japonicus. High divergence was observed among the members of large gene families, most containing transcription factors, indicating the accumulation of gene copies and gene divergence during evolutionary adaptations to environmental changes.

Genome-Wide Identification of the VQ Protein Gene Family of Tobacco (Nicotiana tabacum L.) and Analysis of Its Expression in Response to Phytohormones and Abiotic and Biotic Stresses

“…The number of synonymous (Ks) and nonsynonymous (Ka) substitutions of duplicated VQ genes was computed by using the KaKs_calculator 2.0 with the MYN method [45]. The divergence time (T) was calculated using the formula T = Ks/(2 × 6.1 × 10 −9 ) × 10 −6 million years ago (MYA) with a mutation rate of 1 × 10 −8 [46,47].…”

The Chickpea Early Flowering 1 (Efl1) Locus Is an Ortholog of Arabidopsis ELF3

“…qdf-LD4 and qdf-SD4 had one flanking marker in common, while qdf-LD5 and qdf-SD5 shared the same markers, suggesting that these two loci confer earlier flowering under both LD and SD. Comparative and functional genomic analyses have revealed that the functions of many Arabidopsis flowering time genes are conserved in legumes (Hecht et al, 2005;Kim et al, 2013;Weller and Ortega, 2015). Accordingly, we constructed a physical map with the positions of 138 chickpea orthologs of Arabidopsis flowering time genes, including those implicated in light signaling, the circadian clock, photoperiod sensing, and the autonomous pathways (Fig.…”

QTL detection for flowering time in faba bean and the responses to ambient temperature and photoperiod

“…Three flowering QTLs have been detected on M. truncatula chromosome 8 (Pierre et al 2008) and two on chickpea chromosome 8 (Rehman et al 2011;Varshney et al 2014). Sixteen flowering related genes have been identified on M. truncatula chromosome 8 by Kim et al (2013), including the photoperiod pathway genes: Casein kinase alpha 1 (CKA1); Casein kinase II, alpha chain 2 (CKA2); and Chryptochrome-interacting basic-helix-loop-helix 1 (CIB1). These are the most plausible candidate genes, given the association the QTL has with photoperiod response, however, fine mapping would have to be carried out in order to narrow the possibilities.…”

“…As well as being syntenic with M. truncatula chromosome 1, Chr-III.1 is syntenic with chickpea chromosome 4 and pea chromosome 2 (Hecht et al 2005;Kaur et al 2014). M. truncatula chromosome 1 and chickpea chromosome 4 contain the flowering genes: GI (orthologous to the GIGANTEA gene in A. thaliana), Phytochrome A (PHYA), Cryptochrome 2 (CRY2) and Flowering Locus D (FLD) (Deokar et al 2015;Hecht et al 2005;Kim et al 2013;Weller and Ortega 2015). Additionally, pea chromosome 2 contains Photoperiod (PPD) and Late Flowering (LF) (Liew et al 2014;Weller et al 1997;Weller and Ortega 2015).…”