Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response

Abstract

Nuclear factor-Y (NF-Y), a heterotrimeric transcription factor, is composed of NF-YA, NF-YB and NF-YC proteins. In plants, there are usually more than 10 genes for each family and their members have been identified to be key regulators in many developmental and physiological processes controlling gametogenesis, embryogenesis, nodule development, seed development, abscisic acid (ABA) signaling, flowering time, primary root elongation, blue light responses, endoplasmic reticulum (ER) stress response and drought tolerance. Taking the advantages of the recent soybean genome draft and information on functional characterizations of nuclear factor Y (NF-Y) transcription factor family in plants, we identified 21 GmNF-YA, 32 GmNF-YB, and 15 GmNF-YC genes in the soybean (Glycine max) genome. Phylogenetic analyses show that soybean’s proteins share strong homology to Arabidopsis and many of them are closely related to functionally characterized NF-Y in plants. Expression analysis in various tissues of flower, leaf, root, seeds of different developmental stages, root hairs under rhizobium inoculation, and drought-treated roots and leaves revealed that certain groups of soybean NF-Y are likely involved in specific developmental and stress responses. This study provides extensive evaluation of the soybean NF-Y family and is particularly useful for further functional characterization of GmNF-Y proteins in seed development, nodulation and drought adaptation of soybean.Electronic supplementary materialThe online version of this article (doi:10.1007/s00438-014-0978-2) contains supplementary material, which is available to authorized users.

CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer

“…In mammals, invertebrates, and fungi, there are one or two genes coding for each subunit. Instead, plants have dramatically expanded the number of NF-Y genes: Typically, there are 8 to 14 gene family members for each subunit, conferring an enormous combinatorial capacity on the trimer; some are expressed in a tissue-restricted manner, and many are relatively ubiquitous (Gusmaroli et al, 2001(Gusmaroli et al, , 2002Stephenson et al, 2007;Siefers et al, 2009;Cao et al, 2011b;Hilioti et al, 2014;Liang et al, 2012Liang et al, , 2014Quach et al, 2015;Rípodas et al, 2015;Zhang et al, 2015;Qu et al, 2015;Feng et al, 2015;Ren et al, 2016;Malviya et al, 2016;Li et al, 2016;Yang et al, 2016;Zhang et al, 2016). Typical features of other plant TFs, such as the presence of duplicate members with similar functions and neofunctionalization of specific genes, were determined by genetic experiments, mostly performed in Arabidopsis thaliana (reviewed in Laloum et al, 2013;Petroni et al, 2012).…”

Genome-wide identification and annotation of the Nuclear-factor YA gene family in cassava (Manihot esculenta Crantz)

“…In comparison with recent annotated dicot species, a total of 21 GmNF-YA genes were identified in soybean [5], while 10 NF-YA genes were computationally predicted in tomato [7]. More recently, the genome-wide identification of eight NF-YA genes has been reported in grape [8].…”

“…To date, the NF-Y gene family has been found and characterized in many plant species such as rice (Oryza sativa) [2], canola (Canola napus) [3,4], soybean (Glycine max) [5], and foxtail millet (Setaria italica) [6]. Recently, the family has also been recorded in tomato (Solanum lycopersicum) [7], grape (Vitis vinifera) [8], and sorghum (Sorghum bicolor) [9].…”

Identification and characterization of NF-YB family genes in tung tree

“…Flowering regulation Kumimoto et al (2008) Arabidopsis thaliana Seed maturation, Fatty acid synthesis Mu et al (2008) Arabidopsis thaliana Drought tolerance Nelson et al (2007) Arabidopsis thaliana Root elongation Ballif et al (2011) Arabidopsis thaliana Abscisic acid (ABA) signaling transduction Warpeha et al (2007) Zea mays Embryo development; Seed oil accumulation Zhang et al (2002) Zea mays Drought tolerance Nelson et al (2007) Carrot Embryo development Shibukawa et al (2009) Helianthus annuus Embryo development Fambrini et al (2006) Vitis vinifera L. Embryo development Schellenbaum et al (2008) Triticum aestivum Drought adaptation Stephenson et al (2007) Triticum aestivum Photosynthesis regulation Stephenson et al (2011) Theobroma cacao Partial rescue of lec1 mutant Alemanno et al (2008) Oryza sativa L. Flowering regulation; plant height; yield potential Wei et al (2010) Oryza sativa L. Chloroplast biogenesis regulation Thirumurugan et al (2008) Oryza sativa L. Floral meristem identity Ito et al (2011) Populus Drought tolerance Cohen et al (2010) Brachypodium distachyon Flowering regulation Cao et al (2011) Glycine max Specific development; drought response Quach et al (2014) complexes? To answer these questions, it will be important to identify and characterize NF-YA and NF-YC genes in tung tree in future studies.…”

“…For example, there are at least 10 NF-YB genes in Arabidopsis, (Edwards et al 1998;Gusmaroli et al 2001Gusmaroli et al , 2002, 11 NF-YB genes in wheat (Triticum aestivum) and rice (Stephenson et al 2007;Thirumurugan et al 2008), and 17 NF-YB genes in Brachypodium (Cao et al 2011). Recently, 14 NF-YB genes have been identified and characterized in canola (Liang et al 2014) and 32 NF-YB genes in soybean (Quach et al 2014). The occurrence of multi-member gene families in plants suggests that there is genetic redundancy or functional divergence.…”