Genomic Organization, Phylogenetic Comparison, and Differential Expression of the Nuclear Factor-Y Gene Family in Apple (Malus Domestica)

Abstract

The nuclear factor Y (NF-Y) as a transcription factor plays an important role in plants growth and development, and response to stress. However, few genome-wide analyzes and functional research of the NF-Y family has been undertaken in apple (Malus domestica Borkh.) so far. In this study, we comprehensively identified the 43 MdNF-Y genes in apple, which dispersedly distributed among the three subgroups based on their sequence alignment analysis, including 11 MdNF-YAs, 22 MdNF-YBs and 10 MdNF-YCs. The members in the same subgroups had similar evolution relationships, gene structures, and conserved motifs. The gene duplication analysis suggested that all the genes were dispersed followed by 27 segmental duplication. Moreover, based on synteny analysis of MdNF-Ys with eight plant species results suggested that some ortholog genes were preserved during the evolution of these species. Cis-element analysis showed potential functions of MdNF-Ys in apple growth and development and responded to abiotic stress. Furthermore, the interaction among MdNF-Ys protein were investigated in yeast two-hybrid assays. The expression patterns of MdNF-Ys in tissue-specific response reveled divergence and might play important role in apple growth and development. Subsequently, whole MdNF-Y genes family was carried out for RT-PCR in response to five abiotic stress (ABA, drought, heat, cold, and salinity) to identify their expression patterns. Taken together, our study will provide a foundation for the further study to the molecular mechanism of apple in growing development and response to abiotic stresses.

Expression of the Malus sieversii NF-YB21 Encoded Gene Confers Tolerance to Osmotic Stresses in Arabidopsis thaliana

“…We speculate that these differences in gene numbers might be linked to variations in genome size, as apples and soybeans have larger genomes. Strikingly, the number of NF-YA and NF-YC genes was different from the number found by Qu et al [ 38 ]. For NF-YA , two candidate genes (MD02G1309800 and MD12G1042100) identified in Qu et al [ 38 ] did not have a complete NF-YA domain in our analysis; thus, we removed these two genes.…”

“…Strikingly, the number of NF-YA and NF-YC genes was different from the number found by Qu et al [ 38 ]. For NF-YA , two candidate genes (MD02G1309800 and MD12G1042100) identified in Qu et al [ 38 ] did not have a complete NF-YA domain in our analysis; thus, we removed these two genes. For NF-YC , we added two more candidate genes (MD02G1273400 and MD07G1042300) because of E-values less than 10 −10 .…”

“…Although many NF-Y family members have been identified in plants (including apple trees [ 38 ]), most of these studies have been limited to structural characterization and expression analysis under abiotic stress. The biological functions of the NF-Ys or the molecular properties of these TFs still remain unclear.…”

Identification and Comprehensive Analysis of the Nuclear Factor-Y Family Genes Reveal Their Multiple Roles in Response to Nutrient Deficiencies in Brassica napus

“…The NF-Y genes are trimeric transcription factors in plants, containing the NF-YA , NF-YB and NF-YC subfamilies which include multiple genes [ 2 ]. Recently, the NF-Y families have been identified and characterized in several plant species, including Arabidopsis [ 5 ], rice [ 6 ], soybean [ 7 ], sorghum [ 10 ], barley [ 13 ], apple [ 15 ] and more. Previously, the NF-Y genes were identified and characterized in B. napus based on an expressed sequence tag database and the completed B. napus genome sequence in the CoGe database [ 42 , 43 ].…”

“…Likewise, in rice ( Oryza sativa ), 10, 11, and 7 members were identified in the NF-YA , NF-YB , and NF-YC subfamilies, respectively [ 6 ]. To date, the number of identified members of the three subfamilies in other crop plants have previously been studied, such as soybean [ 7 ], tomato [ 8 ], maize [ 9 ], sorghum [ 10 , 11 ], citrus [ 12 ], barley [ 13 ], cucumber [ 14 ], and apple [ 15 ]. The results indicate that the numbers of NF-Y family members have increased in plants.…”