Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses

Abstract

The SQUAMOSA promoter binding-like protein (SPL) is a specific transcription factor that affects plant growth and development. The SPL gene family has been explored in various plants, but information about these genes in alfalfa is limited. This study, based on the whole genome data of alfalfa SPL, the fundamental physicochemical properties, phylogenetic evolution, gene structure, cis-acting elements, and gene expression of members of the MsSPL gene family were analyzed by bioinformatics methods. We identified 82 SPL sequences in the alfalfa, which were annotated into 23 genes, including 7 (30.43%) genes with four alleles, 10 (43.47%) with three, 3 (13.04%) with two, 3 (13.04%) with one allele. These SPL genes were divided into six groups, that are constructed from A. thaliana, M. truncatula and alfalfa. Chromosomal localization of the identified SPL genes showed arbitary distribution. The subcellular localization predictions showed that all MsSPL proteins were located in the nucleus. A total of 71 pairs of duplicated genes were identified, and segmental duplication mainly contributed to the expansion of the MsSPL gene family. Analysis of the Ka/Ks ratios indicated that paralogs of the MsSPL gene family principally underwent purifying selection. Protein–protein interaction analysis of MsSPL proteins were performed to predict their roles in potential regulatory networks. Twelve cis-acting elements including phytohormone and stress elements were detected in the regions of MsSPL genes. We further analyzed that the MsSPLs had apparent responses to abiotic stresses such as drought and salt and the biotic stress of methyl jasmonate. These results provide comprehensive information on the MsSPL gene family in alfalfa and lay a solid foundation for elucidating the biological functions of MsSPLs. This study also provides valuable on the regulation mechanism and function of MsSPLs in response to biotic and abiotic stresses.

Genome-wide analysis of SPL/miR156 module and their expression analysis in vegetative and reproductive organs of oil palm (Elaeis guineensis)

“…All the identi ed SPLs contained at least one intron and varied among them. Our results are consistent with the previous reports on identi cation of SPL genes in Jatropha [16], Soybean [40], Alfalfa [13] and sweet cherry [12]. The presence of SBP domain is the key feature in SPL gene family [9].…”

“…Phylogenetic analysis of 24 oil palm SPLs with Arabidopsis and rice SPLs suggested the diversi cation of oil palm SPL members among model-to-crop plants during evolution process. The uneven distribution of 24 SPL genes on 16 chromosomes of oil palm also coinciding with the previous reports on SPL gene family distribution on sweet cherry, Alfalfa and foxtail millet genomes [12,13,14]. SPL genes encode plant-speci c transcription factors that play important roles in ower development, including vegetative to reproductive growth [48] .…”

“…The motifs related to the SBP domain are found in all the identi ed EgSPL proteins. Conserved motif analysis revealed the occurrence of 10 motifs in oil palm SPL genes as reported in other plants including foxtail millet [14], Alfalfa [13] and Quinoa [37]. The post transcriptional regulation of SPLs by miR156 determines ne-tune functions of SPLs [45].…”

“…In this study, we identi ed a total of 24 SPL genes in oil palm genome through bioinformatics approach and dissected the expression of 14 SPLs in male and female in orescences of oil palm plants through experimental approach. The number of identi ed SPLs (24) in this study are fewer than the number of SPLs identi ed in sweet cherry (16SPLs) [12], alfalfa (23SPLs) [13], foxtail millet (18 SPLs) [14], jatropha (15 SPLs) [16] and lesser than the number of SPLs identi ed in soybean(41 SPLs) [40], owering cherry (32 SPLs) [43], wheat(56 SPLs) [38], populus (33 SPLs) [41], trifolium(37 SPLs) [15] genomes. Present information on oil palm SPLs would elucidate the evolutionary process of SPLs across various plants.…”

“…SPLs are plant-speci c transcription factors with highly conserved SBP domain and involved in regulating growth and development of plants. Various number of SPL genes were identi ed and characterized their expression in various crops including sweet cherry [12], alfalfa [13], Quinoa [37], Foxtail millet [14], wheat [38], pecan [39] , soybean [40], populas [41], Jatropha [16]. However, some of the studies were carried out to characterize SPL gene expression during reproductive tissue development in various crops including Pecan [39], Tartary Buckwheat [20], Rice [42], owering cherry [43], Trifolium [15] and Petunia [44].…”