De Novo Characterization of Fall Dormant and Nondormant Alfalfa (Medicago sativa L.) Leaf Transcriptome and Identification of Candidate Genes Related to Fall Dormancy

Abstract

Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage legumes worldwide. Fall dormancy is an adaptive character related to the biomass production and winter survival in alfalfa. The physiological, biochemical and molecular mechanisms causing fall dormancy and the related genes have not been well studied. In this study, we sequenced two standard varieties of alfalfa (dormant and non-dormant) at two time points and generated approximately 160 million high quality paired-end sequence reads using sequencing by synthesis (SBS) technology. The de novo transcriptome assembly generated a set of 192,875 transcripts with an average length of 856 bp representing about 165.1 Mb of the alfalfa leaf transcriptome. After assembly, 111,062 (57.6%) transcripts were annotated against the NCBI non-redundant database. A total of 30,165 (15.6%) transcripts were mapped to 323 Kyoto Encyclopedia of Genes and Genomes pathways. We also identified 41,973 simple sequence repeats, which can be used to generate markers for alfalfa, and 1,541 transcription factors were identified across 1,350 transcripts. Gene expression between dormant and non-dormant alfalfa at different time points were performed, and we identified several differentially expressed genes potentially related to fall dormancy. The Gene Ontology and pathways information were also identified. We sequenced and assembled the leaf transcriptome of alfalfa related to fall dormancy, and also identified some genes of interest involved in the fall dormancy mechanism. Thus, our research focused on studying fall dormancy in alfalfa through transcriptome sequencing. The sequencing and gene expression data generated in this study may be used further to elucidate the complete mechanisms governing fall dormancy in alfalfa.

De novo assembly and characterization of leaf transcriptome for the development of EST-SSR markers of the non-model species Indigofera szechuensis

“…These results are consistent with previous results for dicots such as Ricinus communis L (Qiu et al, 2010). and Haloxylon ammodendron (Zhang et al, 2015).…”

“…In this study, in addition to the more common dinucleotide, trinucleotide, tetranucleotide, and other nucleotide repeats that were included in the selection, mononucleotide repeat SSRs were also included. The proportion of mononucleotide repeat SSRs was the most abundant type, followed by trinucleotide, dinucleotide, and tetranucleotide repeats, consistent with previous reports (Du et al, 2013;Long et al, 2014;Zhang et al, 2015). The most abundant dinucleotide and trinucleotide motifs were AG/TC and GAA/TTC, respectively.…”

“…Mey.) Bunge (N50 ¼ 1345 bp, average length ¼ 728 bp) (Long et al, 2014), and Medicago sativa L. (N50 ¼ 1451 bp, average length ¼ 856 bp) (Zhang et al, 2015). More than half of the unigenes (27,320, 62.2%) identified were successfully annotated using BLAST searches of the public Nr, COG, GO, KEGG, KOG, PFAM, and SWISS-PROT databases, given the absence of genomic information on I. szechuensis (Table 2).…”

Genetics and Genomics of Cultivated Eggplants and Wild Relatives

“…These higher numbers of unigenes has been observed in other plant transcriptomes recently published (Groves et al, 2015;Zhang J. et al, 2015;Zhang S. et al, 2015) in which the number of raw reads obtained was quite large. In the outer histogram, depicted in green for S. incanum and in red for S. aethiopicum, are represented the assembled unigenes along the eggplant genome (yellow ring).…”

Insights into Seasonal Dormancy of Perennial Herbaceous Forages

“…Based on plant regrowth in autumn, there are 11 standard classes of fall dormancy and the classes are assigned based on regression with standard checks [48]. The 11 FD classes are divided into sub-categories: dormant, 1 -4 FD; semi dormant, 5 -7; and non-dormant, 8 -11 [63]. However, defining fall dormancy (FD) classes in alfalfa is time-consuming due to its complexity and the influence of different environmental factors and their interactions.…”