Small RNA and Transcriptome Deep Sequencing Proffer Insight into Pistil Gene Regulation in an Alfalfa Multi-Pistil Mutant and Its Wild Type.

Alfalfa (Medicago sativa L.) multi-pistil mutant mp-1 exhibited two to three pistils compared with its wild-type plant. Our previous research revealed that mp-1 was partial-female-sterile, significantly decreasing the production yield. Thus, mp-1 is highly valuable in the study of floral development in alfalfa. In this study, we conducted high-throughput sequencing of the miRNAs and transcriptomes of the alfalfa mutant florets (mp-1) and its wild-type florets (WT) to gain insights into pistil development in alfalfa. A total of 151, 359 putative unigenes with mean length of 631 bp were generated from WT and mp-1 transcriptomes. The unigenes were annotated in NR, NT, KO, Swiss-Prot, PFAM, GO, and KOG databases. Comparative profiling showed that 2306 differentially expressed genes were identified in mp-1 Vs WT, including 1100 upregulated unigenes and 1206 downregulated unigenes. In addition, a total of 148 known miRNAs, belonging to 72 families, were identified from two small RNA libraries of mp-1 and WT. Comparative profiling revealed that 110 miRNAs exhibited differential expression between mp-1 and WT, 43 of them were novel and 67 of them were known miRNAs. The correlation analysis of small RNA and transcriptome reveled that 18 highly differentially expressed miRNAs and their 27 target genes were closely associated with pistil development. KEGG pathway and GO annotation indicated that high-ranking miRNA target genes were involved in the metabolic and signal transduction pathways. Our work provides a comprehensive genetic resource which can be used to better understand alfalfa pistil development and to identify candidate genes for female sterility in alfalfa.