Identification of the regulatory networks and hub genes controlling alfalfa floral pigmentation variation using RNA-sequencing analysis

Abstract

Background: To understand the gene expression networks controlling flower color formation in alfalfa, flowers anthocyanins were identified using two materials with contrasting flower colors, namely Defu and Zhongtian No. 3, and transcriptome analyses of PacBio full-length sequencing combined with RNA sequencing were performed, across four flower developmental stages.Results: Malvidin and petunidin glycoside derivatives were the major anthocyanins in the flowers of Defu, which were lacking in the flowers of Zhongtian No. 3. The two transcriptomic datasets provided a comprehensive and systems-level view on the dynamic gene expression networks underpinning alfalfa flower color formation. By weighted gene coexpression network analyses, we identified candidate genes and hub genes from the modules closely related to floral developmental stages. PAL, 4CL, CHS, CHR, F3'H, DFR, and UFGT were enriched in the important modules. Additionally, PAL6, PAL9, 4CL18, CHS2, 4 and 8 were identified as hub genes. Thus, a hypothesis explaining the lack of purple color in the flower of Zhongtian No. 3 was proposed. Conclusions: These analyses identified a large number of potential key regulators controlling flower color pigmentation, thereby providing new insights into the molecular networks underlying alfalfa flower development. Background Flower color is an important horticultural trait of higher plants [1]. Variation in flower color can fulfill an important ecological function by attracting pollinator's visitation and influencing reproductive success in flowering plants [2], can protect the plant and its reproductive organs from UV damage, pests, and pathogens [3, 4], and has been of paramount importance in plant evolution [5, 6]. Furthermore, flower color is associated with the agronomic characters of plants directly or indirectly, and classical breeding methods have been extensively used to develop cultivars with flowers varying in color [7]. Three species of the genus Medicago L. are the most typical representatives of meadow ecosystems in the central part of European Russia: alfalfa (M. sativa L.), yellow lucerne (M. falcata L.), and black medic (M. lupulina L.), which are widely cultivated and grow easily in the wild [8,9,10]. The obvious 3 differences in these species are their morphological features, among which flower color is the main trait used to distinguish them [11,12,13]. Understanding the differences in the growth period, botanical characteristics, agronomic characteristics, quality, and photosynthetic characteristics of different alfalfa germplasm materials associated with flower color would have great significance in alfalfa breeding [14,15].Of the above-mentioned Medicago species, purple-flowered alfalfa is the most productive perennial legume with high biomass productivity, an excellent nutritional profile, and adequate persistence [16,17]. Yellow lucerne, which has yellow flowers, is closely related to alfalfa and exhibits better cold tolerance than alfalfa [18,19]. Furthermore, the wild plants of M. varia with m...

Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

“…Quintana et al [30] suggested that there is a mutation in the early stage of the anthocyanin pathway, leading to no anthocyanidins in white flowers of Anagallis monellin. Duan et al [11] reported that malvidin and petunidin were detected in purple alfalfa flowers, whereas no color anthocyanidins occurred in cream alfalfa flowers. In this study, we found that 6 types of common anthocyanin pigments were present simultaneously in white flowers of S. miltiorrhiza.…”

“…The biosynthesis of anthocyanin is catalyzed by a series of enzymes in the phenylpropanoid and flavonoid biosynthetic pathways [7,8]. The genes involved in the biosynthesis of anthocyanin have been reported in many plant species such as Arabidopsis [9], spinach [10], and alfalfa [11]. Studies have found that color mutations are often found in fruits, flowers, and leaves.…”