Development and characterization of genic-SSR markers from different Asia lotus (Nelumbo nucifera) types by RNA-seq

Abstract

ABSTRACT. Nelumbo nucifera is an important economic vegetable and traditional medicine, but available genetic resources remain limited. Next generation sequencing has proven to be a rapid and effective means of identifying genic simple sequence repeat (genic-SSR) markers. This study developed genic-SSRs for N. nucifera using Illumina sequencing technology to assess diversity across cultivated and wild lotus. A total of 105,834 uni-contigs were produced with an average read length of 722 bp. Exactly 11,178 genic-SSR loci were identified in 9523 uni-contigs. Di-nucleotide (64.5%) was the most abundant SSR, followed by trinucleotide (23%), tetra-nucleotide (8.9%), penta-nucleotide (2.5%), and hexa-nucleotide (1%) repeat types. The most common di-and tri-nucleotide repeat motifs were AG/CT (51%) and AAG/CTT (8%), respectively. Based on these SSRs sequences, 6568 primer pairs were designed, of which 72 primers were randomly selected for synthesis and validation, and 38 in-silico polymorphic primers were obtained using in-house perl scripts. A total of 110 primers were screened in the lotus samples and the results showed that 101 primers yielded amplification products, of which 80 were polymorphs. The number of alleles ranged from 2 to 17 and the PIC (polymorphism information content) ranged from 0.19 to 0.87 with a mean value of 0.55. An Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram based on Jaccard's similarity coefficients showed that the correlation between geographical source and genotype was low. This study describes the distribution of genic-SSRs in the expressed portion of the lotus genome. These genic-SSRs have an important role to play in molecular mapping, diversity analysis, and marker-assisted selection strategies in Nelumbo.

Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology

“…Flowering and tuberization are the representatives of reproductive and vegetative growth, respectively, which share an overlapping plant energy allocation. AP2 and AP2-like genes are involved in the initiation of flower growth [64][65][66][67], and some of them cause inhibition of flowering in various flowering plants, including rice, Arabidopsis, and Arabis alpina [48,68,69]. Flowering and tuber formation were triggered by certain overlapping signals in potato (Solanum tuberosum) [70], and the transition between flowering and tuberization was induced by 'florigen' and 'tuberigen', which share similar signaling pathway [71,72].…”

Genome-Wide Survey and Analysis of Microsatellites in Waterlily, and Potential for Polymorphic Marker Development

“…In previous studies, SSR markers were effectively applied to the diversity of local and wild lotus varieties [ 45 , 46 , 47 ]. To analyze the genetic relationships between nine waterlily cultivars, a total of 13 pairs of primers targeting polymorphic SSR markers were screened out.…”