Genome-wide SSR markers in bottle gourd: development, characterization, utilization in assessment of genetic diversity of National Genebank of India and synteny with other related cucurbits

Abstract

Lagenaria siceraria (Molina) Standley is an important cultivated crop with its immense importance in pharmaceutical industry and as vegetable. Its seed, root, stem, leaves, ower and fruit are used as an ointment for ailment of various diseases throughout Asia. Despite its worldwide importance, informative co-dominant microsatellite markers in the bottle gourd crop are very restricted, impeding genetic improvement, cultivar identi cation and phylogenetic studies. Next generation sequencing has revolutionized the approaches for discovery, assessment and validation of molecular markers. We conducted a genome wide analysis, for developing SSR markers by utilizing restriction site-associated DNA sequencing (RAD-Seq) data.By performing in silico mining of microsatellite repeat-motifs, we developed 45,066 perfect SSR markers. Of which 203 markers were successfully validated and 101 (49.75%) polymorphic primer pairs were utilized for an in depth genetic diversity and population structure analysis of 96 accessions from the National Genebank of India. Tetranucleotide repeats (∼34.3%) were the most prevalent followed by trinucleotide repeats (∼30.73%), further 21.03%, 9.6% and 4.3% of di-, penta-and hexa-nucleotide repeats in the bottle gourd genome. Synteny of SSR markers on 11 bottle gourd linkage groups was correlated with the 7 chromosomes of cucumber (93.2%), 12 chromosomes of melon (87.4%) and 11 watermelon (90.8%). The generated SSR markers provide a valuable tool for germplasm characterization, genetic linkage map construction, studying synteny, gene discovery and for breeding in bottle gourd and other cucurbits species. Key MessageDevelopment of 45,066 perfect microsatellite markers as a valuable tool for marker assisted selection (MAS) in plant breeding.

Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes

“…SSRs have been deemed as promising candidate markers for population genetics and germplasm identification in plants due to their hypervariability, high information content and codominance [ 45 , 46 , 47 ]. With the rapid development of next-generation sequencing technology, whole-genome SSR identification becomes much more effective and comprehensive [ 2 , 48 ]. In this study, whole-genome SSR identification and comparative analysis were carried out in five bamboo species including two herbaceous bamboos and three woody bamboos representing three tribes.…”

Development of SSR molecular markers and genetic diversity analysis of Clematis acerifolia from Taihang Mountains

“…SSR markers were used for investigating the genetic relationship among 43 individuals of 11 Clematis species [30], and performing the genetic investigation of Clematis finetiana, Clematis chinensis, and Clematis heracleifolia [31][32][33]. Restriction site-associated DNA sequencing (RAD-seq) is an inexpensive method for developing SSR markers, and have been used in genetic studies of several species [34][35][36].…”

Transcriptomic Insights and the Development of Microsatellite Markers to Assess Genetic Diversity in the Broodstock Management of Litopenaeus stylirostris

“…Furthermore, the identification of microsatellites from transcriptome data offers a powerful tool for genetic analysis and management in aquaculture. These markers can be utilized to assess genetic diversity, population structure, and relatedness among individuals, aiding in the development of effective breeding strategies and conservation efforts [ 25 , 26 ].…”