Large-scale microsatellite development in grasspea (Lathyrus sativus L.), an orphan legume of the arid areas

Abstract

BackgroundGrasspea (Lathyrus sativus L., 2n = 14), a member of the family Leguminosae, holds great agronomic potential as grain and forage legume crop in the arid areas for its superb resilience to abiotic stresses such as drought, flood and salinity. The crop could not make much progress through conventional breeding in the past, and there are hardly any detailed molecular biology studies due to paucity of reliable molecular markers representative of the entire genome.ResultsUsing the 454 FLX Titanium pyrosequencing technique, 651,827 simple sequence repeat (SSR) loci were identified and 50,144 nonredundant primer pairs were successfully designed, of which 288 were randomly selected for validation among 23 L. sativus and one L. cicera accessions of diverse provenance. 74 were polymorphic, 70 monomorphic, and 144 with no PCR product. The number of observed alleles ranged from two to five, the observed heterozygosity from 0 to 0.9545, and Shannon’s information index ranged from 0.1013 to 1.0980, respectively. The dendrogram constructed by using unweighted pair group method with arithmetic mean (UPGMA) based on Nei's genetic distance, showed obvious distinctions and understandable relationships among the 24 accessions.ConclusionsThe large number of SSR primer pairs developed in this study would make a significant contribution to genomics enabled improvement of grasspea.

Development of Species-Specific Microsatellite Markers for Broomcorn Millet (Panicum miliaceum L.) via High-Throughput Sequencing

“…Of the SSR-containing reads, mononucleotide, dinucleotide, and trinucleotide repeat motifs are dominated in the broomcorn millet genomic sequences. This result is Similar to the findings in other crops [21,43]. The (AG/CT) n repeat was accounting for 45.8% of total identified SSRs, and was the predominant repeat motif in the whole genome of broomcorn millet.…”

“…454 GS-FLX technology (next-generation sequencing) provides new opportunities for microsatellite isolation due to its high throughput, low cost of operation, and more thorough representation of the genome [15,41]. To date, several crops have developed high-throughput and novel genomic SSR markers via 454 GS-FLX sequencing [18][19][20][21]42]. In this study, massively parallel sequencing technology was adopted and hoped to discovery numerous SSR with high quality from genome of broomcorn millet quickly.…”

“…In conjunction with selective hybridization, NGS technologies can be used in highthroughput applications to develop and identify sequences that flank simple sequence repeat (SSR) regions. Species-specific SSR markers in mung beans [18], endangered dwarf bulrushes [19], fava beans [20], and grass peas [21] have been identified using this method and can be…”

Development and use of molecular markers: past and present

“…The advent of NGS has simplified the process of isolation of microsatellites a great deal, facilitating high throughput development of markers even in non-model species (Abdelkrim et al, 2009;Barnes et al, 2014;Gardner et al, 2011;Pukk et al, 2014;Yang et al, 2014) in a time and cost-effective manner (Csenscics et al, 2010). Microsatellites are still mined using the common software programs such as Msatcommander, E-TRA, msatfinder, that were used to search sequences obtained using first generation sequencers.…”

β-N-oxalyl-L-2,3-diaminopropionic acid, L-homoarginine, and asparagine contents in the seeds of different genotypes Lathyrus sativus L. as determined by UHPLC-MS/MS

“…In the face of climate change challenges, researchers recently started to pay attention to the grass pea, which is considered a model crop for sustainable agriculture. [1][2][3][4] Lathyrus sativus L. is a legume crop from the genus Lathyrus that constitutes 187 species and subspecies. Lathyrus sativus L. is widely cultivated as food and feed in Central, Southern, and Eastern Europe, North Africa the Mediterranean, and across Asia.…”