Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut

Abstract

With the aim to increase the number of functional markers in resource poor crop like cultivated peanut (Arachis hypogaea), large numbers of available expressed sequence tags (ESTs) in the public databases, were employed for the development of novel EST derived simple sequence repeat (SSR) markers. From 16424 unigenes, 2784 (16.95%) SSRs containing unigenes having 3373 SSR motifs were identified. Of these, 2027 (72.81%) sequences were annotated and 4124 gene ontology terms were assigned. Among different SSR motif-classes, tri-nucleotide repeats (33.86%) were the most abundant followed by di-nucleotide repeats (27.51%) while AG/CT (20.7%) and AAG/CTT (13.25%) were the most abundant repeat-motifs. A total of 2456 EST-SSR novel primer pairs were designed, of which 366 unigenes having relevance to various stresses and other functions, were PCR validated using a set of 11 diverse peanut genotypes. Of these, 340 (92.62%) primer pairs yielded clear and scorable PCR products and 39 (10.66%) primer pairs exhibited polymorphisms. Overall, the number of alleles per marker ranged from 1-12 with an average of 3.77 and the PIC ranged from 0.028 to 0.375 with an average of 0.325. The identified EST-SSRs not only enriched the existing molecular markers kitty, but would also facilitate the targeted research in marker-trait association for various stresses, inter-specific studies and genetic diversity analysis in peanut.

De novo sequencing and comparative analysis of leaf transcriptomes of diverse condensed tannin-containing lines of underutilized Psophocarpus tetragonolobus (L.) DC

“…Our result showed 2237 SSRs in HCTW and 1618 SSRs in LCTW, which was near to transcript data showed by other legumes19. Trinucleotide repeats were more predominantly present in our data like other legumes medicago trancatula and Arachis hypogaea 4445.…”

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers

“…Of these, tri-nucleotide repeats were the most abundant, a sensible result given the coding nature of the transcriptome [82]. Other legumes exhibit the same trend, including the winged bean [29] and peanut [83]. …”

Advancements in molecular marker development and their applications in the management of biotic stresses in peanuts

“…However, the available transcriptome sequences are not complete; many have low N50 values, ranging from 500 to 750 bp Chopra et al, 2014). On the basis of gene annotations, Bosamia et al (2015) has identified 2784 SSR containing sequences, of which, 2027 (72.81%) were annotated and assigned in 4124 gene ontology terms and 31.91% sequences were found to be associated with response to stimulus encompassing biotic as well as abiotic stresses.…”

“…From 16424 unigenes, using MISA (MIcroSAtellite identification tool) search, a total of 2456 novel EST-SSR primer pairs were designed; of which 366 unigenes, having relevance to various stresses and other functions were PCR validated using a set of 11 diverse peanut genotypes (both resistant and susceptible to various diseases). Of these, 340 primer pairs yielded clear and scorable PCR products and 39 primer pairs exhibited polymorphisms which are of potential use for the resistance breeding programme (Bosamia et al, 2015). Out of 411 sorghum EST-SSR (SbEST-SSR) markers tested in peanuts, 39% could be successfully amplified, of which 14% showed polymorphism among resistant and susceptible cultivars for rust and LLS diseases (Savadi et al, 2012).…”

“…RILs are being developed to map various genes/QTLs underlying these traits. Currently, more than 14,000 SSR markers are available from different sources; however, substantial efforts are still required to develop sufficient PCR-based markers for the construction of a high-density genetic linkage map and for routine applications in the molecular breeding of peanuts Bosamia et al, 2015).…”