Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications

Autoři: Ratna Kumari aff001;  Dhammaprakash Pandhari Wankhede aff001;  Akansha Bajpai aff001;  Avantika Maurya aff001;  Kartikay Prasad aff001;  Dikshant Gautam aff001;  Parimalan Rangan aff001;  M. Latha aff001;  Joseph John K. aff001;  Suma A. aff001;  Kangila V. Bhat aff001;  Ambika B. Gaikwad aff001
Působiště autorů: ICAR-National Bureau of Plant Genetic Resources, New Delhi, India aff001
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article


Black pepper is one of the most valued and widely used spices in the world and dominates multi-billion dollar global spices trade. India is amongst the major producers, consumers and exporters of black pepper. In spite of its commercial and cultural importance, black pepper has received meagre attention in terms of generation of genomic resources. Availability of markers distributed throughout the genome would facilitate and accelerate genetic studies, QTL identification, genetic enhancement and crop improvement in black pepper. In this perspective, the sequence information from the recently sequenced black pepper (Piper nigrum) genome has been used for identification and characterisation of Simple Sequence Repeats (SSRs). Total 69,126 SSRs were identified from assembled genomic sequence of P. nigrum. The SSR frequency was 158 per MB making it, one SSR for every 6.3 kb in the assembled genome. Among the different types of microsatellite repeat motifs, dinucleotides were the most abundant (48.6%), followed by trinucleotide (23.7%) and compound repeats (20.62%). A set of 85 SSRs were used for validation, of which 74 produced amplification products of expected size. Genetic diversity of 30 black pepper accessions using 50 SSRs revealed four distinct clusters. Further, the cross species transferability of the SSRs was checked in nine other Piper species. Out of 50 SSRs used, 19 and 31 SSRs were amplified in nine and seven species, respectively. Thus the identified SSRs may have application in other species of the genus Piper where genome sequence is not available yet. Present study reports the first NGS based genomic SSRs in black pepper and thus constitute a valuable resource for a whole fleet of applications in genetics and plant breeding studies such as genetic map construction, QTL identification, map-based gene cloning, marker-assisted selection and evolutionary studies in Piper nigrum and related species.

Klíčová slova:

Comparative genomics – Crop genetics – Evolutionary genetics – Gene mapping – Genomic libraries – India – Microsatellite loci – Sequence motif analysis


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