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

Abstract

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.

Genome-wide identification of microsatellite markers and their application in genetic studies of wolfberry (Lycium barbarum)

“…Pentanucleotides, tetranucleotides, and hexanucleotides were less abundant, together accounting for 25.26% (Figure 2A) in the wolfberry genome. Similar results have been reported for several other plant species (Cheng et al, 2016; Kumari et al, 2019; Liu et al, 2018; Pandey et al, 2013). Previous studies have reported that tetranucleotide, pentanucleotide, and hexanucleotide repeats are the most common repeat in the cucumber (Cavagnaro et al, 2010), peanut (Lu et al, 2019), and Gossypium (Wang et al, 2015) genomes, respectively.…”

“…It is noteworthy that the nature of the most abundant dinucleotide repeat sequences of differs among plant species. For example, AG/CT is most abundant in tea (Liu et al, 2018), foxtail millet (Pandey et al, 2013), and Chinese spring wheat (Han et al, 2015), whereas AT/TA is most abundant in watermelon (Zhu et al, 2016), black pepper (Kumari et al, 2019), and cucumber (Cavagnaro et al, 2010).…”

Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)

“…With the emergence of NGS technology, the large-scale development of SSR markers based on genome-wide analysis directly or indirectly promotes the rapid development of marker-assisted breeding. A substantial number of SSR markers have been widely recognized in a variety of plants, including black pepper, pepper, pear, bitter gourd, bread wheat, Camellia sinensis and eggplant, by the analysis of genome-wide sequence data generated ( Cui et al, 2017 ; Liu et al, 2018 ; Portis et al, 2018 ; Xue et al, 2018 ; Kumari et al, 2019 ; Uncu, 2019 ; Ahmed et al, 2020 ). In this study, a large number of SSR primer sets were the first ones to be comprehensively and successfully designed from the whole genome of cabbage, which is specific to previous studies.…”

Genome-wide characterization of simple sequence repeats in Palmae genomes

“…The high mutation rates of SSRs make them highly informative and useful for a wide range of applications such as evolutionary research, population genotyping, and markerassisted breeding. Recent studies have utilized genomewide approaches for the development of SSR markers in plants (Shi et al 2014;Deng et al 2016;Kumari et al 2019). Perhaps the main advantage of this strategy is to produce a large number of SSR markers distributed evenly throughout the genome.…”