First de novo genome-specific development, characterization and validation of simple sequence repeat (SSR) markers in Bambusa polymorpha, a commercially important bamboo of India.

Abstract

The natural population of Bambusa polymorpha have not been genetically enumerated due to a lack of genome sequence information or robust species-specific molecular marker. The present study was conducted to develop and validate genome-wide de novo simple sequence repeat (SSRs) markers in B. polymorpha through shallow-pass genome sequencing. The genome sequence data of about 13 Gb was generated using Illumina technology, and high-quality sequence reads were de novo assembled into 1,390,995 contigs with GC content 42.34%, contig N 50 value 1047 bp. The Benchmark Universal Single-Copy Ortholog (BUSCO) analysis indicated 75.29% of complete and single-copy genome assembly. By scanning of genome assembly, a total of 73,468 simple sequence repeats (SSRs) were identified, and 44,383 primer pairs were designed. Repeat analysis revealed that the dinucleotide and trinucleotide repeats were most abundantly distributed in the genome with 52.95 and 41.17%, respectively. A subset of 33 SSRs was randomly selected for their PCR amplification and polymorphism in 16 random individuals. Of these, 29 SSRs were successfully amplified with the expected product size and 20 showed polymorphic banding patterns. Polymorphic SSRs were characterized by high expected heterozygosity (H _e = 0.72) and polymorphism information content (PIC = 0.68). The clustering pattern obtained using the neighbor joining (NJ) dendrogram revealed the genotypes were clustered in accordance with their geographical locations. The genomic and marker information generated in this study are novel and useful for future studies for genetic improvement and conservation of B. polymorpha.