Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

Abstract

Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.

Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes

“…It indicated that P. equestris, has AT-rich genome with approximately 47,007 genes. In general, GC% in monocot plant ranges from 33.6 to 48.9% (Jiangfeng et al 2014). The GC% in the four orchids species in the present investigation indicates that they have little higher GC% that signifies complex genome architecture compared to other plant groups.…”

“…Total sequence read was 553.3 Kbp in Geodorum (submitted to NCBI SRA archive with Table 1). The GC content was 35.95% in case of Phalaenopsis equestris based on whole genome sequencing report (Jiangfeng et al 2014) with genome size 1600 Mb (Diploid chromosome number 2n = 38, with 3.37 pg DNA/diploid genome). It indicated that P. equestris, has AT-rich genome with approximately 47,007 genes.…”

“…Partial genome sequence was carried out in one important orchid (Phalaenopsis equestris) (Hsu et al 2011) and then whole genome was completely sequenced for its characterization and phylogenetic analysis (Cai et al 2015). But reduced representation of the genomic segment has been sequenced in many organism using RAD, ddRAD, GBS methods based on NGS technology for genetic diversity and phylogenetic relationship using SNPs marker (Baird et al 2008;Etter et al 2011;Peterson et al 2012;Jiangfeng et al 2014;Wataru et al 2014).…”

Generation and Characterisation of a Reference Transcriptome for Phalaris (Phalaris aquatica L.)

“…In the latter category, individual marker loci are likely to be of limited value, as for most other forage species, due to a relative paucity of agronomic traits under simple genetic control. As genomic selection requires a very large number of sequence polymorphism evenly distributed across the entire genome, genotyping-by-sequencing (GBS) methods provide the method of choice [46]. A GBS methodology based on sampling of the expressed component of the genome by RNA-Seq has previously been reported [47].…”

DNA markers reveal genetic structure and localized diversity of Ethiopian sorghum landraces

“…These markers have been widely used for reliable and robust characterization of crop genetic resources (Godwin et al, 1997;Pejic et al, 1998;Smith et al, 2000;Wen et al, 2002;Uptmoor et al, 2003;Medraoui et al, 2007;Weerasooriya et al, 2016). With the development of high-throughput sequencing (or next-generation sequencing-NGS) technologies in recent years, marker techniques such as single nucleotide polymorphism (SNPs) and genotyping by sequencing (GBS) have become very useful for exploring the diversity within plant species, constructing haplotype maps and performing genome-wide association studies as well as genomicsassisted breeding (He et al, 2014). The exploitation of molecular markers in characterizing the variability of Ethiopian sorghums is very limited.…”