The massive power of the NGS technology for rapid and large scale marker discovery laid the foundation for the super-fast development of markers linked to the target gene Lanr1 demonstrated in this study.
The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs.
Since our study examined the distribution of allelic frequencies on a larger scale (markers were spaced about every 10 Kb in genes) and the regions found are much larger (average size = 107 Kb, 95% C.I. = 5 977, from a lognormal distribution), recombination cold spots are unlikely to explain the regions we have discovered.
Herein we report a high-density genetic map for soybean, which is constructed based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq).
Information from these large-scale markers will serve as a foundation for constructing high-density genetic maps, cloning and mapping of important genes, improving gene prediction and annotation, and elucidating the interspecific divergence in different cotton species.
High-throughput genotyping technology and phenotyping platforms have enabled large-scale marker-trait association analysis, such as genome-wide association studies, to precisely dissect the genetic architecture of plant traits.
Hence, the PLUG system is an effective tool for large-scale marker development.
Although a large number of SNPs can be readily discovered from these resources, large-scale marker development and evaluation are seldom performed for such in silico predicted SNPs.
Restriction site-associated DNA sequencing (RAD-Seq) is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing.
Consequently, SLAF-seq is an ideal strategy for large-scale marker developing and genotyping for species which is lack of reference genome information, such as wax gourd.
Future work with large-scale marker development and mapping, and physical anchoring with monosomic oat hybrids, should help to resolve this question.
