Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice

Abstract

Background Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers’ nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection results. Results Evaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7–8 ng/μL) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F 6 ) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~ 99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost–benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations. Conclusion This study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development. Electronic supplementary material The online version of this article (10.1186/s13007-019-0464-2) contains supplementary material, which is available to authorized users.

Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing

“…Because we arrived at broadly similar conclusions regardless of sampling methods for most applications, we do not believe the additional information obtained by genotyping 5–15 individuals justify the multi-fold increase in cost. Furthermore, sampling of 5–15 individuals per accession across thousands of accessions raises another concern in that the technical feasibility of sampling, processing, and tracking so many individuals, followed by managing the high-density genotypic data, will be extremely challenging 85 – 87 . Recently, our team genotyped 4,115 rice accessions with ~ 32,000 SNPs using DArTseq, which generated 650-megabytes of data.…”

QTL Validation and Development of SNP-based High Throughput Molecular Markers Targeting a Genomic Region Conferring Narrow Root Cone Angle in Aerobic Rice Production Systems

“…These other SNP genotyping platforms were also available but KASP has been in the forefront of these as it is more preferred due to its cost effectivity, assay conversion rate, accuracy, and exibility (Semagn et al 2014), especially in the context of marker assisted backcrossing and marker assisted recurrent selection applications. KASP technology have also been shown to work using single seed genotyping in rice, further facilitating its adoption in breeding programs by allowing breeders to combine rapid generation advance techniques more effectively (Arbelaez et al 2019b). To our knowledge, these are the rst high throughput SNP markers targeting root growth angle traits developed, whether in traditional ooded or in AP systems.…”

Opportunities and challenges of speed breeding: A review

“…The advantages of the SSD selection method include less growing area and labour being required for the handling of early generations. It allows for the advancement of progeny under high‐density plantings in small nurseries, growth chambers or greenhouses (Arbelaez et al., 2019; Funada et al., 2013). The negative aspect is that SSD carries forward more inferior progenies than pure line, pedigree and recurrent selection methods.…”