1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice

Juan David Arbelaez, Maria Stefanie Dwiyanti, Erwin Tandayu, Krizzel Llantada, Annalhea Jarana, John Carlos Ignacio, John Damien Platten, Joshua Cobb, Jessica Elaine Rutkoski, Michael J. Thomson, Tobias Kretzschmar

Research output: Contribution to journalArticle

Abstract

Background: While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs. Results: Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications. Conclusions: This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications.

Original languageEnglish (US)
Article number55
JournalRice
Volume12
Issue number1
DOIs
StatePublished - Dec 1 2019
Externally publishedYes

Fingerprint

genotyping
rice
breeding
assay
assays
genomics
marker-assisted selection
customs
genome
cost
MAS
prediction
germplasm
marker
subpopulation
repeatability
genetic relationships
flowering
gene frequency
quantitative trait loci

Keywords

  • Amplicon-based next generation sequencing
  • Breeding and genotyping
  • Genomic selection
  • Indica
  • Marker-assisted selection (MAS)
  • Oryza sativa
  • Single nucleotide polymorphism (SNP)
  • SNP fingerprinting

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Soil Science
  • Plant Science

Cite this

1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice. / Arbelaez, Juan David; Dwiyanti, Maria Stefanie; Tandayu, Erwin; Llantada, Krizzel; Jarana, Annalhea; Ignacio, John Carlos; Platten, John Damien; Cobb, Joshua; Rutkoski, Jessica Elaine; Thomson, Michael J.; Kretzschmar, Tobias.

In: Rice, Vol. 12, No. 1, 55, 01.12.2019.

Research output: Contribution to journalArticle

Arbelaez, JD, Dwiyanti, MS, Tandayu, E, Llantada, K, Jarana, A, Ignacio, JC, Platten, JD, Cobb, J, Rutkoski, JE, Thomson, MJ & Kretzschmar, T 2019, '1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice', Rice, vol. 12, no. 1, 55. https://doi.org/10.1186/s12284-019-0311-0
Arbelaez, Juan David ; Dwiyanti, Maria Stefanie ; Tandayu, Erwin ; Llantada, Krizzel ; Jarana, Annalhea ; Ignacio, John Carlos ; Platten, John Damien ; Cobb, Joshua ; Rutkoski, Jessica Elaine ; Thomson, Michael J. ; Kretzschmar, Tobias. / 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice. In: Rice. 2019 ; Vol. 12, No. 1.
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AU - Tandayu, Erwin

AU - Llantada, Krizzel

AU - Jarana, Annalhea

AU - Ignacio, John Carlos

AU - Platten, John Damien

AU - Cobb, Joshua

AU - Rutkoski, Jessica Elaine

AU - Thomson, Michael J.

AU - Kretzschmar, Tobias

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N2 - Background: While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs. Results: Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications. Conclusions: This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications.

AB - Background: While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs. Results: Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications. Conclusions: This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications.

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KW - Indica

KW - Marker-assisted selection (MAS)

KW - Oryza sativa

KW - Single nucleotide polymorphism (SNP)

KW - SNP fingerprinting

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