Development of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) species

Ndjiondjop, Marie Noëlle; Semagn, Kassa; Zhang, Jian Wei; Gouda, Arnaud Comlan; Kpeki, Sèdjro Bienvenu; Goungoulou, Alphonse; Wambugu, Peterson W.; Dramé, Khady Nani; Bimpong, Isaac Kofi; Zhao, Di

doi:10.1007/s11032-018-0885-z

Cited by 27 publications

(45 citation statements)

References 36 publications

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“…They recommended a set of 50-100 SNPs for routine QC after finding about 29% heterogeneity in inbred lines. In rice, [2] recommended a subset of 24-36 SNP markers filtered from DArTSeq developed markers for genetic purity analyses. In sweetpotato, QA/QC problems in breeding operations have been shown in the current manuscript by monitoring the rate of misclassification as materials moved through different stages of breeding trialing.…”

Section: Plos Onementioning

confidence: 99%

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Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

et al. 2020

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Quality assurance and control (QA/QC) is an essential element of a breeding program's optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)'s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping studies. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers' fields. The study also enabled evaluation of CIP's global breeding population structure and the effect of some of the most devastating stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato.

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Section: Plos Onementioning

confidence: 99%

“…Development of user-friendly, low-cost, high-throughput markers for quality assurance and control (QA/QC) in a genomic-assisted breeding (GAB) era is a critically important aspect in crop improvement and germplasm conservation [1,2]. This is because genetic fidelity and trueness-to-type are often not phenotypically obvious.…”

Section: Introductionmentioning

confidence: 99%

Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

et al. 2020

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“…They recommended a set of 50-100 SNPs for routine QC after finding about 29% heterogeneity in inbred lines. In rice, Ndjiondjop et al 2018 recommended a subset of 24-36 SNP markers filtered from DArTSeq developed markers for genetic purity analyses. In sweetpotato, QA/QC problems have recently been acknowledged ( Gemenet et al 2019a ) by monitoring the rate of misclassification as materials moved through different stages of breeding trialing.…”

Section: Discussionmentioning

confidence: 99%

“…Development of user-friendly, low-cost, high-throughput markers for quality assurance and control (QA/QC) in a genomic-assisted breeding era is a critically important aspect in crop improvement and germplasm conservation ( Semagn et al 2012; Ndjiondjop et al 2018 ). This is because genetic fidelity and trueness-to-type are often not phenotypically obvious.…”

Section: Introductionmentioning

confidence: 99%

Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

Gemenet¹,

Kitavi²,

David³

et al. 2019

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AbstractQuality assurance and control (QA/QC) is an essential element of a breeding program’s optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)’s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers fields. The study also enabled evaluation of CIP’s global breeding population structure and the effect of some of the most devastating biotic stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato.Key MessageA 36-SNP diagnostic marker set has been developed for quality assurance and control to support global sweetpotato breeding optimization efforts. Breeding population structure is shaped by sweetpotato virus disease prevalence.

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“…About 92% of the African rice (Ndjiondjop et al 2017 ) and 43% of the Asian rice (Ndjiondjop et al 2018a ) samples had been previously used for genetic diversity and population structure studies conducted within each species. Nearly, all samples had also been used for identification of species- and subspecies-diagnostic SNPs for routine genotyping quality control analysis to minimize errors during germplasm collection, acquisition and routine genebank operations (Ndjiondjop et al 2018b ). The detailed procedures for genomic DNA extraction and SNP genotyping using DArTseq™ were described in our previous study (Ndjiondjop et al 2017 ).…”

Section: Methodsmentioning

confidence: 99%

Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice

et al. 2018

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Key message The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Abstract Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice ( Oryza glaberrima Steud.) as compared to its wild progenitor ( O. barthii A. Chev.) and to Asian rice ( O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii , respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1–32.1 and 16.3–37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10 −4 , which is not only 20-fold smaller than the value estimated from all genomewide SNPs ( π = 1.6 × 10 −2 ), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii , lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use. Electronic supplementary material The online version of this article (10.1007/s00122-018-3268-2) contains supplementary material, which is available to authorized users.

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Development of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) species

Cited by 27 publications

References 36 publications

Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice

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