The 90 K iSelect array developed by Illumina CSPro (San Diego, CA, USA) as described by Wang et al. [35 (link)] was used to genotype the two parental lines and the 423 DH lines. Details on the genotyping and high density linkage map construction on this population were reported by Sari et al. (2018). Briefly, the genetic linkage map developed by Sari et al. [34 (link)] and used here consisted of 2,943 SNP markers in 19 linkage groups with an average marker density of 0.6 cM. The total length of the map was 1,808.4 cM.
90k iselect array
Manufactured by Illumina
Sourced in United States
The 90K iSelect array is a high-throughput genotyping tool designed for large-scale genetic studies. It allows the simultaneous analysis of up to 90,000 genetic markers across the human genome. The array provides a comprehensive and cost-effective solution for researchers interested in exploring genetic variations and associations.
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Lab products found in correlation
4 protocols using 90k iselect array
1
High-density Linkage Mapping of Crop Population
2
Wheat Genome Genotyping Protocol
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Genomic DNA was extracted from fresh leaves of field grown non-infected plants at seedling stage using the CTAB method [52 (link)]. The association mapping population was genotyped from the wheat Illumina 90 K iSelect array with 81,587 SNPs (Wang et al. 2014) at the Biotechnology Center, Department of Plant Sciences, University of California, USA, using the Illumina SNP genotyping platform and BeadArray Microbead Chip [53 (link)]. To avoid spurious marker-trait associations (MTAs), SNP markers with minor allele frequencies (MAF) < 0.05 and missing data > 10% were excluded from subsequent analyses. The physical positions of SNP markers were obtained from Chinese Spring reference genome sequences at the International Wheat Genome Sequencing Consortium website (IWGSC, http://www.wheatgenome.org/ ).
3
Constructing Genetic Maps of Wheat Populations
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A genetic map constructed with 398 DArT and PCR-based markers was available for the CirNeo population [53 (link)]. For the CicSve [38 (link)], LatMG [54 (link)] and NCCR [38 (link)] populations, genetic maps were previously developed with SNP markers from the Illumina wheat 90K iSelect array [59 (link)].
For all the maps, the marker segregation data were used for chi-square analyses to determine the segregation ratio and the deviation from the expected 1:1 ratio of each marker at p > 0.001. All markers with more than 10% missing data, and a null allele at one parent that was segregating for presence/absence in the mapping population, were excluded from further analysis. Physically mapped markers onto the reference durum genome [32 (link)] and marker data from the durum wheat consensus map [60 (link)] were used as anchor loci to compare the QTL map position across the four mapping populations.
For all the maps, the marker segregation data were used for chi-square analyses to determine the segregation ratio and the deviation from the expected 1:1 ratio of each marker at p > 0.001. All markers with more than 10% missing data, and a null allele at one parent that was segregating for presence/absence in the mapping population, were excluded from further analysis. Physically mapped markers onto the reference durum genome [32 (link)] and marker data from the durum wheat consensus map [60 (link)] were used as anchor loci to compare the QTL map position across the four mapping populations.
4
Genotyping of RIL Mapping Population
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The 90K iSelect array developed by Illumina CSPro® (San Diego, CA, USA) and described by Wang et al. (2014) (link) was used to survey 81,587 SNP sequences across the two parental lines and the whole RIL mapping population. Genotyping was performed on 1 μg of genomic DNA at “TraitGenetics” GmbH (Gatersleben, Germany)1 following the manufacturer’s recommendations as described by Akhunov et al. (2009) (link). The genotyping assays were carried out on the Illumina iScan reader and performed using GenomeStudio software v 2011.1 (Illumina CS Pro®). Each marker was tested for deviation from the expected 1:1 ratio by Chi-square analysis. Linkage analysis and map construction were performed by the JoinMap software v. 4.0 (Van Ooijen and Voorrips, 2001 ) and the Kosambi mapping function was used to calculate map distances (Kosambi, 1944 (link)). Linkage groups (LGs) were established using a minimum LOD score of 10.0 after preliminary analysis using LOD scores ranging from 3 to 5.
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