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Build off exposed and disguised Marey maps

June 25, 2023 SwingingHeaven visitors

Build off exposed and disguised Marey maps

SNP genotyping

Bulk samples of dried leaves or kernels from up to eight Dstep 1 plants derived from the same D0, were used for DNA extraction using the cetyl trimethylammonium bromide (CTAB) procedure. DNA samples were adjusted to 50 to 70 ng/?l and 200 ng per sample were used for genotyping. DH line purity and integrity was first checked using a custom 96plex VeraCode assay (Illumina ® , San Diego, CA, USA) with genome-wide SNP markers to ensure that the lines carried only one of the parental alleles at each SNP, that they did not carry alleles of the inducer line and that they were derived from true F1 plants. For a subset of DH lines, 13 proprietary SNP markers assayed with the KASP™ technology (LGC Genomics, Berlin, Germany) were used for testing line purity and integrity. True DH lines were then used for genotyping with the Illumina ® MaizeSNP50 BeadChip on an Illumina ® iScan platform. Array hybridization and raw data processing were performed according to manufacturer’s instructions (Illumina ® ). Raw data were analyzed in Illumina ® ‘s Genome Studio software version v2011 (Illumina ® ) using an improved version of the public cluster file (MaizeSNP50_B.egt, ). SNP data were filtered based on the GTscore using a threshold of 0.7. Heterozygous SNPs were set to missing values (NA) and only markers with a minor allele frequency >0.1 per population were used for mapping. For each population, the allele of the central line was coded as the ‘A’ allele, and the allele of the founder line was coded as ‘B’ allele (Additional file 4). Raw https://datingranking.net/pl/swingingheaven-recenzja/ genotyping data of parents and DH lines are available at NCBI Gene Expression Omnibus as dataset GSE50558 .

Study off parental hereditary variety

Hereditary assortment between parental traces is analyzed which have genome-wider SNP markers by dominant coordinate research, team analysis, by a beneficial pairwise genome inspect to possess polymorphism between the parents of each society. Getting facts, come across Even more document 8.

Hereditary chart design

Hereditary charts were developed for each personal populace just like the described prior to playing with CarthaGene named out of individualized R scripts. In the first step, mathematically sturdy scaffold maps were constructed with marker ranges away from within least ten cM. When you look at the an extra step, ework maps who has as numerous markers to, while keeping good LOD rating >step three.0 towards robustness off marker orders. Finally, the entire maps was in fact gotten from the placement of extra indicators using bin-mapping . CentiMorgan (cM) ranges was in fact determined using Haldane’s mapping form . Personal genetic maps and you will genotypic data useful framework of one’s charts (More file 4) were transferred at MaizeGDB beneath the investment acronym CORNFED .

Physical map coordinates of SNPs

Chromosome and you may updates tasks off SNPs of your own MaizeSNP50 BeadChip offered by the manufacturer (Illumina ® , North park, Ca, USA), are based on the new B73 AGPv1 system with many markers not having an excellent chromosome and you can/otherwise position recommendations. We thus performed another type of mapping of SNPs to the B73 AGPv2 set-up playing with BWA . The latest projects were utilized for everyone analyses amongst the physical mapping recommendations. Projects appear in Extra file 4.

Given an excellent chromosome additionally the relevant hereditary chart of individuals people, i calculated the brand new marker ranking on B73 construction. From the physical and you can genetic ranking, we constructed a first Marey map that contains all syntenic indicators. Which Marey map are smoothed using cubic spline interpolations , creating a ‘bare’ Marey map that was compelled to become monotonic. Up coming regions where mapping advice was without having (instance, segments IBD regarding mothers) was disguised, generating ‘masked’ Marey maps (Additional document nine). This new detailed techniques is informed me inside the More file 8.

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