Journal: PLoS Genetics

Article Title: A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muffs and Beard Phenotype in Chickens

doi: 10.1371/journal.pgen.1006071

Figure Lengend Snippet: (A) The log 2 fold-change values from whole genome re-sequencing data illustrating the read depth differences between the HB and HQLA breeds. This analysis validates the presence of the CNVs on GGA27 in chickens with the Muffs and beard phenotype that were previously identified using a CGH array experiment. (B) Schematic illustration of the CNV rearrangements in the Mb locus on GGA27. (C) Genes located within the three duplicated CNV regions include the 3’ sequence of PSMC5 and entire SMARCD2 in CNV1 (green shadow), entire HOXB8 and HOXB7 in CNV2 (blue shadow), 5’ sequence of CCR7 , 3’ sequence of KRT222 , and entire SMARCE1 in CNV3 (pink shadow).

Article Snippet: Sequencing libraries (170-bp paired-end, 400-bp paired-end and 3-kb mate-pair) were constructed, and whole-genome re-sequencing was performed using the Illumina HiSeq 2000 platform by BGI (Shenzhen).

Techniques: Sequencing

Journal: PLoS Genetics

Article Title: A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muffs and Beard Phenotype in Chickens

doi: 10.1371/journal.pgen.1006071

Figure Lengend Snippet: The duplicated regions identified by array-CGH are illustrated by green (CNV1), blue (CNV2) and pink (CNV3) boxes, respectively. (A) The boundaries of the CNVs were tested using 8 primers indicated by the arrows located in the known duplicated region of CNV1 and CNV3. All possible amplifications were considered and performed in both Mb and wild-type chickens. (B) The breakpoints of both CNV1_3’ (1,721,521 bp) and CNV3_5’ (4,470,331 bp) were identified after sequencing the specifically-amplified PCR product obtained in Mb chickens using primer F1 and R2. An overlap of two nucleotides was detected in the junction region. Outward facing primers (green and pink arrows) were designed to analyze the other boundary of CNV1 and CNV3. (C) CNV2 was found to be located next to CNV3 in chickens with the Mb phenotype using a genome-walking strategy. The breakpoints of both CNV3_3’ (4,503,417 bp) and CNV2_5’ (3,578,409 bp) were verified by sequencing. A two-nucleotide insertion was found in the junction region. (D) The breakpoints of both CNV2_3’ (3,592,890 bp) and CNV1_5’ (1,702,269 bp) were confirmed through unmapped read alignment of whole genome re-sequencing data. An eight-base insertion was detected in the junction.

Article Snippet: Sequencing libraries (170-bp paired-end, 400-bp paired-end and 3-kb mate-pair) were constructed, and whole-genome re-sequencing was performed using the Illumina HiSeq 2000 platform by BGI (Shenzhen).

Techniques: Sequencing, Amplification

Journal: Frontiers in Plant Science

Article Title: Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat

doi: 10.3389/fpls.2019.01787

Figure Lengend Snippet: Primer sequences for kompetitive allele-specific PCR (KASP) markers designed from SNP sequences that showed association with Lr49 on chromosome 4BL and SNPs discovered from the sqeuences of flow sorted chromosome 4B of parental genotypes.

Article Snippet: The alignment of the flow-sorted chromosome paired-end sequence reads from each parent to the reference genome assembly of Chinese Spring using GYDLE software revealed the presence of two distinct sequence haplotypes in the susceptible parent WL711 that spanned the entire Lr49 region delineated by markers sunKASP_21 and sunKASP_36379 .

Techniques: Marker

Journal: Frontiers in Plant Science

Article Title: Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat

doi: 10.3389/fpls.2019.01787

Figure Lengend Snippet: Genetic linkage map of chromosome 4BL for the VL404/WL711 RIL population (A) Bansal et al. (2008) , (B) present study (resistance gene is shown in red text), and (C) high resolution map of VL404/Avocet S (number of recombinants is given on the left).

Article Snippet: The alignment of the flow-sorted chromosome paired-end sequence reads from each parent to the reference genome assembly of Chinese Spring using GYDLE software revealed the presence of two distinct sequence haplotypes in the susceptible parent WL711 that spanned the entire Lr49 region delineated by markers sunKASP_21 and sunKASP_36379 .

Techniques:

Journal: Frontiers in Plant Science

Article Title: Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat

doi: 10.3389/fpls.2019.01787

Figure Lengend Snippet: Comparison of Lr49 genetic linkage map with the 585 to 617 Mbp interval of Chinese Spring chromosome 4B physical map using Pretzel, a genetic map viewing software ( http://plantinformatics.io ). Markers distal to sunKASP _26 are colinear with the physical map (green connections). The genetic map order of markers proximal to sunKASP _21 does not reflect the physical map order in Chinese Spring (black connections).

Article Snippet: The alignment of the flow-sorted chromosome paired-end sequence reads from each parent to the reference genome assembly of Chinese Spring using GYDLE software revealed the presence of two distinct sequence haplotypes in the susceptible parent WL711 that spanned the entire Lr49 region delineated by markers sunKASP_21 and sunKASP_36379 .

Techniques: Comparison, Software

Journal: Frontiers in Plant Science

Article Title: Fine Mapping of Lr49 Using 90K SNP Chip Array and Flow-Sorted Chromosome Sequencing in Wheat

doi: 10.3389/fpls.2019.01787

Figure Lengend Snippet: Diagrammatic representation of the Lr49 interval and flanking region on chromosome 4B. Both VL404 (resistant parent) and WL711 (susceptible parent) have two sequence haplotypes outside the Lr49 region, while VL404 has only one sequence haplotype within the Lr49 interval. Chinese Spring has only one sequence haplotype across entire region. Each unique sequence haplotype is represented by a different color. Markers mapping within the Lr49 interval are ordered based on their physical mapping location. The Lr49 genetic map does not reflect the physical mapping order as illustrated by comparison of genetic and physical map order across the Lr49 interval. Differences in sequence haplotype structure and physical-genetic map order in VL404 and WL711, relative to Chinese Spring, suggests structural rearrangement or copy number variation (CNV) relative to Chinese Spring.

Article Snippet: The alignment of the flow-sorted chromosome paired-end sequence reads from each parent to the reference genome assembly of Chinese Spring using GYDLE software revealed the presence of two distinct sequence haplotypes in the susceptible parent WL711 that spanned the entire Lr49 region delineated by markers sunKASP_21 and sunKASP_36379 .

Techniques: Sequencing, Comparison