Search

Additional file 5: Figure S5. Manhattan and Q-Q plots of non-significant GWAS results. GWAS was performed with FarmCPU software and a significant p-value threshold set at P = 10–7. Four of the 10 traits studied, milk yield (MY), fat yield (FY), protein percentage (PP), and age at first calving (AFC), resulted in no SNPs passing the Bonferroni threshold, as illustrated by the Manhattan plots on the left. On the right, Q-Q plots are displayed as scatter plots of true and expected log p-values.

Additional file 6: Figure S6. Manhattan and Q-Q plots of GWAS results, without considering population structure. These Manhattan plots (left) illustrate results from an association analysis model that did not consider population structure. GWAS was performed with FarmCPU software and a significant p-value threshold set at P = 10–7. Q-Q plots (right) are displayed as scatter plots of true and expected log p-values. Milk traits include milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FP), protein percentage (PP), and somatic cell score (SCS). Reproductive traits include age at first service (AFS), age at first calving (AFC), gestation length (GL), and calving interval (CI).

Additional file 7: Table S1. Genomic inflation factor (lambda) of each trait.

Additional file 4: Figure S4. Scatter plot between principal components and trait phenotypes. We used these plot to determine which traits were correlated with population structure, represented by principal components (PC). Columns represent the first three principal components, rows represent each trait. Milk traits include milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FP), protein percentage (PP). and somatic cell score (SCS). Reproductive traits include age at first service (AFS), age at first calving (AFC), gestation length (GL), and calving interval (CI).

Additional file 1: Figure S1. Correlations and distributions of phenotypes, EBVs (estimated breeding values), and residuals. The histograms on the diagonal are the distributions for each trait: MY = milk yield, FY = fat yield, PY = protein yield, FP = fat percentage, PP = protein percentage, SCS = somatic cell score, AFS = age at first service, AFC = age of first calving, GL = gestation length, and CI = calving interval. The upper triangle is comprised of the correlation coefficients among traits. The lower triangle is comprised of the pairwise scatter plots. Graphs a, b, c illustrate milk trait phenotypes, EBVs, and residuals, respectively. Graphs d, e, f illustrate reproduction trait phenotypes, EBVs, and residuals, respectively.

Additional file 3: Figure S3. Display of significant markers as visible bands at different width. The number significant markers were determined by the P-value cut off with three levels illustrated on the left. The significant markers are displayed as bands with width indicated on the top starting from 100 kb to 10,000 kb. More bands are visible with wider bands than narrow bands. Wide band and less stringent P value threshold (e.g. to right) demonstrate pleiotropy of significant markers across traits. These traits include milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FP), protein percentage (PP), and somatic cell score (SCS). Reproductive traits include age at first service (AFS), age at first calving (AFC), gestation length (GL), and calving interval (CI).

Additional file 4: Figure S1. Manhattan and Q–Q plots of genome-wide association analyses for TeW and TeP, generated with GAPIT, EMMAX, GenABEL (GRAMMAR) and GEMMA software. The solid line indicates genome-wide significance of association (P value

Additional file 3: Table S3. Primer sequences used to analyze gene expression.

with legends. GWAS results of individual traits and the correlation of different traits. (PDF 21,979Â kb) (PDF 21766Â kb)

Additional file 5: Figure S2. Scatter plots of the expression level ( $$ 2^{{ -\Delta C_{\text{t}} }} $$ 2 - Î C t ) of the TCF21 gene in testis tissue versus testis weight (TeW) in the lean and fat lines from G19 using two different housekeeping genes as internal references. TeWÂ =Â testis weight.

Additional file 1: Table S1. Generations of NEAUHLF chickens used for the different analyses in the current study.

Additional file 2: Table S2. Number of SNPs and average density on each chromosome.

Whole-genome SNP and INDEL distribution. (PDF 133Â kb)

Whole-genome SNP and INDEL distribution. (PDF 133Â kb)

Additional file 7: Table S5. Summary of statistics for core haplotypes with P

Additional file 8 Known functions of the remaining eight candidate genes. Description: This file describes the basic functions of the other eight genes detected in the GWAS and their possible involvement in spermatogenesis [39â 82].

Additional file 6: Table S4. Alignment of chicken TCF21 protein sequences with those of other species.

Joint QTL validation between the CN-NAM and US-NAM populations under the WW and WS conditions. (DOCX 18Â kb)

Statistical analysis of the seven drought-related traits value under WW and WS within the US-NAM population. (DOCX 19Â kb)

Correlation of the seven drought-related traits under the WW (above diagonal) and WS (under diagonal) conditions within the CN-NAM population. (DOCX 19Â kb)

Joint QTL validation between the CN-NAM and US-NAM populations under the WW and WS conditions. (DOCX 18Â kb)

Statistical analysis of the seven drought-related traits value under WW and WS within the US-NAM population. (DOCX 19Â kb)

Statistical analysis of the seven drought-related traitsâ BLUP values under the WW and WS conditions within the CN-NAM population. (DOCX 19Â kb)

Correlation of the seven drought-related traits under the WW (above diagonal) and WS (under diagonal) conditions within the CN-NAM population. (DOCX 19Â kb)

Correlation of the seven drought-related traits under the WW (above diagonal) and WS (under diagonal) conditions within the US-NAM population. (DOCX 19Â kb)

The overlap or linkage relationship of peak SNP and known QTL associated with SCN resistance. (PDF 242 kb)

Sources and distributions of 440 soybean accessions. (PDF 433 kb)