An ISSR-based genetic diversity analysis of Malus sieversii in Tienshan Mountains in Xinjiang, China and Kyrgyzstan

Malus sieversii constitute a valuable genetic resource in wild apple ecosystems. The aim of this study was to use inter-simple sequence repeat (ISSR) primers as an accessible tool to investigate the genetic diversity in Malus sieversii species. The experimental materials include 34 samples from Kyrgyzstan and Xinjiang of China. A total of 125 bands and 98 polymorphic bands were amplified using 47 ISSR primers. The polymorphism rate was 78.4%. The genetic similarity coefficient of Kyrgyzstan and Xinjiang of China population was 0.68; the genetic similarity coefficient of various populations in Xinjiang was 0.72~0.94. The samples in same population got into a category, but some samples in faraway geographic locations have cross clustering. Geographical isolation hindered the gene exchange of Malus sieversii in different populations for a long time, and Malus sieversii developed along the natural selection environment direction and generate genetic differentiation after that

DataSheet_1_Rediscover and Refine QTLs for Pig Scrotal Hernia by Increasing a Specially Designed F3 Population and Using Whole-Genome Sequence Imputation Technology.pdf

Pig scrotal hernia is one of the most common congenital defects triggered by both genetic and environmental factors, leading to severe economic loss as well as poor animal welfare in the pig industry. Identification and implementation of genomic regions controlling scrotal hernia in breeding is of great appeal to reduce incidences of hernia in pig production. The aim of this study was to identify such regions or molecular markers affecting scrotal hernia in pigs. First of all, we summarized and analyzed the results of some international teams on scrotal hernia and designed a specially population which contains 246 male individuals. We then performed genome-wide association study (GWAS) in this specially designed population using two scenarios, i.e., the target panel data before and after imputation, which contain 42,365 SNPs and 18,756,672 SNPs, respectively. In addition, a series of methods including genetic differentiation analysis, linkage disequilibrium and linkage analysis (LDLA), and haplotype sharing analysis were appropriate to provide for further analysis to identify the potential gene underlying the QTL. The GWAS in this report detected a highly significant region affecting scrotal hernia within a 24.8Mb region (114.1–138.9Mb) on SSC8. And the result of genetic differentiation analysis also showed a strong genetic differentiation signal between 116.1 and 132.7Mb on SSC8. In addition, the QTL interval was refined to 2.99Mb by combining LDLA and genetic differentiation analysis. Finally, two susceptibility haplotypes were identified through haplotype sharing analysis, with one potential causal gene in it. Our study provided deeper insights into the genetic architecture of pig scrotal hernia and contributed to further fine-mapping and characterize haplotype and gene that influence scrotal hernia in pigs.</p

Additional file 9 of Identification and validation of a regulatory mutation upstream of the BMP2 gene associated with carcass length in pigs

Additional file 9. Table S5. The associations between some candidate casual mutations and carcass length in all three DLY populations (N=1501)

DataSheet_2_Rediscover and Refine QTLs for Pig Scrotal Hernia by Increasing a Specially Designed F3 Population and Using Whole-Genome Sequence Imputation Technology.docx

Pig scrotal hernia is one of the most common congenital defects triggered by both genetic and environmental factors, leading to severe economic loss as well as poor animal welfare in the pig industry. Identification and implementation of genomic regions controlling scrotal hernia in breeding is of great appeal to reduce incidences of hernia in pig production. The aim of this study was to identify such regions or molecular markers affecting scrotal hernia in pigs. First of all, we summarized and analyzed the results of some international teams on scrotal hernia and designed a specially population which contains 246 male individuals. We then performed genome-wide association study (GWAS) in this specially designed population using two scenarios, i.e., the target panel data before and after imputation, which contain 42,365 SNPs and 18,756,672 SNPs, respectively. In addition, a series of methods including genetic differentiation analysis, linkage disequilibrium and linkage analysis (LDLA), and haplotype sharing analysis were appropriate to provide for further analysis to identify the potential gene underlying the QTL. The GWAS in this report detected a highly significant region affecting scrotal hernia within a 24.8Mb region (114.1–138.9Mb) on SSC8. And the result of genetic differentiation analysis also showed a strong genetic differentiation signal between 116.1 and 132.7Mb on SSC8. In addition, the QTL interval was refined to 2.99Mb by combining LDLA and genetic differentiation analysis. Finally, two susceptibility haplotypes were identified through haplotype sharing analysis, with one potential causal gene in it. Our study provided deeper insights into the genetic architecture of pig scrotal hernia and contributed to further fine-mapping and characterize haplotype and gene that influence scrotal hernia in pigs.</p

Additional file 8 of Identification and validation of a regulatory mutation upstream of the BMP2 gene associated with carcass length in pigs

Additional file 8. Figure S4. Haplotype block view of the region from 15.395 to 15.487 Mb. Haplotype structures viewed using Haploview software. The red mark was the top SNP rs345818757

Additional file 2 of Identification and validation of a regulatory mutation upstream of the BMP2 gene associated with carcass length in pigs

Additional file 2. Figure S1. LD (r2) decay as a function of inter-SNP distance in the DLY-P1 population. LD decay is a fast and effective tool for linkage disequilibrium decay analysis based on variants. LD (r2) dropped below 0.2 at distances greater than 200 kb in the DLY-P1 population

Additional file 4 of Identification and validation of a regulatory mutation upstream of the BMP2 gene associated with carcass length in pigs

Additional file 4. Table S3. Mutations identified by sequencing the BMP2 cDNA from ten DLY pigs with AA or GA genotypes at the GWAS tag SNP rs80965549

Additional file 1 of Identification and validation of a regulatory mutation upstream of the BMP2 gene associated with carcass length in pigs

Additional file 1. Table S1. Sequence information for primers used for cDNA and DNA sequencing of the BMP2 gene

Additional file 5 of Identification and validation of a regulatory mutation upstream of the BMP2 gene associated with carcass length in pigs

Additional file 5. Table S4. List of differentially expressed genes identified in cartilage between different QTL genotypes (Qq vs. qq)

Additional file 6 of Identification and validation of a regulatory mutation upstream of the BMP2 gene associated with carcass length in pigs

Additional file 6. Figure S2. Transcriptome analysis of cartilage tissue. a Volcano plot of differentially expressed genes (DEG). b Allelic expression ratio (AER) analysis with a transcribed SNP rs45434988 (G>A) in BMP2 from four heterozygotes (Qq) and one wild-type homozygote (qq) for the SSC17 QTL. The five individuals were all heterozygous for rs45434988. The Y-axis represents the ratio of RNA-seq reads carrying different alleles of rs45434988 (G/A) in a sample. Allelic expression imbalance was determined by an AER greater than 1.2 or less than 0.8, indicated by dotted lines