Population data and genetic diversity analysis of 17 Y-STR loci in Saudi population

Background The Y chromosome polymorphism has been widely studied for human migrations, population genetics, forensic applications, and paternity analysis. However, studies regarding genetic lineage and population genetic structure of the Y chromosome in different regions of Saudi Arabia are limited. Aim This study aimed to analyze the distribution of Y chromosome haplotypes in a sample of 125 native Saudi males from different geographic regions of Saudi Arabia and compare to previously published Y chromosome haplotype data from Saudi Arabia and some neighboring Arab populations. Materials and methods Buccal swabs were collected from 125 healthy unrelated native Saudi males from different geographic regions of Saudi Arabia. Genomic DNA was extracted by Chelex®100; 17 Y-STR loci were amplified using the AmpFℓlSTR Yfiler PCR amplification kit and detected on the 3130 Genetic AnalyzerTM. Allele frequency and gene diversity were calculated with online tool STRAF. The Saudi population data were compared with the neighboring populations using pairwise genetic distances and associated probability values were calculated using the Y Chromosome Haplotype Reference Database Website (YHRD) software. Results and conclusion One hundred six YSTR haplotypes and 102 YSTR alleles (excluding 4 null alleles) were identified having a discrimination capacity (DC) of 85.8%. The highest haplotype diversity (HD) and gene diversity (GD) were observed at the loci DYS 458 (0.817) and DYS385b (0.807), respectively. According to our results, the Iraqi and Qena (Egypt) populations appeared to have closer relatedness to the Saudi population as compared with Yemen. The UAE and Kuwait populations showed the same degree of relatedness to the Saudi population followed by Bahrain. On the contrary, the Adnanit and Qahtanit populations of Jordan demonstrated low genetic distance from the Saudi population. In short, studying a population sample of pure Saudi ethnicity enabled us to identify a unique set of haplotypes which may help in establishing genetic relatedness between Saudi and the neighboring Arab populations. The present paper, therefore, highlights the importance of ensuring ethnic originality of the study sample while conducting population genetics studies.

GWAS and co-expression network combination uncovers multigenes with close linkage effects on oleic acid content accumulation in Brassica napus

Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We use the 60K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes ( BnmtACP2-A02 , BnABCI13-A02 and BnECI1-A02 ) in the A02 chromosome haplotype region and two genes ( BnFAD8-C02 and BnSDP1-C02 ) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

GWAS and co-expression network combination uncovers multigenes with close linkage effects on oleic acid content accumulation in Brassica napus

Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We use the 60K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes ( BnmtACP2-A02 , BnABCI13-A02 and BnECI1-A02 ) in the A02 chromosome haplotype region and two genes ( BnFAD8-C02 and BnSDP1-C02 ) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

GWAS and co-expression network combination uncovers multigenes with close linkage effects on oleic acid content accumulation in Brassica napus

Abstract Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS in combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We used the 60K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02 and C03. Additionally, whole-genome sequencing of 50 rapeseed lines revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

GWAS and co-expression network combination uncovers multigenes with close linkage effects on oleic acid content accumulation in Brassica napus

Abstract Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS in combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We used the 60K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02 and C03. Additionally, whole-genome sequencing of 50 rapeseed lines revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

GWAS and co-expression network combination uncovers multigenes with close linkage effects on oleic acid content accumulation in Brassica napus

Abstract Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS in combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We used the 60K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02 and C03. Additionally, whole-genome sequencing of 50 rapeseed lines revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.

Determination of complete chromosomal haplotypes by bulk DNA sequencing

Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. Determining the haplotype phase requires knowledge of both the genotypes at variant sites and their linkage across each chromosome. Haplotype linkage can be either inferred statistically from a genotyped population, or determined by long-range sequencing of an individual genome. However, extending haplotype inference to the whole-chromosome scale remains challenging and usually requires special experimental techniques. Here we describe a general computational strategy to determine complete chromosomal haplotypes using a combination of bulk long-range sequencing and Hi-C sequencing. We demonstrate that this strategy can resolve the haplotypes of parental chromosomes in diploid human genomes at high precision (99%) and completeness (98%), and is further able to assemble the syntenic organization of aneuploid genomes (“digital karyotype”).