Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait

Abstract Background Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt. Results Based on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. We furthermore directly link the T-13910 haplotype with the Lactase Persistence phenotype through a Genome Wide Association study (GWAS) and identify another genomic region in the vicinity of the SPRY2 gene associated with glycaemic measurements after lactose intake. Conclusions Our findings suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first GWAS of the lactase persistence trait. We also explored other signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.

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Population history and genetic adaptation of the Fulani nomads: Inferences from genome-wide data and the lactase persistence trait

10.1101/650986 ◽

2019 ◽

Author(s):

Mário Vicente ◽

Edita Priehodová ◽

Issa Diallo ◽

Eliska Podgorná ◽

Estella S. Poloni ◽

...

Keyword(s):

Genome Wide Association Study ◽

Population History ◽

Lactase Persistence ◽

Control Element ◽

Genetic Adaptation ◽

North African ◽

Life Styles ◽

Genome Wide ◽

Genome Wide Data ◽

North African Population

AbstractHuman population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt. Based on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. Our findings further suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first Genome Wide Association study (GWAS) of the lactase persistence trait. We also further explored signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.

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Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽

10.3390/agronomy11010027 ◽

2020 ◽

Vol 11 (1) ◽

pp. 27

Author(s):

Archana Khadgi ◽

Courtney A. Weber

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genomic Region ◽

Rubus Idaeus ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Red Raspberry ◽

Genome Wide ◽

A Genome ◽

Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

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An FGA Frameshift Variant Associated with Afibrinogenemia in Dachshunds

Genes ◽

10.3390/genes12071065 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1065

Author(s):

Reinhard Mischke ◽

Julia Metzger ◽

Ottmar Distl

Keyword(s):

Protein Sequence ◽

Sanger Sequencing ◽

Selective Breeding ◽

Genome Wide Association Study ◽

Frameshift Mutation ◽

Homozygosity Mapping ◽

Genomic Region ◽

Severe Bleeding ◽

Genome Wide ◽

A Genome

Congenital fibrinogen disorders are very rare in dogs. Cases of afibrinogenemia have been reported in Bernese Mountain, Bichon Frise, Cocker Spaniel, Collie, Lhasa Apso, Viszla, and St. Bernard dogs. In the present study, we examined four miniature wire-haired Dachshunds with afibrinogenemia and ascertained their pedigree. Homozygosity mapping and a genome-wide association study identified a candidate genomic region at 50,188,932–64,187,680 bp on CFA15 harboring FGB (fibrinogen beta chain), FGA (fibrinogen alpha chain), and FGG (fibrinogen gamma-B chain). Sanger sequencing of all three fibrinogen genes in two cases and validation of the FGA-associated mutation (FGA:g.6296delT, NC_006597.3:g.52240694delA, rs1152388481) in pedigree members showed a perfect co-segregation with afibrinogenemia-affected phenotypes, obligate carriers, and healthy animals. In addition, the rs1152388481 variant was validated in 393 Dachshunds and samples from 33 other dog breeds. The rs1152388481 variant is predicted to modify the protein sequence of both FGA transcripts (FGA201:p.Ile486Met and FGA-202:p.Ile555Met) leading to proteins truncated by 306 amino acids. The present data provide evidence for a novel FGA truncating frameshift mutation that is very likely to explain the cases of severe bleeding due to afibrinogenemia in a Dachshund family. This mutation has already been spread in Dachshunds through carriers before cases were ascertained. Genetic testing allows selective breeding to prevent afibrinogenemia-affected puppies in the future.

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A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries)

Scientific Reports ◽

10.1038/srep21111 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 7

Author(s):

Xue Ren ◽

Guang-Li Yang ◽

Wei-Feng Peng ◽

Yong-Xin Zhao ◽

Min Zhang ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Close Association ◽

Significant Snps ◽

Genomic Region ◽

Ovis Aries ◽

Genome Wide Association ◽

Chromosome 2 ◽

Genome Wide ◽

A Genome

Abstract Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0–133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.

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Germline variants at SOHLH2 influence multiple myeloma risk

Blood Cancer Journal ◽

10.1038/s41408-021-00468-6 ◽

2021 ◽

Vol 11 (4) ◽

Author(s):

Laura Duran-Lozano ◽

Gudmar Thorleifsson ◽

Aitzkoa Lopez de Lapuente Portilla ◽

Abhishek Niroula ◽

Molly Went ◽

...

Keyword(s):

Multiple Myeloma ◽

Genome Wide Association Study ◽

Plasma Cells ◽

Genomic Region ◽

Open Chromatin ◽

Risk Variant ◽

Inherited Susceptibility ◽

Genome Wide ◽

A Genome ◽

Insight Into

AbstractMultiple myeloma (MM) is caused by the uncontrolled, clonal expansion of plasma cells. While there is epidemiological evidence for inherited susceptibility, the molecular basis remains incompletely understood. We report a genome-wide association study totalling 5,320 cases and 422,289 controls from four Nordic populations, and find a novel MM risk variant at SOHLH2 at 13q13.3 (risk allele frequency = 3.5%; odds ratio = 1.38; P = 2.2 × 10−14). This gene encodes a transcription factor involved in gametogenesis that is normally only weakly expressed in plasma cells. The association is represented by 14 variants in linkage disequilibrium. Among these, rs75712673 maps to a genomic region with open chromatin in plasma cells, and upregulates SOHLH2 in this cell type. Moreover, rs75712673 influences transcriptional activity in luciferase assays, and shows a chromatin looping interaction with the SOHLH2 promoter. Our work provides novel insight into MM susceptibility.

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A genome-wide association study reveals a genomic region associated with the carrot root shape

Acta Horticulturae ◽

10.17660/actahortic.2019.1264.15 ◽

2019 ◽

pp. 129-134

Author(s):

A. Macko-Podgórni ◽

K. Stelmach ◽

K. Kwolek ◽

D. Senalik ◽

P.W. Simon ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genomic Region ◽

Genome Wide Association ◽

Carrot Root ◽

Genome Wide ◽

A Genome

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Clusters of polymorphic transmembrane genes control resistance to schistosomes in snail vectors

eLife ◽

10.7554/elife.59395 ◽

2020 ◽

Vol 9 ◽

Author(s):

Jacob A Tennessen ◽

Stephanie R Bollmann ◽

Ekaterina Peremyslova ◽

Brent A Kronmiller ◽

Clint Sergi ◽

...

Keyword(s):

Genome Wide Association Study ◽

Genomic Region ◽

Amino Acid Residues ◽

Rna Seq ◽

Intermediate Hosts ◽

Genome Wide ◽

A Genome ◽

Snail Proteins ◽

Genome Assemblies ◽

Host Parasite

Schistosomiasis is a debilitating parasitic disease infecting hundreds of millions of people. Schistosomes use aquatic snails as intermediate hosts. A promising avenue for disease control involves leveraging innate host mechanisms to reduce snail vectorial capacity. In a genome-wide association study of Biomphalaria glabrata snails, we identify genomic region PTC2 which exhibits the largest known correlation with susceptibility to parasite infection (>15 fold effect). Using new genome assemblies with substantially higher contiguity than the Biomphalaria reference genome, we show that PTC2 haplotypes are exceptionally divergent in structure and sequence. This variation includes multi-kilobase indels containing entire genes, and orthologs for which most amino acid residues are polymorphic. RNA-Seq annotation reveals that most of these genes encode single-pass transmembrane proteins, as seen in another resistance region in the same species. Such groups of hyperdiverse snail proteins may mediate host-parasite interaction at the cell surface, offering promising targets for blocking the transmission of schistosomiasis.

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