Dataset Information

Characterizing a region on BTA11 affecting ?-lactoglobulin content of milk using high-density genotyping and haplotype grouping.

ABSTRACT: Milk ?-lactoglobulin (?-LG) content is of interest as it is associated with nutritional and manufacturing properties. It is known that milk ?-LG content is strongly affected by genetic factors. In cattle, most of the genetic differences are associated with a chromosomal region on BTA11, which contains the ?-LG gene. The aim of this study was to characterize this region using 777 k SNP data (BovineHDbeadChip) and perform a haplotype-based association study. A statistical approach was developed to build haplotypes that capture the genetic variation associated with this genomic region.The SNP with the most significant effect on ?-lactoglobulin content was one of the 2 causal mutations responsible for the ?-lactoglobulin protein variants A/B. Haplotypes based on 2 to 5 selected lead SNP were clustered in groups with different effects on ?-lactoglobulin content. Four different groups were identified suggesting that ?-lactoglobulin variant A and B can be further refined in A1, A2, B1 and B2.This study showed that ?-lactoglobulin protein variants A/B do not explain all genetic variation associated with the tail part of BTA11 but this region contains more than one mutation with an effect on ?-lactoglobulin content. These findings can be used for selection of cows with higher cheese yield, which is desirable for the dairy industry.

SUBMITTER: Bedere N

PROVIDER: S-EPMC5320657 | biostudies-other | 2017 Feb

REPOSITORIES: biostudies-other

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Characterizing a region on BTA11 affecting β-lactoglobulin content of milk using high-density genotyping and haplotype grouping.

Bedere Nicolas N Bovenhuis Henk H

BMC genetics 20170222 1

<h4>Background</h4>Milk β-lactoglobulin (β-LG) content is of interest as it is associated with nutritional and manufacturing properties. It is known that milk β-LG content is strongly affected by genetic factors. In cattle, most of the genetic differences are associated with a chromosomal region on BTA11, which contains the β-LG gene. The aim of this study was to characterize this region using 777 k SNP data (BovineHDbeadChip) and perform a haplotype-based association study. A statistical approa ...[more]

PMID: 28222684

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Project description:BACKGROUND:Plasmodium knowlesi is a simian malaria parasite that has been reported to cause malaria in humans in Southeast Asia. This parasite invades the erythrocytes of humans and of its natural host, the macaque Macaca fascicularis, via interaction between the Duffy binding protein region II (PkDBP?RII) and the Duffy antigen receptor on the host erythrocytes. In contrast, the P. knowlesi gamma protein region II (Pk?RII) is not involved in the invasion of P. knowlesi into humans. Pk?RII, however, mediates the invasion of P. knowlesi into the erythrocytes of M. mulata, a non-natural host of P. knowlesi via a hitherto unknown receptor. The haplotypes of PkDBP?RII in P. knowlesi isolates from Peninsular Malaysia and North Borneo have been shown to be genetically distinct and geographically clustered. Also, the PkDBP?RII was observed to be undergoing purifying (negative) selection. The present study aimed to determine whether similar phenomena occur in Pk?RII. METHODS:Blood samples from 78 knowlesi malaria patients were used. Forty-eight of the samples were from Peninsular Malaysia, and 30 were from Malaysia Borneo. The genomic DNA of the samples was extracted and used as template for the PCR amplification of the Pk?RII. The PCR product was cloned and sequenced. The sequences obtained were analysed for genetic diversity and natural selection using MEGA6 and DnaSP (version 5.10.00) programmes. Genetic differentiation between the Pk?RII of Peninsular Malaysia and North Borneo isolates was estimated using the Wright's FST fixation index in DnaSP (version 5.10.00). Haplotype analysis was carried out using the Median-Joining approach in NETWORK (version 4.6.1.3). RESULTS:A total of 78 Pk?RII sequences was obtained. Comparative analysis showed that the Pk?RII have similar range of haplotype (Hd) and nucleotide diversity (?) with that of PkDBP?RII. Other similarities between Pk?RII and PkDBP?RII include undergoing purifying (negative) selection, geographical clustering of haplotypes, and high inter-population genetic differentiation (FST index). The main differences between Pk?RII and PkDBP?RII include length polymorphism and no departure from neutrality (as measured by Tajima's D statistics) in the Pk?RII. CONCLUSION:Despite the biological difference between Pk?RII and PkDBP?RII, both generally have similar genetic diversity level, natural selection, geographical haplotype clustering and inter-population genetic differentiation index.

Dataset Information

Characterizing a region on BTA11 affecting ?-lactoglobulin content of milk using high-density genotyping and haplotype grouping.

Publications

Characterizing a region on BTA11 affecting β-lactoglobulin content of milk using high-density genotyping and haplotype grouping.

Similar Datasets

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