Identification of the amino acids in the Major Histocompatibility Complex class II region of Scottish Blackface sheep that are associated with resistance to nematode infection

Lambs with the Major Histocompatibility Complex DRB1*1101 allele have been shown to produce fewer nematode eggs following natural and deliberate infection. These sheep also possess fewer adult Teladorsagia circumcincta than sheep with alternative alleles at the DRB1 locus. However, it is unclear if this allele is responsible for the reduced egg counts or merely acts as a marker for a linked gene. This study defined the MHC haplotypes in a population of naturally infected Scottish Blackface sheep by PCR amplification and sequencing, and examined the associations between MHC haplotypes and faecal egg counts by generalised linear mixed modelling. The DRB1*1101 allele occurred predominately on one haplotype and a comparison of haplotypes indicated that the causal mutation or mutations occurred in or around this locus. Additional comparisons with another resistant haplotype indicated that mutations in or around the DQB2*GU191460 allele were also responsible for resistance to nematode infections. Further analyses identified six amino acid substitutions in the antigen binding site of DRB1*1101 that were significantly associated with reductions in the numbers of adult T. circumcincta.     

Female house mice avoid fertilization by t haplotype incompatible males in a mate choice experiment

The t haplotype in house mice is a well‐known selfish genetic element with detrimental, nonadditive fitness consequences to its carriers: recessive lethal mutations cause t/t homozygotes to perish in utero. Given the severe genetic incompatibility imposed by the t haplotype, we predict females to avoid fertilization by t haplotype incompatible males. Indeed, some of the strongest evidence for compatibility mate choice is related to the t haplotype in house mice. However, all previous evidence for compatibility mate choice in this system is based on olfactory preference. It is so far unknown how general these preferences are and whether they are relevant in an actual mating context. Here, we assess female compatibility mate choice related to t haplotypes in a setting that – for the first time – allowed females to directly interact and mate with males. This approach enabled us to analyse female behaviour during the testing period, and the resulting paternity success and fitness consequences of a given choice. We show that genetic incompatibilities arising from the t haplotype had severe indirect fitness consequences and t females avoided fertilization by t incompatible males. The results are inconclusive whether this avoidance of t fertilization by t females was caused by pre‐ or post‐copulatory processes.     

A simple procedure for directly obtaining haplotype sequences of diploid genomes

Background

Almost all genome sequencing projects neglect the fact that diploid organisms contain two genome copies and consequently what is published is a composite of the two. This means that the relationship between alternate alleles at two or more linked loci is lost. We have developed a simplified method of directly obtaining the haploid sequences of each genome copy from an individual organism.

Results

The diploid sequences of three groups of cattle samples were obtained using a simple sample preparation procedure requiring only a microscope and a haemocytometer. Samples were: 1) lymphocytes from a single Angus steer; 2) sperm cells from an Angus bull; 3) lymphocytes from East African Zebu (EAZ) cattle collected and processed in a field laboratory in Eastern Kenya. Haploid sequence from a fosmid library prepared from lymphocytes of an EAZ cow was used for comparison. Cells were serially diluted to a concentration of one cell per microlitre by counting with a haemocytometer at each dilution. One microlitre samples, each potentially containing a single cell, were lysed and divided into six aliquots (except for the sperm samples which were not divided into aliquots). Each aliquot was amplified with phi29 polymerase and sequenced. Contigs were obtained by mapping to the bovine UMD3.1 reference genome assembly and scaffolds were assembled by joining adjacent contigs that were within a threshold distance of each other. Scaffolds that appeared to contain artefacts of CNV or repeats were filtered out leaving scaffolds with an N50 length of 27–133 kb and a 88–98 % genome coverage. SNP haplotypes were assembled with the Single Individual Haplotyper program to generate an N50 size of 97–201 kb but only ~27–68 % genome coverage. This method can be used in any laboratory with no special equipment at only slightly higher costs than conventional diploid genome sequencing. A substantial body of software for analysis and workflow management was written and is available as supplementary data.

Conclusions

We have developed a set of laboratory protocols and software tools that will enable any laboratory to obtain haplotype sequences at only modestly greater cost than traditional mixed diploid sequences.     

Mitochondrial genetic structure reflects the geographical variation of elytral polymorphism frequency in Cheilomenes sexmaculata (Coleoptera: Coccinellidae)

Many ladybird species are known to have an elytral colour polymorphism, which indicates geographical variation. The ladybird beetle Cheilomenes sexmaculata (Fabricius) exhibits elytral colour polymorphism and has expanded its distribution from 33°N to 36°N in Japan over 100 years since 1900. The mitochondrial COI gene haplotypes were integrated into two haplotype groups, with one group existing at higher frequencies in lower latitudes, the other group appearing at higher frequencies in higher latitudes. In addition, the dark morph types of this species increase with latitude, whereas the light types appear at higher relative frequencies in lower latitudes.In the present study, we first determined the morph types of individuals and examined the mitochondrial DNA COI gene. Second, we investigated the relationship between the genetic population structure based on the mitochondrial DNA COI gene and the morph types’ geographical variation. Results indicated that the mtCOI genetic structure was associated with the morph types by latitude; specifically, the haplotype group existing at higher frequencies in lower latitudes tended to be light morph types. In contrast, the haplotype dominant in higher latitudes more frequently exhibited dark morph types, indicating that dark morph types in the higher latitude genetic group may have led the distributional expansion toward higher latitudes since 1900 rather than the lower latitude light morph types.     

Effective haplotype assembly via maximum Boolean satisfiability

The haplotype assembly problem seeks the haplotypes of an individual from which a set of aligned SNP fragments are available. The problem is important as the haplotypes contain all the SNP information, which is essential to such studies as the analysis of the association between specific diseases and their potential genetic causes. Using Minimum Error Correction as the objective function, the problem is NP-hard, which raises the demand for effective yet affordable solutions. In this paper, we propose a new method to solve the problem by providing a novel Max-2-SAT formulation for the problem. The proposed method is compared with several well-known algorithms proposed for the problem in the literature on a recent extensive benchmark, outperforming them all by achieving solutions of higher average quality.     

A novel replicated association between FXYD6 gene and schizophrenia

FXYD6 gene is located in chromosome region 11q22–q24 where previous studies have shown an association with schizophrenia. However, the subsequent studies failed to replicate this finding. To investigate the relationship between FXYD6 locus and schizophrenia in Chinese population, we genotyped six single-nucleotide polymorphisms (SNPs) in this region of FXYD6 in 1142 Han Chinese subjects (576 cases and 566 controls), and performed an association analysis. Significant associations with schizophrenia and the marker rs11544201 (P = 0.0028) and the haplotype rs10790212–rs11544201 (global P = 0.005) were found. Our results support that FXYD6 is a susceptibility gene of schizophrenia. Replication of larger samples and functional analysis of FXYD6 are needed.     

A polymorphism of matrix Gla protein gene is associated with kidney stone in the Chinese Han population

Purpose

Matrix Gla protein (MGP) is a molecular determinant regulating the extracellular matrix calcification. To further confirm whether the MGP genetic polymorphism was universally associated with the risk of kidney stone, we investigated the association of genetic polymorphisms of MGP with kidney stone in the Chinese Han population.

Materials and methods

728 subjects were recruited for the study. We firstly re-sequenced the human genomic MGP gene including the 1500 bp promoter, 5′-UTR, 4 exons and 3′-untranslated regions, identified single nucleotide polymorphisms (SNPs) in MGP, and performed an association analysis with kidney stones in 54 subjects of the Chinese Han population. A candidate tag SNP was genotyped in total subjects using an allele specific PCR, and further analyzed the association with kidney stone.

Results

We identified 18 polymorphisms including four tag SNPs. A tag SNPrs4236 was associated with kidney stones. The G allele carrier had a 1.373-fold reduced kidney stone risk compared with A allele carriers in SNPrs4236 (odds ratios (OR) = 1.373; 95%CI, 1.051–1.793; p = 0.019). However, we did not find an association between the polymorphism and clinical characteristics of kidney stones.

Conclusions

Our findings showed that SNPrs4236 of the MGP gene is associated with kidney stones in the Chinese Han population, and influences the genetic susceptibility to kidney stones. In the future, functional assays of the polymorphism should permit a better understanding of the role of MGP genetic variants and kidney stones.     

云南地区恒河猴线粒体DNA控制区遗传多态性研究

目的从分子水平探讨云南地区恒河猴遗传多样性,为今后开展恒河猴遗传资源的保护及合理利用提供借鉴和背景资料。方法采用PCR直接测序法测定云南地区恒河猴96份样品的线粒体DNA控制区全序列,用Mege 4.0和DNA SP软件对变异位点数、简约信息位点数、单倍型、单倍型多样度、核苷酸多样度等遗传信息进行分析,基于邻接法（neighbor-joining,NJ）和最小进化法（minimum-evolution,ME）构建系统发生树。结果在96份样品中,共检测出了149个多态性位点,定义了46种单倍型,单倍型多样度（Hd）为0.968±0.007,核苷酸多样度（Pi）为0.020。结论云南地区恒河猴存在着较丰富的遗传多态性。     

Molecular evolution and functional characterisation of haplotypes of an important rubber biosynthesis gene in Hevea brasiliensis

Hydroxy‐methylglutaryl coenzyme‐A synthase (HMGS) is a rate‐limiting enzyme in the cytoplasmic isoprenoid biosynthesis pathway leading to natural rubber production in Hevea brasiliensis (rubber). Analysis of the structural variants of this gene is imperative to understand their functional significance in rubber biosynthesis so that they can be properly utilised for ongoing crop improvement programmes in Hevea. We report here allele richness and diversity of the HMGS gene in selected popular rubber clones. Haplotypes consisting of single nucleotide polymorphisms (SNPs) from the coding and non‐coding regions with a high degree of heterozygosity were identified. Segregation and linkage disequilibrium analysis confirmed that recombination is the major contributor to the generation of allelic diversity, rather than point mutations. The evolutionarily conserved nature of some SNPs was identified by comparative DNA sequence analysis of HMGS orthologues from diverse taxa, demonstrating the molecular evolution of rubber biosynthesis genes in general. In silico three‐dimensional structural studies highlighting the structural positioning of non‐synonymous SNPs from different HMGS haplotypes revealed that the ligand‐binding site on the enzyme remains impervious to the reported sequence variations. In contrast, gene expression results indicated the possibility of association between specific haplotypes and HMGS expression in Hevea clones, which may have a downstream impact up to the level of rubber production. Moreover, haplotype diversity of the HMGS gene and its putative association with gene expression can be the basis for further genetic association studies in rubber. Furthermore, the data also show the role of SNPs in the evolution of candidate genes coding for functional traits in plants.     

Whole-genome linkage disequilibrium screening for complex traits in horses

The identification of candidate genes for significant traits is crucial. In this study, we developed and tested effective and systematic methods based on linkage disequilibrium (LD) for the identification of candidate regions for genes with Mendelian inheritance and those associated with complex traits. Our approach entailed the combination of primary screening using pooled DNA samples based on ΔTAC, secondary screening using an individual typing method and tertiary screening using a permutation test based on the differences in the haplotype frequency between two neighbouring microsatellites. This series of methods was evaluated using horse coat colour traits (chestnut/non-chestnut) as a simple Mendelian inheritance model. In addition, the methods were evaluated using a complex trait model constructed by mixing samples from chestnut and non-chestnut horses. Using both models, the methods could detect the expected regions for the horse coat colour trait. The results revealed that LD extends up to several centimorgans in horses, indicating that whole-genome LD screening in horses could be performed systematically and efficiently by combining the above-mentioned methods. Since genetic maps based on microsatellites have been constructed for many other species, the approaches present here could have wide applicability.