Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population

Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms(SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here,we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs(FROH), homozygosity(FHOM), genomic relationship matrix(FGRM)and pedigree(FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.Results: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes(SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_totaland FHOM, while the lowest was-0.083 between FGRMand FPED. The correlations between FPEDand FROHusing four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes(SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4.Conclusion: FROHcan be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROHcan provide an alternative to inbreeding estimates.Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.

Genome-wide detection for runs of homozygosity analysis in three pig breeds from Chinese Taihu Basin and Landrace pigs by SLAF-seq data

Erhualian(E),Meishan(MS)and Mi(MI)pigs are excellent indigenous pig breeds in Chinese Taihu Basin,which have made great contributions to the genetic improvement of commercial pigs.Investigation of the genetic structure and inbreeding level of the 3 pig breeds is of great significance for the sustainable breeding of commercial pigs.The length and number of runs of homozygosity(ROH)as well as the frequency of genomes covered by ROH can be used as indicators to evaluate the level of inbreeding and the origin of the population.In this study,the ROH characteristics of E,MS,MI and Landrace(L)pigs were analyzed by SLAF-seq data,and the inbreeding coefficient based on ROH(F_(ROH))was calculated.In addition,we have identified candidate genes in the genomic regions associated with ROH.A total of10568 ROH were detected in 116 individuals of 4 pig breeds.The analysis showed that there were significant differences in genetic structure between 3 Taihu Basin pig breeds and L,and the genetic structure of E and MI was similar.The results of F_(ROH)showed that the inbreeding level of MS was the highest(0.25±0.07),while E and MI were lower than L.Compared with the other 3 pig populations,MS showed a higher frequency of long ROH(>5 Mb),indicating higher inbreeding in MS in recent generations.A large number of candidate genes related to reproductive traits are located in the genomic regions with a high frequency of ROH,and these genes are expected to be used as candidate genes in marker-assisted selection(MAS)breeding programs.Our findings can provide theoretical support for genetic conservation and genetic improvement of 3 pig breeds in Chinese Taihu Basin.

Homozygosity mapping of a consanguineous Pakistani family affected with oculocutaneous albinism to Tyrosinase gene

Dear Sir,Iam Haiba Kaul,from the Department of Biochemistry,University of Health Sciences,Lahore,Pakistan.I write to present a study of oculocutaneous albinism（OCA）in consanguineous Pakistani families.OCA is a genetic defect of melanin biosynthesis that mainly affects eyes,skin and hair.

Genome-wide analysis of runs of homozygosity identifies new susceptibility regions of lung cancer in Han Chinese

Runs of homozygosity （ROHs） are a class of important but poorly studied genomic variations and may be in- volved in individual susceptibility to diseases. To better understand ROH and its relationship with lung cancer, we performed a genome-wide ROH analysis of a subset of a previous genome-wide case-control study （1,473 cases and 1,962 controls） in a Han Chinese population. ROHs were classified into two classes, based on lengths, intermedi- ate and long ROils, to evaluate their association with lung cancer risk using existing genome-wide single nucleofide polymorphism （SNP） data. We found that the overall level of intermediate ROHs was significantly associated with a decreased risk of lung cancer （odds ratio = 0.63; 95% confidence interval： 0.51-0.77; P = 4.78 × 10-6 ）, while the long ROHs seemed to be a risk factor of lung cancer. We also identified one ROH region at 14q23A that was con- sistently associated with lung cancer risk in the study. These results indicated that ROHs may be a new class of variation which may be associated with lung cancer risk, and genetic variants at 14q23.1 may be involved in the development of lung cancer.

Comment on homozygosity mapping of a consanguineous Pakistani family affected with oculocutaneous albinism to Tyrosinase gene

Dear Editor,I have carefully read the article entitled ＂Homozygosity mapping of a consanguineous Pakistani family affected with oculocutaneous albinism to Tyrosinase gene＂,published by Shakil et al in 2016 and found it very interesting for the scientific community.

Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,and putative introgression.Here we generated the first chromosome-level genome of the endangered Chinese hazelnut,Corylus chinensis,and compared the genomic signatures with its sympatric widespread C.kwechowensis-C yunnanensis complex.We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation.Population genomics revealed that both C.chinensis and the C.kwechowensis-C.yunnanensis complex had diverged into two genetic lineages,forming a consistent pattern of southwestern-northern differentiation.Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene,whereas the widespread northern lineages have remained stable(C.chinensis) or have even recovered from population bottlenecks(C.kwechowensis-C.yunnanensis complex) during the Quaternary.Compared with C.kwechowensis-C. yunnanensis complex,C.chinensis showed significantly lower genomic diversity and higher inbreeding level.However,C.chinensis carried significantly fewer deleterious mutations than C.kwechowensis-C. yunnanensis complex,as more effective purging selection reduced the accumulation of homozygous variants.We also detected signals of positive selection and adaptive introgression in different lineages,which facilitated the accumulation of favorable variants and formation of local adaptation.Hence,both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C.chinensis.Overall,our study provides critical insights into lineage differentiation,local adaptation,and the potential for future recovery of endangered trees.

Genome-wide detection of selective signatures in a Jinhua pig population

The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig genome.These results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production traits.In the present study,we performed extended haplotype homozygosity(EHH)tests to identify significant core regions in 202 Jinhua pigs.A total of 26161 core regions spanning 636.42 Mb were identified,which occupied approximately 28%of the genome across all autosomes,and 1158 significant(P<0.01)core haplotypes were selected.Genes in these regions were related to several economically important traits,including meat quality,reproduction,immune responses and exterior traits.A panel of genes including ssc-mir-365-2,KDM8,RABEP2,GSG1L,RHEB,RPH3AL and a signal pathway of PI3K-Akt were detected with the most extreme P-values.The findings in our study could draw a comparatively genome-wide map of selection signature in the pig genome,and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.

Ectopic expression of antifreeze protein gene from Ammopiptanthus nanus confers chilling tolerance in maize

Improved chilling tolerance is important for maize production. Previous efforts in transgenics and marker-assisted breeding have not achieved practical results. In this study, the antifreeze protein(AnAFP) from the super-xerophyte Ammopiptanthus nanus was aligned to KnS-type dehydrins.Phosphorylation in vitro and subcellular localization showed that AnAFP was phosphorylated by maize casein kinase II and translocated from nucleus to cytoplasm under chilling stress. AnAFP also increased lactate dehydrogenase activity. A parent line of commercial maize hybrids was transformed with the AnAFP gene. Based on thermal asymmetric interlaced PCR, one hemizygous and two homozygous integration sites were identified in one T_(1) line. Ectopic expression of AnAFP in transgenic lines was confirmed by quantitative real-time PCR, RNA-seq, and Western blotting. After chilling treatment, the transgenic lines showed significantly improved phenotype, higher kernel production, survival rate and biomass, and lower relative electrolyte leakage and superoxide dismutation than the untransformed line. Thus, ectopic expression of AnAFP gene improved chilling tolerance in the transgenic lines, which could be used to apply for further safety assessment for commercial breeding.

Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds

Background:A run of homozygosity(ROH)is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents.Genomic inbreeding can be quantified based on ROH.Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands.We carried out ROH analyses in five Chinese indigenous sheep breeds;Altay sheep(n=50 individuals),Large-tailed Han sheep(n=50),Hulun Buir sheep(n=150),Short-tailed grassland sheep(n=150),and Tibetan sheep(n=50),using genotypes from an Ovine Infinium HD SNP BeadChip.Results:A total of 18,288 ROH were identified.The average number of ROH per individual across the five sheep breeds ranged from 39(Hulun Buir sheep)to 78(Large-tailed Han sheep)and the average length of ROH ranged from 0.929 Mb(Hulun Buir sheep)to 2.544 Mb(Large-tailed Han sheep).The effective population size(Ne)of Altay sheep,Large-tailed Han sheep,Hulun Buir sheep,Short-tailed grassland sheep and Tibetan sheep were estimated to be 81,78,253,238 and 70 five generations ago.The highest ROH-based inbreeding estimate(FROH)was 0.0808 in Large-tailed Han sheep,whereas the lowest F_(ROH)was 0.0148 in Hulun Buir sheep.Furthermore,the highest proportion of long ROH fragments(>5 Mb)was observed in the Large-tailed Han sheep breed which indicated recent inbreeding.In total,49 ROH islands(the top 0.1% of the SNPs most commonly observed in ROH)were identified in the five sheep breeds.Three ROH islands were common to all the five sheep breeds,and were located on OAR2:12.2-12.3 Mb,OAR12:78.4-79.1 Mb and OAR13:53.0-53.6 Mb.Three breed-specific ROH islands were observed in Altay sheep(OAR15:3.4-3.8 Mb),Large-tailed Han sheep(ORA17:53.5-53.8 Mb)and Tibetan sheep(ORA5:19.8-20.2 Mb).Collectively,the ROH islands harbored 78 unique genes,including 19 genes that have been documented as having associations with tail types,adaptation,growth,body size,reproduction or immune response.Conclusion:Different ROH patterns were observed in five Chinese indigenous sheep breeds,which reflected their different population histories.Large-tailed Han sheep had the highest genomic inbreeding coefficients and the highest proportion of long ROH fragments indicating recent inbreeding.Candidate genes in ROH islands could be used to illustrate the genetic characteristics of these five sheep breeds.Our findings contribute to the understanding of genetic diversity and population demography,and help design and implement breeding and conservation strategies for Chinese sheep.

Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marek's disease

Background: Marek's disease(MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. However, the mechanisms of genetic resistance for MD are complex and not fully understood. MD-resistant line 6_3 and MD-susceptible line 7_2 are two highly inbred progenitor lines of White Leghorn. Recombinant Congenic Strains(RCS) were developed from these two lines, which show varied susceptibility to MD.Results: We investigated genetic structure and genomic signatures across the genome, including the line 6_3 and line7_2, six RCSs, and two reciprocally crossed flocks between the lines 6_3 and 7_2(F1 6_3× 7_2 and F1 7_2× 6_3) using Affymetrix~? Axiom~? HD 600 K genotyping array. We observed 18 chickens from RCS lines were specifically clustered into resistance sub-groups distributed around line 6_3. Additionally, homozygosity analysis was employed to explore potential genetic components related to MD resistance, while runs of homozygosity(ROH) are regions of the genome where the identical haplotypes are inherited from each parent. We found several genes including SIK, SOX1, LIG4, SIK1 and TNFSF13B were contained in ROH region identified in resistant group(line 6_3 and RCS), and these genes have been reported that are contribute to immunology and survival. Based on F_(ST) based population differential analysis, we also identified important genes related to cell death and anti-apoptosis, including AKT1, API5, CDH13, CFDP and USP15,which could be involved in divergent selection during inbreeding process.Conclusions: Our findings offer valuable insights for understanding the genetic mechanism of resistance to MD and the identified genes could be considered as candidate biomarkers in further evaluation.

Selection signatures in Canchim beef cattle

Background： Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism（SNP） panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures（SS）. The SS are detectable by different methods, such as the extended haplotype homozygosity（EHH）; and the integrated haplotype score（i HS）, which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle（composite breed）, genotyped with high-density SNP panel.Results： A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The i HS statistic for each marker was transformed into pi HS for better interpretation of the results.Chromosomes BTA5 and BTA14 showed pi HS 〉 5, with 39 and nine statistically significant SNPs（P 〈 0.00001）,respectively. For the candidate selection regions, i HS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism,melanin biosynthesis（pigmentation）, and embryonic and bone development.Conclusions： The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds（i.e. Charolais）, are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization.

Effect of Cold-Mediated Pretreatment on Microspore Culture in Winter and Spring Wheat

Microspore culture of wheat generates completely homozygous (doubled haploid) plants in a single generation thereby reducing the time required for wheat variety development. Success of microspore culture in spring wheat is relatively higher than that in winter wheat. Cold mediated pretreatment was reported to improve response of microspore culture in wheat. The objective of the study was to determine and compare the influence of cold pretreatment on microspore culture in spring and winter wheat. Three spring (“Chris”, “Express”, and “Macon”) and three winter (“Anton”, “Antelope”, and “Camelot”) wheat cultivars were used. In cold pretreatment, excised anthers were incubated in solution B at 25°C-28°C for 4-5 days followed by cold treatment at 4°C for 5 days and were compared with the no-cold pretreatment at 25°C-28°C for 4-5 days. Isolated microspores were cultured in induction medium (MMS4) at 27°C-28°C for 25-30 days in the dark. Embryos (1-2 mm size) were transferred to regeneration medium (MMS5). Numbers of multicellular structures, transferable embryos and green plants were counted and data were used for analysis of variance using a generalized linear model. It was observed that cold pretreatment increased multicellular structures, transferable embryos and green plants in both spring and winter wheat. However, the degree of improvement was higher in spring wheat compared to winter wheat. The cultivars within spring and winter wheat responded differently. Development of embryos from pro-embryos was 4-5 folds lower in winter wheat than that in spring wheat, indicating requirement of a possibly different hormonal composition in induction medium for improving embryo induction in winter wheat. This report may provide future direction of research to improve microspore culture response in winter wheat.

Hereditary Immunity and the Origin of Atherosclerosis

This paper tries to present new confirmation for the opinion about the infectious origin of atherosclerosis from the viewpoint of the current knowledge of hereditary immunity. The performed integrative investigation included the reinterpretation of known clinical and epidemiological observations, supported by immunological, molecular ecological, genetic, and genomic discoveries. The revealed body of firstly achieved information is compatible with the concept that infectious agents contribute the clue step to the development of atherosclerosis over its initial stage performed during the triggering of the arterial endothelial wall by the molecular agent of proposed infectious origin.

Molecular diagnosis of autosomal recessive cerebellar ataxia in the whole exome/genome sequencing era

Autosomal recessive cerebellar ataxias(ARCA) are a clinically and genetically heterogeneous group of rare neurodegenerative disorders characterized by autosomal recessive inheritance and an early age of onset. Progressive ataxia is usually the prominent symptom and is often associated with other neurological or additional features. ARCA classification still remains controversial even though different approaches have been proposed over the years. Furthermore, ARCA molecular diagnosis has been a challenge due to phenotypic overlap and increased genetic heterogeneity observed within this group of disorders. Friedreich's ataxia and ataxia telangiectasia have been reported as the most frequent and well-studied forms of ARCA. Significant progress in understanding the genetic etiologies of the ARCA has been achieved during the last 15 years. The methodological revolution that has been observed in genetics over the last few years has contributed significantly to the molecular diagnosis of rare diseases including the ARCAs. Development of high throughput technologies has resulted in the identification of new ARCA genes and novel mutations in known ARCA genes. Therefore,an improvement in the molecular diagnosis of ARCA is expected. Moreover, based on the fact that many patients still remain undiagnosed, additional forms of ataxia are expected to be identified. We hereby review the current knowledge on the ARCAs, focused on the genetic findings of the most common forms that were molecularly characterized before the whole exome/genome era, as well as the most recently described forms that have been elucidated with the use of these novel technologies. The significant contribution of wholeexome sequencing or whole-genome sequencing in the molecular diagnosis of ARCAs is discussed.

Autozygosity Mapping by Genome-wide Single Nucleotide Polymorphism Array Identifies a Novel Homozygous HR Mutation in a Consanguineous Family with Universal Hereditary Hair Loss

Objective:Isolated hereditary hypotrichosis is caused by mutations in as many as 11 different genes.The conventional mutation detection strategy consists of sequencing of individual candidate genes separately,a time consuming and costly approach.In this study,we perform genome-wide single nucleotide polymorphism(SNP)array to identify candidate genes of hereditary hypotrichosis.Methods:A consanguineous family with two patients with hereditary hypotrichosis was enrolled,and autozygosity mapping by genome-wide SNP array was utilized to identify candidate genes.Results:Autozygosity mapping delineated runs of homozygosity,and alignment of the 11 genes identified the hairless(HR)gene as the candidate gene.Nucleotide sequencing revealed a novel homozygous mutation c.381delT,p.Ser127ArgfsTer40.Conclusion:This study illustrates how autozygosity mapping by a high-density SNP array streamlines mutation detection in heritable skin diseases.

Genetic analysis of four consanguineous multiplex families with inflammatory bowel disease

Background:Family studies support a genetic predisposition to inflammatory bowel diseases(IBD),but known genetic variants only partially explain the disease heritability.Families withmultiple affected individuals potentially harbour rare and highimpact causal variants.Long regions of homozygosity due to recent inbreedingmay increase the risk of individuals bearing homozygous loss-of-function variants.This study aimed to identify rare and homozygous genetic variants contributing to IBD.Methods:Four families with known consanguinity and multiple cases of IBD were recruited.In a family-specific analysis,we utilised homozygosity mapping complemented by whole-exome sequencing.Results:We detected a single region of homozygosity shared by Crohn’s disease cases from a family of Druze ancestry,spanning 2.6Mb containing the NOD2 gene.Whole-exome sequencing did not identify any potentially damaging variants within the region,suggesting that non-coding variation may be involved.In addition,affected individuals in the families harboured several rare and potentially damaging homozygous variants in genes with a role in autophagy and innate immunity including LRRK1,WHAMM,DENND3,and C5.Conclusion:This study examined the potential contribution of rare,high-impact homozygous variants in consanguineous families with IBD.While the analysis was not designed to achieve statistical significance,our findings highlight genes or loci that warrant further research.Non-coding variants affecting NOD2 may be of importance in Druze patients with Crohn’s disease.