Host genomic influence on bacterial composition in the switchgrass rhizosphere

AbstractHost genetic variation can shape the diversity and composition of associated microbiomes, which may reciprocally influence host traits and performance. While the genetic basis of phenotypic diversity of plant populations in nature has been studied, comparatively little research has investigated the genetics of host effects on their associated microbiomes. Switchgrass (Panicum virgatum) is a highly outcrossing, perennial, grass species with substantial locally adaptive diversity across its native North American range. Here, we compared 383 switchgrass accessions in a common garden to determine the host genotypic influence on rhizosphere bacterial composition. We hypothesized that the composition and diversity of rhizosphere bacterial assemblages would differentiate due to genotypic differences between hosts (potentially due to root phenotypes and associated life history variation). We observed higher alpha diversity of bacteria associated with upland ecotypes and tetraploids, compared to lowland ecotypes and octoploids, respectively. Alpha diversity correlated negatively with flowering time and plant height, indicating that bacterial composition varies along switchgrass life history axes. Narrow-sense heritability (h2) of the relative abundance of twenty-one core bacterial families was observed. Overall compositional differences among tetraploids, due to genetic variation, supports wide-spread genotypic influence on the rhizosphere microbiome. Lastly, a genome-wide association study identified 1,861 single-nucleotide polymorphisms associated with 110 families and genes containing them related to potential regulatory functions. Our findings suggest that switchgrass genomic and life-history variation influences bacterial composition in the rhizosphere, potentially due to host adaptation to local environments.

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Genetic variation in recombination rate in the pig

Genetics Selection Evolution ◽

10.1186/s12711-021-00643-0 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Martin Johnsson ◽

Andrew Whalen ◽

Roger Ros-Freixedes ◽

Gregor Gorjanc ◽

Ching-Yi Chen ◽

...

Keyword(s):

Genetic Variation ◽

Recombination Rate ◽

Large Scale ◽

Genome Wide Association Study ◽

Genetic Material ◽

A Genome ◽

Pig Genome ◽

Genetic Length ◽

Trait Locus ◽

Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

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Genetic variation rs10484761 on 6p21.1 derived from a genome-wide association study is associated with gastric cancer survival in a Chinese population

Gene ◽

10.1016/j.gene.2013.11.087 ◽

2014 ◽

Vol 536 (1) ◽

pp. 59-64 ◽

Cited By ~ 10

Author(s):

Meiyun Kang ◽

Xiaojie Ding ◽

Ming Xu ◽

Haixia Zhu ◽

Sang Liu ◽

...

Keyword(s):

Gastric Cancer ◽

Genetic Variation ◽

Association Study ◽

Chinese Population ◽

Genome Wide Association Study ◽

Cancer Survival ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

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Genetic variation associated with chromosomal aberration frequency: A genome-wide association study

Environmental and Molecular Mutagenesis ◽

10.1002/em.22236 ◽

2018 ◽

Vol 60 (1) ◽

pp. 17-28 ◽

Cited By ~ 5

Author(s):

Yasmeen Niazi ◽

Hauke Thomsen ◽

Bozena Smolkova ◽

Ludmila Vodickova ◽

Sona Vodenkova ◽

...

Keyword(s):

Genetic Variation ◽

Association Study ◽

Chromosomal Aberration ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Aberration Frequency ◽

Genome Wide ◽

A Genome

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Loci, genes, and gene networks associated with life history variation in a model ecological organism,Daphnia pulex(complex)

10.1101/436733 ◽

2018 ◽

Author(s):

Jacob W. Malcom ◽

Thomas E. Juenger ◽

Mathew A. Leibold

Keyword(s):

Gene Expression ◽

Genetic Variation ◽

Life History ◽

Molecular Basis ◽

Life History Traits ◽

Evolutionary Dynamics ◽

Daphnia Pulex ◽

Life History Trait ◽

Life History Variation ◽

Trait Variation

ABSTRACTBackgroundIdentifying the molecular basis of heritable variation provides insight into the underlying mechanisms generating phenotypic variation and the evolutionary history of organismal traits. Life history trait variation is of central importance to ecological and evolutionary dynamics, and contemporary genomic tools permit studies of the basis of this variation in non-genetic model organisms. We used high density genotyping, RNA-Seq gene expression assays, and detailed phenotyping of fourteen ecologically important life history traits in a wild-caught panel of 32Daphnia pulexclones to explore the molecular basis of trait variation in a model ecological species.ResultsWe found extensive phenotypic and a range of heritable genetic variation (~0 < H2< 0.44) in the panel, and accordingly identify 75-261 genes—organized in 3-6 coexpression modules—associated with genetic variation in each trait. The trait-related coexpression modules possess well-supported promoter motifs, and in conjunction with marker variation at trans- loci, suggest a relatively small number of important expression regulators. We further identify a candidate genetic network with SNPs in eight known transcriptional regulators, and dozens of differentially expressed genes, associated with life history variation. The gene-trait associations include numerous un-annotated genes, but also support several a priori hypotheses, including an ecdysone-induced protein and several Gene Ontology pathways.ConclusionThe genetic and gene expression architecture ofDaphnialife history traits is complex, and our results provide numerous candidate loci, genes, and coexpression modules to be tested as the molecular mechanisms that underlieDaphniaeco-evolutionary dynamics.

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An association between chronic widespread pain and the gut microbiome

Rheumatology ◽

10.1093/rheumatology/keaa847 ◽

2020 ◽

Author(s):

Maxim B Freidin ◽

Maria A Stalteri ◽

Philippa M Wells ◽

Genevieve Lachance ◽

Andrei-Florin Baleanu ◽

...

Keyword(s):

Gut Microbiome ◽

Genome Wide Association Study ◽

Meta Analysis ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Chronic Widespread Pain ◽

Mendelian Randomisation ◽

Total N ◽

16S Rrna Amplicon Sequencing ◽

A Genome

Abstract Objectives Chronic widespread musculoskeletal pain (CWP) is a characteristic symptom of fibromyalgia, which has been shown to be associated with an altered gut microbiome. Microbiome studies to date have not examined the milder CWP phenotype specifically nor have they explored the role of raised BMI. The aim of this study was to investigate whether the microbiome is abnormal in CWP. Methods CWP was assessed using a standardized screening questionnaire in female volunteers from the TwinsUK cohort including 113 CWP cases and 1623 controls. The stool microbiome was characterised using 16S rRNA amplicon sequencing and amplicon sequence variants (ASVs), and associations with CWP examined using linear mixed-effects models adjusting for BMI, age, diet, family relatedness and technical factors. Results Alpha diversity was significantly lower in CWP cases than controls (Mann–Whitney test, p-values 2.3e-04 and 1.2e-02, respectively). The species Coprococcus comes was significantly depleted in CWP cases (p.adj = 3.04e-03). A genome-wide association study (GWAS) performed for C. comes in TwinsUK followed by meta-analysis with three Dutch cohorts (total n = 3521) resulted in nine suggestive regions, with the most convincing on chromosome 4 near the TRAM1L1 gene (rs76957229, p= 7.4e-8). A Mendelian randomisation study based on the results of the GWAS did not support a causal role for C. comes on the development of CWP. Conclusions We have demonstrated reduced diversity in the microbiome in CWP, indicating an involvement of the gut microbiota in CWP; prospectively the microbiome may offer therapeutic opportunities for this condition.

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Inherited genetic variation in EPHA5, FGD4, and NRDG1 and paclitaxel (P)-induced peripheral neuropathy (PN): Results from a genome-wide association study (GWAS) in CALGB 40101.

Journal of Clinical Oncology ◽

10.1200/jco.2010.28.15_suppl.3021 ◽

2010 ◽

Vol 28 (15_suppl) ◽

pp. 3021-3021 ◽

Cited By ~ 7

Author(s):

D. L. Kroetz ◽

R. M. Baldwin ◽

K. Owzar ◽

C. Jiang ◽

H. Zembutsu ◽

...

Keyword(s):

Genetic Variation ◽

Peripheral Neuropathy ◽

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

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Aegilops sharonensis: Origin, genetics, diversity, and potential for wheat improvement

Botany ◽

10.1139/b09-040 ◽

2009 ◽

Vol 87 (8) ◽

pp. 740-756 ◽

Cited By ~ 16

Author(s):

Pablo D. Olivera ◽

Brian J. Steffenson

Keyword(s):

Agricultural Intensification ◽

Phenotypic Diversity ◽

Grass Species ◽

Wheat Diseases ◽

B Genome ◽

Diverse Species ◽

Wheat Improvement ◽

Aegilops Sharonensis ◽

Variable Environments ◽

A Genome

Aegilops sharonensis Eig (Sharon goatgrass; section Sitopsis) is an annual diploid grass species growing endemically in the coastal plains of Israel and southern Lebanon. It is a wild relative of wheat, with a genome closely related to the B genome of cultivated bread wheat. With the most limited distribution of any species in the genus Aegilops, Ae. sharonensis is rapidly losing its habitats, owing to the combined effects of modern agricultural intensification and expansion of urban and industrial areas. Aegilops sharonensis is known to be a rich source of genes providing resistance to important wheat diseases and abiotic stresses, but it has not been widely exploited. The presence of gametocidal genes that control preferential transmission of chromosome 4Ssh increases the difficulty of introgressing genes from Ae. sharonensis into wheat. However, successful introgression of the genes for resistance to leaf rust, stripe rust, and powdery mildew has been achieved. Studies on genetic and phenotypic diversity indicated that Ae. sharonensis is a highly diverse species, comparable with others that have a wider geographic distribution and more variable environments. Targeting the regions and sites with the highest diversity in Ae. sharonensis will facilitate the capture of the greatest variability and also the identification of novel and diverse genes for wheat improvement.

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Response to selection for photoperiod responsiveness on the density and location of mature GnRH-releasing neurons

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00562.2004 ◽

2005 ◽

Vol 288 (5) ◽

pp. R1226-R1236 ◽

Cited By ~ 16

Author(s):

Mauricio Avigdor ◽

Shannon D. Sullivan ◽

Paul D. Heideman

Keyword(s):

Genetic Variation ◽

Life History ◽

Wild Population ◽

Gonadotropin Releasing Hormone ◽

Short Photoperiod ◽

Life History Trait ◽

Complex Method ◽

Life History Variation ◽

Releasing Hormone ◽

Gnrh Neurons

Natural variation in neuroendocrine traits is poorly understood, despite the importance of variation in brain function and evolution. Most rodents in the temperate zones inhibit reproduction and other nonessential functions in short winter photoperiods, but some have little or no reproductive response. We tested whether genetic variability in reproductive seasonality is related to individual differences in the neuronal function of the gonadotropin-releasing hormone network, as assessed by the number and location of mature gonadotropin-releasing hormone-secreting neurons under inhibitory and excitatory photoperiods. The experiments used lines of Peromyscus leucopus previously developed by selection from a wild population. One line contained individuals reproductively inhibited by short photoperiod, and the other line contained individuals nonresponsive to short photoperiod. Expression of mature gonadotropin-releasing hormone (GnRH) immunoreactivity in the brain was detected using SMI-41 antibody in the single-labeled avidin-biotin-peroxidase-complex method. Nonresponsive mice had 50% more immunoreactive GnRH neurons than reproductively inhibited mice in both short- and long-day photoperiods. The greatest differences were in the anterior hypothalamus and preoptic areas. In contrast, we detected no significant within-lines differences in the number or location of immunoreactive GnRH neurons between photoperiod treatments. Our data indicate that high levels of genetic variation in a single wild population for a specific neuronal trait are related to phenotypic variation in a life history trait, i.e., winter reproduction. Variation in GnRH neuronal activity may underlie some of the natural reproductive and life history variation observed in wild populations of P. leucopus. Similar genetic variation in neuronal traits may be present in humans and other species.

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Host life-history variation in response to parasitism

Parasitology ◽

10.1017/s0031182000049143 ◽

1985 ◽

Vol 90 (1) ◽

pp. 205-216 ◽

Cited By ~ 270

Author(s):

D. J. Minchella

Keyword(s):

Genetic Variation ◽

Life History ◽

Parasitic Infection ◽

Host Susceptibility ◽

Life History Variation ◽

Susceptible Host ◽

Finite Set ◽

Host Life ◽

Host Parasite ◽

Parasite Populations

Over half of all living species of plants and animals are parasitic, which by definition involves intimate association with and unfavourable impact on hosts (Price, 1980). This paper will only consider parasites whose ‘unfavourable impact’ adversely affects the birth and/or mortality rates of their hosts (Anderson, 1978). Most organisms are potential hosts and must deal with the problem of parasitism. The probability of parasitic infection of a host is influenced by both environmental and genetic factors. Traditionally it was assumed that a host was either resistant or susceptible to a particular parasite and therefore the interaction between a parasite and potential host had only two possible outcomes: either the resistant host rebuffed the parasitic attack and remained uninfected or the parasite successfully invaded and significantly reduced the reproductive success of the susceptible host. This approach, however, ignored the intraspecific genetic variation present within both host and parasite populations (Wakelin, 1978). Since the outcome is determined by the interaction of a finite set of host genes and parasite genes, genetic variation in host susceptibility and parasite infectivity (Richards, 1976; Wakelin, 1978) suggests that more than two outcomes are possible. Variation in host and parasite genomes does not begin and end at the susceptibility/infectivity loci. Other genes may also influence the outcome of host–parasite interactions by altering the life-history patterns of hosts and parasites, and lead to a variety of outcomes.

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