Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)

Globodera pallida is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since it was discovered in Idaho in 2006, eradication efforts have aimed to contain and eradicate G. pallida through phytosanitary action and soil fumigation. In this study, we investigated genome-wide patterns of G. pallida genetic variation across Idaho fields to evaluate whether the infestation resulted from a single or multiple introduction(s) and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples (~1,042,000 individuals) were collected and analyzed, representing five different fields in Idaho, a greenhouse population, and a field in Scotland that was used for external comparison. According to genome-wide allele frequency and fixation index (Fst) analyses, most of the genetic variation was shared among the G. pallida populations in Idaho fields pre-fumigation, indicating that the infestation likely resulted from a single introduction. Temporal patterns of genome-wide polymorphisms involving (1) pre-fumigation field samples collected in 2007 and 2014 and (2) pre- and post-fumigation samples revealed nucleotide variants (SNPs, single-nucleotide polymorphisms) with significantly differentiated allele frequencies indicating genetic differentiation. This study provides insights into the genetic origins and adaptive potential of G. pallida invading new environments.

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Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

BMC Ecology and Evolution ◽

10.1186/s12862-020-01739-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Kelly B. Klingler ◽

Joshua P. Jahner ◽

Thomas L. Parchman ◽

Chris Ray ◽

Mary M. Peacock

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Sierra Nevada ◽

Spatial Genetic Structure ◽

Spatial Scales ◽

Thermal Sensitivity ◽

Genomic Variation ◽

Genome Wide ◽

A Genome ◽

American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

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Quantitative Trait Loci for the Monoamine-Related Traits Heart Rate and Headless Behavior inDrosophila melanogaster

Genetics ◽

10.1093/genetics/157.1.283 ◽

2001 ◽

Vol 157 (1) ◽

pp. 283-294 ◽

Cited By ~ 2

Author(s):

Kristie Ashton ◽

Ana Patricia Wagoner ◽

Roland Carrillo ◽

Greg Gibson

Keyword(s):

Heart Rate ◽

Genetic Variation ◽

Recombinant Inbred Lines ◽

Model Organism ◽

Interval Mapping ◽

Activity Levels ◽

Environmental Variance ◽

Genome Wide ◽

A Genome ◽

Monoamine Receptors

AbstractDrosophila melanogaster appears to be well suited as a model organism for quantitative pharmacogenetic analysis. A genome-wide deficiency screen for haploinsufficient effects on prepupal heart rate identified nine regions of the genome that significantly reduce (five deficiencies) or increase (four deficiencies) heart rate across a range of genetic backgrounds. Candidate genes include several neurotransmitter receptor loci, particularly monoamine receptors, consistent with results of prior pharmacological manipulations of heart rate, as well as genes associated with paralytic phenotypes. Significant genetic variation is also shown to exist for a suite of four autonomic behaviors that are exhibited spontaneously upon decapitation, namely, grooming, grasping, righting, and quivering. Overall activity levels are increased by application of particular concentrations of the drugs octopamine and nicotine, but due to high environmental variance both within and among replicate vials, the significance of genetic variation among wild-type lines for response to the drugs is difficult to establish. An interval mapping design was also used to map two or three QTL for each behavioral trait in a set of recombinant inbred lines derived from the laboratory stocks Oregon-R and 2b.

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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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Effect of herbicides on black pigweed and sesbania pea, and yields of five grain sorghum cultivars in central Queensland

Australian Journal of Experimental Agriculture ◽

10.1071/ea9880327 ◽

1988 ◽

Vol 28 (3) ◽

pp. 327

Author(s):

SR Walker ◽

WH Hazard ◽

AF Mich ◽

BA Silver

Keyword(s):

Grain Yield ◽

Sorghum Bicolor ◽

Grain Sorghum ◽

Effective Control ◽

General Control ◽

Sesbania Cannabina ◽

Trianthema Portulacastrum ◽

Delayed Flowering

Six experiments were conducted in central Queensland to compare the efficacy of some post-emergence herbicides and mixtures in controlling black pigweed (Trianthema portulacastrum) and sesbania pea (Sesbania cannabina). The herbicides tested were atrazine, 2,4-D, dicamba, picloram plus 2,4-D, and fluroxypyr and mixtures of atrazine with 2,4-D, dicamba, picloram plus 2,4-D, fluroxypyr or tridiphane. In addition, 4 experiments were conducted to assess the tolerance of 5 sorghum cultivars (Sorghum bicolor) to some of these individual herbicides and atrazine mixtures. Small black pigweed and sesbania pea (< 10 cm diameter) were controlled with atrazine at 1.0 kg a.i./ ha, while for larger black pigweed (up to 15 cm diameter) atrazine at 2.25 kg/ha and atrazine mixtures were effective and for sesbania pea (up to 12 cm high) atrazine at 2.25 kg/ha, picloram plus 2,4-D at 35 + 140 g a.i./ha, fluroxypyr at 0.3 kg a.i./ha and atrazine mixtures were effective. In general, control of both weeds by mixtures with atrazine at 1.0 kg/ha was as effective as atrazine at 2.25 kg/ha alone. In the tolerance experiments the treatments were applied at 18-20 days after planting when the number of sorghum leaves was 4-6. Spraying with 2,4-D, dicamba, MCPA, picloram plus 2,4-D and atrazine mixtures with 2,4-D, dicamba and picloram plus 2,4-D consistently caused injury symptoms, delayed flowering and sometimes reduced grain yield. However, the susceptibility of sorghum to these treatments varied with seasons and cultivars. Overall, yield reductions were less when 2,4-D, dicamba and MCPA were applied at lower rates in the atrazine mixtures than when applied alone. All sorghum cultivars were tolerant of atrazine at 4.5 kg/ha. For effective control of both weeds, for crop safety and for minimum atrazine residues after harvest, we recommend that the weeds black pigweed and sesbania pea be sprayed when less than 10 cm in diameter or height, respectively, with atrazine at 1.0 kg/ha.

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