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51.
Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum)
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Amanda J. Burridge Paul A. Wilkinson Mark O. Winfield Gary L. A. Barker Alexandra M. Allen Jane A. Coghill Christy Waterfall Keith J. Edwards 《Plant biotechnology journal》2018,16(4):867-876
Wheat breeders and academics alike use single nucleotide polymorphisms (SNP s) as molecular markers to characterize regions of interest within the hexaploid wheat genome. A number of SNP ‐based genotyping platforms are available, and their utility depends upon factors such as the available technologies, number of data points required, budgets and the technical expertise required. Unfortunately, markers can rarely be exchanged between existing and newly developed platforms, meaning that previously generated data cannot be compared, or combined, with more recently generated data sets. We predict that genotyping by sequencing will become the predominant genotyping technology within the next 5–10 years. With this in mind, to ensure that data generated from current genotyping platforms continues to be of use, we have designed and utilized SNP ‐based capture probes from several thousand existing and publicly available probes from Axiom® and KASP ? genotyping platforms. We have validated our capture probes in a targeted genotyping by sequencing protocol using 31 previously genotyped UK elite hexaploid wheat accessions. Data comparisons between targeted genotyping by sequencing, Axiom® array genotyping and KASP ? genotyping assays, identified a set of 3256 probes which reliably bring together targeted genotyping by sequencing data with the previously available marker data set. As such, these probes are likely to be of considerable value to the wheat community. The probe details, full probe sequences and a custom built analysis pipeline may be freely downloaded from the CerealsDB website (http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB /sequence_capture.php). 相似文献
52.
Marmoset phylogenetics, conservation perspectives, and evolution of the mtDNA control region 总被引:3,自引:1,他引:2
Tagliaro CH; Schneider MP; Schneider H; Sampaio IC; Stanhope MJ 《Molecular biology and evolution》1997,14(6):674-684
Marmosets (genus Callithrix) are a diverse group of platyrrhine primates
with 13-15 purported taxa, many of them considered endangered.
Morphological analyses constitute most of the basis for recognition of
these forms as distinct taxa. The purpose of this study was to provide a
molecular view, based on mitochondrial control region sequences, of the
evolutionary history of the marmosets, concomitant with a molecular
phylogenetic perspective on species diversity within the group. An
additional purpose was to provide the first comparative examination of a
complete New World monkey control region sequence with those of other
mammals. The phylogenetic analyses provide convincing support for a split
between the Atlantic forest and Amazonian marmosets, with the inclusion of
the pygmy marmoset (Cebuella pygmaea) at the base of the Amazonian clade.
The earliest branch of the Atlantic forest group was C. aurita. In the
Amazonian group, the analyses do not support the recognition of C.
humeralifer and the recently described C mauesi as distinct taxa. They do,
however, support a clear distinction between C. argentata and a strongly
supported mixed clade of C. humeralifer and C. mauesi. In the Atlantic
forest group, the phylogenetic tree suggests mixing between C. penicillata,
C. kuhli, and possibly C. jacchus. Most of the sequence features
characteristic of other mammal control regions were also evident in
marmosets, with the exception that conserved sequence blocks (CSBs) 2 and 3
were not clearly identifiable. Tandem repeat units often associated with
heteroplasmy in a variety of other mammals were not evident in the marmoset
sequences.
相似文献
53.
Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae) 总被引:5,自引:0,他引:5
Campbell CS; Wojciechowski MF; Baldwin BG; Alice LA; Donoghue MJ 《Molecular biology and evolution》1997,14(1):81-90
Individual plants of several Amelanchier taxa contain many polymorphic
nucleotide sites in the internal transcribed spacers (ITS) of nuclear
ribosomal DNA (nrDNA). This polymorphism is unusual because it is not
recent in origin and thus has resisted homogenization by concerted
evolution. Amelanchier ITS sequence polymorphism is hypothesized to be the
result of gene flow between two major North American clades resolved by
phylogenetic analysis of ITS sequences. Western North American species plus
A. humilis and A. sanguinea of eastern North America form one clade (A),
and the remaining eastern North American Amelanchier make up clade B. Five
eastern North American taxa are polymorphic at many of the nucleotide sites
where clades A and B have diverged and are thought to be of hybrid origin,
with A. humilis or A. sanguinea as one parent and various members of clade
B as the other parent. Morphological evidence suggests that A. humilis is
one of the parents of one of the polymorphic taxa, a microspecies that we
refer to informally as A. "erecta." Sequences of 21 cloned copies of the
ITS1- 5.8S gene-ITS2 region from one A. "erecta" individual are identical
to A. humilis sequence or to the clade B consensus sequence, or they are
apparent recombinants of A. humilis and clade B ITS repeats. Amelanchier
"erecta" and another polymorphic taxon are suspected to be relatively old
because both grow several hundred kilometers beyond the range of one of
their parents. ITS sequence polymorphisms have apparently persisted in
these two taxa perhaps because of polyploidy and/or agamospermy (asexual
seed production), which are prevalent in the genus.
相似文献
54.
55.
Landscape genetics is a rapidly growing discipline that examines how heterogeneous landscapes and other environmental factors influence population genetic variation. We conducted a systematic review of the landscape genetic literature which demonstrates that birds are severely under‐represented relative to their species diversity and general publication prevalence. Most avian studies were on species that have relatively low dispersal ability, and we suggest that this reflects an assumed high vagility of birds that precludes spatial genetic variation relatable to landscape heterogeneity. However, spatial genetic variation exists in several bird species with very high dispersal ability, but this has not been considered in the context of landscape features. Genetic patterns may also relate to landscape due to breeding habitat selection and territorial behaviour, despite the fact that species may be able to move throughout different landscape elements with minimal movement costs. Habitat loss and fragmentation are continuing globally and are strongly related to declines in bird populations. Landscape genetic studies provide a means to understand, predict and mitigate the effects of anthropogenic landscape change on birds. This review promotes the need for landscape genetic studies of birds, such that a greater understanding of the drivers of their genetic structuring can be developed and generalizations can be made from landscape genetic studies that apply more broadly across taxa. 相似文献
56.
JA Nboyine S Boyer D Saville MJ Smith SD Wratten 《New Zealand journal of zoology.》2016,43(4):336-350
The endemic New Zealand ground wētā (Hemiandrus sp. ‘promontorius’) has a Naturally Uncommon conservation status. This is because of the paucity of information on its density and distribution. Here, the biology, density and distribution of a population of this wētā found in and around vineyards in the Awatere Valley, Marlborough was studied. Wētā density was assessed in vineyards, paddocks and shrublands in this valley. Soil moisture, penetration resistance, pH and organic matter were recorded at locations with and without wētā. Wētā density in vineyards was significantly higher than in either paddocks or shrub habitats. In vineyards, the density of this insect was significantly higher under-vines than in the inter-rows. Higher numbers of this wētā were found in moist soils that required lower force to burrow. Females laid an average of 55 eggs between March and April, which hatched in September. These findings highlight the intersection between agriculture and conservation. 相似文献
57.
H Zhang L Wang S Kao I P Whitehead M J Hart B Liu K Duus K Burridge C J Der L Su 《Current biology : CB》1999,9(21):1271-1274
The long cytoplasmic tail of the human immunodeficiency virus (HIV)-1 transmembrane protein gp41 (gp41C) is implicated in the replication and cytopathicity of HIV-1 [1]. Little is known about the specific functions of gp41C, however. HIV-1 or simian immunodeficiency virus (SIV) mutants with defective gp41C have cell-type- or species-dependent phenotypes [2] [3] [4] [5] [6]. Thus, host factors are implicated in mediating the functions of gp41C. We report here that gp41C interacted with the carboxy-terminal regulatory domain of p115-RhoGEF [7], a specific guanine nucleotide exchange factor (GEF) and activator of the RhoA GTPase, which regulates actin stress fiber formation, activation of serum response factor (SRF) and cell proliferation [8] [9]. We demonstrate that gp41C inhibited p115-mediated actin stress fiber formation and activation of SRF. An amphipathic helix region with a leucine-zipper motif in gp41C is involved in its interaction with p115. Mutations in gp41C leading to loss of interaction with p115 impaired HIV-1 replication in human T cells. These findings suggest that an important function of gp41C is to modulate the activity of p115-RhoGEF and they thus reveal a new potential anti-HIV-1 target. 相似文献
58.
T F Peter E C Anderson M J Burridge B D Perry S M Mahan 《The Journal of parasitology》1999,85(3):468-472
Three species of wild African ruminants, impala (Aepyceros melampus), sable (Hippotragus equinus), and tsessebe (Damaliscus lunatus), were experimentally inoculated with in vitro culture-derived Cowdria ruminantium organisms, the tick-borne causative agent of heartwater in domestic ruminants, to determine their susceptibility to infection. No clinical disease was observed in any of the ruminants. However, C. ruminantium was detected in the sable by the transmission of heartwater to susceptible sheep, through the tick vector Amblyomma hebraeum, at 10 and 37 days postinfection (PI). Attempts to detect infection in the impala and tsessebe by tick transmission at 54 days PI failed. The impala and tsessebe were reinoculated with C. ruminantium organisms at 146 days after the first inoculation; however, a tick transmission attempt at 66 days after the reinoculation also failed. Seroconversion, as detected by immunoblotting, was demonstrated in the sable and the tsessebe but not in the impala. The results demonstrate that sable can be carriers of C. ruminantium. The susceptibility of tsessebe and impala, however, remains undetermined. 相似文献
59.
Intrinsic factors drive spatial genetic variation in a highly vagile species,the wedge‐tailed eagle Aquila audax,in Tasmania
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Christopher P. Kozakiewicz Scott Carver Jeremy J. Austin Jill M. Shephard Christopher P. Burridge 《Journal of avian biology》2017,48(7):1025-1034
Knowledge of dispersal in a species, both its quantity and the factors influencing it, are crucial for our understanding of ecology and evolution, and for species conservation. Here we quantified and formally assessed the potential contribution of extrinsic factors on individual dispersal in the threatened Tasmanian population of wedge‐tailed eagle Aquila audax. As successful breeding by these individuals appears strongly related to habitat, we tested the effect of landscape around sampling sites on genetic diversity and spatial genetic variation, as these are influenced by patterns of dispersal. Similarly, we also tested whether habitat intervening sampling sites could explain spatial genetic variation. Twenty microsatellites were scored, but only a small proportion of spatial genetic variation (4.6%) could be explained by extrinsic factors, namely habitat suitability and elevation between sites. However, significant clinal genetic variation was evident across Tasmania, which we explain by intrinsic factors, likely high natal philopatry and occasional long‐distance dispersal. This study demonstrates that spatial genetic variation can be detected in highly vagile species at spatial scales that are small relative to putative dispersal ability, although here there was no substantial relationship with landscape factors tested. 相似文献
60.
Swenson-Fields KI Sandquist JC Rossol-Allison J Blat IC Wennerberg K Burridge K Means AR 《Molecular cell》2008,32(1):43-56
Mixed lineage kinase 3 (MLK3) is a MAP3K that activates the JNK-dependent MAPK pathways. Here, we show that MLK3 is required for cell migration in a manner independent of its role as a MAP3K or MLK3 kinase activity. Rather, MLK3 functions in a regulated way to limit levels of the activated GTPase Rho by binding to the Rho activator, p63RhoGEF/GEFT, which, in turn, prevents its activation by Galphaq. These findings demonstrate a scaffolding role for MLK3 in controlling the extent of Rho activation that modulates cell migration. Moreover, they suggest that MLK3 functions as a network hub that links a number of signaling pathways. 相似文献