Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep

Diez-Tascón, Cristina; Keane, Orla M.; Wilson, Theresa; Zadissa, Amonida; Hyndman, D. L.; Baird, David; McEwan, John C.; Crawford, A. M.

doi:10.1152/physiolgenomics.00257.2004

Cited by 107 publications

(93 citation statements)

References 62 publications

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“…by challenging cells derived from these individuals to disease in vitro) is available. But few published studies have yet described how the response of large numbers of genes differs between resistant and susceptible animals (Duncan et al, 2002;Diez-Tascon et al, 2005;Keane et al, 2006;Glass and Jensen, 2007;Jensen et al, 2008). Also, we do not know what the predictive ability of tests for such genes might be as few individuals (11 or less) have been used in these studies, equations describing the relationship between gene expression and disease resistance have not been derived and the predictive ability of such gene expression profiles has not been tested.…”

Section: Discussionmentioning

confidence: 99%

Use of gene expression data for predicting continuous phenotypes for animal production and breeding

Robinson

Goddard

Hayes

2008

Animal

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Traits such as disease resistance are costly to evaluate and slow to improve using current methods. Analysis of gene expression profiles (e.g. DNA microarrays) has potential for predicting such phenotypes and has been used in an analogous way to classify cancer types in human patients. However, doubts have been raised regarding the use of classification methods with microarray data for this purpose. Here we propose a method using random regression with cross validation, which accounts for the distribution of variation in the trait and utilises different subsets of patients or animals to perform a complete validation of predictive ability. Published breast tumour data were used to test the method. Despite the small dataset (n , 100), the new approach resulted in a moderate but significant correlation between the predicted and actual phenotypes (0.32). Binary classification of the predicted phenotypes yielded similar classification error rates to those found by other authors (35%). Unlike other methods, the new method gave a quantitative estimate of phenotype that could be used to rank animals and select those with extreme phenotypic performance. Use of the method in an optimal way using larger sample sizes, and combining DNA microarrays and other testing platforms, is recommended.

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Section: Discussionmentioning

confidence: 99%

Use of gene expression data for predicting continuous phenotypes for animal production and breeding

Robinson

Goddard

Hayes

2008

Animal

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“…When the genes for resistance and their functions are identified, this will provide valuable insights into the molecular basis of the host resistance to GINs. Microarray studies have been very helpful to detect genetic variability between resistant and susceptible animals (Diez-Tascon et al 2005). Following infection, gene expression differs between resistant and susceptible breeds or between infected and noninfected animals (Mackinnon et al 2009).…”

Section: Resistant Genesmentioning

confidence: 99%

Small ruminant resistance against gastrointestinal nematodes: a case of Haemonchus contortus

et al. 2011

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Gastrointestinal nematode (GIN) infections are a common constraint to small ruminant industry throughout the world, and among those, haemonchosis has its own significance. Control of GIN primarily relies on the use of anthelmintics, but this approach has become less reliable due to the development of resistance in GINs against commonly used anthelmintics and an increased consumer demand for environmentally friendly animal products. These issues have stimulated investigations to find alternative sustainable control strategies, which are less reliant on anthelmintic input. One of such strategies is breeding of small ruminants for their resistance to the GINs. The susceptibility and resistance of animals to GIN infections varies within and between breeds. Various parasitological, biochemical and immunological parameters are employed to evaluate natural resistance status of animals both in natural pasture and artificial infections. The immune mechanisms responsible for resistance are not completely understood, but it has a significant effect in inherited resistance. Relatively resistant or tolerant animals show better local and generalised immune response as compared to susceptible. Immune response against GINs is influenced by many physiological factors. Determination of specific genes linked with host resistance will provide a valuable approach to find out the molecular mechanism of host resistance to GINs. Resistance has been reported to reduce pasture contamination, which in turn reduces re-infection and thus the requirement of the frequent anthelmintic treatments. The efficiency of control can be increased through objective and accurate identification of genetically tolerant individuals by natural and artificial infections with GINs. Complete resistance is the ultimate solution, but this has generally been ignored as a commercial reality. This paper reviews the published reports on natural resistance in small ruminants and discusses the prospects of developing small ruminants, which could be resistant to GINs.

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“…In addition, the close evolutionary relationship between sheep and cattle has allowed several groups to use bovine microarrays for functional studies in sheep with some success [e.g. Tao et al, 2004;Diez-Tascón et al, 2005;Cao et al, 2006]. A first draft of the sheep genome sequence assembly (version 1.0) that corresponds to 2,784.6 Mbp of DNA sequence generated from 6 diverse animals has been produced in another ISGC project and has been made available at http://www.livestockgenomics.csiro.au/perl/ gbrowse.cgi/oar1.0/.…”

Section: Genetic and Physical Analysis Of The Sheep Genomementioning

confidence: 99%

Molecular Cytogenetics and Gene Mapping in Sheep (<i>Ovis aries, </i>2n = 54)

Goldammer¹,

Meo

Lühken

et al. 2009

Cytogenet Genome Res

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The development of a completely annotated sheep genome sequence is a key need for understanding the phylogenetic relationships and genetic diversity among the many different sheep breeds worldwide and for identifying genes controlling economically and physiologically important traits. The ovine genome sequence assembly will be crucial for developing optimized breeding programs based on highly productive, healthy sheep phenotypes that are adapted to modern breeding and production conditions. Scientists and breeders around the globe have been contributing to this goal by generating genomic and cDNA libraries, performing genome-wide and trait-associated analyses of polymorphism, expression analysis, genome sequencing, and by developing virtual and physical comparative maps. The International Sheep Genomics Consortium (ISGC), an informal network of sheep genomics researchers, is playing a major role in coordinating many of these activities. In addition to serving as an essential tool for monitoring chromosome abnormalities in specific sheep populations, ovine molecular cytogenetics provides physical anchors which link and order genome regions, such as sequence contigs, genes and polymorphic DNA markers to ovine chromosomes. Likewise, molecular cytogenetics can contribute to the process of defining evolutionary breakpoints between related species. The selective expansion of the sheep cytogenetic map, using loci to connect maps and identify chromosome bands, can substantially contribute to improving the quality of the annotated sheep genome sequence and will also accelerate its assembly. Furthermore, identifying major morphological chromosome anomalies and micro-rearrangements, such as gene duplications or deletions, that might occur between different sheep breeds and other Ovis species will also be important to understand the diversity of sheep chromosome structure and its implications for cross-breeding. To date, 566 loci have been assigned to specific chromosome regions in sheep and the new cytogenetic map is presented as part of this review. This review will also summarize the current cytogenomic status of the sheep genome, describe current activities in the sheep cytogenomics research sector, and will discuss the cytogenomics data in context with other major sheep genomics projects.

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Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep

Abstract: . Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep.

Cited by 107 publications

References 62 publications

Use of gene expression data for predicting continuous phenotypes for animal production and breeding

Use of gene expression data for predicting continuous phenotypes for animal production and breeding

Small ruminant resistance against gastrointestinal nematodes: a case of Haemonchus contortus

Molecular Cytogenetics and Gene Mapping in Sheep (<i>Ovis aries, </i>2n = 54)

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