scholarly journals Expression biomarkers used for the selective breeding of complex polygenic traits

2016 ◽  
Author(s):  
M. Marta Guarna ◽  
Shelley E. Hoover ◽  
Elizabeth Huxter ◽  
Heather Higo ◽  
Kyung-Mee Moon ◽  
...  
Keyword(s):  
Selective Breeding ◽  
Nucleotide Polymorphisms ◽  
Protein Markers ◽  
Three Generations ◽  
Livestock Breeding ◽  
Polygenic Traits ◽  
Genomic Markers ◽  
Resistance Trait ◽  
Agricultural Species ◽  
Better Than

AbstractWe present a novel way to select for highly polygenic traits. For millennia, humans have used observable phenotypes to selectively breed stronger or more productive livestock and crops. Selection on genotype, using single-nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs), is also now applied broadly in livestock breeding programs; however, selection on protein or mRNA expression markers have not been proved useful yet. Here we demonstrate the utility of protein markers to select for disease-resistant behaviour in the European honey bees (Apis melliferaL.). Robust, mechanistically-linked protein expression markers, by integrating cis and trans effects from many genomic loci, may overcome limitations of genomic markers to allow for selection. After three generations of selection, the resulting stock performed as well or better than bees selected using phenotype–based assessment of this trait, when challenged with disease. This is the first demonstration of the efficacy of protein markers for selective breeding in any agricultural species, plant or animal.Significance statementThe honey bee has been in the news a lot recently, largely because of world-wide die-offs due to the parasitic Varroa mite, which is becoming resistant to the chemical controls the bee industry uses. In this study, we show that robust expression biomarkers of a disease-resistance trait can be used, in an out-bred population, to select for that trait. After three generations of selection, the resulting stock performed as well or better than bees selected using the phenotypic best method for assessing this trait when challenged with disease. This is the first demonstration of an expression marker for selective breeding in any agricultural species, plant or animal. This also represents a completely novel way to select for highly polygenic traits.

scholarly journals Genome-wide shifts in climate-related variation underpin responses to selective breeding in a widespread conifer

2021 ◽  
Vol 118 (10) ◽  
pp. e2016900118
Author(s):  
Ian R. MacLachlan ◽  
Tegan K. McDonald ◽  
Brandon M. Lind ◽  
Loren H. Rieseberg ◽  
Sam Yeaman ◽  
...  
Keyword(s):  
Gene Flow ◽  
Selective Breeding ◽  
Natural Populations ◽  
Cold Injury ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Differences ◽  
Climatic Regions ◽  
Breeding Populations ◽  
Trade Offs ◽  
Growth Initiation

Locally adapted temperate tree populations exhibit genetic trade-offs among climate-related traits that can be exacerbated by selective breeding and are challenging to manage under climate change. To inform climatically adaptive forest management, we investigated the genetic architecture and impacts of selective breeding on four climate-related traits in 105 natural and 20 selectively bred lodgepole pine populations from western Canada. Growth, cold injury, growth initiation, and growth cessation phenotypes were tested for associations with 18,600 single-nucleotide polymorphisms (SNPs) in natural populations to identify “positive effect alleles” (PEAs). The effects of artificial selection for faster growth on the frequency of PEAs associated with each trait were quantified in breeding populations from different climates. Substantial shifts in PEA proportions and frequencies were observed across many loci after two generations of selective breeding for height, and responses of phenology-associated PEAs differed strongly among climatic regions. Extensive genetic overlap was evident among traits. Alleles most strongly associated with greater height were often associated with greater cold injury and delayed phenology, although it is unclear whether potential trade-offs arose directly from pleiotropy or indirectly via genetic linkage. Modest variation in multilocus PEA frequencies among populations was associated with large phenotypic differences and strong climatic gradients, providing support for assisted gene flow polices. Relationships among genotypes, phenotypes, and climate in natural populations were maintained or strengthened by selective breeding. However, future adaptive phenotypes and assisted gene flow may be compromised if selective breeding further increases the PEA frequencies of SNPs involved in adaptive trade-offs among climate-related traits.

scholarly journals Population Genomics of Bettongia lesueur: Admixing Increases Genetic Diversity with no Evidence of Outbreeding Depression

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 851 ◽  
Author(s):  
Kate Rick ◽  
Kym Ottewell ◽  
Cheryl Lohr ◽  
Rujiporn Thavornkanlapachai ◽  
Margaret Byrne ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Threatened Species ◽  
Population Genomics ◽  
Fold Increase ◽  
Recruitment Rate ◽  
Outbreeding Depression ◽  
Nucleotide Polymorphisms ◽  
Isolated Populations ◽  
Genomic Markers ◽  
Founder Populations

Small and isolated populations are subject to the loss of genetic variation as a consequence of inbreeding and genetic drift, which in turn, can affect the fitness and long-term viability of populations. Translocations can be used as an effective conservation tool to combat this loss of genetic diversity through establishing new populations of threatened species, and to increase total population size. Releasing animals from multiple genetically diverged sources is one method to optimize genetic diversity in translocated populations. However, admixture as a conservation tool is rarely utilized due to the risks of outbreeding depression. Using high-resolution genomic markers through double-digest restriction site-associated sequencing (ddRAD-seq) and life history data collected over nine years of monitoring, this study investigates the genetic and fitness consequences of admixing two genetically-distinct subspecies of Bettongia lesueur in a conservation translocation. Using single nucleotide polymorphisms (SNPs) identified from 215 individuals from multiple generations, we found an almost 2-fold increase in genetic diversity in the admixed translocation population compared to the founder populations, and this was maintained over time. Furthermore, hybrid class did not significantly impact on survivorship or the recruitment rate and therefore we found no indication of outbreeding depression. This study demonstrates the beneficial application of mixing multiple source populations in the conservation of threatened species for minimizing inbreeding and enhancing adaptive potential and overall fitness.

scholarly journals First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes (Canis latrans)

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 66 ◽  
Author(s):  
Javier Monzón
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Markers ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Canis Latrans ◽  
Regional Analysis ◽  
Model Organism ◽  
Nucleotide Polymorphisms ◽  
Genomic Markers

Previous genetic studies of eastern coyotes (Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

scholarly journals Using triallelic SNPs for determining parentage in North American yak (Bos grunniens) and estimating cattle (B. taurus) introgression

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1096
Author(s):  
Ted Kalbfleisch ◽  
Jessica L. Petersen ◽  
R. G. Tait Jr. ◽  
Jiansheng Qiu ◽  
Veronica Basnayake ◽  
...  
Keyword(s):  
North American ◽  
Species Conservation ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
F1 Hybrid ◽  
Bos Grunniens ◽  
Three Generations ◽  
Animal Identification ◽  
Flanking Sequences ◽  
Zoological Park

Background: Genetic testing for pedigree accuracy is critical for managing genetic diversity in North American (NA) yak (Bos grunniens), a population expanded mostly from imported zoological park specimens.  DNA testing also enhances species conservation by identifying recent B. taurus F1 hybrid ancestors (within three generations).  Biallelic single nucleotide polymorphisms (SNPs) can accomplish either task, but increases the marker count and costs necessary to achieve both.  Our aim was to identify novel, multifunctional, triallelic yak SNPs (tySNPs), with each having two alleles for yak parentage testing, and a third allele for identifying recent cattle introgression.  Methods:  Genome sequences were aligned to the cattle UMD3.1 assembly and SNPs were screened for 1) heterozygosity in a NA and a Chinese yak, 2) a third allele at high frequency in cattle, and 3) flanking sequences conserved in both species.  Subsequently, tySNPs were filtered for unique alignment to the haplotype-resolved F1 yak assembly.  Allele frequencies were estimated in a subset of 87 tySNPs by genotyping 170 NA yak. Results:  We identified 610 autosomal tySNPs, distributed in 441 clusters with 5 Mb average genome spacing.  The average NA yak minor allele frequency was high (0.296), while average introgressed cattle alleles were low (0.004).  In simulations with tySNPs, 28 were sufficient for globally-unique animal identification (PI=5.81x10-12), 87 were able to exclude 19 random bulls from parentage at the 99% level without using the dam’s genotype (PE=5.3x10-4), and 87 were able to detect F1 hybridization events after three generations of yak backcrosses (1/16th B. taurus germplasm). Conclusions:  Identifying animals, determining parentage and detecting recent hybridization events was efficient with as few as 87 tySNPs.  A similar triallelic approach could be used with other bottlenecked Bos species that hybridize with cattle, such as NA plains bison (B. bison).

scholarly journals Revisiting Schizophrenia from an Evolutionary Perspective: An Association Study of Recent Evolutionary Markers and Schizophrenia

2020 ◽  
Author(s):  
Upasana Bhattacharyya ◽  
Smita N Deshpande ◽  
Triptish Bhatia ◽  
B K Thelma
Keyword(s):  
Heritability Estimate ◽  
Asian Population ◽  
Human Populations ◽  
Nucleotide Polymorphisms ◽  
South Asian Population ◽  
Disease Etiology ◽  
Expression Of Genes ◽  
Genomic Markers ◽  
Functional Relevance ◽  
Human Accelerated Regions

Abstract The persistence of schizophrenia in human populations at a high prevalence and with a large heritability estimate despite reduced fertility and increased mortality rate is a Darwinian paradox. This may be likely if the genomic components that predispose to schizophrenia are also advantageous for the acquisition of important human traits, such as language and cognition. Accordingly, an emerging group of genomic markers of recent evolution in humans, namely human accelerated regions (HARs), since our divergence from chimpanzees, are gaining importance for neurodevelopmental disorders, such as schizophrenia. We hypothesize that variants within HARs may affect the expression of genes under their control, thus contributing to disease etiology. A total of 49 HAR single nucleotide polymorphisms (SNPs) were prioritized from the complete repertoire of HARs (n = 2737) based on their functional relevance and prevalence in the South Asian population. Test of association using 2 independent schizophrenia case-control cohorts of north Indian ethnicity (discovery: n = 930; replication: n = 1104) revealed 3 SNPs (rs3800926, rs3801844, and rs764453) from chromosome 7 and rs77047799 from chromosome 3 to be significantly associated (combined analysis: Bonferroni corrected P < .002–.000004). Of note, these SNPs were found to alter the expression of neurodevelopmental genes such as SLC25A13, MAD1L1, and ULK4; a few from the HOX gene family; and a few genes that are implicated in mitochondrial function. These SNPs may most likely alter binding sites of transcription factors, including TFCP2, MAFK, SREBF2, E2F1, and/or methylation signatures around these genes. These findings reiterate a neurodevelopmental basis of schizophrenia and also open up a promising avenue to investigate HAR-mediated mitochondrial dysfunction in schizophrenia etiology.

Grain yield in Composite Cross Five of barley: effects of natural selection

2002 ◽  
Vol 138 (2) ◽  
pp. 171-176 ◽  
Author(s):  
E. Y. DANQUAH ◽  
J. A. BARRETT
Keyword(s):  
Natural Selection ◽  
Grain Yield ◽  
Commercial Variety ◽  
Low Input ◽  
Three Generations ◽  
Low Input Agriculture ◽  
Better Than

A range of three generations from each of three populations of Cambridge Composite Cross Five of barley spanning a period of 18 years of cultivation in Cambridge was evaluated for grain yield over 2 years in the field in 1991 and 1992. The design of the experiment was a randomized complete block with two replications. In 1991, the yield of the best composite cross generation was 78% that of Atem, a commercial variety bred for N.W. European conditions. In the drought-affected year, 1992, three of the composite cross generations performed better than Atem. It is suggested that composite cross populations may be useful in deriving lines for low-input agriculture.

scholarly journals Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland

2019 ◽  
Author(s):  
S. Eryn McFarlane ◽  
Darren C. Hunter ◽  
Helen V. Senn ◽  
Stephanie L. Smith ◽  
Rebecca Holland ◽  
...  
Keyword(s):  
Cervus Elaphus ◽  
Native Species ◽  
Red Deer ◽  
Cervus Nippon ◽  
Natural Process ◽  
Nucleotide Polymorphisms ◽  
Ancestry Informative Markers ◽  
Pure Species ◽  
Single Nucleotide ◽  
Better Than

AbstractHybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here we use 44,999 single nucleotide polymorphisms and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set, and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.

scholarly journals Population-based analysis of ocularChlamydia trachomatisin trachoma-endemic West African communities identifies genomic markers of disease severity

2017 ◽  
Author(s):  
AR Last ◽  
H Pickering ◽  
Ch Roberts ◽  
F Coll ◽  
J Phelan ◽  
...  
Keyword(s):  
Disease Severity ◽  
Disease Transmission ◽  
Population Based ◽  
Genomic Diversity ◽  
Ocular Tissue ◽  
Nucleotide Polymorphisms ◽  
Functional Protein ◽  
Transmitted Infection ◽  
Genomic Markers ◽  
Treatment Naïve

ABSTRACTChlamydia trachomatis(Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. UsingCtwhole genome sequences obtained directly from conjunctival swabs, we studiedCtgenomic diversity and associations betweenCtgenetic polymorphisms with ocular localization and disease severity in a treatment-naïve trachoma-endemic population in Guinea Bissau, West Africa. All sequences fall within the T2 ocular clade phylogenetically. This is consistent with the presence of the characteristic deletion intrpAresulting in a truncated non-functional protein and the ocular tyrosine repeat regions present intarPassociated with ocular tissue localization. We have identified twenty-oneCtnon-synonymous single nucleotide polymorphisms (SNPs) associated with ocular localization, including SNPs withinpmpD(OR=4.07,p*=0.001) andtarP(OR=0.34,p*=0.009). Eight SNPs associated with disease severity were found inyjfH (rlmB)(OR=0.13,p*=0.037),CTA0273(OR=0.12,p*=0.027),trmD(OR=0.12,p*=0.032),CTA0744(OR=0.12,p*=0.041),glgA(OR=0.10,p*=0.026),alaS(OR=0.10,p*=0.032),pmpE(OR=0.08,p*=0.001) and the intergenic regionCTA0744-CTA0745(OR=0.13,p*=0.043). This study demonstrates the extent of genomic diversity within a naturally circulating population of ocularCt, and the first to describe novel genomic associations with disease severity. These findings direct investigation of host-pathogen interactions that may be important in ocularCtpathogenesis and disease transmission.

Characterization of Chlorsulfuron Resistant and Susceptible Kochia (Kochia scoparia)

1994 ◽  
Vol 8 (3) ◽  
pp. 470-476 ◽  
Author(s):  
Curtis R. Thompson ◽  
Donald C. Thill ◽  
Carol A. Mallory-Smith ◽  
Bahman Shafii
Keyword(s):  
North Dakota ◽  
Nuclear Gene ◽  
Shoot Biomass ◽  
Dominant Trait ◽  
Kochia Scoparia ◽  
Three Generations ◽  
Resistance Trait ◽  
Chlorsulfuron Resistance

Kansas and North Dakota kochia populations identified as chlorsulfuron resistant (R) contained 20 and 30% susceptible (S) plants, respectively. Biotypes that were chlorsulfuron R or S were selected from each field R or S collection and selfed through three generations in the greenhouse. Chlorsulfuron at 7.6 and 17.8 g ai/ha suppressed shoot biomass of the Kansas and North Dakota R biotypes by 50%, respectively, which was a 30- and 105-fold greater dose than that required to reduce the respective S biotypes growth 50%. The R and S kochia biotypes are diploid with 2N = 18 chromosomes. Chlorsulfuron resistance is inherited in kochia as a dominant trait controlled by a single nuclear gene. Thus, the resistance trait can be spread by seed and pollen.

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