Genomics Facilitates Evaluation and Monitoring of McCloud River Redband Trout ( Oncorhynchus mykiss stonei )

2021 ◽  
Author(s):  
Ensieh Habibi ◽  
Michael R. Miller ◽  
Daphne Gille ◽  
Leigh Sanders ◽  
Jeff Rodzen ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Introgressive Hybridization ◽  
Principal Component ◽  
Snp Markers ◽  
Rad Sequencing ◽  
Sequencing Data ◽  
Major Threat ◽  
Redband Trout ◽  
Evaluation And Monitoring

Abstract The McCloud River Redband Trout (MRRT; Oncorhynchus mykiss stonei ) is a unique subspecies of rainbow trout that inhabits the isolated Upper McCloud River of Northern California. A major threat to MRRT is introgressive hybridization with non-native rainbow trout from historical stocking and contemporary unauthorized introductions . To help address this concern, we collected RAD-sequencing data on 308 total individuals from MRRT and other California O. mykiss populations and examined population structure using Principal Component and admixture analyses. Our results are consistent with previous studies; we found that populations of MRRT in Sheepheaven, Swamp, Edson, and Moosehead creeks are nonintrogressed. Additionally, we saw no evidence of introgression in Dry Creek, and suggest further investigation to determine if it can be considered a core MRRT conservation population. Sheepheaven Creek was previously thought to be the sole historical lineage of MRRT, but our analysis identified three: Sheepheaven, Edson, and Dry creeks, all of which should be preserved. Finally, we discovered diagnostic and polymorphic SNP markers for monitoring introgression and genetic diversity in MRRT. Collectively, our results provide a valuable resource for the conservation and management of MRRT.

scholarly journals Multi-Approach Assessment for Stress Evaluation in Rainbow Trout Females, Oncorhynchus mykiss (Walbaum, 1792) from Three Different Farms during the Summer Season

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1810
Author(s):  
Paul Uiuiu ◽  
Călin Lațiu ◽  
Tudor Păpuc ◽  
Cristina Craioveanu ◽  
Andrada Ihuț ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Biochemical Parameters ◽  
Principal Component ◽  
Environmental Parameters ◽  
Blood Parameters ◽  
Summer Season ◽  
Farmed Fish ◽  
Blood Profile ◽  
Blood Biochemical

Blood biochemistry parameters are valuable tools for monitoring fish health. Their baseline values are still undefined for a multitude of farmed fish species. In this study, changes in the blood profile of rainbow trout females (Oncorhynchus mykiss) from three farms were investigated using different biomarkers during the summer season. In the given context, the main water physicochemical parameters were investigated and twelve biochemical parameters were measured from blood samples of rainbow trout reared in the Fiad, Șoimul de Jos, and Strâmba farms. We selected these farms because the genetic background of the rainbow trout is the same, with all studied specimens coming from the Fiad farm, which has an incubation station. Forty-five samples were collected monthly (May to August) throughout summer to observe the changes in the blood profile of rainbow trout. Principal component analysis showed a clear separation both among the studied farms and months. Furthermore, significant correlations (p < 0.05) between the majority of the biochemical parameters were found, indicating that the environmental parameters can influence several blood parameters at the same time. The present study provides several useful norms for assessing the welfare of rainbow trout, indicating that the relationships among different parameters are important factors in interpreting the blood biochemical profiles.

scholarly journals Development and Application of Novel Indel Markers in Flax (Linum Usitatissimum L.) Through Whole-genome Re-sequencing

2021 ◽  
Author(s):  
Hui Jiang ◽  
Gen Pan ◽  
Touming Liu ◽  
Li Chang ◽  
Siqi Huang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Snp Markers ◽  
Diversity Analysis ◽  
Whole Genome ◽  
Chromosome 2 ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Genetic Diversity Analysis ◽  
Indel Markers

Abstract Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87-3 and 84-3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

scholarly journals Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Heshan Du ◽  
Jingjing Yang ◽  
Bin Chen ◽  
Xiaofen Zhang ◽  
Jian Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relatedness ◽  
Principal Component ◽  
Shape Index ◽  
Fruit Shape ◽  
Snp Markers ◽  
Variety Identification ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Multiplex Amplification

Abstract Background The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties. Results The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index (p < 0.0001). Conclusions Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.

scholarly journals Long-Term Assessment of Baseline Blood Biochemistry Parameters in Rainbow Trout (Oncorhynchus mykiss) Maintained under Controlled Conditions

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1466
Author(s):  
Paolo Pastorino ◽  
Stefania Bergagna ◽  
Daniela Dezzutto ◽  
Raffaella Barbero ◽  
Marzia Righetti ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Biochemical Parameters ◽  
Linear Regression Analysis ◽  
Principal Component ◽  
Gamma Glutamyl Transferase ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Controlled Conditions ◽  
Baseline Values ◽  
Glutamyl Transferase

Twelve biochemical parameters were measured in serum blood samples from rainbow trout (Oncorhynchus mykiss) maintained under controlled conditions. Forty-five samples were taken every 3 months (T1–T4) over the course of one year to define baseline values. The effect of fish total weight (TW) was also evaluated. Principal component analysis showed a clear separation between T4 and T1, and T2 and T3, indicating an increase in certain biochemical parameters with weight. Linear regression analysis showed how TW significantly explained 11–67% of the variability observed for nine parameters out of 12. Pearson’s correlation matrix showed a significant positive correlation (p < 0.05) between TW and albumin, alkaline phosphatase, alanine-aminotransferase, creatinine, gamma-glutamyl transferase, magnesium, phosphorus and total protein. Furthermore, significant correlations (p < 0.05) between the majority of the biochemical parameters were found, indicating that growth can influence several parameters at the same time. The present study provides several useful baseline values for assessing the health of O. mykiss, indicating that fish weight is an important factor for interpreting the blood biochemical profile.

scholarly journals Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8009
Author(s):  
Yu Lin ◽  
Qianzi Tang ◽  
Yan Li ◽  
Mengnan He ◽  
Long Jin ◽  
...  
Keyword(s):  
Principal Component ◽  
Snp Markers ◽  
Specific Pattern ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Heterozygous Snps ◽  
Specific Expression ◽  
Origin Effects ◽  
Crossbred Pigs

Crossbreeding is widely used aimed at improving crossbred performance for poultry and livestock. Alleles that are specific to different purebreds will yield a large number of heterozygous single-nucleotide polymorphisms (SNPs) in crossbred individuals, which are supposed to have the power to alter gene function or regulate gene expression. For pork production, a classic three-way crossbreeding system of Duroc × (Landrace × Yorkshire) (DLY) is generally used to produce terminal crossbred pigs with stable and prominent performance. Nonetheless, little is known about the breed-of-origin effects from purebreds on DLY pigs. In this study, we first estimated the distribution of heterozygous SNPs in three kinds of three-way crossbred pigs via whole genome sequencing data originated from three purebreds. The result suggested that DLY is a more effective strategy for three-way crossbreeding as it could yield more stably inherited heterozygous SNPs. We then sequenced a DLY pig family and identified 95, 79, 132 and 42 allele-specific expression (ASE) genes in adipose, heart, liver and skeletal muscle, respectively. Principal component analysis and unrestricted clustering analyses revealed the tissue-specific pattern of ASE genes, indicating the potential roles of ASE genes for development of DLY pigs. In summary, our findings provided a lot of candidate SNP markers and ASE genes for DLY three-way crossbreeding system, which may be valuable for pig breeding and production in the future.

Wavelength-dependent waveform characteristics of tectal evoked potentials in rainbow trout

2004 ◽  
Vol 82 (10) ◽  
pp. 1614-1620 ◽  
Author(s):  
C G McDonald ◽  
T J Haimberger ◽  
C W Hawryshyn
Keyword(s):  
Principal Component Analysis ◽  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Evoked Potentials ◽  
Significant Contribution ◽  
Principal Component ◽  
Component Analysis ◽  
Colour Discrimination ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Neural Processes

Wavelength-dependent properties of tectal evoked potentials (TEPs) in rainbow trout, Oncorhynchus mykiss (Walbaum, 1792), were examined. It was found that TEP waveforms show distinct variation as a function of wavelength. In addition, the data suggest that the On and Off channels of the tectum each possess different wavelength-dependent characteristics. Middle wavelength stimulation typically evoked a waveform similar to that reported for another anamniote vertebrate, the toad (genus Bufo Laurenti, 1768). For the On and Off responses, this waveform comprised two negative deflections, N1 and N2, which were interrupted by a positive deflection, P2. The N2 deflection was followed by a final positive deflection, P3. Principal component analysis revealed that the N2–P3 complex of the On response was significantly more pronounced at longer wavelengths. In contrast, the N2–P3 complex was most pronounced at middle wavelengths for the Off response. The N1 deflection was relatively invariant with respect to wavelength. Should colour-opponent tectal units provide a significant contribution to the TEP, it is probable that its waveform characteristics provide signs of underlying neural processes which facilitate colour discrimination.

scholarly journals Development and Application of Novel InDel Markers in Flax (Linum usitatissimum L.) Through Whole-Genome Re-Sequencing

2021 ◽  
Author(s):  
Hui Jiang ◽  
Gen Pan ◽  
Touming Liu ◽  
Li Chang ◽  
Siqi Huang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Snp Markers ◽  
Diversity Analysis ◽  
Whole Genome ◽  
Chromosome 2 ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Genetic Diversity Analysis ◽  
Indel Markers

Abstract Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87 − 3 and 84 − 3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

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