Nucleotide polymorphisms related to altitude and physiological traits in contrasting provenances of Norway spruce (Picea abies)

Biologia ◽  
2012 ◽  
Vol 67 (5) ◽  
Author(s):  
Ivana Romšáková ◽  
Elena Foffová ◽  
Jaroslav Kmeť ◽  
Roman Longauer ◽  
Marian Pacalaj ◽  
...  
Keyword(s):  
Picea Abies ◽  
Norway Spruce ◽  
Nucleotide Diversity ◽  
Growth Traits ◽  
Physiological Traits ◽  
Stem Volume ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Budburst Phenology

AbstractVariation of sequences of six EST-derived markers was investigated in three Norway spruce (Picea abies [L.] Karst.) provenances originating from different altitudes growing at two contrasting trial plots in Slovakia (Veľký Lom 450 m a.s.l., Mútne-Zákamenné 1,250 m a.s.l.) within a spin-off experiment of the IUFRO 1964/68 Inventory Provenance Experiment with Norway spruce. Single nucleotide polymorphisms (SNP) were identified and differences in allele frequencies at polymorphic sites were tested against altitude or associated with physiological and growth traits (chlorophyll a fluorescence, frost resistance, height, diameter, budburst phenology).Overall, 5.1% of sites (190 in total) were polymorphic in the studied material. Although there were no differences in nucleotide diversity among provenances, the differentiation was highly significant (the overall between-population variance component assessed by the AMOVA based on both extreme populations P1 and P49 was 6.53%). Only 4 polymorphic sites differed significantly between populations after Bonferroni correction. Four sites showed significant association with phenotypic traits (breast-height diameter, stem volume, chlorophyll fluorescence). In contrast to earlier analyses of growth and physiological traits based on the same material, significant associations with polymorphic sites indicate the effect of local adaptation.

Differences in fibre properties in cloned Norway spruce (Picea abies)

2008 ◽  
Vol 38 (5) ◽  
pp. 1071-1082 ◽  
Author(s):  
A. Zubizarreta Gerendiain ◽  
H. Peltola ◽  
P. Pulkkinen ◽  
R. Jaatinen ◽  
A. Pappinen
Keyword(s):  
Picea Abies ◽  
Norway Spruce ◽  
Wood Density ◽  
Growth Traits ◽  
Fibre Length ◽  
Stem Volume ◽  
Fibre Properties ◽  
Phenotypic Correlations ◽  
Fibre Width ◽  
Selection For

In forest breeding programmes, growth has typically been used as a selection trait of prime importance in Norway spruce ( Picea abies (L.) Karst.), whereas less attention has been given to the wood and fibre characteristics. In the above context, we investigated phenotypic relationships between different fibre properties and growth and wood density traits in 20 cloned Norway spruce based on a clonal trial established in the 1970s in southeastern Finland. We found that fibre width showed, on average (2.9%), the lowest phenotypic variation followed by fibre wall thickness (3.4%), coarseness (5.5%), and fibre length (8.1%). All of the phenotypic correlations between the fibre properties were also positive (p < 0.05), ranging from moderate to strong, suggesting that selection for one trait could simultaneously affect the other traits. The phenotypic correlations, on average, were quite weak but positive between growth and fibre properties and slightly negative or weak positive between wood density and different fibre properties (p < 0.05). Individually, some of the clones showed negative correlation between growth traits and fibre length. As a result, selection for fibre properties alone could also reduce overall stem volume (or stem mass) and would not directly indicate wood density traits and vice versa.

scholarly journals Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1510
Author(s):  
Salvatore Mastrangelo ◽  
Rosalia Di Gerlando ◽  
Maria Teresa Sardina ◽  
Anna Maria Sutera ◽  
Angelo Moscarelli ◽  
...  
Keyword(s):  
Conservation Status ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Local Populations ◽  
Genomic Technologies ◽  
Fitness Traits ◽  
Genome Wide ◽  
Breeding Schemes ◽  
Genomic Inbreeding

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.

scholarly journals Melanocortin-4 Receptor (MC4R) gene polymorphism and its effect on growth traits in Madura cattle

2019 ◽  
Vol 44 (1) ◽  
pp. 38
Author(s):  
P. W. Prihandini ◽  
S. Sumadi ◽  
G. Suparta ◽  
D. Maharani
Keyword(s):  
Growth Traits ◽  
Balance Control ◽  
Direct Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Mc4r Gene ◽  
Melanocortin 4 Receptor ◽  
Pcr Rflp ◽  
Reverse Primer ◽  
Selection For

Melanocortin-4 receptor (MC4R) gene has an important role in the regulation of feed intake and energy balance control. The objective of this study was to identify the single nucleotide polymorphisms (SNPs) of MC4R gene and their association with growth traits in Madura cattle. A total of 198 calves were used in this study.Forward primer: 5’-GTCGGGCGTCTTGTTCATC-3’and reverse primer: 5’-GCTTGTGTTTAGCATCGCGT-3’ were used to amplify approximately 493 bp of MC4R gene. The results showed that two SNPs, g.1133C>G and g.1108C>T were identified by direct sequencing. The PCR-RFLP method was performed to genotype all individuals studied based on SNP g.1133C>G, and its SNP was significantly associated with shoulder height (SH) at yearling age (P<0.05). Animals with GG genotype had a higher SH (110.35±6.40cm) than those with CC (102.00±8.00 cm) and CG genotype (105.96±6.23 cm). The SNP g.1133 C>G changed amino acid from valine to leucine. In conclusion, the SNP g.1133C>G of the MC4R gene may be used as a marker-assisted selection for SH trait in Madura cattle.

scholarly journals Progressive effects of single-nucleotide polymorphisms on 16 phenotypic traits based on longitudinal data

2020 ◽  
Vol 42 (4) ◽  
pp. 393-403
Author(s):  
Donghe Li ◽  
Hahn Kang ◽  
Sanghun Lee ◽  
Sungho Won
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Longitudinal Data ◽  
Density Lipoprotein ◽  
Phenotypic Traits ◽  
Chromosome 2 ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Longitudinal Changes ◽  
Genome Wide ◽  
A Genome

Abstract Background There are many research studies have estimated the heritability of phenotypic traits, but few have considered longitudinal changes in several phenotypic traits together. Objective To evaluate the progressive effect of single nucleotide polymorphisms (SNPs) on prominent health-related phenotypic traits by determining SNP-based heritability ($$h_{snp}^{2}$$hsnp2) using longitudinal data. Methods Sixteen phenotypic traits associated with major health indices were observed biennially for 6843 individuals with 10-year follow-up in a Korean community-based cohort. Average SNP heritability and longitudinal changes in the total period were estimated using a two-stage model. Average and periodic differences for each subject were considered responses to estimate SNP heritability. Furthermore, a genome-wide association study (GWAS) was performed for significant SNPs. Results Each SNP heritability for the phenotypic mean of all sixteen traits through 6 periods (baseline and five follow-ups) were significant. Gradually, the forced vital capacity in one second (FEV1) reflected the only significant SNP heritability among longitudinal changes at a false discovery rate (FDR)-adjusted 0.05 significance level ($$h_{snp}^{2} = 0.171$$hsnp2=0.171, FDR = 0.0012). On estimating chromosomal heritability, chromosome 2 displayed the highest heritability upon periodic changes in FEV1. SNPs including rs2272402 and rs7209788 displayed a genome-wide significant association with longitudinal changes in FEV1 (P = 1.22 × 10−8 for rs2272402 and P = 3.36 × 10−7 for rs7209788). De novo variants including rs4922117 (near LPL, P = 2.13 × 10−15) of log-transformed high-density lipoprotein (HDL) ratios and rs2335418 (near HMGCR, P = 3.2 $$\times$$× 10−9) of low-density lipoprotein were detected on GWAS. Conclusion Significant genetic effects on longitudinal changes in FEV1 among the middle-aged general population and chromosome 2 account for most of the genetic variance.

A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome

Genome ◽  
2004 ◽  
Vol 47 (2) ◽  
pp. 389-398 ◽  
Author(s):  
Joanne Russell ◽  
Allan Booth ◽  
John Fuller ◽  
Brian Harrower ◽  
Peter Hedley ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Wild Barley ◽  
Genomic Ssrs ◽  
Dna Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Change ◽  
Single Nucleotide ◽  
Single Nucleotide Change ◽  
Haplotype Data ◽  
Fertile Crescent

Direct estimates of sequence diversity provides an abundant source of DNA polymorphisms based on single nucleotide polymorphisms (SNPs). The frequency and distribution of nucleotide diversity within 23 genes associated with grain germination in barley were determined in a sample of accessions representing European cultivars, landraces, and wild barley accessions from throughout the fertile crescent. The overall nucleotide diversity ranged from 0.0021 to 0.0189 with a single nucleotide change being detected every 78 bp and insertion–deletion events being observed every 680 bp. Within the cultivated (H. vulgare) genepool, a small number of haplotypes were detected, the total number of haplotypes observed in H. spontaneum was almost double that detected in H. vulgare (46 and 26, respectively). Distinct haplotypes were observed in the H. spontaneum and landrace genepools, which are highly divergent from H. vulgare. A comparison of SNP-based haplotype data with EST-derived SSRs and genomic SSRs revealed a similar trend of decreasing variability in the cultivated genepool. However, the number of unique alleles identified in the cultivated sample was much greater with genomic SSRs (18%) compared with only 2.1% for SNPs and 3.8% for EST-derived SSRs. The potential utility of SNPs and EST-derived SSRs for association mapping in barley is discussed.Key words: SNPs, haplotype, SSRs, barley.

Associations of single nucleotide polymorphisms in the bovine prolactin gene with phenotypic traits in beef cattle

Agri Gene ◽  
2017 ◽  
Vol 5 ◽  
pp. 7-11 ◽  
Author(s):  
Laura Meyer ◽  
Jeremy Powell ◽  
Bryan Kutz ◽  
Michael Looper ◽  
A. Hayden Brown ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Beef Cattle ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Prolactin Gene

Differences in growth and wood property traits in cloned Norway spruce (Picea abies)

2007 ◽  
Vol 37 (12) ◽  
pp. 2600-2611 ◽  
Author(s):  
A. Zubizarreta Gerendiain ◽  
H. Peltola ◽  
P. Pulkkinen ◽  
R. Jaatinen ◽  
A. Pappinen ◽  
...  
Keyword(s):  
Picea Abies ◽  
Norway Spruce ◽  
Wood Density ◽  
Volume Growth ◽  
Wood Property ◽  
Growth Yield ◽  
Stem Volume ◽  
Forest Tree Breeding ◽  
Wood Processing ◽  
Selection For

Volume growth has typically been used as a selection trait of prime importance in forest tree breeding. Less attention has been given to the genetic or phenotypic relationships between the growth or yield and wood density traits. In the above context, we aimed to investigate the phenotypic relationships among different growth, yield, and wood density traits of 20 Norway spruce ( Picea abies (L.) Karst.) clones grown in southeastern Finland, in order to identify whether a high growth rate was associated with low wood density in any of the clones. Compared with growth or yield traits, the wood density traits showed lower phenotypic variations. The phenotypic correlations between growth, yield, and wood density traits were, on average, from moderate to high, suggesting that selection for one trait would simultaneously affect the other traits. Compared with volume production, selection based on stem mass could be more profitable if a clonal stand is managed for pulpwood rather than mechanical wood processing and vice versa; whereas selection for overall wood density alone would reduce both the stem volume and stem mass. However, by compromising the gain or loss in wood density and stem volume, clones with high stem volume and a relatively high wood density could be found.

Sign in / Sign up

Export Citation Format

Share Document