scholarly journals Genomic prediction informed by biological processes expands our understanding of the genetic architecture underlying free amino acid traits in dry Arabidopsis seeds

2018 ◽  
Author(s):  
Sarah D. Turner-Hissong ◽  
Kevin A. Bird ◽  
Alexander E. Lipka ◽  
Elizabeth G. King ◽  
Timothy M. Beissinger ◽  
...  
Keyword(s):  
Amino Acid ◽  
Free Amino Acid ◽  
Candidate Genes ◽  
Genomic Prediction ◽  
Free Amino ◽  
Amino Acid Content ◽  
Predictive Ability ◽  
Search Space ◽  
Biological Processes ◽  
Branched Chain

ABSTRACTPlant growth, development, and nutritional quality depends upon amino acid homeostasis, especially in seeds. However, our understanding of the underlying genetics influencing amino acid content and composition remains limited, with only a few candidate genes and quantitative trait loci identified to date. Improved knowledge of the genetics and biological processes that determine amino acid levels will enable researchers to use this information for plant breeding and biological discovery. Towards this goal, we used genomic prediction to identify biological processes that are associated with, and therefore potentially influence, free amino acid (FAA) composition in seeds of the model plant Arabidopsis thaliana. Markers were split into categories based on metabolic pathway annotations and fit using a genomic partitioning model to evaluate the influence of each pathway on heritability explained, model fit, and predictive ability. Selected pathways included processes known to influence FAA composition, albeit to an unknown degree, and spanned four categories: amino acid, core, specialized, and protein metabolism. Using this approach, we identified associations for pathways containing known variants for FAA traits, in addition to finding new trait-pathway associations. Markers related to amino acid metabolism, which are directly involved in the FAA regulation, improved predictive ability for branched chain amino acids and histidine. The use of genomic partitioning also revealed patterns across biochemical families, in which serine-derived FAAs were associated with protein related annotations and aromatic FAAs were associated with specialized metabolic pathways. Taken together, these findings provide evidence that genomic partitioning is a viable strategy to uncover the relative contributions of biological processes to FAA traits in seeds, offering a promising framework to guide hypothesis testing and narrow the search space for candidate genes.

scholarly journals Genomic Prediction Informed by Biological Processes Expands Our Understanding of the Genetic Architecture Underlying Free Amino Acid Traits in Dry Arabidopsis Seeds

2020 ◽  
Vol 10 (11) ◽  
pp. 4227-4239
Author(s):  
Sarah D. Turner-Hissong ◽  
Kevin A. Bird ◽  
Alexander E. Lipka ◽  
Elizabeth G. King ◽  
Timothy M. Beissinger ◽  
...  
Keyword(s):  
Amino Acid ◽  
Free Amino Acid ◽  
Candidate Genes ◽  
Genomic Prediction ◽  
Free Amino ◽  
Amino Acid Content ◽  
Predictive Ability ◽  
Search Space ◽  
Biological Processes ◽  
Branched Chain

Plant growth, development, and nutritional quality depends upon amino acid homeostasis, especially in seeds. However, our understanding of the underlying genetics influencing amino acid content and composition remains limited, with only a few candidate genes and quantitative trait loci identified to date. Improved knowledge of the genetics and biological processes that determine amino acid levels will enable researchers to use this information for plant breeding and biological discovery. Toward this goal, we used genomic prediction to identify biological processes that are associated with, and therefore potentially influence, free amino acid (FAA) composition in seeds of the model plant Arabidopsis thaliana. Markers were split into categories based on metabolic pathway annotations and fit using a genomic partitioning model to evaluate the influence of each pathway on heritability explained, model fit, and predictive ability. Selected pathways included processes known to influence FAA composition, albeit to an unknown degree, and spanned four categories: amino acid, core, specialized, and protein metabolism. Using this approach, we identified associations for pathways containing known variants for FAA traits, in addition to finding new trait-pathway associations. Markers related to amino acid metabolism, which are directly involved in FAA regulation, improved predictive ability for branched chain amino acids and histidine. The use of genomic partitioning also revealed patterns across biochemical families, in which serine-derived FAAs were associated with protein related annotations and aromatic FAAs were associated with specialized metabolic pathways. Taken together, these findings provide evidence that genomic partitioning is a viable strategy to uncover the relative contributions of biological processes to FAA traits in seeds, offering a promising framework to guide hypothesis testing and narrow the search space for candidate genes.

scholarly journals Changes in Free Amino Acid Content in ‘Jonagold’ Apple Fruit as Related to Branched-chain Ester Production, Ripening, and Senescence

2011 ◽  
Vol 136 (6) ◽  
pp. 429-440 ◽  
Author(s):  
Nobuko Sugimoto ◽  
A. Daniel Jones ◽  
Randolph Beaudry
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Free Amino Acid ◽  
Acid Content ◽  
Free Amino ◽  
Amino Acid Content ◽  
Apple Fruit ◽  
Free Amino Acid Content ◽  
Threonine Deaminase ◽  
Branched Chain

The relationship among the free amino acid content, the expression of genes related to branched-chain amino acid metabolism {branched-chain aminotransferase [BCAT], α-keto acid decarboxylase [pyruvate decarboxylase (PDC)], and threonine deaminase [TD]}, and the production of branched-chain (BC) esters during ripening and senescence in ‘Jonagold’ apple fruit (Malus ×domestica) was studied. Eighteen amino acids were measured by liquid chromatography coupled with tandem mass spectrometry. The content for all amino acids changed with developmental stage and some shared similar patterns of accumulation/diminution. The pattern for isoleucine differed from all other amino acids, increasing more than 20-fold during the ripening process. The onset of the increase was concomitant with the onset of increasing ethylene and BC ester production and the content remained elevated even during senescence. The elevated isoleucine levels are consistent with an increase in the flux through the pathway leading to the formation and degradation of the isoleucine precursor α-keto-β-methylvalerate, which is used for production of BC esters containing 2-methylbutanol and 2-methylbutanoate moieties. Unexpectedly, the content of threonine, the amino acid from which isoleucine is thought to be derived in plants, did not change in concert with isoleucine, but rather declined somewhat after ripening was well underway. Patterns in the expression of some, but not all, of the putative BCAT and PDC genes appeared to reflect the rise and fall in ester formation; however, the expression of putative TD genes did not change during ripening. The patterns in gene expression and amino acid content are interpreted to suggest that the synthesis of α-keto-β-methylvalerate and isoleucine during apple ripening may depend on an as yet uncharacterized pathway that bypasses threonine, similar to the citramalate pathway found in some bacteria.

Evaluation of seed amino acid content and its correlation network analysis in wild soybean (Glycine soja) germplasm in Japan

2021 ◽  
Vol 19 (1) ◽  
pp. 35-43
Author(s):  
Awatsaya Chotekajorn ◽  
Takuyu Hashiguchi ◽  
Masatsugu Hashiguchi ◽  
Hidenori Tanaka ◽  
Ryo Akashi
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Free Amino Acid ◽  
Acid Content ◽  
Free Amino ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Amino Acid Content ◽  
Soybean Seeds ◽  
Free Amino Acid Content

AbstractWild soybean (Glycine soja) is a valuable genetic resource for soybean improvement. Seed composition profiles provide beneficial information for the effective conservation and utilization of wild soybeans. Therefore, this study aimed to assess the variation in free amino acid abundance in the seeds of wild soybean germplasm collected in Japan. The free amino acid content in the seeds from 316 accessions of wild soybean ranged from 0.965 to 5.987 mg/g seed dry weight (DW), representing a 6.2-fold difference. Three amino acids had the highest coefficient of variation (CV): asparagine (1.15), histidine (0.95) and glutamine (0.94). Arginine (0.775 mg/g DW) was the predominant amino acid in wild soybean seeds, whereas the least abundant seed amino acid was glutamine (0.008 mg/g DW). A correlation network revealed significant positive relationships among most amino acids. Wild soybean seeds from different regions of origin had significantly different levels of several amino acids. In addition, a significant correlation between latitude and longitude of the collection sites and the total free amino acid content of seeds was observed. Our study reports diverse phenotypic data on the free amino acid content in seeds of wild soybean resources collected from throughout Japan. This information will be useful in conservation programmes for Japanese wild soybean and for the selection of accessions with favourable characteristics in future legume crop improvement efforts.

scholarly journals Free amino acid content in muscle tissue of bighead carp and wels catfish

2016 ◽  
Vol 72 (10) ◽  
pp. 632-636 ◽  
Author(s):  
Renata Pyz-Łukasik ◽  
Maria Szpetnar ◽  
Waldemar Paszkiewicz ◽  
Marcin R. Tatara ◽  
Adam Brodzki
Keyword(s):  
Amino Acid ◽  
Free Amino Acid ◽  
Muscle Tissue ◽  
Acid Content ◽  
Free Amino ◽  
Amino Acid Content ◽  
Bighead Carp ◽  
Predatory Fish ◽  
Free Amino Acid Content ◽  
Natural Diet

The present research was aimed at a comparative analysis of free amino acid (FAA) levels in the muscle tissue of herbivorous and predatory fish. The FAA concentration in the muscle tissue samples from bighead carp and wels catfish was determined by ion-exchange chromatography. The bighead carp muscle tissue, as compared to that of wels catfish, showed significantly higher concentrations of arginine, histidine, methionine, phenyloalanine, alanine, asparagine, serine, glycine, and taurine, but significantly lower levels of isoleucine, leucine, threonine, valine, glutamine, cystationine, β-alanine, ethanoloamine, as well as aspartic, glutamic, cysteic, α- and γ-aminobutyric acids. The muscle tissues of bighead carp and wels catfish did not differ significantly in the levels of cystine, lysine, tryptophan, tyrosine, α-aminoadipic acid, cytrulline, ornithine and 1-methyl-histidine. Proline was detected only in the wels catfish muscle. The results obtained have shown differences in free amino acid concentration in muscle tissue of examined fish. A differentiated natural diet induces changes in free amino acid content in fish tissues. Knowledge of levels of free amino acids which are precursors for biogenic amines facilitates setting the safety criteria for fish and fishery products from species other than those mentioned in the Commission Regulation No 2073/2005

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