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Genes, Genomes, and Systems Biology in Agriculture
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Genes, Genomes, and Systems Biology in Agriculture

A Special Issue of Genes (ISSN 2073-4425) belonging to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: 25 October 2026 | Viewed by 1822

Editors

Dr. Nick Hudson

E-Mail Website
Guest Editor
School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD, Australia
Interests: genetic variability; black slavonian; swine; genotype; best linear unbiased prediction; breeding value
Dr. Pâmela A. Alexandre

E-Mail Website
Guest Editor
Animal Genomics, Livestock & Aquaculture, Agriculture & Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Queensland Bioscience Precinct, Dutton Park, QLD 4160, Australia
Interests: transcriptomics; computational multi-omics; systems biology; co-expression networks; livestock production
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Agriculture is undergoing a data-driven transformation, with crop and livestock sectors facing urgent challenges and exciting opportunities. Pressures to improve efficiency and resilience amid resource constraints and global instability are supported by the promise of new technologies to enhance sustainability, productivity, and food security.

A key opportunity lies in harnessing ‘Big Data’ from high-throughput omics platforms. Millions of SNPs now support genomic selection, while RNA sequencing enables digital quantification of diverse RNA species, offering molecular insights into tissue states and trait expression.

Since the first crop and livestock genomes—rice (2002) and chicken (2004)—data generation has accelerated, with mature genome assemblies and affordable, genome-wide post-genomic technologies now widely available. These tools offer unprecedented resolution into the biology of complex traits, yet extracting actionable insights remains a major challenge.

Barriers include incomplete molecular annotation, difficulties in multi-omic integration, limitations in modelling approaches, and the complexity of quantitative traits shaped by many interacting genes. Emergent properties at the whole-organism level often defy reductionist interpretation from molecular data alone.

This Special Issue will showcase advances in molecular modelling and systems biology that support sustainable, high-yield, and environmentally responsible agriculture. We invite contributions spanning integrative omics, predictive modelling, and systems-level insights into crop and livestock traits.

Dr. Nick Hudson
Dr. Pâmela A. Alexandre
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • systems biology
  • modelling
  • omics technologies
  • big data
  • machine learning
  • genetics
  • genomics
  • transcriptomics
  • microbiome
  • metabolomics

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Published Papers (2 papers)

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Research

21 pages, 1950 KB  
Article
Post-Transcriptional Gene Regulation by MicroRNAs During Barley Malting
by Sarah J. Whitcomb, Marcus A. Vinje and Ramamurthy Mahalingam
Genes 2026, 17(6), 676; https://doi.org/10.3390/genes17060676 - 9 Jun 2026
Cited by 1 | Viewed by 734
Abstract
Background/Objectives: Barley malting is an agro-industrial process that produces malt, an essential ingredient for the brewing and distilling industries. Previously, tran-scriptome profiling has revealed mRNA changes during malting but less is known about their regulation. Methods: The spring 2-row barley variety ‘Conrad’ was [...] Read more.
Background/Objectives: Barley malting is an agro-industrial process that produces malt, an essential ingredient for the brewing and distilling industries. Previously, tran-scriptome profiling has revealed mRNA changes during malting but less is known about their regulation. Methods: The spring 2-row barley variety ‘Conrad’ was sampled at five stages of malt-ing. Using small RNA (sRNA)-sequencing and degradome-sequencing data from these malting stages, de novo discovery of mature microRNA (miRNA), as well as cognate mRNAs targeted for slicing, was identified. ShortStack v4.1.0 was used to map sRNA reads to the Hordeum vulgare Morex V3 genome. Results: In total, 33 expressed MIRs were identified, six of which may be novel. Using the degradome-sequencing data from the same malting stages, CleaveLand4 v4.5 pre-dicted 64 sliced mRNA targets, predominantly transcription factors associated with root development. Conclusions: This study provides an overview of post-transcriptional modulations of miRNAs-cognate mRNA targets, as well as plausible interactions between miRNAs during barley malting. Full article
(This article belongs to the Special Issue Genes, Genomes, and Systems Biology in Agriculture)
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16 pages, 1781 KB  
Article
Liver Mitochondrial Transcriptomic Responses to Dietary Crude Protein and Phosphorus Deficiencies and Feed Restriction in Wethers
by Elmer E. Fernandez, David J. Innes, Walter G. Bottje, Marina R. S. Fortes, Dennis P. Poppi, Simon P. Quigley, Jude J. Bond and Nicholas J. Hudson
Genes 2026, 17(6), 644; https://doi.org/10.3390/genes17060644 - 31 May 2026
Viewed by 457
Abstract
Background/Objectives: Seasonal crude protein (CP) and phosphorus (P) deficiency in northern Australian pastures reduces feed intake and growth of grazing ruminants, but the hepatic mitochondrial mechanisms underlying this response remain unclear. We characterized the hepatic mitochondrial transcriptome of sheep exposed to CP-P deficiency [...] Read more.
Background/Objectives: Seasonal crude protein (CP) and phosphorus (P) deficiency in northern Australian pastures reduces feed intake and growth of grazing ruminants, but the hepatic mitochondrial mechanisms underlying this response remain unclear. We characterized the hepatic mitochondrial transcriptome of sheep exposed to CP-P deficiency or matched-intake feed restriction. Methods: Merino wethers were assigned for 63 d to one of three treatments (n = 8/group): High CP-P, Low CP-P, or Restricted, in which High CP-P feed was offered at the same energy intake as the Low CP-P group. Liver RNA was sequenced, and transcripts encoding mitochondrial proteins were identified using MitoCarta 3.0. Differentially expressed genes (DEGs) were defined as adjusted p < 0.05 and |log2FC| ≥ 0.585. Results: Of 804 mitochondrial genes detected, 83 were differentially expressed in at least one pairwise comparison. The greatest transcriptional response occurred in contrasts against High CP-P (Low CP-P vs. High CP-P: 38 DEGs in 8 enriched pathways; Restricted vs. High CP-P: 37 DEGs in 10 enriched pathways). In both low-intake treatments, ALDH1L2, ALDH1L1, SHMT2, and DMGDH were upregulated, suggesting altered folate-mediated one-carbon metabolism. Restricted sheep also showed higher expression of several SLC25A transporters (SLC25A4, SLC25A28, SLC25A29, SLC25A33, and SLC25A34), indicative of enhanced mitochondrial nucleotide and metabolite exchange under CP-P adequate energy restriction. In contrast, Low CP-P sheep showed higher expression of SLC25A15 and SLC25A25 relative to either High CP-P or Restricted sheep, a nutrient-deficiency specific transporter response. CKMT2 expression was also higher in Restricted sheep than in both other groups. Conclusions: These findings suggest that reduced metabolizable energy intake was associated with the bulk of the hepatic mitochondrial transcriptional response, particularly in folate-mediated one-carbon metabolism, whereas CP-P deficiency was associated with a smaller but distinct transporter signature. The liver mitochondrial transcriptome may provide mechanistic insight into nutritional adaptation under CP and P deficiency in grazing sheep. Full article
(This article belongs to the Special Issue Genes, Genomes, and Systems Biology in Agriculture)
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