**Integrative Analysis of Metabolomic and Transcriptomic Profiles Uncovers Biological Pathways of Feed E**ffi**ciency in Pigs**

#### **Priyanka Banerjee, Victor Adriano Okstoft Carmelo and Haja N. Kadarmideen \***

Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; priyankabnrj@gmail.com(P.B.);vaocar@dtu.dk(V.A.O.C.)

 **\*** Correspondence<EMAIL_ADDRESS>Tel.: +45-45255223

Received: 21 May 2020; Accepted: 4 July 2020; Published: 6 July 2020

**Abstract:** Feed efficiency (FE) is an economically important trait. Thus, reliable predictors would help to reduce the production cost and provide sustainability to the pig industry. We carried out metabolome-transcriptome integration analysis on 40 purebred Duroc and Landrace uncastrated male pigs to identify potential gene-metabolite interactions and explore the molecular mechanisms underlying FE. To this end, we applied untargeted metabolomics and RNA-seq approaches to the same animals. After data quality control, we used a linear model approach to integrate the data and find significant differently correlated gene-metabolite pairs separately for the breeds (Duroc and Landrace) and FE groups (low and high FE) followed by a pathway over-representation analysis. We identified 21 and 12 significant gene-metabolite pairs for each group. The valine-leucine-isoleucine biosynthesis/degradation and arginine-proline metabolism pathways were associated with unique metabolites. The unique genes obtained from significant metabolite-gene pairs were associated with sphingolipid catabolism, multicellular organismal process, cGMP, and purine metabolic processes. While some of the genes and metabolites identified were known for their association with FE, others are novel and provide new avenues for further research. Further validation of genes, metabolites, and gene-metabolite interactions in larger cohorts will elucidate the regulatory mechanisms and pathways underlying FE.

**Keywords:** feed efficiency; linear model; metabolomics; pigs; transcriptomics


**4. Impact of anthropogenic activities on the species diversity, composition, and ecosystem functioning**

For more than two million years, the structure of the African savanna ecosystems has been affected by anthropogenic activities [93]. Human beings impact the structure of savanna ecosystems directly by cultivating and cutting woody species. They also indirectly impact the structure because of their ability to alter fire and herbivore numbers and distribution through hunting and livestock management [79].

#### **4.1 Anthropogenic activities and species diversity**

Human activities have time in memorial influenced the diversity of species in African savannas. Refs. [94, 95] reported that the annual burning of savannas tends to increase species richness. On the other hand, Ref. [96] reported a negative correlation between fire frequencies and woody plant species richness where it was stated that high frequencies of fire reduce woody plant species devoid of producing substantial upsurges in species richness of grass and forb. Fires have been said to alter and restrain tree crown cover and diversity by sporadically killing the tree crown canopy. Fires also restrict the sapling growth into the crown cover canopy and eradicate the regeneration of the tree species, which are intolerant to fire but tolerant to shade [96].

#### *Contextualizing the Factors Affecting Species Diversity and Composition in the African Savanna DOI: http://dx.doi.org/10.5772/intechopen.108413*

The dominance of the woody plant growing on savannas with finer textured soils may be decreased due to fires which may ultimately reduce the species' richness. The occurrence of fires may harm the woody plants and reduce their cover of the woody plants. It may also reduce the frequencies of woody species, thereby declining the species diversity [97–99]. On the other hand, low fire frequencies have been reported to maximize the understory woody species richness because high fire frequencies damage the seedlings and saplings, which are species sensitive to fire. This inhibits seedlings and saplings' growth into tree crown cover, harming overstory trees over time and limiting the species mix of overstory trees to extremely fire-resistant oaks [96]. The savanna ecosystem houses huge heterogeneous communities because the plant composition communities differ across fine-scale environmental slopes connected to the variability in tree canopy cover throughout space [53, 100].

#### **4.2 Anthropogenic activities and species composition and ecosystem functioning**

Ceballos et al. & Steffen et al. [101, 102] denoted that anthropogenic activities have rapidly exacerbated the rate of loss in global biological diversity in the past. Loss of habitat has been the principal driver of this decline globally and is reported to be accountable for almost 67% of the terrestrial land surface, having passed a suggested "safe limit" of the extinction of local species [103].

These declines in biological diversity adversely affect the local functioning and services of an ecosystem and pose a major threat to mankind [12]. On the other hand, biodiversity in flora and fauna has a positive relationship with the productivity of plants as well as soil health [104, 105], thereby enhancing the sequestration ability of atmospheric carbon [104]. Besides, mitigation of alarming carbon dioxide levels may be decelerated due to the loss of diversity which may undermine the progress on limiting climate change. On the other hand, increased crop production and resilience to distress are connected to higher species diversity in agricultural lands [106]. Conservation of biodiversity is thus key to safeguarding the availability of food in light of rising demand and fluctuating environmental conditions.

The structure and functioning of the savanna ecosystem are also affected by the selective removal of trees in several ways. Mostly, the selective removal of trees forms gaps in the crown canopy may lead to increased diversity and abundance because the competition for water and nutrients, as well as increased availability of light, may be reduced [79]. Loss in biological diversity has also been reported by Ref. [18] to reduce the efficiency by which ecological communities capture biologically essential resources, produce biomass, decompose and recycle biologically essential nutrients. Advances have also been made in under-studied areas, such as soils and exhibiting, for instance, that cycling of nitrogen and diversity of plants can be reduced due to the reduced soil biodiversity [107–109].

#### **4.3 Land use change and species diversity and composition**

In the past 20 years, the emergence of change in land science has sought to understand the dynamics of anthropogenic activities on the earth through the changes in land use and land cover [110]. Conversion of land to agriculture is reported by Refs. [111, 112] to be a key driver of universal biological loss, with implications for the functioning of an ecosystem, thereby disrupting species diversity and composition. According to Ref. [113], the human population is much higher across the savannas, implying that the more anthropogenic activities, the more pressure on savanna

degradation, cover loss, a continued downward trend in species diversity, and composition. Ref. [114] adds that globally land-use change is the principal influence of biological diversity loss.

Taubert et al. [115] note that agricultural expansion and its impact on the loss and disintegration of native habitats causes a reduction in the habitat areas. This also leads to increased predation, a decline in population, extinctions in species, and alterations in species compositions [112, 116]. Nevertheless, these effects change according to the species characteristics and the spatial structure of the habitat. The effects also change according to the surrounding human-modified landscape (matrix) [117]. However, land-use change in African savannas poses a threat to the tenacity of biotic diversity through wildlife grazing loss and dispersal area to agriculture, as well as enlarged disturbance of wildlife around human inhabitation [118].


*2.4. Other Arylalkyne Substrates*

In 2013, Ye et al., described a gold(I)/acid-catalyzed methodology for the syntheses of anthracenes using *o*-alkynyl diarylmethanes with 21 examples and 58–80% yields (Scheme 11) [32]. Coordination of alkynes by gold catalysts triggered the attack of electronrich benzene rings to furnish vinyl–gold intermediates (**43**) via 6-*exo*-dig cyclization. After protodeauration and [Au]+/H+ promoted isomerization, anthracenes (**45**) were obtained. An alternative pathway was also proposed; the alkyne of the substrates (**42**) was hydrolyzed under gold-catalyzed conditions to yield intermediates (**44**) that were converted to products (**45**) by an acid-mediated cyclodehydration. In addition, the products (**45**) were further modified into a variety of potentially valuable anthracene derivatives.

**Scheme 11.** Gold(I)-catalyzed syntheses of anthracene derivatives.

In 2017, a gold(I)-catalyzed tandem cycloisomerization, Diels–Alder, and retro-Diels– Alder reactions were reported by the Liu lab (Scheme 12) [33]. Activation of alkyne in substrates (**46**) initiated the first cycloisomerization to yield furopyran intermediates (**47**). A subsequent Diels–Alder reaction of dienes (**47**) and dienophiles occurred to form highly strained intermediates (**48**), which underwent a retro-Diels–Alder reaction to provide biaryl products (**49**) by releasing acetaldehyde (HCHO). The above pathways were reasonably explained by density functional theory (DFT).

**Scheme 12.** Gold(I)-catalyzed syntheses of biaryl derivatives.

In 2021, the Hashmi group reported the syntheses of *meta*- and *para*dihydroxynaph thalenes based on diazoalkynes through a regiodivergent gold-catalyzed cyclization (Scheme 13) [34]. The activated triple bonds of substrates (**50**) were attacked by diazocarbon to generate intermediates (**51**), followed by the formation of quinoid gold carbene intermediates (**52**) via the release of nitrogen. At this stage, two different reaction paths occurred via the addition of water or Et3N(HF)3. Under the condition of water as an additive (path a), *meta*dihydroxynaphthalenes (**54**) were produced via carbene insertion of water after protodeauration. When H2O and Et3N(HF)3 were used as additives, *para*dihydroxynaphthalenes (**56**) were obtained via Michael-type addition of quinoid carbene species, 1,2-phenyl migration, and protodeauration. Moreover, when only Et3N(HF)3 was used as an additive, "F−" was inserted instead of water for gold carbene to generate the α-fluoronaphthalenes.

**Scheme 13.** Gold(I)-catalyzed syntheses of meta- and paradihydroxynaphthalene derivatives.

Gold(I)-catalyzed arylalkyne annulations provide abundant strategies for the syntheses of benzene derivatives, including the strategies shown in this chapter and several other intramolecular or intermolecular strategies [35–47].


**Author details**

Jack Denur Electric & Gas Technology, Inc., Rowlett, Texas, USA

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*Improving Heat-Engine Performance by Employing Multiple Heat Reservoirs DOI: http://dx.doi.org/10.5772/intechopen.89047*