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    Exploring innovative ways, based on skin thickness and brown adipose tissue metabolism, for genetic improvement of new-born lamb survival : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science, Massey University, Palmerston North, New Zealand
    (Massey University, 2023) Graña Baumgartner, Andrea
    A major cause of new-born lamb mortality under pastoral conditions is starvation/exposure. Heritability for lamb survival is low and indirect selection for a trait that is both correlated with lamb survival and is heritable, may provide a more efficacious way to improve lamb survival. In addition to selecting for a lamb that can withstand cold environments, the ability to produce heat via non-shivering thermogenesis through brown adipose tissue (BAT) is essential. Consequently, the main aims of this thesis were to investigate the potential selection for skin thickness and temperature to indirectly improve lamb survival, to examine their interactions with other traits of importance, and to characterise the transcriptome and lipidome of BAT in new-born lambs exposed to a cold environment. Heritability estimates were moderate for skin thickness and low for skin temperature when considering all sheep data from the FocusPrime, Texel, Romney and Highlander breeds. Positive and favourable correlations between skin thickness and other known insulation traits such as fat depth were found, as well as negative and favourable correlations between skin thickness and skin temperature. Therefore, selecting for thicker skinned lambs could enhance the lamb’s insulation characteristics and survival. A short-term cold challenge in new-born lambs was carried out to perform a ribonucleic acid sequencing (RNAseq) analysis to characterize the transcriptome of BAT and thyroid tissue. There was no evidence of thermogenic activity from any of the key thermogenic genes, such as UCP1 (uncoupling protein 1) or any of the thyroid receptors. This may suggest that the heat production peak under cold exposure occurs swiftly and thus results in being undetectable in BAT by day three of life. These changes in expression might give way to the whitening process of the adipose tissue, concluding the non-shivering thermogenesis period. Within the same experimental short-term cold challenge, BAT and plasma samples were collected to identify lipidomic profiles. Profound changes were found after cold exposure, where significant increases in the lipid composition of glycerolipids, glycerophospholipids, sphingolipids and sterol lipids were observed. In some cases, an exponential increase of certain metabolites was recorded through the time of exposure, implying that their increase may be generated as a consequence of BAT activity. The overall differences in lipid types found could be associated with the improvement of lipid metabolism via BAT thermogenic activation, and adipocyte survival during cold adaptation. In summary, this thesis suggests an alternative pathway to improve lamb survival and provides useful insights into molecular mechanisms and lipidomic composition of thermogenic tissues in new-born lambs.
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    Skin thickness as a potential indirect trait for genetic improvement of lamb survival : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand
    (Massey University, 2021) Soltanighombavani, Masoud
    Lamb survival, as a trait of great economic importance with low heritability, might show more response to indirect selection for traits of higher heritability that are genetically correlated with lamb survival, as a trait of high economic importance. The main objective of this thesis was to explore if ultrasonographically measured skin thickness (ST) at about nine months of age could be considered as an alternative to direct selection for lamb survival from birth to weaning (SBW). For this purpose, in the first step, the reliability of ultrasonography as an accurate and noninvasive method for measurement of ST was validated using plicometry and histometry. In the second experiment, the heritability of ultrasonographically measured ST at an age of about 9 months was estimated to be 0.21 ± 0.03 and 0.20 ± 0.03, respectively from analyses with and without adjustment for live weight at scanning (LWS), implying that the trait would respond to genetic selection. Estimates of genetic correlation of ST with SBW from the analyses with LWS considered as a covariate for ST ranged from 0.16 to 0.35 depending on the minimum number of progeny per sire for each trait, while the corresponding estimates from the analyses with LWS excluded ranged from 0.08 to 0.27. When correction was made for LWS, ST showed genetic correlations of 0.21 ± 0.07, -0.13 ± 0.09, -0.32 ± 0.12, -0.23 ± 0.09, -0.10 ± 0.10, 0.02 ± 0.11, and 0.20 ± 0.11 with fat depth (FD), eye muscle depth (EMD), weights at weaning (WWT), 8 months (LW8), scanning (LWS), and 12 months (LW12), and fleece weight at 12 months (FW12), respectively. The corresponding estimates when no adjustment was made for LWS, were respectively 0.24 ± 0.08, -0.08 ± 0.10, -0.01 ± 0.12, 0.09 ± 0.09, 0.19 ± 0.09, 0.30 ± 0.10, and 0.20 ± 0.11. In the third experiment, the role of skin thickness in thermoregulation through its effect on surface heat loss and a few other indices of cold resistance was explored in two groups of new-born lambs with the thickest skin (thick-skinned category) and the thinnest skin (thin-skinned category) exposed to cold-stress. As a result of lower skin surface temperature (as an indicator of heat loss) in thick-skinned lambs compared to thin-skinned lambs, the first group had higher rectal temperature and were more likely to maintain body temperature during cold stress, even though they produced significantly less heat (W Kg-1). This means there is less need to consume body reserves as a source of energy and consequently better conservation of body reserves in the thick-skinned lambs. In the fourth experiment, skin thickness measured at six to eight months of age was revealed to be a moderately reliable indicator of skin thickness at birth. This is of high importance from both practical and economic points of views. Measuring skin thickness at six to eight months of age is much easier than at birth for sheep farmers/breeders. Furthermore, ultrasound measurement of skin thickness at these ages facilitates simultaneous recording of other traits of importance like fat depth and eye muscle depth, which are normally taken at these ages. In the final study, the effects of genetic variation in the uncoupling protein 1 (UCP1), prolactin (PRL), and prolactin receptor (PRLR) genes on the indices of cold resistance were tested in new-born lambs exposed to cold stress. Although significant effects on some of the indices were observed at/during some time-points/periods of the cold stress, they seem to be mostly due to biases resulting from low number of lambs rather than being real. Considering all the findings, it could be generally concluded that ultrasonographically measured skin thickness at about nine months of age could be considered as a supplement to direct selection for lamb survival in genetic improvement programs. Nevertheless, the large standard errors of the correlations of ST with SBW as well as the unfavorable correlation of ST with other traits should also be considered.
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    Pachycladon species evolved traits to adapt to New Zealand habitats : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology at Massey University, Manawatū, New Zealand
    (Massey University, 2021) Dong, Yanni
    P. cheesemanii is a close relative of A. thaliana and is an allotetraploid perennial herb that is widespread in the South Island of New Zealand. It grows at altitudes of up to 1,000 m where it is subject to relatively high levels of UV-B radiation. However, to date the origin of this species and the mechanisms underlying its tolerance to its harsh living environmental conditions such as moderate–high UV-B radiation, cold and drought is unclear. To gain the first insights into how Pachycladon copes with UV-B stress, I sequenced the P. cheesemanii genome and compared the UV-B tolerance of plants from Wye Creek (~300-m altitude) and Kingston (~500-m altitude) with that of A. thaliana from Col-0 (~100-m altitude) and Kondara (1,000–1,100-m altitude). A high-quality draft genome of P. cheesemanii was assembled with a high percentage of conserved single-copy plant orthologues. A synteny analysis involving genomes from other species of the Brassicaceae family suggested that the two subgenomes of P. cheesemanii may have the same origin as species from Brassicaceae Lineage I and EII. While UV-B radiation caused greater growth reduction in A. thaliana Col-0 and Kondara than in P. cheesemanii Wye Creek, growth was not reduced in P. cheesemanii Kingston. Homologues of the A. thaliana UV-B radiation response genes have multiple copies in P. cheesemanii, and an expression analysis of those genes indicated that the tolerance mechanism in P. cheesemanii Wye Creek and Kingston may differ from that in A. thaliana. Although the P. cheesemanii genome shows close similarity with that of A. thaliana, the uniqueness of the strongly UV-B-induced UVR8-independent pathway in P. cheesemanii may help this species to tolerate relatively high UV-B radiation. Next, to understand the different stress responses of A. thaliana and P. cheesemanii, I designed a project to build multiple-stress transcriptomes for A. thaliana and P. cheesemanii. Since plant responses to salt and drought are related and have overlapping mechanisms, and salt stress can easily be applied in the laboratory, high salinity rather than drought stress was used to stress A. thaliana and P. cheesemanii plants in this study. Transcriptomes of A. thaliana and P. cheesemanii plants in response to cold, salt and UV-B radiation stresses were created. A high-quality de novo transcriptome assembly of allopolyploid P. cheesemanii was obtained by using multiple assemblers with further downstream processing. Differential expression analysis revealed a strong bias, in terms of the number of DEGs, towards upregulation in both A. thaliana and P. cheesemanii in responding to salt stress, as well as in P. cheesemanii’s cold and UV-B treatment responses. Meanwhile, in each species, a number of DEGs was shared between stresses, although the majority were unique in responding to each stress in upregulation and downregulation, respectively. Further, GO enrichment analysis revealed that these responsive genes were involved in some biological processes shared by A. thaliana and P. cheesemanii. Immune system processes, response to stimuli, signalling, developmental processes, growth, negative regulation of biological processes, multi-organism processes, biological regulation, secondary metabolic processes, cell communication, and cellular aromatic compound metabolic processes were common in the responses of both A. thaliana and P. cheesemanii to all three stresses. In both A. thaliana and P. cheesemanii, a number of these biological processes were also stress specific. First of all, in A. thaliana, cold stress may easily affect photomorphogenesis in cold responses, while the majority of the P. cheesemanii unique cold responses occurred in root differentiation, floral whorl development and regulation of programmed cell death. Second, A. thaliana responses to salt stress affected starch metabolism and lipid modification, whereas disaccharide and polysaccharide metabolism, as well as microtubule structure, were affected by salt stress uniquely in P. cheesemanii. Finally, A. thaliana responses to UV-B radiation involved a combination of physical and biological defences, including cell wall modification defence, stomatal movement, vitamin B6 metabolic processes and oxygen metabolic processes. In contrast, seed germination biological regulation was affected in P. cheesemanii under UV-B radiation stress. Further, P. cheesemanii had a larger number of unique GO enrichments in cold responses than did A. thaliana. There was a wide range of crosstalk among the biological processes in responding to the three stresses in A. thaliana, while only one main cluster was identified in crosstalk for the three stress responses in P. cheesemanii. In this main cluster, the biosynthetic process for anthocyanins was in the centre position, and it was found that multiple stress-responsive biological processes probably involved anthocyanins in P. cheesemanii. Thus, although the P. cheesemanii genome shows close similarity with that of A. thaliana, it appears to have evolved novel strategies such as a highly UV-B-activated UVR8-independent pathway, allowing the plant to tolerate relatively high UV-B radiation. The stress process is highly conserved in plant species under various stresses, but species also develop a few unique characteristics that may help them adapt to their own ecological niche and survive particular environmental stresses.