Genetic polymorphism and association study of milk production related genes and transcriptome analysis of mammary tissue at different stages of lactation in Indian Goat Breeds

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dc.contributor.advisorSatyendra Pal Singh
dc.contributor.authorKumar, Avneesh
dc.date.accessioned2024-08-06T10:55:37Z
dc.date.available2024-08-06T10:55:37Z
dc.date.issued2024-07-26
dc.description.abstractGoat husbandry plays a crucial role in Indian agriculture, it has become indispensable for millions of small farmers, landless laborers, and rural households. This sector accounts for 4.2% of rural employment in India, providing economic empowerment and livelihood options. However, tackling issues such as inadequate healthcare services, restricted access to high-quality breeding stock, and insufficient scientific knowledge among farmers is vital for the sustainable development of goat husbandry. The genetic diversity of native goat breeds is diminishing due to the slaughtering of superior bucks and does for meat, posing challenges for enhancing goat milk production. Conventional selection methods are time-consuming, but advances in molecular and whole genome sequencing techniques enable swift and effective selection of economically significant milk production traits via marker assisted selection. Nonetheless, data on the genetic diversity of economically crucial genes is scarce, and the interaction of genes and molecular pathways associated with milk production remains limited. This research sought to explore the correlation between genetic variations in established milk-related genes and disparities in gene expression within the mammary glands of Indian goat breeds throughout various lactation stages. The present investigation examined the polymorphism of PIT1, PITX2, GH, and MTHFR genes in 100 adult female goats of the Barbari breed at the University Goat Farm, Department of Physiology, DUVASU, Mathura. PCR-RFLP assay was utilized to analyze gene polymorphism, with restriction enzymes confirming restriction sites and indel sequences in the PCR products by sequencing. Standard methods were employed to estimate allelic and genotypic frequencies and association studies on milk-related traits were conducted using data from the University Goat Farm, DUVASU, Mathura. Differential mRNA expression was analyzed through transcriptome profiling of the mammary gland alveolar parenchyma in Jamnapari indigenous goats. Mammary tissue samples were obtained from Indian goats during different lactation stages (early, mid, and late) for evaluating gene expression variations. Total RNA was extracted, assessed for quality, and converted into cDNA libraries for Next Generation Sequencing RNA-Seq. The raw reads were quality-checked, and aligned with the reference genome (Capra hircus) using Hisat2. Abundance estimation was performed with featureCounts, and differential expression analysis and visualization were carried out using the edgeR package. Gene ontology and pathway enrichment analyses identified biological pathways enriched in differentially expressed genes. RT-qPCR validated the gene expression differences found in RNA-Seq. After investigating genetic polymorphisms in PIT1, PITX2, GH and MTHFR genes their associations with milk traits like daily milk yield, fat%, SNF%, lactose% and protein% was carried out. While GH and PITX2 polymorphisms did not show significant links to milk traits, while PIT1 and MTHFR genes were found monomorphic. The transcriptome study was helpful in providing cognizance regarding the interplay and dynamics of key genes also it gave acumen about the molecular pathway in the important biological process and function the current study identified 26 uniquely and significantly upregulated genes during mid-lactation, while 14 uniquely and significantly upregulated genes were found during the late lactation period. Interestingly, ten genes that were uniquely downregulated during mid-lactation were significantly upregulated in late lactation. Furthermore, the research revealed that 427 unique genes were significantly upregulated in mid-lactation but were shut down in the late lactation period. These results show how gene expression changes during different stages of lactation. This gives us more information about how the mammary glands in dairy goats are controlled at the molecular level. Examination of gene expression across lactation stages highlighted key genes (CRABP1, CDA, CXCL9 and SPP1) crucial for mammary gland development. The analyses underscored vital mechanisms governing milk production. This detailed analysis lays the groundwork for targeted breeding efforts to enhance the milk production in Indian goat breeds
dc.external.URLhttps://krishikosh.egranth.ac.in/
dc.identifier.citationSelf, Advisor, books, reports praticals etc./U.P. Pandit Deen Dayal Upadhyaya pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU) Mathura Uttar Pradesh India-281001
dc.identifier.otherU.P. Pandit Deen Dayal Upadhyaya pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU) Mathura Uttar Pradesh India-281001
dc.identifier.urihttps://krishikosh.egranth.ac.in/handle/1/5810212961
dc.language.isoEnglish
dc.pages189p
dc.publisherU.P. Pandit Deen Dayal Upadhyaya pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU) Mathura Uttar Pradesh India-281001
dc.relation.ispartofseriesPh.D. Thesis; Ph.D. Thesis
dc.research.problem Investigated the polymorphism of milk production-related genes PIT1, PITX2, GH and MTHFR using PCR-RFLP assay and explore their association with milk-related traits in Indian goat breed Barbari.  Performed transcriptome profiling of the mammary gland to examine differential gene expressions, interactions and key pathways activated or deactivated in early, mid, and late lactation in Indian goat breed Jamnapari.  The polymorphism study revealed that the screened Barbari goat population under study was monomorphic for PIT1 and MTHFR w.r.t. RE digestion with PstI, and BsaHI, respectively  The polymorphism study revealed that the screened Barbari goat population under study was polymorphic for GH and PITX2 gene w.r.t. RE digestion with HaeIII enzyme and presence of 22bp indel mutation, respectively.  The 22 bp indel mutation and its association with milk production traits were first time explored in Indian goat Barbari population.  The PITX2 Indel mutation gene exhibited genotypic frequencies of 32.0% II (n=32), 45.0% ID (n=45), and 23.0% DD (n=23), with allelic frequencies of 0.545 for I and 0.455 for D.  There were not found any significant association between the polymorphic genotypes of GH and PITX2 gene with milk production traits in the population under study.  There were significant differences in the expression levels of mRNA genes between the control (early lactation) and treated groups (mid and late lactation), with a large number of genes being upregulated or downregulated across different comparisons.  Twenty six uniquly and significantly upregualted genes were identified during mid/peak lactation while 14 uniquly and significantly upregualted genes were identified during late lactation period.  Ten uniquly genes in mid lactation were down regulated significantly while these were upregulated significantly in late lactation  Four hundred twenty seven unique genes were significantly up regulated in mid lactation while they were shut down in late lactation.  In transcriptome analysis, SPP1, FGF4, LCN2 and WNT8A genes were significantly expressed and found to have significant roles in the development of the mammary gland and presumably in lactation.  In the comparison between early and mid-lactation 764 long non coding RNAs (lncRNA) were found to be significantly differentially expressed. Among the significant lncRNAs, 319 were upregulated and 216 were downregulated. Nine control-specific lncRNA, and one early lactation stage (T1) specific lncRNA was identified.  In the comparison between early and late lactation, 690 lncRNA were significantly differentially expressed, with 260 upregulated and 221 downregulated. Additionally, 4 control-specific lncRNA, and one lncRNA specific to the late lactation stage (T2) was identified.  For the comparison between mid and late lactation 633 lncRNA were significantly differentially expressed, with 168 upregulated and 252 downregulated. Five lncRNA specific to the mid lactation stage (T1) were identified, and 4 lncRNA specific to the late lactation stage (T2) were identified.  The top three GO terms pertaining to biological process (BP), cellular components (CC) and molecular function (MF) in each stage showed concurrence with normal trend of lactation cycle.  Several pathways related to mammary gland development and milk production identified such as protein processing in ER, Oxidative phosphorylation, ECM-receptor interaction etc. were identified.
dc.subAnimal Genetics and Breeding
dc.themeGenetic polymorphism and association study of milk production related genes and transcriptome analysis of mammary tissue at different stages of lactation in Indian Goat Breeds
dc.these.typePh.D
dc.titleGenetic polymorphism and association study of milk production related genes and transcriptome analysis of mammary tissue at different stages of lactation in Indian Goat Breeds
dc.typeThesis
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