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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Date
2024-07-26
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U.P. Pandit Deen Dayal Upadhyaya pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU) Mathura Uttar Pradesh India-281001
Abstract
Goat 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
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Self, 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