POLYMORPHISM STUDY ON MILK PRODUCTION TRAITS IN GOATS USING DOUBLE DIGEST RESTRICTION ASSOCIATED DNA SEQUENCE
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Date
2019
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College of Veterinary and animal Science,Mannuthy
Abstract
Native goat breeds of Kerala; namely Attappady Black and Malabari,
apparently varied in milk production capacity. Milk production data was collected
from 100 each of Malabari and Attappady Black goats and the data analysed.
Parity (p≤0.01), breed (p≤0.05) and herd (p≤0.01) showed significant influence on
milk production. Fat per cent showed significant (p≤0.05) breed differences
during early, middle and late lactation. Double digest Restriction Associated DNA
Sequencing (ddRADseq) is a modern approach for identification of Single
Nucleotide Polymorphisms (SNP) across populations. The ddRADseq technique
was performed in three pooled samples (ten each) of high and low milk producing
Malabari and Attappady Black goats. The SNPs discovered were analysed using
bioinformatics tool Venny 3. A total of 4141 and 2192 variants were observed in
Malabari and Attappady Black goats respectively. A panel of 42 candidate genes
affecting milk production were screened and 26 SNPs were discovered in 22
genes comprising of 19 intron, five downstream and two upstream variants. From
a set of 11 milk production related genes, 11 SNPs were identified based on the
difference in allelic distribution of SNPs between the two groups. NRXN3, LPL,
GLI2 were selected for validation studies. Intronic variant c.301+155748C>T of
NRXN3 was validated using High Resolution Melting analysis and showed
significant (p≤0.01) association, with mean daily milk yield (mL) of 558.17±4.58,
462.21 ±16.53 and 416.62 ±11.13 for CC, CT and TT genotypes, respectively. In
Attappady Black goats, CC genotype was absent as indicated by ddRADseq
results. Intronic variant c.243+1082C>T LPL, was validated using Polymerase
Chain Reaction-Single Strand Conformation Polymorphism and further
sequencing. It had significant (p≤0.05) association with mean daily milk yield
(mL) of 437.12±12.85, 494.72±11.60 and 467.63 ± 19.86 for CC, CT and TT
genotypes respectively. The GLI2 variant c.64T>G revealed monomorphic pattern
in PCR-RFLP. Expression study of BTN1A1 revealed significantly (p≤0.05)
higher expression (6.74 fold) in Malabari than Attappady Black. Current study
emphasized the relevance of ddRADseq in identifying novel SNPs in candidate
and unexplored genes influencing economic traits.