INSERTION/ DELETION (InDel) POLYMORPHISMS IN CANDIDATE GENES AND ITS ASSOCIATION WITH BODY MEASUREMENT TRAITS IN NATIVE GOAT BREEDS OF KERALA
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Date
2023-02-02
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COLLEGE OF VETERINARY AND ANIMAL SCIENCS, POOKODE, WAYANAD, KERALA VETERINARY AND ANIMAL SCIENCES UNIVERSITY
Abstract
India has 34 well-defined goat breeds in their genetic database which is distributed among four major regions: the temperate Himalayas, the north-western regions, the southern peninsulas and the eastern regions. Goats are highly valued as multipurpose animals capable of boosting rural economies, as much as they are involved in food production. India has a high demand for goat meat, which is one of the choicest and most sought-after meats in the country. Kerala is home to two goat breeds- Attappady Black, which is known for its disease resistance and Malabari, which is known for its prolificacy. Livestock are increasingly selected for economic traits using genetic markers like single nucleotide polymorphism (SNP) and insertion/deletion polymorphisms (InDel). A total of 60 Malabari goats maintained in the University farm, Pookode, 67 Attappady Black and 50 Malabari goats maintained in the university farm, Mannuthy and 43 Attappady Black and 17 Malabari goats maintained in the Livestock research farm (LRS), Thiruvazhamkunnu were the experimental animals included in the study. Among those breeds, the animals were grouped into yearling(18-month-old), matured but not yet mated and adult (36-month-old), kidded at least once. From each goat, body measurements including body length (BL), heart girth (HG), body weight (BW), height, chest width (ChW), chest depth (ChD), cannon circumference (CC), hip width (HW) and height at the hip cross (HHC) were taken. From those measurements, calculated the body measurement indices such as the body trunk index (BTI), the body length index (BLI), the heart girth index (HGI), the cannon circumference index (CCI) and the chest width index (ChWI). For our polymorphic study, blood samples were collected from each goat, DNA extracted from blood, amplify the DNA and genotyping study was done.The study investigated five InDel polymorphisms in four candidate genes in Attappady Black and Malabari goats viz., two InDel polymorphisms in PR/SET domain family 6 (PRDM6), one InDel polymorphism each in myostatin (MSTN), insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) and growth hormone receptor (GHR) and found that 15bp insertion and unidentified insertion were detected within the intron2 region of goat IGF2BP1 gene, 9bp insertion was
detected within the upstream region of goat PRDM6 gene, 5bp insertion was detected within 5’UTR of goat myostatin gene, 12bp deletion was detected within the intron 1 region of PRDM6P1 gene and 14bp deletion was not detected within the intron 1 region of goat GHR gene. Body measurement traits and their ratios were significantly different across breeds, ages and breed x age interactions (p <0.05). Especially in adult Attappady Black goats, body length, body weight and chest depth were found to be significantly different (p<0.05) and in yearling Attappady Black goats, cannon circumference index was found to be significantly different (p<0.05). In adult Malabari goat, body length, body weight and hip width were found to be significantly different (p<0.05) and yearling Malabari, body height were found to be significantly different (p<0.05). Body weight was found to be significantly different (p<0.05) in breed* age interaction. An association study was conducted between identified InDel and body measurement traits. It was revealed that no significant association between body measurement traits and detected InDel in IGF2BP1 gene, PRDM6 gene and MSTN gene. But in PRDM6P1 gene, body height, cannon circumference and cannon circumference index were found to be
significantly associated with 12bp InDel polymorphism. A Chi square test was also used to determine whether Hardy-Weinberg equilibrium (HWE) existed in the screened population. In both Attappady Black and Malabari goat breeds, IGF2BP1gene, MSTN gene and PRDM6P1 gene were deviated from the state of HWE (p <0.05). In Attappady Black goats, PRDM6 gene was deviated from the state of HWE (p <0.05) but in Malabari PRDM6 gene was in the state of Hardy- Weinberg equilibrium (p >0.05). A number of other population genetic parameters were also calculated, including allele frequency, genotype frequency, observed heterozygosity (Ho), heterozygosity (He) and the polymorphic information content (PIC). It was found that the allele frequencies of IGF2BP1 gene, the frequencies of insertion “I” allele was greater than the deletion “D” allele in both breeds. In PRDM6 gene, the frequencies of deletion “D” allele was higher than insertion “I” allele in Malabari goats and vice-versa in Attappady Black goat breeds. In both MSTN gene
and PRDM6P1 gene, the frequencies of insertion “I” allele was lower than the deletion “D” allele in both breeds. found that the expected heterozygosity (He) in the PRDM6 and PRDM6P1 genes in both breeds was higher than the observed heterozygosity (Ho).This may have been caused by large proportion of inbreeding. As a result of mixing two isolated populations, observed heterozygosity (Ho) for the IGF2BP1 gene and MSTN gene was greater than expected heterozygosity (He). The polymorphic information content was examined and found that, the polymorphic information content (PIC) was examined and found that, it was moderate level of genetic diversity in Attappady Black goats and high level of genetic diversity in Malabari goats in IGF2BP1 gene, while in PRDM6 and MSTN
gene, it was found that high and low level of genetic diversity respectively. in case of PRDM6P1 gene, it was low level of genetic diversity in Attappady Black goats and moderate level of genetic diversity in Malabari goats.From these findings, it was concluded that InDel markers found in the present study may provide a theoretical basis for use of InDel as a marker for marker assisted selection of growth traits among Attappady Black and Malabari goats. Especially PRDM6P1 gene may be directly used as an InDel marker for the selection of goat based on body height, cannon circumference and cannon circumference for meat production as well as growth aspects