GENOME WIDE ASSOCIATION STUDY OF UDDER TYPE TRAITS AND MILK PRODUCTION IN GIR CATTLE
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Date
2018
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DEPARTMENT OF ANIMAL GENETICS AND BREEDING POSTGRADUATE INSTITUTE OF VETERINARY EDUCATION AND RESEARCH KAMDHENU UNIVERSITY, GANDHINAGAR
Abstract
Gir cattle are among top milch cattle breeds of India. The present study was conducted to study nine different udder type traits and 305 day milk yield and, genome wide association study (GWAS) of udder type traits and 305 day milk yield in Gir cattle based on SNP genotyping. The records comprised of data pertaining to udder type traits collected from field area of Bhavnagar and Gir-Somnath Districts on 635 Gir cows and milk production performance data was obtained from INAPH database based on monthly test day milk records generated under Gir Pedigree Selection Programme being implemented by Sabarmati Ashram Gaushala, Bidaj under National Dairy Plan-I. The animals were genotyped using the customized Illumina Bovine HD microarray chip assay INDUSCHIP 1, as designed by NDDB, Anand.
Nine udder type traits (fore udder attachment, central ligament, fore teat placement, rear teat placement, rear udder height, rear udder width, teat length, and udder depth and teat thickness) and 305 day milk yield were considered under the present study. The descriptive statistics for udder type traits and 305 day milk yield were calculated using statistical software R (v3.4.0). The data on genotype and phenotypes were used for genome wide association study (GWAS). The genome wide association study was carried out with PLINK (v1.90b4.4) software.
The means and standard error of fore udder attachment, central ligament, fore teat placement, rear teat placement, rear udder height (cm), rear udder width (cm), teat length (cm) and udder depth (cm) and teat thickness were 5.43±0.08, 4.91±0.06, 4.06±0.05, 4.25±0.07, 13.19±0.12, 7.27±0.06, 7.90±0.10, 13.75±0.14 and 4.14±0.07 respectively. The mean for 305 day lactation milk yield (kg) was 2051.42±31.38.
The phenotypic correlation between the 305day milk yield and udder type traits were low to moderate. The higher phenotypic correlation of 305 day milk yield with teat length (0.46), rear udder width (0.35) and teat thickness (0.30) were observed in present study. While negative correlation of 305day milk yield and fore udder attachment (-0.34), fore teat placement (-0.12), rear teat placement (-0.14) and udder depth (-0.33) were observed.
The phenotypic correlations among the udder traits were low to medium in range. The highest positive phenotypic correlation between teat length and teat thickness was 0.50. The correlations between fore udder attachment, central ligament, rear udder height, teat length, udder depth and teat thickness were found to be highly significant (p<0.001). The correlations of rear udder width with teat length, udder depth and teat thickness were also highly significant. The fore udder attachment was negatively correlated with central ligament (-0.13), fore teat placement (-0.09), rear teat placement (-0.02), rear udder height (-0.14), rear udder width (-0.11), teat length (-0.33) and teat thickness (-0.24) except udder depth (0.47) which was positive.
Genome wide association study identified 838 significant SNPs associated with udder type traits and 305 day milk yield in Gir cattle. Number of SNPs found to be significantly associated with (p< 0.0001) fore udder attachment, central ligament, fore teat placement, rear teat placement, rear udder height, rear udder width, teat length, udder depth and teat thickness and 305 day milk yield were 11, 6, 3, 7, 7, 38, 166, 14, 89 and 497 respectively.
The chromosome with the highest number of associated SNP was chromosome 5 which had highest number of SNPs associated with fore udder attachment, central ligament, rear udder width, teat length, udder depth, teat thickness and 305day milk yield which were 1, 2, 2, 31, 1, 17and 59 significantly associated SNPs respectively.
Most of the udder type traits in Gir cows were of intermediate nature and of desirable type but have good amount of variation The phenotypic correlations amongst the most of udder type traits were low to moderate but significant (p<0.05) and positive. Thus, present study on udder type traits and 305 day milk yield and their GWAS in Gir cattle using INDUSCHIP1 a customized SNP chip has provided the base line data for incorporation of udder type traits in Genomic Selection. The Genomic Selection approach would improve the accuracy of selection followed by rapid genetic progress in this important milch breed of India.