title: Polymorphism of BMP4 gene in Indian goat breeds differing in prolificacy.
abstract: Bone morphogenetic proteins (BMPs) are members of the TGF-β (transforming growth factor-beta) superfamily, of which BMP4 is the most important due to its crucial role in follicular growth and differentiation, cumulus expansion and ovulation. Reproduction is a crucial trait in goat breeding and based on the important role of BMP4 gene in reproduction it was considered as a possible candidate gene for the prolificacy of goats. The objective of the present study was to detect polymorphism in intronic, exonic and 3' un-translated regions of BMP4 gene in Indian goats. Nine different goat breeds (Barbari, Beetal, Black Bengal, Malabari, Jakhrana (Twinning>40%), Osmanabadi, Sangamneri (Twinning 20-30%), Sirohi and Ganjam (Twinning<10%)) differing in prolificacy and geographic distribution were employed for polymorphism scanning. Cattle sequence (AC_000167.1) was used to design primers for the amplification of a targeted region followed by direct DNA sequencing to identify the genetic variations. Single nucleotide polymorphisms (SNPs) were not detected in exon 3, the intronic region and the 3' flanking region. A SNP (G1534A) was identified in exon 2. It was a non-synonymous mutation resulting in an arginine to lysine change in a corresponding protein sequence. G to A transition at the 1534 locus revealed two genotypes GG and GA in the nine investigated goat breeds. The GG genotype was predominant with a genotype frequency of 0.98. The GA genotype was present in the Black Bengal as well as Jakhrana breed with a genotype frequency of 0.02. A microsatellite was identified in the 3' flanking region, only 20 nucleotides downstream from the termination site of the coding region, as a short sequence with more than nineteen continuous and repeated CA dinucleotides. Since the gene is highly evolutionarily conserved, identification of a non-synonymous SNP (G1534A) in the coding region gains further importance. To our knowledge, this is the first report of a mutation in the coding region of the caprine BMP4 gene. But whether the reproduction trait of goat is associated with the BMP4 polymorphism, needs to be further defined by association studies in more populations so as to delineate an effect on it.
authors.affiliation: National Bureau of Animal Genetic Resources, Karnal 132001, India. Electronic address: rekvik@gmail.com.
authors.forename: Rekha
authors.initials: R
authors.lastname: Sharma
authors.forename: Sonika
authors.initials: S
authors.lastname: Ahlawat
authors.forename: A
authors.initials: A
authors.lastname: Maitra
authors.forename: Manoranjan
authors.initials: M
authors.lastname: Roy
authors.forename: S
authors.initials: S
authors.lastname: Mandakmale
authors.forename: M S
authors.initials: MS
authors.lastname: Tantia
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D001120:Arginine / Q000235:genetics; D055415:Bone Morphogenetic Protein 4 / Q000235:genetics*; D001947:Breeding; D005091:Exons; D005260:Female; D005298:Fertility / Q000235:genetics; D005787:Gene Frequency; D006041:Goats / Q000235:genetics / Q000502:physiology*; D008239:Lysine / Q000235:genetics; D018895:Microsatellite Repeats; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D012098:Reproduction / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; D055415:Bone Morphogenetic Protein 4; D001120:Arginine; D008239:Lysine
keywords: 3′ UTR; 3′ Un-Translated Region; BLAST; BMP15; BMP4; BMPR1B; BMPs; Basic Local Alignment Search Tool; Bone Morphogenetic Protein 15; Bone Morphogenetic Protein 4; Bone Morphogenetic Protein Receptor type 1B; Bone Morphogenetic Proteins; CDS; Coding DNA Sequence; DNA; Deoxyribonucleic acid; EDTA; Ethylene Diamine Tetra Acetic acid; FSH; Fec; Fecundity; Follicle Stimulating Hormone; GDF9; Growth Differentiation Factor 9; ICAR; Indian Council of Agricultural Research; Indian goat; MAS; Magnesium Chloride; Marker Assisted Selection; MgCl(2); Microsatellite; NCBI; National Centre for Biotechnology Information; OD; Optical Density; PCR; PCR-RFLP; PCR-SSCP; Polymerase Chain Reaction; Polymerase Chain Reaction-Restriction Fragment Length Polymorphism; Polymerase Chain Reaction-Single Strand Conformation Polymorphism; Polymorphism; SNP; SNPs; Single Nucleotide Polymorphism; TGF-β; Transforming Growth Factor β; UPGMA; Unweighted Pair Group Method with Arithmetic Mean; Variations