According to the presumption made for this study, an attempt was made to study the variants of exon II region of
PHKA2 gene present on X chromosome and to associate with udder traits in Bos Indicus for the first time. Primers for exon 2 and its flanking region of bovine
PHKA2 gene were used for amplification of genomic DNA of 100 Sahiwal cows. A 437 bp band was successfully amplified by PCR in all DNA samples providing a clear band with good specificity (Fig 1). This gene is present on bovine X chromosome. Various studies on X chromosome polymorphic regions associated with udder traits have been reported
(Yan et al., (2020), Devani et al., (2020), Ogorevc et al., (2009). In Charolais cattle,
myostatin gene (
GDF8) was significantly associated with udder volume and teat size
(Vallee et al., 2016). According to
Cole et al., (2011), the X chromosome was highly variable and the most significant X chromosome SNP effects were associated with udder attachment, rear teat placement, specifically in context of udder traits.
DNA sequence analysis revealed three-point mutations
i.
e g.124497381C>T in exon 2, X:124497248G>A and X: 124497189 C>T in our targeted population. Chromatogram changes in
PHKA2 gene in targeted regions are shown in Fig 2-4. Genetic architecture of targeted loci in resource population exhibited very low ranging frequency of mutant allele (from 0.02 to 0.08). Detailed genotypic and allelic frequencies are presented in Table 1. Chi-square test showed that SNP X: 124497248G>A; X: 124497189 C>T were not in Hardy-Weinberg equilibrium (p<0.05) due to the kind of genetic architecture. The recessive homozygotes were negligible and therefore the variant could be seen in the heterozygote genotypes only. This specific kind of selection for dominant homozygotes in the present population against recessive gene might be an example of directional selection. The unfavourable form (recessive allele) might probably have been present in the previous generations, which now is in process of removal by selection. Also, selection against recessive alleles must have been very efficient initially, which generally becomes slower as larger proportion of the latter is protected in heterozygotes. Also, these variants in non-coding region might have role in the gene activity, protein assembly
etc. Noncoding DNA has wide implications for a range of phenotypic traits such as cell size, growth rate, metabolism and life history and is an important yet often neglected part of the genotype-phenotype link
(Hessen, 2017).
However, an association analysis was performed and least square means of udder traits grouped based on genotype at different loci were analysed (Table 2). It was observed that SNP g.124497381C>T was significantly (p<0.05) associated with DBT and CL. It is inferred that selection of heterozygote genotype will help to select the animal having more distance between teats and shallower CL than homozygote animals. The homozygote animals were having closely placed teats and deeper udder cleft which is a very desirable udder conformation. Widely placed teats are undesirable as is evident by various reports.
Turkyilmaz et al., (2018) found a negative relationship between distance between udder teat places and milk components in sheep.
Berry et al., (2004) stated that teats at either extremity of the scale in cows increases the likelihood of being culled while long CL stipulates a strong median suspensory ligament.
Additionally, SNP X: 124497248G>A was significantly (p<0.05) associated with RUW, FUA, UD, UL and TL. Homozygote genotype were having higher values for RUW, UL, FUA and TL than heterozygote animals except UD. Furthermore, SNP X: 124497189C>T was significantly (p<0.05) associated with UL and RUH.
Homozygote genotype were selected and favoured in the population. Higher the RUW, higher is the udder capacity. Medium range positive phenotypic correlation was reported between RUW and 305-day milk yield and between UL and Milk yield by
Khan and Khan (2016). FUA indicates how strongly the fore udder is attached to the body wall
via lateral ligaments. The strong and tight fore udder attachment is the most desirable
(Godara et al., 2015). In context of TL, intermediate values of TL are preferred over smaller TL agreeing with the findings of study. Short teats cause problem for milking machines
(Icar, 2001) while more longer teats are genetically predisposed to a higher incidence of mastitis.
Klein et al. (2005) and
Paulrud and Rasmussen (2004) stated that teat length and thickness play an important role in preventing mastitis, since the longer the canal length, the more pronounced the keratin cap, acting as a natural barrier, prevents contamination with the pathogens causing mastitis. Therefore, it is crucial to establish a balance between functionality and health for this trait, given that extremes are undesirable
(Panetto et al., 2017). However, lower value of UD which is not advantageous. This condition might have happened in the resource population because of selection of high milk producing cows eventually resulting in deep udders. Shallow udder depth is most desirable. Cows with deeper udders have more chances of udder injury and mastitis
(Rogers, 1993). Cows with deeper udders and less udder clearance are more susceptible to high SCS
(Carlstrom et al., 2016; Dadpasand et al., 2012; Stefani et al., 2018). Similar to RUW, high rear udder attachment is also an index of more udder capacity, so higher values are beneficial.
