Assessing the Effect of SNPs on Litter Traits in Pigs

Island demographics and trait associations in white-tailed deer

When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force and results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number (~50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.

Candidate genes associated with reproductive traits in rabbits

In the era of scientific advances and genetic progress, opportunities in the livestock sector are constantly growing. The application of molecular-based methods and approaches in farm animal breeding would accelerate and improve the expected results. The current work aims to comprehensively review the most important causative mutations in candidate genes that affect prolificacy traits in rabbits. Rabbits are a source of excellent-tasting meat that is high in protein and low in fat. Their early maturity and intensive growth are highly valued all over the world. However, improving reproductive traits and prolificacy in rabbits could be very tricky with traditional selection. Therefore, traditional breeding programs need new methods based on contemporary discoveries in molecular biology and genetics because of the complexity of the selection process. The study and implementation of genetic markers related to production in rabbits will help to create populations with specific productive traits that will produce the desired results in an extremely short time. Many studies worldwide showed an association between different genes and productive traits in rabbits. The study of these polymorphisms and their effects could be useful for molecular-oriented breeding, particularly marker-assisted selection programs in rabbit breeding.

Allelic to genome wide perspectives of swine genetic variation to litter size and its component traits

Litter size is a complex and sex limited trait that depends on various biological, managemental and environmental factors. Owing to its low heritability it is inefficaciously selected by traditional methods. However, due to higher heritability of ovulation rate and embryo survival, selection based on component traits of litter size is advocated. QTL analysis and candidate gene approach are among the various supplementary/alternate strategies for selection of litter size. QTL analysis is aimed at identifying genomic regions affecting trait of interest significantly. Candidate gene approach necessitates identification of genes potentially affecting the trait. There are various genes that significantly affect litter size and its component traits viz. ESR, LEP, BF, IGFBP, RBP4, PRLR, CTNNAL1, WNT10B, TCF12, DAZ, and RNF4. These genes affect litter size in a complex interacting manner. Lately, genome wide association study (GWAS) have been utilized to unveil the genetic and biological background of litter traits, and elucidate the genes governing litter size. Favorable SNPs in these genes have been identified and offers a scope for inclusion in selection programs thereby increasing breeding efficiency and profit in pigs. The review provides a comprehensive coverage of investigations carried out globally to unravel the genetic variation in litter size and its component traits in pigs, both at allelic and genome wide level. It offers a current perspective on different strategies including the profiling of candidate genes, QTLs, and genome wide association studies as an aid to efficient selection for litter size and its component traits.

Research Note: Association of Single Nucleotide Polymorphism of AKT3 with Egg Production Traits in White Muscovy Ducks (Cairina moschata)

Prior studies on transcriptomes of hypothalamus and ovary revealed that AKT3 is one of the candidate genes that might affect egg production in White Muscovy ducks. The role of AKT3 in the uterus during reproductive processes cannot be overemphasized. However, functional role of this gene in the tissues and on egg production traits of Muscovy ducks remains unknown. To identify the relationship between AKT3 and egg production traits in ducks, relative expression profile was first examined prior to identifying the variants within AKT3 that may underscore egg production traits [age at first egg (AFE), number of eggs at 300 d (N300D), and number of eggs at 59 wk (N59W)] in 549 ducks. The mRNA expression of AKT3 gene in high producing (HP) ducks was significantly higher than low producing (LP) ducks in the ovary, oviduct, and hypothalamus (P < 0.05 or 0.001). Three variants in AKT3 (C-3631A, C-3766T, and C-3953T) and high linkage block between C-3766T and C-3953T which are significantly (P < 0.05) associated with N300D and N59W were discovered. This study elucidates novel knowledge on the molecular mechanism of AKT3 that might be regulating egg production traits in Muscovy ducks.

Identification of polymorphism of FecX gene in indigenous sheep of Meghalaya

Fecundity gene such as FecX, govern fertility and litter size in sheep. Selection of animals with the help of molecular markers through identification of polymorphism of fecundity genes is an impactful method of genetic improvement. The present study was carried out to identify the polymorphism of FecX gene in indigenous sheep of Meghalaya. Blood samples were collected from 50 randomly selected ewes from 2 districts of Meghalaya namely, East Khasi Hills and West Khasi Hills. Genomic DNA was extracted from the samples and PCR amplification of FecX gene with specific primer set was done. PCR product size of 141 bp was obtained. Further, digestion of the PCR product with restriction enzyme HinfI through PCR-RFLP technique was conducted to identify the variants in FecX gene. Upon digestion, 2 types of fragment pattern identified, arbitrarily designated as AA and AB genotype, where AA genotype yielded one fragment (141 bp) and AB genotype yielded 2 fragments (100 and 41 bp). Presence of polymorphism can be an important indicator for selection with the help of molecular markers.