# Survey of SNPs Associated with Total Number Born and Total Number Born Alive in Pig
## 1 Introduction  
In the early 1990s the work on mapping the pig genome started and maps containing more than 1200 microsatellite markers appeared due to the development of the international project \"PiGMap\" and projects of the US Department of Agriculture and American agricultural institutes. These maps were used to identify the Quantitative Trait Loci (QTL) underlying the genetic architecture of pig productivity traits [1; 2; 3]. To date, an extended database has been created--Pig Quantitative Trait Locus Database (PigQTLdb), which presents 30170 QTLs for 688 pig trait of deferent classes [4].  
The sows' reproductive potential is the basis for continuous and efficient production. In recent decades, the BLUP (Best linear unbiased prediction) method has made a significant contribution to improving reproduction rates [5; 6]. However, low heritability coefficients of reproductive traits and their sex-limited phenotypic exhibition lead to developing new approaches revealing the biological nature of reproductive performance. Great hopes are pinned on GWAS (Genome-Wide Association Studies) to solve the problems associated with studying the genetic architecture of reproductive traits of pigs [7; 8; 9; 10].  
GWAS results can be represented by the information on detected associations with various genetic aberrations: chromosomal mutations (whole chromosomes or their fragments), large inserts or deletions (100-100,000 nucleotides), small inserts or deletions (1 to 100), single nucleotide polymorphisms (SNP) [11]. Each SNP is represented by at least two alleles: minor (rarer) and major. Genetic variations with minor allele frequency exceeding 0.01% are numbered and assigned to rs index [12].  
Currently SNP BeadChip technology is more affordable for genome-wide research than sequencing is. SNP BeadChips have been developed to include high (HD), medium (MD), or low (LD) genome distribution of markers. Rigid structure is noted as a disadvantage, which allows us to analyze only what is already predetermined by the BeadChip design and in this connection the potentially important information can be omitted [13]. Markers do not have the same density across all chromosomes and not fully track structural genetic variations such as insertions and deletions [13]. However, despite these shortcomings, SNP BeadChip has recently gained great popularity in studies of the genetic architecture of quantitative traits of farm animals and pigs in particular [14; 15; 16].  
The first SNP BeadChips with a resolution of about 60 thousand markers covering all autosomal and X chromosome genes PorcineSNP60 BeadChip v2 were presented by the American company Illumina (San Diego, CA, USA). In addition to SNP BeadChip with high density, LD SNP BeadChip with low density have been proposed to reduce genotyping costs. Commercial LD SNP BeadChip <<GeneSeek/Neogen GPP-Porcine LD Illumina Bead Chip panel>> were also developed by <<GeneSeek/Neogen>> (Lincoln, NE, USA). Besides this, the company introduced HD SNP BeadChips with a higher density (about 70 thousand markers). HD SNP BeadChips containing about 650 thousand markers and including all markers of the <<Illumina PorcineSNP60 BeadChip v2>> array, were produced by <<Affymetrix>> (Santa Clara, CA, USA). It should be noted that SNP BeadChip can be custom made including specific SNPs associated with given traits of productivity.  
Reproductive productivity depend on a complex set of characteristics. The number of piglets at birth (Total number born, Litter size, TNB) and the number of alive piglets at birth (Total number born alive, NBA) are the main indicators of the reproductive productivity of sows in pig breeding [17; 18; 19; 20; 21]. These indicators reflect the level of all physiological processes associated with fertilization, intrauterine development of the fetus and a sow's labor, and are also quite easy to account for.