Association of single nucleotide polymorphisms in candidate genes with economically useful traits in chickens (Gallus gallus domesticus L.) (review)

Economically useful traits of chickens associated with productivity are inherited polygenically. With the discovery of numerous DNA regions characterized by single nucleotide polymorphism (SNP) and the development of modern genomic technologies, a detailed assessment of the results of breeding in poultry farming has become possible to successfully predict the effect of breeding (L. Wang et al., 2011; C.M. Seabury et al., 2017). This review summarizes data on genes and SNP markers used in domestic chicken breeding and describes new polymorphic allelic variants in genes that are associated with integrated productivity indicators in chickens from the world gene pool. In Russia, domestic meat, egg and dual-purpose chicken breeds are currently subjected to thorough genotyping. Polymorphic variants of key genes LCORL ( ligand dependent nuclear receptor core-pressor-like ) and NCAPG ( non-SMC condensin I complex, subunit G ) that affect egg-laying performance has been found. Differences in SNP between egg and meat and egg and decorative chickens were revealed (T.A. Larkina et al., 2021). For the NCAPG gene, a significant association of rs14991030 alleles with shell weight, percentage of shell weight to egg weight, and shell thickness was identified (O.Yu. Barkova et al., 2016). In Russian White chickens, single nucleotide polymorphisms of the dysferlin gene ( DYSF ) were identified and their association with economically valuable traits was studied (O.Yu. Barkova et al., 2021). For safe breeding and selection of chicken populations and breeds, it important to prevent the spreading of genetic diseases and to ensure the maintenance of heterozygosity of the domestic gene pool. In the Smena 8 broiler meat cross line B5, typing SNPs in the DMA , RACK1 , and CD1B genes responsible for a higher IgY titer revealed the fixation of an allele of a lower IgY titer at the Gga_rs15788237 locus and the predominance of an unfavorable allele at the Gga_rs15788101 locus and a favorable allele at the Gga17_rs160 locus. Changes in the Gga_rs16057130 and Gga_rs15788101 loci in the B5 broiler line bred at Smena State Breeding Center (Moscow Province) are most likely associated with selection for productivity traits (А.М. Borodin et al., 2020). Poultry genome studies are currently focused on analyzing large datasets across several generations to find associations (GWAS, genome-wide association studies) between SNPs and economically important traits such as growth rate, egg quantity and quality, meat and fat deposition. (A. Wolc, 2014; S.K. Zhu et al., 2014; J.H. Ouyang et al., 2008). Genome-wide genotyping using a high-density SNP array revealed candidate genes GRB14 and GALNT1 whose single nucleotide polymorphisms had statistically significant associations with egg production and egg quality parameters, including egg weight, eggshell weight, yolk weight, eggshell thickness and strength, albumen height and Haugh value for hens aged 40-60 weeks (W. Liu et al., 2011). GWAS analysis identified candidate genes ZAR1 , STARD13 , ACER1b , ACSBG2 , and DHRS12 which were associated with the weight of yolk, follicles, and ovaries of hens from the beginning of oviposition to 72 weeks of age. As estimated by SNP analysis, the heritability was moderate for yolk weight (h2 of 0.25-0.38) and relatively low for follicle weight (h2 = 0.16) and ovary weight (h2 = 0.20) (C. Sun et al., 2015). Two genes, MSX2 and DRD1 are associated with embryonic and ovarian development and contain significant SNPs associated with egg quality, i,e,, height of albumen and Haugh value. Three genes, the RHOA , SDF4 , and TNFRSF4 have been identified as candidate genes for eggshell coloration (Z. Liu et al., 2018). It has been reported (S.A. Azmal et al., 2019) that in the Chinese chicken breed Jing Hong, SNPs in the RAPGEF6 gene are associated with the egg laying rate during late oviposition. Several studies support the notion of dopamine involvement in the regulation of egg production in birds. Four SNPs (G+123A, T+198C, G+1065A, C+1107T) in dopamine receptor gene ( DRD1 ) were found which significantly affect the age of the first oviposition (it characterizes the rate of puberty of hens), the weight of the first egg and the yield of standard eggs (H. Xu et al., 2010). The VIP (receptor for vasoactive intestinal peptide-1) gene polymorphisms are associated with brooding instinct and egg production rate (M. Zhou et al., 2010). X. Li et al., (2019) found five polymorphisms in the promoter region of the FSHR (follicle-stimulating hormone receptor) gene and determined their association with the total egg production for 43 weeks of life and with the age of laying the first egg. H. Zhou et al. (2005) found significant associations of single nucleotide polymorphism in the IGF1 (insulin-like growth factor 1) gene promoter with growth rate, body composition, skeletal condition and physiological parameters of chickens.