Comparative genomic analysis uncovers candidate genes related with milk production and adaptive traits in goat breeds

Abstract

During the process of animal domestication, both natural and artificial selection cause variation in allele frequencies among populations. Identifying genomic areas of selection in domestic animals may aid in the detection of genomic areas linked to ecological and economic traits. We studied genomic variation in 140 worldwide goat individuals, including 75 Asian, 30 African and 35 European goats. We further carried out comparative population genomics to detect genomic regions under selection for adaptability to harsh conditions in local Asian ecotypes and also milk production traits in European commercial breeds. In addition, we estimated the genetic distances among 140 goat individuals. The results showed that among all studied goat groups, local breeds from West and South Asia emerged as an independent group. Our search for selection signatures in local goats from West and South Asia revealed candidate genes related to adaptation to hot climate (HSPB6, HSF4, VPS13A and NBEA genes) and immune response (IL7, IL5, IL23A and LRFN5) traits. Furthermore, selection signatures in European commercial goats involved several milk production related genes, such as VPS13C, NCAM2, TMPRSS15, CSN3 and ABCG2. The identified candidate genes could be the fundamental genetic resource for enhancement of goat production and environmental-adaptive traits, and as such they should be used in goat breeding programs to select more efficient breeds.

Genomic analysis uncovers novel candidate genes related to adaptation to tropical climates and milk production traits in native goats

“…2 C). The r 2 values found in this investigation ranged from – 0.53 to – 0.57 at a marker pair distance of 120 Kb, which were consistent with those previously reported for Iranian and Chinese native goat groups [ 16 , 42 ]. Furthermore, the results demonstrated that Pakistani goats had much higher levels of LD across all genomic lengths than other goat groups, which could be due to recent artificial selection for economic traits in these breeds [ 43 ].…”

“…These results agree with those of the earlier research, which suggested that the genomic architecture of the goat populations from Southwest Asia has been affected by broad historical processes such as gene flow from ancient periods [ 2 ]. In line with previous studies on different species [ 3 , 16 , 26 , 42 ], we discovered that all groups experienced the same pattern of reduction in LD decay as the genomic distance (Kb) increased, while a relatively rapid change in LD over increasing physical distance was detected in the African population (Fig. 2 C).…”

“…Another gene associated with milk, LPL , was found in one of the selection regions of chromosome 8, which is a crucial potential gene that plays a central role in human plasma triglyceride metabolism [ 61 ]. Previous studies have reported that genetic mutations in the LPL gene are related to milk production traits (e.g., milk yield, fat content, and protein yield) and composition traits (protein and fat percentages) in dairy goats and also in different livestock species [ 16 , 62 ].…”

Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat

“…Among the immune response-related genes screened, DOCK8 was investigated for its ability to confer immunity as a positively selected gene in Yunling goats ( Kim et al, 2016 ). The IL1R1 gene is regarded as a candidate gene for the induction of autoimmune responses in goats ( Amiri Ghanatsaman et al, 2023 ); similarly, the IL7 gene is the top signaling gene for the induction of immunological responses in the worldwide goat population ( Crisà et al, 2016 ). Among milk production- and composition-related attributes, SPP1 ( Li et al, 2020 ), TLL1 and ERBB4 , which are related to colostrum and lactation regulation ( Chen et al, 2020 ), respectively, have been studied previously.…”

Genome-Wide Association Study of Milk Composition in Karachai Goats

“…With the development of the GoatSNP50 BeadChip by Illumina Inc. [27], GWASs (genome-wide association studies) became available for goats of different productivity directions [9,21]. Through these studies, it has been possible to identify certain genes associated with various economically important traits in goats, such as fiber productivity, including fiber color [28][29][30], meat productivity traits [31][32][33], reproduction [34][35][36], and adaptation ability [37][38][39]. Several studies have focused on identifying genes associated with milk production traits in goats, as well as exterior traits that have a greater impact on level of their development [40][41][42].…”