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Simple Summary: Genomic selection (GS) is defined as a marker-assisted selection method that uses high-density molecular markers covering the entire genome combined with phenotypic data to estimate genomic estimated breeding values (GEBV). This paper reviews the principles, methods, and influencing factors of GS for breeding by using phenotypic information and genetic relationships simultaneously. It also covers the research progress of GS in meat, fiber, dairy, and reproductive traits in sheep and goats. Compared to other livestock, especially cattle, sheep and goat breeding is relatively small-scale and has lagged behind. GS combined with genomic information can help promote the breeding process and development in commercial farming of sheep and goats. We highlight the potential for phenotypic information and genetic relationships to work together to drive the breeding process, providing valuable insights for implementing GS in sheep and goat breeding. The advancement of sequencing technology and molecular breeding methods has provided technical support and assurance for accurate breeding. Genomic Selection (GS) utilizes genomic information to improve livestock breeding, and it is more accurate and more efficient than traditional selection methods. GS has been widely applied in domestic animal breeding, especially in cattle. However, there are still limited studies on the application and research of GS in sheep and goats. This paper outlines the principles, analysis methods, and influential factors of GS and elaborates on the research progress, challenges, and prospects of applying GS in sheep and goat breeding. Through the review of these aspects, this paper is expected to provide valuable references for the implementation of GS in the field of sheep and goat breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: To explore the genomic variations associated with goats' body conformation traits, we performed a genome-wide association study (GWAS) on Tashi goats. We assessed eight body conformation traits in 155 Tashi goats and performed whole-genome sequencing on 100 of them. We obtained 1676.4 Gb of raw data and identified 11,257,923 qualified single nucleotide polymorphisms (SNPs). GWAS revealed 109, 20, 52, 14, 62, 51, 70, and 7 SNPs significantly associated with body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference, respectively. We annotated 183 genes based on the significant SNPs' physical locations. Notably, several SNPs have been identified multiple times in two regions, chr.10:25988403-26102739 and chr.11:88216493-89250659, where candidate genes such as FNTB, CHURC1, and RNF144 could be crucial for goat body conformation traits. Our findings offer significant insights into body conformation and support the use of molecular breeding in meat goats. Identifying genetic markers of economically valuable traits has practical benefits for the meat goat industry. To better understand the genomic variations influencing body conformation traits, a genome-wide association study was performed on Tashi goats, an indigenous Chinese goat breed. A total of 155 Tashi goats were phenotyped for eight body conformation traits: body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Then, 100 Tashi goats were randomly selected for whole-genome sequencing and genotyped. We obtained 1676.4 Gb of raw data with an average sequencing depth of 6.2X. Clean reads were aligned to the ARS1.2 reference genome, and 11,257,923 single nucleotide polymorphisms (SNPs) were identified. The structure analysis showed that these Tashi goats were almost not genetically related. The 109, 20, 52, 14, 62, 51, 70, and 7 SNPs were significantly associated with body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Within the ±500 kb region of significant SNPs, 183 genes were annotated. The most significantly enriched KEGG pathway was "olfactory transduction", and the most significantly enriched gene ontology (GO) terms were "cellular process", "cellular anatomical entity", and "molecular transducer activity". Interestingly, we found several SNPs on chromosomes 10 and 11 that have been identified multiple times for all eight body conformation traits located in two fragments (114 kb and 1.03 Mb). In chr.10:25988403-26102739, the six SNPs were tightly linked, the TACTAG genotype was the highest at 91.8%, and the FNTB (Farnesyltransferase, CAAX Box Beta) and CHURC1 (Churchill Domain Containing 1) genes were located. In chr.11:88216493-89250659, ten SNPs were identified with several dependent linkage disequilibrium (LD) blocks, and seven related genes were annotated, but no significant SNP was located in them. Our results provide valuable biological information for improving growth performance with practical applications for genomic selection in goats. [ABSTRACT FROM AUTHOR]

Yudong black goats (YDGs) are a local breed in southwest China that possess unique meat qualities and produce a high meat yield, making them ideal models for studying goat meat quality. Castration may decrease off-odors, significantly change metabolites and improve meat quality. Using multi-omics techniques, this study focused on Yudong black goat wethers (YDW, n = 4) and Yudong black bucks (YDB, n = 4). The findings revealed that 33 differentially expressed genes (DEGs) and 279 significantly changed metabolites (SCMs) influenced goat meat quality by affecting fat accumulation and lipolysis regulatory processes. Herein, several candidate genes (IGF1, TNNT2, PPP2R2C, MAPK10 and VNN1, etc.) were identified that play a role in regulating meat quality, non-castrated and castrated, alongside a series of metabolites that may serve as potential meat quality biomarkers. Lipids (triglycerides, oxidized lipids_5-iso PGF2VI, ceramide (t18:1/36:2(2OH)) and Carnitine C20:5, etc.) were significantly higher in the castrated goats. These results revealed that lipids and hydrophilic metabolites were affected by castration, which might be beneficial in terms of goat meat quality. This study aimed to investigate the differences in meat quality between uncastrated and castrated male goats and the possible molecular regulatory mechanisms. [ABSTRACT FROM AUTHOR]

Reproductive traits are essential economic traits in goats. This study aimed to analyze the relationship between single nucleotide polymorphisms (SNPs) within the genes of GLRB, GRIA2, and GASK1B, and reproductive traits (kidding traits and placental traits) in goats. We used the resequencing data of 150 Dazu Black Goats to perform correlation analysis with the average litter size. We screened thirteen SNPs loci in introns and then used the Sanger method to genotype the remaining 150 Dazu Black Goats. The results showed that a total of six SNPs were screened. Three SNPs related to litter size and live litter size (g.28985790T > G, g.28986352A > G, and g.28987976A > G); one SNP related to total cotyledon area (g.29203243G > A); two SNPs related to placental efficiency (g.30189055G > A and g.30193974C > T); one SNP associated with cotyledon support efficiency (g.30193974C > T). The qPCR results showed that GLRB, GRIA2, and GASK1B were all highly expressed in the udder, kidney, uterus, and ovary. It indicated that these three candidate genes might affect the reproductive traits, which could be used as candidate markers for reproductive traits in Dazu Black Goats. Moreover, association studies on a large scale are still needed to figure out what effect these SNPs have on reproductive traits. [ABSTRACT FROM AUTHOR]

Reproductive traits are the basic economic traits of goats and important indicators in goat breeding. In this study, Dazu black goats (DBGs; n = 150), an important Chinese local goat breed with excellent reproductive performance, were used to screen for important variation loci and genes of reproductive traits. Through genome-wide association studies (GWAS), 18 SNPs were found to be associated with kidding traits (average litter size, average litter size in the first three parity, and average litter size in the first six parity), and 10 SNPs were associated with udder traits (udder depth, teat diameter, teat length, and supernumerary teat). After gene annotation of the associated SNPs and in combination with relevant references, the candidate genes, namely ATP1A1, LRRC4C, SPCS2, XRRA1, CELF4, NTM, TMEM45B, ATE1, and FGFR2, were associated with udder traits, while the ENSCHIG00000017110, SLC9A8, GLRB, GRIA2, GASK1B, and ENSCHIG00000026285 genes were associated with litter size. These SNPs and candidate genes can provide useful biological information for improvement of the reproductive traits of goats. [ABSTRACT FROM AUTHOR]

Embryo implantation is a critical step in the establishment of pregnancy. However, the mechanisms of embryo implantation during early pregnancy in goats remain unclear due to the lack of published studies examining the genes involved in embryo implantation. As a popular goat breed in southwest China, Dazu black goats (DBGs) are highly adaptable and exhibit high fertility, making this breed a good model in which to study reproductive performance of goats. Here, morphological analysis showed that compared with the non-pregnant (NP) groups, the endometrial thickness of the goats in the P15 and P19 groups (15 and 19-day pregnant groups, respectively) were increased (P < 0.01). Proliferating Cell Nuclear Antigen (PCNA) staining showed that PCNA was expressed in the NP, P15, and P19 groups. Transcriptome analysis was then conducted to identify gene expression patterns in uterine tissue during DBG embryo implantation. By comparing uterine tissue at different stages of embryonic implantation, 48 in NP_vs._P15, 318 in NP_vs._P19, and 1439 in P15_vs._P19, differentially expressed mRNAs were identified. Gene Ontology (GO) enrichments of the differentially expressed genes were enriched in the extracellular region, extracellular space, transporter activity, extracellular region, immune system process, immune response, and defense response etc. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the biological metabolic pathways with which the differentially expressed genes are associated were explored. Through KEGG analysis, the DBGs were associated with oxidative phosphorylation, complement and coagulation cascades, arginine and proline metabolism, metabolic pathways, arachidonic acid metabolism, and ECM-receptor interaction. These candidate genes (CSF1 , C1S , CST6 , SLC24A4 , HOXA10 , HOXA11 , MMP9 , and ITGA11) and enriched signaling pathways could be valuable references for exploring the molecular mechanisms underlying goat embryo implantation. [ABSTRACT FROM AUTHOR]

The aim of this study was to determine the properties and quality characteristics of hair and cashmere fibres of three goat breeds raised in Southwest China, namely; Dazu black goat (DBG, n = 203; ♂99, ♀104), Inner Mongolia cashmere goat (IMCG, n = 65; 21♂, 44♀) and their first cross (F1, n = 79; 39♂, 40♀). Totals of 5219, 2130 and 2981 fibre samples, from the three breeds respectively, were taken prior to shearing at 32.5 ± 01.25 months of age from four body sites; shoulder, side-portion, abdomen and leg. Breed effect was significant (P < 0.01) for most hair and cashmere properties. IMCG and F1 hair lengths were longer (P < 0.001) with less variable lengths than DBG. Shoulder hair diameters of the three breeds were not different (P > 0.05) but biggest of the side-portion and abdomen sites of DBG were bigger (P > 0.01), however, the biggest (P < 0.001) hair diameter was recorded for the leg site of F1 and the smallest (P > 0.01) for IMCG. IMCG recorded the longest value for cashmere lengths followed by DBG, while F1 recorded the lowest (P = 0.001), whilst F1 recorded the biggest (P = 0.001) diameter whereas no differences existed between parents' breeds. The cortical cell lengths of IMCG and DBG were 94.57 and 86.85 μm without significant difference detected between breeds. Differences between hair length and diameter for body sites of the studied goat breeds were significant (P < 0.01) but between whiteness, cashmere diameter and diameter of cortical cells were not. Sex had no significant effect on all hair/cashmere properties. Quality characteristics of cashmere fibres from IMCG and F1 were better (P < 0.001) than from DBG. Leg hair diameter, curl recovery rate and cashmere diameter were superior in the crossbred F1 compared to pure breed parents, and DBG was superior to IMCG for fibre elasticity and intensity traits. FGF-5 gene was detected as a candidate gene for hair and cashmere traits in IMCG breed. Whilst, KIT gene was found to be associated with coat colour in the studied breeds. Extra investigations to examine more cashmere goat breeds and crosses are needed to discover genetic variability in cashmere production locally and worldwide. [ABSTRACT FROM AUTHOR]

Simple Summary: Boer goat is a world-famous meat-type goat breed that underwent long-term artificial selection from African indigenous animals. The current study displayed the genome-wide selection signature analyses of South African indigenous goat (AF), African Boer (BH), and Australian Boer (AS), to investigate the hereditary basis of artificial selection in different stages. Moreover, the θπ, FST, and XP-CLR methods were used to search for the candidate signatures of positive selection in Boer goats. Ten genes (e.g., BMPR1B, DNER, ITGAL, and KIT) under selection in both groups were identified and are potentially responsible for reproduction, metabolism, growth, and development. This study provided a comprehensive overview of genomic variations in Boer goat, which may provide a basis for further resource protection and improvement of this breed. Boer goats, as kemp in meat-type goats, are selected and bred from African indigenous goats under a long period of artificial selection. Their advantages in multiple economic traits, particularly their plump growth, have attracted worldwide attention. The current study displayed the genome-wide selection signature analyses of South African indigenous goat (AF), African Boer (BH), and Australian Boer (AS) to investigate the hereditary basis of artificial selection in different stages. Four methods (principal component analysis, nucleotide diversity, linkage disequilibrium decay, and neighbor-joining tree) implied the genomic diversity changes with different artificial selection intensities in Boer goats. In addition, the θπ, FST, and XP-CLR methods were used to search for the candidate signatures of positive selection in Boer goats. Consequently, 339 (BH vs. AF) and 295 (AS vs. BH) candidate genes were obtained from SNP data. Especially, 10 genes (e.g., BMPR1B, DNER, ITGAL, and KIT) under selection in both groups were identified. Functional annotation analysis revealed that these genes are potentially responsible for reproduction, metabolism, growth, and development. This study used genome-wide sequencing data to identify inheritance by artificial selection. The results of the current study are valuable for future molecular-assisted breeding and genetic improvement of goats. [ABSTRACT FROM AUTHOR]

Simple Summary: Body conformation traits are economically important in the goat meat industry. Good growth performance in goats, including an accelerated growth rate, can improve carcass weight and meat yield. The identification of genetic variants associated with these traits provides a basis for the genetic improvement of growth performance. In this study, we measured six body conformation traits, including body height, body length, cannon circumference, chest depth, chest width, and heart girth. By a genome-wide association study of a Chinese meat goat breed, 53 significant single nucleotide polymorphisms and 42 candidate genes associated with these traits were detected. These findings improve our understanding of the genetic basis of body conformation traits in goats. Identifying associations between genetic markers and economic traits has practical benefits for the meat goat industry. To better understand the genomic regions and biological pathways contributing to body conformation traits of meat goats, a genome-wide association study was performed using Dazu black goats (DBGs), a Chinese indigenous goat breed. In particular, 150 DBGs were genotyped by whole-genome sequencing, and six body conformation traits, including body height (BH), body length (BL), cannon circumference (CC), chest depth (CD), chest width (CW), and heart girth (HG), were examined. In total, 53 potential SNPs were associated with these body conformation traits. A bioinformatics analysis was performed to evaluate the genes located close to the significant SNPs. Finally, 42 candidate genes (e.g., PSTPIP2, C7orf57, CCL19, FGF9, SGCG, FIGN, and SIPA1L) were identified as components of the genetic architecture underlying body conformation traits. Our results provide useful biological information for the improvement of growth performance and have practical applications for genomic selection in goats. [ABSTRACT FROM AUTHOR]

Despite the significant advantages of using indigenous Chinese goat breeds in cashmere production, yield improvement is an ongoing challenge to cashmere goat breeding. This study aimed to investigate the occupied proportion of hair follicle group (HFG) and examine its influence on total hair follicle density (THFD). A total of 459 skin samples from the Inner Mongolia cashmere goat were processed for paraffin embedment, transverse sectioning, and H&E staining. An image of 9.26 mm2 was captured for each sample. All hair follicles were marked as color dots and the areas occupied by HFGs were filled by color blocks. Color blocks and the corresponding color dots were then analysed to calculate parameters. Our results showed that those samples with the higher THFD had the following characteristics: the size of the HFG (Size-HFG) was smaller, the HFGs (Num-HFG) was denser, the area proportion of the HFGs (Ratio-HFG) was larger, and the hair follicle density within HFG (Int-THFD) was higher. For each sample, its THFD was directly determined by the Int-THFD and Ratio-HFG. By improving one or both of Int-THFD and Ratio-HFG, a higher THFD can be achieved, thereby increasing the cashmere yield. This work implied that the Inner Mongolia cashmere goat still has upward potential for THFD improvement. • Histological image analysis was done on 459 skin samples of Inner Mongolia cashmere goat. • The total hair follicle density (THFD) of Inner Mongolia cashmere goats varied greatly. • The occupied proportion of hair follicle groups (Ratio-HFG) in goat skin was investigated. • The higher the Ratio-HFG, the higher the THFD. • The Inner Mongolia cashmere goat has upward potential for THFD improvement. [ABSTRACT FROM AUTHOR]

• Kisspeptin/GPR54 was expressed in Leydig, Sertoli and germ cells of goat testes. • Kisspeptin plays a direct regulation role on testosterone secretion in Leydig cells. • Kisspeptin can directly stimulate Kiss1 / GPR54 mRNA expression in Leydig cells. • Kisspeptins play an autocrine role in goat Leydig cells. Kisspeptin, encoded by the Kiss1 gene, and its receptor GPR54 have a central regulatory role in the male reproduction. However, their functions in peripheral tissues, such as testes, remain unclear. This study investigated the local expressions and function of Kiss1 / GPR54 in goats' testes. The mRNA expression of Kiss1 / GPR54 in pubertal goat Leydig cells was detected through reverse transcriptase PCR (RT-PCR), and its protein expression in Leydig cells or the testis was examined by immunohistochemistry and Western blot analysis. Isolated and cultured Leydig cells were treated with different concentration of kisspeptin (0, 1, 10 and 100 μM) and kisspeptin antagonist for 4, 24 or 72 h. The direct effect of kisspeptin on testosterone secretion and Kiss1 / GPR54 mRNA expression was evaluated by ELISA and RT-PCR. Kiss1 / GPR54 mRNA and protein were expressed in Leydig cells and spermatids, and GPR54 were expressed in Sertoli cells. Kisspeptin treatment significantly stimulated testosterone secretion in Leydig cells, with the highest levels found under 24 h of treatment with 10 μM kisspeptin. Treatment with kisspeptin + kisspeptin antagonist significantly reduced the kisspeptin-stimulated testosterone secretion in Leydig cells. Kisspeptin treatment significantly enhanced the expression of Kiss1 / GPR54 mRNA in Leydig cells. These data suggest the local expressions of Kiss1 / GPR54 in goats' testes and its autocrine role in Leydig cells, which is helpful in understanding the regulation role of kisspeptin/GPR54 system in other peripheral tissues. [ABSTRACT FROM AUTHOR]