Two strongly linked single nucleotide polymorphisms (Q320P and V397I) in GDF9 gene are associated with litter size in cashmere goats

Guo

et al. 2020

Animals

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Simple Summary: Genome-wide association studies found that the PR/SET Domain 6 (PRDM6) gene mutation was associated with bone development, bone density, and body mass index. This study found a 12 bp deletion variation within the PRDM6 gene in Shaanbei white cashmere goats in a large sample size (n = 1044). This variation polymorphism was associated with multiple goat growth traits in the yearling period, including heart girth (p = 0.027), cannon circumference (p = 0.008), chest depth (p = 2.10 × 10 −5 ), chest width (p = 0.004), body height (p = 0.032), body length (p = 0.044), and hip-width (p = 0.014). The effects of the 12 bp variation were found to make no difference on adult goat growth traits. Taken together, these results demonstrate that the 12 bp deletion variant plays an important role in the early growth and development of goats and could be considered as a useful and effective molecular marker for goat breeding selection in the growth stage.Abstract: By genome-wide association studies, the PRDM6 gene has been shown to affect multiple, apparently unrelated inherited traits, including bone density and body mass index. Therefore, it is considered a potentially pleiotropic gene. In this study, we identified a 12 bp deletion variant (NC_030814.1:rs651603667, g: 79985625-79985636delTTGACTGATCCA) within the PRDM6 gene in a large sample (SBWC goats; n = 1044). All goat samples were collected in Shaanxi province in July 2018. The frequency of the wt allele was higher than the frequency of the del allele, and this mutation polymorphism confirmed to be consistent with the Hardy-Weinberg equilibrium (p > 0.05). Further results showed that in a group of goats in the yearling period (18 months old, n = 567), this deletion variant of the PRDM6 gene was associated with heart girth (p = 0.027), cannon circumference (p = 0.008), chest depth (p = 2.10 × 10 −5 ), chest width (p = 0.004), body height (p = 0.032), body length (p = 0.044) and hip-width (p = 0.014). For adult SBWC goats (36 months old, n = 477), the effects of the 12 bp variation on growth-related traits were found to make no difference. These findings show that the 12 bp deletion within the goat PRDM6 gene plays an important role in the early growth and development of goats. Using the 12 bp mutation, breeders can quickly and effectively select excellent individual goats at an early stage.

Section: Introductionmentioning

confidence: 99%

Screening of Deletion Variants within the Goat PRDM6 Gene and Its Effects on Growth Traits

Guo

et al. 2020

Animals

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“…Many reports have proved different gene mutation sites could regulate phenotypes of organism through LD (Gibson et al, 2013;Lynch et al, 2014;Wang et al, 2019). Based on multiplex PCR method and LD analysis, this study first discovered CFAP69-P4 and CFAP69-P6 were in complete LD (D' = 0.999, r 2 = 1.000) (Fig.1), suggesting there was certain combination of these two loci in the process of SBWC goat evolutionary selection.…”

Section: Discussionmentioning

confidence: 67%

“…Population indexes (Ho, homozygosity; He, heterozygosity; PIC, polymorphism information content) were calculated following Nei's methods (Nei, 1973). The chi-square (χ 2 ) test and hardy-Weinberg equilibrium (HWE) were performed using SHEsis (http://analysis.bio-x.cn) and Linkage disequilibrium (LD) structure was evaluated across these five indel mutations (Wang et al, 2019). The r 2 value was known as a pairwise measure of LD.…”

Section: Discussionmentioning

confidence: 99%

Detection of genetic variations of five MMAF-related genes and their associations with litter size in goat

Peng

et al. 2019

Preprint

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Background: Multiple morphological abnormalities of the sperm flagella (MMAF) makes an assignable contribution to male infertility, including QRICH2 , CFAP43 , CFAP44 , CFAP69 , CCDC39 , AKAP4 and DNAH1 gene. This work studied 28 putative indel mutations of MMAF related genes including QRICH2 , CFAP69 , CFAP43 , CCDC39 and DNAH1 gene and their correlation with the first-born litter sizes of 769 Shaanbei white cashmere (SBWC) goats. Results: Electrophoresis and DNA sequencing analysis showed the 11-bp indel within QRICH2 ( QRICH2 -P4), the three indel variations in CFAP69 ( CFAP69 -P4, CFAP69 -P6 and CFAP69 -P7) and the 27-bp indel of DNAH1 ( DNAH1 -P1) were found to be polymorphic. The 27-bp indel variation within DNAH1 was not in consistent with HWE and the other four indel of QRICH2 and CFAP69 were in consistent with HWE. The linkage disequilibrium (LD) analysis showed the 8-bp indel ( CFAP69 -P4) and the 6-bp indel ( CFAP69- P6) within CFAP69 were in complete LD with each other (D'=0.99, r 2 =1.00). The 27-bp indel mutation within DNAH1 was strongly significantly associated with first-born litter sizes of SBWC goats ( P ＜0.01) and the average litter size of II genotype was significantly greater than ID and DD genotypes ( P = 0.003). In single-lamb and multi-lamb of goat groups, the genotype distributions of the 27-bp indel was significantly different ( P = 0.002). While the 11-bp indel variation of QRICH2 and three indel mutations (P4, P6 and P7) of CFAP69 identified were not ( P ＞0.05). Conclusions: These findings suggest the 27-bp indels in the goat DNAH1 can be used as an effective molecular marker for marker-assisted selection of goats reproduction breeding in the future.

“…where Y ijk is the observation of the milk performance indices, µ is the overall mean of each index, L i is the effect due to i th lactation, G j is the fixed effect of j th genotype, (LG) ij is interaction between the i th lactation and the j th genotype, and ε ijk is the random error [33]. Meanwhile, for the body measurement traits, the GLM was calculated as follows: Y il = µ + A i + G l + ε il , where Y il represents the observations of the body measurement traits, µ is the population mean, A i is the fixed effect of age, G l is the fixed effect of genotype, and ε il is the random error [39,40]. The model excluded the effects of farm, sex, and season of birth, which had no significant effects on the variation of traits in this population [40].…”

Section: Discussionmentioning

confidence: 99%

An 11-bp Indel Polymorphism within the CSN1S1 Gene Is Associated with Milk Performance and Body Measurement Traits in Chinese Goats

Zhang

Liu

et al. 2019

Animals

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Simple Summary: In the field of animal breeding, selection using molecular genetic markers, such as insertions/deletions (indels), is a novel method to reduce the generation interval and more accurately improve performance. The casein alpha s1 (CSN1S1) gene is one of the major genes regulating the milk performance of mammals, and it is also relevant to body development. Previous studies have shown that an 11-bp indel in this gene was strongly associated with goat litter size, however, its effects on milk performance and body measurement traits have not been studied. In this study, this indel was genotyped in three Chinese goat breeds, and further analysis results revealed that this indel polymorphism was significantly associated with milk performance in dairy goats, as well as affecting the body measurement traits in all three breeds. These findings hint that the 11-bp indel within CSN1S1 gene could be utilized for effectively selecting goats with excellent performances in terms of production and breeding.Abstract: The casein alpha s1 (CSN1S1) gene encodes α-s1 casein, one of the proteins constituting milk, which affects milk performance, as well as improving the absorption of calcium and bone development in mammals. A previous study found that an 11-bp insertion/deletion (indel) of this gene strongly affected litter size in goats. However, to our knowledge, the relationships between this polymorphism and the milk performance and body measurement traits of goats have not been reported. In this paper, the previously identified indel has been recognized in three Chinese goat breeds, namely the Guanzhong dairy goat (GZDG; n = 235), Shaanbei white cashmere goat (SBWC; n = 1092), and Hainan black goat (HNBG; n = 278), and the following three genotypes have been studied for all of the breeds: insertion/insertion (II), deletion/deletion (DD), and insertion/deletion (ID). The allele frequencies analyzed signified that the frequencies of the "D" allele were higher (47.8%-65.5%), similar to the previous report, which indicates that this polymorphism is genetically stable in different goat breeds. Further analysis showed that this indel was markedly associated with milk fat content, total solids content, solids-not-fat content, freezing point depression, and acidity in GZDG (p < 0.05), and also affected different body measurement traits in all three breeds (p < 0.05). The goats with II genotypes had superior milk performance, compared with the others; however, goats with DD genotypes had better body measurement sizes. Hence, it may be necessary to select goats with an II or DD genotype, based on the desired traits, while breeding. Our study Animals 2019, 9, 1114 2 of 11 provides information on the potential impact of the 11-bp indel polymorphism of the CSN1S1 gene for improving the milk performance and body measurement traits in goats.