A 14-bp functional deletion within the CMTM2 gene is significantly associated with litter size in goat

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: Statistical Analysesmentioning

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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“…Thus, to establish optimal breeding programs, plenty of candidate genes, as well as their genetic variations should be appropriately used [4][5][6][7]. Maker-assisted selection (MAS) can satisfy the need to screen crucial genes and consider the relation between their polymorphisms and growth-related traits [8][9][10][11]. Herein, establishing a MAS system and performing candidate genes analyses will speed up the development of goat breeding [12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Myostatin (MSTN) Gene Indel Variation and Its Associations with Body Traits in Shaanbei White Cashmere Goat

Feng

et al. 2020

Animals

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Myostatin (MSTN) gene, also known as growth differentiation factor 8 (GDF8), is a member of the transforming growth factor-beta super-family and plays a negative role in muscle development. It acts as key points during pre- and post-natal life of amniotes that ultimately determine the overall muscle mass of animals. There are several studies that concentrate on the effect of a 5 bp insertion/deletion (indel) within the 5’ untranslated region (5’ UTR) of goat MSTN gene in goats. However, almost all sample sizes were below 150 individuals. Only in Boer goats, the sample sizes reached 482. Hence, whether the 5 bp indel was still associated with the growth traits of goats in large sample sizes which were more reliable is not clear. To find an effective and dependable DNA marker for goat rearing, we first enlarged the sample sizes (n = 1074, Shaanbei White Cashmere goat) which would enhance the robustness of the analysis and did the association analyses between the 5 bp indel and growth traits. Results uncovered that the 5 bp indel was significantly related to body height, height at hip cross, and chest width index (p < 0.05). In addition, individuals with DD genotype had a superior growing performance than those with the ID genotype. These findings suggested that the 5 bp indel in MSTN gene are significantly associated with growth traits and the specific genotype might be promising for maker-assisted selection (MAS) of goats.

“…DNAH1 has been reported to be associated with MMAF and Primary ciliary dyskinesia (PCD) et al (Zariwala et al, 2011;Ben Khelifa et al, 2014;Imtiaz et al, 2015). MMAF makes an assignable contribution to male infertility and recent studies have also certified some male related genes also expressed in female reproductive structure and might were able to affect female reproduction (Zariwala et al, 2011;Kang et al, 2019a;Kang et al, 2019b).…”

Section: Discussionmentioning

confidence: 99%

“…Because most traits associated with reproduction are quantitative traits with low heritability, it is difficult to improve these traits by traditional breeding selection methods (Shaat et al, 2009). On the contrary, marker-assisted selection (MAS) can bred high yields and superior quality breeding quickly to enhance economic traits (Collard et al, 2008;Kang et al, 2019b;Knorst et al, 2019). Now, natural genetic variations were divided into insertion/deletion (indel), single nucleotide polymorphism (SNP) and larger structural variants (SV) (Cui et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…According to Shen's report (Shen et al, 2019), to date, mutations in only seven genes have been determined in humans related to MMAF: QRICH2 (Glutamine Rich 2), CFAP43 (Cilia And Flagella (Baccetti et al, 2005;Merveille et al, 2011;Ben Khelifa et al,2014;Coutton et al,2015;Tang et al, 2017;Coutton et al, 2018;Dong et al, 2018;Shen et al, 2019). Recent studies have also certified some male related genes also expressed in female reproductive structure and might were able to affect female reproduction (Zariwala et al, 2011;Kang et al, 2019a;Kang et al, 2019b). Meanwhile, there were studies confirmed QRICH2, CFAP44, CFAP69, CCDC39 and DNAH1 were broad spectrum expression including in testis, ovaries and placentas (Fagerberg et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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.