Insertion/Deletion Within the KDM6A Gene Is Significantly Associated With Litter Size in Goat

Abstract

A previous whole-genome association analysis identified lysine demethylase 6A (KDM6A), which encodes a type of histone demethylase, as a candidate gene associated to goat fecundity. KDM6A gene knockout mouse disrupts gametophyte development, suggesting that it has a critical role in reproduction. In this study, goat KDM6A mRNA expression profiles were determined, insertion/deletion (indel) variants in the gene identified, indel variants effect on KDM6A gene expression assessed, and their association with first-born litter size analyzed in 2326 healthy female Shaanbei white cashmere goats. KDM6A mRNA was expressed in all tissues tested (heart, liver, spleen, lung, kidney, muscle, brain, skin and testis); the expression levels in testes at different developmental stages [1-week-old (wk), 2, 3 wk, 1-month-old (mo), 1.5 and 2 mo] indicated a potential association with the mitosis-to-meiosis transition, implying that KDM6A may have an essential role in goat fertility. Meanwhile, two novel intronic indels of 16 bp and 5 bp were identified. Statistical analysis revealed that only the 16 bp indel was associated with first-born litter size (P < 0.01), and the average first-born litter size of individuals with an insertion/insertion genotype higher than that of those with the deletion/deletion genotype (P < 0.05). There was also a significant difference in genotype distributions of the 16 bp indel between mothers of single-lamb and multi-lamb litters in the studied goat population (P = 0.001). Consistently, the 16 bp indel also had a significant effect on KDM6A gene expression. Additionally, there was no significant linkage disequilibrium (LD) between these two indel loci, consistent with the association analysis results. Together, these findings suggest that the 16 bp indel in KDM6A may be useful for marker-assisted selection (MAS) of goats.

Nucleotide variants in prion-related protein (testis-specific) gene (PRNT) and effects on Chinese and Mongolian sheep phenotypes

“…Polymorphism information content (PIC) was calculated by Nei's method implemented in the GDIcall Online Calculator (http://www.msrcall.com/ Gdicall.aspx) [20]. Distribution differences for genotypic and allelic frequencies among/between different breeds were calculated with the x2 test implemented in SPSS (Version 18.0, IBM Corp., Armonk, NY, USA) [21]. Additionally, linkage equilibrium on the population of the seven pairs of alleles and haplotypes of seven polymorphic loci were also analyzed (http:// analysis.bio-x.cn) [22][23].…”

“…When necessary, the Bonferroni correction for multiple comparisons was performed. Particularly, data that did not follow a normal distribution and homogeneity of variances were analyzed by the non-parametric (Kruskal-Wallis) test in SPSS (version 18.0) [21]. P < 0.05 was considered to indicate statistical significance and all statistical tests were two-sided.…”

Detection of insertion/deletions (indels) of the &lt;i&gt;ATBF1&lt;/i&gt; gene and their effects on growth-related traits in three indigenous goat breeds

“…The AT motif-binding factor (ATBF1), also known as zinc finger homeobox 3 (ZFHX3), is a crucial cancer suppressor gene. It is worth mentioning that ATBF1 could promote the expression levels of the growth hormone prolactin and TSH-β by binding to the enhancers of POU1F1 (also known as Pit1) and PROP1 (Darling et al, 1998;Qi et al, 2008;Araujo et al, 2013;Yan et al, 2018). These studies showed that the ATBF1 gene was hypothesized to produce important effects on cell differentiation and early development, suggesting that the ATBF1 gene would affect the growth traits in animals.…”

Association of a new 99-bp indel of the CEL gene promoter region with phenotypic traits in chickens

“…Interspecific comparisons of genes and proteins have shown that the CEL gene retains essentially similar properties, structures and key sequences across species 12 . Previous studies have shown that variable numbers of tandem repeat (VNTR) mutations and copy number variants (CNVs) located in CEL exon 11 can lead to MODY-pancreatic exocrine syndrome 3,13,14 , alcoholic cirrhosis 15 , insulin-dependent diabetes mellitus or noninsulin dependent diabetes mellitus 13 , pancreatic cancer 16 , alcoholic pancreatitis and other pancreatic exocrine diseases 17,18 .The above facets of the role and mutation of CEL in mammalian species have been extensively studied; however, although high CEL expression in layer chickens has been found only in pancreatic tissues 19 , no research on CEL gene mutations in chickens and livestock has yet been reported.Insertion/deletion (indel) is one of the main sources of molecular-level evolutionary variation, and has been used widely as a major molecular marker in the study of economic traits in livestock and poultry 20,21 . Chickens are an economically important poultry species, prompting great interest in improving the qualitative and quantitative traits of poultry 22 .…”

“…Insertion/deletion (indel) is one of the main sources of molecular-level evolutionary variation, and has been used widely as a major molecular marker in the study of economic traits in livestock and poultry 20,21 . Chickens are an economically important poultry species, prompting great interest in improving the qualitative and quantitative traits of poultry 22 .…”