Nerve Growth Factor gene ovarian expression, polymorphism identification, and association with litter size in goats

Thomas, Naicy; Venkatachalapathy, R. Thirupathy; Aravindakshan, T. V.; Radhika, G.; Raghavan, K.C.; Mini, M.; Shyama, K.

doi:10.1016/j.theriogenology.2016.07.011

Cited by 23 publications

(8 citation statements)

References 24 publications

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“…Currently, natural genetic variations are divided into three forms: SNPs (single nucleotide polymorphisms), indels and SVs (larger structural variants; Julienne et al, 2010 ). Unlike other genetic variations, indels can be directly detected by simple PCR amplification and agarose gel electrophoresis, making them convenient and practical (Naicy et al, 2016 ). Therefore, indel variants in the KDM6A gene were identified and their associations with first-born litter size investigated in a large commercial population of 2,326 Shaanbei white cashmere goats.…”

Section: Discussionmentioning

confidence: 99%

“…Improvements in female fertility are of critical importance for the goat industry. As one of the most important factors restricting female fertility, increasing litter size has received much more consideration (Naicy et al, 2016 ; Yang et al, 2017 ). However, litter size is a trait with low heritability in many livestock animals, including pigs (Córdoba et al, 2015 ) and goats (Shaat and Mäki-Tanila, 2009 ); therefore, traditional direct selection is ineffective.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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“…SNPs in NCOA1 were associated with litter size in Icelandic sheep [21]. Two SNPs in NGF were associated with litter size in goat [39]. In accordance with these studies, seven SNPs ( KIT : g.70199073A>G, KITLG : g.124520653G>C, ADAMTS1 : g.127753565T>C, ADAMTS1 : g.127754640G>T; NCOA1 : g.31928165C>T, NCOA1 : g.32140565G>A, and NGF : g.91795933T>C) in five genes were significantly associated with litter size in Hu sheep or Small-tailed Han sheep.…”

Section: Discussionmentioning

confidence: 99%

Association of Polymorphisms in Candidate Genes with the Litter Size in Two Sheep Breeds

Yuan

Zhang

et al. 2019

Animals

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Simple SummaryIncreasing litter size is critical for the intensive sheep production system. Genetic marker-assisted selection (MAS) based on proven molecular indicators could enhance the efficacy of sheep selection with improving litter size traits. Many single nucleotide polymorphisms (SNPs) linked with litter size in Hu sheep and Small-tailed Han sheep have been identified. However, they usually explain a small portion of genetic variation and additional genetic markers linked with litter size have not been found. The present study investigated the potential SNPs in ten genes as candidate markers for improved litter size in sheep. As a result, nine SNPs in six out of ten genes can be served as useful genetic markers to improve the selection of litter size since they are significantly associated with litter size either in Hu sheep or Small-tailed Han sheep. Further, a combined haplotypes analysis of the two loci (LIFR: g.35862868C>T and LIFR: g.35862947G>T) revealed that H2H3 (CTTT) combined haplotypes had the largest litter size than the rest combined haplotypes and more than those with either mutation alone in Small-tailed Han sheep. Our knowledge is essential to implement the MAS in sheep and further to increase the profitability in the sheep industry.AbstractHu sheep and Small-tailed Han sheep are the most widely raised and most famous maternal sheep breeds in China, which are known for precocious puberty, perennial oestrus and high fecundity (1–6 lambs each parity). Therefore, it is crucial to increase litter size of these two breeds for intensive sheep industry. The objective of this study was to identify potential genetic markers linked with sheep litter size located at ten genes. This study collected blood sample of 537 Hu sheep and 420 Small-tailed Han sheep with litter size of first parity. The average litter sizes in Hu sheep and Small-tailed Han sheep were 2.21 and 1.93. DNA-pooling sequencing method was used for detecting the potential single nucleotide polymorphisms (SNPs) in ten genes related to follicle development and female reproduction. SNPscan® was used for individually genotyping. As a result, a total of 78 putative SNPs in nine out of ten candidate genes (except NOG) were identified. In total, 50 SNPs were successfully genotyped in Hu sheep and Small-tailed Han sheep. After quality control, a total of 42 SNPs in Hu sheep and 44 SNPs in Small-tailed Han sheep were finally used for further analysis. Association analysis revealed that nine SNPs within six genes (KIT: g.70199073A>G, KITLG: g.124520653G>C, ADAMTS1: g.127753565T>C, ADAMTS1: g.127754640G>T, NCOA1: g.31928165C>T, NCOA1: g.32140565G>A, LIFR: g.35862868C>T, LIFR: g.35862947G>T and NGF: g.91795933T>C) were significantly associated with litter size in Hu sheep or Small-tailed Han sheep. A combined haplotypes analysis of the two loci (LIFR: g.35862868C>T and LIFR: g.35862947G>T) revealed that H2H3 (CTTT) combined haplotypes had the largest litter size than the rest combined haplotypes and more than those with either mutation alone in Sma...

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“…The main genetic variations are insertion/deletions (indels), SNPs, and CNVs, among others. Among them, insertion/deletions (indels) are easily identified by simple PCR amplification and agarose gel electrophoresis [20], and extensively exist in eukaryotic genomes. Indels were used in marker-assisted selection (MAS), forming a convenient and efficient method for breeding selection that is not affected by the environment [21].…”

Section: Introductionmentioning

confidence: 99%

Detection of a 4 bp Mutation in the 3′UTR Region of Goat Sox9 Gene and Its Effect on the Growth Traits

Wang

et al. 2020

Animals

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The SRY-type HMG box 9 (Sox9) gene plays an important role in chondrocyte development as well as changes in hypertrophic chondrocytes, indicating that Sox9 can regulate growth in animals. However, no studies to date have examined the correlation between variations in Sox9 and growth traits in goats. Here, we found a 4 bp indel in the 3′UTR of Sox9 and verified its association with growth traits in Shaanbei white cashmere goats (n = 1109). The frequencies of two genotypes (ID and II) were 0.397 and 0.603, respectively, and polymorphic information content (PIC) values showed that the indel had a medium PIC (PIC > 0.25). The 4 bp indel was significantly correlated with body length (p = 0.006), heart girth (p = 0.001), and hip width (p = 4.37 × 10 −4). Notably, individuals with the ID genotype had significantly superior phenotypic traits compared with individuals bearing the II genotype. Hence, we speculated that the 4 bp indel is an important mutation affecting growth traits in goat, and may serve as an effective DNA molecular marker for marker-assisted selection in goat breeding programs.

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Nerve Growth Factor gene ovarian expression, polymorphism identification, and association with litter size in goats

Cited by 23 publications

References 24 publications

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

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

Association of Polymorphisms in Candidate Genes with the Litter Size in Two Sheep Breeds

Detection of a 4 bp Mutation in the 3′UTR Region of Goat Sox9 Gene and Its Effect on the Growth Traits

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