Identification and Function Prediction of Novel MicroRNAs in Laoshan Dairy Goats

Ji, Zhibin; Wang, Guizhi; Zhang, Chunlan; Xie, Zhijing; Liu, Zhaohua; Wang, Jianmin

doi:10.5713/ajas.2012.12422

Cited by 12 publications

(12 citation statements)

References 24 publications

(25 reference statements)

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“…In the present study, mammary gland tissues in early, peak and late lactation periods from five dairy goats were selected, and sequenced based on the Illumina HiSeq™ 2000 platform. To better connect with our previous study [17,18], and the integrated analysis of multiomics data in the next step, the method of mixing pools of samples in the same period was also adopted in the current study. According to the quality control results, the construction and sequencing were successful, high quality data were obtained in three libraries, and 2381 lncRNAs and 37,249 mRNAs were identified.…”

Section: Discussionmentioning

confidence: 99%

“…In our previous studies, miRNAomics and transcriptomics of dairy goat mammary glands at different lactating stages were analyzed using RNA sequencing [17,18]. In the current study, for enhanced identification and characterization of the lncRNA profiles and function at the genome level, dairy goat mammary gland tissues in early lactation ((10th day after parturition), peak lactation (90th day after parturition) and late lactation (210th day after parturition) were collected, and the distribution, expression abundance and differential expression patterns of lncRNAs among different lactating periods of mammary gland development were tested and identified.…”

Section: Introductionmentioning

confidence: 99%

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Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Chao

Liu

et al. 2020

BMC Genomics

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Background: The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined. Result: In the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism. Conclusions: Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Chao

Liu

et al. 2020

BMC Genomics

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“…In China, dairy goats are mainly distributed in the northern region, and more concentrated, mainly in Shandong, Shaxi, Hebei, Henan, Xinjiang, Inner Mongolia, and other provinces. Laoshan dairy goat, with the characteristic of strong adaptability, roughage resistance and good quality milk, is an important domestic animal in Chinese agricultural industry due to its use in milk and meat production(Ji et al., ).…”

Section: Introductionmentioning

confidence: 99%

Milk compositional changes of Laoshan goat milk from partum up to 261 days postpartum

Chen

Zhao

et al. 2018

Animal Science Journal

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Despite the global increasing demand for goat milk, no data exist on the nutrient potential of Laoshan goat milk and limited information exists on its composition according to lactation period. In this study, the measured indicators, including dry matter, protein, immunoglobulin, lactoferrin, fat, ash, lactose, calcium, titratable acidity and pH from partum to 261 days postpartum of Laoshan goat milk, followed the same law of change. There was a significant difference over the first 5 days postpartum, after which no significant difference was observed until days 225 postpartum. However, days 255 postpartum was like a turning point, after which their values showed either an increasing or decreasing trend. We concluded that the colostrum for Laoshan dairy goat was considered from days 1 to 5 postpartum and after 5 days it was as transitioned to milk when all measured parameters were according to the normal ranges as described in this study. This work provided updated information on the current nutritive characteristics of Laoshan goat milk, which may be of importance in the fields of milk production, food technology, and nutritional mutual replenishment.

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“…In the present study we focused on Laoshan dairy goats4. They have the characteristics of seasonal estrus, milk yields reaching up to 800 kg in 270 days, litter sizes averaging 1.7 kids, and are mainly distributed in the eastern part of Shandong Province in China412. We selected extreme populations in order to help disseminate the genetic differences.…”

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confidence: 99%

Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus)

Lai

Zhai²,

Cheng

et al. 2016

Sci Rep

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Dairy goats are one of the most utilized domesticated animals in China. Here, we selected extreme populations based on differential fecundity in two Laoshan dairy goat populations. Utilizing deep sequencing we have generated 68.7 and 57.8 giga base of sequencing data, and identified 12,458,711 and 12,423,128 SNPs in the low fecundity and high fecundity groups, respectively. Following selective sweep analyses, a number of loci and candidate genes in the two populations were scanned independently. The reproduction related genes CCNB2, AR, ADCY1, DNMT3B, SMAD2, AMHR2, ERBB2, FGFR1, MAP3K12 and THEM4 were specifically selected in the high fecundity group whereas KDM6A, TENM1, SWI5 and CYM were specifically selected in the low fecundity group. A sub-set of genes including SYCP2, SOX5 and POU3F4 were localized both in the high and low fecundity selection windows, suggesting that these particular genes experienced strong selection with lower genetic diversity. From the genome data, the rare nonsense mutations may not contribute to fecundity, whereas nonsynonymous SNPs likely play a predominant role. The nonsynonymous exonic SNPs in SETDB2 and CDH26 which were co-localized in the selected region may take part in fecundity traits. These observations bring us a new insights into the genetic variation influencing fecundity traits within dairy goats.

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Identification and Function Prediction of Novel MicroRNAs in Laoshan Dairy Goats

Cited by 12 publications

References 24 publications

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

Milk compositional changes of Laoshan goat milk from partum up to 261 days postpartum

Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus)

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