哺乳期默拉水牛的全血转录组分析,以比较不同基因对产奶量的影响

IF 2.1 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Frontiers in animal science Pub Date : 2023-06-22 DOI:10.3389/fanim.2023.1135429
P. Sikka, Kunwar Pal Singh, I. Singh, D. Mishra, S. S. Paul, A. Balhara, J. Andonissamy, K. K. Chaturvedi, A. Rao, Anil Rai
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引用次数: 1

摘要

通过全血转录组分析,对Murrah水牛(Bubalus bubalis)的产奶性状进行了功能基因组分析,比较了产奶量高和产奶量低(5 -6胎)动物的RNA-seq数据。这些水牛反映了在后代测试计划下由极高端和低端公牛所生的女儿遗传的遗传优点,并根据估计的繁殖价值进行排名。高产、低产水牛胎次305 d的平均标准产奶量分别为2909.50L±492.63 l和1869.57±189.36L。“参考”组装数据来自一组水牛(n=16)的转录组文库,这些水牛由不同生理状态的动物组成。与“参考”组合相比,在高、低遗传优势动物的每个类别中选择的重复显示出高阶相关系数(R2=0.98)。选定水牛的序列数据,绘制在地中海水牛基因组上,揭示了差异表达基因(DEGs)通过热图和火山图得到了两类动物的明确描述,通过袖扣分析确定了超过25,000个基因。deg共包含83个下调基因和142个上调基因(p<0.05, FDR<0.05)。deg的功能分类揭示了生物过程的精细网络,主要是细胞信号传导、细胞增殖、细胞分化、RNA剪接、脂肪代谢和炎性体的产生。这些过程受TNF - α信号通路、nf - κ B信号通路和MAPK - PI3K-AKT信号通路/级联网络覆盖下的转录因子和结合蛋白调控。出现的途径揭示了代谢和细胞发育过程中非常复杂的调节,这些过程汇聚到水牛的产奶过程中。利用无创全血转录组分析方法获得高产和低产奶量水牛的分离基因表达模式,已成为一种有前途的资源,包括基因网络和蛋白质-蛋白质相互作用,主要涉及哺乳。转录因子和结合蛋白在乳腺组织的所有发育阶段促进表观遗传调控的协同作用,在最佳喂养管理下诱导乳腺生成和乳生成反应,从而促进随后的乳汁分泌。这些发现可能有助于改进育种策略,以实现默拉水牛所需的产奶量。
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Whole blood transcriptome analysis of lactating Murrah buffaloes divergent to contrasting genetic merits for milk yield
Functional genome profiling of Murrah buffaloes (Bubalus bubalis) was performed for milk-production trait by whole blood transcriptome analysis comparing RNA-seq data assembled from high and low milk producing multiparous (5 -6 parity) animals. These buffaloes reflected the genetic merit inherited as daughters born to extremely high- and low-end bulls evaluated under a progeny testing scheme and ranked by the estimated breeding value. The average standard milk yield (SMY) over the 305 d during the parity was recorded as 2909.50L ± 492.63 and 1869.57 ± 189.36L in high- and low-performance buffaloes, respectively. The “reference” assembly data was assembled from transcriptome libraries of a group of buffaloes (n=16), comprising of animals in different physiological states. Replicates selected within each category of the high and low genetic merit animals showed a correlation coefficient of high order (R2=0.98) while comparing with the `reference' assembly. The sequence data of selected buffaloes, mapped over the Mediterranean water buffalo genome, revealed differentially expressed genes (DEGs) distinctly depicted via heat maps and volcano plots obtained for two categories of animals, determining more than 25,000 genes via the Cufflink analysis. DEGs included 83 down-regulating and 142 up-regulating genes (p<0.05, FDR<0.05). Functional classification of the DEGs revealed a fine networking of biological processes, primarily cell signaling, cell proliferation, cell differentiation, RNA splicing, fat metabolism, and inflammasome generation. These processes are regulated by transcription factors and binding proteins covered under the network of TNF alpha signaling, NF-kappa B signaling and MAPK PI3K-AKT signaling pathways/ cascade emerged as main biological pathways. Emerged pathways revealed remarkably intricate tuning of metabolic and cell development processes converging into milk production in buffaloes. Segregated patterns of gene expression obtained for high and low milk producing buffaloes using the non-invasive method of whole blood transcriptome analysis has emerged as a promising resource comprising gene network and protein -protein interactions, primarily involved in lactation. Synergism of transcription factors and binding proteins promoting epigenetic regulation at all development stages of mammary tissue induce mammogenic and lactogenic responses for subsequent milk secretion under optimum feeding management. These findings may help improve breeding strategies to achieve the desired milk yield in Murrah buffaloes.
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