论文题名(中文): | 基于群体基因组学揭示产热相关基因PRDM16的突变与家养牛耐寒性的关系 |
作者: | |
学号: | 2017001052 |
保密级别: | 公开 |
论文语种: | chi |
学科代码: | 090501 |
学科名称: | 农学 - 畜牧学 - 动物遗传育种与繁殖 |
学生类型: | 博士 |
学位: | 农学博士 |
学校: | 延边大学 |
院系: | |
专业: | |
第一导师姓名: | |
第一导师学校: | |
论文完成日期: | 2022-06-01 |
论文答辩日期: | 2022-05-22 |
论文题名(外文): | Population genomics reveal that the relationship between the thermogenesis related gene PRDM16 mutation and cold tolerance in domestic cattle |
关键词(中文): | |
关键词(外文): | Population genomics Cattle Cold tolerance PRDM16 Brown adipose tissue |
论文文摘(中文): |
哺乳动物是恒温动物,它们需要恒定的体温来确保最佳的生活状态。这就给哺乳动物颤抖性产热和非颤抖性产热在内的产热系统带来了巨大的选择压力。在中国,由于南北方的纬度相差大,造成年平均气温相差较大,导致许多物种生活在不同的温度环境中,包括家养牛在内。在夏季,中国南方地区的温度明显高于北方地区,这使中国南方牛被暴露在极热的环境中,相反,北方牛的生活环境比较凉爽。在冬季,中国北方地区的温度比南方地区的温度低的很多,因此中国北方的牛暴露在极冷的生活环境中,相比中国北方牛,南方牛的生活环境相对温和。这些生活环境恰好驱动了北方牛可以抵抗急剧寒冷环境和南方牛可以抵抗炎热环境的特性。与牛耐热性研究相比,目前关于牛耐寒性调控机制的研究很少。然而,犊牛出生时的冷应激导致的新生犊牛死亡率是全世界寒冷地区养牛业关注的主要问题,它对畜牧业造成了巨大的经济损失,而且在畜牧业发展中带来了的一个主要的难题。因此,筛选与产热相关基因的SNP标记将为家养牛的遗传育种提供策略并减少寒冷暴露所引起的死亡率。为了探讨家养牛对环境温度的适应性机制,本研究利用全基因组重测序技术探索了家养牛产热相关候选基因,主要研究内容如下: 1. 对28头分布在中国寒冷地区和温暖地区牛(14头南方牛和14头北方牛)进行了全基因组重测序。通过群体遗传学分析(进化树构建,PCA分析,LD分析和群体结构分析)和种群历史重建(PSMC),确定了北方和南方牛可以分别组成两个遗传簇,并且,两种种群的祖先有效群体大小在5千年和7万年前呈现最高值,3千年和4万年前呈现出最小值。 2. 为了揭示耐寒品种的产热相关通路中潜在的选择候选基因,首先按50 kb窗口,25 kb步长进行划窗,计算每个窗口内的FST值,取前5%的FST值,识别为高度分化区域。高度分化区域中被识别出的基因外显子区域非同义SNPs进行Fisher’s精确检验,取q < 0.01为最终候选基因。通过对寒冷地区和温暖地区牛基因组进行选择性扫描获得了197个候选基因,并发现一些产热相关通路中的基因受到选择作用。其中,只有2个候选基因(PRDM16和CPT2)是与产热通路相关的,而且可以促进产热关键因子UCP1的候选基因—PRDM16为排名最靠前(FST = 0.52,Fisher’s exact test P = 3.76 × 10-11)。 3. 通过PRDM16的SNPs 系统发育树分析揭示出耐寒牛和非耐寒牛PRDM16基因的不同进化历史,同时在耐寒牛和非耐寒牛之间发现了一共5个非同义SNVs,其中最高的突变率达到了93%(c.2336 T > C, p. L779P)。我们通过比较耐寒牛,非耐寒牛和不同物种PRDM16该位点的基因序列,得到了耐寒牛的基因型(PRDM16 779L)与拥有完整的棕色脂肪功能的物种相同(小鼠,大鼠和仓鼠),而非耐寒牛的基因型(PRDM16 779P)与不完整或者没有棕色脂肪功能的物种相同(羊,猪,鲸,马和人等),发现PRDM16基因的突变模式(c.2336 T > C, p. L779P)在全球范围的牛基因组中也是相同的。 4. 利用3T3-L1细胞构建了耐寒牛基因型PRDM16 和非耐寒牛基因型PRDM16 MU(c.2336 T > C, L779P mutation of PRDM16)过表达细胞系,并进行了棕色化分化。结果发现,虽然两组之间的形态学特征上没有差异,但PRDM16 MU组在棕色脂肪相关基因的mRNA水平(C/EBPb, PGC1-a, CIDEA, UCP1)与蛋白水平(UCP1)上明显低于PRDM16组;发现了PRDM16的突变(p.L779P)会导致基因功能受损,最终影响了非耐寒牛棕色脂肪细胞的形成,表明该基因在耐寒性方面发挥了重要作用。 总之,我们的结果为研究牛对环境温度变化的适应性机制提供了理论基础,为家养牛的遗传育种提供了更有效的策略。 |
文摘(外文): |
Temperature is one of the most important environmental factors that drive evolutionary changes in diverse organisms. Mammals are endotherms; they require a constant body temperature to ensure optimal biological activity. This leads to strong selection pressure on the heat production system, including shivering and non-shivering thermogenesis. In China, due to the large latitude difference between the South and north, the annual average temperature is greatly different. Therefore, there is a vast difference in the annual average temperature of the habitats among mammals and the domestication, including cattle. In summer, southern cattle are exposed to extreme heat environment compared to northern cattle, and in winter, northern cattle are exposed to extreme cold environment compared to southern cattle. These living conditions just drive the characteristics that resistance of northern cattle can tolerant extremely cold environment and southern cattle can tolerant extremely hot environment. Compared with the research on heat tolerance of cattle, there are few studies on the regulation mechanism of cold tolerance of cattle. 1. We sequenced genomes of 28 cattle, including 14 cold-tolerant cattle lineages (annual average temperature of habitat: 2–6℃) and 14 cold-intolerant cattle lineages (annual average temperature of habitat: 20–25℃). The Neighbor-joining trees, PCA, LD and population structure analysis were clearly indicated that cattle samples could be classified into northern and southern groups and PSMC analysis showed two bottlenecks and two expansions, with population peaks at ~50 and ~700 kilo years ago (Kya) and population bottlenecks at ~30 and 400 Kya, respectively. 2. Selective sweeps analyses were performed over whole genomes based on the distribution of population-differentiation statistic (FST) values. First, we identified highly differentiated regions using FST, and then determined the top 5% calculated in 50 kb windows in 25 kb steps. Then, final candidate genes were determined and ranked using Fisher’s exact test (q < 0.01). A total of 197 candidate genes had strong selective sweep signals and Among genes with signals of selective sweep, two candidate genes (PRDM16 and CPT2) were involved in thermogenesis; PRDM16 was of the most interest as it is known to increase thermogenesis by promoting the expression of the key gene UCP1. PRDM16 had the lowest P-value (Fisher’s exact test P = 3.8×10-11) and the highest FST (0.52) among genes related to thermogenesis. 3. The PRDM16 genotypes found in northern and southern cattle were well-distinguished and consistent with the phylogenetic tree created using the SNPs of this gene. We discovered five nonsynonymous single nucleotide variants (SNVs), of which one (c.2336 T > C, p.L779P) was found at a higher level (93%) in southern cattle than northern cattle. we compared the PRDM16 protein sequences to other species, and found that the substitution that occurred at position Leu779 of the PRDM16 gene in northern cattle is the same as that in species that have complete BAT function (e.g., mouse, rat, and hamster). Conversely, the substitution in southern cattle, which is proline, was the same as that in species with an incomplete or null BAT function (sheep, pig, whale, horse, platypus, elephant, sirenian, marsupial, human and rabbit). Moreover, we also explored the genetic pattern of these substitutions (c.2336 T > C, p.L779P) across cattle genomes worldwide, and found that cattle in cold regions have a high frequency of the c.2336 C > T mutation, consistent with the pattern in China. 4. In biochemical experiment, despite the similar differentiation efficiency between the two ectopic PRDM16-overexpressing groups, the mRNA expression levels of four BAT-selective genes (UCP1, C/EBPb, PGC1-a, and CIDEA) were significantly lower in the PRDM16 MU (c.2336 T > C, L779P mutation of PRDM16) group than in the PRDM16 group. Moreover, overexpression of PRDM16 increased UCP1 expression to a much greater degree than PRMD16 MU. In general, on the one hand, well-functioning PRDM16 in northern cattle is required to resist extreme cold, and on the other, the functional inactivation of PRDM16 impairs beige adipocyte formation, which is beneficial for the environmental adaptability of southern cattle. These results could improve understanding of adaptive genetic variations in cattle and other livestock species living in regions different temperatures. |
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开放日期: | 2022-06-11 |