Analysis of four complete linkage sequence variants within a novel lncRNA located in a growth QTL on chromosome 1 related to growth traits in chickens
Analysis of four complete linkage sequence variants within a novel lncRNA located in a growth QTL on chromosome 1 related to growth traits in chickens
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DOI：
10.1093/jas/skaa122
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发表时间：
2020-05-01
影响因子：
3.3
通讯作者：
Li, Zhuanjian
中科院分区：
文献类型：
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作者：
Li, Wenya;Jing, Zhenzhu;Li, Zhuanjian
越来越多的研究表明，不同鸡品种和群体中1号染色体末端的数量性状位点（qtl）对鸡的生长性状有重要影响。然而，QTL效应背后的因果基因仍然知之甚少。利用更新的基因数据库，在1号染色体末端发现了一个新的lncRNA（命名为LncFAM），位于生长和消化QTL中。本研究发现，LncFAM在高体重胰腺组织中的表达水平显著高于低体重胰腺组织，说明LncFAM的表达水平与生长速度、体重等多种生长表型指标呈正相关。多态性筛选在LncFAM中发现了4个具有强连锁不平衡的多态性：第二个外显子的5-bp突变，A/G碱基突变，以及第二个内含子的7-bp和97-bp突变。97 bp的研究在第二内含子插入使用一个F2资源人口由安卡和固始鸡鸡表明,突变基因型个体的二值最高的体重(BW)在0天,2,4,6,8,10,12周,柄周长(SG) 4、8和12周,胸宽(CW) 4、8和12周,身体倾斜长度在8 - 12周(声波测井),和骨盆宽度(PW) 4、8和12周,其次是ID和DD基因型。对F2鸡资源群体、西川乌骨鸡、鲁氏绿壳鸡、东乡绿壳鸡、长顺绿壳鸡、固始鸡等双型鸡和罗斯308、AA、科布、哈贝德等商品肉鸡2716只鸡进行扩增分型，结果表明ⅱ型为优势基因型。有趣的是，在商业肉鸡的测试群体中只存在基因型II。罗斯308鸡胰腺组织中的表达量显著高于固始鸡胰腺组织（P < 0.001），这可能与不同鸡间的转化率有关。对LncFAM靶基因的预测和验证表明，LncFAM可能通过顺式表达调控其靶基因FAM48A的表达。我们的结果为LncFAM的突变提供了有用的信息，可以作为潜在的分子育种标记。
An increasing number of studies have shown that quantitative trait loci (QTLs) at the end of chromosome 1 identified in different chicken breeds and populations exert significant effects on growth traits in chickens. Nevertheless, the causal genes underlying the QTL effect remain poorly understood. Using an updated gene database, a novel lncRNA (named LncFAM) was found at the end of chromosome 1 and located in a growth and digestion QTL. This study showed that the expression level of LncFAM in pancreas tissues with a high weight was significantly higher than that in pancreas tissues with a low weight, which indicates that the expression level of LncFAM was positively correlated with various growth phenotype indexes, such as growth speed and body weight. A polymorphism screening identified four polymorphisms with strong linkage disequilibrium in LncFAM: a 5-bp indel in the second exon, an A/G base mutation, and 7-bp and 97-bp indels in the second intron. A study of a 97-bp insertion in the second intron using an F2 chicken resource population produced by Anka and Gushi chickens showed that the mutant individuals with genotype II had the highest values for body weight (BW) at 0 days and 2, 4, 6, 8, 10 and 12 weeks, shank girth (SG) at 4, 8 and 12 weeks, chest width (CW) at 4, 8 and 12 weeks, body slant length (BSL) at 8 and 12 weeks, and pelvic width (PW) at 4, 8 and 12 weeks, followed by ID and DD genotypes. The amplification and typing of 2,716 chickens from ten different breeds, namely, the F2 chicken resource population, dual-type chickens, including Xichuan black-bone chickens, Lushi green-shell layers, Dongxiang green-shell layers, Changshun green-shell layers, and Gushi chickens, and commercial broilers, including Ross 308, AA, Cobb and Hubbard broilers, revealed that II was the dominant genotype. Interestingly, only genotype II existed among the tested populations of commercial broilers. Moreover, the expression level in the pancreas tissue of Ross 308 chickens was significantly higher than that in the pancreas tissue of Gushi chickens (P < 0.001), which might be related to the conversion rates among different chickens. The prediction and verification of the target gene of LncFAM showed that LncFAM might regulate the expression of its target gene FAM48A through cis-expression. Our results provide useful information on the mutation of LncFAM, which can be used as a potential molecular breeding marker.