Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, People's Republic of China.
College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China.
Sci Rep. 2024 Oct 24;14(1):25184. doi: 10.1038/s41598-024-76685-3.
This study was performed on Micropterus salmoides to determine growth-linked gene and single nucleotide polymorphism (SNP) markers under carbohydrate diet and varying temperature through RNA-seq and whole-genome re-sequencing. The results showed that growth-related genes were primarily enriched in the fat digestion and absorption signaling pathway, playing a role in lipid transport and metabolism. Fatty acid binding protein 6, bile salt-activated lipase-like, lysophosphatidylcholine acyltransferase 2, phospholipase A2, minor isoenzyme-like, and phospholipase A2, group IB (pancreas) were identified as the crucial genes. The differentially expressed genes between high and low temperatures were enriched in the pentose phosphate pathway, with carbohydrate transport and metabolism were most affected by temperature. Major facilitator superfamily domain containing 10, phosphogluconate dehydrogenase, fructose-1,6-bisphosphatase 1a, and spinster homolog 3 transcript variant X1(spns3) were the shared genes affected by temperature. From all the common genes, 10 growth-associated SNP markers were identified. The TT genotype at rs7781 was associated with lower body weight, while AA genotype at rs31434173 and CC genotype at rs31435313 showed positive correlation with body weight. Analogously, the GG genotype at rs31436887 and AA genotype at rs31438769 also found to characterize better growth performance. At low temperature, individuals with the AA genotype at rs11506587 and rs31435313 exhibited the slowest growth. For the genotypes labeled with rs11510589, the GG individual grew faster than the AA individual, whereas the opposite phenomenon occurred in these genotypes when labeled with rs11511314. The genotypes at rs32970704 and rs32967921 showed no growth correlation. The AA genotype at rs31435313 in spns3 had the slowest growth under a carbohydrate-rich diet regardless of the temperature. Our study presents candidate genes and SNP markers associated with growth influenced by carbohydrate and temperature, providing basis for the development of M. salmoides strain that better accepts carbohydrate diets at varying temperature.
本研究以斑点叉尾鮰为研究对象，通过 RNA-seq 和全基因组重测序，在碳水化合物饮食和不同温度下确定了与生长相关的基因和单核苷酸多态性（SNP）标记。结果表明，与生长相关的基因主要富集在脂肪消化吸收信号通路中，在脂质转运和代谢中发挥作用。鉴定出脂肪酸结合蛋白 6、胆盐激活的脂肪酶样、溶血磷脂酰基转移酶 2、磷脂酶 A2、小同工酶样和磷脂酶 A2、IB 组（胰腺）为关键基因。高温和低温之间差异表达的基因富集在戊糖磷酸途径中，碳水化合物的运输和代谢受温度影响最大。主要易化因子超级家族结构域包含 10、磷酸葡萄糖酸脱氢酶、果糖-1,6-二磷酸酶 1a 和旋毛虫同源物 3 转录变体 X1（spns3）是受温度影响的共享基因。从所有常见基因中，鉴定出 10 个与生长相关的 SNP 标记。rs7781 的 TT 基因型与体重较低相关，而 rs31434173 的 AA 基因型和 rs31435313 的 CC 基因型与体重呈正相关。类似地，rs31436887 的 GG 基因型和 rs31438769 的 AA 基因型也被发现具有更好的生长性能。在低温下，rs11506587 和 rs31435313 基因型为 AA 的个体生长最慢。对于标记为 rs11510589 的基因型，GG 个体比 AA 个体生长更快，而在标记为 rs11511314 的基因型中则相反。rs32970704 和 rs32967921 的基因型与生长无相关性。spns3 中 rs31435313 的 AA 基因型在富含碳水化合物的饮食下无论温度如何生长速度都最慢。本研究提供了与碳水化合物和温度影响生长相关的候选基因和 SNP 标记，为开发在不同温度下更好地接受碳水化合物饮食的斑点叉尾鮰品系提供了基础。
