Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (12): 2794-2808.DOI: 10.3969/j.issn.1004-1524.20221710
• Animal Science • Previous Articles Next Articles
LI Yanyan1(), BU Jianhua2, HAN Liyun1, WANG Chuanchuan3, MU Tong3,*(
)
Received:
2022-11-29
Online:
2023-12-25
Published:
2023-12-27
CLC Number:
LI Yanyan, BU Jianhua, HAN Liyun, WANG Chuanchuan, MU Tong. Identification and functional analysis of key candidate genes for milk fat metabolism in dairy cattle[J]. Acta Agriculturae Zhejiangensis, 2023, 35(12): 2794-2808.
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URL: http://www.zjnyxb.cn/EN/10.3969/j.issn.1004-1524.20221710
基因登录号 GenBank ID | 基因 Gene | 上游引物序列 Forward primer sequence(5’→3’) | 下游引物序列 Reverse primer sequence(5’→3’) | 产物长度 Product length/bp | 退火温度 Annealing temperature/℃ |
---|---|---|---|---|---|
NM_001034034.2 | GAPDH | TCGGAGTGAACGGATTCGG | TGATGACGAGCTTCCCGTTC | 192 | 60.0 |
NM_173893.3 | B2M | ACACCCACCAGAAGATGGAAAG | CAGGTCTGACTGCTCCGATTTA | 124 | 60.0 |
NR_036642.1 | 18S RNA | ACTTTCGATGGTAGTCGCTGTGC | TCCTTGGATGTGGTAGCCGTTT | 105 | 60.0 |
NM_001167834.1 | CES4A | TTTGAGCACTACGCTCCTGG | CCACCATTGGGGTTTCCTGT | 188 | 58.2 |
NM_001163802.3 | ATP8A2 | GCCCACAGCTGGAGAAGATA | GTACTTGGCCGTGCTGATCT | 189 | 59.4 |
NM_001034385.2 | CTSH | CGCCCAGAACTTCAACAACC | TACTTGCAGTCACCATCCTGG | 132 | 59.4 |
NM_001100297.1 | APOL3 | GCAGACTCCTGGGGTGAAAC | TGGACAAATCAGCCTCGGTC | 247 | 58.2 |
NM_001205544.1 | DKK1 | ATTGACAACCACCAGCCGTA | AGAAGGCATGCATATCCCGT | 189 | 59.4 |
NM_001080293.1 | ENPP2 | TCACTTTTGCCGTCGGTGTCAA | AATCAGGGGGTCCAGCCTCTTG | 174 | 58.0 |
NM_001083644.1 | BCAT1 | TGTGTTGTTTGCCCTGTTTC | GTCGCTCTCTTCTCTTCCGT | 138 | 59.5 |
NM_001113261.1 | PTPRR | TGAGGACAAGACAGCCAACAG | AAAGGAGAAGGGCAGACAGAG | 129 | 56.4 |
NM_001075477 | U6 | CTCGCTTCGGCAGCACA | AACGCTTCACGAATTTGCGT | 132 | 58.2 |
NM_173979.3 | β-actin | CATCGGCAATGAGCGGTTCC | ACCGTGTTGGCGTAGAGGTC | 80 | 60.0 |
NM_001083706.1 | PDGFD | GTGAAAAAGTACCACGAGGTGT | TAAGTTCGGTTGCTGGTGGG | 237 | 58.2 |
NM_174680.2 | KCNMA1 | CTAACCTGGAGCTGGAAGCCT | ACGCATCTGCTGACTCTATCTTGA | 117 | 58.2 |
XM_005208272.4 | ZFYVE28 | ACCGCCTGTTTGTCTGTATCTC | TTCCTTGTCGTCCGTCTCTG | 128 | 58.2 |
NM_001100316.1 | PI4K2A | CGGAACCCCTTCCTGAGAAC | CCAGTCTGTGTCCCGAGAGT | 161 | 58.2 |
NM_001100316.1 | PI4K2A(CDS) | ATGGACGAGACGAGCCCACT | CTACCACCAGGAGAAGAAGGG | 1 440 | 58.0 |
NM_001097568.2 | ID1 | CTGGGATCTGGAGTTGGAGC | GGAACACACGCCGCCTCT | 135 | 58.2 |
NM_001101043.2 | VEGFD | CCACTCGCAGGAATGGAAGATCAC | GAAAGGGGCATCTGTCCTCACA | 238 | 58.2 |
NM_001037319.1 | SLC16A1 | TGGCAGCACCTTTATCCTCTAC | ACTCCACAATGGTCACCAATCC | 160 | 58.2 |
Table 1 Primer sequence and annealing temperature
基因登录号 GenBank ID | 基因 Gene | 上游引物序列 Forward primer sequence(5’→3’) | 下游引物序列 Reverse primer sequence(5’→3’) | 产物长度 Product length/bp | 退火温度 Annealing temperature/℃ |
---|---|---|---|---|---|
NM_001034034.2 | GAPDH | TCGGAGTGAACGGATTCGG | TGATGACGAGCTTCCCGTTC | 192 | 60.0 |
NM_173893.3 | B2M | ACACCCACCAGAAGATGGAAAG | CAGGTCTGACTGCTCCGATTTA | 124 | 60.0 |
NR_036642.1 | 18S RNA | ACTTTCGATGGTAGTCGCTGTGC | TCCTTGGATGTGGTAGCCGTTT | 105 | 60.0 |
NM_001167834.1 | CES4A | TTTGAGCACTACGCTCCTGG | CCACCATTGGGGTTTCCTGT | 188 | 58.2 |
NM_001163802.3 | ATP8A2 | GCCCACAGCTGGAGAAGATA | GTACTTGGCCGTGCTGATCT | 189 | 59.4 |
NM_001034385.2 | CTSH | CGCCCAGAACTTCAACAACC | TACTTGCAGTCACCATCCTGG | 132 | 59.4 |
NM_001100297.1 | APOL3 | GCAGACTCCTGGGGTGAAAC | TGGACAAATCAGCCTCGGTC | 247 | 58.2 |
NM_001205544.1 | DKK1 | ATTGACAACCACCAGCCGTA | AGAAGGCATGCATATCCCGT | 189 | 59.4 |
NM_001080293.1 | ENPP2 | TCACTTTTGCCGTCGGTGTCAA | AATCAGGGGGTCCAGCCTCTTG | 174 | 58.0 |
NM_001083644.1 | BCAT1 | TGTGTTGTTTGCCCTGTTTC | GTCGCTCTCTTCTCTTCCGT | 138 | 59.5 |
NM_001113261.1 | PTPRR | TGAGGACAAGACAGCCAACAG | AAAGGAGAAGGGCAGACAGAG | 129 | 56.4 |
NM_001075477 | U6 | CTCGCTTCGGCAGCACA | AACGCTTCACGAATTTGCGT | 132 | 58.2 |
NM_173979.3 | β-actin | CATCGGCAATGAGCGGTTCC | ACCGTGTTGGCGTAGAGGTC | 80 | 60.0 |
NM_001083706.1 | PDGFD | GTGAAAAAGTACCACGAGGTGT | TAAGTTCGGTTGCTGGTGGG | 237 | 58.2 |
NM_174680.2 | KCNMA1 | CTAACCTGGAGCTGGAAGCCT | ACGCATCTGCTGACTCTATCTTGA | 117 | 58.2 |
XM_005208272.4 | ZFYVE28 | ACCGCCTGTTTGTCTGTATCTC | TTCCTTGTCGTCCGTCTCTG | 128 | 58.2 |
NM_001100316.1 | PI4K2A | CGGAACCCCTTCCTGAGAAC | CCAGTCTGTGTCCCGAGAGT | 161 | 58.2 |
NM_001100316.1 | PI4K2A(CDS) | ATGGACGAGACGAGCCCACT | CTACCACCAGGAGAAGAAGGG | 1 440 | 58.0 |
NM_001097568.2 | ID1 | CTGGGATCTGGAGTTGGAGC | GGAACACACGCCGCCTCT | 135 | 58.2 |
NM_001101043.2 | VEGFD | CCACTCGCAGGAATGGAAGATCAC | GAAAGGGGCATCTGTCCTCACA | 238 | 58.2 |
NM_001037319.1 | SLC16A1 | TGGCAGCACCTTTATCCTCTAC | ACTCCACAATGGTCACCAATCC | 160 | 58.2 |
Fig.1 Resuscitation culture of BMECs A, BMECs after 24 h of resuscitation culture, the green arrow points to the secreted milk droplet; B, BMECs after 3 d of resuscitation culture, with green arrows pointing to the bulge after cell contact.
Fig.2 Results of total RNA extraction from different tissues and BMECs of dairy cow A, 1-7 are the results of total RNA extraction from the small intestine, liver, kidney, uterus, heart, ovary and mammary gland of cow, respectively; B, 1 and 2 are the results of total RNA extraction from BMECs. M is DL 2000 DNA marker.
Fig.3 Stability of different internal reference genes A, Standard deviation and coefficient of variation of Cq values of different internal reference genes; B, Cq values of different internal reference genes.
Fig.4 Relative expression levels of candidate differential genes of milk fat metabolism in different tissues of dairy cow The bars marked without the same lowercase letter indicated significant differences at P<0.05. The same as below.
Fig.5 The expression differences of candidate differential genes of milk fat metabolism in mammary gland (A) and BMECs (B) * represented significant difference compared with other genes.
Fig.7 Cloning of PI4K2A gene A, Results of PCR amplification of CDS region of PI4K2A gene, 1 and 2 are amplification products; B, Results of amplification product recovery and purification, 1 and 2 are recovered products; C, Results of bacteria amplification of PI4K2A gene, 1-8 are amplification products. M is DL2000 DNA marker.
Fig.9 Function prediction of PI4K2A protein A, Hydrophobicity/hydrophilicity prediction; B, Signal peptide prediction; C, Transmembrane structure prediction; D, Phosphorylation site prediction.
预测软件 Prediction software | 预测含量Prediction content/% | |||||
---|---|---|---|---|---|---|
细胞质 Cytoplasm | 细胞核 Cell nucleus | 线粒体 Mitochondria | 液泡 Vacuole | 高尔基体 Golgi apparatus | 细胞骨架 Cytoskeleton | |
Euk-mPLOC 2.0 | 100 | 0 | 0 | 0 | 0 | 0 |
YLoc | 87.1 | 12.8 | 0.1 | 0 | 0 | 0 |
MultiLoc2 | 86.0 | 13.0 | 1.0 | 0 | 0 | 0 |
PSORT II Prediction | 34.8 | 26.1 | 21.8 | 8.7 | 4.3 | 4.3 |
Table 2 Subcellular localization prediction of PI4K2A protein
预测软件 Prediction software | 预测含量Prediction content/% | |||||
---|---|---|---|---|---|---|
细胞质 Cytoplasm | 细胞核 Cell nucleus | 线粒体 Mitochondria | 液泡 Vacuole | 高尔基体 Golgi apparatus | 细胞骨架 Cytoskeleton | |
Euk-mPLOC 2.0 | 100 | 0 | 0 | 0 | 0 | 0 |
YLoc | 87.1 | 12.8 | 0.1 | 0 | 0 | 0 |
MultiLoc2 | 86.0 | 13.0 | 1.0 | 0 | 0 | 0 |
PSORT II Prediction | 34.8 | 26.1 | 21.8 | 8.7 | 4.3 | 4.3 |
Fig.10 Total RNA extraction from nucleus and plasma of BMECs and subcellular localization of PI4K2A mRNA A, Results of nuclear and plasma total RNA extraction from BMECs; B, The distribution of PI4K2A in BMECs.
物种 Species | 占比Percentage/% | |||
---|---|---|---|---|
α螺旋 α-Helix | 延伸链 Extended chain | β转角 β-Turn | 无规则卷曲 Random coil | |
牛Bos taurus | 34.66 | 14.61 | 6.47 | 44.26 |
绵羊Ovis aries | 32.57 | 14.61 | 6.26 | 46.56 |
山羊Capra hircus | 32.99 | 14.61 | 6.26 | 46.14 |
水牛 | 33.40 | 15.24 | 6.89 | 44.47 |
Bubalus bubalis | ||||
人Homo sapiens | 35.07 | 14.41 | 6.05 | 44.47 |
猪Sus scrofa | 34.86 | 14.61 | 5.01 | 45.51 |
小鼠Mus musculus | 32.36 | 15.45 | 5.43 | 46.76 |
大鼠 | 33.26 | 15.27 | 6.49 | 44.98 |
Rattus norvegicus | ||||
原鸡Gallus gallus | 34.12 | 14.59 | 6.01 | 45.28 |
Table 3 Predicted secondary structure of PI4K2A protein in different species
物种 Species | 占比Percentage/% | |||
---|---|---|---|---|
α螺旋 α-Helix | 延伸链 Extended chain | β转角 β-Turn | 无规则卷曲 Random coil | |
牛Bos taurus | 34.66 | 14.61 | 6.47 | 44.26 |
绵羊Ovis aries | 32.57 | 14.61 | 6.26 | 46.56 |
山羊Capra hircus | 32.99 | 14.61 | 6.26 | 46.14 |
水牛 | 33.40 | 15.24 | 6.89 | 44.47 |
Bubalus bubalis | ||||
人Homo sapiens | 35.07 | 14.41 | 6.05 | 44.47 |
猪Sus scrofa | 34.86 | 14.61 | 5.01 | 45.51 |
小鼠Mus musculus | 32.36 | 15.45 | 5.43 | 46.76 |
大鼠 | 33.26 | 15.27 | 6.49 | 44.98 |
Rattus norvegicus | ||||
原鸡Gallus gallus | 34.12 | 14.59 | 6.01 | 45.28 |
Fig.12 Similarity analysis of the spatial structure of PI4K2A protein in different species Red arrows indicate the locations where the spatial structure of PI4K2A protein changes in other species relative to that of cattle.
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