Identification of hub genes in meat quality of grass carp (Ctenopharyngodon idellus) fed with faba bean by muscle tissue transcriptomic analysis

Figures & data

Table 1. Muscle physical and texture parameters of grass carp after 120-days feeding experiment.

Parameters	Crisp grass carp	Ordinary grass carp
pH	6.56 ± 0.09	6.66 ± 0.01
Water holding capacity, %	7.19 ± 1.62^b	10.94 ± 2.49^a
Cooking loss, %	24.12 ± 2.33	27.03 ± 2.58
Hardness, kg	1.23 ± 0.29^a	0.75 ± 0.12^b
Springiness, mm	4.98 ± 0.01^a	3.08 ± 0.56^b
Gumminess, kg	0.89 ± 0.08^a	0.61 ± 0.15^b
Chewiness, mJ	38.18 ± 5.98	29.56 ± 6.19
Cohesiveness, mm	0.55 ± 0.03	0.49 ± 0.07

Results are presented as the mean ± SEM (n = 5). Values with different letters in the same line indicate significant differences (p < .05).

Table 2. Summary statistics of transcriptome sequencing from muscle tissue between ordinary grass carp and the crisp carp group.

Sample	Raw reads	Raw bases, bp	Clean reads	Clean data, bp	Total_Mapped	Q20, %	Q30, %
Group_A1	40,564,018	6,125,166,718	37,910,970	5,724,556,470	94.82%	98.06	94.49
Group_A2	44,425,106	6,708,191,006	41,601,388	6,281,809,588	94.82%	98.41	95.26
Group_A3	42,834,600	6,468,024,600	39,930,392	6,029,489,192	94.77%	98.22	94.83
Group_B1	44,106,208	6,660,037,408	41,239,048	6,227,09,6248	94.91%	98.35	95.19
Group_B2	44,332,974	6,694,279,074	41,533,704	6,271,589,304	95.14%	98.16	94.7
Group_B3	43,989,620	6,642,432,620	41,083,156	6,203,556,556	94.28%	98.26	94.93

Group_A1, Group_A2 and Group_A3: Crisp carp group; Group_B1,Group_B2 and Group_B3: Ordinary grass carp.

Figure 1. Volcano map and heat map of clustering of differentially expressed genes in Ctenopharyngodon idellus.

Figure 2. Classify and analysis according to gene function. (A) GO enrichment of top 20 up-regulated and down-regulated DEGs. (B) KEGG enrichment of top 20 up-regulated and down-regulated DEGs.

Table 3. Differentially expressed genes (DEGs) identified in the muscle tissue between ordinary grass carp and the crisp carp group (Top20).

Gene name	log2FoldChange	pval	padj	Up/down
SLC43A2	5.064656592	6.80492E–33	1.08032E–28	Up
SLC15A4	4.705924222	9.08516E–33	1.08032E–28	Up
CTSL	4.48421604	2.04893E–32	1.62425E–28	Up
ASB18	4.302901408	9.31283E–27	5.53694E–23	Up
PRODH	4.288735951	3.07603E–24	1.21923E–20	Up
RETREG1	3.646621252	8.11353E–24	2.75651E–20	Up
SYT13	3.444645426	6.42403E–22	1.69751E–18	Up
TMEM117	5.606150055	8.53125E–21	1.44922E–17	Up
KLHL38	3.684010648	1.02518E–20	1.62538E–17	Up
ALSIN2	3.786370075	2.1948E–20	3.2623E–17	Up
FBXO30	4.343309036	3.60615E–20	4.76452E–17	Up
SLC16A9	3.556296732	4.43136E–20	5.54666E–17	Up
CCDC129	4.02000405	2.2623E–19	2.562E–16	Up
MSTO1	3.413871711	7.10594E–19	7.34755E–16	Up
FBXO32	3.077803356	7.81533E–19	7.74434E–16	Up
SLC7A8	6.709140063	3.72444E–18	3.54299E–15	Up
NFKBIE	3.46188969	1.66097E–17	1.46301E–14	Up
ABHD2B	3.200719079	4.2128E–17	3.45478E–14	Up
SLC1A5	2.850515434	7.89862E–17	6.05951E–14	Up
ARRDC2	2.88068052	1.1498E–16	8.54514E–14	Up
LDHA	−4.36656894	1.39724E–26	6.64581E–23	Down
AGL	−3.66368887	8.47661E–23	2.51988E–19	Down
SMARCD3	−3.80962945	7.67351E–22	1.82491E–18	Down
ABI3BP	−3.708319297	9.88402E–22	2.13693E–18	Down
TP53BP1	−3.619697977	7.4131E–21	1.38612E–17	Down
MR1	−8.336943833	7.57699E–21	1.38612E–17	Down
COL1A1	−3.294263698	3.21588E–20	4.49883E–17	Down
PDK3	−3.414423635	6.83228E–20	8.12427E–17	Down
FNDC1	−3.225926906	2.96302E–17	2.51666E–14	Down
AAMM50B	−4.606184319	7.56746E–17	5.99898E–14	Down
COL1A2	−2.887803272	2.56396E–16	1.7437E–13	Down
PGK1	−2.819612167	5.67971E–16	3.57571E–13	Down
TNNT3	−2.865108634	7.9281E–16	4.71365E–13	Down
HP1BP3	−3.648142909	1.11962E–15	6.33972E–13	Down
AHSA1	−3.432529968	7.74482E–15	4.09305E–12	Down
ADH1	−3.698975919	9.94866E–15	5.14346E–12	Down
BCL2L13	−2.932306208	1.93091E–14	9.62513E–12	Down
SMTN	−2.671925777	3.06599E–14	1.45831E–11	Down
KYAT1	−3.349710817	4.46425E–14	2.08174E–11	Down
MYOM1	−2.728438474	6.16919E–14	2.71696E–11	Down

Figure 3. (A) GO enrichment of DEGs. (B) GO enrichment of up-regulated DEGs. (C) GO enrichment of down-regulated DEGs.

Figure 4. (A) KEGG pathway enrichment of DEGs. (B) KEGG pathway enrichment of up-regulated DEGs. (C) KEGG pathway enrichment of down-regulated DEGs.

Figure 5. PPI network construction and hub gene screening.

Figure 6. (A) Correlation analysis between the top 10 hub genes and meat quality. (B) Comparison between RNA-Seq result and qRT-PCR validation result. The y-axis is the relative fold change. Data are presented as mean ± SEM.

Data availability statement

The data that support the fundings of this study are available from the corresponding author upon reasonable request.