Phenotypic differences between inbred and outbred OFFs
The outbred population had higher genetic heterozygosity (F1,7=4.324, p =0.33) and a larger number of SNPs (F1,7 = 4.323, p = 0.33) than the inbred population (Fig. 2A and B). Additionally, the outbred population had a higher pupal weight (F1,156 =591.78, p < 0.001) than the inbred population, with an increase of 7.32% (Fig. 2C). However, diet intake volume and the development rate did not differ between the two populations (F1,156 =591.78, p < 0.001, Fig. S1). Additionally, adult female ovaries in the outbred population were 34.47% larger than those of the inbred population at 15 days post-emergence (F1,87=99.45, P<0.001) (Fig. 2D). The ovary length and width in the outbred population were 23.15% (F1,87=52.14, P<0.001) and 55.02% (F1,87 = 117.74, p < 0.001) longer and wider than those in the inbred population, respectively.
The survival curve of the outbred population was significantly lower than that of the inbred population (F1,7=64.73, P <0.05) (Fig. 2E). Regarding cohort fecundity, the outbred population laid a significantly larger number of eggs per female than the inbred population (F1,7=12.52, P<0.01), indicating that the reproductive potential was enhanced after population mixing (Fig. 2F). In total, the accumulated egg number in the outbred population was 26.12% higher than that in the inbred population (p<0.01). The innate rate decreased from 0.33±0.00 in the inbred population to 0.32±0.01 in the outbred population (p=0.257), while the doubling time in the outbred population was 2.82% lower than that in the inbred population (p=0.242) (Table S2). Pharyngeal bone length (p=0.174) and food intake (p=0.275) showed no significant differences between the inbred population and outbred population (Fig. S1 A and B).
Microbiome differences between inbred and outbred OFFs
In total, 367,190 and 367,190 high-quality fungal and bacterial sequences were obtained, respectively. The mean base pair lengths of each sequence were 227 bp and 417 bp, respectively. The microbiome OTU analysis revealed 113 species, 67 families, and 8 phyla. In the inbred population, intestinal fungi were mainly distributed in Eurotiales (43.03%), Saccharomycetales (35.35%), Trichosporonales (7.43%), Hypocreales (5.63%), Tremellales (1.05%), and others (7.51%). In the outbred population, fungi were mainly distributed in Saccharomycetales (87.95%), Trichosporonales (2.27%), Hypocreales (2.20%), Eurotiales (1.04%), and others (6.54%). The abundance of Saccharomycetales in the outbred population was 148.80% higher than that in the inbred population (P=0.046) (Fig. 3A). Regarding intestinal fungal LEfSe, Diutina rugosa (P=0.009) showed the most significant difference between the outbred and inbred groups (Fig. 3C).
The number of intestinal bacteria OTUs was 2,571, with 1,651 species, 516 families, and 47 phyla. The intestinal bacteria in the inbred population mainly belonged to Lactobacillales (14.32%), Pseudomonadales (5.89%), Burkholderiales (4.62%), and Acetobacterales (0.68%). The intestinal bacteria in the outbred population mainly belonged to Lactobacillales (45.78%), Acetobacterales (16.44%), Burkholderiales (3.64%), Sphingomonadales (2.20%), and Pseudomonadales (2.17%). The abundance of Lactobacillales in the outbred population was 219.70% higher than that in the inbred population (P=0.023). (Fig. 3B). Regarding intestinal bacteria LEfSe between the outbred and inbred groups, Komagataeibacter saccharivorans (P=0.017) was the most significantly different between the two populations (Fig. 3D).
When the outbred and inbred populations were fed each other's diet, the pupal weight in the inbred population was 1.06% higher than the original pupal weight (F1,63=0.472, P <0.05). The pupal weight in the outbred population was 6.28% lower than the original pupal weight (F1,74=0.853, P <0.001) (Fig. S1 C). The concentrations of histidine, arginine, glutamine, glutamate, isoleucine, and valine in the intestine in the outbred population were significantly higher than those in the intestine in the inbred population (Fig. 3E).
The pupal weight in the inbred population was significantly increased after adding glutamic acid and histidine to diets. In contrast, there was no significant difference in pupal weight between the inbred subpopulation with no diet composition change and those fed diets supplemented with arginine, isoleucine and valine. The pupal weights in those fed diets supplemented with histidine and glutamic acid were 9.23% and 8.10% higher, respectively, than that in those fed a diet with no amino acid supplementation (F1,202=10.066, P <0.001; F1,202=10.037, P <0.001). The pupal weights in inbred subpopulations fed diets supplemented with valine and isoleucine were 14.76±0.04 mg and 14.63±0.05 mg, respectively, which was not significantly different from the pupal weight in those fed the normal diet (F1,202=28.818, P =0.904; F1,202=22.995, P =0.200) (Fig. S1 C).
Transcriptomic differences between inbred and outbred OFFs
Genomic material of the inbred and outbred populations were sequenced on the Illumina platform, and 46.83×106, 49.30×106, 50.33×106, and 49.65×106 high-quality sequences were obtained. Each sample generated approximately 7 G of data, with the Q20 value reaching 98%. A total of 24,000 genes and 36,955 transcripts were obtained after assembly. The longest transcript was 16,079 bp, the shortest was 201 bp, and the average length was 1082.85 bp. Most of the transcripts were distributed between 200 and 500 bps, and the length of N50 was 2,156 bp.
A false discovery rate (FDR) ≤0.05 and fold-change ≥ 2 were applied to compare unigenes between the inbred and outbred populations. The results showed that 784 unigenes were differentially expressed in the transcriptomes of the inbred and outbred populations, of which 637 unigenes were upregulated and 147 unigenes were downregulated (Fig. 4A).
Thirty-four functional components and 147 downregulated unigenes in the outbred population were obtained based on 309 annotations. Among them, 95 annotations were attributed to molecular function, 110 to biological processes, and 104 to cellular components. In the molecular function category, binding (GO:0005488) (27.21%) and catalytic activity (GO:0003824) (22.45%) were the most enriched. Cellular process (GO:0009987) (19.05%) and metabolic process (GO:0005488) (14.97%) were the most involved biological processes. Cell part (GO:0008152) (23.13%) and membrane part (GO:0044425) (14.97%) were the most upregulated cellular components (Fig. 4B).
Some downregulated differential genes that may affect phenotypic differentiation were screened considering p<0.05. The expression levels of the CRYAB gene in the inbred and outbred populations were 750.15±36.49 and 101.47±47.49, respectively. The expression levels of HSPA1S in the inbred and outbred populations were 617.63±336.22 and 14.04±2.09, respectively. The expression levels of the HSPA5 gene in the inbred and outbred populations were 136.90±51.12 and 22.25±0.98, respectively. The expression levels of the CYP6 gene in the inbred and outbred populations were 22.76±3.58 and 4.18±0.09, respectively. The expression levels of CYP18A1 in the inbred and outbred populations were 4.96±33.13 and 0.02±0.00, respectively. The expression levels of FOXA2 in the inbred and outbred populations were 3.57±0.05 and 0.64±0.01, respectively (Fig. 4C).
Based on the KEGG database of 122 metabolic pathways, 60 downregulated genes were obtained, among which 10 pathways were significantly enriched in the outbred population (FDR≤0.05). The immune system pathway, including the antigen processing and presentation pathway, had the most significant differences between the two populations (P=0.0019). Additionally, the longevity regulating pathway-multiple species pathway (P=0.0021) and protein processing in the endoplasmic reticulum pathway (P=0.0022) and the MAPK signalling pathway (P=0.0033) showed significant differences. Thus, the expression of the HSPA1S gene in the MAPK pathway was downregulated, which led to upregulation of the JNK pathway. Additionally, the CYP18A1 gene, which regulates the insect hormone synthesis pathway, namely, the ecdysone pathway, was significantly downregulated, but the pathway was not significantly enriched (Table 1, Fig. 4D).
Table 1 KEGG enrichment pathways and descriptions
Pathway ID
|
Description
|
P value
|
map04612
|
Antigen processing and presentation
|
0.0019
|
map04213
|
Lifespan regulation pathway - multiple species
|
0.0021
|
map04141
|
Protein processing in endoplasmic reticulum
|
0.0022
|
map03040
|
spliceosome
|
0.039
|
map04010
|
MAPK signalling pathway
|
0.045
|