Screening of genes related to auto-sexing on feather color based on RNA-seq technology

doi:10.3969/j.issn.1004-1524.2022.03.10

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (3): 498-506.DOI: 10.3969/j.issn.1004-1524.2022.03.10

• Animal Science • Previous Articles Next Articles

Screening of genes related to auto-sexing on feather color based on RNA-seq technology

WANG Qiankun¹(), ZHANG Xiaohui¹^,², PANG Youzhi¹^,²^,^*(), QI Yanxia¹^,², LEI Ying¹^,², BAI Junyan¹^,², HU Yunqi¹, ZHAO Yiwei¹, YUAN Zhiwen¹, WANG Tao¹

1. College of Animal Science, Henan University of Science and Technology, Luoyang 471003, Henan, China
2. Luoyang Key Laboratory of Animal Genetic and Breeding, Luoyang 471003, Henan,China

Received:2021-07-12 Online:2022-03-25 Published:2022-03-30
Contact: PANG Youzhi

Abstract

Abstract:

The phenomenon of auto-sexingby feather color in quail is determined by genes on the sex chromosomes, but the specific molecular mechanism is unknown. In this study, Beijing male white feather quail and female maroon feather quail were selected as research animals.The transcriptome of F₁ male and F₁ female quails at the 10th day of embryo stage were analyzed by RNA-seq technique, and the key genes associated with feather color were screened and verified by qRT-PCR. The results showed that a total of 38.94 G of raw reads were obtained in RNA-seq, with an average of 6.49 G for each sample. And the Q30 of the six libraries was above 90%, average of GC content was 49.7%.At least 89% of the reads from the tested sample were aligned to the reference genome.A total of 16 013 genes were obtained through database comparison, of which 69 were up-regulated genes and 22 were down-regulated genes.GO enrichment analysis revealed that 13 841 genes were annotated into the GO database, including 78 differentially expressed genes.KEGG enrichment results showed that 22 differentially expressed genes were enriched in 38 pathways. All differentially expressed genes were screened and seven genes related to feather color phenotype were obtained: DCT, MLANA, SLC45A2, TYRP1, TRPM1, FAM174A and KIT. According to the results of qRT-PCR, the candidate genes were highly expressed in maroon feather quail, which was consistent with RNA-seq results.The seven candidate genes obtained in this study might be related to auto-sexing.

Key words: quail, feather color, auto-sexing, transcriptome, gene expression

CLC Number:

S839

WANG Qiankun, ZHANG Xiaohui, PANG Youzhi, QI Yanxia, LEI Ying, BAI Junyan, HU Yunqi, ZHAO Yiwei, YUAN Zhiwen, WANG Tao. Screening of genes related to auto-sexing on feather color based on RNA-seq technology[J]. Acta Agriculturae Zhejiangensis, 2022, 34(3): 498-506.

Figures/Tables 8

References 31

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基因 Gene	上游引物 Forward primer(5'→3')	下游引物 Reverse primer(5'→3')	产物长度 Product length/bp	退火温度 Annealing temperature/℃
KIT	TCATTCAAGGGCTGCTACCA	GCTTGTACGCTGCTATCCAC	197	59
DCT	TGATGAGTGGATGAAGCGGT	GCAGGTCAATGGCATAGGTG	170	59
MLANA	AAGGACGCACCTATTTCACA	GTTGCTCCCTCACTCACCAC	178	57
FAM174A	CAGTGCGGCTCAGAAGAAAT	TTGAGTGCATTCTGTTCCGA	163	60
SLC45A2	AATGGTACGAGTAAGCCG	GGTAGCGATAATGGGATG	118	54
TYRP1	TGAGGGACCTGCTTTCGT	GATTTCTGCGGATGGGAC	299	56
TRPM1	AGCAGGTCTTAGTGCCTCTTAC	TCCTTTATAGTCTTGGCTTTCC	156	56
EIF4E	GACTGCGTCAAGCAATCG	CAGAAGTACAAGACAAAGGCG	139	56

基因 Gene	上游引物 Forward primer(5'→3')	下游引物 Reverse primer(5'→3')	产物长度 Product length/bp	退火温度 Annealing temperature/℃
KIT	TCATTCAAGGGCTGCTACCA	GCTTGTACGCTGCTATCCAC	197	59
DCT	TGATGAGTGGATGAAGCGGT	GCAGGTCAATGGCATAGGTG	170	59
MLANA	AAGGACGCACCTATTTCACA	GTTGCTCCCTCACTCACCAC	178	57
FAM174A	CAGTGCGGCTCAGAAGAAAT	TTGAGTGCATTCTGTTCCGA	163	60
SLC45A2	AATGGTACGAGTAAGCCG	GGTAGCGATAATGGGATG	118	54
TYRP1	TGAGGGACCTGCTTTCGT	GATTTCTGCGGATGGGAC	299	56
TRPM1	AGCAGGTCTTAGTGCCTCTTAC	TCCTTTATAGTCTTGGCTTTCC	156	56
EIF4E	GACTGCGTCAAGCAATCG	CAGAAGTACAAGACAAAGGCG	139	56

样本名称 Sample	原始数据 Raw reads/M	过滤后数据 Clean reads/M	分析数据 Clean bases/G	Q30/%	GC含量 GC content/%	总比对读段 Total mapped reads	多位点比对读段 Multiple mapped	唯一比对读段 Uniquely mapped
BF1	46.16	44.44	6.19	91.25	49.74	40 037 396(90.08%)	1 269 910(2.86%)	38 767 486(87.23%)
BF2	47.33	45.61	6.35	91.47	49.78	41 019 585(89.93%)	1 239 218(2.72%)	39 780 367(87.21%)
BF3	49.89	48.13	6.68	91.78	49.87	43 274 927(89.91%)	1 321 985(2.75%)	41 952 942(87.16%)
LF1	50.57	48.39	6.67	90.75	50.04	43 467 145(89.83%)	1 365 790(2.82%)	42 101 355(87.01%)
LF2	47.27	45.35	6.35	90.96	49.21	41 127 739(90.68%)	1 255 232(2.77%)	39 872 507(87.92%)
LF3	49.85	47.80	6.70	90.90	49.23	43 289 872(90.56%)	1 332 581(2.79%)	41 957 291(87.77%)

样本名称 Sample	原始数据 Raw reads/M	过滤后数据 Clean reads/M	分析数据 Clean bases/G	Q30/%	GC含量 GC content/%	总比对读段 Total mapped reads	多位点比对读段 Multiple mapped	唯一比对读段 Uniquely mapped
BF1	46.16	44.44	6.19	91.25	49.74	40 037 396(90.08%)	1 269 910(2.86%)	38 767 486(87.23%)
BF2	47.33	45.61	6.35	91.47	49.78	41 019 585(89.93%)	1 239 218(2.72%)	39 780 367(87.21%)
BF3	49.89	48.13	6.68	91.78	49.87	43 274 927(89.91%)	1 321 985(2.75%)	41 952 942(87.16%)
LF1	50.57	48.39	6.67	90.75	50.04	43 467 145(89.83%)	1 365 790(2.82%)	42 101 355(87.01%)
LF2	47.27	45.35	6.35	90.96	49.21	41 127 739(90.68%)	1 255 232(2.77%)	39 872 507(87.92%)
LF3	49.85	47.80	6.70	90.90	49.23	43 289 872(90.56%)	1 332 581(2.79%)	41 957 291(87.77%)

通路注释 Description	通路ID Pathway accession	基因数量 Gene numbers	基因名称 Gene name	P值 P-vaule
黑色素生成Melanogenesis	gga04916	3	TYRP1,DCT,KIT	0.001 717
酪氨酸代谢Tyrosine metabolism	gga00350	2	TYRP1,DCT	0.003 700
神经活性配体受体相互作用Neuroactive ligand-receptor interaction	gga04080	4	C3,GRP,CCK,HRH3	0.010 209
苯丙氨酸、酪氨酸和伤寒杆菌生物合成	gga00400	1	PAH	0.014 978
Phenylalanine, tyrosine and typtohan biosynthesis
MAPK信号通路MAPK signaling pathway	gga04010	3	CACNGS,AMHR2,KIT	0.028 778
苯丙氨酸代谢Phenylalanine metabolism	gga00360	1	PAH	0.037 033

Screening of genes related to auto-sexing on feather color based on RNA-seq technology

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