东乡绿壳蛋鸡与白来航鸡资源群体开产体重、开产日龄性状遗传解析

doi:10.11843/j.issn.0366-6964.2025.10.012

摘要/Abstract

摘要：

针对蛋鸡开产性状进行遗传评估，旨在解析开产体重、开产日龄遗传结构。表型数据源自东乡绿壳蛋鸡-白来航鸡F₂分离群体。以600K基因芯片对1 534只F₂代试验鸡进行基因型分型。SNPs数据经质量控制后，进行基因型数据填充。以一步法全基因组关联分析获得开产性状关联的遗传标记。对显著性位点进行基因注释以及GO富集分析，进一步理解这些候选基因的生物学含义。鸡开产体重属于高遗传力性状，遗传力在0.62~0.65之间；开产日龄属于中等偏高遗传力性状，遗传力在0.35与0.42之间；开产体重与开产日龄遗传相关系数为0.24~0.37。鸡1号染色体5-羟色胺受体2A(5-hydroxytryptamine receptor 2A, HTR2A)、钙结合蛋白样39(calcium binding protein 39 like, CAB39L)附近存在与开产体重显著关联的QTL，另有343个支持位点超过基因组显著水平，显著性SNPs分别解释11.74%、9.34%开产体重表型方差；4号染色体筛选到开产体重QTL，候选基因为非SMC凝聚素Ⅰ型复合物G亚基(non-SMC condensin Ⅰ complex subunit G，NCAPG)，可解释5.68%表型方差，附近有89个SNPs超过基因组显著水平阈值；鸡9号染色体G蛋白偶联受体149 (G protein-coupled receptor 149, GPR149)附近存在开产体重QTL，可解释1.33%的表型方差。开产日龄QTL位于5号染色体石蛋白2(stonin 2, STON2)基因附近以及9号染色体Mg²⁺/Mn²⁺依赖性蛋白磷酸酶样1(protein phosphatase, Mg²⁺/Mn²⁺ dependent 1L, PPM1L)附近，分别解释1.80%、1.22%表型方差。应用一步法GWAS，在鸡9号染色体物理位置22 Mb附近新发现与开产体重、开产日龄关联的遗传座位，还在5号染色体物理位置40 Mb附近新发现一个开产日龄关联的遗传座位。GO富集分析进一步表明，开产体重表型变异与性腺发育相关，开产日龄表型变异与钙离子转运相关。

关键词: 开产体重, 开产日龄, 遗传力, 全基因组关联分析, GO富集分析

Abstract:

The aims of this study was to dissect the genetic architecture of body weight and age at the first egg. Phenotypic data were collected from an F₂ segregation population of Dongxiang blue-shelled chickens and White Leghorn. The 1 534 hens in F₂ generation were genotyped using 600K gene microarray. The SNPs data were quality cleaned. Missing data was imputed with BEAGLE software. SNPs associated with traits of onset of lay were obtained with single-step GWAS. Gene annotation and GO enrichment analysis were carried out on the significant SNPs to elucidate the biological roles of candidate genes. The body weight at first egg (BWFE) showed high levels of heritability. The heritability on BWFE ranged from 0.62 to 0.65. The age at first egg (AFE) showed moderate to high levels of heritability. The heritability on AFE ranged from 0.35 to 0.42. The genetic correlation coefficients between traits of onset of lay ranged from 0.24 to 0.37. There were one or more QTLs close to HTR2A or CAB39L on chromosome 1 that was significantly associated with the BWFE, which was supported by the additional 343 SNPs over the threshold of significant level. These QTL explained 11.74% and 9.34% of the phenotypic variance of BWFE, respectively. On chromosome 4, region close to NCAPGwas significantly associated with the BWFE, and reinforced by the additional 89 SNPs. The region explained 5.68% of the phenotypic variance. On chromosome 9, QTL was identified nearby the GPR149, and explained 1.33% of the phenotypic variance. Furthermore, QTL on AFE were identified near the STON2 gene on chromosome 5 and the PPM1L gene on chromosome 9, explaining 1.80% and 1.22% of the phenotypic variance of AFE, respectively. Single-step GWAS was used to detect the genetic structure of traits of onset of lay. Two novel QTL, mapped on 40 Mb of chromosome 5 and 22 Mb of chromosome 9, were identified with BWFE and AFE. GO enrichment analysis showed that the variations on BWFE were related to gonadal development, and the phenotypic variations on AFE was related to calcium ion transport.

Key words: body weight at first egg, age at first egg, heritability, GWAS, GO enrichment analysis

中图分类号:

S831.2

郭军, 邵丹, 马猛, 卢建, 窦套存, 胡玉萍, 王星果, 王强, 李永峰, 郭伟, 童海兵, 曲亮. 东乡绿壳蛋鸡与白来航鸡资源群体开产体重、开产日龄性状遗传解析[J]. 畜牧兽医学报, 2025, 56(10): 4903-4913.

GUO Jun, SHAO Dan, MA Meng, LU Jian, DOU Taocun, HU Yuping, WANG Xingguo, WANG Qiang, LI Yongfeng, GUO Wei, TONG Haibing, QU Liang. Genetic Dissection on Body Weight and Age at the first Egg in Resource Population between White Leghorn and Dongxiang Blue Shelled Chickens[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(10): 4903-4913.

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参考文献 48

1	GARCIAR L. Onset of laying: A key period in the productive lives of layers[J]. Avinews Int, 2019 (4)
2	TANY G,XUX L,CAOH Y,et al. Effect of age at first egg on reproduction performance and characterization of the hypothalamo-pituitary-gonadal axis in chickens[J]. Poult Sci, 2021, 100 (9):101325. doi: 10.1016/j.psj.2021.101325
3	郭军,王克华. 鸡开产日龄遗传调控研究进展[J]. 中国畜牧兽医, 2015, 42 (4): 997-1003.
	GUOJ,WANGK H. Genetic studies on age at the first egg in chicken: A review[J]. China Animal Husbandry & Veterinary Medicine, 2015, 42 (4): 997- 1003.
4	TONGSIRIS,JEYARUBANM G,VAN DER WERFJ H J. Genetic parameters for egg production traits in purebred and hybrid chicken in a tropical environment[J]. Brit Poul Sci, 2015, 56 (6): 613- 620. doi: 10.1080/00071668.2015.1099614
5	PEELERR J,GLAZENERE W,BLOWW L. The heritability of broiler weight and weight and age at sexual maturity and the genetic and environmental correlations between these traits[J]. Poult Sci, 1955, 34 (2): 420- 426. doi: 10.3382/ps.0340420
6	FANQ,WUP,DAIG,et al. Identification of 19 loci for reproductive traits in a local chinese chicken by genome-wide study[J]. Genet Mol Res, 2017, 16 (1): 1- 8.
7	YANGQ,LUX,LIG,et al. Genetic analysis of egg production traits in Luhua chickens: Insights from a multi-trait animal model and a genome-wide association study[J]. Genes, 2024, 15 (6): 796. doi: 10.3390/genes15060796
8	CHENA,ZHAOX,WENJ,et al. Genetic parameter estimation and molecular foundation of chicken egg-laying trait[J]. Poult Sci, 2024, 103 (6): 103627. doi: 10.1016/j.psj.2024.103627
9	MAX,YINGF,LIZ,et al. New insights into the genetic loci related to egg weight and age at first egg traits in broiler breeder[J]. Poult Sci, 2024, 103 (5): 103613. doi: 10.1016/j.psj.2024.103613
10	LIUZ,YANGN,YANY,et al. Genome-wide association analysis of egg production performance in chickens across the whole laying period[J]. BMC Genet, 2019, 20, 1- 9.
11	YUANJ,SUNC,DOUT,et al. Identification of promising mutants associated with egg production traits revealed by genome-wide association study[J]. PLoS One, 2015, 10 (10): e0140615. doi: 10.1371/journal.pone.0140615
12	YIG,SHENM,YUANJ,et al. Genome-wide association study dissects genetic architecture underlying longitudinal egg weights in chickens[J]. BMC Genomics, 2015, 16 (1): 746. doi: 10.1186/s12864-015-1945-y
13	LEGARRAA,AGUILARI,MISZTALI. A relationship matrix including full pedigree and genomic information[J]. J Dairy Sci, 2009, 92 (9): 4656- 4663. doi: 10.3168/jds.2009-2061
14	VANRADENP M. Efficient methods to compute genomic predictions[J]. J Dairy Sci, 2008, 91 (11): 4414- 4423. doi: 10.3168/jds.2007-0980
15	BARRETTJ C,FRYB,MALLERJ,et al. Haploview: Analysis and visualization of LD and haplotype maps[J]. Bioinformatics, 2005, 21 (2): 263- 265. doi: 10.1093/bioinformatics/bth457
16	MUH,CHENJ,HUANGW,et al. Omicshare tools: A zero-code interactive online platform for biological data analysis and visualization[J]. iMeta, 2024, 3 (5): e228. doi: 10.1002/imt2.228
17	HAYESB J,BOWMANP J,CHAMBERLAINA C,et al. Accuracy of genomic breeding values in multi-breed dairy cattle populations[J]. Genet Sel Evol, 2009, 41 (1): 51. doi: 10.1186/1297-9686-41-51
18	MUNOZP R,RESENDEJR M F,HUBERD A,et al. Genomic relationship matrix for correcting pedigree errors in breeding populations: Impact on genetic parameters and genomic selection accuracy[J]. Crop Sci, 2014, 54 (3): 1115- 1123. doi: 10.2135/cropsci2012.12.0673
19	YANGJ,BENYAMINB,MCEVOYB P,et al. Common SNPs explain a large proportion of the heritability for human height[J]. Nat Genet, 2010, 42 (7): 565- 569. doi: 10.1038/ng.608
20	SANGB D,KONGH S,KIMH K,et al. Estimation of genetic parameters for economic traits in Korean native chickens[J]. Asian-Australas J Anim Sci, 2006, 19 (3): 319- 323. doi: 10.5713/ajas.2006.319
21	BEYIHAYOG A,KUGONZAD R,NDYOMUGYENYIE K,et al. Genetic and phenotypic parameter estimates for selection within Ugandan indigenous chickens[J]. Trop Anim Health Prod, 2023, 55 (2): 100. doi: 10.1007/s11250-023-03513-7
22	郭军,曲亮,邵丹,等. 基于一步法全基因组关联分析解析蛋黄比率遗传结构[J]. 中国农业科学, 2024, 57 (21): 4356- 4366.
	GUOJ,QUL,SHAOD,et al. Dissecting the genetic architecture of yolk ratio with single-step genome-wide association study[J]. Scientia Agricultura Sinica, 2024, 57 (21): 4356- 4366.
23	曲亮,郭军,窦套存,等. 应用REML方法评估蛋鸡哈氏单位遗传参数[J]. 中国家禽, 2019, 41 (7): 11- 14.
	QUL,GUOJ,DOUT C,et al. Genetic parameters for Haugh Unit estimated by restricted maximum likelihood approaches[J]. China Poultry, 2019, 41 (7): 11- 14.
24	GUOJ,MAM,QUL,et al. Estimation of genetic parameters related to eggshell strength using random regression models[J]. Brit Poul Sci, 2015, 56 (6): 645- 650. doi: 10.1080/00071668.2015.1113503
25	NIKNAFSS,NEJATI-JAVAREMIA,MEHRABANI-YEGANEHH,et al. Estimation of genetic parameters for body weight and egg production traits in Mazandaran native chicken[J]. Trop Anim Health Prod, 2012, 44 (7): 1437- 1443. doi: 10.1007/s11250-012-0084-6
26	SEWALEMA,JOHANSSONK,CARLGRENA B,et al. Are reproductive traits impaired by selection for egg production in hens?[J]. J Anim Breed and Genet, 1998, 115 (1-6): 281- 297. doi: 10.1111/j.1439-0388.1998.tb00349.x
27	SZYDȽOWSKIM,SZWACZKOWSKIT. Bayesian segregation analysis of production traits in two strains of laying chickens[J]. Poult Sci, 2001, 80 (2): 125- 131. doi: 10.1093/ps/80.2.125
28	WOLCA,ARANGOJ,SETTARP,et al. Genetic parameters of egg defects and egg quality in layer chickens[J]. Poult Sci, 2012, 91 (6): 1292- 1298. doi: 10.3382/ps.2011-02130
29	FUM,WUY,SHENJ,et al. Genome-wide association study of egg production traits in Shuanglian chickens using whole genome sequencing[J]. Genes(Basel), 2023, 14 (12): 2129.
30	LIUZ,YANGN,YANY,et al. Genome-wide association analysis of egg production performance in chickens across the whole laying period[J]. BMC Genet, 2019, 20 (1): 67. doi: 10.1186/s12863-019-0771-7
31	CAOX,WANGY,SHUD,et al. Food intake-related genes in chicken determined through combinatorial genome-wide association study and transcriptome analysis[J]. Anim Genet, 2020, 51 (5): 741- 751. doi: 10.1111/age.12980
32	MOREIRAG C M,POLETIM D,PÉRTILLEF,et al. Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach[J]. BMC Genet, 2019, 20 (1): 83. doi: 10.1186/s12863-019-0783-3
33	BUL,WANGY,TANL,et al. Haplotype analysis incorporating ancestral origins identified novel genetic loci associated with chicken body weight using an advanced intercross line[J]. Genet Sel Evol, 2024, 56 (1): 78. doi: 10.1186/s12711-024-00946-y
34	ZHONGC H,LIX C,GUAND L,et al. Age-dependent genetic architectures of chicken body weight explored by multidimensional GWAS and molQTL analyses[J]. Age-dependent genetic architectures of chicken body weight explored by multidimensional GWAS and molQTL analyses, 2024, 51 (12): 1423- 1434.
35	WANGJ,LIUZ S,CAOD G,et al. Elucidation of the genetic determination of clutch traits in chinese local chickens of the Laiwu Black breed[J]. BMC Genomics, 2023, 24, 686. doi: 10.1186/s12864-023-09798-0
36	TETENSJ,WIDMANNP,KVHNC,et al. A genome-wide association study indicates LCORL/NCAPG as a candidate locus for withers height in german warmblood horses[J]. Anim Genet, 2013, 44 (4): 467- 471. doi: 10.1111/age.12031
37	KARIML,TAKEDAH,LINL,et al. Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature[J]. Nat Genet, 2011, 43 (5): 405- 413. doi: 10.1038/ng.814
38	MATIKAO,RIGGIOV,ANSELME-MOIZANM,et al. Genome-wide association reveals QTL for growth, bone and in vivo carcass traits as assessed by computed tomography in scottish blackface lambs[J]. Genet Sel Evol, 2016, 48, 1- 15. doi: 10.1186/s12711-015-0181-x
39	GUX,FENGC,MAL,et al. Genome-wide association study of body weight in chicken F₂ resource population[J]. PLoS One, 2011, 6 (7): e21872. doi: 10.1371/journal.pone.0021872
40	GUOJ,QUL,DOUT-C,et al. Genome-wide association study provides insights into the genetic architecture of bone size and mass in chickens[J]. Genome, 2020, 63 (3): 133- 143. doi: 10.1139/gen-2019-0022
41	骆娜,安炳星,魏立民,等. 全基因关联分析筛选文昌鸡体尺性状相关分子标记[J]. 中国农业科学, 2024, 57 (10): 2046- 2060.
	LUON,ANB X,WEIL M,et al. Identification of molecular markers associated with body size traits through genome-wide association analysis in Wenchang Chickens[J]. Scientia Agricultura Sinica, 2024, 57 (10): 2046- 2060.
42	EDSONM A,LINY N,MATZUKM M. Deletion of the novel oocyte-enriched gene, GPR149, leads to increased fertility in mice[J]. Endocrinol, 2010, 151 (1): 358- 368. doi: 10.1210/en.2009-0760
43	WANGC,WANGH Y,ZHANGY,et al. Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in chinese domestic pigs[J]. Mol Ecol Res, 2015, 15 (2): 414- 424. doi: 10.1111/1755-0998.12311
44	WYLERS,CAON,MERCHANTW,et al. GPR149 is involved in energy homeostasis in the male mouse[J]. Peer J, 2024, 12, e16739. doi: 10.7717/peerj.16739
45	CHENY,ZHUJ,LUMP Y,et al. Variations in DNA elucidate molecular networks that cause disease[J]. Nature, 2008, 452 (7186): 429- 435. doi: 10.1038/nature06757
46	LUG,OTAA,RENS,et al. PPM1l encodes an inositol requiring-protein 1 (IRE1) specific phosphatase that regulates the functional outcome of the ER stress response[J]. Mol Metab, 2013, 2 (4): 405- 416. doi: 10.1016/j.molmet.2013.07.005
47	MERHIZ,POLOTSKYA J,BRADFORDA P,et al. Adiposity alters genes important in inflammation and cell cycle division in human cumulus granulosa cell[J]. Reprod Sci, 2015, 22 (10): 1220- 1228. doi: 10.1177/1933719115572484
48	ABDELMANOVAA S,DOTSEVA V,ROMANOVM N,et al. Unveiling comparative genomic trajectories of selection and key candidate genes in egg-type russian White and meat-type white Cornish chickens[J]. Biology, 2021, 10 (9): 876. doi: 10.3390/biology10090876

遗传参数 Genetic parameter	系谱遗传关系矩阵 Pedigree relationship	杂交遗传关系矩阵 Hybrid relationship	基因组遗传关系矩阵 Genomic relationship
开产体重遗传力Age at first egg	0.646±0.041	0.652±0.030	0.615±0.041
开产日龄遗传力Body weight at first egg	0.395±0.046	0.416±0.038	0.350±0.043
开产性状遗传相关系数	0.243±0.076	0.370±0.061	0.333±0.074
Genetic correlations coefficients between AFE and BWFE

代码 Code	染色体 Chromosome	物理位置^* /bp Position	候选基因 Candidate	基因内位置 Within gene	碱基替换 Allele	单倍型片段 Length of block	P值 Pvalue
rs317496170	1	168 272 709	HTR2A	上游15.6 kb	T/A	10 kb	7.15×10^-15
rs313913043	1	169 040 953	CAB39L	内含子	A/G	57 kb	1.88×10^-16
rs315201454	4	75 435 186	NCAPG	内含子	G/A	17 kb	2.51×10^-17
rs15988610	9	22 892 481	GPR149	3′端UTR外显子	C/T	172 kb	1.87×10^-7

代码 Code	染色体 Chromosome	物理位置^*/bp Position	候选基因 Candidate	基因内位置 Within gene	碱基替换 Allele	单倍型片段/kb Length of block	P值 Pvalue
rs312299419	5	40 398 485	STON2	内含子/增强子	T/G	45	5.91×10^-11
rs317291556	9	21 782 606	PPM1L	内含子	A/C	8	2.08×10^-7

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