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

Abstract

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

CLC Number:

S831.2

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.

Figures/Tables 8

Fig. 1

Table 1

Table 2

Fig. 2

Fig. 3

Table 3

Fig. 4

Fig. 5

References 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

[1]	WU Jiahao, WU Ziyi, DOU Tengfei, BAI Liyao, ZHANG Yongqian, DONG Lianhe, LI Pengfei, LI Xinjian, HAN Xuelei, LI Xiuling. Genome-wide Association Study of Copy Number Variation in Growth-Related Traits of Yunong-Black Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(3): 1110-1119.
[2]	ZHOU Taizeng, YANG Yiting, ZHU Yuehua, QIAN Hongxi, LIU Yihui, GAN Mailin, ZHU Li, SHEN Linyuan. Genome-wide Association Study of Stillbirths and Mummies in Sows [J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(3): 1231-1241.
[3]	CAO Yu, ZHOU Bohan, XU Qi, YUAN Zi'ao, SU Rui, LÜ Qi, LI Jinquan, ZHANG Yanjun, WANG Ruijun, WANG Zhiying. Research Progress on Integrated eQTL-GWAS Data Analysis for Potential Functional Genetic Loci Identification in Animal Breeding [J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(10): 4759-4773.
[4]	MA Jing'e, WAN Shuxing, LEI Wenjing, ZHANG Yingzhi, YU Zixuan, LIU Zige, XU Jiguo. Identification of Candidate Genes and Key Pathways Associated with Body Weight at 16 Weeks of Age in Kangle Yellow Chickens Based on Omics Data [J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(10): 4889-4902.
[5]	DUAN Yixin, ZHANG Linyun, ZHAO Yongju. The Evaluated Methods and Influencing Factors of SNP Heritability and Its Application in Farmer Animal Breeding [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 1854-1865.
[6]	XIA Shuwen, CHEN Kunlin, SHEN Yangyang, AN Zhenjiang, ZHAO Fang, DING Qiang, ZHONG Jifeng, LIN Zhiping, WANG Huili. The Estimation of Genetic Parameters for Longevity Traits of Holstein Cows in Jiangsu Region [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(3): 1030-1039.
[7]	ZHANG Xiaoke, LIAO Weili, CHEN Xinyou, LI Tingting, YUAN Xiaolong, LI Jiaqi, HUANG Xiang, ZHANG Hao. Genome-wide Association Study for Identifying Candidate Genes of Growth Traits in Duroc Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1868-1876.
[8]	WU Jun, CAI Xiaodian, LIN Qing, ZHONG Zhanming, YE Haoqiang, WEI Chen, XU Zhiting, WU Xibo, SI Jinglei, ZHANG Zhe, LI Jiaqi. Weighted Single-step GWAS of Eye Muscle Area, Predicted Lean Meat Percentage and Average Backfat Thickness in A Yorkshire Pig Population [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1403-1414.
[9]	ZHANG Gaomeng, DING Jiqiang, LIU Yuhong, ZHENG Maiqing, WEN Jie, ZHAO Guiping, LI Qinghe. Genome-wide Association Study Reveals the Genetic Basis of Hatching Traits in White-feathered Broilers [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 534-544.
[10]	LI Haodong, MIN Xiangyu, ZHOU Ya, ZHANG Heyang, ZHENG Junjun, LIU Linling, WANG Ping, WANG Yanmei, YANG Fuhe, WANG Guiwu. Comparison of Prediction Accuracy of Genomic Selection for Growth-related Traits in Sika Deer (Cervus Nippon) based on GBLUP and other Models [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 608-616.
[11]	FAN Chenyu, SHAN Yanju, ZHANG Ming, JI Gaige, JU Xiaojun, TU Yunjie, HE Xi, SHU Jingting, LIU Yifan, ZHANG Haihan. Genome-wide Association Study of Body Weight and Meat Quality Traits in Lihua Mahuang Chickens [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 4982-4992.
[12]	ZHANG Changzheng, LI Desen, HUANG Min, FANG Xiaomin, ZHAO Weimin, REN Shouwen, DONG Huansheng, REN Jun, ZHOU Lisheng. An Imputed Whole-genome Sequence-based GWAS Approach Pinpoints Genetic Loci for Body Conformation at Birth and Teat Number Traits in Sushan Pig Population [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(1): 88-102.
[13]	WU Pingxian, CHEN Li, LONG Xi, CHAI Jie, ZHANG Tinghuan, XU Shunlai, GUO Zongyi, WANG Jinyong. Genome-wide Association Studies for Reproductive Traits at First Farrowing in Rongchang Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(1): 103-112.
[14]	DU Yongwang, HUANG Chao, WANG Yidong, LI Sen, WEN Jie, CHEN Zhiwu, ZHAO Guiping, ZHENG Maiqing. Genomic Selection for RFI in Broiler Combining GWAS Prior Marker Information [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(10): 3403-3411.
[15]	CHEN Zuoquan, RAO Lin, XIE Lei, YAO Tianxiong, ZHANG Zhiyan. Transmission Ratio Distortion Analysis of SNP in a Duroc×Erhualian Intercross Pigs Population [J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(9): 2384-2393.

Genetic Dissection on Body Weight and Age at the first Egg in Resource Population between White Leghorn and Dongxiang Blue Shelled Chickens

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 8

References 48

Related Articles 15

Recommended Articles

Metrics

Comments