中国农业科学 ›› 2023, Vol. 56 ›› Issue (3): 572-586.doi: 10.3864/j.issn.0578-1752.2023.03.014

• 畜牧·兽医 • 上一篇    

龙岩山麻鸭蛋品质性状的全基因组关联研究

孙艳发1,2(), 吴琼1,2, 林如龙3, 陈红萍3, 甘秋云1, 沈玥1, 王亚茹1, 薛鹏飞1, 陈飞帆1, 刘健涛1, 周陈鑫1, 兰诗诗1, 潘浩哲1, 邓凡1,5, 岳稳3, 江宵兵4(), 李焰1,2()   

  1. 1龙岩学院生命科学学院,福建龙岩 364012
    2龙岩学院/福建省家畜传染病防治与生物技术重点实验室/预防兽医学与生物技术福建省高校重点实验室,福建龙岩 364012
    3龙岩市新罗区农业局山麻鸭原种场,福建龙岩 364031
    4福建省畜牧总站,福州 350003
    5福建农林大学动物科学学院(蜂学学院),福州 350002
  • 收稿日期:2021-10-20 接受日期:2022-11-16 出版日期:2023-02-01 发布日期:2023-02-14
  • 通信作者: 江宵兵,Tel:13960752743;E-mail:fzjxb@163.com。 李焰,Tel:13860217279;E-mail:529783204@qq.com
  • 联系方式: 孙艳发,Tel:18250071633;E-mail:boysun2010@163.com。
  • 基金资助:
    福建省种业创新与产业化工程(2021-2025);农业良种重大科研育种攻关与产业化工程项目(zycxny20211014);福建省科技厅对外合作项目(2021I0045);福建省科技厅引导性科技项目(2020N0034);龙岩学院科研博士启动基金(LB2019001)

Genome-Wide Association Study of Egg Quality Traits in Longyan Shan-Ma Duck

SUN YanFa1,2(), WU Qiong1,2, LIN RuLong3, CHEN HongPing3, GAN QiuYun1, SHEN Yue1, WANG YaRu1, XUE PengFei1, CHEN FeiFan1, LIU JianTao1, ZHOU ChenXin1, LAN ShiShi1, PAN HaoZhe1, DENG Fan1,5, YUE Wen3, JIANG XiaoBing4(), LI Yan1,2()   

  1. 1College of Life Sciences, Longyan University, Longyan 364012, Fujian
    2Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology/Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology/Longyan University, Longyan 364012, Fujian
    3Longyan Shan-Ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan 364031, Fujian
    4Fujian Provincial Animal Husbandry Headquarters, Fuzhou 350003
    5College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002
  • Received:2021-10-20 Accepted:2022-11-16 Published:2023-02-01 Online:2023-02-14

摘要:

【目的】通过全基因组关联研究(genome-wide association study,GWAS)技术筛选和鉴定鸭蛋品质性状的单核苷酸多态性(single nucleotide polymorphisms,SNPs)位点及候选基因,为龙岩山麻鸭蛋品质性状分子育种提供参考。【方法】试验测定产蛋后期235只龙岩山麻鸭母鸭蛋品质性状,包括蛋重(egg weight,EW)、蛋形指数(egg shaped index,ESI)、蛋壳厚(eggshell thickness,EST)、蛋壳强度(eggshell strength,ESS)、蛋壳颜色L*、a*、b*值(eggshell colour L*, a*, b*,ESCL、ESCA和ESCB)、蛋白高度(albumin height,AH)、哈氏单位(Haugh unit,HU)、蛋黄颜色(egg yolk colour,EYC)、蛋黄重(egg yolk weight,EYW)和蛋黄比例(egg yolk percentage relative to egg weight,EYP)。使用ASReml-R 4.1软件多性状动物模型对蛋品质性状进行遗传参数估计。使用简化基因组测序技术对鸭血液基因组DNA进行SNP分型,分型后进行蛋品质性状与这些SNPs间的GWAS研究。【结果】龙岩山麻鸭蛋品质性状中,EW、ESI、EST、ESL、ESA和AU具有中高等的遗传力,遗传力在0.21—0.70之间。EW与AU存在较强的正遗传相关(rg = 0.91±0.37)。ESI与EYC存在较强的遗传负相关(rg = -0.98±1.03)。EST与ESS具有表型正相关(rp = 0.41±0.06),与ESA具有遗传和表型负相关(rg = -0.86±0.25和rp = -0.15±0.07),与ESB具有遗传和表型正相关(rg= 0.96±0.37和rp = 0.18±0.07)。ESA与ESB具有遗传和表型负相关(rg = -0.64±0.28和rp = -0.31±0.06)。GWAS研究结果表明,7个SNPs位点与ESI、EST和EYC达到5%基因组水平显著关联(P<4.74×10-6),涉及6个候选基因。与ESI关联的SNP(chr20:11135563:G:C)位点位于20号染色体含有75A富含亮氨酸重复序列(leucine rich repeat containing 75A)基因内。与EST关联的2个SNPs(chr13:5766560:A:G和chrZ:968819:C:T)位点分别位于13号LOC106014427下游6.86 kb处和Z染色体转录因子4(transcription factor 4)基因内。与EYC关联的4个SNPs位点,其中1个(chr2:38155965:G:A)位于2号染色体钾电压门控通道亚家族H成员8(potassium voltage-gated channel subfamily H member 8)基因内;3个SNPs位于9号染色体上的位点,2个(chr9:22623156:G:A和chr9:22623155:T:C)位于胰岛素受体底物1(insulin receptor substrate 1)内、1个(chr9:22490158:A:T)位于LOC106018641内。同时发现81个SNPs位点与蛋品质性状达到基因组水平潜在关联(P<9.48×10-5)。13个与EYC关联的SNPs位点集中在9号染色体0.84 Mb(22.16—23.00 Mb)区域内。【结论】估计了龙岩山麻鸭蛋品质性状的遗传参数,通过蛋品质性状GWAS研究鉴定了影响ESI、EST和EYC性状的7个显著的SNPs位点、6个候选基因和1个候选基因区域,这些结果为龙岩山麻鸭蛋品质性状分子育种提供参考信息。

关键词: 龙岩山麻鸭, 蛋品质, 遗传参数, 单核苷酸多态性, 全基因组关联研究

Abstract:

【Objective】Single nucleotide polymorphisms (SNPs) and candidate genes for egg quality traits in duck were identified through genome-wide association study (GWAS) technology, so as to provide reference for molecular breeding to improve egg quality traits of Longyan Shan-Ma Duck.【Method】Egg quality traits of 235 female Longyan Shan-Ma Duck were measured, including egg weight (EW), egg shaped index (ESI), eggshell thickness (EST), eggshell strength (ESS), eggshell colour L* (ESCL), a* (ESCA), b* (ESCB), albumin height (AH), Haugh unit (HU), egg yolk colour (EYC), egg yolk weight (EYW), and egg yolk percentage relative to egg weight (EYP). Genetic parameters of these traits were estimated using multi-trait animal model by ASReml-R 4.1 software. Blood genomic DNAs of these ducks were genotyped using genotyping-by-sequencing (GBS) technology. The GWAS between egg quality traits of the late laying period and SNPs were performed. 【Result】 The heritability of EW, ESI, EST, ESL, ESA and AU was higher among the egg quality traits of Longyan Shan-Ma Duck, and ranged from 0.21 to 0.70. There was a strong positive genetic correlation (rg = 0.91±0.37) between EW and AU, a strong negative genetic correlation (rg = -0.98±1.03) between ESI and EYC. EST had a positive phenotypic correlation (rp = 0.41±0.06) with ESS, negative genetic and phenotypic correlations with ESA (rg = -0.86±0.25 and rp = -0.15±0.07), and positive genetic and phenotypic correlations with ESB (rg= 0.96±0.37 and 0.18±0.07). There were negative genetic and phenotypic correlations between ESA and ESB (rg = -0.64±0.28 and rp = -0.31±0.06). Results from the GWAS showed that seven SNPs were significantly associated with ESI, EST and yolk color (YC) at 5% Bonferroni-corrected genome-wide significance level (P<4.74×10-6), involving six candidate genes. One SNP, chr20:11135563: G:C, was associated with ESI, which was in leucine rich repeat containing 75A gene, located on chromosome 20. Two SNPs, chr13:5766560:A:G and chrZ:968819:C:T, were associated with EST, which were located on chromosome 13, downstream 6.86 Kb of LOC106014427 and in transcription factor 4 gene, respectively. Four SNPs were associated with EYC, one SNP chr2: 38155965:G:A in potassium voltage-gated channel subfamily H member 8 gene located on chromosome 2; three SNPs located on chromosome 9, two SNPs, chr9:22623156:G:A and chr9:22623155:T:C, in insulin receptor substrate 1 gene, and one SNP, chr9:22490158:A:T, in LOC106018641 gene. Eighty-one SNPs associated with egg quality traits reached at suggestive genome-wide significance level (P<9.48×10-5) were also found. Thirteen SNPs associated with YC were distributed in the 0.84 Mb (22.16-23.00 Mb) region of chromosome 9.【Conclusion】In this study, genetic parameters of egg quality traits of Longyan Shan-Ma Duck were estimated. Seven significant SNPs, six candidate genes, and one candidate region affecting ESI, EST and EYC traits were identified through GWAS. The findings from the present study provided a reference for the molecular breeding of egg quality traits in Longyan Shan-Ma Duck.

Key words: Longyan Shan-Ma Duck, egg quality traits, genetic parameter, SNPs, GWAS