基于靶向捕获测序的猪单倍型基因组选择效果研究

doi:10.3864/j.issn.0578-1752.2024.11.015

中国农业科学 ›› 2024, Vol. 57 ›› Issue (11): 2243-2253.doi: 10.3864/j.issn.0578-1752.2024.11.015

基于靶向捕获测序的猪单倍型基因组选择效果研究

刘燕玲¹(), 邱奥¹(), 张梓鹏¹, 王雪¹, 都鹤鹤¹, 罗文学², 王贵江², 魏霞³, 施文颖³, 丁向东¹()

¹ 中国农业大学动物科学技术学院/畜禽育种国家工程实验室/农业农村部动物遗传育种与繁殖重点实验室，北京 100193
² 河北省畜牧良种工作总站，石家庄 050061
³ 张家口大好河山新农业开发有限公司，河北张家口 076250

收稿日期:2023-12-12 接受日期:2024-03-01 出版日期:2024-06-01 发布日期:2024-06-07
通信作者:
丁向东，E-mail：xding@cau.edu.cn
联系方式: 刘燕玲，E-mail：liuyanl2022@163.com。邱奥，E-mail：956482319@qq.com。刘燕玲与邱奥为同等贡献作者。
基金资助:
财政部和农业农村部：国家现代农业产业技术体系(CARS-35); 山东省农业良种工程项目(2022LZGC003); 河北省重点研发计划(19226376D)

The Efficiency of Haplotype-Based Genomic Selection Using Genotyping by Target Sequencing in Pigs

LIU YanLing¹(), QIU Ao¹(), ZHANG ZiPeng¹, WANG Xue¹, DU HeHe¹, LUO WenXue², WANG GuiJiang², WEI Xia³, SHI WenYing³, DING XiangDong¹()

¹ College of Animal Science and Technology, China Agricultural University/National Engineering Laboratory of Animal Breeding/ Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing 100193
² Hebei Animal Husbandry Extension Station, Shijiazhuang 050061
³ Zhangjiakou Dahaoheshan New Agricultural Development Co., Ltd., Zhangjiakou 076250, Hebei

Received:2023-12-12 Accepted:2024-03-01 Published:2024-06-01 Online:2024-06-07

摘要/Abstract

摘要：

【目的】探索靶向捕获测序技术的猪单倍型基因组选择研究效果，为我国猪分子育种提供借鉴。【方法】收集了1 267头大白猪的生长性能测定记录和800头大白猪的繁殖记录，利用基于靶向捕获测序技术（genotyping by target sequencing，GBTS）开发的猪50K液相芯片（液相50K）以及靶向捕获重测序数据进行基因型分型，对靶向捕获重测序数据进行单倍型分析，比较固定SNP数目、固定物理间距和靶向block三种单倍型区块划分方法以及单个SNP数据的基因组选择准确性。其中靶向block方法是基于靶向捕获测序技术设计的一种单倍型区块划分方法，通过将靶位点与其上下游400 bp 内SNP（mSNP）组合为一个block的方式构建单倍型。本研究对每个单倍型区块采用Beagle5.1进行单倍型推断后，将不同单倍型重新编码为单倍型等位基因，然后利用单倍型剂量模型构建单倍型基因型矩阵，采用一步法模型（ssGBLUP），估计达百公斤体重日龄(AGE)、百公斤活体背膘厚(BF)和总产仔数(TNB)三个性状的基因组育种值。对两个生长性状（AGE和BF）使用双性状动物模型进行估计，对总产仔数性状使用单性状重复力模型。使用年轻群体验证和5倍交叉验证两种验证方法，计算基因组估计育种值与育种值之间的相关系数和基因组估计育种值对估计育种值的回归系数，分别评价单倍型基因组预测准确性和无偏性。【结果】年轻群体作为验证群体的基因组预测结果表明，相较于液相50K SNP，基因型质量控制后，靶向捕获重测序标记数由液相50K 的42 302增加到了88 105，但其对三个性状的基因组选择准确性反而有所下降。通过靶向block方法划分的单倍型区块平均包含SNP 2.08个、单倍型等位基因5.67个。基于三种单倍型区块划分方法进行的单倍型基因组选择准确性都得到了提高，其中靶向block提升幅度最大，AGE、BF和TNB三个性状准确性比液相50K分别提高了4.80%，1.98%和6.04%，靶向block多数情况下基因组预测无偏性最优。交叉验证结果与年轻群体验证相似，靶向block方法相较于单标记SNP和其他单倍型区块划分方法均有一定优势，固定间距400 bp划分单倍型的基因组选择效果与靶向block单倍型接近但计算时间增加；固定2个和5个SNP单倍型区块划分方法单倍型基因组预测准确性较单个SNP均有一定提升，但低于靶向block单倍型。【结论】由于液相芯片标记的特点，靶向重测序数据mSNP与液相50K SNP芯片标记多数处于高度连锁不平衡状态，利用靶向block划分的单倍型基因组选择准确性优于50K SNP以及其他两种单倍型区块划分方法，进一步利用了液相芯片的技术优势，拓宽了基于GBTS技术的液相芯片在基因组分析方面的应用。

关键词: 猪, 液相芯片, 基因组选择, 单倍型, 靶向捕获测序

Abstract:

【Objective】This study explored the efficiency of haplotype-based genomic selection using genotyping by target sequencing technology in order to provide the useful experience for molecular breeding of pigs in China.【Method】The growth traits records of 1 267 Large White pigs and the reproduction trait records of 800 Large White pigs were collected and genotyped by using the porcine 50K liquid-phase SNP panel (liquid-phase 50K) based on the Genotyping by Target Sequencing (GBTS) as well as its target resequencing data. Three strategies for haplotype block partition, including fixed SNP number, fixed length, and target block, were proposed to construct haplotypes, and the corresponding haplotype-based genomic prediction were compared with single SNP genomic prediction. The target block partition strategy was mainly based on target resequencing data obtained by the GBTS, and one haplotype block contained one target site in liquid-phase 50K and its upstream and downstream SNPs (mSNP) within 400 bp from target resequencing data. In this study, after phasing haplotype using Beagle 5.1 within each haplotype block, the different haplotypes were recoded as haplotype alleles, and then haplotype allele matrix was constructed using haplotype dosage model. A single-step GBLUP model (ssGBLUP) was then used to estimate genomic breeding values for three traits of days at 100 kg body weight (AGE), backfat thickness at 100 kg (BF), and total number of born (TNB). A two-trait animal model was implemented for two growth traits of AGE and BF, and repeatability model for TNB. Younger validation population and five-fold cross validation were carried out to assess the efficiency of genomic prediction. The correlation coefficients between estimated breeding values and genomic estimated breeding values were measured as the accuracy of genomic prediction, and the regression coefficients of genomic estimated breeding values on estimated breeding values were measured unbiasedness, respectively.【Result】The results from the younger validation population showed that the target resequencing data yielded lower accuracies of genomic selection on three traits than liquid-phase 50K SNP, even its number of SNP after genotype quality control was increased from 42 302 in liquid phase 50K to 88 105. The haplotype blocks partitioned by target block strategy contained 2.08 SNPs and 5.67 haplotype alleles on average. The accuracies of haplotype-based genomic selection based on all three haplotype block partition strategies were improved, and the target block gained the largest improvement, yielding 4.80%, 1.98% and 6.04% higher accuracies on AGE, BF and TNB than liquid- phase 50K, respectively. In addition, the target block strategy generated the lowest bias in most scenarios as well. The five-fold cross-validation obtained similar results as younger validation population did, target block gained advantages over both single SNP and other haplotype block partition methods. The fixed length of 400 bp block partition strategy performed comparable with target block, while it was time demanding. Although fixed 2 and 5 SNP haplotype block partition methods performed better than single SNP method, they were worse than target block.【Conclusion】Due to the short length, the linkage disequilibrium between most of the target sites in liquid-phase 50K SNPs and their mSNPs in same blocks are strong, resulting in target block strategy obtained higher accuracy in haplotype-based genomic selection than single SNP and other haplotype block partition strategies, which could make use of the technique advantage of GBTS, and further broaden the application of liquid-phase chip.

Key words: pig, liquid chip, genomic selection, haplotype, genotyping by target sequencing

刘燕玲, 邱奥, 张梓鹏, 王雪, 都鹤鹤, 罗文学, 王贵江, 魏霞, 施文颖, 丁向东. 基于靶向捕获测序的猪单倍型基因组选择效果研究[J]. 中国农业科学, 2024, 57(11): 2243-2253.

LIU YanLing, QIU Ao, ZHANG ZiPeng, WANG Xue, DU HeHe, LUO WenXue, WANG GuiJiang, WEI Xia, SHI WenYing, DING XiangDong. The Efficiency of Haplotype-Based Genomic Selection Using Genotyping by Target Sequencing in Pigs[J]. Scientia Agricultura Sinica, 2024, 57(11): 2243-2253.

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	达百公斤日龄 Age at 100 kg weight	达百公斤背膘厚 Backfat thickness at 100 kg weight	总产仔数 Total born number
表型数据量Number of phenotype records	1267	1267	2898
测定年份Year	2019-2021	2019-2021	2016-2021
系谱记录数Number of pedigree animals	42198

统计量 Statistic	2 SNPs/ block	5 SNPs/ block	400 bp/ block	靶向block Targeting block
单倍型等位基因数Number of haplotype alleles	153367	210348	238449	240015
单倍型区块数Number of haplotype blocks	44053	17621	42473	42302
每个单倍型区块的平均SNP数 The average number of SNPS per haplotype block	2	5	2.07	2.08
每个单倍型区块的平均单倍型等位基因数 The average number of haplotype alleles per haplotype block	3.48	11.94	5.61	5.67
每个单倍型区块的最大SNP数 The maximum number of SNPS per haplotype block	2	5	7	7
每个单倍型区块的最小SNP数 The minimum number of SNPs per haplotype block	2	5	1	1
SNP大于等于2的单倍型区块数 The number of haplotype blocks with more than or equal to two SNPs	44052	17621	21066	21089

SNP/单倍型 SNP/Haplotype	单倍型等位基因数或SNP标记数 The number of haplotype alleles or SNP markers	AGE		BF		TNB
SNP/单倍型 SNP/Haplotype		准确性 Accuracy	无偏性 Unbiasedness	准确性Accuracy	无偏性 Unbiasedness	准确性Accuracy	无偏性Unbiasedness
液相50K SNP Liquid phase 50K SNP	42302	0.562	1.139	0.607	1.020	0.596	0.744
靶向重测序mSNP Target sequencing mSNP	88105	0.554	1.172	0.599	1.011	0.578	0.745
2 SNPs/block	153367	0.563	1.150	0.608	1.039	0.612	0.736
5 SNPs/block	210348	0.557	1.153	0.604	1.107	0.606	0.743
400 bp/block	238449	0.589	1.134	0.619	1.010	0.632	0.745
靶向block Target block	240015	0.589	1.134	0.619	1.010	0.633	0.745

SNP/单倍型 SNP/Haplotype	AGE		BF		TNB
SNP/单倍型 SNP/Haplotype	准确性 Accuracy	无偏性 Unbiasedness	准确性 Accuracy	无偏性 Unbiasedness	准确性 Accuracy	无偏性 Unbiasedness
液相50K SNP Liquid phase 50K SNP	0.785±0.004	0.735±0.09	0.736±0.008	0.688±0.11	0.740±0.010	0.929±0.12
靶向重测序mSNP Target sequencing mSNP	0.780±0.003	0.756±0.09	0.730±0.007	0.704±0.12	0.725±0.012	0.903±0.11
2 SNPs/block	0.792±0.003	0.744±0.08	0.746±0.007	0.700±0.12	0.751±0.012	0.895±0.11
5 SNPs/block	0.787±0.004	0.747±0.09	0.740±0.007	0.710±0.12	0.746±0.011	0.884±0.11
400 bp/block	0.796±0.003	0.739±0.09	0.748±0.007	0.992±0.48	0.756±0.012	0.897±0.11
靶向 block Target block	0.796±0.003	0.739±0.09	0.748±0.007	0.992±0.48	0.756±0.012	0.897±0.11

基于靶向捕获测序的猪单倍型基因组选择效果研究

The Efficiency of Haplotype-Based Genomic Selection Using Genotyping by Target Sequencing in Pigs

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