SNPs for parentage testing and traceability in globally diverse breeds of sheep.
SNPs for parentage testing and traceability in globally diverse breeds of sheep.
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DOI：
10.1371/journal.pone.0094851
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
International Sheep Genomics Consortium
中科院分区：
文献类型：
--
作者：
Heaton MP;Leymaster KA;Kalbfleisch TS;Kijas JW;Clarke SM;McEwan J;Maddox JF;Basnayake V;Petrik DT;Simpson B;Smith TP;Chitko-McKown CG;International Sheep Genomics Consortium
基于DNA的亲子鉴定通过提高系谱准确性来加速绵羊的遗传改良。单核苷酸多态性（SNP）标记可用于确定亲子关系，并为追踪羊产品的来源提供独特的分子标识符。然而，特定“亲本SNP”的效用因品种而异，这取决于其次要等位基因频率（MAF）及其序列背景。我们的目标是确定具有特殊品质的亲本SNP，用于全球不同的品种，并开发一个子集用于北美绵羊。从国际绵羊基因组学联盟（ISGC）提供的2，915只绵羊和74个品种组的基因型开始，我们通过多个标准分析了47，693个常染色体SNP，并选择了163个具有理想特性的亲子鉴定。平均而言，在48±5个品种组中，163个SNP中的每一个都是高度信息化的（MAF≥0.3）。通过对来自54个品种群的166只绵羊进行全基因组和桑格测序，确定了可能混淆遗传检测的邻近多态性。开发了具有163个亲本SNP中的109个的遗传测试用于基质辅助激光解吸/电离飞行时间质谱。在一组北美绵羊中，这109个SNPs的评分率和准确性大于99%。在一组96个家庭（父亲，母亲，和非同卵双胞胎羔羊）的盲法，每只羔羊的每一个父母被确定，而不使用其他父母的基因型。在74个ISGC品种组中，对于109个SNP组合，两只动物之间巧合匹配的概率（PI）和排除亲子关系的潜在成年动物比例（PE）的中位数估计值分别为1.1×10（-39）和0.999987。一组163个亲本SNP的良好表征的可用性促进了高通量遗传技术的发展，用于在世界上许多绵羊品种中实施准确和经济的亲子鉴定和可追溯性。
DNA-based parentage determination accelerates genetic improvement in sheep by increasing pedigree accuracy. Single nucleotide polymorphism (SNP) markers can be used for determining parentage and to provide unique molecular identifiers for tracing sheep products to their source. However, the utility of a particular “parentage SNP” varies by breed depending on its minor allele frequency (MAF) and its sequence context. Our aims were to identify parentage SNPs with exceptional qualities for use in globally diverse breeds and to develop a subset for use in North American sheep. Starting with genotypes from 2,915 sheep and 74 breed groups provided by the International Sheep Genomics Consortium (ISGC), we analyzed 47,693 autosomal SNPs by multiple criteria and selected 163 with desirable properties for parentage testing. On average, each of the 163 SNPs was highly informative (MAF≥0.3) in 48±5 breed groups. Nearby polymorphisms that could otherwise confound genetic testing were identified by whole genome and Sanger sequencing of 166 sheep from 54 breed groups. A genetic test with 109 of the 163 parentage SNPs was developed for matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry. The scoring rates and accuracies for these 109 SNPs were greater than 99% in a panel of North American sheep. In a blinded set of 96 families (sire, dam, and non-identical twin lambs), each parent of every lamb was identified without using the other parent’s genotype. In 74 ISGC breed groups, the median estimates for probability of a coincidental match between two animals (PI), and the fraction of potential adults excluded from parentage (PE) were 1.1×10(−39) and 0.999987, respectively, for the 109 SNPs combined. The availability of a well-characterized set of 163 parentage SNPs facilitates the development of high-throughput genetic technologies for implementing accurate and economical parentage testing and traceability in many of the world’s sheep breeds.
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影响因子：
3.5
作者：
Fisher, P. J.;Malthus, B.;Spelman, R. J.
通讯作者：
Spelman, R. J.
影响因子：
2.6
作者：
Heaton, Michael P.;Leymaster, Kreg A.;Laegreid, William W.
通讯作者：
Laegreid, William W.
影响因子：
2.6
作者：
Heaton, Michael P.;Keele, John W.;Harhay, Gregory P.;Richt, Juergen A.;Koohmaraie, Mohammad;Wheeler, Tommy L.;Shackelford, Steven D.;Casas, Eduardo;King, D. Andy;Sonstegard, Tad S.;Van Tassell, Curtis P.;Neibergs, Holly L.;Chase, Chad C., Jr.;Kalbfleisch, Theodore S.;Smith, Timothy P. L.;Clawson, Michael L.;Laegreid, William W.
通讯作者：
Laegreid, William W.
影响因子：
9.8
作者：
Kijas JW;Lenstra JA;Hayes B;Boitard S;Porto Neto LR;San Cristobal M;Servin B;McCulloch R;Whan V;Gietzen K;Paiva S;Barendse W;Ciani E;Raadsma H;McEwan J;Dalrymple B;International Sheep Genomics Consortium Members
通讯作者：
International Sheep Genomics Consortium Members
影响因子：
3.5
作者：
Hayes, B. J.
通讯作者：
Hayes, B. J.