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用于杏仁的Axiom 60K单核苷酸多态性芯片的开发与评估（）。

Development and Evaluation of an Axiom 60K SNP Array for Almond ().

作者信息

Duval Henri, Coindre Eva, Ramos-Onsins Sebastian E, Alexiou Konstantinos G, Rubio-Cabetas Maria J, Martínez-García Pedro J, Wirthensohn Michelle, Dhingra Amit, Samarina Anna, Arús Pere

机构信息

Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRAE (French National Research Institute for Agriculture, Food and Environment), 84143 Montfavet, France.

Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain.

出版信息

Plants (Basel). 2023 Jan 5;12(2):242. doi: 10.3390/plants12020242.

DOI:10.3390/plants12020242
PMID:36678957
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9866729/
Abstract

A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the (nematode resistance) and (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits.

摘要

高密度单核苷酸多态性（SNP）阵列对于加快植物育种以培育新品种至关重要。在这方面，我们通过对81份杏仁种质进行重测序，开发了一种Axiom 60K杏仁SNP阵列。为了验证该阵列，对一组210份种质进行了基因分型，82.8%的SNP被归类为最佳推荐SNP。杏仁种质的缺失数据率在0.4%至2.7%之间，少数桃和野生种质的缺失数据率低于15.5%，这表明该阵列可用于桃以及种间杂交种桃×杏仁的遗传研究。与（抗线虫）和（苦味）基因连锁的两个SNP的值是一致的。我们还对一个杏仁F2后代的49个杂交种进行了基因分型，并利用一组1159个SNP构建了遗传图谱。通过比较重复样本以及检测F2后代中偏离孟德尔遗传的情况，评估出错误率低于1%。这种杏仁阵列已商业化，应该是一种经济高效的基因分型工具，有助于寻找控制农艺性状的新基因和数量性状位点（QTL）。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c5e/9866729/e4a73e8cd25b/plants-12-00242-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c5e/9866729/d2d1f4c204e3/plants-12-00242-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c5e/9866729/48640b9c8b6f/plants-12-00242-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c5e/9866729/6b563e179cd7/plants-12-00242-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c5e/9866729/e4a73e8cd25b/plants-12-00242-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c5e/9866729/d2d1f4c204e3/plants-12-00242-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c5e/9866729/48640b9c8b6f/plants-12-00242-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c5e/9866729/6b563e179cd7/plants-12-00242-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c5e/9866729/e4a73e8cd25b/plants-12-00242-g004.jpg

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