The use of SNP markers for linkage mapping in diploid and tetraploid peanuts.
The use of SNP markers for linkage mapping in diploid and tetraploid peanuts.
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DOI：
10.1534/g3.113.007617
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发表时间：
2014-01-10
期刊：
影响因子：
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通讯作者：
Moretzsohn MC
中科院分区：
文献类型：
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作者：
Bertioli DJ;Ozias-Akins P;Chu Y;Dantas KM;Santos SP;Gouvea E;Guimarães PM;Leal-Bertioli SC;Knapp SJ;Moretzsohn MC
单核苷酸多态性标记（SNP）在遗传作图和标记辅助育种中具有吸引力，因为它们可以在平行测定中以有利的成本进行评分。然而，在多倍体植物如花生中对SNP标记进行评分是有问题的，因为从与被测定的DNA碱基同源的DNA碱基产生的干扰信号。本研究使用了先前构建的1536 GoldenGate SNP检测，该检测是使用在两个A.杜兰种质在这项研究中，该测定的性能进行了测试，两个RIL定位群体，一个二倍体（A。杜兰属× A. stenosperma）和一个四倍体[A.海波盖亚Runner IAC 886 ×人工四倍体（A. Ipaënsis × A. duranensis）4×]。使用软件GenomeStudio 2011.1版进行评分。对于二倍体，多态性标记提供了极好的基因分型分数与默认的软件参数。在四倍体中，正如预期的那样，大多数多态性标记提供的信号强度图与二倍体模式相比是扭曲的，并且使用默认参数进行了错误的评分。然而，使用GenomeStudio软件很容易校正这些评分。扭曲的程度变化很大。在多态性标记中，约10%的标记完全没有表现出单剂量标记的预期行为，另外30%的标记表现出低失真，可以被认为是高质量的。基因型标记被纳入花生的二倍体和四倍体遗传图谱，在后者的情况下，几乎完全位于A基因组连锁群。
Single nucleotide polymorphic markers (SNPs) are attractive for use in genetic mapping and marker-assisted breeding because they can be scored in parallel assays at favorable costs. However, scoring SNP markers in polyploid plants like the peanut is problematic because of interfering signal generated from the DNA bases that are homeologous to those being assayed. The present study used a previously constructed 1536 GoldenGate SNP assay developed using SNPs identified between two A. duranensis accessions. In this study, the performance of this assay was tested on two RIL mapping populations, one diploid (A. duranensis × A. stenosperma) and one tetraploid [A. hypogaea cv. Runner IAC 886 × synthetic tetraploid (A. ipaënsis × A. duranensis)4×]. The scoring was performed using the software GenomeStudio version 2011.1. For the diploid, polymorphic markers provided excellent genotyping scores with default software parameters. In the tetraploid, as expected, most of the polymorphic markers provided signal intensity plots that were distorted compared to diploid patterns and that were incorrectly scored using default parameters. However, these scorings were easily corrected using the GenomeStudio software. The degree of distortion was highly variable. Of the polymorphic markers, approximately 10% showed no distortion at all behaving as expected for single-dose markers, and another 30% showed low distortion and could be considered high-quality. The genotyped markers were incorporated into diploid and tetraploid genetic maps of Arachis and, in the latter case, were located almost entirely on A genome linkage groups.