Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max.
Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max.
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基于特定长度扩增片段测序（SLAF-seq）大规模标记的高密度遗传图谱构建及其在大豆异黄酮含量QTL分析中的应用
DOI：
10.1186/1471-2164-15-1086
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发表时间：
2014-12-10
期刊：
影响因子：
4.4
通讯作者：
Sun J
中科院分区：
文献类型：
--
作者：
Li B;Tian L;Zhang J;Huang L;Han F;Yan S;Wang L;Zheng H;Sun J
背景数量性状基因座(QTL)定位是发现复杂数量性状遗传结构的有效途径。然而，遗传图谱中分子标记密度较低，限制了QTL定位的效率和准确性。本研究利用基于下一代测序的高通量SNP发现和基因分型新策略--特定长度扩增片段测序法(SLAF-SEQ)，利用重组自交系(RILS，鲁黑豆2号 × 南恢早，F5：8)构建了大豆高密度遗传图谱。结果共获得23 GB数据，包含87,604,858对端读数。每个SLAF标记的平均覆盖率分别是母本的11.20倍、父本的12.51倍和RILs的3.98倍。在获得的116,216个高质量的SLAF中，9948个是多态的。最终的图谱由20个连锁群上的5785个SLAF组成，基因组大小为2255.18 cM，相邻标记之间的平均距离为0.43 cM。比较基因组分析显示，20 lGs与大豆参考基因组有较高的共线性。根据该图谱，共检测到41个与异黄酮含量相关的QTL。在这些基因座中发现了编码异黄酮生物合成酶的基因，证明了该图谱的高效性和准确性。此外，在这41个QTL中，有11个QTL(包括6个新的基因座)与不同环境中的异黄酮含量有关。其中，qIF20-2对不同环境中的大多数异黄酮组分有贡献，并解释了较高的表型差异(8.7%-35.3%)。这代表了一个新的大豆异黄酮含量的主效QTL。结论在此，我们报道了一个大豆高密度遗传图谱。该地图具有较高的分辨率和精度。这将有助于鉴定大豆主要农艺性状的基因和QTL。这一新的大豆异黄酮含量主效QTL不仅为进一步研究大豆异黄酮积累的遗传基础，而且为今后大豆分子标记辅助选择(MAS)奠定了基础。
BackgroundQuantitative trait locus (QTL) mapping is an efficient approach to discover the genetic architecture underlying complex quantitative traits. However, the low density of molecular markers in genetic maps has limited the efficiency and accuracy of QTL mapping. In this study, specific length amplified fragment sequencing (SLAF-seq), a new high-throughput strategy for large-scale SNP discovery and genotyping based on next generation sequencing (NGS), was employed to construct a high-density soybean genetic map using recombinant inbred lines (RILs, Luheidou2 × Nanhuizao, F5:8). With this map, the consistent QTLs for isoflavone content across various environments were identified.ResultsIn total, 23 Gb of data containing 87,604,858 pair-end reads were obtained. The average coverage for each SLAF marker was 11.20-fold for the female parent, 12.51-fold for the male parent, and an average of 3.98-fold for individual RILs. Among the 116,216 high-quality SLAFs obtained, 9,948 were polymorphic. The final map consisted of 5,785 SLAFs on 20 linkage groups (LGs) and spanned 2,255.18 cM in genome size with an average distance of 0.43 cM between adjacent markers. Comparative genomic analysis revealed a relatively high collinearity of 20 LGs with the soybean reference genome. Based on this map, 41 QTLs were identified that contributed to the isoflavone content. The high efficiency and accuracy of this map were evidenced by the discovery of genes encoding isoflavone biosynthetic enzymes within these loci. Moreover, 11 of these 41 QTLs (including six novel loci) were associated with isoflavone content across multiple environments. One of them,qIF20-2, contributed to a majority of isoflavone components across various environments and explained a high amount of phenotypic variance (8.7% - 35.3%). This represents a novel major QTL underlying isoflavone content across various environments in soybean.ConclusionsHerein, we reported a high-density genetic map for soybean. This map exhibited high resolution and accuracy. It will facilitate the identification of genes and QTLs underlying essential agronomic traits in soybean. The novel major QTL for isoflavone content is useful not only for further study on the genetic basis of isoflavone accumulation, but also for marker-assisted selection (MAS) in soybean breeding in the future.
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影响因子：
6.1
作者：
Di, X.;Yu, L.;Dixon, D.
通讯作者：
Dixon, D.
影响因子：
7.4
作者：
Deavours, BE;Dixon, RA
通讯作者：
Dixon, RA
影响因子：
5.1
作者：
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Sleper, David A.
影响因子：
5.4
作者：
Kato, Shin;Sayama, Takashi;Ishimoto, Masao
通讯作者：
Ishimoto, Masao