Genome-wide evaluation of genetic diversity and linkage disequilibrium in winter and spring triticale (x Triticosecale Wittmack).
Genome-wide evaluation of genetic diversity and linkage disequilibrium in winter and spring triticale (x Triticosecale Wittmack).
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DOI：
10.1186/1471-2164-13-235
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发表时间：
2012-06-12
期刊：
影响因子：
4.4
通讯作者：
Würschum T
中科院分区：
文献类型：
--
作者：
Alheit KV;Maurer HP;Reif JC;Tucker MR;Hahn V;Weissmann EA;Würschum T
高密度标记基因分型技术的最新进展使作物全基因组基因组分析成为可能。详细描述群体结构和连锁不平衡（LD）对于基因组方法的应用和基于知识的育种是必不可少的。在这项研究中，我们使用的小黑麦特定的DArT阵列分析的人口结构，遗传多样性和LD在全球范围内设置的161个冬，春小黑麦系。主坐标分析表明，第一主坐标将小黑麦群体按其生长习性分为两类。前十个主要坐标的密度分布显示，有几个显示出人口结构的分布指示。此外，我们观察到的相关性内的生长习性，这是较高的春季类型之间的冬季类型。全基因组多态信息含量（PIC）分析表明，PIC在染色体间和沿着染色体上是可变的，尤其是春型的R基因组具有较低的遗传多样性。我们还发现，几条染色体显示出两种生长习性之间的高遗传距离区域，这表明了趋异选择。关于连锁不平衡，A和B基因组显示紧密连锁标记的相似LD为0.24，并且衰减在约12 cM内。LD在R基因组中较低，为0.19，并在约5 cM的较短图谱距离内衰减。LD的程度一般是较高的春季类型相比，冬季类型。此外，我们观察到LD沿着染色体的强变异性。研究结果表明，冬、春季生长习性是影响小黑麦群体结构的主要因素，两种生长类型均存在家系结构。在这些类型中观察到的遗传多样性的具体模式，如一些黑麦染色体上的春季习性的低多样性，提供了一个基础，有针对性地扩大可用的育种种质。此外，对LD的程度和模式的全基因组分析将有助于科学家和育种家在小黑麦中实施和解释关联作图。
Recent advances in genotyping with high-density markers nowadays enable genome-wide genomic analyses in crops. A detailed characterisation of the population structure and linkage disequilibrium (LD) is essential for the application of genomic approaches and consequently for knowledge-based breeding. In this study we used the triticale-specific DArT array to analyze population structure, genetic diversity, and LD in a worldwide set of 161 winter and spring triticale lines. The principal coordinate analysis revealed that the first principal coordinate divides the triticale population into two clusters according to their growth habit. The density distributions of the first ten principal coordinates revealed that several show a distribution indicative of population structure. In addition, we observed relatedness within growth habits which was higher among the spring types than among the winter types. The genome-wide analysis of polymorphic information content (PIC) showed that the PIC is variable among and along chromosomes and that especially the R genome of spring types possesses a reduced genetic diversity. We also found that several chromosomes showed regions of high genetic distance between the two growth habits, indicative of divergent selection. Regarding linkage disequilibrium, the A and B genomes showed a similar LD of 0.24 for closely linked markers and a decay within approximately 12 cM. LD in the R genome was lower with 0.19 and decayed within a shorter map distance of approximately 5 cM. The extent of LD was generally higher for the spring types compared to the winter types. In addition, we observed strong variability of LD along the chromosomes. Our results confirm winter and spring growth habit are the major contributors to population structure in triticale, and a family structure exists in both growth types. The specific patterns of genetic diversity observed within these types, such as the low diversity on some rye chromosomes of spring habits, provide a basis for targeted broadening of the available breeding germplasm. In addition, the genome-wide analysis of the extent and the pattern of LD will assist scientists and breeders alike in the implementation and the interpretation of association mapping in triticale.
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影响因子：
5.4
作者：
HILL W G;ROBERTSON A
通讯作者：
ROBERTSON A
影响因子：
3.8
作者：
Lexer, C.;Buerkle, C. A.;Fay, M. F.
通讯作者：
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影响因子：
3.3
作者：
Breseghello, F;Sorrells, ME
通讯作者：
Sorrells, ME
影响因子：
5.4
作者：
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Dweikat, I
影响因子：
5.4
作者：
Bus, Anja;Koerber, Niklas;Stich, Benjamin
通讯作者：
Stich, Benjamin