Novel genomic approaches unravel genetic architecture of complex traits in apple.
Novel genomic approaches unravel genetic architecture of complex traits in apple.
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DOI：
10.1186/1471-2164-14-393
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发表时间：
2013-06-12
期刊：
影响因子：
4.4
通讯作者：
Volz RK
中科院分区：
文献类型：
--
作者：
Kumar S;Garrick DJ;Bink MC;Whitworth C;Chagné D;Volz RK
了解数量性状的遗传结构对于开发基于基因组的作物改良方法非常重要。全基因组关联研究（GWAS）是挖掘新功能变异的强大技术。我们采用基于家系的设计，对 1,200 个苹果 (Malus × Domestica Borkh.) 幼苗进行 8K SNP 阵列基因分型，首次系统评估了不同基因组区域对与食用质量和对某些生理疾病的易感性相关的各种性状的相对贡献。将单 SNP 分析模型（无论是否考虑群体结构）与同时拟合所有标记的模型进行比较。还研究了连锁不平衡（LD）的模式。即使标记之间的距离较长，也可以观察到高度的 LD，并且连续几代的 LD 衰减模式相似。确定了基因组区域，其中一些与已知的候选基因一致，对各种性状具有显着影响。通过全基因组扫描识别的基因座解释的表型变异在不同性状中的范围为 3% 至 25%，同时拟合所有标记通常提供与基于谱系分析的遗传力估计值接近的遗传力估计值。 “Q+K”和“K”模型的结果非常相似，表明基于 SNP 的亲属关系矩阵捕获了大部分潜在的种群结构。对于所有性状，从单标记和全标记分析中获得的等位基因替代效应之间的相关性约为 0.90。在线性混合模型中使用 SNP 衍生的已实现关系提供了比基于谱系的预期关系更好的拟合优度。具有可能的多效性效应的基因组区域得到相应的较高连锁群（LG）水平估计遗传相关性的支持。通过使用更精确的标记衍生的已实现关系系数估计，可以提高植物物种人工选择的准确性。间接解释群体和谱系结构的全标记分析将成为 GWAS 中单 SNP 分析的可靠替代方案。这项研究揭示了苹果果实性状遗传结构的巨大差异，这里确定的标记-性状关联将有助于开发基于基因组的苹果品种育种方法。
Understanding the genetic architecture of quantitative traits is important for developing genome-based crop improvement methods. Genome-wide association study (GWAS) is a powerful technique for mining novel functional variants. Using a family-based design involving 1,200 apple (Malus × domestica Borkh.) seedlings genotyped for an 8K SNP array, we report the first systematic evaluation of the relative contributions of different genomic regions to various traits related to eating quality and susceptibility to some physiological disorders. Single-SNP analyses models that accounted for population structure, or not, were compared with models fitting all markers simultaneously. The patterns of linkage disequilibrium (LD) were also investigated. A high degree of LD even at longer distances between markers was observed, and the patterns of LD decay were similar across successive generations. Genomic regions were identified, some of which coincided with known candidate genes, with significant effects on various traits. Phenotypic variation explained by the loci identified through a whole-genome scan ranged from 3% to 25% across different traits, while fitting all markers simultaneously generally provided heritability estimates close to those from pedigree-based analysis. Results from ‘Q+K’ and ‘K’ models were very similar, suggesting that the SNP-based kinship matrix captures most of the underlying population structure. Correlations between allele substitution effects obtained from single-marker and all-marker analyses were about 0.90 for all traits. Use of SNP-derived realized relationships in linear mixed models provided a better goodness-of-fit than pedigree-based expected relationships. Genomic regions with probable pleiotropic effects were supported by the corresponding higher linkage group (LG) level estimated genetic correlations. The accuracy of artificial selection in plants species can be increased by using more precise marker-derived estimates of realized coefficients of relationships. All-marker analyses that indirectly account for population- and pedigree structure will be a credible alternative to single-SNP analyses in GWAS. This study revealed large differences in the genetic architecture of apple fruit traits, and the marker-trait associations identified here will help develop genome-based breeding methods for apple cultivar development.
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DOI：
10.1111/j.1365-313x.2006.02964.x
发表时间：
2007-02
期刊：
The Plant journal : for cell and molecular biology
影响因子：
--
作者：
Espley RV;Hellens RP;Putterill J;Stevenson DE;Kutty-Amma S;Allan AC
通讯作者：
Allan AC
影响因子：
2
作者：
Iwanami, Hiroshi;Moriya, Shigeki;Abe, Kazuyuki
通讯作者：
Abe, Kazuyuki
影响因子：
3.7
作者：
Chagné D;Crowhurst RN;Troggio M;Davey MW;Gilmore B;Lawley C;Vanderzande S;Hellens RP;Kumar S;Cestaro A;Velasco R;Main D;Rees JD;Iezzoni A;Mockler T;Wilhelm L;Van de Weg E;Gardiner SE;Bassil N;Peace C
通讯作者：
Peace C
影响因子：
5.4
作者：
HILL W G;ROBERTSON A
通讯作者：
ROBERTSON A
影响因子：
3.7
作者：
Kumar S;Chagné D;Bink MC;Volz RK;Whitworth C;Carlisle C
通讯作者：
Carlisle C