Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness.
Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness.
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DOI：
10.1111/pbi.13516
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发表时间：
2021-05
影响因子：
13.8
通讯作者：
Sreenivasulu N
中科院分区：
文献类型：
--
作者：
Misra G;Badoni S;Parween S;Singh RK;Leung H;Ladejobi O;Mott R;Sreenivasulu N
质量被评为优秀的水稻品种，其籽粒垩白率（PGC）较低，为2%及以下，碾磨时全粒产量较高，从而为农民带来更高的经济回报。我们使用籼稻和粳稻品种的组合群体进行了全基因组关联研究（GWAS），并确定了总共746个与白垩表型强烈相关的单核苷酸多态性（SNP），覆盖了78个数量性状位点（QTL）区域。其中，21个是高值QTL，因为它们解释了至少10%的PGC表型方差。采用上位性分析和GWAS相结合的方法对这一复杂垩白性状进行遗传分析，并利用基因调控网络验证其调控级联。在第6号染色体（PGC6.1）和第7号染色体（PGC7.8）的基因座之间发现了有希望的新的上位性相互作用，这有助于降低PGC。单倍型挖掘结果表明，只有少数现代水稻品种与低垩白性状混淆，且这些品种具有多个PGC QTL。PGC6.1的重要性通过多亲本高世代互交得到验证，并鉴定了几个具有上级单倍型的低垩白品系。这项研究的结果已经破译了潜在的遗传网络，可以将PGC降低到2%，因此将支持未来的育种计划，以提高具有高产潜力的精英遗传材料的谷物质量。
Rice varieties whose quality is graded as excellent have a lower percent grain chalkiness (PGC) of two per cent and below with higher whole grain yields upon milling, leading to higher economic returns for farmers. We have conducted a genome‐wide association study (GWAS) using a combined population panel of indica and japonica rice varieties, and identified a total of 746 single nucleotide polymorphisms (SNPs) that were strongly associated with the chalk phenotype, covered 78 Quantitative Trait Loci (QTL) regions. Among them, 21 were high‐value QTLs, as they explained at least 10 % of the phenotypic variance for PGC. A combined epistasis and GWAS was applied to dissect the genetics of the complex chalkiness trait, and its regulatory cascades were validated using gene regulatory networks. Promising novel epistatic interactions were found between the loci of chromosomes 6 (PGC6.1) and 7 (PGC7.8) that contributed to lower PGC. Based on haplotype mining only a few modern rice varieties confounded with a lower chalkiness, and they possess several PGC QTLs. The importance of PGC6.1 was validated through multi‐parent advanced generation intercrosses and several low‐chalk lines possessing superior haplotypes were identified. The results of this investigation have deciphered the underlying genetic networks that can reduce PGC to 2%, and will thus support future breeding programs to improve the grain quality of elite genetic material with high‐yielding potentials.
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WGCNA：用于加权相关网络分析的 R 包。
影响因子：
3
作者：
Langfelder P;Horvath S
通讯作者：
Horvath S
影响因子：
13.8
作者：
Anacleto, Roslen;Badoni, Saurabh;Sreenivasulu, Nese
通讯作者：
Sreenivasulu, Nese
影响因子：
9.2
作者：
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通讯作者：
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影响因子：
7.4
作者：
Gocal, GFW;Sheldon, CC;King, RW
通讯作者：
King, RW
使用加权多个线性回归来估计by-qtl上位效应。
影响因子：
2.1
作者：
Bocianowski J
通讯作者：
Bocianowski J