Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population
Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population
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DOI：
10.1186/s12864-019-5427-5
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发表时间：
2019-02-06
期刊：
影响因子：
4.4
通讯作者：
Florane, Christopher B.
中科院分区：
文献类型：
--
作者：
Naoumkina, Marina;Thyssen, Gregory N.;Florane, Christopher B.
背景：提高棉纤维长度而不降低产量是棉花育种的主要目标之一。然而，由于现代棉花品种遗传多样性狭窄，纤维品质与产量性状呈负相关关系，棉花纤维长度的遗传改良一直面临挑战。通过随机交配形成的多亲本高代杂交（MAGIC）群体为数量性状位点（QTL）和致病基因的鉴定提供了良好的遗传资源。结果：利用来自11个不同品种的550个重组自交系（RILs）组成的陆地棉MAGIC群体，鉴定了纤维长度qtl和导致纤维变长的潜在基因。基因组广泛关联研究（GWAS）在染色体（Chr.）上发现了一个单核苷酸多态性（SNPs）簇。D11与纤维长度显著相关。对人权的进一步评价。MAGIC群体的D11基因组区域检测到90%的RILs具有与参考基因组TM-1相似的D11单倍型（D11-ref），而10%的RILs继承了来自父母一方的替代单倍型（D11-alt）。D11-alt基因的纤维平均长度明显短于D11-ref基因，说明D11-alt基因的等位基因导致了D11-alt基因的纤维质量较差。对D11-ref和D11-alt群体中纤维长度最长和最短的ril进行RNAseq分析，鉴定出949个显著差异表达基因（DEGs）。基因集富集分析显示，不同功能类别的基因在纤维伸长过程中被过度代表。我们发现12个非同义snp （non-synonymous SNPs, nsSNPs）基因与纤维长度显著相关，其中3个基因高度显著，聚集在d11:24 mb，包括D11G1928、D11G1929和D11G1931。结论：本研究结果为棉花纤维长度遗传变异的分子机制提供了新的思路，并为棉花改良提供了候选基因。
Background: Improving cotton fiber length without reducing yield is one of the major goals of cotton breeding. However, genetic improvement of cotton fiber length by breeding has been a challenge due to the narrow genetic diversity of modern cotton cultivars and negative correlations between fiber quality and yield traits. A multi-parent advanced generation inter-cross (MAGIC) population developed through random mating provides an excellent genetic resource that allows quantitative trait loci (QTL) and causal genes to be identified.Results: An Upland cotton MAGIC population, consisting of 550 recombinant inbred lines (RILs) derived from eleven different cultivars, was used to identify fiber length QTLs and potential genes that contribute to longer fibers. A genome wide association study (GWAS) identified a cluster of single nucleotide polymorphisms (SNPs) on chromosome (Chr.) D11 that is significantly associated with fiber length. Further evaluation of the Chr. D11 genomic region among lines of the MAGIC population detected that 90% of RILs have a D11 haplotype similar to the reference TM-1 genome (D11-ref), whereas 10% of RILs inherited an alternative haplotype from one of the parents (D11-alt). The average length of fibers of D11-alt RILs was significantly shorter compared to D11-ref RILs, suggesting that alleles in the D11-alt haplotype contributed to the inferior fiber quality. RNAseq analysis of the longest and shortest fiber length RILs from D11-ref and D11-alt populations identified 949 significantly differentially expressed genes (DEGs). Gene set enrichment analysis revealed that different functional categories of genes were over-represented during fiber elongation between the four selected RILs. We found 12 genes possessing non-synonymous SNPs (nsSNPs) significantly associated with the fiber length, and three that were highly significant and were clustered at D11:24-Mb, including D11G1928, D11G1929 and D11G1931.Conclusion: The results of this study provide insights into molecular aspects of genetic variation in fiber length and suggests candidate genes for genetic manipulation for cotton improvement.