Ren Yanjing, Zhang Ning, Li Ru, Ma Xiaomin, Zhang Lugang
Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China.
Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, China.
PeerJ. 2021 Mar 4;9:e10770. doi: 10.7717/peerj.10770. eCollection 2021.
Seed coat color is an important horticultural trait in crops, which is divided into two categories: brown/black and yellow. Seeds with yellow seed coat color have higher oil quality, higher protein content and lower fiber content. Yellow seed coat color is therefore considered a desirable trait in hybrid breeding of and .
Comprehensive analysis of the abundance transcripts for seed coat color at three development stages by RNA-sequencing (RNA-seq) and corresponding flavonoids compounds by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were carried out in .
We identified 41,286 unigenes with 4,989 differentially expressed genes between brown seeds (B147) and yellow seeds (B80) at the same development stage. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified 19 unigenes associated with the phenylpropanoid, flavonoid, flavone and flavonol biosynthetic pathways as involved in seed coat color formation. Interestingly, expression levels of early biosynthetic genes (, , , and ) in the flavonoid biosynthetic pathway were down-regulated while late biosynthetic genes (, and ) were hardly or not expressed in seeds of B80. At the same time, and were down-regulated in B80. Results of LC-MS also showed that epicatechin was not detected in seeds of B80. We validated the accuracy of our RNA-seq data by RT-qPCR of nine critical genes. Epicatechin was not detected in seeds of B80 by LC-MS/MS.
The expression levels of flavonoid biosynthetic pathway genes and the relative content of flavonoid biosynthetic pathway metabolites clearly explained yellow seed color formation in . This study provides a foundation for further research on the molecular mechanism of seed coat color formation.
种皮颜色是作物中一项重要的园艺性状，可分为两类：棕色/黑色和黄色。种皮颜色为黄色的种子具有更高的油质、更高的蛋白质含量和更低的纤维含量。因此，黄色种皮颜色被认为是[作物名称1]和[作物名称2]杂交育种中一个理想的性状。
通过RNA测序（RNA-seq）对三个发育阶段种皮颜色的丰度转录本进行综合分析，并通过液相色谱-串联质谱（LC-MS/MS）对相应的类黄酮化合物进行分析。
我们鉴定出41286个单基因，在同一发育阶段的棕色种子（B147）和黄色种子（B80）之间有4989个差异表达基因。京都基因与基因组百科全书富集分析确定了19个与苯丙烷类、类黄酮、黄酮和黄酮醇生物合成途径相关的单基因参与种皮颜色形成。有趣的是，类黄酮生物合成途径中的早期生物合成基因（[基因名称1]、[基因名称2]、[基因名称3]、[基因名称4]和[基因名称5]）的表达水平下调，而晚期生物合成基因（[基因名称6]、[基因名称7]和[基因名称8]）在B80种子中几乎不表达或不表达。同时，[基因名称9]和[基因名称10]在B80中下调。LC-MS的结果还表明，在B80种子中未检测到表儿茶素。我们通过对9个关键基因进行RT-qPCR验证了RNA-seq数据的准确性。通过LC-MS/MS在B80种子中未检测到表儿茶素。
类黄酮生物合成途径基因的表达水平和类黄酮生物合成途径代谢物的相对含量清楚地解释了[作物名称1]中黄色种子颜色的形成。本研究为进一步研究种皮颜色形成的分子机制提供了基础。
