Graduate School Experimental Plant Sciences, Wageningen, The Netherlands.
Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, The Netherlands.
BMC Plant Biol. 2018 Jan 23;18(1):20. doi: 10.1186/s12870-018-1229-1.
Recent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species. To get more insight into the genetic factors underlying variation in quality traits related to carbohydrate and starch metabolism and cold sweetening, we determined the protein content and composition in potato tubers using 2D-gel electrophoresis in a diploid potato mapping population. Upon analyzing we made sure that the proteins from the patatin family were excluded to ensure a better representation of the other proteins.
We subsequently performed pQTL analyses for all other proteins with a sufficient representation in the population and established a relationship between proteins and 26 potato tuber quality traits (e.g. flesh colour, enzymatic discoloration) by co-localization on the genetic map and a direct correlation study of protein abundances and phenotypic traits. Over 1643 unique protein spots were detected in total over the two harvests. We were able to map pQTLs for over 300 different protein spots some of which co-localized with traits such as starch content and cold sweetening. pQTLs were observed on every chromosome although not evenly distributed over the chromosomes. The largest number of pQTLs was found for chromosome 8 and the lowest for chromosome number 10. For some 20 protein spots multiple QTLs were observed.
From this analysis, hotspot areas for protein QTLs were identified on chromosomes three, five, eight and nine. The hotspot on chromosome 3 coincided with a QTL previously identified for total protein content and had more than 23 pQTLs in the region from 70 to 80 cM. Some of the co-localizing protein spots associated with some of the most interesting tuber quality traits were identified, albeit far less than we had anticipated at the onset of the experiments.
转录组学、代谢组学和蛋白质组学等组学技术的最新进展以及基因分型分析，使得对非模式物种的复杂性状（如品质性状）进行遗传剖析成为可能。为了更深入地了解与碳水化合物和淀粉代谢及冷甜相关的品质性状变异的遗传因素，我们使用 2D 凝胶电泳在二倍体马铃薯作图群体中测定了马铃薯块茎中的蛋白质含量和组成。在分析过程中，我们确保排除了 patatin 家族的蛋白质，以确保更好地代表其他蛋白质。
我们随后对群体中具有足够代表性的所有其他蛋白质进行了 pQTL 分析，并通过在遗传图谱上的共定位以及蛋白质丰度和表型性状的直接相关研究，建立了蛋白质与 26 个马铃薯块茎品质性状（如果肉颜色、酶促变色）之间的关系。在两个收获期共检测到超过 1643 个独特的蛋白质斑点。我们能够对超过 300 个不同蛋白质斑点进行 pQTL 作图，其中一些与淀粉含量和冷甜等性状共定位。pQTL 存在于每条染色体上，但在染色体上的分布不均匀。第 8 号染色体上观察到的 pQTL 数量最多，第 10 号染色体上观察到的 pQTL 数量最少。对于大约 20 个蛋白质斑点，观察到多个 QTL。
从这项分析中，确定了染色体 3、5、8 和 9 上蛋白质 QTL 的热点区域。第 3 号染色体上的热点区域与先前鉴定的总蛋白质含量 QTL 相吻合，在 70 到 80 cM 的区域内有超过 23 个 pQTL。尽管远少于实验开始时的预期，但我们确定了一些与最有趣的块茎品质性状相关的共定位蛋白质斑点。
