He Kunhui, Zhao Zheng, Ren Wei, Chen Zhe, Chen Limei, Chen Fanjun, Mi Guohua, Pan Qingchun, Yuan Lixing
College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, MOE, China Agricultural University, Beijing, 100193, China.
Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China.
Theor Appl Genet. 2023 May 15;136(6):127. doi: 10.1007/s00122-023-04376-0.
A new strategy that integrated multiple public data resources was established to construct root gene co-expression network and mine genes regulating root system architecture in maize. A root gene co-expression network, containing 13,874 genes, was constructed. A total of 53 root hub genes and 16 priority root candidate genes were identified. One priority root candidate was further functionally verified using overexpression transgenic maize lines. Root system architecture (RSA) is crucial for crops productivity and stress tolerance. In maize, few RSA genes are functionally cloned, and effective discovery of RSA genes remains a great of challenge. In this work, we established a strategy to mine maize RSA genes by integrating functionally characterized root genes, root transcriptome, weighted gene co-expression network analysis (WGCNA) and genome-wide association analysis (GWAS) of RSA traits based on public data resources. A total of 589 maize root genes were collected by searching well-characterized root genes in maize or homologous genes of other species. We performed WGCNA to construct a maize root gene co-expression network containing 13874 genes based on public available root transcriptome data, and further discovered the 53 hub genes related to root traits. In addition, by the prediction function of obtained root gene co-expression network, a total of 1082 new root candidate genes were explored. By further overlapping the obtained new root candidate gene with the root-related GWAS of RSA candidate genes, 16 priority root candidate genes were identified. Finally, a priority root candidate gene, Zm00001d023379 (encodes pyruvate kinase 2), was validated to modulate root open angle and shoot-borne roots number using its overexpression transgenic lines. Our results develop an integration analysis method for effectively exploring regulatory genes of RSA in maize and open a new avenue to mine the candidate genes underlying complex traits.
建立了一种整合多种公共数据资源的新策略，以构建根基因共表达网络并挖掘调控玉米根系结构的基因。构建了一个包含13874个基因的根基因共表达网络。共鉴定出53个根枢纽基因和16个优先根候选基因。利用过表达转基因玉米品系对一个优先根候选基因进行了功能验证。根系结构（RSA）对作物生产力和胁迫耐受性至关重要。在玉米中，很少有RSA基因被功能克隆，有效发现RSA基因仍然是一个巨大的挑战。在这项工作中，我们基于公共数据资源，通过整合功能特征明确的根基因、根转录组、加权基因共表达网络分析（WGCNA）和RSA性状的全基因组关联分析（GWAS），建立了一种挖掘玉米RSA基因的策略。通过搜索玉米中功能特征明确的根基因或其他物种的同源基因，共收集了589个玉米根基因。我们进行了WGCNA，基于公开可用的根转录组数据构建了一个包含13874个基因的玉米根基因共表达网络，并进一步发现了53个与根性状相关的枢纽基因。此外，通过所获得的根基因共表达网络的预测功能，共探索了1082个新的根候选基因。通过将获得的新根候选基因与RSA候选基因的根相关GWAS进一步重叠，鉴定出16个优先根候选基因。最后，利用其过表达转基因品系验证了一个优先根候选基因Zm00001d023379（编码丙酮酸激酶2）可调节根张开角度和茎生根数量。我们的结果开发了一种有效探索玉米RSA调控基因的整合分析方法，并为挖掘复杂性状潜在候选基因开辟了一条新途径。
