Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Rd, Cambridge, CB3 0LE, UK.
Planta. 2024 Nov 18;260(6):142. doi: 10.1007/s00425-024-04577-x.
Association analysis identified 77 marker-trait associations (MTAs) for PUE traits, of which 10 were high-confidence MTAs. Candidate-gene mining and in-silico expression analysis identified 13 putative candidate genes for PUE traits. Bread wheat (Triticum aestivum L.) is a major cereal crop affected by phosphorus (P) deficiency, which affects root characteristics, plant biomass, and other attributes related to P-use efficiency (PUE). Understanding the genetic mechanisms of PUE traits helps in developing bread wheat cultivars that perform well in low-P environments. With this objective, we evaluated a bread wheat panel comprising 304 accessions for 14 PUE traits with high-throughput phenotyping under low-P and optimum-P treatments and observed a significant genetic variation among germplasm lines for studied traits. Genome-wide association study (GWAS) using 14,025 high-quality single-nucleotide polymorphisms identified 77 marker-trait associations (MTAs), of which 10 were chosen as high-confidence MTAs as they had > 10% phenotypic variation with logarithm of odds (LOD) scores of more than five. Candidate-gene (CG) mining from high-confidence MTAs identified 180 unique gene models, of which 78 were differentially expressed (DEGs) with at least twofold change in expression under low-P over optimum-P. Of the 78-DEGs, 13 were thought to be putative CGs as they exhibited functional relevance to PUE traits. These CGs mainly encode for important proteins and their products involved in regulating root system architecture, P uptake, transport, and utilization. Promoter analysis from 1500 bp upstream of gene start site for 13 putative CGs revealed the presence of light responsive, salicylic-acid responsive, gibberellic-acid (GA)-responsive, auxin-responsive, and cold responsive cis-regulatory elements. High-confidence MTAs and putative CGs identified in this study can be employed in breeding programs to improve PUE traits in bread wheat.
关联分析鉴定了 77 个与 PUE 性状相关的标记-性状关联 (MTA)，其中 10 个是高置信度的 MTA。候选基因挖掘和计算机表达分析鉴定了 13 个与 PUE 性状相关的假定候选基因。普通小麦 (Triticum aestivum L.) 是一种受磷 (P) 缺乏影响的主要粮食作物，这会影响根系特征、植物生物量和其他与磷利用效率 (PUE) 相关的属性。了解 PUE 性状的遗传机制有助于开发在低 P 环境下表现良好的普通小麦品种。为此，我们使用高通量表型分析评估了由 304 个品种组成的普通小麦群体，在低 P 和最佳 P 处理下对 14 个 PUE 性状进行了评估，并观察到供试品系之间存在显著的遗传变异。使用 14025 个高质量的单核苷酸多态性进行全基因组关联研究 (GWAS)，鉴定了 77 个标记-性状关联 (MTA)，其中 10 个被选为高置信度的 MTA，因为它们的表型变异超过 10%，对数优势 (LOD) 分数超过 5。从高置信度的 MTA 中挖掘候选基因 (CG) 确定了 180 个独特的基因模型，其中 78 个在低 P 下的表达水平与最佳 P 相比至少有两倍的变化，这些差异表达的基因 (DEGs) 显示出与 PUE 性状相关的功能相关性。在 78 个 DEGs 中，有 13 个被认为是假定的 CG，因为它们表现出与 PUE 性状相关的功能相关性。这些 CG 主要编码参与调节根系结构、P 吸收、运输和利用的重要蛋白质及其产物。对 13 个假定 CG 的基因起始位点上游 1500bp 的启动子分析表明，存在光响应、水杨酸响应、赤霉素 (GA)-响应、生长素响应和冷响应顺式作用元件。本研究中鉴定的高置信度的 MTA 和假定的 CG 可用于小麦的育种计划，以提高 PUE 性状。
