Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach
Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach
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DOI：
10.1007/s00122-021-03953-5
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发表时间：
2021-10-08
影响因子：
5.4
通讯作者：
Shobbar, Zahra-Sadat
中科院分区：
文献类型：
--
作者：
Daryani, Parisa;Darzi Ramandi, Hadi;Shobbar, Zahra-Sadat
应用整合的Meta分析方法获得了与水稻根系构型相关的Meta-QTL/候选基因，可用于MQTL辅助育种/根部性状基因工程。根系构型(RSA)是促进深层土壤水分和养分吸收和适应干旱胁迫条件的重要因素。本研究采用综合荟萃分析方法寻找与水稻RSA性状相关的候选基因和基因组区域。对过去20年在对照和干旱胁迫条件下控制RSA性状的34个独立试验中报告的425个初始QTL进行了全基因组Meta分析。在12条水稻染色体上共检测到64个一致偏QTL(MQTL)，分布不均。获得的QTL的可信区间为0.11~14.23 cM，平均为3.79 cM，比原始QTL的平均可信区间窄3.88倍。有趣的是，52个MQTL与水稻全基因组关联研究中报道的SNP峰位共定位于根形态性状。基于RNA-SEQ和微阵列数据，对这些与RSA相关的MQTL中的基因进行检测和探索，以寻找水稻根中的干旱响应基因。在这些MQTL中发现了多个与RSA和耐旱性相关的基因，包括与生长素生物合成或信号转导相关的基因(如Yucca、WOX、AUX/IAA、ARF)、根角度(DRO1相关基因)、侧根发育(如DSR、WRKY)、根直径(如OsNAC5)、植物细胞壁(如EXPA)和木质化(如C4H、PAL、PRX和CAD)。位于RSA的SNP峰位和QTL概述峰位的基因被认为是进一步功能分析的新的候选基因。这些有希望的候选基因和MQTL可以作为基因工程和MQTL辅助育种的基础，以提高产量潜力、稳定性和在水分胁迫环境中的表现。
Key message Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA-related MQTLs were detected and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance-associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA), and lignification (e.g. C4H, PAL, PRX and CAD). The genes located within both the SNP peak positions and the QTL-overview peaks for RSA are suggested as novel candidate genes for further functional analysis. The promising candidate genes and MQTLs can be used as basis for genetic engineering and MQTL-assisted breeding of root phenotypes to improve yield potential, stability and performance in a water-stressed environment.