Mining candidate genes for rice cadmium accumulation in the shoot through a genome-wide association study and transcriptomic analysis.
Mining candidate genes for rice cadmium accumulation in the shoot through a genome-wide association study and transcriptomic analysis.
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通过全基因组关联研究和转录组分析挖掘水稻地上部镉积累的候选基因
DOI：
10.3389/fgene.2022.944529
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发表时间：
2022
影响因子：
3.7
通讯作者：
Zhao, Junliang
中科院分区：
文献类型：
--
作者：
Wang, Jian;Yang, Wu;Zhang, Shaohong;Dong, Jingfang;Yang, Tifeng;Ma, Yamei;Zhou, Lian;Chen, Jiansong;Liu, Bin;Zhao, Junliang
水稻中镉的高富集严重威胁着人类的健康。水稻Cd积累的遗传机制非常复杂。为了确定水稻种质资源Cd低积累的遗传机制，探索Cd积累的遗传机制，挖掘对水稻低Cd积累品种育种有重要意义的精英基因，本研究对水稻茎部Cd浓度进行了全基因组关联研究（GWAS）。从1568份籼稻材料中筛选出315份不同的籼稻材料，共含有70万个snp。在高速率的连锁不平衡（LD）衰减中，鉴定出8个与水稻Cd积累有关的qtl。转录组学分析显示，根中有799个差异表达基因（deg），茎中有857个差异表达基因（deg），这可能是造成Cd富集高、低品种间Cd积累差异显著的原因。在qCd11-1中，我们检测到一个关键的候选基因LOC_Os11g11050，该基因编码一个起始因子，在高Cd积累品种和低Cd积累品种的根中表达不同。Cd处理下，LOC_Os11g11050在Cd积累高、低品种中的表达量均显著降低。序列比较和qRT-PCR结果显示，LOC_Os11g11050启动子区存在与LOC_Os11g11050表达水平相关的indel序列和碱基置换，以及高、低Cd积累材料地上部Cd浓度表型差异。LOC_Os11g11050可能在Cd积累中起重要作用。本研究结果为籼稻低Cd积累和候选功能基因的研究以及籼稻Cd积累的分子机制提供了宝贵的资源。利用籼稻Cd积累的遗传结构，可以进一步利用籼稻低Cd基因降低水稻Cd积累。
High cadmium (Cd) accumulation in rice is a serious threat to human health. The genetic mechanism of Cd accumulation in rice is highly complicated. To identify the low Cd accumulation in rice germplasm, investigate the genetic mechanism underlying Cd accumulation, and mine the elite genes of significant importance for rice breeding of low Cd accumulation varieties, we performed a genome-wide association study (GWAS) for rice Cd concentration in the shoot. The rice accessions were 315 diverse indica rice accessions selected from the 1568 rice accessions with 700,000 SNPs. Within the high rate of linkage disequilibrium (LD) decay, eight QTLs related to rice Cd accumulation were identified. Transcriptomic analysis showed there were 799 differentially expressed genes (DEGs) in the root and 857 DEGs in the shoot, which are probably considered to be the cause of the significant difference in Cd accumulation between high and low Cd accumulation varieties. In qCd11-1, we detected a crucial candidate gene, LOC_Os11g11050, which encodes an initiation factor, expressed differently in the root between the high and low Cd accumulation varieties. Furthermore, under Cd treatment, the expression levels of LOC_Os11g11050 significantly decreased in both the high and low Cd accumulation varieties. Sequence comparison and qRT-PCR revealed that there were indel sequences and base substitutions in the promoter region of LOC_Os11g11050 correlated with the LOC_Os11g11050 expression level, as well as the phenotype of Cd concentration differences in shoot between the high and low Cd accumulation accessions. LOC_Os11g11050 might play important roles in Cd accumulation. The results of our study provide valuable resources for low Cd accumulation in indica varieties and the candidate functional gene, as well as molecular mechanisms for Cd accumulation in indica rice. The genetic architecture underlying Cd accumulation in indica can be used for further applying the low Cd gene existing in indica for decreasing Cd accumulation in rice.
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影响因子：
4.6
作者：
Tang L;Mao B;Li Y;Lv Q;Zhang L;Chen C;He H;Wang W;Zeng X;Shao Y;Pan Y;Hu Y;Peng Y;Fu X;Li H;Xia S;Zhao B
通讯作者：
Zhao B
agriGO v2.0：农业社区的 GO 分析工具包，2017 年更新
影响因子：
14.9
作者：
Tian T;Liu Y;Yan H;You Q;Yi X;Du Z;Xu W;Su Z
通讯作者：
Su Z
DOI：
10.1186/s12284-021-00530-8
发表时间：
2021-10-24
期刊：
Rice (New York, N.Y.)
影响因子：
--
作者：
Tang L;Dong J;Tan L;Ji Z;Li Y;Sun Y;Chen C;Lv Q;Mao B;Hu Y;Zhao B
通讯作者：
Zhao B
影响因子：
2
作者：
Nakanishi, Hiromi;Ogawa, Ippei;Nishizawa, Naoko K.
通讯作者：
Nishizawa, Naoko K.
影响因子：
3.7
作者：
Gu, Haiyong;Liang, Shihu;Zhao, Junliang
通讯作者：
Zhao, Junliang