Genome-Wide Association Study and Genomic Prediction Elucidate the Distinct Genetic Architecture of Aluminum and Proton Tolerance in Arabidopsis thaliana
Genome-Wide Association Study and Genomic Prediction Elucidate the Distinct Genetic Architecture of Aluminum and Proton Tolerance in Arabidopsis thaliana
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DOI：
10.3389/fpls.2020.00405
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发表时间：
2020-04
影响因子：
5.6
通讯作者：
Yuki Nakano;Kazutaka Kusunoki;O. Hoekenga;Keisuke Tanaka;S. Iuchi;Y. Sakata;Masatomo Kobayashi;Yoshiharu Y. Yamamoto;H. Koyama;Yuriko Kobayashi
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文献类型：
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作者：
Yuki Nakano;Kazutaka Kusunoki;O. Hoekenga;Keisuke Tanaka;S. Iuchi;Y. Sakata;Masatomo Kobayashi;Yoshiharu Y. Yamamoto;H. Koyama;Yuriko Kobayashi
在酸性土壤条件下，会发生铝胁迫和质子胁迫，降低根系的生长和功能。然而，这些压力源是不同的，对每一种压力源的耐受性由多种生理过程控制。为了更好地了解这些巧合但实验上可分离的压力的基础基因，全基因组关联研究（GWAS）和基因组预测（GP）模型创建了约200个不同的拟南芥加入。GWAS和基因组预测分别确定了140/160个与Al和质子耐受性相关的SNP，这解释了观察到的约70%的方差。基因座中基因的反向遗传学鉴定了新的铝和质子耐受性基因，包括TON 1-受体基序28（AtTRM 28）和硫氧还蛋白H型1（AtTRX 1），以及已知与耐受性相关的基因，如铝激活的苹果酸转运蛋白AtALMT 1。此外，铝耐受性的变化部分解释了由顺式调节等位基因变异引起的AtALMT 1和AtTRX 1的表达水平多态性。这些结果表明，我们成功地确定了调控铝和质子耐受性的位点。此外，由GWAS确定的Al和质子耐受性共享非常少量的位点。基因组预测的耐铝表型与观察到的耐铝表型之间存在显著差异。这表明GWAS检测不到的遗传因素（例如，稀有等位基因突变）对耐铝性的影响比对耐质子性的影响更大。这项研究提供了重要的新见解的遗传结构，产生变异的酸性土壤的耐受性。
Under acid soil conditions, Al stress and proton stress can occur, reducing root growth and function. However, these stressors are distinct, and tolerance to each is governed by multiple physiological processes. To better understand the genes that underlie these coincidental but experimentally separable stresses, a genome-wide association study (GWAS) and genomic prediction (GP) models were created for approximately 200 diverse Arabidopsis thaliana accessions. GWAS and genomic prediction identified 140/160 SNPs associated with Al and proton tolerance, respectively, which explained approximately 70% of the variance observed. Reverse genetics of the genes in loci identified novel Al and proton tolerance genes, including TON1-RECRUITING MOTIF 28 (AtTRM28) and THIOREDOXIN H-TYPE 1 (AtTRX1), as well as genes known to be associated with tolerance, such as the Al-activated malate transporter, AtALMT1. Additionally, variation in Al tolerance was partially explained by expression level polymorphisms of AtALMT1 and AtTRX1 caused by cis-regulatory allelic variation. These results suggest that we successfully identified the loci that regulate Al and proton tolerance. Furthermore, very small numbers of loci were shared by Al and proton tolerance as determined by the GWAS. There were substantial differences between the phenotype predicted by genomic prediction and the observed phenotype for Al tolerance. This suggested that the GWAS-undetectable genetic factors (e.g., rare-allele mutations) contributing to the variation of tolerance were more important for Al tolerance than for proton tolerance. This study provides important new insights into the genetic architecture that produces variation in the tolerance of acid soil.