Identification of Major QTL for Waterlogging Tolerance Using Genome-Wide Association and Linkage Mapping of Maize Seedlings
Identification of Major QTL for Waterlogging Tolerance Using Genome-Wide Association and Linkage Mapping of Maize Seedlings
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利用玉米幼苗全基因组关联和连锁图谱鉴定耐涝主要 QTL
DOI：
10.1007/s11105-012-0526-3
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发表时间：
2012-11
影响因子：
2.1
通讯作者：
Yue, Bing
中科院分区：
文献类型：
--
作者：
Qiu, Fazhan;Tang, Bin;Yu, Feng;Li, Liu;Wang, Ming;Xue, Yadong;Zhang, Zuxin;Yan, Jianbing;Yue, Bing
为了探讨玉米幼苗对渍水反应的遗传基础，我们利用45,868个SNPs对144个玉米自交系进行了全基因组关联研究，测量了正常和淹水条件下玉米幼苗的根和茎的长度、鲜重和干重。根据种群结构结果将该小组划分为三个亚组，LD衰变距离为180kb。还利用双亲先进回交(AB)群体检测了数量性状座位(QTL)。在对16种不同模型的比较中，主成分分析(主成分分析/TOP PC3) + K被发现最能减少进一步分析的假阳性关联。全基因组扫描在第5、6和9染色体上检测到4个与受涝反应显著相关的峰信号(P<； 2.18 × 10−5)。SNP4784、SNP200、SNP298和SNP6314在受涝条件下与相应的性状显著相关，分别解释了14.99~19.36%、15.75~17.64%、16.08%和15.44%的表型变异。已鉴定的SNP分别位于GRMZM2G012046、GRMZM2G009808、GRMZM2G137108和GRMZM2G369629(AGPV1)。SNP4784(GRMZM2G012046)与AB群体中具有相同性状的主QTL共定位。在关联图谱中发现了4 7个与6个性状显著相关的SNP(P<； 2.18 × 10−4)，其中33个SNP已被文献报道为与内涝有关的性状。这些结果将有助于阐明玉米自交系对湿涝胁迫的差异反应和耐性的遗传基础，并为利用分子标记辅助选择改良玉米自交系的耐涝能力提供新的基因座。
To investigate the genetic basis of maize seedling response to waterlogging, we performed a genome-wide association study in 144 maize inbred lines, measuring length, fresh and dry weight of roots and shoots under normal and waterlogged conditions using 45,868 SNPs. This panel was divided into three subgroups based on the population structure results and the LD decay distance was 180 kb. A biparental advanced backcross (AB) population was also used to detect quantitative trait loci (QTL). In a comparison of 16 different models, principal components analysis (PCA/top PC3) + K was found to be best for reduction of false-positive associations for further analysis. A whole-genome scan detected four strong peak signals (P< 2.18 × 10−5) significantly associated with the waterlogging response on chromosomes 5, 6 and 9. SNP4784, SNP200, SNP298, and SNP6314 showed significant association with corresponding traits under waterlogging and explained 14.99–19.36 %, 15.75–17.64 %, 16.08 % and 15.44 % of the phenotypic variation, respectively. The identified SNPs were located in GRMZM2G012046, GRMZM2G009808, GRMZM2G137108 and GRMZM2G369629 (AGPV1). SNP4784 (GRMZM2G012046) was colocalized with the major QTL that was identified with the same traits in the AB population. Forty-seven SNPs significantly associated (P< 2.18 × 10−4) with six traits in association mapping were identified and, among these, 33 SNPs were already reported in literature as waterlogging-related traits. These results will help elucidate the genetic basis of differential responses and tolerance to waterlogging stress among maize inbred lines, and provide novel loci for improvement of waterlogging tolerance of maize inbred lines using marker-assisted selection.
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影响因子：
56.9
作者：
T. Mackay
通讯作者：
T. Mackay
影响因子：
5.8
作者：
P. H. Zaidi;S. Rafique;P. Rai;N. Singh;G. Srinivasan
通讯作者：
P. H. Zaidi;S. Rafique;P. Rai;N. Singh;G. Srinivasan
影响因子：
2.9
作者：
Ching A;Caldwell KS;Jung M;Dolan M;Smith OS;Tingey S;Morgante M;Rafalski AJ
通讯作者：
Rafalski AJ
影响因子：
--
作者：
Ming Wang;Xiaobo Zhang;Jiuran Zhao;Wei Song;Yong-lian Zheng
通讯作者：
Ming Wang;Xiaobo Zhang;Jiuran Zhao;Wei Song;Yong-lian Zheng
影响因子：
3.3
作者：
Breseghello, F;Sorrells, ME
通讯作者：
Sorrells, ME