Phenotypic characterization and genetic dissection of nine agronomic traits in Tokachi nagaha and its derived cultivars in soybean (Glycine max (L.) Merr.).
By using the soybean founder parent Tokachi nagaha and its 137 derived cultivars as materials, a genome-wide association analysis was performed to identify the single nucleotide polymorphisms (SNPs) underlying soybean yield and quality related traits at two planting densities. Results of ANOVA showed that genotype, environment, and genotype by environment interaction effects were all significant for each trait. The Tokachi nagaha-derived soybean population could be divided into two subpopulations based on molecular data, and accessions in each subpopulation were almost all from the same Chinese province. Relatedness was detected between pair-wise accessions within the population. Linkage disequilibrium was obvious and the level of intra-chromosome linkage disequilibrium was about 8370kb. A total of 40 SNPs with significant signal were detected and distributed across 18 chromosomes. Some SNP markers were located in or near regions where QTLs have been previously mapped by linkage analysis. Nineteen SNPs were identified both in low- and high- density planting treatments, indicating those loci were common and sTable Sixteen SNPs were co-associated with two or more different traits, suggesting that some of the QTLs/genes underlying those identified SNPs were likely to be pleiotropic.
National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China. Electronic address: liuzhangxiong@caas.cn.
Zhangxiong
Z
Liu
National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China. Electronic address: lihuihui@caas.cn.
Huihui
H
Li
Institute of Soybean Research, Jilin Academy of Agricultural Sciences, Changchun 130124, China. Electronic address: fxher@126.com.
Xuhong
X
Fan
Tonghua Academy of Agricultural Sciences, Meihekou 135007, China. Electronic address: huangwen_110@163.com.
Wen
W
Huang
Jilin City Academy of Agricultural Sciences, Jilin 132101, China. Electronic address: jlyangjiyu@163.com.
Jiyu
J
Yang
Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, USA. Electronic address: wzxsoy@msu.edu.
Zixiang
Z
Wen
National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China. Electronic address: liyinghui@caas.cn.
Yinghui
Y
Li
National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China. Electronic address: guanrongxia@caas.cn.
Rongxia
R
Guan
National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China. Electronic address: guoyong@caas.cn.
Yong
Y
Guo
National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China. Electronic address: rx_guan@sina.com.
Ruzhen
R
Chang
Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, USA. Electronic address: wangdech@msu.edu.
Dechun
D
Wang
Department of Crop, Soil and Environment Sciences, University of Arkansas, Fayetteville 72701, USA. Electronic address: pchen@uark.edu.
Pengyin
P
Chen
Institute of Soybean Research, Jilin Academy of Agricultural Sciences, Changchun 130124, China. Electronic address: shumingw@263.net.
Shuming
S
Wang
National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China. Electronic address: qiulijuan@caas.cn.
Li-Juan
LJ
Qiu
D000383:Agriculture; D000704:Analysis of Variance; D002681:China; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D018556:Crops, Agricultural / Q000235:genetics; D004777:Environment; D017343:Genes, Plant; D056726:Genetic Association Studies; D008040:Genetic Linkage; D058685:Genetic Pleiotropy; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D015810:Linkage Disequilibrium; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D013025:Glycine max / Q000235:genetics* / Q000254:growth & development; D013045:Species Specificity
Agronomic traits; Cultivars; Genome-wide association mapping; Soybean