Integrating QTL mapping and transcriptomics identifies candidate genes underlying QTLs associated with soybean tolerance to low-phosphorus stress.
Soybean is a high phosphorus (P) demand species that is sensitive to low-P stress. Although many quantitative trait loci (QTL) for P efficiency have been identified in soybean, but few of these have been cloned and agriculturally applied mainly due to various limitations on identifying suitable P efficiency candidate genes. Here, we combined QTL mapping, transcriptome profiling, and plant transformation to identify candidate genes underlying QTLs associated with low-P tolerance and response mechanisms to low-P stress in soybean. By performing QTL linkage mapping using 152 recombinant inbred lines (RILs) that were derived from a cross between a P-efficient variety, Nannong 94-156, and P-sensitive Bogao, we identified four major QTLs underlying P efficiency. Within these four QTL regions, 34/81 candidate genes in roots/leaves were identified using comparative transcriptome analysis between two transgressive RILs, low-P tolerant genotype B20 and sensitive B18. A total of 22 phosphatase family genes were up-regulated significantly under low-P condition in B20. Overexpression of an acid phosphatase candidate gene, GmACP2, in soybean hairy roots increased P efficiency by 15.43-24.54 % compared with that in controls. Our results suggest that integrating QTL mapping and transcriptome profiling could be useful for rapidly identifying candidate genes underlying complex traits, and phosphatase-encoding genes, such as GmACP2, play important roles involving in low-P stress tolerance in soybean.
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, People's Republic of China. zhangd@henau.edu.cn.
Dan
D
Zhang
Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA.
Hengyou
H
Zhang
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, People's Republic of China.
Shanshan
S
Chu
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, People's Republic of China.
Hongyan
H
Li
National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
Yingjun
Y
Chi
Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA.
Daniella
D
Triebwasser-Freese
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, People's Republic of China.
Haiyan
H
Lv
National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, No. 1 Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
Deyue
D
Yu
D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D005838:Genotype; D010744:Phosphoric Monoester Hydrolases / Q000235:genetics / Q000378:metabolism; D010758:Phosphorus / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D040641:Quantitative Trait Loci; D013025:Glycine max / Q000235:genetics* / Q000502:physiology; D013312:Stress, Physiological
D010940:Plant Proteins; D010758:Phosphorus; D010744:Phosphoric Monoester Hydrolases
GmACP2; Low-phosphorus stress; Phosphatases; Quantitative trait locus mapping; Soybean; Transcriptome profiling