QTL mapping for aluminum tolerance in RIL population of soybean (Glycine max L.) by RAD sequencing

Xinxin Wang; Yanbo Cheng; Ce Yang; Cunyi Yang; Yinghui Mu; Qiuju Xia; Qibin Ma

doi:10.1371/journal.pone.0223674

QTL mapping for aluminum tolerance in RIL population of soybean (Glycine max L.) by RAD sequencing

PLoS One. 2019 Oct 29;14(10):e0223674. doi: 10.1371/journal.pone.0223674. eCollection 2019.

Authors

Xinxin Wang^{1

2

3}, Yanbo Cheng^{1

2

3}, Ce Yang^{1

2

3}, Cunyi Yang^{1

2

3}, Yinghui Mu^{1

2

3}, Qiuju Xia⁴, Qibin Ma^{1

2

3}

Affiliations

¹ The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
² The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
³ The National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, Guangdong, China.
⁴ The Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.

Abstract

Aluminum (Al3+) toxicity is a typical abiotic stress that severely limits crop production in acidic soils. In this study, an RIL (recombinant inbred line, F12) population derived from the cross of Zhonghuang 24 (ZH 24) and Huaxia 3 (HX 3) (160 lines) was tested using hydroponic cultivation. Relative root elongation (RRE) and apical Al3+ content (AAC) were evaluated for each line, and a significant negative correlation was detected between the two indicators. Based on a high-density genetic linkage map, the phenotypic data were used to identify quantitative trait loci (QTLs) associated with these traits. With composite interval mapping (CIM) of the linkage map, five QTLs that explained 39.65% of RRE and AAC variation were detected on chromosomes (Chrs) Gm04, Gm16, Gm17 and Gm19. Two new QTLs, qRRE_04 and qAAC_04, were located on the same region of bin93-bin94 on Chr Gm04, which explained 7.09% and 8.98% phenotypic variation, respectively. Furthermore, the results of the expression analysis of candidate genes in the five genetic regions of the QTLs showed that six genes (Glyma.04g218700, Glyma.04g212800, Glyma.04g213300, Glyma.04g217400, Glyma.04g216100 and Glyma.04g220600) exhibited significant differential expression between the Al3+ treatment and the control of two parents. The results of qRT-PCR analysis indicated that Glyma.04g218700 was upregulated by Al3+ treatment with the hundreds-fold increased expression level and may be a candidate gene with potential roles in the response to aluminum stress. Therefore, our efforts will enable future functional analysis of candidate genes and will contribute to the strategies for improvement of aluminum tolerance in soybean.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adaptation, Biological / genetics*
Aluminum / toxicity*
Biological Variation, Population
Chromosome Mapping*
Computational Biology / methods
Gene Ontology
Genetic Linkage
Glycine max / drug effects*
Glycine max / genetics*
High-Throughput Nucleotide Sequencing
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci*
Quantitative Trait, Heritable*
Sequence Analysis, DNA

Substances

Aluminum

Grants and funding

This work was supported by The Project of Science and Technology of Guangzhou (201804020015)-(Hai Nian, prepared the soybean materials used in this study); The Major Project of New Varieties Cultivation of Genetically Modified Organisms (2016ZX08004002-007)-(Qibin Ma, designed the research program; The Project of Molecular Design Breeding for Major Economic Crops (2016YFD0101901)-(Cunyi Yang, designed the research program; The Project of the National Natural Sciences Foundation of China (31771816)-(Qibin Ma); The Project of the National Key R and D Program of China (2017YFD0101500)-(Hai Nian); The Project of the China Agricultural Research System (CARS-04-PS09)-(Hai Nian.