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

• Published in: PloS one 2019-10, Vol.14 (10), p.e0223674
• Main Authors: Wang, Xinxin, Cheng, Yanbo, Yang, Ce, Yang, Cunyi, Mu, Yinghui, Xia, Qiuju, Ma, Qibin
• Format: Article
• Language: English
• Subjects: Acidic soils; Adaptation, Biological - genetics; Agricultural production; Agriculture; Aluminum; Aluminum - toxicity; Barley; Biological Variation, Population; Biology and Life Sciences; Chromosome Mapping; Chromosomes; Computational Biology - methods; Computer-integrated manufacturing; Crop production; Crops; Cultivars; Cultivation; Ecology and Environmental Sciences; Elongation; Engineering research; Functional analysis; Gene expression; Gene mapping; Gene Ontology; Genes; Genetic Linkage; Genomes; Genomics; Glycine max - drug effects; Glycine max - genetics; High-Throughput Nucleotide Sequencing; Hydroponics; Inbreeding; Laboratories; Loam soils; Mapping; Phenotype; Phenotypic variations; Physical Sciences; Physiology; Pollution tolerance; Polymorphism; Polymorphism, Single Nucleotide; Quantitative genetics; Quantitative Trait Loci; Quantitative Trait, Heritable; Research and Analysis Methods; Sequence Analysis, DNA; Signal transduction; Soils; Soybeans; Toxicity; Wheat
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0223674

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.