Quantitative trait loci mapping for flooding tolerance at an early growth stage of soybean recombinant inbred line population

Abstract

Flooding stress causes a significant yield reduction in soybean. The early growth of soybean in Korea coincides with the rainy season, potentially exposing to flooding stress. Greenhouse experiments were conducted to map the quantitative trait loci (QTL) for flooding tolerance in soybean and to identify and investigate candidate genes near the QTL hot spots. Flood stress was imposed at V1–V2 stage on a recombinant inbred line population (‘Paldalkong’ × ‘NTS1116’), and leaf chlorophyll content (CC) and shoot dry weight (DW) were measured under control and flooded conditions. The genetic map was constructed using 180K Axiom® SoyaSNP markers. The QTL were analysed under control and flooded conditions as well as for index (ratio of CC or DW under flooded to control, CCI and DWI) and flooding tolerance index (FTI, mean of CCI and DWI). A total of 20 QTL with LOD scores 3.59–19.73 causing 5.8%–33.3% phenotypic variation were identified on nine chromosomes. Chromosomes 10, 12 and 13 harboured relatively more stable QTL. Results of this study could be useful to further understand the genetic basis of soybean's flooding tolerance and applied in breeding programmes.

Analysis of differentially expressed genes in soybean leaf tissue of tolerant and susceptible cultivars under flooding stress revealed by RNA sequencing

“…The results of some stress-related DEGs by RNA-Seq in this study were comparatively analyzed with putative genes in the QTL associated with flooding tolerance (Dhungana et al 2020). Several genes located in the QTL regions were also found by RNA-Seq to contribute to flooding and other abiotic tolerance.…”

“…The recombinant inbred line (RIL) populations for QTL were developed using the tolerant ('Paldalkong' and 'Danbaekkong') and susceptible ('NTS1116') cultivars as parents which were also used for RNA-Seq in this study. The QTL result of one of the RIL populations was published (Dhungana et al 2020). QTL map-based identification of DEGs may allow us to find the putative genes related to flooding tolerance and to verify the results of RNA-Seq study.…”

Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean

“…For seed-flooding tolerance, four QTLs were detected based on examination of germination rate and normal seedling rate [ 142 ], and 33 QTLs were identified using relative seedling length as a flooding tolerance indicator [ 143 ]. At the early vegetative growth stage, seven [ 13 ] and 20 QTLs [ 144 ] associated with flooding tolerance were obtained through phenotypic analyses of chlorophyll content, dry weight of shoot, and seed weight. Notably, seven QTLs were mapped for hypoxia-tolerant index of root development traits [ 145 ].…”

“…Furthermore, a tolerant allele of qWT_Gm03 promoted soybean growth under waterlogging stress through regulation of root architecture and plasticity [ 146 ]. Chromosome region analysis showed that these QTLs for flooding tolerance were mainly located on chromosomes 4, 9, 10, 12, 13, and 14 [ 144 , 145 , 146 ]. In addition, proteomic studies indicated that chromosomes 5, 10, 11, and 13 contained abundant flooding response genes [ 20 , 23 ]; however, chromosome 17 contained more tolerant genes [ 23 ].…”

Integrating RNA Sequencing and Quantitative Trait Locus Mapping to Identify Potential Candidate Genes for Flooding Tolerance in Soybean

“…At the seed germination stage, two studies have identified 25 (Yu et al 2019) and four (Sayama et al 2009) QTLs for seed-flooding tolerance. Recently, 20 QTLs for flooding tolerance at the V1-V2 stages of soybean have been identified on nine chromosomes (Dhungana et al 2020a). In another QTL study conducted at early growth stage has reported seven QTLs (Githiri et al 2006).…”