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

Abstract

Flooding stress causes a significant reduction in soybean yield. The development of flood-tolerant cultivars is an effective way to minimize yield loss due to flooding. Information on candidate genes for flooding tolerance is useful for developing tolerant lines. The objective of this study was to identify potential candidate genes for flooding tolerance in soybean by integrating the results of a quantitative trait locus analysis and RNA sequencing. A total of 19 genes showed good amplification in capillary electrophoresis and were further analyzed through a reverse transcription quantitative polymerase chain reaction (qRT-PCR); two of these genes showed differential expression among tolerant and susceptible lines. The expression of Glyma.12g030900 and Glyma.10g050300 in leaf and root tissues, respectively, was higher in several tolerant lines than in the susceptible lines under flooding stress. The chlorophyll index of the tolerant lines was also consistently higher than that of the susceptible lines over two years, supporting the qRT-PCR results. This study provides useful information on flooding tolerance in soybeans.

The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean – An review

“…GsCNGC20-f, GsCNGC20-g Enhanced calcium cascade (Li et al, 2022) GSNOR, NR Improved the cellular SNO level (Imran et al, 2022) Glyma.04g240800 Alcohol dehydrogenases (ADH) contributed to flooding tolerance (Lai et al, 2021) Glyma.12g030900, Glyma.10g050300 Showed higher expression in tolerant lines (Dhungana et al, 2021c) Glyma.01G2 31200, Glyma.08G083300…”

“…The tolerant soybean cultivar (I27) showed higher expression of genes involved in energy metabolism and detoxification and indicated a flood tolerance mechanism ( Casarotto et al., 2019 ). Two flood-tolerant genes ( Glyma.12g030900 , Glyma.10g050300 ) identified in leaf and root tissues showed higher expression in tolerant lines than in susceptible lines ( Dhungana et al., 2021c ). Core clock SUB1 and ABAR genes mediated flood tolerance in soybean by alternate splicing.…”