Abstract
The number of four-seed pods is one of the most important agronomic traits affected by gene and environment that can potentially improve soybean (Glycine max) yield. However, the gene regulatory network that affects the ratio of four-seed pod (the ratio of the number of four-seed pods to the total number of pods in each individual plant) is yet unclear. Here, we performed bulked segregant RNA sequencing (BSR-seq) on a series of recombinant inbred lines (RILs) derived from hybrid progenies between Heinong 48 (HN48), a cultivar with a high ratio of four-seed pod, and Henong 64 (HN64), a cultivar with a low ratio of four-seed pod. Two tissues, flower bud and young pod, at two different growth stages, R1 and R3, were analyzed under the ratios of four-seed pod at less than 10% and greater than 30%, respectively. To identify the potential gene regulation pathways associated with the ratio of soybean four-seed pod, we performed differentially expressed analysis on the four bulked groups. A differentially expressed gene (DEG) encoding a photosystem II 5-kDa protein had the function of participating in the energy conversion of photosynthesis. In addition, 79 common DEGs were identified at different developmental stages and under different ratios of four-seed pod. Among them, four genes encoding calcium-binding proteins and a WRKY transcription factor were enriched in the plant–pathogen interaction pathway, and they showed a high level of expression in roots. Moreover, 10 DEGs were identified in the reported quantitative trait locus (QTL) interval of four-seed pod, and two of them were significantly enriched in the pentose and glucuronate interconversion pathway. These findings provide basic insights into the understanding of the underlying gene regulatory network affected by specific environment and lay the foundation for identifying the targets that affect the ratio of four-seed pod in soybean.
Highlights
Soybean (Glycine max [L.] Merr.) is one of the most important protein and oil crops worldwide (Wang and Tian, 2015)
To research the genetic mechanism of the ratio of four-seed pod, two soybean cultivars, the variety Henong 64 (HN64) with a low ratio of fourseed pods (Supplementary Figure 1A and Figure 1) and the variety Heinong 48 (HN48) with a high ratio of four-seed pods (Supplementary Figure 1B and Figure 1), were crossed and further inbred for over five generations to construct the recombinant inbred lines (RILs) population
Recent genetic studies have identified Ln gene and many main effect quantitative trait locus (QTL) that affect the trait of the four-seed pod, but it is essential to further study the main effect genes affecting the ratios of four-seed pod
Summary
Soybean (Glycine max [L.] Merr.) is one of the most important protein and oil crops worldwide (Wang and Tian, 2015). Six stable main effect quantitative trait loci (QTLs) controlling the number of four-seed pods have been identified among 11 different environments (Asakura et al, 2012; Yang et al, 2013). Ln gene affects the external outline of the formation of four-seed pod, while the exploration of gene regulation pathways in specific environment is to understand the internal details of the formation of four-seed pod under different four-seed pod ratios. This implies the phenotypic effect of environment conditions, namely, environmental adaptability, and is an important aspect of adaptive breeding
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