Identification of Potential Gene Regulatory Pathways Affecting the Ratio of Four-Seed Pod in Soybean

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.

Identification of quantitative trait loci for lodging and related agronomic traits in soybean (Glycine max [L.] Merr.)

“…Notably, the primary QTLs for these traits consistently align with the main QTL for lodging score (qLD-4-1). In summary, many QTLs associated with lodging identi ed in this study show correlations with prior research results [21,22,30,35,37,[52][53][54][55][56][59][60][61][62][63][64][65][66][67][68][69][70]. The presence of shared QTL loci for various traits, such as growth period, seed type, grain weight per plant, number of pods per plant, stem diameter, and plant height, suggests the reliability of the QTL mapping in this study.…”

“…Comparing the results of this study with previous research, it was discovered that the Glyma.04G050200 gene within the major QTL (qLD-4-1) for lodging score has been previously associated with controlling the growth period. Its physical location corresponds to a range of 4075901 to 4081260 bp, suggesting a potential link between genes regulating lodging and those governing the growth period [52][53][54]. Furthermore, QTLs for three lodging scores (qLD-4-2, qLD-7-2, and qLD-19-2) overlap or coincide with loci related to growth stage traits from previous studies [39,55,56].…”

Integrated Bioinformatics Analyses of PIN1, CKX, and Yield-Related Genes Reveals the Molecular Mechanisms for the Difference of Seed Number Per Pod Between Soybean and Cowpea

“…Candidate SNPP genes in this and previous ( Schwarz et al, 2020 ; Fang et al, 2021 ) studies and known gene Ln were used to construct interaction networks in soybean and cowpea. All the results are shown in Figure 5 and Supplementary Table 7 .…”

“…In soybean network, low SNPP may be due to two reasons. First, four-seed-pod-related gene Glyma.10G002200 , in Fang et al (2021) , was interacted with GmCBP-1 and GmCBP-2 , while its homology Vigun07g002900 in cowpea was interacted with VuCBP-1 , VuCP1 , and VuCAM4. The five interacted genes in soybean and cowpea belong to the calmodulin and calcium-binding protein gene ( CBP) family.…”

Analysis of Genetic Diversity in Adzuki Beans (Vigna angularis): Insights into Environmental Adaptation and Early Breeding Strategies for Yield Improvement

“…Ovule fertility, pollen/pollen tube development, and interaction determine the fertilization rate of the ovule. The process of ovule development into seeds after fertilization is affected by the physiological conditions of the plant and the external environment [ 18 ]. The number of pods per plant in legumes is largely regulated by the number of pods in a single node [ 19 , 20 , 21 , 22 ].…”