Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent Latitude Distribution

Narrowing down a major QTL region reveals Phytochrome E (PHYE) as the candidate gene controlling flowering time in mungbean (Vigna radiata)

Flowering time is an important agronomic trait that is highly correlated with plant height, maturity time and yield in mungbean. Up to present, however, molecular basis of flowering time in mungbean is poorly understood. Previous studies demonstrated that flowering time in mungbean is largely controlled by a major QTL on linkage group 2 (LG2). In this study, the QTL on the LG2 in mungbean was investigated using F2 and F2:3 populations derived from a cross between mungbean cultivar Kamphaeng Saen 2 (KPS2) and wild mungbean accession ACC41. The QTL was narrowed down to a genome region of 164.87 Kb containing a phytochrome gene, designated VrPHYE, encoding phytochrome E (phyE), a known photoreceptor modulating flowering time. Compared to VrPHYE of the wild ACC41, VrPHYE of KPS2 contained several single nucleotide polymorphisms (SNPs) causing amino acid changes. Those SNPs were also found in other mungbean cultivars. Some amino acid changes were predicted to occur in the regulatory region of phytochromes. Gene expression analysis revealed that VrPHYE in KPS2 was expressed significantly higher than that in ACC41. These results showed that VrPHYE is the candidate gene controlling flowering time in the mungbean.

Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean

BACKGROUND

Mung bean (Vigna radiata (L.) Wilczek), is an important pulse crop in the global south. Early flowering and maturation are advantageous traits for adaptation to northern and southern latitudes. This study investigates the genetic basis of the Days-to-Flowering trait (DTF) in mung bean, combining genome-wide association studies (GWAS) in mung bean and comparisons with orthologous genes involved with control of DTF responses in soybean (Glycine max (L) Merr) and Arabidopsis (Arabidopsis thaliana).

RESULTS

The most significant associations for DTF were on mung bean chromosomes 1, 2, and 4. Only the SNPs on chromosomes 1 and 4 were heavily investigated using downstream analysis. The chromosome 1 DTF association is tightly linked with a cluster of locally duplicated FERONIA (FER) receptor-like protein kinase genes, and the SNP occurs within one of the FERONIA genes. In Arabidopsis, an orthologous FERONIA gene (AT3G51550), has been reported to regulate the expression of the FLOWERING LOCUS C (FLC). For the chromosome 4 DTF locus, the strongest candidates are Vradi04g00002773 and Vradi04g00002778, orthologous to the Arabidopsis PhyA and PIF3 genes, encoding phytochrome A (a photoreceptor protein sensitive to red to far-red light) and phytochrome-interacting factor 3, respectively. The soybean PhyA orthologs include the classical loci E3 and E4 (genes GmPhyA3, Glyma.19G224200, and GmPhyA2, Glyma.20G090000). The mung bean PhyA ortholog has been previously reported as a candidate for DTF in studies conducted in South Korea.

CONCLUSION

The top two identified SNPs accounted for a significant proportion (~ 65%) of the phenotypic variability in mung bean DTF by the six significant SNPs (39.61%), with a broad-sense heritability of 0.93. The strong associations of DTF with genes that have orthologs with analogous functions in soybean and Arabidopsis provide strong circumstantial evidence that these genes are causal for this trait. The three reported loci and candidate genes provide useful targets for marker-assisted breeding in mung beans.

Loss-of-function of an α-SNAP gene confers resistance to soybean cyst nematode

Plant-parasitic nematodes are one of the most economically impactful pests in agriculture resulting in billions of dollars in realized annual losses worldwide. Soybean cyst nematode (SCN) is the number one biotic constraint on soybean production making it a priority for the discovery, validation and functional characterization of native plant resistance genes and genetic modes of action that can be deployed to improve soybean yield across the globe. Here, we present the discovery and functional characterization of a soybean resistance gene, GmSNAP02. We use unique bi-parental populations to fine-map the precise genomic location, and a combination of whole genome resequencing and gene fragment PCR amplifications to identify and confirm causal haplotypes. Lastly, we validate our candidate gene using CRISPR-Cas9 genome editing and observe a gain of resistance in edited plants. This demonstrates that the GmSNAP02 gene confers a unique mode of resistance to SCN through loss-of-function mutations that implicate GmSNAP02 as a nematode virulence target. We highlight the immediate impact of utilizing GmSNAP02 as a genome-editing-amenable target to diversify nematode resistance in commercially available cultivars.

Going north: adaptation of soybean to long-day environments

This article comments on:

Zhu X, Leiser WL, Hahn V, Würschum T. 2023. The genetic architecture of soybean photothermal adaptation to high latitudes. Journal of Experimental Botany 74,2987–3002

In plant breeding, understanding genetic variation in the photoperiodic control of flowering time of crop plants such as soybean is a prerequisite for managing adaptation to new environments. Zhu et al. (2023) analyzed a large diversity panel of >1500 early maturity soybean lines to disclose the genetic architecture behind the timing of flowering and maturity. Their findings confirm known maturity loci and reveal new candidate genes and alleles as well as environmental interactions of individual quantitative trait loci (QTLs) for flowering and maturity time. The results shed light on the complexity of the regulatory network which controls the timing of flowering in soybean. This supports the fine-tuning of plant architectures through the combination of stem termination and flowering genes towards a better adaptation of soybean to high latitudes or other stressful environments.