Yanzhu Su, Zhipeng Zhang, Jianbo He, Weiying Zeng, Zhaoyan Cai, Zhenguang Lai, Yongpeng Pan, Xiaoshuai Hao, Guangnan Xing, Wubin Wang, Jiaoping Zhang, Yan Li, Zudong Sun & Junyi Gai

Theoretical and Applied Genetics July 2023; vol. 136, Article number: 152 

Figure: Demonstrations of the diversity in the CWLGC. (a) Flower color variations [40]. (b) Using Kunitz trypsin inhibitor, different KTi forms were detected in Korean G. soja accessions by nondenaturing PAGE. Lanes 1-9 are: Tia protein standard (Sigma), Tia, Tib, Tia/Tib, Tibi7-1, Tia, Tibi5, Tib, and Tia, respectively [111]. (c) Comparison of saponin composition phenotypes in seed -  Wild Soybean Germplasm (MA Nawaz et al. 2020)

Key message

Fifty-three shade tolerance genes with 281 alleles in the SCSGP were identified directly using gene–allele sequence as markers in RTM GWAS, from which optimized crosses, evolutionary motivators, and gene–allele networks were explored.

Abstract

Shade tolerance is a key for optimal cultivation of soybean inter/relay-cropped with corn. To explore the shade tolerance gene–allele system in the southern China soybean germplasm, we proposed using gene–allele sequence markers (GASMs) in a restricted two-stage multi-locus model genome-wide association study (GASM-RTM-GWAS). A representative sample with 394 accessions was tested for their shade tolerance index (STI), in Nanning, China. Through whole-genome re-sequencing, 47,586 GASMs were assembled. From GASM-RTM-GWAS, 53 main-effect STI genes with 281 alleles (2–13 alleles/gene) (totally 63 genes with 308 alleles, including 38 G × E genes with 191 alleles) were identified and then organized into a gene–allele matrix composed of eight submatrices corresponding to geo-seasonal subpopulations. The population featured mild STI changes (1.69 → 1.56–1.82) and mild gene–allele changes (92.5% alleles inherited, 0% alleles excluded, 7.5% alleles emerged) from the primitive (SA_III) to the derived seven subpopulations, but large transgressive recombination potentials and optimal crosses were predicted. The 63 STI genes were annotated into six biological categories (metabolic process, catalytic activity, response to stresses, transcription and translation, signal transduction and transport and unknown functions), interacted as gene networks. From the STI gene–allele system, 38 important alleles of 22 genes were nominated for further in-depth study. GASM-RTM-GWAS performed powerful and efficient in germplasm population genetic study comparing to other procedures through facilitating direct and thorough identification of its gene–allele system, from which genome-wide breeding by design could be achieved, and evolutionary motivators and gene–allele networks could be explored.

See https://link.springer.com/article/10.1007/s00122-023-04390-2