Gene–allele system of shade tolerance in southern China soybean germplasm revealed by genome-wide association study using gene–allele sequence as markers

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

doi:10.1007/s00122-023-04390-2

Cited by 7 publications

(8 citation statements)

References 31 publications

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“…The direct comparison procedure in studying the motivator of population evolution was suggested originally by Fu et al [ 35 ], which is based on the relative thorough identification of the genes/QTLs and their corresponding alleles in an evolutionary or geographic population. This procedure has been used effectively by Liu et al [ 2 ] and Su et al [ 22 ].…”

Section: Discussionmentioning

confidence: 99%

“…In the present study, it was achieved by using the GASM-RTM-GWAS procedure [ 21 ], with GASMs as markers such that the 132 ATI genes with their 359 alleles were identified directly. The GASM-RTM-GWAS procedure features two major innovations [ 22 ]. The first is using multiple allele markers to fit the requirement of multiple alleles in the germplasm population or breeding population (previously SNPLDB and at present GASM), so it can detect gene loci as well as their alleles.…”

Section: Discussionmentioning

confidence: 99%

“…As indicated in the present study, 132 genes with their 359 alleles were identified; GASM-RTM-GWAS is more powerful and efficient than the other procedures, such as SNP-MLM-GWAS and SNPLDB-RTM-GWAS [ 22 ]. Thus, the GASM-RTM-GWAS procedure fits especially well with the germplasm populations, with multiple alleles per locus, enabling an understanding of the complete gene–allele system in population evolutionary study.…”

Section: Discussionmentioning

confidence: 99%

“…This procedure has been used to identify QTLs of soybean isoflavones, 100-seed weight, flowering date, etc. [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

“…In this case, the identified QTL is in fact the gene marker itself, without additional requirement to infer from a QTL to a gene. This RTM-GWAS based on a gene–allele segment marker (GASM) is called GASM-RTM-GWAS, which has been used in identifying the gene–allele system for shade tolerance under soybean–maize inter-/relay-cropping in the southern China soybean germplasm [ 22 ]. These studies have demonstrated that the GASM-RTM-GWAS procedure was powerful and efficient in identifying a gene–allele system of complex traits and in predicting optimal crosses.…”

Section: Introductionmentioning

confidence: 99%

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Identification of Gene–Allele System Conferring Alkali-Tolerance at Seedling Stage in Northeast China Soybean Germplasm

Zong,

Zhao,

Wang

et al. 2024

IJMS

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Salinization of cultivated soils may result in either high salt levels or alkaline conditions, both of which stress crops and reduce performance. We sampled genotypes included in the Northeast China soybean germplasm population (NECSGP) to identify possible genes that affect tolerance to alkaline soil conditions. In this study, 361 soybean accessions collected in Northeast China were tested under 220 mM NaHCO3:Na2CO3 = 9:1 (pH = 9.8) to evaluate the alkali-tolerance (ATI) at the seedling stage in Mudanjiang, Heilongjiang, China. The restricted two-stage multi-locus model genome-wide association study (RTM-GWAS) with gene–allele sequences as markers (6503 GASMs) based on simplified genome resequencing (RAD-sequencing) was accomplished. From this analysis, 132 main effect candidate genes with 359 alleles and 35 Gene × Environment genes with 103 alleles were identified, explaining 90.93% and 2.80% of the seedling alkali-tolerance phenotypic variation, respectively. Genetic variability of ATI in NECSGP was observed primarily within subpopulations, especially in ecoregion B, from which 80% of ATI-tolerant accessions were screened out. The biological functions of 132 candidate genes were classified into eight functional categories (defense response, substance transport, regulation, metabolism-related, substance synthesis, biological process, plant development, and unknown function). From the ATI gene–allele system, six key genes–alleles were identified as starting points for further study on understanding the ATI gene network.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…This procedure has been used to identify QTLs of soybean isoflavones, 100-seed weight, flowering date, etc. [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%