QTL Mapping and Genomic Selection of Stem and Branch Diameter in Soybean ( L.)

Overview

Journal Front Plant Sci

Date 2024 Jun 17

PMID 38882575

Authors

Jing Wang

Qichao Yang

Yijie Chen

Kanglin Liu

Zhiqing Zhang

Yajun Xiong

Huan Yu

Yingdong Yu

Jun Wang

Jian Song

Lijuan Qiu

Affiliations

Soon will be listed here.

Abstract

Introduction: Soybean stem diameter (SD) and branch diameter (BD) are closely related traits, and genetic clarification of SD and BD is crucial for soybean breeding.

Methods: SD and BD were genetically analyzed by a population of 363 RIL derived from the cross between Zhongdou41 (ZD41) and ZYD02878 using restricted two-stage multi-locus genome-wide association, inclusive composite interval mapping, and three-variance component multi-locus random SNP effect mixed linear modeling. Then candidate genes of major QTLs were selected and genetic selection model of SD and BD were constructed respectively.

Results And Discussion: The results showed that SD and BD were significantly correlated (r = 0.74, P < 0.001). A total of 93 and 84 unique quantitative trait loci (QTL) were detected for SD and BD, respectively by three different methods. There were two and ten major QTLs for SD and BD, respectively, with phenotypic variance explained (PVE) by more than 10%. Within these loci, seven genes involved in the regulation of phytohormones (IAA and GA) and cell proliferation and showing extensive expression of shoot apical meristematic genes were selected as candidate genes. Genomic selection (GS) analysis showed that the trait-associated markers identified in this study reached 0.47-0.73 in terms of prediction accuracy, which was enhanced by 6.56-23.69% compared with genome-wide markers. These results clarify the genetic basis of SD and BD, which laid solid foundation in regulation gene cloning, and GS models constructed could be potentially applied in future breeding programs.

Citing Articles

Dynamic QTL mapping reveals the genetic architecture of stem diameter across developmental stages in foxtail millet.

Wang C, Liu D, Han H, Chai S, Li S, Wu Y Planta. 2025; 261(4):70.

PMID: 40014161 DOI: 10.1007/s00425-025-04640-1.

References

Ghasemi A, Zahediasl S . Normality tests for statistical analysis: a guide for non-statisticians. Int J Endocrinol Metab. 2013; 10(2):486-9. PMC: 3693611. DOI: 10.5812/ijem.3505. View

Gonda I, Ashrafi H, Lyon D, Strickler S, Hulse-Kemp A, Ma Q . Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection. Plant Genome. 2019; 12(1). DOI: 10.3835/plantgenome2018.02.0010. View

Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q . Progress in soybean functional genomics over the past decade. Plant Biotechnol J. 2021; 20(2):256-282. PMC: 8753368. DOI: 10.1111/pbi.13682. View

Kibe M, Nyaga C, Nair S, Beyene Y, Das B, L M S . Combination of Linkage Mapping, GWAS, and GP to Dissect the Genetic Basis of Common Rust Resistance in Tropical Maize Germplasm. Int J Mol Sci. 2020; 21(18). PMC: 7555316. DOI: 10.3390/ijms21186518. View

Van Lijsebettens M, Vanderhaeghen R, De Block M, Bauw G, Villarroel R, Van Montagu M . An S18 ribosomal protein gene copy at the Arabidopsis PFL locus affects plant development by its specific expression in meristems. EMBO J. 1994; 13(14):3378-88. PMC: 395235. DOI: 10.1002/j.1460-2075.1994.tb06640.x. View

Contreras-Soto R, Mora F, de Oliveira M, Higashi W, Scapim C, Schuster I . A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis. PLoS One. 2017; 12(2):e0171105. PMC: 5289539. DOI: 10.1371/journal.pone.0171105. View

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, Bender D . PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81(3):559-75. PMC: 1950838. DOI: 10.1086/519795. View

Ravelombola W, Qin J, Shi A, Song Q, Yuan J, Wang F . Genome-wide association study and genomic selection for yield and related traits in soybean. PLoS One. 2021; 16(8):e0255761. PMC: 8362977. DOI: 10.1371/journal.pone.0255761. View

Hirsch S, Oldroyd G . GRAS-domain transcription factors that regulate plant development. Plant Signal Behav. 2009; 4(8):698-700. PMC: 2801379. DOI: 10.4161/psb.4.8.9176. View

10.

Wang L, Cheng Y, Ma Q, Mu Y, Huang Z, Xia Q . QTL fine-mapping of soybean (Glycine max L.) leaf type associated traits in two RILs populations. BMC Genomics. 2019; 20(1):260. PMC: 6444683. DOI: 10.1186/s12864-019-5610-8. View

11.

VanRaden P . Efficient methods to compute genomic predictions. J Dairy Sci. 2008; 91(11):4414-23. DOI: 10.3168/jds.2007-0980. View

12.

Sun R, Sun B, Tian Y, Su S, Zhang Y, Zhang W . Dissection of the practical soybean breeding pipeline by developing ZDX1, a high-throughput functional array. Theor Appl Genet. 2022; 135(4):1413-1427. PMC: 9033737. DOI: 10.1007/s00122-022-04043-w. View

13.

Song Q, Hyten D, Jia G, Quigley C, Fickus E, Nelson R . Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS One. 2013; 8(1):e54985. PMC: 3555945. DOI: 10.1371/journal.pone.0054985. View

14.

Hong J, Ro N, Lee H, Kim G, Kwon J, Yamamoto E . Genomic Selection for Prediction of Fruit-Related Traits in Pepper ( spp.). Front Plant Sci. 2020; 11:570871. PMC: 7655793. DOI: 10.3389/fpls.2020.570871. View

15.

Dang D, Guan Y, Zheng H, Zhang X, Zhang A, Wang H . Genome-Wide Association Study and Genomic Prediction on Plant Architecture Traits in Sweet Corn and Waxy Corn. Plants (Basel). 2023; 12(2). PMC: 9867343. DOI: 10.3390/plants12020303. View

16.

Li M, Zhang Y, Zhang Z, Xiang Y, Liu M, Zhou Y . A compressed variance component mixed model for detecting QTNs and QTN-by-environment and QTN-by-QTN interactions in genome-wide association studies. Mol Plant. 2022; 15(4):630-650. DOI: 10.1016/j.molp.2022.02.012. View

17.

An Y, Chen L, Li Y, Li C, Shi Y, Zhang D . Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize. BMC Plant Biol. 2020; 20(1):490. PMC: 7590725. DOI: 10.1186/s12870-020-02676-x. View

18.

Li Y, Qin C, Wang L, Jiao C, Hong H, Tian Y . Genome-wide signatures of the geographic expansion and breeding of soybean. Sci China Life Sci. 2022; 66(2):350-365. DOI: 10.1007/s11427-022-2158-7. View

19.

Cui Y, Li R, Li G, Zhang F, Zhu T, Zhang Q . Hybrid breeding of rice via genomic selection. Plant Biotechnol J. 2019; 18(1):57-67. PMC: 6920338. DOI: 10.1111/pbi.13170. View

20.

Zhao X, Ebert B, Zhang B, Liu H, Zhang Y, Zeng W . UDP-Api/UDP-Xyl synthases affect plant development by controlling the content of UDP-Api to regulate the RG-II-borate complex. Plant J. 2020; 104(1):252-267. DOI: 10.1111/tpj.14921. View