NDLI: Genome-wide association studies of plant architecture-related traits and 100-seed weight in soybean landraces

Content Provider	Springer Nature : BioMed Central
Author	Zhang, Xiaoli Ding, Wentao Xue, Dong Li, Xiangnan Zhou, Yang Shen, Jiacheng Feng, Jianying Guo, Na Qiu, Lijuan Xing, Han Zhao, Jinming
Abstract	Background Plant architecture-related traits (e.g., plant height (PH), number of nodes on main stem (NN), branch number (BN) and stem diameter (DI)) and 100-seed weight (100-SW) are important agronomic traits and are closely related to soybean yield. However, the genetic basis and breeding potential of these important agronomic traits remain largely ambiguous in soybean (Glycine max (L.) Merr.). Results In this study, we collected 133 soybean landraces from China, phenotyped them in two years at two locations for the above five traits and conducted a genome-wide association study (GWAS) using 82,187 single nucleotide polymorphisms (SNPs). As a result, we found that a total of 59 SNPs were repeatedly detected in at least two environments. There were 12, 12, 4, 4 and 27 SNPs associated with PH, NN, BN, DI and 100-SW, respectively. Among these markers, seven SNPs (AX-90380587, AX-90406013, AX-90387160, AX-90317160, AX-90449770, AX-90460927 and AX-90520043) were large-effect markers for PH, NN, BN, DI and 100-SW, and 15 potential candidate genes were predicted to be in linkage disequilibrium (LD) decay distance or LD block. In addition, real-time quantitative PCR (qRT-PCR) analysis was performed on four 100-SW potential candidate genes, three of them showed significantly different expression levels between the extreme materials at the seed development stage. Therefore, Glyma.05 g127900, Glyma.05 g128000 and Glyma.05 g129000 were considered as candidate genes with 100-SW in soybean. Conclusions These findings shed light on the genetic basis of plant architecture-related traits and 100-SW in soybean, and candidate genes could be used for further positional cloning.
Related Links	https://bmcgenomdata.biomedcentral.com/counter/pdf/10.1186/s12863-021-00964-5.pdf
Ending Page	14
Page Count	14
Starting Page	1
File Format	HTM / HTML
ISSN	27306844
DOI	10.1186/s12863-021-00964-5
Journal	BMC Genomic Data
Issue Number	1
Volume Number	22
Language	English
Publisher	BioMed Central
Publisher Date	2021-03-06
Access Restriction	Open
Subject Keyword	Life Sciences Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genetics and Population Dynamics Soybean Glycine max (L.) Merr.) Plant architecture-related traits 100-seed weight GWAS Candidate genes
Content Type	Text
Resource Type	Article
Subject	Health Informatics Genetics
Journal Impact Factor	1.9/2023
5-Year Journal Impact Factor	1.9/2023

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