Xiaoli Zhang1, Wentao Ding1, Dong Xue1, Xiangnan Li1, Yang Zhou1, Jiacheng Shen1, Jianying Feng1, Na Guo1, Lijuan Qiu2, Han Xing1, Jinming Zhao3. 1. National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China. 2. The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. 3. National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China. xingyuan_2013@163.com.
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.
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.
Authors: Mônica T V Labate; Kenton Ko; Zdenka W Ko; Luciana S R Costa Pinto; Maria J U D Real; Marcelo Ribeiro Romano; Paulo Roxo Barja; Antonio Granell; Giulia Friso; Klaas J van Wijk; Enrico Brugnoli; Carlos A Labate Journal: Plant Mol Biol Date: 2004-07 Impact factor: 4.076
Authors: Edward S Buckler; James B Holland; Peter J Bradbury; Charlotte B Acharya; Patrick J Brown; Chris Browne; Elhan Ersoz; Sherry Flint-Garcia; Arturo Garcia; Jeffrey C Glaubitz; Major M Goodman; Carlos Harjes; Kate Guill; Dallas E Kroon; Sara Larsson; Nicholas K Lepak; Huihui Li; Sharon E Mitchell; Gael Pressoir; Jason A Peiffer; Marco Oropeza Rosas; Torbert R Rocheford; M Cinta Romay; Susan Romero; Stella Salvo; Hector Sanchez Villeda; H Sofia da Silva; Qi Sun; Feng Tian; Narasimham Upadyayula; Doreen Ware; Heather Yates; Jianming Yu; Zhiwu Zhang; Stephen Kresovich; Michael D McMullen Journal: Science Date: 2009-08-07 Impact factor: 47.728