Seed weight differences between wild and domesticated soybeans are associated with specific changes in gene expression.
Chao Yu, Zhipeng Qu, Yueting Zhang, Xifeng Zhang, Tingting Lan, David L Adelson, Dong Wang, Youlin Zhu
Author Information
Chao Yu: State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330031, Jiangxi, China.
Zhipeng Qu: Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
Yueting Zhang: Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China.
Xifeng Zhang: Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China.
Tingting Lan: Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China.
David L Adelson: Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
Dong Wang: Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China. dongwangbio@gmail.com.
Youlin Zhu: State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330031, Jiangxi, China. ylzhu1999@aliyun.com.
KEY MESSAGE: Our study systematically explored potential genes and molecular pathways as candidates for differences in seed weight resulting from soybean domestication. In addition, potential contributions of lncRNAs to seed weight were also investigated. Soybeans have a long history of domestication in China, and there are several significant phenotypic differences between cultivated and wild soybeans, for example, seeds of cultivars are generally larger and heavier than those from wild accessions. We analyzed seed transcriptomes from thirteen soybean samples, including six landraces and seven wild accessions using strand-specific RNA sequencing. Differentially expressed genes related to seed weight were identified, and some of their homologs were associated with seed development in Arabidopsis. We also identified 1251 long intergenic noncoding RNAs (lincRNAs), 243 intronic RNAs and 81 antisense lncRNAs de novo from these soybean transcriptomes. We then profiled the expression patterns of lncRNAs in cultivated and wild soybean seeds, and found that transcript levels of a number of lncRNAs were sample-specific. Moreover, gene transcript and lincRNA co-expression network analysis showed that some soybean lincRNAs might have functional roles as they were hubs of co-expression modules. In conclusion, this study systematically explored potential genes and molecular pathways as candidates for differences in seed weight resulting from soybean domestication, and will provide a useful future resource for molecular breeding of soybeans.
