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Li G, Xie J, Zhang W, Meng F, Yang M, Fan X, Sun X, Zheng Y, Zhang Y, Wang M, Chen Q, Wang S, Jiang H. Integrated examination of the transcriptome and metabolome of the gene expression response and metabolite accumulation in soybean seeds for seed storability under aging stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1437107. [PMID: 39040511 PMCID: PMC11261460 DOI: 10.3389/fpls.2024.1437107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/24/2024]
Abstract
Soybean quality and production are determined by seed viability. A seed's capacity to sustain germination via dry storage is known as its seed life. Thus, one of the main objectives for breeders is to preserve genetic variety and gather germplasm resources. However, seed quality and germplasm preservation have become significant obstacles. In this study, four artificially simulated aging treatment groups were set for 0, 24, 72, and 120 hours. Following an aging stress treatment, the transcriptome and metabolome data were compared in two soybean lines with notable differences in seed vigor-R31 (aging sensitive) and R80 (aging tolerant). The results showed that 83 (38 upregulated and 45 downregulated), 30 (19 upregulated and 11 downregulated), 90 (52 upregulated and 38 downregulated), and 54 (25 upregulated and 29 downregulated) DEGs were differentially expressed, respectively. A total of 62 (29 upregulated and 33 downregulated), 94 (49 upregulated and 45 downregulated), 91 (53 upregulated and 38 downregulated), and 135 (111 upregulated and 24 downregulated) differential metabolites accumulated. Combining the results of transcriptome and metabolome investigations demonstrated that the difference between R31 and R80 responses to aging stress was caused by genes related to phenylpropanoid metabolism pathway, which is linked to the seed metabolite caffeic acid. According to this study's preliminary findings, the aging-resistant line accumulated more caffeic acid than the aging-sensitive line, which improved its capacity to block lipoxygenase (LOX) activity. An enzyme activity inhibition test was used to demonstrate the effect of caffeic acid. After soaking seeds in 1 mM caffeic acid (a LOX inhibitor) for 6 hours and artificially aging them for 24 hours, the germination rates of the R31 and R80 seeds were enhanced. In conclusion, caffeic acid has been shown to partially mitigate the negative effects of soybean seed aging stress and to improve seed vitality. This finding should serve as a theoretical foundation for future research on the aging mechanism of soybean seeds.
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Affiliation(s)
- Guang Li
- Jilin Academy of Agricultural Sciences (China Agricultural Science and Technology Northeast Innovation Center), Soybean Research Institute, Changchun, China
| | - Jianguo Xie
- Jilin Academy of Agricultural Sciences (China Agricultural Science and Technology Northeast Innovation Center), Soybean Research Institute, Changchun, China
| | - Wei Zhang
- Jilin Academy of Agricultural Sciences (China Agricultural Science and Technology Northeast Innovation Center), Soybean Research Institute, Changchun, China
| | - Fanfan Meng
- Jilin Academy of Agricultural Sciences (China Agricultural Science and Technology Northeast Innovation Center), Soybean Research Institute, Changchun, China
| | - Mingliang Yang
- Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xuhong Fan
- Jilin Academy of Agricultural Sciences (China Agricultural Science and Technology Northeast Innovation Center), Soybean Research Institute, Changchun, China
| | - Xingmiao Sun
- Jilin Academy of Agricultural Sciences (China Agricultural Science and Technology Northeast Innovation Center), Soybean Research Institute, Changchun, China
| | - Yuhong Zheng
- Jilin Academy of Agricultural Sciences (China Agricultural Science and Technology Northeast Innovation Center), Soybean Research Institute, Changchun, China
| | - Yunfeng Zhang
- Jilin Academy of Agricultural Sciences (China Agricultural Science and Technology Northeast Innovation Center), Soybean Research Institute, Changchun, China
| | - Mingliang Wang
- Jilin Academy of Agricultural Sciences (China Agricultural Science and Technology Northeast Innovation Center), Soybean Research Institute, Changchun, China
| | - Qingshan Chen
- Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Shuming Wang
- Jilin Academy of Agricultural Sciences (China Agricultural Science and Technology Northeast Innovation Center), Soybean Research Institute, Changchun, China
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences (China Agricultural Science and Technology Northeast Innovation Center), Soybean Research Institute, Changchun, China
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Jong C, Yu Z, Zhang Y, Choe K, Uh S, Kim K, Jong C, Cha J, Kim M, Kim Y, Han X, Yang M, Xu C, Hu L, Chen Q, Liu C, Qi Z. Multi-Omics Analysis of a Chromosome Segment Substitution Line Reveals a New Regulation Network for Soybean Seed Storage Profile. Int J Mol Sci 2024; 25:5614. [PMID: 38891802 PMCID: PMC11171932 DOI: 10.3390/ijms25115614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 06/21/2024] Open
Abstract
Soybean, a major source of oil and protein, has seen an annual increase in consumption when used in soybean-derived products and the broadening of its cultivation range. The demand for soybean necessitates a better understanding of the regulatory networks driving storage protein accumulation and oil biosynthesis to broaden its positive impact on human health. In this study, we selected a chromosome segment substitution line (CSSL) with high protein and low oil contents to investigate the underlying effect of donor introgression on seed storage through multi-omics analysis. In total, 1479 differentially expressed genes (DEGs), 82 differentially expressed proteins (DEPs), and 34 differentially expressed metabolites (DEMs) were identified in the CSSL compared to the recurrent parent. Based on Gene Ontology (GO) term analysis and the Kyoto Encyclopedia of Genes and Genomes enrichment (KEGG), integrated analysis indicated that 31 DEGs, 24 DEPs, and 13 DEMs were related to seed storage functionality. Integrated analysis further showed a significant decrease in the contents of the seed storage lipids LysoPG 16:0 and LysoPC 18:4 as well as an increase in the contents of organic acids such as L-malic acid. Taken together, these results offer new insights into the molecular mechanisms of seed storage and provide guidance for the molecular breeding of new favorable soybean varieties.
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Affiliation(s)
- Cholnam Jong
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Zhenhai Yu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
- Heilongjiang Green Food Science Research Institute, Harbin 150000, China
| | - Yu Zhang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Kyongho Choe
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Songrok Uh
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Kibong Kim
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Chol Jong
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Jinmyong Cha
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Myongguk Kim
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Yunchol Kim
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Xue Han
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Mingliang Yang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Chang Xu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Limin Hu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Qingshan Chen
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Chunyan Liu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Zhaoming Qi
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
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3
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Wang W, Zhang T, Liu C, Liu C, Jiang Z, Zhang Z, Ali S, Li Z, Wang J, Sun S, Chen Q, Zhang Q, Xie L. A DNA demethylase reduces seed size by decreasing the DNA methylation of AT-rich transposable elements in soybean. Commun Biol 2024; 7:613. [PMID: 38773248 PMCID: PMC11109123 DOI: 10.1038/s42003-024-06306-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Understanding how to increase soybean yield is crucial for global food security. The genetic and epigenetic factors influencing seed size, a major crop yield determinant, are not fully understood. We explore the role of DNA demethylase GmDMEa in soybean seed size. Our research indicates that GmDMEa negatively correlates with soybean seed size. Using CRISPR-Cas9, we edited GmDMEa in the Dongnong soybean cultivar, known for small seeds. Modified plants had larger seeds and greater yields without altering plant architecture or seed nutrition. GmDMEa preferentially demethylates AT-rich transposable elements, thus activating genes and transcription factors associated with the abscisic acid pathway, which typically decreases seed size. Chromosomal substitution lines confirm that these modifications are inheritable, suggesting a stable epigenetic method to boost seed size in future breeding. Our findings provide insights into epigenetic seed size control and suggest a strategy for improving crop yields through the epigenetic regulation of crucial genes. This work implies that targeted epigenetic modification has practical agricultural applications, potentially enhancing food production without compromising crop quality.
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Affiliation(s)
- Wanpeng Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Chunyu Liu
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhenfeng Jiang
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhaohan Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shahid Ali
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Zhuozheng Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Jiang Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shanwen Sun
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China.
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China.
| | - Linan Xie
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China.
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
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4
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Wei S, Yu Z, Du F, Cao F, Yang M, Liu C, Qi Z, Chen Q, Zou J, Wang J. Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:908. [PMID: 38592937 PMCID: PMC10975824 DOI: 10.3390/plants13060908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent 'Suinong14' (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean.
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Affiliation(s)
- Siming Wei
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Zhenhai Yu
- Heilongjiang Province Green Food Science Institute, Harbin 150028, China;
| | - Fangfang Du
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Fubin Cao
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Mingliang Yang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Chunyan Liu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Zhaoming Qi
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Qingshan Chen
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Jianan Zou
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Jinhui Wang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
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5
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Wei S, Yong B, Jiang H, An Z, Wang Y, Li B, Yang C, Zhu W, Chen Q, He C. A loss-of-function mutant allele of a glycosyl hydrolase gene has been co-opted for seed weight control during soybean domestication. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2469-2489. [PMID: 37635359 DOI: 10.1111/jipb.13559] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 08/29/2023]
Abstract
The resultant DNA from loss-of-function mutation can be recruited in biological evolution and development. Here, we present such a rare and potential case of "to gain by loss" as a neomorphic mutation during soybean domestication for increasing seed weight. Using a population derived from a chromosome segment substitution line of Glycine max (SN14) and Glycine soja (ZYD06), a quantitative trait locus (QTL) of 100-seed weight (qHSW) was mapped on chromosome 11, corresponding to a truncated β-1, 3-glucosidase (βGlu) gene. The novel gene hsw results from a 14-bp deletion, causing a frameshift mutation and a premature stop codon in the βGlu. In contrast to HSW, the hsw completely lost βGlu activity and function but acquired a novel function to promote cell expansion, thus increasing seed weight. Overexpressing hsw instead of HSW produced large soybean seeds, and surprisingly, truncating hsw via gene editing further increased the seed size. We further found that the core 21-aa peptide of hsw and its variants acted as a promoter of seed size. Transcriptomic variation in these transgenic soybean lines substantiated the integration hsw into cell and seed size control. Moreover, the hsw allele underwent selection and expansion during soybean domestication and improvement. Our work cloned a likely domesticated QTL controlling soybean seed weight, revealed a novel genetic variation and mechanism in soybean domestication, and provided new insight into crop domestication and breeding, and plant evolution.
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Affiliation(s)
- Siming Wei
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Yong
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongwei Jiang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
- Jilin Academy of Agricultural Sciences, Changchun, 130022, China
| | - Zhenghong An
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Bingbing Li
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ce Yang
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiwei Zhu
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Chaoying He
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
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6
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Yong B, Zhu W, Wei S, Li B, Wang Y, Xu N, Lu J, Chen Q, He C. Parallel selection of loss-of-function alleles of Pdh1 orthologous genes in warm-season legumes for pod indehiscence and plasticity is related to precipitation. THE NEW PHYTOLOGIST 2023; 240:863-879. [PMID: 37501344 DOI: 10.1111/nph.19150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
Pod dehiscence facilitates seed dispersal in wild legumes but results in yield loss in cultivated legumes. The evolutionary genetics of the legume pod dehiscence trait remain largely elusive. We characterized the pod dehiscence of chromosome segment substitution lines of Glycine max crossed with Glycine soja and found that the gene underlying the predominant quantitative trait locus (QTL) of soybean pod-shattering trait was Pod dehiscence 1 (Pdh1). A few rare loss-of-function (LoF) Pdh1 alleles were identified in G. soja, while only an allele featuring a premature stop codon was selected for pod indehiscence in cultivated soybean and spread to low-precipitation regions with increased frequency. Moreover, correlated interactions among Pdh1's haplotype, gene expression, and environmental changes for the developmental plasticity of the pod dehiscence trait were revealed in G. max. We found that orthologous Pdh1 genes specifically originated in warm-season legumes and their LoF alleles were then parallel-selected during the domestication of legume crops. Our results provide insights into the convergent evolution of pod dehiscence in warm-season legumes, facilitate an understanding of the intricate interactions between genetic robustness and environmental adaptation for developmental plasticity, and guide the breeding of new legume varieties with pod indehiscence.
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Affiliation(s)
- Bin Yong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Weiwei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Siming Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Bingbing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Nan Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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7
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Sun M, Wei S, Liu J, Wang L, Zhang Y, Hu L, Piao J, Liang Z, Jiang H, Xin D, Zhao Y, Chen Q, Foyer CH, Liu C, Qi Z. The impact of GmTSA and GmALS on soybean salt tolerance: uncovering the molecular landscape of amino acid and secondary metabolism pathways. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:212. [PMID: 37740151 DOI: 10.1007/s00122-023-04461-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/08/2023] [Indexed: 09/24/2023]
Abstract
KEY MESSAGE GmTSA and GmALS were screened out for salt stress in soybean and explore the poteintial amino acid secondary metabolism pathways. Soybean (Glycine max L.) is an oil and protein crop of global importance, and salinity has significant effects on soybean growth. Here, a population of soybean chromosome segment substitution lines was screened to identify highly salt-tolerant lines. In total, 24 quantitative trait loci (QTLs) on seven chromosomes were associated with salt tolerance, and CSSL_R71 was selected for further analysis. Although numerous genes were differentially expressed in CSSL_R71 in response to salt statically no differently, transcript levels of classical salt-response genes, including those of the salt overly sensitive pathway. Rather, salt tolerance in CSSL_R71 was associated with changes in amino acid and lipid metabolism. In particular, changes in p-coumaric acid, shikimic acid, and pyrrole-2-carboxylic acid levels accompanied salt tolerance in CSSL_R71. Eleven differentially expressed genes (DEGs) related to amino acid and secondary metabolism were identified as candidate genes on the substituted chromosome fragment. Six of these showed differences in coding sequence between the parental genotypes. Crucially, overexpression of GmTSA (Glyma.03G158400, tryptophan synthase) significantly enhanced salt tolerance in soybean hairy roots, whereas overexpression of GmALS (Glyma.13G241000, acetolactate synthase) decreased salt tolerance. Two KASP markers were developed for GmALS and used to genotype salt-tolerant and salt-sensitive lines in the CSSL population. Non-synonymous mutations were directly associated with salt tolerance. Taken together, these data provide evidence that changes in amino acid and secondary metabolism have the potential to confer salt tolerance in soybean.
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Affiliation(s)
- Minghao Sun
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Siming Wei
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jiarui Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Luyao Wang
- Institute of Rural Revitalization Science and Technology, Heilongjiang Academy of Agricultural Sciences, Harbin, 150028, China
| | - Yu Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Limin Hu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jingxi Piao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhao Liang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, 130033, China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Ying Zhao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, UK.
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
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8
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Identifications of QTLs and Candidate Genes Associated with Pseudomonas syringae Responses in Cultivated Soybean ( Glycine max) and Wild Soybean ( Glycine soja). Int J Mol Sci 2023; 24:ijms24054618. [PMID: 36902050 PMCID: PMC10003559 DOI: 10.3390/ijms24054618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 03/06/2023] Open
Abstract
Soybeans (Glycine max) are a key food crop, serving as a valuable source of both oil and plant-derived protein. Pseudomonas syringae pv. glycinea (Psg) is among the most aggressive and prevalent pathogens affecting soybean production, causing a form of bacterial spot disease that impacts soybean leaves and thereby reduces crop yields. In this study, 310 natural soybean varieties were screened for Psg resistance and susceptibility. The identified susceptible and resistant varieties were then used for linkage mapping, BSA-seq, and whole genome sequencing (WGS) analyses aimed at identifying key QTLs associated with Psg responses. Candidate Psg-related genes were further confirmed through WGS and qPCR analyses. Candidate gene haplotype analyses were used to explore the associations between haplotypes and soybean Psg resistance. In addition, landrace and wild soybean plants were found to exhibit a higher degree of Psg resistance as compared to cultivated soybean varieties. In total, 10 QTLs were identified using chromosome segment substitution lines derived from Suinong14 (cultivated soybean) and ZYD00006 (wild soybean). Glyma.10g230200 was found to be induced in response to Psg, with the Glyma.10g230200 haplotype corresponding to soybean disease resistance. The QTLs identified herein can be leveraged to guide the marker-assisted breeding of soybean cultivars that exhibit partial resistance to Psg. Moreover, further functional and molecular studies of Glyma.10g230200 have the potential to offer insight into the mechanistic basis for soybean Psg resistance.
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9
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Song S, Wang J, Yang X, Zhang X, Xin X, Liu C, Zou J, Cheng X, Zhang N, Hu Y, Wang J, Chen Q, Xin D. GsRSS3L, a Candidate Gene Underlying Soybean Resistance to Seedcoat Mottling Derived from Wild Soybean (Glycine soja Sieb. and Zucc). Int J Mol Sci 2022; 23:ijms23147577. [PMID: 35886929 PMCID: PMC9318458 DOI: 10.3390/ijms23147577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/27/2022] Open
Abstract
Soybeans are a major crop that produce the best vegetable oil and protein for use in food and beverage products worldwide. However, one of the most well-known viral infections affecting soybeans is the Soybean Mosaic Virus (SMV), a member of the Potyviridae family. A crucial method for preventing SMV damage is the breeding of resistant soybean cultivars. Adult resistance and resistance of seedcoat mottling are two types of resistance to SMV. Most studies have focused on adult-plant resistance but not on the resistance to seedcoat mottling. In this study, chromosome segment-substituted lines derived from a cross between Suinong14 (cultivated soybean) and ZYD00006 (wild soybean) were used to identify the chromosome region and candidate genes underlying soybean resistance to seed coat mottling. Herein, two quantitative trait loci (QTLs) were found on chromosome 17, and eighteen genes were found in the QTL region. RNA-seq was used to evaluate the differentially expressed genes (DEGs) among the eighteen genes located in the QTLs. According to the obtained data, variations were observed in the expression of five genes following SMV infection. Furthermore, Nicotiana benthamiana was subjected to an Agrobacterium-mediated transient expression assay to investigate the role of the five candidate genes in SMV resistance. It has also been revealed that Glyma.17g238900 encoding a RICE SALT SENSITIVE 3-like protein (RSS3L) can inhibit the multiplication of SMV in N.benthamiana. Moreover, two nonsynonymous single-nucleotide polymorphisms (SNPs) were found in the coding sequence of Glyma.17g238900 derived from the wild soybean ZYD00006 (GsRSS3L), and the two amino acid mutants may be associated with SMV resistance. Hence, it has been suggested that GsRSS3L confers seedcoat mottling resistance, shedding light on the mechanism of soybean resistance to SMV.
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10
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Zheng H, Hou L, Xie J, Cao F, Wei R, Yang M, Qi Z, Zhu R, Zhang Z, Xin D, Li C, Liu C, Jiang H, Chen Q. Construction of Chromosome Segment Substitution Lines and Inheritance of Seed-Pod Characteristics in Wild Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:869455. [PMID: 35783974 PMCID: PMC9247457 DOI: 10.3389/fpls.2022.869455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Genetic populations provide the basis for genetic and genomic research, and chromosome segment substitution lines (CSSLs) are a powerful tool for the fine mapping of quantitative traits, new gene mining, and marker-assisted breeding. In this study, 213 CSSLs were obtained by self-crossing, backcrossing, and marker-assisted selection between cultivated soybean (Glycine max [L.] Merr.) variety Suinong14 (SN14) and wild soybean (Glycine soja Sieb. et Zucc.) ZYD00006. The genomes of these 213 CSSLs were resequenced and 580,524 single-nucleotide polymorphism markers were obtained, which were divided into 3,780 bin markers. The seed-pod-related traits were analyzed by quantitative trait locus (QTL) mapping using CSSLs. A total of 170 QTLs were detected, and 32 QTLs were detected stably for more than 2 years. Through epistasis analysis, 955 pairs of epistasis QTLs related to seed-pod traits were obtained. Furthermore, the hundred-seed weight QTL was finely mapped to the region of 64.4 Kb on chromosome 12, and Glyma.12G088900 was identified as a candidate gene. Taken together, a set of wild soybean CSSLs was constructed and upgraded by a resequencing technique. The seed-pod-related traits were studied by bin markers, and a candidate gene for the hundred-seed weight was finely mapped. Our results have revealed the CSSLs can be an effective tool for QTL mapping, epistatic effect analysis, and gene cloning.
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Affiliation(s)
| | - Lilong Hou
- Northeast Agricultural University, Harbin, China
| | - Jianguo Xie
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, China
| | - Fubin Cao
- Northeast Agricultural University, Harbin, China
| | - Ruru Wei
- Northeast Agricultural University, Harbin, China
| | | | - Zhaoming Qi
- Northeast Agricultural University, Harbin, China
| | | | | | - Dawei Xin
- Northeast Agricultural University, Harbin, China
| | - Candong Li
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Chunyan Liu
- Northeast Agricultural University, Harbin, China
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, China
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11
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Wang J, Ma C, Ma S, Zheng H, Feng H, Wang Y, Wang J, Liu C, Xin D, Chen Q, Yang M. GmARP is Related to the Type III Effector NopAA to Promote Nodulation in Soybean (Glycine max). Front Genet 2022; 13:889795. [PMID: 35692823 PMCID: PMC9184740 DOI: 10.3389/fgene.2022.889795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/05/2022] [Indexed: 11/23/2022] Open
Abstract
Type III effectors secreted by rhizobia regulate nodulation in the host plant and are important modulators of symbiosis between rhizobia and soybean (Glycine max), although the underlying mechanisms are poorly understood. Here, we studied the type III effector NopAA in Sinorhizobium fredii HH103, confirming its secretion into the extracellular environment under the action of genistein. The enzyme activity of NopAA was investigated in vitro, using xyloglucan and β-glucan as substrates. NopAA functions were investigated by the generation of a NopAA mutant and the effects of NopAA deficiency on symbiosis were analyzed. Soybean genes associated with NopAA were identified in a recombinant inbred line (RIL) population and their functions were verified. NopAA was confirmed to be a type III effector with glycosyl hydrolase activity, and its mutant did not promote nodulation. Quantitative trait locus (QTL) analysis identified 10 QTLs with one, Glyma.19g074200 (GmARP), found to be associated with NopAA and to positively regulate the establishment of symbiosis. All these results support the hypothesis that type III effectors interact with host proteins to regulate the establishment of symbiosis and suggest the possibility of manipulating the symbiotic soybean–rhizobia interaction to promote efficient nitrogen fixation.
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Affiliation(s)
- Jinhui Wang
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Chao Ma
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Shengnan Ma
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Haiyang Zheng
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Haojie Feng
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yue Wang
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Jiangxu Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chunyan Liu
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Dawei Xin
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
- *Correspondence: Dawei Xin, ; Qingshan Chen, ; Mingliang Yang,
| | - Qingshan Chen
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
- *Correspondence: Dawei Xin, ; Qingshan Chen, ; Mingliang Yang,
| | - Mingliang Yang
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
- *Correspondence: Dawei Xin, ; Qingshan Chen, ; Mingliang Yang,
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12
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Han X, Li J, Zhao Y, Zhang Z, Jiang H, Wang J, Feng X, Zhang Y, Du Z, Wu X, Chen Q, Qi Z. Integrated transcriptomic and proteomic characterization of a chromosome segment substitution line reveals a new regulatory network controlling the seed storage profile of soybean. Food Energy Secur 2022. [DOI: 10.1002/fes3.381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Xue Han
- College of Agriculture Northeast Agricultural University Harbin China
- Heilongjiang Academy of Land Reclamation Sciences Harbin China
| | - Jiapeng Li
- College of Agriculture Northeast Agricultural University Harbin China
| | - Yabin Zhao
- College of Agriculture Northeast Agricultural University Harbin China
| | - Zhanguo Zhang
- College of Agriculture Northeast Agricultural University Harbin China
| | - Hongwei Jiang
- Soybean Research Institute Jilin Academy of Agricultural Sciences Changchun China
| | - Jinxing Wang
- Suihua Branch Institute, HeiLongJiang Academy of Agricultural Sciences Suihua China
| | - Xuezhen Feng
- College of Agriculture Northeast Agricultural University Harbin China
| | - Yu Zhang
- College of Agriculture Northeast Agricultural University Harbin China
| | - Ziyue Du
- College of Agriculture Northeast Agricultural University Harbin China
| | - Xiaoxia Wu
- College of Agriculture Northeast Agricultural University Harbin China
| | - Qingshan Chen
- College of Agriculture Northeast Agricultural University Harbin China
| | - Zhaoming Qi
- College of Agriculture Northeast Agricultural University Harbin China
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13
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Dong L, Cheng Q, Fang C, Kong L, Yang H, Hou Z, Li Y, Nan H, Zhang Y, Chen Q, Zhang C, Kou K, Su T, Wang L, Li S, Li H, Lin X, Tang Y, Zhao X, Lu S, Liu B, Kong F. Parallel selection of distinct Tof5 alleles drove the adaptation of cultivated and wild soybean to high latitudes. MOLECULAR PLANT 2022; 15:308-321. [PMID: 34673232 DOI: 10.1016/j.molp.2021.10.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/27/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor. In particular, the genetic basis of the adaptation in wild soybean remains poorly understood. In this study, by combining whole-genome resequencing and genome-wide association studies we identified a novel locus, Time of Flowering 5 (Tof5), which promotes flowering and enhances adaptation to high latitudes in both wild and cultivated soybean. By genomic, genetic and transgenic analyses we showed that Tof5 encodes a homolog of Arabidopsis thaliana FRUITFULL (FUL). Importantly, further analyses suggested that different alleles of Tof5 have undergone parallel selection. The Tof5H1 allele was strongly selected by humans after the early domestication of cultivated soybean, while Tof5H2 allele was naturally selected in wild soybean, and in each case facilitating adaptation to high latitudes. Moreover, we found that the key flowering repressor E1 suppresses the transcription of Tof5 by binding to its promoter. In turn, Tof5 physically associates with the promoters of two important FLOWERING LOCUS T (FT), FT2a and FT5a, to upregulate their transcription and promote flowering under long photoperiods. Collectively, our findings provide insights into how wild soybean adapted to high latitudes through natural selection and indicate that cultivated soybean underwent changes in the same gene but evolved a distinct allele that was artificially selected after domestication.
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Affiliation(s)
- Lidong Dong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China.
| | - Qun Cheng
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Chao Fang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Lingping Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Hui Yang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Zhihong Hou
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China; College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163000, China
| | - Yongli Li
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Haiyang Nan
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Yuhang Zhang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Qingshan Chen
- Department of Agriculture, Northeast Agricultural University, Harbin 150000, China
| | - Chunbao Zhang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Kun Kou
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Tong Su
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Lingshuang Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Shichen Li
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Haiyang Li
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China; National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoya Lin
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Yang Tang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Xiaohui Zhao
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Sijia Lu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China.
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China; The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China; The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
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14
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Li C, Jiang H, Li Y, Liu C, Qi Z, Wu X, Zhang Z, Hu Z, Zhu R, Guo T, Wang Z, Zheng W, Zhang Z, Zhao H, Wang N, Shan D, Xin D, Luan F, Chen Q. Identification of Finely Mapped Quantitative Trait Locus and Candidate Gene Mining for the Three-Seeded Pod Trait in Soybean. FRONTIERS IN PLANT SCIENCE 2021; 12:715488. [PMID: 34899770 PMCID: PMC8663486 DOI: 10.3389/fpls.2021.715488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/19/2021] [Indexed: 06/14/2023]
Abstract
The three-seeded pod number is an important trait that positively influences soybean yield. Soybean variety with increased three-seeded pod number contributes to the seed number/plant and higher yield. The candidate genes of the three-seeded pod may be the key for improving soybean yield. In this study, identification and validation of candidate genes for three-seeded pod has been carried out. First, a total of 36 quantitative trait locus (QTL) were detected from the investigation of recombinant inbred lines including 147 individuals derived from a cross between Charleston and Dongning 594 cultivars. Five consensus QTLs were integrated. Second, an introgressed line CSSL-182 carrying the target segment for the trait from the donor parent was selected to verify the consensus QTL based on its phenotype. Third, a secondary group was constructed by backcrossing with CSSL-182, and two QTLs were confirmed. There were a total of 162 genes in the two QTLs. The mining of candidate genes resulted in the annotation of eight genes with functions related to pod and seed sets. Finally, haplotype analysis and quantitative reverse transcriptase real-time PCR were carried to verify the candidate genes. Four of these genes had different haplotypes in the resource group, and the differences in the phenotype were highly significant. Moreover, the differences in the expression of the four genes during pod and seed development were also significant. These four genes were probably related to the development process underlying the three-seeded pod in soybean. Herein, we discuss the past and present studies related to the three-seeded pod trait in soybean.
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Affiliation(s)
- Candong Li
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
- College of Life Science, Northeast Agricultural University, Harbin, China
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hongwei Jiang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yingying Li
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Chunyan Liu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhaoming Qi
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xiaoxia Wu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhanguo Zhang
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhenbang Hu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Rongsheng Zhu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Tai Guo
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Zhixin Wang
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Wei Zheng
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Zhenyu Zhang
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Haihong Zhao
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Nannan Wang
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Dapeng Shan
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Dawei Xin
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Feishi Luan
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Qingshan Chen
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
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15
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Huang M, Qin R, Li C, Liu C, Jiang Y, Yu J, Chang D, Roberts PA, Chen Q, Wang C. Transgressive resistance to Heterodera glycines in chromosome segment substitution lines derived from susceptible soybean parents. THE PLANT GENOME 2021; 14:e20091. [PMID: 33817979 DOI: 10.1002/tpg2.20091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Chromosome segment substitution lines (CSSLs) are valuable genetic resources for quantitative trait loci (QTL) mapping of complex agronomic traits especially suitable for minor effect QTL. Here, 162 BC3 F7 -BC7 F3 CSSLs derived from crossing two susceptible parent lines, soybean [Glycine max (L.) Merr.] 'Suinong14' (recurrent parent) × wild soybean (G. soja Siebold & Zucc.) ZYD00006, were used for QTL mapping of soybean cyst nematode (SCN, Heterodera glycine Ichinohe) resistance based on female index (FI) and cysts per gram root (CGR) through phenotypic screening and whole-genome resequencing of CSSLs. Phenotypic results displayed a wide range of distribution and transgressive lines in both HG Type 2.5.7 FI and CGR and demonstrated a higher correlation between CGR and root weight (R2 = .5424) compared with than between FI and CGR (R2 = .0018). Using the single-marker analysis nonparametric mapping test, 33 significant QTL were detected on 18 chromosomes contributing resistance to FI and CGR. Fourteen QTL contributing 5.6-15.5% phenotypic variance (PVE) to FI were revealed on 11 chromosomes, and 16 QTL accounting for 6.1-36.2% PVE in CGR were detected on 14 chromosomes with strong additive effect by multiple-QTL model (MQM) mapping. Twenty-five and 13 out of all 38 QTL identified for FI and CGR on 20 chromosomes were from ZYD00006 and Suinong14, respectively. The CSSLs with the combination of positive alleles for FI, CGR, and root weight exhibited low nematode reproduction. For the first time, QTL associated with CGR have been detected, and both FI and CGR should be considered for breeding purposes in the absence of strong resistance genes such as rhg1 and Rhg4.
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Affiliation(s)
- Minghui Huang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruifeng Qin
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunjie Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
| | - Chunyan Liu
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Ye Jiang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinyao Yu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
| | - Doudou Chang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Philip A Roberts
- Department of Nematology, University of California, Riverside, CA, 92521, USA
| | - Qingshan Chen
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Congli Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
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Elattar MA, Karikari B, Li S, Song S, Cao Y, Aslam M, Hina A, Abou-Elwafa SF, Zhao T. Identification and Validation of Major QTLs, Epistatic Interactions, and Candidate Genes for Soybean Seed Shape and Weight Using Two Related RIL Populations. Front Genet 2021; 12:666440. [PMID: 34122518 PMCID: PMC8195344 DOI: 10.3389/fgene.2021.666440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the genetic mechanism underlying seed size, shape, and weight is essential for enhancing soybean cultivars. High-density genetic maps of two recombinant inbred line (RIL) populations, LM6 and ZM6, were evaluated across multiple environments to identify and validate M-QTLs as well as identify candidate genes behind major and stable quantitative trait loci (QTLs). A total of 239 and 43 M-QTLs were mapped by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM) approaches, from which 180 and 18, respectively, are novel QTLs. Twenty-two QTLs including four novel major QTLs were validated in the two RIL populations across multiple environments. Moreover, 18 QTLs showed significant AE effects, and 40 pairwise of the identified QTLs exhibited digenic epistatic effects. Thirty-four QTLs associated with seed flatness index (FI) were identified and reported here for the first time. Seven QTL clusters comprising several QTLs for seed size, shape, and weight on genomic regions of chromosomes 3, 4, 5, 7, 9, 17, and 19 were identified. Gene annotations, gene ontology (GO) enrichment, and RNA-seq analyses of the genomic regions of those seven QTL clusters identified 47 candidate genes for seed-related traits. These genes are highly expressed in seed-related tissues and nodules, which might be deemed as potential candidate genes regulating the seed size, weight, and shape traits in soybean. This study provides detailed information on the genetic basis of the studied traits and candidate genes that could be efficiently implemented by soybean breeders for fine mapping and gene cloning, and for marker-assisted selection (MAS) targeted at improving these traits individually or concurrently.
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Affiliation(s)
- Mahmoud A Elattar
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.,Agronomy Department, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Benjamin Karikari
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shuguang Li
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shiyu Song
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yongce Cao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Muhammed Aslam
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Aiman Hina
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | | | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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17
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Zou J, Zhang Z, Yu S, Kang Q, Shi Y, Wang J, Zhu R, Ma C, Chen L, Wang J, Li J, Li Q, Liu X, Zhu J, Wu X, Hu Z, Qi Z, Liu C, Chen Q, Xin D. Responses of Soybean Genes in the Substituted Segments of Segment Substitution Lines Following a Xanthomonas Infection. FRONTIERS IN PLANT SCIENCE 2020; 11:972. [PMID: 32719700 PMCID: PMC7351525 DOI: 10.3389/fpls.2020.00972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Bacterial blight, which is one of the most common soybean diseases, is responsible for considerable yield losses. In this study, a novel Xanthomonas vasicola strain was isolated from the leaves of soybean plants infected with bacterial blight under field conditions. Sequencing the X. vasicola genome revealed type-III effector-coding genes. Moreover, the hrpG deletion mutant was constructed. To identify the soybean genes responsive to HrpG, two chromosome segment substitution lines (CSSLs) carrying the wild soybean genome, but with opposite phenotypes following Xanthomonas inoculations, were used to analyze gene expression networks based on RNA sequencing at three time points after inoculations with wild-type Xanthomonas or the hrpG deletion mutant. To further identify the hub genes underlying soybean responses to HrpG, the genes located on the substituted chromosome segments were examined. Finally, a combined analysis with the QTLs for resistance to Xanthomonas identified 35 hub genes in the substituted chromosomal segments that may help regulate soybean responses to Xanthomonas and HrpG. Furthermore, two candidate genes in the CSSLs might play pivotal roles in response to Xanthomonas.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Zhaoming Qi
- *Correspondence: Zhaoming Qi, ; Chunyan Liu, ; Qingshan Chen, ; Dawei Xin,
| | - Chunyan Liu
- *Correspondence: Zhaoming Qi, ; Chunyan Liu, ; Qingshan Chen, ; Dawei Xin,
| | - Qingshan Chen
- *Correspondence: Zhaoming Qi, ; Chunyan Liu, ; Qingshan Chen, ; Dawei Xin,
| | - Dawei Xin
- *Correspondence: Zhaoming Qi, ; Chunyan Liu, ; Qingshan Chen, ; Dawei Xin,
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18
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Shi Y, Zhang Z, Wen Y, Yu G, Zou J, Huang S, Wang J, Zhu J, Wang J, Chen L, Ma C, Liu X, Zhu R, Li Q, Li J, Guo M, Liu H, Zhu Y, Sun Z, Han L, Jiang H, Wu X, Wang N, Zhang W, Yin Z, Li C, Hu Z, Qi Z, Liu C, Chen Q, Xin D. RNA Sequencing-Associated Study Identifies GmDRR1 as Positively Regulating the Establishment of Symbiosis in Soybean. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:798-807. [PMID: 32186464 DOI: 10.1094/mpmi-01-20-0017-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In soybean (Glycine max)-rhizobium interactions, the type III secretion system (T3SS) of rhizobium plays a key role in regulating host specificity. However, the lack of information on the role of T3SS in signaling networks limits our understanding of symbiosis. Here, we conducted an RNA sequencing analysis of three soybean chromosome segment substituted lines, one female parent and two derived lines with different chromosome-substituted segments of wild soybean and opposite nodulation patterns. By analyzing chromosome-linked differentially expressed genes in the substituted segments and quantitative trait loci (QTL)-assisted selection in the substituted-segment region, genes that may respond to type III effectors to mediate plant immunity-related signaling were identified. To narrow down the number of candidate genes, QTL assistant was used to identify the candidate region consistent with the substituted segments. Furthermore, one candidate gene, GmDRR1, was identified in the substituted segment. To investigate the role of GmDRR1 in symbiosis establishment, GmDRR1-overexpression and RNA interference soybean lines were constructed. The nodule number increased in the former compared with wild-type soybean. Additionally, the T3SS-regulated effectors appeared to interact with the GmDDR1 signaling pathway. This finding will allow the detection of T3SS-regulated effectors involved in legume-rhizobium interactions.
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Affiliation(s)
- Yan Shi
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Zhanguo Zhang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Yingnan Wen
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Guolong Yu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Jianan Zou
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Shiyu Huang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Jinhui Wang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Jingyi Zhu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Jieqi Wang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Lin Chen
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Chao Ma
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Xueying Liu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Rongsheng Zhu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Qingying Li
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Jianyi Li
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Miaoxin Guo
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Hanxi Liu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Yongxu Zhu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Zhijun Sun
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Lu Han
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Hongwei Jiang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, People's Republic of China
| | - Xiaoxia Wu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Nannan Wang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
- Jiamusi Branch of Heilongjiang Academy of Agricultural, Jiamusi, People's Republic of China
| | - Weiyao Zhang
- Suihua Branch of Heilongjiang Academy of Agricultural, Suihua, China, Crop Breeding Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, People's Republic of China
| | - Zhengong Yin
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
- Suihua Branch of Heilongjiang Academy of Agricultural, Suihua, China, Crop Breeding Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, People's Republic of China
| | - Candong Li
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
- Jiamusi Branch of Heilongjiang Academy of Agricultural, Jiamusi, People's Republic of China
| | - Zhenbang Hu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Zhaoming Qi
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Chunyan Liu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Qingshan Chen
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Dawei Xin
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
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19
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Balakrishnan D, Surapaneni M, Yadavalli VR, Addanki KR, Mesapogu S, Beerelli K, Neelamraju S. Detecting CSSLs and yield QTLs with additive, epistatic and QTL×environment interaction effects from Oryza sativa × O. nivara IRGC81832 cross. Sci Rep 2020; 10:7766. [PMID: 32385410 PMCID: PMC7210974 DOI: 10.1038/s41598-020-64300-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/10/2020] [Indexed: 12/25/2022] Open
Abstract
Chromosome segment substitution lines (CSSLs) are useful tools for precise mapping of quantitative trait loci (QTLs) and the evaluation of gene action and interaction in inter-specific crosses. In this study, a set of 90 back cross lines at BC2F8 generation derived from Swarna x Oryza nivara IRGC81832 was evaluated for yield traits under irrigated conditions in wet seasons of 3 consecutive years. We identified a set of 70 chromosome segment substitution lines, using genotyping data from 140 SSR markers covering 94.4% of O. nivara genome. Among these, 23 CSSLs were significantly different for 7 traits. 22 QTLs were detected for 11 traits with 6.51 to 46.77% phenotypic variation in 90 BILs. Three pleiotropic genomic regions associated with yield traits were mapped on chromosomes 1, 8 and 11. The marker interval RM206-RM144 at chromosome 11 was recurrently detected for various yield traits. Ten QTLs were identified consistently in the three consecutive years of testing. Seventeen pairs of significant epistatic QTLs (E-QTLs) were detected for days to flowering, days to maturity and plant height. Chromosome segments from O. nivara contributed trait enhancing alleles. The significantly improved lines and the stable QTLs identified in this study are valuable resource for gene discovery and yield improvement.
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20
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Sakoda K, Kaga A, Tanaka Y, Suzuki S, Fujii K, Ishimoto M, Shiraiwa T. Two novel quantitative trait loci affecting the variation in leaf photosynthetic capacity among soybeans. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110300. [PMID: 31928682 DOI: 10.1016/j.plantsci.2019.110300] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 05/13/2023]
Abstract
There is a large variation in CO2 assimilation rate per unit of leaf area (A) within or among crop species, which can be exploited to improve A by elucidating the mechanisms underlying such variation. The objective of the present study is to elucidate the genetic factors affecting the variation in leaf photosynthetic capacity among soybeans. Here, we conducted field experiments over three years, using Enrei, a leading variety in Japan, Peking, a landrace from China and the chromosome segment substitution lines derived from their progenies. The gas exchange measurements were conducted to evaluate A among soybean. Peking showed higher A than Enrei after the flowering in all the years. The genetic analysis identified two novel quantitative trait loci (QTLs) related to variation in A, which were located on chromosome 13 (qLPC13) and 20 (qLPC20). The Peking allele at qLPC13 increased A by 8.3 % in the Enrei genetic background, while the Peking allele at qLPC20 decreased A by 15.3 %. The present study is the first report on QTLs affecting a genotypic variation in leaf photosynthetic capacity among field-grown soybeans. The identification of the causal genes in these QTLs can provide a novel strategy to enhance leaf photosynthetic capacity with soybean breeding.
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Affiliation(s)
- Kazuma Sakoda
- Crop Science Laboratory, Graduate School of Agriculture, Kyoto University, Kyoto-city, Kyoto 606-8502, Japan; Research Fellow of Japan Society for the Promotion of Science, Japan.
| | - Akito Kaga
- Soybean and Field Crop Applied Genomics Research Unit, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba-city, Ibaraki, Japan.
| | - Yu Tanaka
- Crop Science Laboratory, Graduate School of Agriculture, Kyoto University, Kyoto-city, Kyoto 606-8502, Japan; JST, PRESTO, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Seita Suzuki
- Crop Science Laboratory, Graduate School of Agriculture, Kyoto University, Kyoto-city, Kyoto 606-8502, Japan.
| | - Kenichiro Fujii
- Soybean and Field Crop Applied Genomics Research Unit, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba-city, Ibaraki, Japan.
| | - Masao Ishimoto
- Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan.
| | - Tatsuhiko Shiraiwa
- Crop Science Laboratory, Graduate School of Agriculture, Kyoto University, Kyoto-city, Kyoto 606-8502, Japan.
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21
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Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs. Sci Rep 2020; 10:214. [PMID: 31937848 PMCID: PMC6959250 DOI: 10.1038/s41598-019-56903-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/10/2019] [Indexed: 11/08/2022] Open
Abstract
The genetic architecture of seed protein content (SPC) and its relationships to agronomic traits in pigeonpea is poorly understood. Accordingly, five F2 populations segregating for SPC and four agronomic traits (seed weight (SW), seed yield (SY), growth habit (GH) and days to first flowering (DFF)) were phenotyped and genotyped using genotyping-by-sequencing approach. Five high-density population-specific genetic maps were constructed with an average inter-marker distance of 1.6 to 3.5 cM, and subsequently, integrated into a consensus map with average marker spacing of 1.6 cM. Based on analysis of phenotyping data and genotyping data, 192 main effect QTLs (M-QTLs) with phenotypic variation explained (PVE) of 0.7 to 91.3% were detected for the five traits across the five populations. Major effect (PVE ≥ 10%) M-QTLs included 14 M-QTLs for SPC, 16 M-QTLs for SW, 17 M-QTLs for SY, 19 M-QTLs for GH and 24 M-QTLs for DFF. Also, 573 epistatic QTLs (E-QTLs) were detected with PVE ranging from 6.3 to 99.4% across traits and populations. Colocalization of M-QTLs and E-QTLs explained the genetic basis of the significant (P < 0.05) correlations of SPC with SW, SY, DFF and GH. The nature of genetic architecture of SPC and its relationship with agronomic traits suggest that genomics-assisted breeding targeting genome-wide variations would be effective for the simultaneous improvement of SPC and other important traits.
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22
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Wang J, Wang J, Ma C, Zhou Z, Yang D, Zheng J, Wang Q, Li H, Zhou H, Sun Z, Liu H, Li J, Chen L, Kang Q, Qi Z, Jiang H, Zhu R, Wu X, Liu C, Chen Q, Xin D. QTL Mapping and Data Mining to Identify Genes Associated With the Sinorhizobium fredii HH103 T3SS Effector NopD in Soybean. FRONTIERS IN PLANT SCIENCE 2020; 11:453. [PMID: 32508850 PMCID: PMC7249737 DOI: 10.3389/fpls.2020.00453] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/27/2020] [Indexed: 05/10/2023]
Abstract
In some legume-rhizobium symbioses, host specificity is influenced by rhizobial type III effectors-nodulation outer proteins (Nops). However, the genes encoding host proteins that interact with Nops remain unknown. In this study, we aimed to identify candidate soybean genes associated with NopD, one of the type III effectors of Sinorhizobium fredii HH103. The results showed that the expression pattern of NopD was analyzed in rhizobia induced by genistein. We also found NopD can be induced by TtsI, and NopD as a toxic effector can induce tobacco leaf death. In 10 soybean germplasms, NopD played a positively effect on nodule number (NN) and nodule dry weight (NDW) in nine germplasms, but not in Kenjian28. Significant phenotype of NN and NDW were identified between Dongnong594 and Charleston, Suinong14 and ZYD00006, respectively. To map the quantitative trait locus (QTL) associated with NopD, a recombinant inbred line (RIL) population derived from the cross between Dongnong594 and Charleston, and chromosome segment substitution lines (CSSLs) derived from Suinong14 and ZYD00006 were used. Two overlapping conditional QTL associated with NopD on chromosome 19 were identified. Two candidate genes were identified in the confident region of QTL, we found that NopD could influence the expression of Glyma.19g068600 (FBD/LRR) and expression of Glyma.19g069200 (PP2C) after HH103 infection. Haplotype analysis showed that different types of Glyma.19g069200 haplotypes could cause significant nodule phenotypic differences, but Glyma.19g068600 (FBD/LRR) was not. These results suggest that NopD promotes S. fredii HH103 infection via directly or indirectly regulating Glyma.19g068600 and Glyma.19g069200 expression during the establishment of symbiosis between rhizobia and soybean plants.
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Affiliation(s)
- Jinhui Wang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jieqi Wang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Chao Ma
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Ziqi Zhou
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Decheng Yang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Junzan Zheng
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Qi Wang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Huiwen Li
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hongyang Zhou
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhijun Sun
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hanxi Liu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jianyi Li
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Lin Chen
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Qinglin Kang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhaoming Qi
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Rongsheng Zhu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xiaoxia Wu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Chunyan Liu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
- *Correspondence: Chunyan Liu,
| | - Qingshan Chen
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
- Qingshan Chen,
| | - Dawei Xin
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin, China
- Dawei Xin,
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23
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Li R, Jiang H, Zhang Z, Zhao Y, Xie J, Wang Q, Zheng H, Hou L, Xiong X, Xin D, Hu Z, Liu C, Wu X, Chen Q. Combined Linkage Mapping and BSA to Identify QTL and Candidate Genes for Plant Height and the Number of Nodes on the Main Stem in Soybean. Int J Mol Sci 2019; 21:E42. [PMID: 31861685 PMCID: PMC6981803 DOI: 10.3390/ijms21010042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
Soybean is one of the most important food and oil crops in the world. Plant height (PH) and the number of nodes on the main stem (NNMS) are quantitative traits closely related to soybean yield. In this study, we used 208 chromosome segment substitution lines (CSSL) populations constructed using "SN14" and "ZYD00006" for quantitative trait locus (QTL) mapping of PH and NNMS. Combined with bulked segregant analysis (BSA) by extreme materials, 8 consistent QTLs were identified. According to the gene annotation of the QTL interval, a total of 335 genes were obtained. Five of which were associated with PH and NNMS, potentially representing candidate genes. RT-qPCR of these 5 candidate genes revealed two genes with differential relative expression levels in the stems of different materials. Haplotype analysis showed that different single nucleotide polymorphisms (SNPs) between the excellent haplotypes in Glyma.04G251900 and Glyma.16G156700 may be the cause of changes in these traits. These results provide the basis for research on candidate genes and marker-assisted selection (MAS) in soybean breeding.
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Affiliation(s)
- Ruichao Li
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun 130033, China;
| | - Zhanguo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Yuanyuan Zhao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Jianguo Xie
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Qiao Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Haiyang Zheng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Lilong Hou
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Xin Xiong
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Zhenbang Hu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
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24
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Li SN, Cheng P, Bai YQ, Shi Y, Yu JY, Li RC, Zhou RN, Zhang ZG, Wu XX, Chen QS. Analysis of Soybean Somatic Embryogenesis Using Chromosome Segment Substitution Lines and Transcriptome Sequencing. Genes (Basel) 2019; 10:E943. [PMID: 31752416 PMCID: PMC6896167 DOI: 10.3390/genes10110943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/05/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
Soybean is an important cash crop that is widely used as a source of vegetable protein and edible oil. The regeneration ability of soybean directly affects the application of biotechnology. In this study, we used the exogenous hormone 2,4-D to treat immature embryos. Different levels of somatic incidence were selected from the chromosome segment substitution lines (CSSLs) constructed by SN14 and ZYD00006. Transcriptome sequencing of extreme materials was performed, and 2666 differentially expressed genes were obtained. At the same time, a difference table was generated by combining the data on CSSL rearrangement. In the extreme materials, a total of 93 differentially expressed genes were predicted and were then analyzed by cluster analysis and Gene Ontology (GO) annotation. After screening and annotating the target genes, three differentially expressed genes with hormone pathways were identified. The expression patterns of the target genes were verified by real-time quantitative PCR (qRT-PCR). Haplotype polymorphism detection and linkage disequilibrium analysis were performed on the candidate gene Glyma.09g248200. This study provided more information on the regulation network of soybean somatic embryogenesis and regeneration processes, and further identified important genes in the soybean regeneration process and provided a theoretical basis for accelerating the application of biotechnology to soybean for improving its breeding efficiency.
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Affiliation(s)
| | | | | | | | | | | | | | - Zhan-Guo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
| | - Xiao-Xia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
| | - Qing-Shan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
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25
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Karikari B, Chen S, Xiao Y, Chang F, Zhou Y, Kong J, Bhat JA, Zhao T. Utilization of Interspecific High-Density Genetic Map of RIL Population for the QTL Detection and Candidate Gene Mining for 100-Seed Weight in Soybean. FRONTIERS IN PLANT SCIENCE 2019; 10:1001. [PMID: 31552060 PMCID: PMC6737081 DOI: 10.3389/fpls.2019.01001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/17/2019] [Indexed: 05/26/2023]
Abstract
Seed-weight is one of the most important traits determining soybean yield. Hence, it is prerequisite to have detailed understanding of the genetic basis regulating seed-weight for the development of improved cultivars. In this regard, the present study used high-density interspecific linkage map of NJIR4P recombinant inbred population evaluated in four different environments to detect stable Quantitative trait loci (QTLs) as well as mine candidate genes for 100-seed weight. In total, 19 QTLs distributed on 12 chromosomes were identified in all individual environments plus combined environment, out of which seven were novel and eight are stable identified in more than one environment. However, all the novel QTLs were minor (R 2 < 10%). The remaining 12 QTLs detected in this study were co-localized with the earlier reported QTLs with narrow genomic regions, and out of these only 2 QTLs were major (R 2 > 10%) viz., qSW-17-1 and qSW-17-4. Beneficial alleles of all identified QTLs were derived from cultivated soybean parent (Nannong493-1). Based on Protein ANalysis THrough Evolutionary Relationships, gene annotation information, and literature search, 29 genes within 5 stable QTLs were predicted to be possible candidate genes that might regulate seed-weight/size in soybean. However, it needs further validation to confirm their role in seed development. In conclusion, the present study provides better understanding of trait genetics and candidate gene information through the use high-density inter-specific bin map, and also revealed considerable scope for genetic improvement of 100-seed weight in soybean using marker-assisted breeding.
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Affiliation(s)
| | | | | | | | | | | | - Javaid Akhter Bhat
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tuanjie Zhao
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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26
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Zhao X, Dong H, Chang H, Zhao J, Teng W, Qiu L, Li W, Han Y. Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill]. BMC Genomics 2019; 20:648. [PMID: 31412769 PMCID: PMC6693149 DOI: 10.1186/s12864-019-6009-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 07/30/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The hundred seed weight (HSW) is one of the yield components of soybean [Glycine max (L.) Merrill] and is especially critical for various soybean food types. In this study, a representative sample consisting of 185 accessions was selected from Northeast China and analysed in three tested environments to determine the quantitative trait nucleotide (QTN) of HSW through a genome-wide association study (GWAS). RESULT A total of 24,180 single nucleotide polymorphisms (SNPs) with minor allele frequencies greater than 0.2 and missing data less than 3% were utilized to estimate linkage disequilibrium (LD) levels in the tested association panel. Thirty-four association signals were identified as associated with HSW via GWAS. Among them, nineteen QTNs were novel, and another fifteen QTNs were overlapped or located near the genomic regions of known HSW QTL. A total of 237 genes, derived from 31 QTNs and located near peak SNPs from the three tested environments in 2015 and 2016, were considered candidate genes, were related to plant growth regulation, hormone metabolism, cell, RNA, protein metabolism, development, starch accumulation, secondary metabolism, signalling, and the TCA cycle, some of which have been found to participate in the regulation of HSW. A total of 106 SNPs from 16 candidate genes were significantly associated with HSW in soybean. CONCLUSIONS The identified loci with beneficial alleles and candidate genes might be valuable for the molecular network and MAS of HSW.
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Affiliation(s)
- Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030 China
| | - Hairan Dong
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030 China
| | - Hong Chang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030 China
| | - Jingyun Zhao
- Zhumadian Academy of Agricultural Sciences, Zhumadian, 463000 China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030 China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030 China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030 China
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27
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Zhang H, Yasmin F, Song BH. Neglected treasures in the wild - legume wild relatives in food security and human health. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:17-26. [PMID: 31085425 PMCID: PMC6817337 DOI: 10.1016/j.pbi.2019.04.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 05/08/2023]
Abstract
The legume family (Fabaceae) is the third-largest flowering family with over 18 000 species worldwide that are rich in proteins, oils, and nutrients. However, the production potential of legume-derived food cannot meet increasing global demand. Wild legumes represent a large group of wild species adaptive to diverse habitats and harbor rich genetic diversity for the improvement of the agronomic, nutritional, and medicinal values of the domesticated legumes. Accumulating evidence suggests that the genetic variation retained in these under-exploited leguminous wild relatives can be used to improve crop yield, nutrient contents, and resistance/tolerance to environmental stresses via the integration of omics, genetics, and genome-editing technologies.
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Affiliation(s)
- Hengyou Zhang
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Farida Yasmin
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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28
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Yu JY, Zhang ZG, Huang SY, Han X, Wang XY, Pan WJ, Qin HT, Qi HD, Yin ZG, Qu KX, Zhang ZX, Liu SS, Jiang HW, Liu CY, Hu ZB, Wu XX, Chen QS, Xin DW, Qi ZM. Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing. Genes (Basel) 2019; 10:E408. [PMID: 31142023 PMCID: PMC6628032 DOI: 10.3390/genes10060408] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 01/05/2023] Open
Abstract
Soybeans are an important cash crop and are widely used as a source of vegetable protein and edible oil. MicroRNAs (miRNA) are endogenous small RNA that play an important regulatory role in the evolutionarily conserved system of gene expression. In this study, we selected four lines with extreme phenotypes, as well as high or low protein and oil content, from the chromosome segment substitution line (CSSL) constructed from suinong (SN14) and ZYD00006, and planted and sampled at three stages of grain development for small RNA sequencing and expression analysis. The sequencing results revealed the expression pattern of miRNA in the materials, and predicted miRNA-targeted regulatory genes, including 1967 pairs of corresponding relationships between known-miRNA and their target genes, as well as 597 pairs of corresponding relationships between novel-miRNA and their target genes. After screening and annotating genes that were targeted for regulation, five specific genes were identified to be differentially expressed during seed development and subsequently analyzed for their regulatory relationship with miRNAs. The expression pattern of the targeted gene was verified by Real-time Quantitative PCR (RT-qPCR). Our research provides more information about the miRNA regulatory network in soybeans and further identifies useful genes that regulate storage during soy grain development, providing a theoretical basis for the regulation of soybean quality traits.
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Affiliation(s)
- Jing-Yao Yu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhan-Guo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Shi-Yu Huang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Xue Han
- Department of Horticulture, Michigan State University, East Lansing 48824, MI, USA.
| | - Xin-Yu Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Wen-Jing Pan
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Hong-Tao Qin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Hui-Dong Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhen-Gong Yin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Ke-Xin Qu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Ze-Xin Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Shan-Shan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Hong-Wei Jiang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Chun-Yan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhen-Bang Hu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Xiao-Xia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
- Green Food Research Institute in Heilongjiang Province, Harbin 150030, Heilongjiang, China.
| | - Qing-Shan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Da-Wei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhao-Ming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
- Department of Plant Soil and Microbe Science, Michigan State University, East Lansing, MI 48824, USA.
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29
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Swarm SA, Sun L, Wang X, Wang W, Brown PJ, Ma J, Nelson RL. Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1195-1209. [PMID: 30607438 DOI: 10.1007/s00122-018-3272-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/20/2018] [Indexed: 05/26/2023]
Abstract
KEY MESSAGE A total of 132 domestication-related QTLs, of which 41 were novel, were identified through genotyping-by-sequencing of two Glycine max × Glycine soja populations. Soybean [Glycine max (L.) Merr.] was domesticated in East Asia from the wild progenitor Glycine soja. The domestication process led to many distinct morphological changes that adapt it to cultivation. These include larger seeds, erect growth, larger stem diameter, reduced pod shattering, and altered growth habit. The objective of this study was to identify QTLs controlling key domestication-related traits (DRTs) using interspecific mapping populations. A total of 151 RILs from Williams 82 × PI 468916 and 510 RILs from Williams 82 × PI 479752 were utilized for QTL mapping. These lines were genotyped using a genotyping-by-sequencing protocol which resulted in approximately 5000 polymorphic SNP markers. The number of QTLs detected for each of the eleven DRTs ranged between 0-4 QTLs in the smaller Williams 82 × PI 468916 population and 3-16 QTLs in the larger Williams 82 × PI 479752 population. A total of 132 QTLs were detected, of which 51 are associated with selective sweeps previously related to soybean domestication. These QTLs were detected across all 20 chromosomes within 42 genomic regions. This study identifies 41 novel QTLs not detected in previous studies using smaller populations while also confirming the quantitative nature for several of the important DRTs in soybeans. These results would enable more effective use of the wild germplasm for soybean improvement.
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Affiliation(s)
- Stephen A Swarm
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beck's Superior Hybrids, Atlanta, IN, 46031, USA
| | - Lianjun Sun
- Department of Agronomy and Center for Plant Biology, Purdue University, West Lafayette, IN, 47906, USA
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xutong Wang
- Department of Agronomy and Center for Plant Biology, Purdue University, West Lafayette, IN, 47906, USA
| | - Weidong Wang
- Department of Agronomy and Center for Plant Biology, Purdue University, West Lafayette, IN, 47906, USA
| | - Patrick J Brown
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Plant Sciences, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Jianxin Ma
- Department of Agronomy and Center for Plant Biology, Purdue University, West Lafayette, IN, 47906, USA.
| | - Randall L Nelson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Urbana, IL, 61801, USA.
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30
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Huang S, Yu J, Li Y, Wang J, Wang X, Qi H, Xu M, Qin H, Yin Z, Mei H, Chang H, Gao H, Liu S, Zhang Z, Zhang S, Zhu R, Liu C, Wu X, Jiang H, Hu Z, Xin D, Chen Q, Qi Z. Identification of Soybean Genes Related to Soybean Seed Protein Content Based on Quantitative Trait Loci Collinearity Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:258-274. [PMID: 30525587 DOI: 10.1021/acs.jafc.8b04602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Increasing the protein content of soybean seeds through a higher ratio of glycinin is important for soybean breeding and food processing; therefore, the integration of different quantitative trait loci (QTLs) is of great significance. In this study, we investigated the collinearity of seed protein QTLs. We identified 192 collinear protein QTLs that formed six hotspot regions. The two most important regions had seed protein 36-10 and seed protein 36-20 as hub nodes. We used a chromosome segment substitution line (CSSL) population for QTL validation and identified six CSSL materials with collinear QTLs. Five materials with higher protein and glycinin contents in comparison to the recurrent parent were analyzed. A total of 13 candidate genes related to seed protein from the QTL hotspot intervals were detected, 8 of which had high expression in mature soybean seeds. These results offer a new analysis method for molecular-assisted selection (MAS) and improvement of soybean product quality.
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Affiliation(s)
- Shiyu Huang
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Jingyao Yu
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Yingying Li
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Jingxin Wang
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Xinyu Wang
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Huidong Qi
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Mingyue Xu
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Hongtao Qin
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Zhengong Yin
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Hongyao Mei
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | | | - Hongxiu Gao
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Shanshan Liu
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Zhenguo Zhang
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Shuli Zhang
- Institute of Wuchang Rice Research , Heilongjiang Academy of Agricultural Sciences , Wuchang , Heilongjiang 150229 , People's Republic of China
| | - Rongsheng Zhu
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Chunyan Liu
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Xiaoxia Wu
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Hongwei Jiang
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Zhenbang Hu
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Dawei Xin
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Qingshan Chen
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
| | - Zhaoming Qi
- College of Agriculture , Northeast Agricultural University , Harbin 150030 , Heilongjiang , People's Republic of China
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31
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Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S. Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1-25. [PMID: 30483819 DOI: 10.1007/s00122-018-3219-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/24/2018] [Indexed: 05/27/2023]
Abstract
CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits. Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross breeding and genome-wide marker-assisted selection followed by selfing. Each line in a CSSL library has a specific marker-defined large donor segment. CSSLs are evaluated for any target phenotype to identify lines significantly different from the parental line. These CSSLs are then used to map quantitative trait loci (QTLs) or causal genes. CSSLs are valuable prebreeding tools for broadening the genetic base of existing cultivars and harnessing the genetic diversity from the wild- and distant-related species. These are resources for genetic map construction, mapping QTLs, genes or gene interactions and their functional analysis for crop improvement. In the last two decades, the utility of CSSLs in identification of novel genomic regions and QTL hot spots influencing a wide range of traits has been well demonstrated in food and commercial crops. This review presents an overview of how CSSLs are developed, their status in major crops and their use in genomic studies and gene discovery.
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Affiliation(s)
- Divya Balakrishnan
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Malathi Surapaneni
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sukumar Mesapogu
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sarla Neelamraju
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India.
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32
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Wang J, Wang J, Liu C, Ma C, Li C, Zhang Y, Qi Z, Zhu R, Shi Y, Zou J, Li Q, Zhu J, Wen Y, Sun Z, Liu H, Jiang H, Yin Z, Hu Z, Chen Q, Wu X, Xin D. Identification of Soybean Genes Whose Expression is Affected by the Ensifer fredii HH103 Effector Protein NopP. Int J Mol Sci 2018; 19:E3438. [PMID: 30400148 PMCID: PMC6274870 DOI: 10.3390/ijms19113438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 01/01/2023] Open
Abstract
In some legume⁻rhizobium symbioses, host specificity is influenced by rhizobial nodulation outer proteins (Nops). However, the genes encoding host proteins that interact with Nops remain unknown. We generated an Ensifer fredii HH103 NopP mutant (HH103ΩNopP), and analyzed the nodule number (NN) and nodule dry weight (NDW) of 10 soybean germplasms inoculated with the wild-type E. fredii HH103 or the mutant strain. An analysis of recombinant inbred lines (RILs) revealed the quantitative trait loci (QTLs) associated with NopP interactions. A soybean genomic region containing two overlapping QTLs was analyzed in greater detail. A transcriptome analysis and qRT-PCR assay were used to identify candidate genes encoding proteins that interact with NopP. In some germplasms, NopP positively and negatively affected the NN and NDW, while NopP had different effects on NN and NDW in other germplasms. The QTL region in chromosome 12 was further analyzed. The expression patterns of candidate genes Glyma.12g031200 and Glyma.12g073000 were determined by qRT-PCR, and were confirmed to be influenced by NopP.
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Affiliation(s)
- Jinhui Wang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Jieqi Wang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Chunyan Liu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Chao Ma
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Changyu Li
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Yongqian Zhang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Zhaoming Qi
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Rongsheng Zhu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Yan Shi
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Jianan Zou
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Qingying Li
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Jingyi Zhu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Yingnan Wen
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Zhijun Sun
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Hanxi Liu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Hongwei Jiang
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Zhengong Yin
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
- Heilongjiang Academy of Agricultural Sciences, Harbin 150030, China.
| | - Zhenbang Hu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Qingshan Chen
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Xiaoxia Wu
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
| | - Dawei Xin
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin 150030, China.
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Yang S, Zhang B, Liu G, Hong B, Xu J, Chen X, Wang B, Wu Z, Hou F, Yue X, Wang J, Zhang Q, King GJ, Liu K. A comprehensive and precise set of intervarietal substitution lines to identify candidate genes and quantitative trait loci in oilseed rape (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2117-2129. [PMID: 29998372 DOI: 10.1007/s00122-018-3140-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/01/2018] [Indexed: 06/08/2023]
Abstract
A set of intervarietal substitution lines were developed in rapeseed by recurrent backcrossing and marker-assisted selection and employed for mapping both qualitative and quantitative traits. Intervarietal substitution lines (ISLs) may be assembled into advanced secondary mapping populations that have remarkable potential for resolving trait loci and mapping candidate genes. To facilitate the identification of important genes in oilseed rape (canola, Brassica napus), we developed 89 ISLs using an elite cultivar 'Zhongyou 821' (ZY821) as the recipient and a re-synthesized line 'No.2127' as the donor. In the whole process of ISLs development, the target chromosome segments were selected based on the genotypes of 300 microsatellite markers evenly distributed across the genome. Eighty-nine ISLs fixed at BC5F4 were genotyped by sequencing using double digestion to survey the lengths of target substitution segments from the donor parent and the background segments from the recurrent parent. The total length of the substituted chromosome segments was 3030.27 Mb, representing 3.56 × of the Darmor-bzh reference genome sequence (version 4.1). Gene mapping was conducted for two qualitative traits, flower colour and seed-coat colour, and nine quantitative traits including yield- and quality-related traits, with 19 QTLs identified for the latter. Overlapping substitution segments were identified for flower colour and seed-coat colour loci, as well as for QTLs consistently detected in 2 or 3 years. These results demonstrate the value of these ISLs for locus resolution and subsequent cloning, targeted mutation or editing of genes controlling important traits in oilseed rape.
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Affiliation(s)
- Shanjing Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Baohua Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsong Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xun Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhikun Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fan Hou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaopeng Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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34
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Jiang H, Li Y, Qin H, Li Y, Qi H, Li C, Wang N, Li R, Zhao Y, Huang S, Yu J, Wang X, Zhu R, Liu C, Hu Z, Qi Z, Xin D, Wu X, Chen Q. Identification of Major QTLs Associated With First Pod Height and Candidate Gene Mining in Soybean. FRONTIERS IN PLANT SCIENCE 2018; 9:1280. [PMID: 30283463 PMCID: PMC6157441 DOI: 10.3389/fpls.2018.01280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/15/2018] [Indexed: 05/11/2023]
Abstract
First pod height (FPH) is a quantitative trait in soybean [Glycine max (L.) Merr.] that affects mechanized harvesting. A compatible combination of the FPH and the mechanized harvester is required to ensure that the soybean is efficiently harvested. In this study, 147 recombinant inbred lines, which were derived from a cross between 'Dongnong594' and 'Charleston' over 8 years, were used to identify the major quantitative trait loci (QTLs) associated with FPH. Using a composite interval mapping method with WinQTLCart (version 2.5), 11 major QTLs were identified. They were distributed on five soybean chromosomes, and 90 pairs of QTLs showed significant epistatic associates with FPH. Of these, 3 were main QTL × main QTL interactions, and 12 were main QTL × non-main QTL interactions. A KEGG gene annotation of the 11 major QTL intervals revealed 8 candidate genes related to plant growth, appearing in the pathways K14486 (auxin response factor 9), K14498 (serine/threonine-protein kinase), and K13946 (transmembrane amino acid transporter family protein), and 7 candidate genes had high expression levels in the soybean stems. These results will aid in building a foundation for the fine mapping of the QTLs related to FPH and marker-assisted selection for breeding in soybean.
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Affiliation(s)
- Hongwei Jiang
- College of Agriculture, Northeast Agricultural University, Harbin, China
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, China
| | - Yingying Li
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hongtao Qin
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Yongliang Li
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Huidong Qi
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Candong Li
- College of Agriculture, Northeast Agricultural University, Harbin, China
- Heilongjiang Academy of Agricultural Sciences, Jiamusi Branch Institute, Jiamusi, China
| | - Nannan Wang
- Heilongjiang Academy of Agricultural Sciences, Jiamusi Branch Institute, Jiamusi, China
| | - Ruichao Li
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Yuanyuan Zhao
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Shiyu Huang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jingyao Yu
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xinyu Wang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Rongsheng Zhu
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhenbang Hu
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, China
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35
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Qi Z, Zhang Z, Wang Z, Yu J, Qin H, Mao X, Jiang H, Xin D, Yin Z, Zhu R, Liu C, Yu W, Hu Z, Wu X, Liu J, Chen Q. Meta-analysis and transcriptome profiling reveal hub genes for soybean seed storage composition during seed development. PLANT, CELL & ENVIRONMENT 2018; 41:2109-2127. [PMID: 29486529 DOI: 10.1111/pce.13175] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/10/2018] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Soybean is an important crop providing edible oil and protein source. Soybean oil and protein contents are quantitatively inherited and significantly affected by environmental factors. In this study, meta-analysis was conducted based on soybean physical maps to integrate quantitative trait loci (QTLs) from multiple experiments in different environments. Meta-QTLs for seed oil, fatty acid composition, and protein were identified. Of them, 11 meta-QTLs were located on hot regions for both seed oil and protein. Next, we selected 4 chromosome segment substitution lines with different seed oil and protein contents to characterize their 3 years of phenotype selection in the field. Using strand-specific RNA-sequencing analysis, we profile the time-course transcriptome patterns of soybean seeds at early maturity, middle maturity, and dry seed stages. Pairwise comparison and K-means clustering analysis revealed 7,482 differentially expressed genes and 45 expression patterns clusters. Weighted gene coexpression network analysis uncovered 46 modules of gene expression patterns. The 2 most significant coexpression networks were visualized, and 7 hub genes were identified that were involved in soybean oil and seed storage protein accumulation processes. Our results provided a transcriptome dataset for soybean seed development, and the candidate hub genes represent a foundation for further research.
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Affiliation(s)
- Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhanguo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhongyu Wang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jingyao Yu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Hongtao Qin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Xinrui Mao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Hongwei Jiang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhengong Yin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Rongsheng Zhu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Wei Yu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Zhenbang Hu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
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36
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Liu D, Yan Y, Fujita Y, Xu D. Identification and validation of QTLs for 100-seed weight using chromosome segment substitution lines in soybean. BREEDING SCIENCE 2018; 68:442-448. [PMID: 30369818 PMCID: PMC6198907 DOI: 10.1270/jsbbs.17127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 06/03/2018] [Indexed: 05/04/2023]
Abstract
The 100-seed weight (100SW) is one of the most important traits that control soybean yield. To identify the quantitative trait loci (QTL) of 100SW, 120 BC3F5 chromosome segment substitution lines (CSSLs) were cultivated over three years. The CSSLs were developed from a cross between the cultivated soybean variety 'Jackson' and the wild soybean accession 'JWS156-1', followed by continuous backcrossing using 'Jackson' variety as a recurrent parent. A total of nine QTLs (qSW8.1, qSW9.1, qSW12.1, qSW13.1, qSW14.1, qSW16.1, qSW17.1, qSW17.2, and qSW20.1) were detected on eight chromosomes. Of these, qSW12.1 (LOD = 6.78-12.31) was detected over the three successive years on chromosome 12 as a novel, stable, and major QTL. To validate the effect of qSW12.1, a residual heterozygous line (RHL), RHL564, which showed heterozygous at the qSW12.1 region, was selected from the BC3F5 population. Of the two homologous genotypes in the progenies produced by self-pollination of RHL564, a higher seed weight was observed in the 'Jackson' genotype plants than that in the 'JWS156-1' genotype plants. qSW12.1 was delimited in an interval of approximately 1,348 kb between the BARCSOYSSR_12_1282 and BARCSOYSSR_12_1347 markers on chromosome 12.
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Affiliation(s)
- Dequan Liu
- Japan International Research Center for Agricultural Science (JIRCAS),
Ohwashi, Tsukuba, Ibaraki 305-8686,
Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba,
Tennodai, Tsukuba, Ibaraki 350-8572,
Japan
| | - Yongliang Yan
- Japan International Research Center for Agricultural Science (JIRCAS),
Ohwashi, Tsukuba, Ibaraki 305-8686,
Japan
- Institute of Crop Germplasm Resources, Xinjiang Academy of Agricultural Sciences,
Urumqi, Xinjiang 830000,
P. R. China
| | - Yasunari Fujita
- Japan International Research Center for Agricultural Science (JIRCAS),
Ohwashi, Tsukuba, Ibaraki 305-8686,
Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba,
Tennodai, Tsukuba, Ibaraki 350-8572,
Japan
| | - Donghe Xu
- Japan International Research Center for Agricultural Science (JIRCAS),
Ohwashi, Tsukuba, Ibaraki 305-8686,
Japan
- Corresponding author (e-mail: )
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37
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Yu M, Liu Z, Jiang S, Xu N, Chen Q, Qi Z, Lv W. QTL mapping and candidate gene mining for soybean seed weight per plant. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1438851] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Meng Yu
- College of Agriculture Department, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Zhangxiong Liu
- Institute of Crop Sciences Department, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Shanshan Jiang
- College of Agriculture Department, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Ning Xu
- Heilongjiang Academy of Land Reclamation Sciences, Harbin, Heilongjiang, PR China
| | - Qingshan Chen
- College of Agriculture Department, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Zhaoming Qi
- College of Agriculture Department, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Wenhe Lv
- College of Agriculture Department, Northeast Agricultural University, Harbin, Heilongjiang, PR China
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