1
|
Klčová B, Balarynová J, Trněný O, Krejčí P, Cechová MZ, Leonova T, Gorbach D, Frolova N, Kysil E, Orlova A, Ihling С, Frolov A, Bednář P, Smýkal P. Domestication has altered gene expression and secondary metabolites in pea seed coat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2269-2295. [PMID: 38578789 DOI: 10.1111/tpj.16734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/09/2024] [Indexed: 04/07/2024]
Abstract
The mature seed in legumes consists of an embryo and seed coat. In contrast to knowledge about the embryo, we know relatively little about the seed coat. We analyzed the gene expression during seed development using a panel of cultivated and wild pea genotypes. Gene co-expression analysis identified gene modules related to seed development, dormancy, and domestication. Oxidoreductase genes were found to be important components of developmental and domestication processes. Proteomic and metabolomic analysis revealed that domestication favored proteins involved in photosynthesis and protein metabolism at the expense of seed defense. Seed coats of wild peas were rich in cell wall-bound metabolites and the protective compounds predominated in their seed coats. Altogether, we have shown that domestication altered pea seed development and modified (mostly reduced) the transcripts along with the protein and metabolite composition of the seed coat, especially the content of the compounds involved in defense. We investigated dynamic profiles of selected identified phenolic and flavonoid metabolites across seed development. These compounds usually deteriorated the palatability and processing of the seeds. Our findings further provide resources to study secondary metabolism and strategies for improving the quality of legume seeds which comprise an important part of the human protein diet.
Collapse
Affiliation(s)
- Barbora Klčová
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
| | - Jana Balarynová
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
| | - Oldřich Trněný
- Agricultural Research Ltd., Zemědělská 1, Troubsko, 664 41, Czech Republic
| | - Petra Krejčí
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Monika Zajacová Cechová
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Daria Gorbach
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Nadezhda Frolova
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Elana Kysil
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Anastasia Orlova
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Сhristian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle (Saale), 06120, Germany
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Petr Bednář
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
| |
Collapse
|
2
|
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.
Collapse
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.)
| |
Collapse
|
3
|
Tayade R, Imran M, Ghimire A, Khan W, Nabi RBS, Kim Y. Molecular, genetic, and genomic basis of seed size and yield characteristics in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1195210. [PMID: 38034572 PMCID: PMC10684784 DOI: 10.3389/fpls.2023.1195210] [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: 03/28/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
Soybean (Glycine max L. Merr.) is a crucial oilseed cash crop grown worldwide and consumed as oil, protein, and food by humans and feed by animals. Comparatively, soybean seed yield is lower than cereal crops, such as maize, rice, and wheat, and the demand for soybean production does not keep up with the increasing consumption level. Therefore, increasing soybean yield per unit area is the most crucial breeding objective and is challenging for the scientific community. Moreover, yield and associated traits are extensively researched in cereal crops, but little is known about soybeans' genetics, genomics, and molecular regulation of yield traits. Soybean seed yield is a complex quantitative trait governed by multiple genes. Understanding the genetic and molecular processes governing closely related attributes to seed yield is crucial to increasing soybean yield. Advances in sequencing technologies have made it possible to conduct functional genomic research to understand yield traits' genetic and molecular underpinnings. Here, we provide an overview of recent progress in the genetic regulation of seed size in soybean, molecular, genetics, and genomic bases of yield, and related key seed yield traits. In addition, phytohormones, such as auxin, gibberellins, cytokinins, and abscisic acid, regulate seed size and yield. Hence, we also highlight the implications of these factors, challenges in soybean yield, and seed trait improvement. The information reviewed in this study will help expand the knowledge base and may provide the way forward for developing high-yielding soybean cultivars for future food demands.
Collapse
Affiliation(s)
- Rupesh Tayade
- Upland Field Machinery Research Center, Kyungpook National University, Daegu, Republic of Korea
| | - Muhammad Imran
- Division of Biosafety, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Jeollabul-do, Republic of Korea
| | - Amit Ghimire
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Waleed Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Rizwana Begum Syed Nabi
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Yoonha Kim
- Upland Field Machinery Research Center, Kyungpook National University, Daegu, Republic of Korea
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Choi H, Jo Y, Chung H, Choi SY, Kim SM, Hong JS, Lee BC, Cho WK. Investigating Variability in Viral Presence and Abundance across Soybean Seed Development Stages Using Transcriptome Analysis. PLANTS (BASEL, SWITZERLAND) 2023; 12:3257. [PMID: 37765420 PMCID: PMC10535271 DOI: 10.3390/plants12183257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Plant transcriptomes offer a valuable resource for studying viral communities (viromes). In this study, we explore how plant transcriptome data can be applied to virome research. We analyzed 40 soybean transcriptomes across different growth stages and identified six viruses: broad bean wilt virus 2 (BBWV2), brassica yellow virus (BrYV), beet western yellow virus (BWYV), cucumber mosaic virus (CMV), milk vetch dwarf virus (MDV), and soybean mosaic virus (SMV). SMV was the predominant virus in both Glycine max (GM) and Glycine soja (GS) cultivars. Our analysis confirmed its abundance in both, while BBWV2 and CMV were more prevalent in GS than GM. The viral proportions varied across developmental stages, peaking in open flowers. Comparing viral abundance measured by viral reads and fragments per kilobase of transcript per million (FPKM) values revealed insights. SMV showed similar FPKM values in GM and GS, but BBWV2 and CMV displayed higher FPKM proportions in GS. Notably, the differences in viral abundance between GM and GS were generally insignificant based on the FPKM values across developmental stages, except for the apical bud stage in four GM cultivars. We also detected MDV, a multi-segmented virus, in two GM samples, with variable proportions of its segments. In conclusion, our study demonstrates the potential of plant transcriptomes for virome research, highlighting their strengths and limitations.
Collapse
Affiliation(s)
- Hoseong Choi
- Plant Health Center, Seoul National University, Seoul 08826, Republic of Korea;
| | - Yeonhwa Jo
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea;
| | - Hyunjung Chung
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea; (H.C.); (S.Y.C.); (S.-M.K.)
| | - Soo Yeon Choi
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea; (H.C.); (S.Y.C.); (S.-M.K.)
| | - Sang-Min Kim
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea; (H.C.); (S.Y.C.); (S.-M.K.)
| | - Jin-Sung Hong
- Department of Applied Biology, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Bong Choon Lee
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea;
| |
Collapse
|
6
|
Li D, Zhang Z, Gao X, Zhang H, Bai D, Wang Q, Zheng T, Li YH, Qiu LJ. The elite variations in germplasms for soybean breeding. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:37. [PMID: 37312749 PMCID: PMC10248635 DOI: 10.1007/s11032-023-01378-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/03/2023] [Indexed: 06/15/2023]
Abstract
The genetic base of soybean cultivars (Glycine max (L.) Merr.) has been narrowed through selective domestication and specific breeding improvement, similar to other crops. This presents challenges in breeding new cultivars with improved yield and quality, reduced adaptability to climate change, and increased susceptibility to diseases. On the other hand, the vast collection of soybean germplasms offers a potential source of genetic variations to address those challenges, but it has yet to be fully leveraged. In recent decades, rapidly improved high-throughput genotyping technologies have accelerated the harness of elite variations in soybean germplasm and provided the important information for solving the problem of a narrowed genetic base in breeding. In this review, we will overview the situation of maintenance and utilization of soybean germplasms, various solutions provided for different needs in terms of the number of molecular markers, and the omics-based high-throughput strategies that have been used or can be used to identify elite alleles. We will also provide an overall genetic information generated from soybean germplasms in yield, quality traits, and pest resistance for molecular breeding.
Collapse
Affiliation(s)
- Delin Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhengwei Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xinyue Gao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dong Bai
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Qi Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Tianqing Zheng
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| |
Collapse
|
7
|
Jin X, Liu J, Wang W, Li J, Liu G, Qiu R, Yang M, Liu M, Yang L, Du X, Lei B. Identification of Age-associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:633-647. [PMID: 35752290 PMCID: PMC9880895 DOI: 10.1016/j.gpb.2022.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/15/2022] [Accepted: 06/13/2022] [Indexed: 01/31/2023]
Abstract
Retinal pigment epithelium (RPE) has essential functions, such as nourishing and supporting the neural retina, and is of vital importance in the pathogenesis of age-related retinal degeneration. However, the exact molecular changes of RPE during aging remain poorly understood. Here, we isolated human primary RPE (hRPE) cells from 18 eye donors distributed over a wide age range (10-67 years old). A quantitative proteomic analysis was performed to analyze changes in their intracellular and secreted proteins. Age-group related subtypes and age-associated proteins were revealed and potential age-associated mechanisms were validated in ARPE-19 and hRPE cells. The results of proteomic data analysis and verifications suggest that RNF123- and RNF149-related protein ubiquitination plays an important role in protecting hRPE cells from oxidative damage during aging. In older hRPE cells, apoptotic signaling-related pathways were up-regulated, and endoplasmic reticulum organization was down-regulated both in the intracellular and secreted proteomes. Our work paints a detailed molecular picture of hRPE cells during the aging process and provides new insights into the molecular characteristics of RPE during aging and under other related clinical retinal conditions.
Collapse
Affiliation(s)
- Xiuxiu Jin
- Henan Eye Institute, Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou 450003, China,Branch of National Clinical Research Center for Ocular Disease, Henan Provincial People’s Hospital, Zhengzhou 450003, China,School of Medicine, Henan Provincial People’s Hospital, Henan University, Zhengzhou 450003, China
| | - Jingyang Liu
- Henan Eye Institute, Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou 450003, China,Branch of National Clinical Research Center for Ocular Disease, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Weiping Wang
- Henan Eye Institute, Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou 450003, China,Branch of National Clinical Research Center for Ocular Disease, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Jiangfeng Li
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Guangming Liu
- Henan Eye Institute, Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou 450003, China,Branch of National Clinical Research Center for Ocular Disease, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Ruiqi Qiu
- Henan Eye Institute, Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou 450003, China,Branch of National Clinical Research Center for Ocular Disease, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Mingzhu Yang
- Henan Eye Institute, Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou 450003, China,Branch of National Clinical Research Center for Ocular Disease, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Meng Liu
- Henan Eye Institute, Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou 450003, China,Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lin Yang
- Henan Eye Institute, Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou 450003, China,Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaofeng Du
- Henan Eye Institute, Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou 450003, China,Branch of National Clinical Research Center for Ocular Disease, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Bo Lei
- Henan Eye Institute, Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou 450003, China,Branch of National Clinical Research Center for Ocular Disease, Henan Provincial People’s Hospital, Zhengzhou 450003, China,Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China,Corresponding author.
| |
Collapse
|
8
|
Quan C, Chen G, Li S, Jia Z, Yu P, Tu J, Shen J, Yi B, Fu T, Dai C, Ma C. Transcriptome shock in interspecific F1 allotriploid hybrids between Brassica species. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2336-2353. [PMID: 35139197 DOI: 10.1093/jxb/erac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Interspecific hybridization drives the evolution of angiosperms and can be used to introduce novel alleles for important traits or to activate heterosis in crop breeding. Hybridization brings together gene expression networks from two different species, potentially causing global alterations of gene expression in the F1 plants which is called 'transcriptome shock'. Here, we explored such a transcriptome shock in allotriploid Brassica hybrids. We generated interspecific F1 allotriploid hybrids between the allotetraploid species Brassica napus and three accessions of the diploid species Brassica rapa. RNA-seq of the F1 hybrids and the parental plants revealed that 26.34-30.89% of genes were differentially expressed between the parents. We also analyzed expression level dominance and homoeolog expression bias between the parents and the F1 hybrids. The expression-level dominance biases of the Ar, An, and Cn subgenomes was genotype and stage dependent, whereas significant homoeolog expression bias was observed among three subgenomes from different parents. Furthermore, more genes were involved in trans regulation than in cis regulation in allotriploid F1 hybrids. Our findings provide new insights into the transcriptomic responses of cross-species hybrids and hybrids showing heterosis, as well as a new method for promoting the breeding of desirable traits in polyploid Brassica species.
Collapse
Affiliation(s)
- Chengtao Quan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Guoting Chen
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Sijia Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Pugang Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| |
Collapse
|
9
|
Huang J, Chen X, He A, Ma Z, Gong T, Xu K, Chen R. Integrative Morphological, Physiological, Proteomics Analyses of Jujube Fruit Development Provide Insights Into Fruit Quality Domestication From Wild Jujube to Cultivated Jujube. FRONTIERS IN PLANT SCIENCE 2021; 12:773825. [PMID: 34899802 PMCID: PMC8653901 DOI: 10.3389/fpls.2021.773825] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/13/2021] [Indexed: 06/12/2023]
Abstract
Jujube (Ziziphus jujuba) was domesticated from wild jujube (Z. jujuba var. spinosa). Here, integrative physiological, metabolomic, and comparative proteomic analyses were performed to investigate the fruit expansion and fruit taste components in a jujube cultivar 'Junzao' and a wild jujube 'Qingjiansuanzao' with contrasting fruit size and taste. We revealed that the duration of cell division and expansion largely determined the final fruit size, while the intercellular space in the mesocarp dictated the ratio of mesocarp volume in mature fruits. The high levels of endogenous gibbereline3 (GA) and zeatin in the growing fruit of 'Junzao' were associated with their increased fruit expansion. Compared with 'Junzao,' wild jujube accumulated lower sugars and higher organic acids. Furthermore, several protein co-expression modules and important member proteins correlated with fruit expansion, sugar synthesis, and ascorbic acid metabolism were identified. Among them, GA20OX involved in GA biosynthesis was identified as a key protein regulating fruit expansion, whereas sucrose-6-phosphate synthase (SPS) and neutral invertase (NINV) were considered as key enzymes promoting sugar accumulation and as major factors regulating the ratio of sucrose to hexose in jujube fruits, respectively. Moreover, the increase of Nicotinamide adenine dinucleotide-Malate dehydrogenase (NAD-MDH) activity and protein abundance were associated with the malic acid accumulation, and the high accumulation of ascorbic acid in wild jujube was correlated with the elevated abundance of GalDH, ZjAPXs, and MDHAR1, which are involved in the ascorbic acid biosynthesis and recycling pathways. Overall, these results deepened the understanding of mechanisms regulating fruit expansion and sugar/acids metabolisms in jujube fruit.
Collapse
Affiliation(s)
- Jian Huang
- Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling, China
| | - Xin Chen
- Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling, China
| | - Aobing He
- Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling, China
| | - Zhibo Ma
- Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling, China
| | - Tianqi Gong
- Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling, China
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, United States
| | - Ruihong Chen
- Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling, China
- Key Laboratory of Shaanxi Province on Jujube, College of Life Science, Yan’an University, Yan’an, China
| |
Collapse
|
10
|
Kohlhase DR, McCabe CE, Singh AK, O’Rourke JA, Graham MA. Comparing Early Transcriptomic Responses of 18 Soybean ( Glycine max) Genotypes to Iron Stress. Int J Mol Sci 2021; 22:11643. [PMID: 34769077 PMCID: PMC8583884 DOI: 10.3390/ijms222111643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/21/2022] Open
Abstract
Iron deficiency chlorosis (IDC) is an abiotic stress that negatively affects soybean (Glycine max [L.] Merr.) production. Much of our knowledge of IDC stress responses is derived from model plant species. Gene expression, quantitative trait loci (QTL) mapping, and genome-wide association studies (GWAS) performed in soybean suggest that stress response differences exist between model and crop species. Our current understanding of the molecular response to IDC in soybeans is largely derived from gene expression studies using near-isogenic lines differing in iron efficiency. To improve iron efficiency in soybeans and other crops, we need to expand gene expression studies to include the diversity present in germplasm collections. Therefore, we collected 216 purified RNA samples (18 genotypes, two tissue types [leaves and roots], two iron treatments [sufficient and deficient], three replicates) and used RNA sequencing to examine the expression differences of 18 diverse soybean genotypes in response to iron deficiency. We found a rapid response to iron deficiency across genotypes, most responding within 60 min of stress. There was little evidence of an overlap of specific differentially expressed genes, and comparisons of gene ontology terms and transcription factor families suggest the utilization of different pathways in the stress response. These initial findings suggest an untapped genetic potential within the soybean germplasm collection that could be used for the continued improvement of iron efficiency in soybean.
Collapse
Affiliation(s)
- Daniel R. Kohlhase
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; (D.R.K.); (A.K.S.)
| | - Chantal E. McCabe
- U.S. Department of Agriculture (USDA)—Agricultural Research Service (ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA;
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; (D.R.K.); (A.K.S.)
| | - Jamie A. O’Rourke
- U.S. Department of Agriculture (USDA)—Agricultural Research Service (ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA;
| | - Michelle A. Graham
- U.S. Department of Agriculture (USDA)—Agricultural Research Service (ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA;
| |
Collapse
|
11
|
Li Q, Qiao X, Jia L, Zhang Y, Zhang S. Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties. Int J Mol Sci 2021; 22:ijms22179622. [PMID: 34502530 PMCID: PMC8456318 DOI: 10.3390/ijms22179622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 11/18/2022] Open
Abstract
Fruit acidity is one of the main determinants of fruit flavor and a target trait in fruit breeding. However, the genomic mechanisms governing acidity variation among different pear varieties remain poorly understood. In this study, two pear varieties with contrasting organic acid levels, ‘Dangshansuli’ (low-acidity) and ‘Amute’ (high-acidity), were selected, and a combination of transcriptome and population genomics analyses were applied to characterize their patterns of gene expression and genetic variation. Based on RNA-seq data analysis, differentially expressed genes (DEGs) involved in organic acid metabolism and accumulation were identified. Weighted correlation network analysis (WGCNA) revealed that nine candidate TCA (tricarboxylic acid)-related DEGs and three acid transporter-related DEGs were located in three key modules. The regulatory networks of the above candidate genes were also predicted. By integrating pear resequencing data, two domestication-related genes were found to be upregulated in ‘Amute’, and this trend was further validated for other pear varieties with high levels of organic acid, suggesting distinct selective sweeps during pear dissemination and domestication. Collectively, this study provides insight into organic acid differences related to expression divergence and domestication in two pear varieties, pinpointing several candidate genes for the genetic manipulation of acidity in pears.
Collapse
|
12
|
Zheng Q, Chen W, Luo M, Xu L, Zhang Q, Luo Z. Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon. BMC PLANT BIOLOGY 2021; 21:356. [PMID: 34325657 PMCID: PMC8323215 DOI: 10.1186/s12870-021-03133-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/01/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Proanthocyanidins (PAs) are important plant secondary metabolites that confer flavor, nutritional value, and resistance to pathogens. Persimmon is one of the PA richest crops. Mature fruits can be inedible because of the astringency caused by high PA levels and need to go through a de-astringency treatment before consumption. The molecular basis for PA accumulation is poorly known, particularly transcriptional regulators. We characterised three genotypes ('Luotiantianshi' (LT), 'Mopanshi' (MP), and 'Youhou' (YH)) with different PA accumulation patterns using an approach that combined PacBio full-length sequencing and Illumina-based RNA sequencing to build high-quality full-length transcriptomes. Additionally, we analysed transcriptome dynamics of the three genotypes (LT, MP, and YH) at four key fruit developmental stages. RESULTS A total of 96,463 transcripts were obtained. We identified 80,075 protein-coding sequences (CDSs), 71,137 simple sequence repeats (SSRs), and 27,845 long noncoding RNAs (lncRNAs). Pearson correlation coefficient (PCC), principal component analysis (PCA), and differentially expressed transcripts (DETs) analyses indicated that the four different developmental stages within a genotype exhibited similar transcriptome activities. A total of 2,164 transcripts specific to each fruit developmental stage were detected. The transcripts specific to early stages were attributed to phenylpropanoid and flavonoid biosynthesis. Co-expression network analyses revealed MEbrown and MEblue modules were strongly associated to PA accumulation. From these two modules, 20 hub TFs are potential regulators for PA accumulation. Among them, Cluster_78388 (SBP protein), Cluster_63454 (bZIP protein), and Cluster_66595 (MYB protein) appear to involve in the PA biosynthesis in Chinese genotypes. CONCLUSIONS This is the first high-quality reference transcriptome for commercial persimmon. Our work provides insights into the molecular pathways underlying PA accumulation and enhances our global understanding of transcriptome dynamics throughout fruit development.
Collapse
Affiliation(s)
- Qingyou Zheng
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Wenxing Chen
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Man Luo
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Liqing Xu
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qinglin Zhang
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhengrong Luo
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| |
Collapse
|
13
|
Yang S, Zhang J, Geng Y, Tang Z, Wang J, Guo F, Meng J, Wang Q, Wan S, Li X. Transcriptome analysis reveals the mechanism of improving erect-plant-type peanut yield by single-seeding precision sowing. PeerJ 2021; 9:e10616. [PMID: 33614263 PMCID: PMC7879956 DOI: 10.7717/peerj.10616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/30/2020] [Indexed: 01/11/2023] Open
Abstract
Background In China, double-seed (DS) sowing (i.e., sowing two seeds per hole) has been conventionally performed towards the erect-plant-type peanuts to increase the low germination rate due to poor seed preservation conditions. However, the corresponding within-hole plant competition usually limits the subsequent plant growth and the final yield. We developed a high-yield cultivation system of single-seed (SS) precision sowing to solve this paradox, saving 20% of seeds and increasing yields by more than 10% relative to the conventional DS sowing. Methods To explore the mechanisms of these two different cropping patterns in peanut yields, we conducted transcriptomic and physiological comparisons in the seeding plant leaf and root tissues between SS precision sowing and standard DS sowing treatments. Results After assembly, each library contained an average of 43 million reads and generated a total of 523,800, 338 clean reads. After GO and Kyoto Encyclopedia of Genes and Genomes pathway analysis, we found the key genes for biotic and abiotic stress showed higher expression in roots of plants grown under the SS precision sowing treatment, including genes encoding disease resistance, oxidation-reduction, hormone related, and stress response transcription factors and signaling regulation proteins. In particular, the resveratrol synthesis genes related to stress and disease resistance appeared induced in roots under the SS sowing treatment. Conclusion These data indicated that Aspergillus flavus resistance and stress tolerance in roots under SS precision sowing were enhanced compared with roots under the DS sowing treatment. This work benefits the development of underground pods and thus increasing peanut yields.
Collapse
Affiliation(s)
- Sha Yang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, China.,Scientific observation and experiment station of crop cultivation in east China, Ministry of Agriculture and Rural Affairs, Dongying, China
| | - Jialei Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, China.,Scientific observation and experiment station of crop cultivation in east China, Ministry of Agriculture and Rural Affairs, Dongying, China
| | - Yun Geng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, China.,Scientific observation and experiment station of crop cultivation in east China, Ministry of Agriculture and Rural Affairs, Dongying, China
| | - Zhaohui Tang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, China.,Scientific observation and experiment station of crop cultivation in east China, Ministry of Agriculture and Rural Affairs, Dongying, China
| | - Jianguo Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, China.,Scientific observation and experiment station of crop cultivation in east China, Ministry of Agriculture and Rural Affairs, Dongying, China
| | - Feng Guo
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, China.,Scientific observation and experiment station of crop cultivation in east China, Ministry of Agriculture and Rural Affairs, Dongying, China
| | - Jingjing Meng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, China.,Scientific observation and experiment station of crop cultivation in east China, Ministry of Agriculture and Rural Affairs, Dongying, China
| | - Quan Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, China.,College of Life Sciences, Shandong Normal University, Ji'nan, China
| | - Shubo Wan
- Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Ji'nan, China
| | - Xinguo Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, China.,Scientific observation and experiment station of crop cultivation in east China, Ministry of Agriculture and Rural Affairs, Dongying, China
| |
Collapse
|
14
|
Li Z, Zhang X, Zhao K, Zhao K, Qu C, Gao G, Gong F, Ma X, Yin D. Comprehensive Transcriptome Analyses Reveal Candidate Genes for Variation in Seed Size/Weight During Peanut ( Arachis hypogaea L.) Domestication. FRONTIERS IN PLANT SCIENCE 2021; 12:666483. [PMID: 34093624 PMCID: PMC8170302 DOI: 10.3389/fpls.2021.666483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/22/2021] [Indexed: 05/05/2023]
Abstract
Seed size/weight, a key domestication trait, is also an important selection target during peanut breeding. However, the mechanisms that regulate peanut seed development are unknown. We re-sequenced 12 RNA samples from developing seeds of two cultivated peanut accessions (Lines 8106 and 8107) and wild Arachis monticola at 15, 30, 45, and 60 days past flowering (DPF). Transcriptome analyses showed that ∼36,000 gene loci were expressed in each of the 12 RNA samples, with nearly half exhibiting moderate (2 ≤ FPKM < 10) expression levels. Of these genes, 12.2% (4,523) were specifically expressed during seed development, mainly at 15 DPF. Also, ∼12,000 genes showed significant differential expression at 30, 45, and/or 60 DPF within each of the three peanut accessions, accounting for 31.8-34.1% of the total expressed genes. Using a method that combined comprehensive transcriptome analysis and previously mapped QTLs, we identified several candidate genes that encode transcription factor TGA7, topless-related protein 2, IAA-amino acid hydrolase ILR1-like 5, and putative pentatricopeptide repeat-containing (PPR) protein. Based on sequence variations identified in these genes, SNP markers were developed and used to genotype both 30 peanut landraces and a genetic segregated population, implying that EVM0025654 encoding a PPR protein may be associated with the increased seed size/weight of the cultivated accessions in comparison with the allotetraploid wild peanut. Our results provide additional knowledge for the identification and functional research into candidate genes responsible for the seed size/weight phenotype in peanut.
Collapse
|
15
|
Chen L, Yun M, Cao Z, Liang Z, Liu W, Wang M, Yan J, Yang S, He X, Jiang B, Peng Q, Lin Y. Phenotypic Characteristics and Transcriptome of Cucumber Male Flower Development Under Heat Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:758976. [PMID: 34745192 PMCID: PMC8570340 DOI: 10.3389/fpls.2021.758976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/13/2021] [Indexed: 05/16/2023]
Abstract
Cucumber (Cucumis sativus L.) is an important vegetable crop, which is thermophilic not heat resistant. High-temperature stress always results in sterility at reproductive stage. In the present study, we evaluate the male flower developmental changes under normal (CK) and heat stress (HS) condition. After HS, the activities of peroxidase (POD) and superoxide dismutase (SOD) and the contents of malondialdehyde (MDA) were increased. In addition, the pollen fertility was significantly decreased; and abnormal tapetum and microspore were observed by paraffin section. Transcriptome analysis results presented that total of 5828 differentially expressed genes (DEGs) were identified after HS. Among these DEGs, 20 DEGs were found at four stages, including DNA binding transcription factor, glycosyltransferase, and wound-responsive family protein. The gene ontology term of carbohydrate metabolic process was significantly enriched in all anther stages, and many saccharides and starch synthase-related genes, such as invertase, sucrose synthase, and starch branching enzyme, were significantly different expressed in HS compared with CK. Furthermore, co-expression network analysis showed a module (midnightblue) strongly consistent with HS, and two hub genes (CsaV3_6G004180 and CsaV3_5G034860) were found with a high degree of connectivity to other genes. Our results provide comprehensive understandings on male flower development in cucumber under HS.
Collapse
Affiliation(s)
- Lin Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Maomao Yun
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Zhenqiang Cao
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Zhaojun Liang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Min Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Jinqiang Yan
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Songguang Yang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Xiaoming He
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Qingwu Peng
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Yu’e Lin
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
- *Correspondence: Yu’e Lin,
| |
Collapse
|
16
|
Xu Y, Magwanga RO, Jin D, Cai X, Hou Y, Juyun Z, Agong SG, Wang K, Liu F, Zhou Z. Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton. BMC PLANT BIOLOGY 2020; 20:518. [PMID: 33183239 PMCID: PMC7664088 DOI: 10.1186/s12870-020-02726-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/31/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Wild species of cotton are excellent resistance to abiotic stress. Diploid D-genome cotton showed abundant phenotypic diversity and was the putative donor species of allotetraploid cotton which produce the largest textile natural fiber. RESULTS A total of 41,053 genes were expressed in all samples by mapping RNA-seq Illumina reads of G. thurberi (D1), G. klotzschianum (D3-k), G. raimondii (D5) and G. trilobum (D8) to reference genome. The numbers of differently expressed genes (DEGs) were significantly higher under cold stress than salt stress. However, 34.1% DEGs under salt stress were overlapped with cold stress in four species. Notably, a potential shared network (cold and salt response, including 16 genes) was mined out by gene co-expression analysis. A total of 47,180-55,548 unique genes were identified in four diploid species by De novo assembly. Furthermore, 163, 344, 330, and 161 positively selected genes (PSGs) were detected in thurberi, G. klotzschianum, G. raimondii and G. trilobum by evolutionary analysis, respectively, and 9.5-17% PSGs of four species were DEGs in corresponding species under cold or salt stress. What's more, most of PSGs were enriched GO term related to response to stimulation. G. klotzschianum showed the best tolerance under both cold and salt stress. Interestingly, we found that a RALF-like protein coding gene not only is PSGs of G. klotzschianum, but also belongs to the potential shared network. CONCLUSION Our study provided new evidence that gene expression variations of evolution by natural selection were essential drivers of the morphological variations related to environmental adaptation during evolution. Additionally, there exist shared regulated networks under cold and salt stress, such as Ca2+ signal transduction and oxidation-reduction mechanisms. Our work establishes a transcriptomic selection mechanism for altering gene expression of the four diploid D-genome cotton and provides available gene resource underlying multi-abiotic resistant cotton breeding strategy.
Collapse
Affiliation(s)
- Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 40070 China
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- School of Biological, Physical, Mathematics and Actuarial sciences (SBPMAS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya
| | - Dingsha Jin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Zheng Juyun
- Economic Crops Research Institute of Xinjiang Academy of Agricultural Science, Urumqi, Xinjiang province China
| | - Stephen Gaya Agong
- School of Biological, Physical, Mathematics and Actuarial sciences (SBPMAS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| |
Collapse
|
17
|
Guo DL, Wang ZG, Pei MS, Guo LL, Yu YH. Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment. BMC Genomics 2020; 21:784. [PMID: 33176674 PMCID: PMC7657363 DOI: 10.1186/s12864-020-07180-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Background In a previous study, the early ripening of Kyoho grape following H2O2 treatment was explored at the physiological level, but the mechanism by which H2O2 promotes ripening at the molecular level is unclear. To reveal the molecular mechanism, RNA-sequencing analysis was conducted on the different developmental stages of Kyoho berry treated with H2O2. Results In the comparison of treatment and control groups, 406 genes were up-regulated and 683 were down-regulated. Time course sequencing (TCseq) analysis showed that the expression patterns of most of the genes were similar between the treatment and control, except for some genes related to chlorophyll binding and photosynthesis. Differential expression analysis and the weighted gene co-expression network were used to screen significantly differentially expressed genes and hub genes associated with oxidative stress (heat shock protein, HSP), cell wall deacetylation (GDSL esterase/lipase, GDSL), cell wall degradation (xyloglucan endotransglucosylase/ hydrolase, XTH), and photosynthesis (chlorophyll a-b binding protein, CAB1). Gene expression was verified with RT-qPCR, and the results were largely consistent with those of RNA sequencing. Conclusions The RNA-sequencing analysis indicated that H2O2 treatment promoted the early ripening of Kyoho berry by affecting the expression levels of HSP, GDSL, XTH, and CAB1 and- photosynthesis- pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07180-y.
Collapse
Affiliation(s)
- Da-Long Guo
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China. .,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China.
| | - Zhen-Guang Wang
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
| | - Mao-Song Pei
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
| | - Li-Li Guo
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
| | - Yi-He Yu
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
| |
Collapse
|
18
|
Zhou XL, Wang YH, Shen SK. Transcriptomic comparison reveals modifications in gene expression, photosynthesis, and cell wall in woody plant as responses to external pH changes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 203:111007. [PMID: 32888586 DOI: 10.1016/j.ecoenv.2020.111007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/13/2020] [Accepted: 07/03/2020] [Indexed: 05/14/2023]
Abstract
Soil acidification is one of the crucial global environmental problems, affecting sustainable land use, crop yield, and ecosystem stability. Previous research reported the tolerance of crops to acid soil stress. However, the molecular response of woody plant to acid conditions remains largely unclear. Rhododendron L. is a widely distributed woody plant genus and prefers to grow in acidic soils. Herein, weighted gene coexpression network analysis was performed on R. protistum var. giganteum seedlings subjected to five pH treatments (3.5, 4.5, 5.5, 6.0, 7.0), and their ecophysiological characteristics were determined for the identification of their molecular responses to acidic environments. Through pairwise comparison, 855 differentially expressed genes (DEGs) associated with photosynthesis, cell wall, and phenylpropanoid metabolism were identified. Most of the DEGs related to photosynthesis and cell wall were up-regulated after pH 4.5 treatment. Results implied that the species improves its photosynthetic abilities and changes its cell wall characteristics to adapt to acidic conditions. Weighted gene co-expression network analyses showed that most of the hub genes were annotated to the biosynthetic pathways of ribosomal proteins and photosynthesis. Expression pattern analysis showed that genes encoding subunit ribosomal proteins decreased at pH 7.0 treatment, suggesting that pH 7.0 treatment led to cell injury in the seedlings. The species regulates protein synthesis in response to high pH stress (pH 7.0). The present study revealed the molecular response mechanism of woody plant R. protistum var. giganteum to acid environments. These findings can be useful in enriching current knowledge of how woody species adapt to soil acidification under global environmental changes.
Collapse
Affiliation(s)
- Xiong-Li Zhou
- School of Ecology and Environmental Sciences & School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, China; Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650091, Yunnan, China
| | - Yue-Hua Wang
- School of Ecology and Environmental Sciences & School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, China; Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650091, Yunnan, China
| | - Shi-Kang Shen
- School of Ecology and Environmental Sciences & School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, China; Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650091, Yunnan, China; Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, 650091, Yunnan, China.
| |
Collapse
|
19
|
Xing S, Liu R, Zhao G, Liu L, Groenen MAM, Madsen O, Zheng M, Yang X, Crooijmans RPMA, Wen J. RNA-Seq Analysis Reveals Hub Genes Involved in Chicken Intramuscular Fat and Abdominal Fat Deposition During Development. Front Genet 2020; 11:1009. [PMID: 33117416 PMCID: PMC7493673 DOI: 10.3389/fgene.2020.01009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/07/2020] [Indexed: 12/22/2022] Open
Abstract
Fat traits are important in the chicken industry where there is a desire for high intramuscular fat (IMF) and low abdominal fat. However, there is limited knowledge on the relationship between the dynamic status of gene expression and the body fat deposition in chicken. Transcriptome data were obtained from breast muscle and abdominal fat of female chickens from nine developmental stages (from embryonic day 12 to hatched day 180). In total, 8,545 genes in breast muscle and 6,824 genes in abdominal fat were identified as developmentally dynamic genes. Weighted correlation network analysis was used to identify gene modules and the hub genes. Twenty-one hub genes were identified, e.g., ENSGALG00000041996, which represents a candidate for high IMF, and CREB3L1, which relates to low abdominal fat weight. The transcript factor L3MBTL1 and the transcript factor cofactors TNIP1, HAT1, and BEND6 related to both high breast muscle IMF and low abdominal fat weight. Our results provide a resource of developmental transcriptome profiles in chicken breast muscle and abdominal fat. The candidate genes can be used in the selection for increased IMF content and/or a decrease in abdominal fat weight which would contribute to the improvement of these traits.
Collapse
Affiliation(s)
- Siyuan Xing
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Ranran Liu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lu Liu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinting Yang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Jie Wen
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
20
|
Pourkheirandish M, Golicz AA, Bhalla PL, Singh MB. Global Role of Crop Genomics in the Face of Climate Change. FRONTIERS IN PLANT SCIENCE 2020; 11:922. [PMID: 32765541 PMCID: PMC7378793 DOI: 10.3389/fpls.2020.00922] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 06/05/2020] [Indexed: 05/05/2023]
Abstract
The development of climate change resilient crops is necessary if we are to meet the challenge of feeding the growing world's population. We must be able to increase food production despite the projected decrease in arable land and unpredictable environmental conditions. This review summarizes the technological and conceptual advances that have the potential to transform plant breeding, help overcome the challenges of climate change, and initiate the next plant breeding revolution. Recent developments in genomics in combination with high-throughput and precision phenotyping facilitate the identification of genes controlling critical agronomic traits. The discovery of these genes can now be paired with genome editing techniques to rapidly develop climate change resilient crops, including plants with better biotic and abiotic stress tolerance and enhanced nutritional value. Utilizing the genetic potential of crop wild relatives (CWRs) enables the domestication of new species and the generation of synthetic polyploids. The high-quality crop plant genome assemblies and annotations provide new, exciting research targets, including long non-coding RNAs (lncRNAs) and cis-regulatory regions. Metagenomic studies give insights into plant-microbiome interactions and guide selection of optimal soils for plant cultivation. Together, all these advances will allow breeders to produce improved, resilient crops in relatively short timeframes meeting the demands of the growing population and changing climate.
Collapse
Affiliation(s)
| | | | | | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
21
|
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.
Collapse
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,
| |
Collapse
|
22
|
Kim JY, Jeong S, Kim KH, Lim WJ, Lee HY, Jeong N, Moon JK, Kim N. Dissection of soybean populations according to selection signatures based on whole-genome sequences. Gigascience 2019; 8:giz151. [PMID: 31869408 PMCID: PMC6927394 DOI: 10.1093/gigascience/giz151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/21/2019] [Accepted: 12/05/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Domestication and improvement processes, accompanied by selections and adaptations, have generated genome-wide divergence and stratification in soybean populations. Simultaneously, soybean populations, which comprise diverse subpopulations, have developed their own adaptive characteristics enhancing fitness, resistance, agronomic traits, and morphological features. The genetic traits underlying these characteristics play a fundamental role in improving other soybean populations. RESULTS This study focused on identifying the selection signatures and adaptive characteristics in soybean populations. A core set of 245 accessions (112 wild-type, 79 landrace, and 54 improvement soybeans) selected from 4,234 soybean accessions was re-sequenced. Their genomic architectures were examined according to the domestication and improvement, and accessions were then classified into 3 wild-type, 2 landrace, and 2 improvement subgroups based on various population analyses. Selection and gene set enrichment analyses revealed that the landrace subgroups have selection signals for soybean-cyst nematode HG type 0 and seed development with germination, and that the improvement subgroups have selection signals for plant development with viability and seed development with embryo development, respectively. The adaptive characteristic for soybean-cyst nematode was partially underpinned by multiple resistance accessions, and the characteristics related to seed development were supported by our phenotypic findings for seed weights. Furthermore, their adaptive characteristics were also confirmed as genome-based evidence, and unique genomic regions that exhibit distinct selection and selective sweep patterns were revealed for 13 candidate genes. CONCLUSIONS Although our findings require further biological validation, they provide valuable information about soybean breeding strategies and present new options for breeders seeking donor lines to improve soybean populations.
Collapse
Affiliation(s)
- Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seongmun Jeong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ho-Yeon Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Namhee Jeong
- National Institute of Crop Science, Rural Development Administration, Nongsaengmyeong-ro 370, Deokjin-gu, Jeon-Ju 54874, Republic of Korea
| | - Jung-Kyung Moon
- National Institute of Crop Science, Rural Development Administration, Nongsaengmyeong-ro 370, Deokjin-gu, Jeon-Ju 54874, Republic of Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| |
Collapse
|
23
|
Wang Y, Gao H, He L, Zhu W, Yan L, Chen Q, He C. The PHOSPHATE1 genes participate in salt and Pi signaling pathways and play adaptive roles during soybean evolution. BMC PLANT BIOLOGY 2019; 19:353. [PMID: 31412775 PMCID: PMC6694516 DOI: 10.1186/s12870-019-1959-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 07/31/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND The PHOSPHATE1 (PHO1) gene family plays diverse roles in inorganic phosphate (Pi) transfer and signal transduction, and plant development. However, the functions and diversification of soybean PHO1 family are poorly understood. RESULTS Cultivated soybean (Glycine max) was domesticated from wild soybean (Glycine soja). To illuminate their roles in this evolutionary process, we comparatively investigated the G. max PHO1 genes (GmPHO1) in Suinong 14 (SN14) and G. soja PHO1 genes (GsPHO1) in ZYD00006 (ZYD6). The sequences of the orthologous Gm-GsPHO1 pairs were grouped into two Classes. The expression of Class I in both SN14 and ZYD6 was widely but relatively high in developing fruits, whereas Class II was predominantly expressed in the roots. The whole family displayed diverse response patterns to salt stresses and Pi-starvation in roots. Between SN14 and ZYD6, most PHO1 genes responded similarly to salinity stresses, and half had sharp contrasts in response to Pi-starvation, which corroborated the differential response capacities to salinity and low-Pi stress between SN14 and ZYD6. Furthermore, in transgenic Arabidopsis plants, most Class II members and GmPHO1;H9 from Class I could enhance salt tolerance, while only two Class II genes (GmPHO1;H4 and GmPHO1;H8) differently altered sensitivity to Pi-starvation. The expression of critical genes was accordingly altered in either salt or Pi signaling pathways in transgenic Arabidopsis plants. CONCLUSIONS Our work identifies some PHO1 genes as promising genetic materials for soybean improvement, and suggests that expression variation is decisive to functional divergence of the orthologous Gm-GsPHO1 pairs, which plays an adaptive role during soybean evolution.
Collapse
Affiliation(s)
- Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093 China
| | - Huihui Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093 China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049 China
| | - Lingli He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 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
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049 China
| | - Lixin Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093 China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049 China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 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
| |
Collapse
|
24
|
Wang ZG, Guo LL, Ji XR, Yu YH, Zhang GH, Guo DL. Transcriptional Analysis of the Early Ripening of 'Kyoho' Grape in Response to the Treatment of Riboflavin. Genes (Basel) 2019; 10:genes10070514. [PMID: 31284601 PMCID: PMC6678464 DOI: 10.3390/genes10070514] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 12/16/2022] Open
Abstract
Previous study has demonstrated that the riboflavin treatment promoted the early ripening of the ‘Kyoho’ grape berry. However, the molecular mechanism causing this was unclear. In order to reveal the regulation mechanism of riboflavin treatment on grape berry development and ripening, the different berry developmental stages of the ‘Kyoho’ berry treated with 0.5 mmol/L of riboflavin was sampled for transcriptome profiling. RNA-seq revealed that 1526 and 430 genes were up-regulated and down-regulated, respectively, for the comparisons of the treatment to the control. TCseq analysis showed that the expression patterns of most of the genes were similar between the treatment and the control, except for some genes that were related to the chlorophyll metabolism, photosynthesis–antenna proteins, and photosynthesis, which were revealed by the enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The differentially expressed genes and weighted gene co-expression network analysis (WGCNA) analysis identified some significantly differentially expressed genes and some hub genes, including up-regulation of the photosynthesis-related ELIP1 and growth and development-related GDSL; and down-regulation of the oxidative stress-related ATHSP22 and berry softening-related XTH32 and GH9B15. The results suggested that the riboflavin treatment resulted in the variations of the expression levels of these genes, and then led to the early ripening of the ‘Kyoho’ berry.
Collapse
Affiliation(s)
- Zhen-Guang Wang
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China
| | - Li-Li Guo
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China
- College of Agriculture, Henan University of Science and Technology, Luoyang 471023, Henan Province, China
| | - Xiao-Ru Ji
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China
| | - Yi-He Yu
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China
| | - Guo-Hai Zhang
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, Henan Province, China.
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China.
| | - Da-Long Guo
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, Henan Province, China.
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, Henan Province, China.
| |
Collapse
|
25
|
Yang S, Miao L, He J, Zhang K, Li Y, Gai J. Dynamic Transcriptome Changes Related to Oil Accumulation in Developing Soybean Seeds. Int J Mol Sci 2019; 20:E2202. [PMID: 31060266 PMCID: PMC6539092 DOI: 10.3390/ijms20092202] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 01/01/2023] Open
Abstract
Soybean is one of the most important oil crops in the world. Revealing the molecular basis and exploring key candidate genes for seed oil synthesis has great significance for soybean improvement. In this study, we found that oil accumulation rates and gene expression levels changed dynamically during soybean seed development. The expression levels of genes in metabolic pathways such as carbon fixation, photosynthesis, glycolysis, and fatty acid biosynthesis were significantly up-regulated during the rapid accumulation of oil in developing soybean seeds. Through weighted correlation network analysis, we identified six co-expression modules associated with soybean seed oil content and the pink module was the most positively correlated (r = 0.83, p = 7 × 10-4) network. Through the integration of differential expression and co-expression analysis, we predicted 124 candidate genes potentially affecting soybean seed oil content, including seven genes in lipid metabolism pathway, two genes involved in glycolysis, one gene in sucrose metabolism, and 12 genes belonged to transcription factors as well as other categories. Among these, three genes (GmABI3b, GmNFYA and GmFAD2-1B) have been shown to control oil and fatty acid content in soybean seeds, and other newly identified candidate genes would broaden our knowledge to understand the molecular basis for oil accumulation in soybean seeds.
Collapse
Affiliation(s)
- Songnan Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
| | - Long Miao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jianbo He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kai Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|