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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.
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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
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Wen Z, Lu X, Wen J, Wang Z, Chai M. Physical Seed Dormancy in Legumes: Molecular Advances and Perspectives. PLANTS (BASEL, SWITZERLAND) 2024; 13:1473. [PMID: 38891282 PMCID: PMC11174410 DOI: 10.3390/plants13111473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Physical dormancy of seeds is a form of dormancy due to the presence of an impermeable seed coat layer, and it represents a feature for plants to adapt to environmental changes over an extended period of phylogenetic evolution. However, in agricultural practice, physical dormancy is problematic. because it prevents timely and uniform seed germination. Therefore, physical dormancy is an important agronomical trait to target in breeding and domestication, especially for many leguminous crops. Compared to the well-characterized physiological dormancy, research progress on physical dormancy at the molecular level has been limited until recent years, due to the lack of suitable research materials. This review focuses on the structure of seed coat, factors affecting physical dormancy, genes controlling physical dormancy, and plants suitable for studying physical dormancy at the molecular level. Our goal is to provide a plethora of information for further molecular research on physical dormancy.
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Affiliation(s)
- Zhaozhu Wen
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xuran Lu
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Zengyu Wang
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Maofeng Chai
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
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Williams OR, Vander Schoor JK, Butler JB, Hecht VFG, Weller JL. Physical seed dormancy in pea is genetically separable from seed coat thickness and roughness. FRONTIERS IN PLANT SCIENCE 2024; 15:1359226. [PMID: 38476691 PMCID: PMC10927720 DOI: 10.3389/fpls.2024.1359226] [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: 12/22/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024]
Abstract
Introduction The seeds of wild pea (Pisum) exhibit marked physical dormancy due to impermeability of the seed coat to water, and the loss of this dormancy is thought to have been critical for domestication. Wild pea seed coats are also notably thick and rough, traits that have also reduced during domestication and are anecdotally linked to increased permeability. However, how these traits specifically interact with permeability is unclear. Methods To investigate this, we examined the genetic control of differences in seed coat characteristics between wild P. sativum ssp. humile and a non-dormant domesticated P. s. sativum accession in a recombinant inbred population. QTL effects were confirmed and their locations refined in segregating F4/5 populations. Results In this population we found a moderate correlation between testa thickness and permeability, and identified loci that affect them independently, suggesting no close functional association. However, the major loci affecting both testa thickness and permeability collocated closely with Mendel's pigmentation locus A, suggesting flavonoid compounds under its control might contribute significantly to both traits. We also show that seed coat roughness is oligogenic in this population, with the major locus independent of both testa thickness and permeability, suggesting selection for smooth seed was unlikely to be due to effects on either of these traits. Discussion Results indicate loss of seed coat dormancy during domestication was not primarily driven by reduced testa thickness or smooth seededness. The close association between major permeability and thickness QTL and Mendel's 'A' warrant further study, particularly regarding the role of flavonoids.
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Affiliation(s)
- Owen R. Williams
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Jacqueline K. Vander Schoor
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Jakob B. Butler
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, TAS, Australia
| | | | - James L. Weller
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, TAS, Australia
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Wang N, Feng S, Ma X, Chen Q, Liu C, Qi Z. Meta-Analysis and Multiomics of a Chromosome Segment Substitution Line Reveal Candidate Genes Associated with Seed Hardness in Soybean. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16840-16854. [PMID: 37821458 DOI: 10.1021/acs.jafc.3c03950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Soybean seed hardness is a key trait that influences planting, nutritional quality, and postharvest processing, but its genetic and molecular mechanisms remain to be clarified. We used meta-analysis to detect 17 meta-quantitative trait locus (QTLs) for soybean seed hardness. We then identified a hard-seeded chromosome segment substitution line, R75, with fragments introduced from hard-seeded wild germplasm in four of the meta-QTL intervals. Observations of the seed coat ultrastructure revealed thicker palisade tissue in R75 than in its soft-seeded recurrent parent. Transcriptomics and proteomics of R75 and its recurrent parent revealed multiple candidate genes associated with seed hardness. Fifty-seven were located on homozygous introduced fragments, 26 in meta-QTL intervals, and one in both (Glyma.02G268600). Five initial candidates were selected for KASP marker development on the basis of their predicted functions and nonsynonymous SNPs. The selection efficiency of the markers was as high as 90% for nonhard lines and 43% for hard lines in the chromosome segment substitution line (CSSL) population.
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Affiliation(s)
- Ning Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Shaowei Feng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Xuntong Ma
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
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Tilhou N, Kucek LK, Carr B, Marion A, Douglas J, Englert J, Ali S, Raasch J, Bhamidimarri S, Mirsky SB, Monteros MJ, Krogman S, Hayes R, Azevedo M, Riday H. Genome-wide association mapping in hairy vetch ( Vicia villosa) discovers a large effect locus controlling seed dormancy. FRONTIERS IN PLANT SCIENCE 2023; 14:1282187. [PMID: 37941659 PMCID: PMC10628312 DOI: 10.3389/fpls.2023.1282187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Hairy vetch (Vicia villosa Roth), a winter-hardy annual legume, is a promising cover crop. To fully leverage its potential, seed production and field performance of V. villosa must be improved to facilitate producer adoption. Two classic domestication traits, seed dormancy (hard seed) and dehiscence (pod shatter), are selection targets in an ongoing breeding program. This study reports a genome-wide association study of 1,019 V. villosa individuals evaluated at two sites (Knox City, Texas and Corvallis, Oregon) for the proportion of dormant seed, visual pod dehiscence scores, and two dehiscence surrogate measures (force to dehiscence and pod spiraling score). Trait performance varied between sites, but reliability (related to heritability) across sites was strong (dormant seed proportion: 0.68; dehiscence score: 0.61; spiraling score: 0.42; force to dehiscence: 0.41). A major locus controlling seed dormancy was found (q-value: 1.29 × 10-5; chromosome 1: position: 63611165), which can be used by breeding programs to rapidly reduce dormancy in breeding populations. No significant dehiscence score QTL was found, primarily due to the high dehiscence rates in Corvallis, Oregon. Since Oregon is a potentially major V. villosa seed production region, further dehiscence resistance screening is necessary.
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Affiliation(s)
- Neal Tilhou
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - Lisa Kissing Kucek
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - Brandon Carr
- James E. “Bud” Smith Plant Materials Center, United States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), Knox City, TX, United States
| | - Annie Marion
- Corvallis Plant Materials Center, USDA-NRCS, Corvallis, OR, United States
| | - Joel Douglas
- Central National Technology Support Center, USDA-NRCS, Fort Worth, TX, United States
| | - John Englert
- National Plant Materials Program, USDA-NRCS, Washington, DC, United States
| | - Shahjahan Ali
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - John Raasch
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | | | - Steven Brian Mirsky
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture-Natural Resources Conservation Service (USDA-ARS), Beltsville, MD, United States
| | | | - Sarah Krogman
- School of Medicine in Kansas, University of Kansas Medical Center, Wichita, KS, United States
| | - Ryan Hayes
- Forage Seed and Cereal Research Unit, USDA-ARS, Corvaillis, OR, United States
| | - Mark Azevedo
- Forage Seed and Cereal Research Unit, USDA-ARS, Corvaillis, OR, United States
| | - Heathcliffe Riday
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
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Ali S, Kucek LK, Riday H, Krom N, Krogman S, Cooper K, Jacobs L, Mehta P, Trammell M, Bhamidimarri S, Butler T, Saha MC, Monteros MJ. Transcript profiling of hairy vetch (Vicia villosa Roth) identified interesting genes for seed dormancy. THE PLANT GENOME 2023; 16:e20330. [PMID: 37125613 DOI: 10.1002/tpg2.20330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Hairy vetch, a diploid annual legume species, has a robust growth habit, high biomass yield, and winter hardy characteristics. Seed hardness is a major constraint for growing hairy vetch commercially. Hard seeded cultivars are valuable as forages, whereas soft seeded and shatter resistant cultivars have advantages for their use as a cover crop. Transcript analysis of hairy vetch was performed to understand the genetic mechanisms associated with important hairy vetch traits. RNA was extracted from leaves, flowers, immature pods, seed coats, and cotyledons of contrasting soft and hard seeded "AU Merit" plants. A range of 31.22-79.18 Gb RNA sequence data per tissue sample were generated with estimated coverage of 1040-2639×. RNA sequence assembly and mapping of the contigs against the Medicago truncatula (V4.0) genome identified 76,422 gene transcripts. A total of 24,254 transcripts were constitutively expressed in hairy vetch tissues. Key genes, such as KNOX4 (a class II KNOTTED-like homeobox KNOXII gene), qHs1 (endo-1,4-β-glucanase), GmHs1-1 (calcineurin-like metallophosphoesterase), chitinase, shatterproof 1 and 2 (SHP1, SHP2), shatter resistant 1-5 (SHAT1-5)(NAC transcription factor), PDH1 (prephenate dehydrogenase 1), and pectin methylesterases with a potential role in seed hardness and pod shattering, were further explored based on genes involved in seed hardness from other species to query the hairy vetch transcriptome data. Identification of interesting candidate genes in hairy vetch can facilitate the development of improved cultivars with desirable seed characteristics for use as a forage and as a cover crop.
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Affiliation(s)
- Shahjahan Ali
- USDA-ARS, US Dairy Forage Research Center, Madison, Wisconsin, USA
| | | | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Sarah Krogman
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | | | - Lynne Jacobs
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Perdeep Mehta
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Michael Trammell
- Oklahoma State University Cooperative Extension, Shawnee, Oklahoma, USA
| | | | - Twain Butler
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Malay C Saha
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
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Takahashi Y, Nasu H, Nakayama S, Tomooka N. Domestication of azuki bean and soybean in Japan: From the insight of archeological and molecular evidence. BREEDING SCIENCE 2023; 73:117-131. [PMID: 37404345 PMCID: PMC10316305 DOI: 10.1270/jsbbs.22074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/05/2023] [Indexed: 07/06/2023]
Abstract
Domestication of azuki bean and soybean has enabled them to acquire non-dormant seeds, non-shattering pods, and larger seed size. Seed remains of the Jomon period recently discovered at archeological sites in the Central Highlands of Japan (6,000-4,000 BP) suggest that the use of azuki bean and soybean and their increase in seed size began earlier in Japan than in China and Korea; molecular phylogenetic studies indicate that azuki bean and soybean originated in Japan. Recent identification of domestication genes indicate that the domestication traits of azuki bean and soybean were established by different mechanisms. Analyses of domestication related genes using DNA extracted from the seed remains would reveal further details about their domestication processes.
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Affiliation(s)
- Yu Takahashi
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroo Nasu
- Faculty of Biosphere-Geosphere Science, Okayama University of Science, Okayama 700-0005, Japan
| | - Seiji Nakayama
- Research Institute of Cultural Properties, Teikyo University, Fuefuki, Yamanashi 406-0032, Japan
| | - Norihiko Tomooka
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
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Bohra A, Tiwari A, Kaur P, Ganie SA, Raza A, Roorkiwal M, Mir RR, Fernie AR, Smýkal P, Varshney RK. The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies. PLANT & CELL PHYSIOLOGY 2022; 63:1554-1572. [PMID: 35713290 PMCID: PMC9680861 DOI: 10.1093/pcp/pcac086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 05/11/2023]
Abstract
Crop domestication is a co-evolutionary process that has rendered plants and animals significantly dependent on human interventions for survival and propagation. Grain legumes have played an important role in the development of Neolithic agriculture some 12,000 years ago. Despite being early companions of cereals in the origin and evolution of agriculture, the understanding of grain legume domestication has lagged behind that of cereals. Adapting plants for human use has resulted in distinct morpho-physiological changes between the wild ancestors and domesticates, and this distinction has been the focus of several studies aimed at understanding the domestication process and the genetic diversity bottlenecks created. Growing evidence from research on archeological remains, combined with genetic analysis and the geographical distribution of wild forms, has improved the resolution of the process of domestication, diversification and crop improvement. In this review, we summarize the significance of legume wild relatives as reservoirs of novel genetic variation for crop breeding programs. We describe key legume features, which evolved in response to anthropogenic activities. Here, we highlight how whole genome sequencing and incorporation of omics-level data have expanded our capacity to monitor the genetic changes accompanying these processes. Finally, we present our perspective on alternative routes centered on de novo domestication and re-domestication to impart significant agronomic advances of novel crops over existing commodities. A finely resolved domestication history of grain legumes will uncover future breeding targets to develop modern cultivars enriched with alleles that improve yield, quality and stress tolerance.
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Affiliation(s)
- Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Abha Tiwari
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kalyanpur, Kanpur 208024, India
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, Santiniketan Road, Bolpur 731235, India
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Sheik Khalifa Bin Zayed Street, Al Ain, Abu Dhabi 15551, UAE
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST, Shalimar, Srinagar 190025, India
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Křížkovského 511/8, Olomouc 78371, Czech Republic
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Zhou J, Li Y, Wang X, Liu Y, David-Schwartz R, Weissberg M, Qiu S, Guo Z, Yang F. Analysis of Elymus nutans seed coat development elucidates the genetic basis of metabolome and transcriptome underlying seed coat permeability characteristics. FRONTIERS IN PLANT SCIENCE 2022; 13:970957. [PMID: 36061807 PMCID: PMC9437961 DOI: 10.3389/fpls.2022.970957] [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: 06/16/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
The seed coat takes an important function in the life cycle of plants, especially seed growth and development. It promotes the accumulation of nutrients inside the seed and protects the seed embryo from mechanical damage. Seed coat permeability is an important characteristic of seeds, which not only affects seed germination, but also hinders the detection of seed vigor by electrical conductivity (EC) method. This research aimed to elucidate the mechanism of seed coat permeability formation through metabolome and transcriptome analysis of Elymus nutans. We collected the samples at 8, 18, and 28 days post-anthesis (dpa), and conducted a seed inclusion exosmosis experiment and observed the seed coat permeability. Moreover, we analyzed the changes in the metabolome and transcriptome during different development stages. Here, taking 8 dpa as control, 252 upregulated and 157 downregulated differentially expressed metabolites (DEMs) were observed and 886 upregulated unigenes and 1170 downregulated unigenes were identified at 18 dpa, while 4907 upregulated unigenes and 8561 downregulated unigenes were identified at 28 dpa. Meanwhile, we observed the components of ABC transporters, the biosynthesis of unsaturated fatty acids, and phenylalanine metabolism pathways. The key metabolites and genes affecting seed coat permeability were thiamine and salicylic acid. Furthermore, there were 13 and 14 genes with correlation coefficients greater than 0.8 with two key metabolites, respectively, and the -log2Fold Change- of these genes were greater than 1 at different development stages. Meanwhile, pathogenesis-related protein 1 and phenylalanine ammonia-lyase play an important role in regulating the formation of compounds. Our results outline a framework for understanding the development changes during seed growth of E. nutans and provide insights into the traits of seed coat permeability and supply a great significance value to seed production and quality evaluation.
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Affiliation(s)
- Jing Zhou
- National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xun Wang
- Qinghai University, Academy of Animal Science and Veterinary Medicine, Xining, China
| | - Yijia Liu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rakefet David-Schwartz
- Volcani Center, Agriculture Research Organization, Institute of Plant Sciences, Beit Dagan, Israel
| | - Mira Weissberg
- Volcani Center, Agriculture Research Organization, Institute of Plant Sciences, Beit Dagan, Israel
| | - Shuiling Qiu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenfei Guo
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Fulin Yang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
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10
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Lu S, Fang C, Abe J, Kong F, Liu B. Current overview on the genetic basis of key genes involved in soybean domestication. ABIOTECH 2022; 3:126-139. [PMID: 36312442 PMCID: PMC9590488 DOI: 10.1007/s42994-022-00074-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/11/2022] [Indexed: 11/28/2022]
Abstract
Modern crops were created through the domestication and genetic introgression of wild relatives and adaptive differentiation in new environments. Identifying the domestication-related genes and unveiling their molecular diversity provide clues for understanding how the domesticated variants were selected by ancient people, elucidating how and where these crops were domesticated. Molecular genetics and genomics have explored some domestication-related genes in soybean (Glycine max). Here, we summarize recent studies about the quantitative trait locus (QTL) and genes involved in the domestication traits, introduce the functions of these genes, clarify which alleles of domesticated genes were selected during domestication. A deeper understanding of soybean domestication could help to break the bottleneck of modern breeding by highlighting unused genetic diversity not selected in the original domestication process, as well as highlighting promising new avenues for the identification and research of important agronomic traits among different crop species.
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Affiliation(s)
- Sijia Lu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Chao Fang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-0808 Japan
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
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11
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Wang F, Sun X, Liu B, Kong F, Pan X, Zhang H. A polygalacturonase gene PG031 regulates seed coat permeability with a pleiotropic effect on seed weight in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1603-1618. [PMID: 35233649 DOI: 10.1007/s00122-022-04057-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/08/2022] [Indexed: 05/26/2023]
Abstract
KEY MESSAGE A QTL gene PG031 regulates the seed coat permeability and seed weight. The critical SNP that can explain the variation of permeability in soybean population can be used for seed improvement. Seed coat permeability is a critical trait for soybean and is tightly associated with seed storage longevity, germination, soy-food processing, and other commercially important traits. However, the molecular mechanism of such an important trait in soybean is largely unclear. In the present study, we uncovered a polygalacturonase (PG) gene, PG031, which controls seed coat permeability in soybean. PG031 exhibited tissue expression specificity in flowers while it was strongly induced in the seed coat and radical upon imbibition. Subcellular localization localized PG031 to the cell wall, suggesting its role specific to the cell wall of the seed coat. Natural variation analysis reveals three haplotypes (PG031289H, PG031289Y, and PG031Hap3) and the single nucleotide polymorphism (SNP) variation for H289Y may explain the variation in permeability in cultivated soybean population. Overexpression of impermeable allele PG031289H significantly reduced the seed coat permeability and 100-seed weight in transgenic seeds through decreasing intracellular spaces of the osteosclereid layer and parenchyma of the seed coat to decline water accessing the seed. PG031 was also located within a quantitative trait locus (QTL) explaining ~ 15% of total phenotypic variation in permeability, nominating it the QTL gene controlling permeability. PG031289Y allele associated with high permeability and high seed weight is experiencing ongoing artificial selection. The results provide insight into the genetic mechanism of seed coat permeability and indicate its potential for the improvement of permeability-associated seed traits in soybean.
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Affiliation(s)
- Feifei Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Xia Sun
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Baohui Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Fanjiang Kong
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Xiangwen Pan
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Hengyou Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
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12
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Yadav NS, Titov V, Ayemere I, Byeon B, Ilnytskyy Y, Kovalchuk I. Multigenerational Exposure to Heat Stress Induces Phenotypic Resilience, and Genetic and Epigenetic Variations in Arabidopsis thaliana Offspring. FRONTIERS IN PLANT SCIENCE 2022; 13:728167. [PMID: 35419019 PMCID: PMC8996174 DOI: 10.3389/fpls.2022.728167] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Plants are sedentary organisms that constantly sense changes in their environment and react to various environmental cues. On a short-time scale, plants respond through alterations in their physiology, and on a long-time scale, plants alter their development and pass on the memory of stress to the progeny. The latter is controlled genetically and epigenetically and allows the progeny to be primed for future stress encounters, thus increasing the likelihood of survival. The current study intended to explore the effects of multigenerational heat stress in Arabidopsis thaliana. Twenty-five generations of Arabidopsis thaliana were propagated in the presence of heat stress. The multigenerational stressed lineage F25H exhibited a higher tolerance to heat stress and elevated frequency of homologous recombination, as compared to the parallel control progeny F25C. A comparison of genomic sequences revealed that the F25H lineage had a three-fold higher number of mutations [single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs)] as compared control lineages, suggesting that heat stress induced genetic variations in the heat-stressed progeny. The F25H stressed progeny showed a 7-fold higher number of non-synonymous mutations than the F25C line. Methylome analysis revealed that the F25H stressed progeny showed a lower global methylation level in the CHH context than the control progeny. The F25H and F25C lineages were different from the parental control lineage F2C by 66,491 and 80,464 differentially methylated positions (DMPs), respectively. F25H stressed progeny displayed higher frequency of methylation changes in the gene body and lower in the body of transposable elements (TEs). Gene Ontology analysis revealed that CG-DMRs were enriched in processes such as response to abiotic and biotic stimulus, cell organizations and biogenesis, and DNA or RNA metabolism. Hierarchical clustering of these epimutations separated the heat stressed and control parental progenies into distinct groups which revealed the non-random nature of epimutations. We observed an overall higher number of epigenetic variations than genetic variations in all comparison groups, indicating that epigenetic variations are more prevalent than genetic variations. The largest difference in epigenetic and genetic variations was observed between control plants comparison (F25C vs. F2C), which clearly indicated that the spontaneous nature of epigenetic variations and heat-inducible nature of genetic variations. Overall, our study showed that progenies derived from multigenerational heat stress displayed a notable adaption in context of phenotypic, genotypic and epigenotypic resilience.
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13
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Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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14
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Tokumitsu Y, Kozu T, Yamatani H, Ito T, Nakano H, Hase A, Sasada H, Takada Y, Kaga A, Ishimoto M, Kusaba M, Nakashima T, Abe J, Yamada T. Functional Divergence of G and Its Homologous Genes for Green Pigmentation in Soybean Seeds. FRONTIERS IN PLANT SCIENCE 2022; 12:796981. [PMID: 35069653 PMCID: PMC8766641 DOI: 10.3389/fpls.2021.796981] [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: 10/18/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
The degradation of chlorophyll in mature soybean seeds is closely related to the development of their yellow color. In this study, we examined G, its homologue G-like (GL), and their mutant alleles and investigated the relationship between these genes and chlorophyll accumulation in the seed coats of mature seeds. Transient expression of G and GL proteins fused with green fluorescent protein revealed that both were localized in plastids. Overexpression of G resulted in the accumulation of chlorophyll in the seed coats and cotyledons of mature seeds, indicating that high expression levels of G result in chlorophyll accumulation that exceeds its metabolism in the seeds of yellow soybean. Analysis of near isogenic lines at the G locus demonstrated a significant difference in the chlorophyll content of the seed coats and cotyledons of mature seeds when G and mutant g alleles were expressed in the d1d2 stay-green genetic background, indicating that the G protein might repress the SGR-independent degradation of chlorophyll. We examined the distribution of mutant alleles at the G and GL loci among cultivated and wild soybean germplasm. The g allele was widely distributed in cultivated soybean germplasm, except for green seed coat soybean lines, all of which contained the G allele. The gl alleles were much fewer in number than the g alleles and were mainly distributed in the genetic resources of cultivated soybean from Japan. None of the landraces and breeding lines investigated in this study were observed to contain both the g and gl alleles. Therefore, in conclusion, the mutation of the G locus alone is essential for establishing yellow soybeans, which are major current soybean breeding lines.
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Affiliation(s)
- Yusuke Tokumitsu
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Takuto Kozu
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hiroshi Yamatani
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takeshi Ito
- Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
| | - Haruna Nakano
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Ayaka Hase
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hiroki Sasada
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yoshitake Takada
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Japan
| | - Akito Kaga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Masao Ishimoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Makoto Kusaba
- Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
| | - Taiken Nakashima
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Jun Abe
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Tetsuya Yamada
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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15
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Chandra S, Taak Y, Rathod DR, Yadav RR, Poonia S, Sreenivasa V, Talukdar A. Genetics and mapping of seed coat impermeability in soybean using inter-specific populations. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2291-2299. [PMID: 33268930 PMCID: PMC7688772 DOI: 10.1007/s12298-020-00906-y] [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: 06/03/2020] [Revised: 09/14/2020] [Accepted: 10/23/2020] [Indexed: 05/31/2023]
Abstract
Seed coat impermeability (SCI) in soybean is associated with seed viability under storage and quality of processed products. Understanding genetics and identification of linked molecular markers would facilitate need-based utilization of seed coat impermeability. Two impermeable wild type (G. soja Sieb. and Zucc.) accessions viz. PI 424079 and PI 136620 were crossed with a permeable cultivated (G. max) variety JS335 to generate the mapping populations. Genetic analysis of the F1:2 and F2:3 seeds of the crosses indicated that SCI is controlled by a single gene/major QTL, and impermeability is dominant over permeability. Presence of seeds with intermediate permeability indicated role of some minor genes/QTLs. A set of 204 inter-specific recombinant inbred line (RILs) (F7) was used to map SCI with 207 SSR markers. Phenotyping through rapid imbibition approach (seed imbibition for 6 h), seven QTLs were mapped on chromosomes (Chrs.) 2, 5, 12, 13 and 16 in the seeds stored for 1-3 years, while through slow imbibition method (seed imbibition for 7 days), five QTLs were mapped on Chrs. 2, 9, 10 and 20. Phenotypic variation explained (PVE) by the QTLs ranged from 5.96 to 39.67%. Two major and stable QTLs viz., qScI-h2-1 and qScI-h2-2 that mapped in tandem on Chr.2 jointly explained 43.09-62.92% of the variations in impermeability. Seven minor QTLs identified here were novel and two (qScI-h5, and qScI-h16) were consistent. It is the first report of mapping impermeability using two imbibition approaches together in 200 plus inter-specific RILs in soybean. The study will pave the way for developing genotypes with restricted permeability, enhanced seed viability, and improved seeds quality.
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Affiliation(s)
- Subhash Chandra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- ICAR-Indian Institute of Soybean Research, Indore, India
| | - Yashpal Taak
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Raju Ratan Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shatakshi Poonia
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - V. Sreenivasa
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Akshay Talukdar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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16
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Desta ZA, de Koning DJ, Ortiz R. Molecular mapping and identification of quantitative trait loci for domestication traits in the field cress (Lepidium campestre L.) genome. Heredity (Edinb) 2020; 124:579-591. [PMID: 32076125 PMCID: PMC7080786 DOI: 10.1038/s41437-020-0296-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 01/08/2023] Open
Abstract
Lepidium campestre (L.) or field cress is a multifaceted oilseed plant, which is not yet domesticated. Moreover, the molecular and genetic mechanisms underlying the domestication traits of field cress remain largely elusive. The overarching goal of this study is to identify quantitative trait loci (QTL) that are fundamental for domestication of field cress. Mapping and dissecting quantitative trait variation may provide important insights into genomic trajectories underlying field cress domestication. We used 7624 single nucleotide polymorphism (SNP) markers for QTL mapping in 428 F2 interspecific hybrid individuals, while field phenotyping was conducted in F2:3 segregating families. We applied multiple QTL mapping algorithms to detect and estimate the QTL effects for seven important domestication traits of field cress. Verification of pod shattering across sites revealed that the non-shattering lines declined drastically whereas the shattering lines increased sharply, possibly due to inbreeding followed by selection events. In total, 1461 of the 7624 SNP loci were mapped to eight linkage groups (LGs), spanning 571.9 cM map length. We identified 27 QTL across all LGs of field cress genome, which captured medium to high heritability, implying that genomics-assisted selection could deliver domesticated lines in field cress breeding. The use of high throughput genotyping can accelerate the process of domestication in novel crop species. This is the first QTL mapping analysis in the field cress genome that may lay a foundational framework for positional or functional QTL cloning, introgression as well as genomics-assisted breeding in field cress domestication.
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Affiliation(s)
- Zeratsion Abera Desta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundesvagen 10 Box 101, 23053, Alnarp, Sweden.
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 75007, Uppsala, Sweden
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundesvagen 10 Box 101, 23053, Alnarp, Sweden
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17
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Sato K, Jitsuyama Y, Yamada T, Liu B, Abe J. Structural features of the aleurone layer of the seed coat associated with imbibition injury in soybean. BREEDING SCIENCE 2019; 69:364-370. [PMID: 31481847 PMCID: PMC6711741 DOI: 10.1270/jsbbs.18181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/26/2019] [Indexed: 06/10/2023]
Abstract
Soybean (Glycine max) seeds are prone to imbibition injury caused by a rapid uptake of water. Genetic variation in imbibition injury tolerance is well documented, but the underlying mechanisms remain unclear. The aim of this study was to clarify the role of the aleurone layer of seed coat in the tolerance and its structural differences between tolerant and susceptible cultivars. Imbibition injury tolerance was closely related to the water absorption rate of seeds, which was regulated by the aleurone layer of the seed coat. Cryo-scanning electron microscopy analysis revealed that water absorbed in seed coats entered the seed preferentially through the aleurone layer of the top area above the raphe. In susceptible cultivars, the cell walls of the aleurone layer facing the cotyledon in this area were thin and the surface showed shallow depression-like structures, a distinct structure different from those of the tolerant cultivars, which had aleurone cells with thick outer cell walls and smooth and stripe-like deposits. The differences in the structural features of the cell walls and surfaces of aleurone cells in the top area of the seed may be responsible for the difference in the extent of imbibition injury between susceptible and tolerant cultivars.
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Affiliation(s)
- Kei Sato
- Research Faculty of Agriculture, Hokkaido University,
Sapporo, Hokkaido 060-8589,
Japan
| | - Yutaka Jitsuyama
- Research Faculty of Agriculture, Hokkaido University,
Sapporo, Hokkaido 060-8589,
Japan
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University,
Sapporo, Hokkaido 060-8589,
Japan
| | - Baohui Liu
- School of Life Sciences, Guangzhou University,
Guangzhou 510006,
China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences,
Harbin 150081,
China
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University,
Sapporo, Hokkaido 060-8589,
Japan
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18
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Janská A, Pecková E, Sczepaniak B, Smýkal P, Soukup A. The role of the testa during the establishment of physical dormancy in the pea seed. ANNALS OF BOTANY 2019; 123:815-829. [PMID: 30534972 PMCID: PMC6526324 DOI: 10.1093/aob/mcy213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 11/08/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND A water-impermeable testa acts as a barrier to a seed's imbibition, thereby imposing dormancy. The physical and functional properties of the macrosclereids are thought to be critical determinants of dormancy; however, the mechanisms underlying the maintenance of and release from dormancy in pea are not well understood. METHODS Seeds of six pea accessions of contrasting dormancy type were tested for their ability to imbibe and the permeability of their testa was evaluated. Release from dormancy was monitored following temperature oscillation, lipid removal and drying. Histochemical and microscopic approaches were used to characterize the structure of the testa. KEY RESULTS The strophiole was identified as representing the major site for the entry of water into non-dormant seeds, while water entry into dormant seeds was distributed rather than localized. The major barrier for water uptake in dormant seeds was the upper section of the macrosclereids, referred to as the 'light line'. Dormancy could be released by thermocycling, dehydration or chloroform treatment. Assays based on either periodic acid or ruthenium red were used to visualize penetration through the testa. Lipids were detected within a subcuticular waxy layer in both dormant and non-dormant seeds. The waxy layer and the light line both formed at the same time as the establishment of secondary cell walls at the tip of the macrosclereids. CONCLUSIONS The light line was identified as the major barrier to water penetration in dormant seeds. Its outer border abuts a waxy subcuticular layer, which is consistent with the suggestion that the light line represents the interface between two distinct environments - the waxy subcuticular layer and the cellulose-rich secondary cell wall. The mechanistic basis of dormancy break includes changes in the testa's lipid layer, along with the mechanical disruption induced by oscillation in temperature and by a decreased moisture content of the embryo.
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Affiliation(s)
- Anna Janská
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - Eva Pecková
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - Bogna Sczepaniak
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - Petr Smýkal
- Department of Botany, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Aleš Soukup
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
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19
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Takahashi Y, Sakai H, Yoshitsu Y, Muto C, Anai T, Pandiyan M, Senthil N, Tomooka N, Naito K. Domesticating Vigna Stipulacea: A Potential Legume Crop With Broad Resistance to Biotic Stresses. FRONTIERS IN PLANT SCIENCE 2019; 10:1607. [PMID: 31867036 PMCID: PMC6909428 DOI: 10.3389/fpls.2019.01607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/15/2019] [Indexed: 05/03/2023]
Abstract
Though crossing wild relatives to modern cultivars is a usual means to introduce alleles of stress tolerance, an alternative is de novo domesticating wild species that are already tolerant to various kinds of stresses. As a test case, we chose Vigna stipulacea Kuntze, which has fast growth, short vegetative stage, and broad resistance to pests and diseases. We developed an ethyl methanesulfonate-mutagenized population and obtained three mutants with reduced seed dormancy and one with reduced pod shattering. We crossed one of the mutants of less seed dormancy to the wild type and confirmed that the phenotype was inherited in a Mendelian manner. De novo assembly of V. stipulacea genome, and the following resequencing of the F2 progenies successfully identified a Single Nucleotide Polymorphism (SNP) associated with seed dormancy. By crossing and pyramiding the mutant phenotypes, we will be able to turn V. stipulacea into a crop which is yet primitive but can be cultivated without pesticides.
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Affiliation(s)
| | | | - Yuki Yoshitsu
- Kenpoku Agricultural Institute, Iwate Agricultural Research Center, Iwate, Japan
| | - Chiaki Muto
- Genetic Resources Center, NARO, Tsukuba, Japan
| | - Toyoaki Anai
- Department of Agriculture, Saga University, Saga, Japan
| | - Muthaiyan Pandiyan
- Agricultural College and Research Institute, Tamil Nadu Agricultural University, Thanjavur, India
| | - Natesan Senthil
- Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | | | - Ken Naito
- Genetic Resources Center, NARO, Tsukuba, Japan
- *Correspondence: Ken Naito,
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20
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Wang M, Li W, Fang C, Xu F, Liu Y, Wang Z, Yang R, Zhang M, Liu S, Lu S, Lin T, Tang J, Wang Y, Wang H, Lin H, Zhu B, Chen M, Kong F, Liu B, Zeng D, Jackson SA, Chu C, Tian Z. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nat Genet 2018; 50:1435-1441. [PMID: 30250128 DOI: 10.1038/s41588-018-0229-2] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 08/07/2018] [Indexed: 12/27/2022]
Abstract
Domesticated species often exhibit convergent phenotypic evolution, termed the domestication syndrome, of which loss of seed dormancy is a component. To date, dormancy genes that contribute to parallel domestication across different families have not been reported. Here, we cloned the classical stay-green G gene from soybean and found that it controls seed dormancy and showed evidence of selection during soybean domestication. Moreover, orthologs in rice and tomato also showed evidence of selection during domestication. Analysis of transgenic plants confirmed that orthologs of G had conserved functions in controlling seed dormancy in soybean, rice, and Arabidopsis. Functional investigation demonstrated that G affected seed dormancy through interactions with NCED3 and PSY and in turn modulated abscisic acid synthesis. Therefore, we identified a gene responsible for seed dormancy that has been subject to parallel selection in multiple crop families. This may help facilitate the domestication of new crops.
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Affiliation(s)
- Min Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhen Li
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chao Fang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fan Xu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Rui Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sijia Lu
- School of Life Sciences, Guangzhou University, Guangzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Tao Lin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiuyou Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiqin Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hongru Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hao Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baoge Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingsheng Chen
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fanjiang Kong
- School of Life Sciences, Guangzhou University, Guangzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Baohui Liu
- School of Life Sciences, Guangzhou University, Guangzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA.
| | - Chengcai Chu
- University of Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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21
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Ramakrishna G, Kaur P, Nigam D, Chaduvula PK, Yadav S, Talukdar A, Singh NK, Gaikwad K. Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits. BMC PLANT BIOLOGY 2018; 18:141. [PMID: 29986650 PMCID: PMC6038289 DOI: 10.1186/s12870-018-1341-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 06/05/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation. RESULTS In the present study, we have analyzed genomic variation between cultivated soybean and its wild progenitor with implications on seed permeability, a trait related to seed storability. Whole genome resequencing of G.max and G. soja, identified SNPs and InDels which were further characterized on the basis of their genomic location and impact on gene expression. Chromosomal density distribution of the variation was assessed across the genome and genes carrying SNPs and InDels were characterized into different metabolic pathways. Seed hardiness is a complex trait that is affected by the allelic constitution of a genetic locus as well as by a tricky web of plant hormone interactions. Seven genes that hold a probable role in the determination of seed permeability were selected and their expression differences at different stages of water imbibition were analyzed. Variant interaction network derived 205 downstream interacting partners of 7 genes confirmed their role in seed related traits. Interestingly, genes encoding for Type I- Inositol polyphosphate 5 phosphatase1 and E3 Ubiquitin ligase could differentiate parental genotypes, revealed protein conformational deformations and were found to segregate among RILs in coherence with their permeability scores. The 2 identified genes, thus showed a preliminary association with the desirable permeability characteristics. CONCLUSION In the light of above outcomes, 2 genes were identified that revealed preliminary, but a relevant association with soybean seed permeability trait and hence could serve as a primary material for understanding the molecular pathways controlling seed permeability traits in soybean.
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Affiliation(s)
- G. Ramakrishna
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Parampreet Kaur
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Deepti Nigam
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Pavan K. Chaduvula
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Sangita Yadav
- ICAR- IARI, Division of Seed Science and Technology, Pusa Campus, New Delhi, 110012 India
| | - Akshay Talukdar
- ICAR- IARI, Division of Genetics, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Kishor Gaikwad
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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22
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Sedivy EJ, Wu F, Hanzawa Y. Soybean domestication: the origin, genetic architecture and molecular bases. THE NEW PHYTOLOGIST 2017; 214:539-553. [PMID: 28134435 DOI: 10.1111/nph.14418] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/28/2016] [Indexed: 05/20/2023]
Abstract
Domestication provides an important model for the study of evolution, and information learned from domestication research aids in the continued improvement of crop species. Recent progress in de novo assembly and whole-genome resequencing of wild and cultivated soybean genomes, in addition to new archeological discoveries, sheds light on the origin of this important crop and provides a clearer view on the modes of artificial selection that drove soybean domestication and diversification. This novel genomic information enables the search for polymorphisms that underlie variation in agronomic traits and highlights genes that exhibit a signature of selection, leading to the identification of a number of candidate genes that may have played important roles in soybean domestication, diversification and improvement. These discoveries provide a novel point of comparison on the evolutionary bases of important agronomic traits among different crop species.
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Affiliation(s)
- Eric J Sedivy
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Faqiang Wu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yoshie Hanzawa
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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23
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Hradilová I, Trněný O, Válková M, Cechová M, Janská A, Prokešová L, Aamir K, Krezdorn N, Rotter B, Winter P, Varshney RK, Soukup A, Bednář P, Hanáček P, Smýkal P. A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea ( Pisum sp.). FRONTIERS IN PLANT SCIENCE 2017; 8:542. [PMID: 28487704 PMCID: PMC5404241 DOI: 10.3389/fpls.2017.00542] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/27/2017] [Indexed: 05/19/2023]
Abstract
The origin of the agriculture was one of the turning points in human history, and a central part of this was the evolution of new plant forms, domesticated crops. Seed dispersal and germination are two key traits which have been selected to facilitate cultivation and harvesting of crops. The objective of this study was to analyze anatomical structure of seed coat and pod, identify metabolic compounds associated with water-impermeable seed coat and differentially expressed genes involved in pea seed dormancy and pod dehiscence. Comparative anatomical, metabolomics, and transcriptomic analyses were carried out on wild dormant, dehiscent Pisum elatius (JI64, VIR320) and cultivated, indehiscent Pisum sativum non-dormant (JI92, Cameor) and recombinant inbred lines (RILs). Considerable differences were found in texture of testa surface, length of macrosclereids, and seed coat thickness. Histochemical and biochemical analyses indicated genotype related variation in composition and heterogeneity of seed coat cell walls within macrosclereids. Liquid chromatography-electrospray ionization/mass spectrometry and Laser desorption/ionization-mass spectrometry of separated seed coats revealed significantly higher contents of proanthocyanidins (dimer and trimer of gallocatechin), quercetin, and myricetin rhamnosides and hydroxylated fatty acids in dormant compared to non-dormant genotypes. Bulk Segregant Analysis coupled to high throughput RNA sequencing resulted in identification of 770 and 148 differentially expressed genes between dormant and non-dormant seeds or dehiscent and indehiscent pods, respectively. The expression of 14 selected dormancy-related genes was studied by qRT-PCR. Of these, expression pattern of four genes: porin (MACE-S082), peroxisomal membrane PEX14-like protein (MACE-S108), 4-coumarate CoA ligase (MACE-S131), and UDP-glucosyl transferase (MACE-S139) was in agreement in all four genotypes with Massive analysis of cDNA Ends (MACE) data. In case of pod dehiscence, the analysis of two candidate genes (SHATTERING and SHATTERPROOF) and three out of 20 MACE identified genes (MACE-P004, MACE-P013, MACE-P015) showed down-expression in dorsal and ventral pod suture of indehiscent genotypes. Moreover, MACE-P015, the homolog of peptidoglycan-binding domain or proline-rich extensin-like protein mapped correctly to predicted Dpo1 locus on PsLGIII. This integrated analysis of the seed coat in wild and cultivated pea provides new insight as well as raises new questions associated with domestication and seed dormancy and pod dehiscence.
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Affiliation(s)
- Iveta Hradilová
- Department of Botany, Palacký University in OlomoucOlomouc, Czechia
| | - Oldřich Trněný
- Department of Plant Biology, Mendel University in BrnoBrno, Czechia
- Agricultural Research, Ltd.Troubsko, Czechia
| | - Markéta Válková
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Monika Cechová
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Anna Janská
- Department of Experimental Plant Biology, Charles UniversityPrague, Czechia
| | - Lenka Prokešová
- Department of Crop Science, Breeding and Plant Medicine, Mendel University in BrnoBrno, Czechia
| | - Khan Aamir
- Research Program-Genetic Gains, ICRISATHyderabad, India
| | | | | | | | | | - Aleš Soukup
- Department of Experimental Plant Biology, Charles UniversityPrague, Czechia
| | - Petr Bednář
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Pavel Hanáček
- Department of Plant Biology, Mendel University in BrnoBrno, Czechia
| | - Petr Smýkal
- Department of Botany, Palacký University in OlomoucOlomouc, Czechia
- *Correspondence: Petr Smýkal
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24
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Abstract
Physical dormancy of seed is an adaptive trait that widely exists in higher plants. This kind of dormancy is caused by a water-impermeable layer that blocks water and oxygen from the surrounding environment and keeps embryos in a viable status for a long time. Most of the work on hardseededness has focused on morphological structure and phenolic content of seed coat. The molecular mechanism underlying physical dormancy remains largely elusive. By screening a large number of Tnt1 retrotransposon-tagged Medicago truncatula lines, we identified nondormant seed mutants from this model legume species. Unlike wild-type hard seeds exhibiting physical dormancy, the mature mutant seeds imbibed water quickly and germinated easily, without the need for scarification. Microscopic observations of cross sections showed that the mutant phenotype was caused by a dysfunctional palisade cuticle layer in the seed coat. Chemical analysis found differences in lipid monomer composition between the wild-type and mutant seed coats. Genetic and molecular analyses revealed that a class II KNOTTED-like homeobox (KNOXII) gene, KNOX4, was responsible for the loss of physical dormancy in the seeds of the mutants. Microarray and chromatin immunoprecipitation analyses identified CYP86A, a gene associated with cutin biosynthesis, as one of the downstream target genes of KNOX4 This study elucidated a novel molecular mechanism of physical dormancy and revealed a new role of class II KNOX genes. Furthermore, KNOX4-like genes exist widely in seed plants but are lacking in nonseed species, indicating that KNOX4 may have diverged from the other KNOXII genes during the evolution of seed plants.
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25
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Considine MJ, Considine JA. On the language and physiology of dormancy and quiescence in plants. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3189-203. [PMID: 27053719 DOI: 10.1093/jxb/erw138] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The language of dormancy is rich and poetic, as researchers spanning disciplines and decades have attempted to understand the spell that entranced 'Sleeping Beauty', and how she was gently awoken. The misleading use of 'dormancy', applied to annual axillary buds, for example, has confounded progress. Language is increasingly important as genetic and genomic approaches become more accessible to species of agricultural and ecological importance. Here we examine how terminology has been applied to different eco-physiological states in plants, and with pertinent reference to quiescent states described in other domains of life, in order to place plant quiescence and dormancy in a more complete context than previously described. The physiological consensus defines latency or quiescence as opportunistic avoidance states, where growth resumes in favourable conditions. In contrast, the dormant state in higher plants is entrained in the life history of the organism. Competence to resume growth requires quantitative and specific conditioning. This definition applies only to the embryo of seeds and specialized meristems in higher plants; however, mechanistic control of dormancy extends to mobile signals from peripheral tissues and organs, such as the endosperm of seed or subtending leaf of buds. The distinction between dormancy, quiescence, and stress-hardiness remains poorly delineated, most particularly in buds of winter perennials, which comprise multiple meristems of differing organogenic states. Studies in seeds have shown that dormancy is not a monogenic trait, and limited study has thus far failed to canalize dormancy as seen in seeds and buds. We argue that a common language, based on physiology, is central to enable further dissection of the quiescent and dormant states in plants. We direct the topic largely to woody species showing a single cycle of growth and reproduction per year, as these bear the majority of global timber, fruit, and nut production, as well being of great ecological value. However, for context and hypotheses, we draw on knowledge from annuals and other specialized plant conditions, from a perspective of the major physical, metabolic, and molecular cues that regulate cellular activity.
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Affiliation(s)
- Michael J Considine
- School of Plant Biology, and The Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia Department of Agriculture and Food Western Australia, South Perth, WA 6151 Australia Centre for Plant Sciences, University of Leeds, Leeds, Yorkshire LS2 9JT, UK
| | - John A Considine
- School of Plant Biology, and The Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
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26
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Huq A, Akter S, Nou IS, Kim HT, Jung YJ, Kang KK. Identification of functional SNPs in genes and their effects on plant phenotypes. ACTA ACUST UNITED AC 2016. [DOI: 10.5010/jpb.2016.43.1.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Amdadul Huq
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Shahina Akter
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Ill Sup Nou
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonam-do, 57922, Korea
| | - Hoy Taek Kim
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonam-do, 57922, Korea
| | - Yu Jin Jung
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Kwon Kyoo Kang
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
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27
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Liu E, Liu Y, Wu G, Zeng S, Tran Thi TG, Liang L, Liang Y, Dong Z, She D, Wang H, Zaid IU, Hong D. Identification of a Candidate Gene for Panicle Length in Rice (Oryza sativa L.) Via Association and Linkage Analysis. FRONTIERS IN PLANT SCIENCE 2016; 7:596. [PMID: 27200064 PMCID: PMC4853638 DOI: 10.3389/fpls.2016.00596] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/18/2016] [Indexed: 05/19/2023]
Abstract
Panicle length (PL) is an important trait for improving panicle architecture and grain yield in rice (Oryza sativa L.). Three populations were used to identify QTLs and candidate genes associated with PL. Four QTLs for PL were detected on chromosomes 4, 6, and 9 through linkage mapping in the recombinant inbred line population derived from a cross between the cultivars Xiushui79 (short panicle) and C-bao (long panicle). Ten SSR markers associated with PL were detected on chromosomes 2, 3, 5, 6, 8, 9, and 10 in the natural population consisting of 540 accessions collected from East and Southeast Asia. A major locus on chromosome 9 with the largest effect was identified via both linkage and association mapping. LONG PANICLE 1 (LP1) locus was delimited to a 90-kb region of the long arm of chromosome 9 through fine mapping using a single segment segregating F2 population. Two single nucleotide polymorphisms (SNPs) leading to amino acid changes were detected in the third and fifth exons of LP1. LP1 encodes a Remorin_C-containing protein of unknown function with homologs in a variety of species. Sequencing analysis of LP1 in two parents and 103 rice accessions indicated that SNP1 is associated with panicle length. The LP1 allele of Xiushui79 leads to reduced panicle length, whereas the allele of C-bao relieves the suppression of panicle length. LP1 and the elite alleles can be used to improve panicle length in rice.
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Affiliation(s)
- Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Yang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Guocan Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Siyuan Zeng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Thu G. Tran Thi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
- College of Agronomy, Hue University of Agriculture and Forestry, Hue UniversityHue, Vietnam
| | - Lijun Liang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Yinfeng Liang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Zhiyao Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Dong She
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Imdad U. Zaid
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Delin Hong
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