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Brindisi LJ, Mattera R, Mudiyala S, Honig J, Simon JE. Genetic linkage mapping and quantitative trait locus (QTL) analysis of sweet basil (Ocimum basilicum L.) to identify genomic regions associated with cold tolerance and major volatiles. PLoS One 2024; 19:e0299825. [PMID: 38593174 PMCID: PMC11003626 DOI: 10.1371/journal.pone.0299825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/15/2024] [Indexed: 04/11/2024] Open
Abstract
Chilling sensitivity is one of the greatest challenges affecting the marketability and profitability of sweet basil (Ocimum basilicum L.) in the US and worldwide. Currently, there are no sweet basils commercially available with significant chilling tolerance and traditional aroma profiles. This study was conducted to identify quantitative trait loci (QTLs) responsible for chilling tolerance and aroma compounds in a biparental mapping population, including the Rutgers advanced breeding line that served as a chilling tolerant parent, 'CB15', the chilling sensitive parent, 'Rutgers Obsession DMR' and 200 F2 individuals. Chilling tolerance was assessed by percent necrosis using machine learning and aroma profiling was evaluated using gas chromatography (GC) mass spectrometry (MS). Single nucleotide polymorphism (SNP) markers were generated from genomic sequences derived from double digestion restriction-site associated DNA sequencing (ddRADseq) and converted to genotype data using a reference genome alignment. A genetic linkage map was constructed and five statistically significant QTLs were identified in response to chilling temperatures with possible interactions between QTLs. The QTL on LG24 (qCH24) demonstrated the largest effect for chilling response and was significant in all three replicates. No QTLs were identified for linalool, as the population did not segregate sufficiently to detect this trait. Two significant QTLs were identified for estragole (also known as methyl chavicol) with only qEST1 on LG1 being significant in the multiple-QTL model (MQM). QEUC26 was identified as a significant QTL for eucalyptol (also known as 1,8-cineole) on LG26. These QTLs may represent key mechanisms for chilling tolerance and aroma in basil, providing critical knowledge for future investigation of these phenotypic traits and molecular breeding.
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Affiliation(s)
- Lara J. Brindisi
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - Robert Mattera
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - Sonika Mudiyala
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - Joshua Honig
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - James E. Simon
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
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2
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Yurkov AP, Kryukov AA, Gorbunova AO, Kudriashova TR, Kovalchuk AI, Gorenkova AI, Bogdanova EM, Laktionov YV, Zhurbenko PM, Mikhaylova YV, Puzanskiy RK, Bagrova TN, Yakhin OI, Rodionov AV, Shishova MF. Diversity of Arbuscular Mycorrhizal Fungi in Distinct Ecosystems of the North Caucasus, a Temperate Biodiversity Hotspot. J Fungi (Basel) 2023; 10:11. [PMID: 38248921 PMCID: PMC10817546 DOI: 10.3390/jof10010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Investigations that are focused on arbuscular mycorrhizal fungus (AMF) biodiversity is still limited. The analysis of the AMF taxa in the North Caucasus, a temperate biodiversity hotspot, used to be limited to the genus level. This study aimed to define the AMF biodiversity at the species level in the North Caucasus biotopes. METHODS The molecular genetic identification of fungi was carried out with ITS1 and ITS2 regions as barcodes via sequencing using Illumina MiSeq, the analysis of phylogenetic trees for individual genera, and searches for operational taxonomic units (OTUs) with identification at the species level. Sequences from MaarjAM and NCBI GenBank were used as references. RESULTS We analyzed >10 million reads in soil samples for three biotopes to estimate fungal biodiversity. Briefly, 50 AMF species belonging to 20 genera were registered. The total number of the AM fungus OTUs for the "Subalpine Meadow" biotope was 171/131, that for "Forest" was 117/60, and that for "River Valley" was 296/221 based on ITS1/ITS2 data. The total number of the AM fungus species (except for virtual taxa) for the "Subalpine Meadow" biotope was 24/19, that for "Forest" was 22/13, and that for "River Valley" was 28/24 based on ITS1/ITS2 data. Greater AMF diversity, as well as number of OTUs and species, in comparison with that of forest biotopes, characterized valley biotopes (disturbed ecosystems; grasslands). The correlation coefficient between "Percentage of annual plants" and "Glomeromycota total reads" r = 0.76 and 0.81 for ITS1 and ITS2, respectively, and the correlation coefficient between "Percentage of annual plants" and "OTUs number (for total species)" was r = 0.67 and 0.77 for ITS1 and ITS2, respectively. CONCLUSION High AMF biodiversity for the river valley can be associated with a higher percentage of annual plants in these biotopes and the active development of restorative successional processes.
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Affiliation(s)
- Andrey P. Yurkov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Alexey A. Kryukov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Anastasiia O. Gorbunova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Tatyana R. Kudriashova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, 194064 St. Petersburg, Russia
| | - Anastasia I. Kovalchuk
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, 194064 St. Petersburg, Russia
| | - Anastasia I. Gorenkova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ekaterina M. Bogdanova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Yuri V. Laktionov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Peter M. Zhurbenko
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Yulia V. Mikhaylova
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Roman K. Puzanskiy
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia;
- Faculty of Ecology, Russian State Hydrometeorological University, 192007 St. Petersburg, Russia;
| | - Tatyana N. Bagrova
- Faculty of Ecology, Russian State Hydrometeorological University, 192007 St. Petersburg, Russia;
| | - Oleg I. Yakhin
- Institute of Biochemistry and Genetics, The Ufa Federal Research Center of the Russian Academy of Sciences, 450054 Ufa, Russia;
| | - Alexander V. Rodionov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Maria F. Shishova
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
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3
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Quattrone A, Yang Y, Yadav P, Weber KA, Russo SE. Nutrient and Microbiome-Mediated Plant-Soil Feedback in Domesticated and Wild Andropogoneae: Implications for Agroecosystems. Microorganisms 2023; 11:2978. [PMID: 38138123 PMCID: PMC10745641 DOI: 10.3390/microorganisms11122978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Plants influence the abiotic and biotic environment of the rhizosphere, affecting plant performance through plant-soil feedback (PSF). We compared the strength of nutrient and microbe-mediated PSF and its implications for plant performance in domesticated and wild grasses with a fully crossed greenhouse PSF experiment using four inbred maize genotypes (Zea mays ssp. mays b58, B73-wt, B73-rth3, and HP301), teosinte (Z. mays ssp. parviglumis), and two wild prairie grasses (Andropogon gerardii and Tripsacum dactyloides) to condition soils for three feedback species (maize B73-wt, teosinte, Andropogon gerardii). We found evidence of negative PSF based on growth, phenotypic traits, and foliar nutrient concentrations for maize B73-wt, which grew slower in maize-conditioned soil than prairie grass-conditioned soil. In contrast, teosinte and A. gerardii showed few consistent feedback responses. Both rhizobiome and nutrient-mediated mechanisms were implicated in PSF. Based on 16S rRNA gene amplicon sequencing, the rhizosphere bacterial community composition differed significantly after conditioning by prairie grass and maize plants, and the final soil nutrients were significantly influenced by conditioning, more so than by the feedback plants. These results suggest PSF-mediated soil domestication in agricultural settings can develop quickly and reduce crop productivity mediated by PSF involving changes to both the soil rhizobiomes and nutrient availability.
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Affiliation(s)
- Amanda Quattrone
- Complex Biosystems Ph.D. Program, University of Nebraska-Lincoln, Lincoln, NE 68583-0851, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118, USA; (Y.Y.)
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68583-0705, USA
| | - Yuguo Yang
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118, USA; (Y.Y.)
| | - Pooja Yadav
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118, USA; (Y.Y.)
| | - Karrie A. Weber
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118, USA; (Y.Y.)
- Department of Earth and Atmospheric Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0340, USA
- Daugherty Water for Food Institute, University of Nebraska, Lincoln, NE 68588-6203, USA
| | - Sabrina E. Russo
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118, USA; (Y.Y.)
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68583-0705, USA
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4
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Li X, Wang X, Ma Q, Zhong Y, Zhang Y, Zhang P, Li Y, He R, Zhou Y, Li Y, Cheng M, Yan X, Li Y, He J, Iqbal MZ, Rong T, Tang Q. Integrated single-molecule real-time sequencing and RNA sequencing reveal the molecular mechanisms of salt tolerance in a novel synthesized polyploid genetic bridge between maize and its wild relatives. BMC Genomics 2023; 24:55. [PMID: 36717785 PMCID: PMC9887930 DOI: 10.1186/s12864-023-09148-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/23/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Tripsacum dactyloides (2n = 4x = 72) and Zea perennis (2n = 4x = 40) are tertiary gene pools of Zea mays L. and exhibit many abiotic adaptations absent in modern maize, especially salt tolerance. A previously reported allopolyploid (hereafter referred to as MTP, 2n = 74) synthesized using Zea mays, Tripsacum dactyloides, and Zea perennis has even stronger salt tolerance than Z. perennis and T. dactyloides. This allopolyploid will be a powerful genetic bridge for the genetic improvement of maize. However, the molecular mechanisms underlying its salt tolerance, as well as the key genes involved in regulating its salt tolerance, remain unclear. RESULTS Single-molecule real-time sequencing and RNA sequencing were used to identify the genes involved in salt tolerance and reveal the underlying molecular mechanisms. Based on the SMRT-seq results, we obtained 227,375 reference unigenes with an average length of 2300 bp; most of the unigenes were annotated to Z. mays sequences (76.5%) in the NR database. Moreover, a total of 484 and 1053 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Functional enrichment analysis of DEGs revealed that multiple pathways responded to salt stress, including "Flavonoid biosynthesis," "Oxidoreductase activity," and "Plant hormone signal transduction" in the leaves and roots, and "Iron ion binding," "Acetyl-CoA carboxylase activity," and "Serine-type carboxypeptidase activity" in the roots. Transcription factors, such as those in the WRKY, B3-ARF, and bHLH families, and cytokinin negatively regulators negatively regulated the salt stress response. According to the results of the short time series-expression miner analysis, proteins involved in "Spliceosome" and "MAPK signal pathway" dynamically responded to salt stress as salinity changed. Protein-protein interaction analysis revealed that heat shock proteins play a role in the large interaction network regulating salt tolerance. CONCLUSIONS Our results reveal the molecular mechanism underlying the regulation of MTP in the response to salt stress and abundant salt-tolerance-related unigenes. These findings will aid the retrieval of lost alleles in modern maize and provide a new approach for using T. dactyloides and Z. perennis to improve maize.
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Affiliation(s)
- Xiaofeng Li
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Xingyu Wang
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Qiangqiang Ma
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yunfeng Zhong
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yibo Zhang
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Ping Zhang
- grid.452857.9Chengdu Research Base of Giant Panda Breeding, Chengdu, 61130 China
| | - Yingzheng Li
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Ruyu He
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yang Zhou
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yang Li
- Mianyang Teachers’ College School of Urban and Rural Construction and Planning, Mianyany, 621000 China
| | - Mingjun Cheng
- grid.412723.10000 0004 0604 889XInstitute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610041 China
| | - Xu Yan
- grid.465230.60000 0004 1777 7721Sericulture Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, 637000 China
| | - Yan Li
- grid.465230.60000 0004 1777 7721Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611041 China
| | - Jianmei He
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Muhammad Zafar Iqbal
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Tingzhao Rong
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Qilin Tang
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
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5
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Sun G, Wase N, Shu S, Jenkins J, Zhou B, Torres-Rodríguez JV, Chen C, Sandor L, Plott C, Yoshinga Y, Daum C, Qi P, Barry K, Lipzen A, Berry L, Pedersen C, Gottilla T, Foltz A, Yu H, O'Malley R, Zhang C, Devos KM, Sigmon B, Yu B, Obata T, Schmutz J, Schnable JC. Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass. Nat Commun 2022; 13:7731. [PMID: 36513676 PMCID: PMC9747981 DOI: 10.1038/s41467-022-35507-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum (Paspalum vaginatum) is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here, we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologues conserved in 6 related grass species places paspalum as an outgroup of the maize-sorghum clade. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibits a significant increase in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, results in autophagy dependent increases in biomass accumulation.
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Affiliation(s)
- Guangchao Sun
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Nishikant Wase
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Biomolecular Analysis Facility. School of Medicine, University of Virginia, Charlottesville, VA, 22903, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Bangjun Zhou
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - J Vladimir Torres-Rodríguez
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Cindy Chen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Laura Sandor
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Yuko Yoshinga
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Luke Berry
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Connor Pedersen
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Thomas Gottilla
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Ashley Foltz
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Huihui Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Ronan O'Malley
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Brandi Sigmon
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Bin Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Toshihiro Obata
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA, 94720, USA.
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
| | - James C Schnable
- Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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6
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Chen L, Luo J, Jin M, Yang N, Liu X, Peng Y, Li W, Phillips A, Cameron B, Bernal JS, Rellán-Álvarez R, Sawers RJH, Liu Q, Yin Y, Ye X, Yan J, Zhang Q, Zhang X, Wu S, Gui S, Wei W, Wang Y, Luo Y, Jiang C, Deng M, Jin M, Jian L, Yu Y, Zhang M, Yang X, Hufford MB, Fernie AR, Warburton ML, Ross-Ibarra J, Yan J. Genome sequencing reveals evidence of adaptive variation in the genus Zea. Nat Genet 2022; 54:1736-1745. [PMID: 36266506 DOI: 10.1038/s41588-022-01184-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/10/2022] [Indexed: 11/09/2022]
Abstract
Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single-nucleotide polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations. We focus on adaptive alleles in highland teosinte and temperate maize, highlighting the key role of flowering-time-related pathways in their adaptation. To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. This work provides an extensive sampling of the genetic diversity of Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.
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Affiliation(s)
- Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Alyssa Phillips
- Center for Population Biology, University of California Davis, Davis, CA, USA.,Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Brenda Cameron
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Julio S Bernal
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Rubén Rellán-Álvarez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Ruairidh J H Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA, USA
| | - Qing Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yuejia Yin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xinnan Ye
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jiali Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaoting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shenshen Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenjie Wei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chenglin Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Min Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Liumei Jian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yanhui Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Maolin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Marilyn L Warburton
- United States Department of Agriculture-Agricultural Research Service: Western Regional Plant Introduction Station, Washington State University, Pullman, WA, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, Center for Population Biology, Genome Center, University of California Davis, Davis, CA, USA.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
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7
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An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time. Proc Natl Acad Sci U S A 2022; 119:e2100036119. [PMID: 35771940 PMCID: PMC9271162 DOI: 10.1073/pnas.2100036119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Native Americans domesticated maize (Zea mays ssp. mays) from lowland teosinte parviglumis (Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 (HPC1), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.
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8
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Chamberlain-Irwin HN, Hufford MB. Convergent domestication: Finding the genes that make crops. Curr Biol 2022; 32:R585-R588. [PMID: 35728534 DOI: 10.1016/j.cub.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A recent study shows that convergent selection of orthologs encoding a WD40 protein in maize and rice occurs during domestication. Knockout of these genes increases yield in both crops with no detectable effects on other agronomic traits. Identification of convergent selection can focus improvement efforts.
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Affiliation(s)
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
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9
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Abraham-Juárez MJ, Barnes AC, Aragón-Raygoza A, Tyson D, Kur A, Strable J, Rellán-Álvarez R. The arches and spandrels of maize domestication, adaptation, and improvement. CURRENT OPINION IN PLANT BIOLOGY 2021; 64:102124. [PMID: 34715472 DOI: 10.1016/j.pbi.2021.102124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
People living in the Balsas River basin in southwest México domesticated maize from the bushy grass teosinte. Nine thousand years later, in 2021, Ms. Deb Haaland - a member of the Pueblo of Laguna tribe of New Mexico - wore a dress adorned with a cornstalk when she was sworn in as the Secretary of Interior of the United States of America. This choice of garment highlights the importance of the coevolution of maize and the farmers who, through careful selection over thousands of years, domesticated maize and adapted the physiology and shoot architecture of maize to fit local environments and growth habits. Some traits such as tillering were directly selected on (arches), and others such as tassel size are the by-products (spandrels) of maize evolution. Here, we review current knowledge of the underlying cellular, developmental, physiological, and metabolic processes that were selected by farmers and breeders, which have positioned maize as a top global staple crop.
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Affiliation(s)
- María Jazmín Abraham-Juárez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Irapuato, 36821, Mexico
| | - Allison C Barnes
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alejandro Aragón-Raygoza
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA; Unidad de Genómica Avanzada, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, Guanajuato, Mexico
| | - Destiny Tyson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Andi Kur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Josh Strable
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Rubén Rellán-Álvarez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA.
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10
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Alseekh S, Scossa F, Wen W, Luo J, Yan J, Beleggia R, Klee HJ, Huang S, Papa R, Fernie AR. Domestication of Crop Metabolomes: Desired and Unintended Consequences. TRENDS IN PLANT SCIENCE 2021; 26:650-661. [PMID: 33653662 DOI: 10.1016/j.tplants.2021.02.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 05/02/2023]
Abstract
The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178 Rome, Italy
| | - Weiwei Wen
- Key laboratory of Horticultural Plant Biology (MOE),College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Hubei, Wuhan 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China; College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-, CI), 71122 Foggia, Italy
| | - Harry J Klee
- Horticultural Sciences, University of Florida, Gainesville, FL, USA
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture - Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
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11
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Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae. G3-GENES GENOMES GENETICS 2020; 10:4387-4398. [PMID: 32988994 PMCID: PMC7718754 DOI: 10.1534/g3.120.401596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size with the latter. Although LTR-retrotransposons were abundant in all species, we observed an expansion of the copia superfamily, specifically in Z. mays and T. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically, copia insertions in Zea and T. dactyloides were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post Zea-Tripsacum divergence. The lack of copia insertions near the orthologous genes in S. bicolor suggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.
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12
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Carvalho DS, Nishimwe AV, Schnable JC. IsoSeq transcriptome assembly of C 3 panicoid grasses provides tools to study evolutionary change in the Panicoideae. PLANT DIRECT 2020; 4:e00203. [PMID: 32128472 PMCID: PMC7047018 DOI: 10.1002/pld3.203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses-Poaceae-have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4 photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and Hymenachne amplexicaulis. Based on alignments to the sorghum genome, we estimate that assembled consensus transcripts from each species capture between 54.2% and 65.7% of the conserved syntenic gene space in grasses. Genes co-opted into C4 were also well represented in this dataset, despite concerns that because these genes might play roles unrelated to photosynthesis in the target species, they would be expressed at low levels and missed by transcript-based sequencing. A combined analysis using syntenic orthologous genes from grasses with published reference genomes and consensus long-read sequences from these wild species was consistent with previously published phylogenies. It is hoped that these data, targeting underrepresented classes of species within the PACMAD grasses-wild species and species utilizing C3 photosynthesis-will aid in future studies of domestication and C4 evolution by decreasing the evolutionary distance between C4 and C3 species within this clade, enabling more accurate comparisons associated with evolution of the C4 pathway.
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Affiliation(s)
- Daniel S. Carvalho
- Department of Agronomy and HorticultureCenter for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Aime V. Nishimwe
- Department of Agronomy and HorticultureCenter for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - James C. Schnable
- Department of Agronomy and HorticultureCenter for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
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