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Zhang W, Benke R, Zhang X, Zhang H, Zhao C, Zhao Y, Xu Y, Wang H, Liu S, Li X, Wu Y. Novel allelic variations in Tannin1 and Tannin2 contribute to tannin absence in sorghum. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:24. [PMID: 38495646 PMCID: PMC10942951 DOI: 10.1007/s11032-024-01463-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/04/2024] [Indexed: 03/19/2024]
Abstract
Sorghum is an important food crop commonly used for brewing, feed, and bioenergy. Certain genotypes of sorghum contain high concentrations of condensed tannins in seeds, which are beneficial, such as protecting grains from herbivore bird pests, but also impair grain quality and digestibility. Previously, we identified Tannin1 and Tannin2, each with three recessive causal alleles, regulate tannin absence in sorghum. In this study, via characterizing 421 sorghum accessions, we further identified three novel recessive alleles from these two genes. The tan1-d allele contains a 12-bp deletion at position 659 nt and the tan1-e allele contains a 10-bp deletion at position 771 nt in Tannin1. The tan2-d allele contains a C-to-T transition, which results in a premature stop codon before the bHLH domain in Tannin2, and was predominantly selected in China. We further developed KASP assays targeting these identified recessive alleles to efficiently genotype large populations. These studies provide new insights in sorghum domestication and convenient tools for breeding programs. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01463-y.
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Affiliation(s)
- Wenbin Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
| | - Ryan Benke
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164 USA
| | - Xiao Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
| | - Huawen Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 China
| | - Cunyuan Zhao
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
| | - Yu Zhao
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
| | - Ying Xu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
| | - Hailian Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 China
| | - Shubing Liu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
| | - Xianran Li
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164 USA
| | - Yuye Wu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
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2
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Jiao Y, Nigam D, Barry K, Daum C, Yoshinaga Y, Lipzen A, Khan A, Parasa SP, Wei S, Lu Z, Tello-Ruiz MK, Dhiman P, Burow G, Hayes C, Chen J, Brandizzi F, Mortimer J, Ware D, Xin Z. A large sequenced mutant library - valuable reverse genetic resource that covers 98% of sorghum genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1543-1557. [PMID: 38100514 DOI: 10.1111/tpj.16582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/08/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
Mutant populations are crucial for functional genomics and discovering novel traits for crop breeding. Sorghum, a drought and heat-tolerant C4 species, requires a vast, large-scale, annotated, and sequenced mutant resource to enhance crop improvement through functional genomics research. Here, we report a sorghum large-scale sequenced mutant population with 9.5 million ethyl methane sulfonate (EMS)-induced mutations that covered 98% of sorghum's annotated genes using inbred line BTx623. Remarkably, a total of 610 320 mutations within the promoter and enhancer regions of 18 000 and 11 790 genes, respectively, can be leveraged for novel research of cis-regulatory elements. A comparison of the distribution of mutations in the large-scale mutant library and sorghum association panel (SAP) provides insights into the influence of selection. EMS-induced mutations appeared to be random across different regions of the genome without significant enrichment in different sections of a gene, including the 5' UTR, gene body, and 3'-UTR. In contrast, there were low variation density in the coding and UTR regions in the SAP. Based on the Ka /Ks value, the mutant library (~1) experienced little selection, unlike the SAP (0.40), which has been strongly selected through breeding. All mutation data are publicly searchable through SorbMutDB (https://www.depts.ttu.edu/igcast/sorbmutdb.php) and SorghumBase (https://sorghumbase.org/). This current large-scale sequence-indexed sorghum mutant population is a crucial resource that enriched the sorghum gene pool with novel diversity and a highly valuable tool for the Poaceae family, that will advance plant biology research and crop breeding.
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Affiliation(s)
- Yinping Jiao
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Deepti Nigam
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Kerrie Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Chris Daum
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Yuko Yoshinaga
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Anna Lipzen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Adil Khan
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Sai-Praneeth Parasa
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | | | - Pallavi Dhiman
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Gloria Burow
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
| | - Chad Hayes
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Jenny Mortimer
- Joint BioEnergy Institute, Emeryville, California, 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, 94720, USA
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, South Australia, 5064, Australia
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
- USDA-ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, New York, 14853, USA
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, Texas, 79424, USA
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3
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Deng CH, Naithani S, Kumari S, Cobo-Simón I, Quezada-Rodríguez EH, Skrabisova M, Gladman N, Correll MJ, Sikiru AB, Afuwape OO, Marrano A, Rebollo I, Zhang W, Jung S. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database (Oxford) 2023; 2023:baad088. [PMID: 38079567 PMCID: PMC10712715 DOI: 10.1093/database/baad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]
Abstract
Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.
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Affiliation(s)
- Cecilia H Deng
- Molecular and Digital Breeding, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland 1025, New Zealand
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
| | - Irene Cobo-Simón
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Institute of Forest Science (ICIFOR-INIA, CSIC), Madrid, Spain
| | - Elsa H Quezada-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maria Skrabisova
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Nick Gladman
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA
| | - Melanie J Correll
- Agricultural and Biological Engineering Department, University of Florida, 1741 Museum Rd, Gainesville, FL 32611, USA
| | | | | | - Annarita Marrano
- Phoenix Bioinformatics, 39899 Balentine Drive, Suite 200, Newark, CA 94560, USA
| | | | - Wentao Zhang
- National Research Council Canada, 110 Gymnasium Pl, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sook Jung
- Department of Horticulture, Washington State University, 303c Plant Sciences Building, Pullman, WA 99164-6414, USA
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4
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An Y, Xia X, Zheng H, Yu S, Jing T, Zhang F. Multi-genome comprehensive identification of SSR/SV and development of molecular markers database to serve Sorghum bicolor (L.) breeding. BMC Genom Data 2023; 24:62. [PMID: 37924022 PMCID: PMC10625204 DOI: 10.1186/s12863-023-01165-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND As an important food and cash crop, identification of DNA molecular markers is of great significance for molecular marker-assisted breeding of Sorghum (Sorghum bicolor (L.) moench). Although some sorghum-related mutation databases have been published, the special SSR and SV databases still need to be constructed and updated. RESULTS In this study, the quality of 18 different sorghum genomes was evaluated, and two genomes were assembled at chromosome level. Through the identification and comparative analysis of SSR loci in these genomes, the distribution characteristics of SSR in the above sorghum genomes were initially revealed. At the same time, five representative reference genomes were selected to identify the structural variation of sorghum. Finally, a convenient SSR/SV database of sorghum was constructed by integrating the above results ( http://www.sorghum.top:8079/ ; http://43.154.129.150:8079/ ; http://47.106.184.91:8079/ ). Users can query the information of related sites and primer pairs. CONCLUSIONS Anyway, our research provides convenience for sorghum researchers and will play an active role in sorghum molecular marker-assisted breeding.
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Affiliation(s)
- Yanlin An
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Xiaobo Xia
- College of Plant Protection , Nanjing Agricultural University, Nanjing, 210095, China
| | - Huayan Zheng
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Shirui Yu
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China.
| | - Feng Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China.
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5
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Yang L, Zhou Q, Sheng X, Chen X, Hua Y, Lin S, Luo Q, Yu B, Shao T, Wu Y, Chang J, Li Y, Tu M. Harnessing the Genetic Basis of Sorghum Biomass-Related Traits to Facilitate Bioenergy Applications. Int J Mol Sci 2023; 24:14549. [PMID: 37833996 PMCID: PMC10573072 DOI: 10.3390/ijms241914549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce biomass in marginal lands with low agronomic inputs, thus representing an important source of bioenergy. Among these grasses, Sorghum bicolor has been recognized as not only a promising bioenergy crop but also a research model due to its diploidy, simple genome, genetic diversity and clear orthologous relationship with other grass genomes, allowing sorghum research to be easily translated to other grasses. Although sorghum molecular genetic studies have lagged far behind those of major crops (e.g., rice and maize), recent advances have been made in a number of biomass-related traits to dissect the genetic loci and candidate genes, and to discover the functions of key genes. However, molecular and/or targeted breeding toward biomass-related traits in sorghum have not fully benefited from these pieces of genetic knowledge. Thus, to facilitate the breeding and bioenergy applications of sorghum, this perspective summarizes the bioenergy applications of different types of sorghum and outlines the genetic control of the biomass-related traits, ranging from flowering/maturity, plant height, internode morphological traits and metabolic compositions. In particular, we describe the dynamic changes of carbohydrate metabolism in sorghum internodes and highlight the molecular regulators involved in the different stages of internode carbohydrate metabolism, which affects the bioenergy utilization of sorghum biomass. We argue the way forward is to further enhance our understanding of the genetic mechanisms of these biomass-related traits with new technologies, which will lead to future directions toward tailored designing sorghum biomass traits suitable for different bioenergy applications.
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Affiliation(s)
- Lin Yang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Qin Zhou
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Xuan Sheng
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiangqian Chen
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Yuqing Hua
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Shuang Lin
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Qiyun Luo
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Boju Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Ti Shao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Yixiao Wu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
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6
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Naithani S, Deng CH, Sahu SK, Jaiswal P. Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes. Biomolecules 2023; 13:1403. [PMID: 37759803 PMCID: PMC10527062 DOI: 10.3390/biom13091403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of crops constructed from various cultivars, accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novel genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding to mitigate the impact of global climate change. Here, we summarize the tools used for pan-genome assembly and annotations, web-portals hosting plant pan-genomes, etc. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and future potential of this emerging field of study.
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Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Cecilia H. Deng
- Molecular & Digital Breeing Group, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand;
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China;
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
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7
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Takanashi H. Genetic control of morphological traits useful for improving sorghum. BREEDING SCIENCE 2023; 73:57-69. [PMID: 37168813 PMCID: PMC10165342 DOI: 10.1270/jsbbs.22069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/14/2022] [Indexed: 05/13/2023]
Abstract
Global climate change and global warming, coupled with the growing population, have raised concerns about sustainable food supply and bioenergy demand. Sorghum [Sorghum bicolor (L.) Moench] ranks fifth among cereals produced worldwide; it is a C4 crop with a higher stress tolerance than other major cereals and has a wide range of uses, such as grains, forage, and biomass. Therefore, sorghum has attracted attention as a promising crop for achieving sustainable development goals (SDGs). In addition, sorghum is a suitable genetic model for C4 grasses because of its high morphological diversity and relatively small genome size compared to other C4 grasses. Although sorghum breeding and genetic studies have lagged compared to other crops such as rice and maize, recent advances in research have identified several genes and many quantitative trait loci (QTLs) that control important agronomic traits in sorghum. This review outlines traits and genetic information with a focus on morphogenetic aspects that may be useful in sorghum breeding for grain and biomass utilization.
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Affiliation(s)
- Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Corresponding author (e-mail: )
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8
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Voelker WG, Krishnan K, Chougule K, Alexander LC, Lu Z, Olson A, Ware D, Songsomboon K, Ponce C, Brenton ZW, Boatwright JL, Cooper EA. Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes. FRONTIERS IN PLANT SCIENCE 2023; 13:1040909. [PMID: 36684744 PMCID: PMC9846640 DOI: 10.3389/fpls.2022.1040909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Sorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations. METHODS Expanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs). RESULTS We show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes. DISCUSSION These resources can be integrated into both ongoing and future mapping and trait discovery for sorghum and its myriad uses including food, feed, bioenergy, and increasingly as a carbon dioxide removal mechanism.
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Affiliation(s)
- William G. Voelker
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Krittika Krishnan
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Kapeel Chougule
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
| | - Louie C. Alexander
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Zhenyuan Lu
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
| | - Andrew Olson
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
| | - Doreen Ware
- Cold Spring Harbor Research Laboratory, Cold Spring Harbor, NY, United States
- United States Department of Agriculture - Agricultural Research Service in the North Atlantic Area (USDA-ARS NAA), Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Kittikun Songsomboon
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Cristian Ponce
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
| | - Zachary W. Brenton
- Carolina Seed Systems, Darlington, SC, United States
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - J. Lucas Boatwright
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Dept. of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Elizabeth A. Cooper
- Dept. of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- North Carolina Research Campus, Kannapolis, NC, United States
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9
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Simons JM, Herbert TC, Kauffman C, Batete MY, Simpson AT, Katsuki Y, Le D, Amundson D, Buescher EM, Weil C, Tuinstra M, Addo‐Quaye C. Systematic prediction of EMS-induced mutations in a sorghum mutant population. PLANT DIRECT 2022; 6:e404. [PMID: 35647479 PMCID: PMC9132608 DOI: 10.1002/pld3.404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/22/2022] [Accepted: 04/24/2022] [Indexed: 05/14/2023]
Abstract
The precise detection of causal DNA mutations (deoxyribonucleic acid) is very crucial for forward genetic studies. Several sources of errors contribute to false-positive detections by current variant-calling algorithms, which impact associating phenotypes with genotypes. To improve the accuracy of mutation detection, we implemented a binning method for the accurate detection of likely ethyl methanesulfonate (EMS)-induced mutations in a sequenced mutant population. We also implemented a clustering algorithm for detecting likely false negatives with high accuracy. Sorghum bicolor is a very valuable crop species with tremendous potential for uncovering novel gene functions associated with highly desirable agronomical traits. We demonstrate the precision of the described approach in the detection of likely EMS-induced mutations from the publicly available low-cost sequencing of the M3 generation from 600 sorghum BTx623 mutants. The approach detected 3,274,606 single nucleotide polymorphisms (SNPs), of which 96% (3,141,908) were G/C to A/T DNA substitutions, as expected by EMS-mutagenesis mode of action. We demonstrated the general applicability of the described method and showed a high concordance, 94% (3,074,759) SNPs overlap between SAMtools-based and GATK-based variant-calling algorithms. Our clustering algorithm uncovered evidence for an additional 223,048 likely false-negative shared EMS-induced mutations. The final 3,497,654 SNPs represent an 87% increase in SNPs detected from the previous analysis of the mutant population, with an average of one SNP per 125 kb in the sorghum genome. Annotation of the final SNPs revealed 10,263 high-impact and 136,639 moderate-impact SNPs, including 7217 stop-gained mutations, which averages 12 stop-gained mutations per mutant, and four high- or medium-impact SNPs per sorghum gene. We have implemented a public search database for this new genetic resource of 30,285 distinct sorghum genes containing medium- or high-impact EMS-induced mutations. Seedstock for a select 486 of the 600 described mutants are publicly available in the Germplasm Resources Information Network (GRIN) database.
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Affiliation(s)
- Jared M. Simons
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Tim C. Herbert
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Coleby Kauffman
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Marc Y. Batete
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Andrew T. Simpson
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
- Present address:
Department of Biological SciencesUniversity of IdahoMoscowIdahoUSA
| | - Yuka Katsuki
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Dong Le
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | - Danielle Amundson
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
| | | | - Clifford Weil
- Department of AgronomyPurdue UniversityWest LafayetteIndianaUSA
| | - Mitch Tuinstra
- Department of AgronomyPurdue UniversityWest LafayetteIndianaUSA
| | - Charles Addo‐Quaye
- Division of Natural Sciences and MathematicsLewis‐Clark State CollegeLewistonIdahoUSA
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