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Choi S, Prabhakar PK, Chowdhury R, Pendergast TH, Urbanowicz BR, Maranas C, Devos KM. A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5532-5546. [PMID: 37402629 PMCID: PMC10540729 DOI: 10.1093/jxb/erad255] [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: 02/15/2023] [Accepted: 07/03/2023] [Indexed: 07/06/2023]
Abstract
Switchgrass, a forage and bioenergy crop, occurs as two main ecotypes with different but overlapping ranges of adaptation. The two ecotypes differ in a range of characteristics, including flowering time. Flowering time determines the duration of vegetative development and therefore biomass accumulation, a key trait in bioenergy crops. No causal variants for flowering time differences between switchgrass ecotypes have, as yet, been identified. In this study, we mapped a robust flowering time quantitative trait locus (QTL) on chromosome 4K in a biparental F2 population and characterized the flowering-associated transcription factor gene PvHd1, an ortholog of CONSTANS in Arabidopsis and Heading date 1 in rice, as the underlying causal gene. Protein modeling predicted that a serine to glycine substitution at position 35 (p.S35G) in B-Box domain 1 greatly altered the global structure of the PvHd1 protein. The predicted variation in protein compactness was supported in vitro by a 4 °C shift in denaturation temperature. Overexpressing the PvHd1-p.35S allele in a late-flowering CONSTANS-null Arabidopsis mutant rescued earlier flowering, whereas PvHd1-p.35G had a reduced ability to promote flowering, demonstrating that the structural variation led to functional divergence. Our findings provide us with a tool to manipulate the timing of floral transition in switchgrass cultivars and, potentially, expand their cultivation range.
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Affiliation(s)
- Soyeon Choi
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Pradeep K Prabhakar
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Ratul Chowdhury
- Chemical Engineering, Penn State University, State College, PA 16801, USA
| | - Thomas H Pendergast
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
| | - Breeanna R Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Costas Maranas
- Chemical Engineering, Penn State University, State College, PA 16801, USA
| | - Katrien M Devos
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
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3
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Devos KM, Qi P, Bahri BA, Gimode DM, Jenike K, Manthi SJ, Lule D, Lux T, Martinez-Bello L, Pendergast TH, Plott C, Saha D, Sidhu GS, Sreedasyam A, Wang X, Wang H, Wright H, Zhao J, Deshpande S, de Villiers S, Dida MM, Grimwood J, Jenkins J, Lovell J, Mayer KFX, Mneney EE, Ojulong HF, Schatz MC, Schmutz J, Song B, Tesfaye K, Odeny DA. Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nat Commun 2023; 14:3694. [PMID: 37344528 DOI: 10.1038/s41467-023-38915-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/19/2023] [Indexed: 06/23/2023] Open
Abstract
Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.
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Affiliation(s)
- Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics, 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.
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, 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
| | - Bochra A Bahri
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Pathology, University of Georgia, Griffin, GA, 30223, USA
| | - Davis M Gimode
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
| | - Katharine Jenike
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Samuel J Manthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
| | - Dagnachew Lule
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
- Ethiopian Agricultural Transformation Agency, Addis Ababa, Bole, Ethiopia
| | - Thomas Lux
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Liliam Martinez-Bello
- Institute of Plant Breeding, Genetics and Genomics, 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
- UR Ventures, University of Rochester, Rochester, NY, 14627, USA
| | - Thomas H Pendergast
- Institute of Plant Breeding, Genetics and Genomics, 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
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Dipnarayan Saha
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- ICAR-Central Research Institute for Jute and Allied Fibers, Kolkata, West Bengal, 700120, India
| | - Gurjot S Sidhu
- Institute of Plant Breeding, Genetics and Genomics, 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
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hao Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hallie Wright
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Jianxin Zhao
- Institute of Plant Breeding, Genetics and Genomics, 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
| | - Santosh Deshpande
- ICRISAT, Patancheru, 502 324, T.S., India
- Hytech Seed India Pvt. Ltd., Ravalkol Village, Medcahl-Malkajgiri Dist-, 501 401, Hubballi, T.S, India
| | - Santie de Villiers
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, 80108, Kenya
- Pwani University Biosciences Research Center (PUBReC), Kilifi, 80108, Kenya
| | - Mathews M Dida
- Department of Crop and Soil Science, Maseno University, P.O. 333, Maseno, Kenya
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - John Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Emmarold E Mneney
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar Es Salaam, Tanzania
- Biotechnology Society of Tanzania, P.O. Box 10257, Dar es Salaam, Tanzania
| | - Henry F Ojulong
- ICRISAT, Matopos Research Station, P.O. Box 776, Bulawayo, Zimbabwe
| | - Michael C Schatz
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bo Song
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
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Long Z, Tu M, Xu Y, Pak H, Zhu Y, Dong J, Lu Y, Jiang L. Genome-wide-association study and transcriptome analysis reveal the genetic basis controlling the formation of leaf wax in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2726-2739. [PMID: 36724105 DOI: 10.1093/jxb/erad047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/01/2023] [Indexed: 06/06/2023]
Abstract
Cuticular wax protects plants from various biotic and abiotic stresses. However, the genetic network of wax biosynthesis and the environmental factors influencing leaf wax production in rapeseed (Brassica napus) remains unclear. Here, we demonstrated the role of leaf wax in the resistance to Sclerotinia infection in rapeseed. We found that leaves grown under high light intensity had higher expression of genes involved in wax biosynthesis, and produced more wax on the leaf surface, compared with those grown under low light conditions. Genome-wide association study (GWAS) identified 89 single nucleotide polymorphisms significantly associated with leaf wax coverage. A cross-analysis between GWAS and differentially expressed genes (DEGs) in the leaf epidermis of the accessions with contrasting differences in wax content revealed 17 candidate genes that control this variation in rapeseed. Selective sweep analysis combined with DEG analysis unveiled 510 candidate genes with significant selective signatures. From the candidate genes, we selected BnaA02.LOX4, a putative lipoxygenase, and BnaCnn.CER1, BnaA02.CER3, BnaC02.CER3, and BnaA01.CER4 (ECERIFERUM1-4) that were putatively responsible for wax biosynthesis, to analyse the allelic forms and haplotypes corresponding to high or low leaf wax coverage. These data enrich our knowledge about wax formation, and provide a gene pool for breeding an ideal leaf wax content in rapeseed.
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Affiliation(s)
- Zhengbiao Long
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Mengxin Tu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Ying Xu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Haksong Pak
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Yang Zhu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Jie Dong
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Yunhai Lu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road 866, 310058, Hangzhou, China
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5
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Yan J, Chen F, Sun P, Liu W, Xie D, Qian Y, Jiang B. Genome-wide association study and genetic mapping of BhWAX conferring mature fruit cuticular wax in wax gourd. BMC PLANT BIOLOGY 2022; 22:539. [PMID: 36401157 PMCID: PMC9675113 DOI: 10.1186/s12870-022-03931-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Wax gourd [Benincasa hispida (Thunb) Cogn. (2n = 2x = 24)] is an economically important vegetable crop of genus Benincasa in the Cucurbitaceae family. Fruit is the main consumption organ of wax gourd. The mature fruit cuticular wax (MFCW) is an important trait in breeding programs, which is also of evolutionary significance in wax gourd. However, the genetic architecture of this valuable trait remains unrevealed. RESULTS In this study, genetic analysis revealed that the inheritance of MFCW was controlled by a single gene, with MFCW dominant over non-MFCW, and the gene was primarily named as BhWAX. Genome-wide association study (GWAS) highlighted a 1.1 Mb interval on chromosome 9 associated with MFCW in wax gourd germplasm resources. Traditional fine genetic mapping delimited BhWAX to a 0.5 Mb region containing 12 genes. Based on the gene annotation, expression analysis and co-segregation analysis, Bhi09G001428 that encodes a membrane bound O-acyltransferase (MBOAT) was proposed as the candidate gene for BhWAX. Moreover, it was demonstrated that the efficiency of a cleaved amplified polymorphic sequences (CAPS) marker in the determination of MFCW in wax gourd reached 80%. CONCLUSIONS In closing, the study identified the candidate gene controlling MFCW and provided an efficient molecular marker for the trait in wax gourd for the first time, which will not only be beneficial for functional validation of the gene and marker-assisted breeding of wax gourd, but also lay a foundation for analysis of its evolutionary meaning among cucurbits.
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Affiliation(s)
- Jinqiang Yan
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, Guangdong, China
| | - Feng Chen
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, Guangdong, China
| | - Piaoyun Sun
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, Guangdong, China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, Guangdong, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, Guangdong, China
| | - Yulei Qian
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, Guangdong, China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China.
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, Guangdong, China.
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6
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Razar RM, Qi P, Devos KM, Missaoui AM. Genotyping-by-Sequencing and QTL Mapping of Biomass Yield in Two Switchgrass F 1 Populations (Lowland x Coastal and Coastal x Upland). FRONTIERS IN PLANT SCIENCE 2022; 13:739133. [PMID: 35665173 PMCID: PMC9162799 DOI: 10.3389/fpls.2022.739133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
The prevalence of genetic diversity in switchgrass germplasm can be exploited to capture favorable alleles that increase its range of adaptation and biomass yield. The objectives of the study were to analyze the extent of polymorphism and patterns of segregation distortion in two F1 populations and use the linkage maps to locate QTL for biomass yield. We conducted genotyping-by-sequencing on two populations derived from crosses between the allotetraploid lowland genotype AP13 (a selection from "Alamo") and coastal genotype B6 (a selection from PI 422001) with 285 progeny (AB population) and between B6 and the allotetraploid upland VS16 (a selection from "Summer") with 227 progeny (BV population). As predictable from the Euclidean distance between the parents, a higher number of raw variants was discovered in the coastal × upland BV cross (6 M) compared to the lowland × coastal AB cross (2.5 M). The final number of mapped markers was 3,107 on the BV map and 2,410 on the AB map. More segregation distortion of alleles was seen in the AB population, with 75% distorted loci compared to 11% distorted loci in the BV population. The distortion in the AB population was seen across all chromosomes in both the AP13 and B6 maps and likely resulted from zygotic or post-zygotic selection for increased levels of heterozygosity. Our results suggest lower genetic compatibility between the lowland AP13 and the coastal B6 ecotype than between B6 and the upland ecotype VS16. Four biomass QTLs were mapped in the AB population (LG 2N, 6K, 6N, and 8N) and six QTLs in the BV population [LG 1N (2), 8N (2), 9K, and 9N]. The QTL, with the largest and most consistent effect across years, explaining between 8.4 and 11.5% of the variation, was identified on 6N in the AP13 map. The cumulative effect of all the QTLs explained a sizeable portion of the phenotypic variation in both AB and BV populations and the markers associated with them may potentially be used for the marker-assisted improvement of biomass yield. Since switchgrass improvement is based on increasing favorable allele frequencies through recurrent selection, the transmission bias within individuals and loci needs to be considered as this may affect the genetic gain if the favorable alleles are distorted.
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Affiliation(s)
- Rasyidah M. Razar
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Genetic Resources and Improvement Unit, RRIM Research Station, Malaysian Rubber Board, Selangor, Malaysia
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Ali M. Missaoui
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
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