1
|
Gao M, Hua T, Niu G, Masabni J, Dewalt W. A locus-dependent mixed inheritance in the segmental allohexaploid sweetpotato ( Ipomoea batatas [L.] Lam). FRONTIERS IN PLANT SCIENCE 2024; 15:1398081. [PMID: 38863536 PMCID: PMC11165125 DOI: 10.3389/fpls.2024.1398081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024]
Abstract
Two interrelated aspects of the sweetpotato genome, its polyploid origin and inheritance type, remain uncertain. We recently proposed a segmental allohexaploid sweetpotato and thus sought to clarify its inheritance type by direct analyses of homoeolog segregations at selected single-copy loci. For such analyses, we developed a digital quantitative PCR genotyping method using one nondiscriminatory and three discriminatory probes for each selected locus to discriminate and quantify three homoeolog-differentiating variation types (homoeolog-types) in genomic DNA samples for genotype fitting and constructed a F2 population for segregation analyses. We confirmed inter-subgenomic distinctions of three identified homoeolog-types at each of five selected loci by their interspecific differentiations among 14 species in Ipomoea section batatas and genotyped the loci in 549 F2 lines, selected F1 progenies, and their founding parents. Segregation and genotype analyses revealed a locus-dependent mixed inheritance (disomic, polysomic, and intermediate types) of the homoeolog-types at 4 loci in the F2 population, displaying estimated disomic-inheritance frequencies of 0, 2.72%, 14.52%, and 36.92%, and probably in the F1 population too. There were also low-frequency non-hexaploid F1 and F2 genotypes that were probably derived from double-reduction recombination or partially unreduced gametes, and F2 genotypes of apparent aneuploids/dysploids with neopolyploid-like frequencies. Additional analyses of homoeolog-type genotypes at the 5 loci in 46 lines from various regions revealed locus-dependent selection biases, favoring genotypes having more of one homoeolog-type, i.e. more of di- or homogenized homoeolog-type composition, and one-direction ploidy trending among apparent aneuploids/dysploids. These inheritance features pointed to an evolving segmental allohexaploid sweetpotato impacted by selection biases.
Collapse
Affiliation(s)
- Ming Gao
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
| | - Tien Hua
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
| | - Genhua Niu
- AgriLife Research and Extension Center at Dallas, Texas A&M University, Dallas, TX, United States
| | - Joe Masabni
- AgriLife Research and Extension Center at Dallas, Texas A&M University, Dallas, TX, United States
| | - Willie Dewalt
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
| |
Collapse
|
2
|
Guo F, Meng X, Hong H, Liu S, Yu J, Huang C, Dong T, Geng H, Li Z, Zhu M. Systematic identification and expression analysis of bHLH gene family reveal their relevance to abiotic stress response and anthocyanin biosynthesis in sweetpotato. BMC PLANT BIOLOGY 2024; 24:156. [PMID: 38424529 PMCID: PMC10905920 DOI: 10.1186/s12870-024-04788-0] [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: 08/23/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND bHLH transcription factors play significant roles in regulating plant growth and development, stress response, and anthocyanin biosynthesis. Sweetpotato is a pivotal food and industry crop, but little information is available on sweetpotato bHLH genes. RESULTS Herein, 227 putative IbbHLH genes were defined on sweetpotato chromosomes, and fragment duplications were identified as the dominant driving force for IbbHLH expansion. These IbbHLHs were divided into 26 subfamilies through phylogenetic analysis, as supported by further analysis of exon-intron structure and conserved motif composition. The syntenic analysis between IbbHLHs and their orthologs from other plants depicted evolutionary relationships of IbbHLHs. Based on the transcriptome data under salt stress, the expression of 12 IbbHLHs was screened for validation by qRT-PCR, and differential and significant transcriptions under abiotic stress were detected. Moreover, IbbHLH123 and IbbHLH215, which were remarkably upregulated by stress treatments, had obvious transactivation activity in yeasts. Protein interaction detections and yeast two-hybrid assays suggested an intricate interaction correlation between IbbHLHs. Besides, transcriptome screening revealed that multiple IbbHLHs may be closely related to anthocyanin biosynthesis based on the phenotype (purple vs. white tissues), which was confirmed by subsequent qRT-PCR analysis. CONCLUSIONS These results shed light on the promising functions of sweetpotato IbbHLHs in abiotic stress response and anthocyanin biosynthesis.
Collapse
Affiliation(s)
- Fen Guo
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Xiaoqing Meng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Haiting Hong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Siyuan Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Jing Yu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Can Huang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Huixue Geng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu Province, 221116, China.
| |
Collapse
|
3
|
Ahmed S, Khan MSS, Xue S, Islam F, Ikram AU, Abdullah M, Liu S, Tappiban P, Chen J. A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato. HORTICULTURE RESEARCH 2024; 11:uhae014. [PMID: 38464477 PMCID: PMC10923648 DOI: 10.1093/hr/uhae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/09/2024] [Indexed: 03/12/2024]
Abstract
Biotic and abiotic stresses negatively affect the yield and overall plant developmental process, thus causing substantial losses in global sweet potato production. To cope with stresses, sweet potato has evolved numerous strategies to tackle ever-changing surroundings and biological and environmental conditions. The invention of modern sequencing technology and the latest data processing and analysis instruments has paved the way to integrate biological information from different approaches and helps to understand plant system biology more precisely. The advancement in omics technologies has accumulated and provided a great source of information at all levels (genome, transcript, protein, and metabolite) under stressful conditions. These latest molecular tools facilitate us to understand better the plant's responses to stress signaling and help to process/integrate the biological information encoded within the biological system of plants. This review briefly addresses utilizing the latest omics strategies for deciphering the adaptive mechanisms for sweet potatoes' biotic and abiotic stress tolerance via functional genomics, transcriptomics, proteomics, and metabolomics. This information also provides a powerful reference to understand the complex, well-coordinated stress signaling genetic regulatory networks and better comprehend the plant phenotypic responses at the cellular/molecular level under various environmental stimuli, thus accelerating the design of stress-resilient sweet potato via the latest genetic engineering approaches.
Collapse
Affiliation(s)
- Sulaiman Ahmed
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | | | - Songlei Xue
- Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng 224000, China
| | - Faisal Islam
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Aziz Ul Ikram
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Muhammad Abdullah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minghang, 200240, Shanghai, China
| | - Shan Liu
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Piengtawan Tappiban
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Jian Chen
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| |
Collapse
|
4
|
Chen L, Liu L, Yang G, Li X, Dai X, Xue L, Yin T. Expression Quantitative Trait Locus of Wood Formation-Related Genes in Salix suchowensis. Int J Mol Sci 2023; 25:247. [PMID: 38203430 PMCID: PMC10778782 DOI: 10.3390/ijms25010247] [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: 11/14/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Shrub willows are widely planted for landscaping, soil remediation, and biomass production, due to their rapid growth rates. Identification of regulatory genes in wood formation would provide clues for genetic engineering of willows for improved growth traits on marginal lands. Here, we conducted an expression quantitative trait locus (eQTL) analysis, using a full sibling F1 population of Salix suchowensis, to explore the genetic mechanisms underlying wood formation. Based on variants identified from simplified genome sequencing and gene expression data from RNA sequencing, 16,487 eQTL blocks controlling 5505 genes were identified, including 2148 cis-eQTLs and 16,480 trans-eQTLs. eQTL hotspots were identified, based on eQTL frequency in genomic windows, revealing one hotspot controlling genes involved in wood formation regulation. Regulatory networks were further constructed, resulting in the identification of key regulatory genes, including three transcription factors (JAZ1, HAT22, MYB36) and CLV1, BAM1, CYCB2;4, CDKB2;1, associated with the proliferation and differentiation activity of cambium cells. The enrichment of genes in plant hormone pathways indicates their critical roles in the regulation of wood formation. Our analyses provide a significant groundwork for a comprehensive understanding of the regulatory network of wood formation in S. suchowensis.
Collapse
Affiliation(s)
| | | | | | | | | | - Liangjiao Xue
- State Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Tongming Yin
- State Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| |
Collapse
|
5
|
Kim TH, Kim S, Park W, Woo KS, Lee K, Chung MN, Lee YH, Lee HU, Lee KH, Nam SS, Jo H, Lee JD. Genome-wide association study to identify novel loci and genes for Fusarium root rot resistance in sweet potato using genotyping-by-sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1251157. [PMID: 37860237 PMCID: PMC10584150 DOI: 10.3389/fpls.2023.1251157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
Fusarium root rot, caused by Fusarium solani, is a major post-harvest disease in sweet potatoes (Ipomoea batatas (L.) Lam.). An effective strategy for controlling this disease is the development of resistant varieties. In this study, a genome-wide association study (GWAS) was conducted on 96 sweet potato genotypes to identify novel candidate loci and dissect the genetic basis of Fusarium root rot resistance. Genotyping was performed using genotyping-by-sequencing (GBS), and 44,255 SNPs were identified after filtering. The genotypes (n = 96) were evaluated through resistance tests in 2021 and 2022, separately and combined. The GWAS identified two significant SNP markers (LG3_22903756 and LG4_2449919) on chromosomes 3 and 4 associated with Fusarium root rot resistance, respectively. Lesion length showed significant differences between homozygous A and G alleles of LG3_22903756, which can potentially be used to develop molecular markers for selecting accessions resistant to Fusarium root rot. Expression analysis of 11 putative genes flanking the significant SNPs revealed the alteration in the expression of nine genes, indicating their possible involvement in Fusarium root rot resistance. The results of this study will aid in the marker-assisted selection and functional analysis of candidate genes for Fusarium root rot resistance in sweet potatoes.
Collapse
Affiliation(s)
- Tae Hwa Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Sujung Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Won Park
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Koan Sik Woo
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Keunpyo Lee
- International Technology Cooperation Center, Technology Cooperation Bureau, Rural Development Administration, Jeonju, Republic of Korea
| | - Mi Nam Chung
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Young Hoon Lee
- Planning and Coordination Division, National Institute of Crop Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Hyeong-Un Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Kyo Hwui Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Sang-Sik Nam
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Hyun Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
6
|
Xu C, Song LY, Zhou Y, Ma DN, Ding QS, Guo ZJ, Li J, Song SW, Zhang LD, Zheng HL. Integration of eQTL and GWAS analysis uncovers a genetic regulation of natural ionomic variation in Arabidopsis. PLANT CELL REPORTS 2023; 42:1473-1485. [PMID: 37516984 DOI: 10.1007/s00299-023-03042-5] [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: 12/27/2022] [Accepted: 06/12/2023] [Indexed: 08/01/2023]
Abstract
KEY MESSAGE This study provided important insights into the genetic architecture of variations in A. thaliana leaf ionome in a cell-type-specific manner. The functional interpretation of traits associated variants by expression quantitative trait loci (eQTL) analysis is usually performed in bulk tissue samples. While the regulation of gene expression is context-dependent, such as cell-type-specific manner. In this study, we estimated cell-type abundances from 728 bulk tissue samples using single-cell RNA-sequencing dataset, and performed cis-eQTL mapping to identify cell-type-interaction eQTL (cis-eQTLs(ci)) in A. thaliana. Also, we performed Genome-wide association studies (GWAS) analyses for 999 accessions to identify the genetic basis of variations in A. thaliana leaf ionome. As a result, a total of 5,664 unique eQTL genes and 15,038 unique cis-eQTLs(ci) were significant. The majority (62.83%) of cis-eQTLs(ci) were cell-type-specific eQTLs. Using colocalization, we uncovered one interested gene AT2G25590 in Phloem cell, encoding a kind of plant Tudor-like protein with possible chromatin-associated functions, which colocalized with the most significant cis-eQTL(ci) of a Mo-related locus (Chr2:10,908,806:A:C; P = 3.27 × 10-27). Furthermore, we prioritized eight target genes associated with AT2G25590, which were previously reported in regulating the concentration of Mo element in A. thaliana. This study revealed the genetic regulation of ionomic variations and provided a foundation for further studies on molecular mechanisms of genetic variants controlling the A. thaliana ionome.
Collapse
Affiliation(s)
- Chaoqun Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Ling-Yu Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Ying Zhou
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
| | - Dong-Na Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qian-Su Ding
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Ze-Jun Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Jing Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Shi-Wei Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Lu-Dan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China.
| |
Collapse
|
7
|
Haque E, Shirasawa K, Suematsu K, Tabuchi H, Isobe S, Tanaka M. Polyploid GWAS reveals the basis of molecular marker development for complex breeding traits including starch content in the storage roots of sweet potato. FRONTIERS IN PLANT SCIENCE 2023; 14:1181909. [PMID: 37342138 PMCID: PMC10277646 DOI: 10.3389/fpls.2023.1181909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/08/2023] [Indexed: 06/22/2023]
Abstract
Given the importance of prioritizing genome-based breeding of sweet potato to enable the promotion of food and nutritional security for future human societies, here, we aimed to dissect the genetic basis of storage root starch content (SC) when associated with a complex set of breeding traits including dry matter (DM) rate, storage root fresh weight (SRFW), and anthocyanin (AN) content in a mapping population containing purple-fleshed sweet potato. A polyploid genome-wide association study (GWAS) was extensively exploited using 90,222 single-nucleotide polymorphisms (SNPs) obtained from a bi-parental 204 F1 population between 'Konaishin' (having high SC but no AN) and 'Akemurasaki' (having high AN content but moderate SC). Through the comparison of polyploid GWAS on the whole set of the 204 F1, 93 high-AN-containing F1, and 111 low-AN-containing F1 populations, a total of two (consists of six SNPs), two (14 SNPs), four (eight SNPs), and nine (214 SNPs) significantly associated signals were identified for the variations of SC, DM, SRFW, and the relative AN content, respectively. Of them, a novel signal associated with SC, which was most consistent in 2019 and 2020 in both the 204 F1 and 111 low-AN-containing F1 populations, was identified in homologous group 15. The five SNP markers associated with homologous group 15 could affect SC improvement with a degree of positive effect (~4.33) and screen high-starch-containing lines with higher efficiency (~68%). In a database search of 62 genes involved in starch metabolism, five genes including enzyme genes granule-bound starch synthase I (IbGBSSI), α-amylase 1D, α-amylase 1E, and α-amylase 3, and one transporter gene ATP/ADP-transporter were located on homologous group 15. In an extensive qRT-PCR of these genes using the storage roots harvested at 2, 3, and 4 months after field transplantation in 2022, IbGBSSI, which encodes the starch synthase isozyme that catalyzes the biosynthesis of amylose molecule, was most consistently elevated during starch accumulation in sweet potato. These results would enhance our understanding of the underlying genetic basis of a complex set of breeding traits in the starchy roots of sweet potato, and the molecular information, particularly for SC, would be a potential platform for molecular marker development for this trait.
Collapse
Affiliation(s)
- Emdadul Haque
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Keisuke Suematsu
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Japan
| | - Hiroaki Tabuchi
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Japan
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Masaru Tanaka
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Japan
| |
Collapse
|
8
|
Li M, Zhou Y, Li K, Guo H. Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes. PLANTS (BASEL, SWITZERLAND) 2023; 12:1731. [PMID: 37111954 PMCID: PMC10140993 DOI: 10.3390/plants12081731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 06/19/2023]
Abstract
Sweet potatoes (Ipomoea batatas) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. R2R3-MYB is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few reports about the R2R3-MYB gene family of sweet potatoes have been released to date. In the present study, a total of 695 typical R2R3-MYB genes were identified in six Ipomoea species, including 131 R2R3-MYB genes in sweet potatoes. A maximum likelihood phylogenetic analysis divided these genes into 36 clades, referring to the classification of 126 R2R3-MYB proteins of Arabidopsis. Clade C25(S12) has no members in six Ipomoea species, whereas four clades (i.e., clade C21, C26, C30, and C36), including 102 members, had no members in Arabidopsis, and they were identified as Ipomoea-specific clades. The identified R2R3-MYB genes were unevenly distributed on all chromosomes in six Ipomoea species genomes, and the collinearity analysis among hexaploid I. batatas and another five diploid Ipomoea species suggested that the sweet potato genome might have undergone a larger chromosome rearrangement during the evolution process. Further analyses of gene duplication events showed that whole-genome duplication, transposed duplication, and dispersed duplication events were the primary forces driving the R2R3-MYB gene family expansion of Ipomoea plants, and these duplicated genes experienced strong purifying selection because of their Ka/Ks ratio, which is less than 1. Additionally, the genomic sequence length of 131 IbR2R3-MYBs varied from 923 bp to ~12.9 kb with a mean of ~2.6 kb, and most of them had more than three exons. The Motif 1, 2, 3, and 4 formed typical R2 and R3 domains and were identified in all IbR2R3-MYB proteins. Finally, based on multiple RNA-seq datasets, two IbR2R3-MYB genes (IbMYB1/g17138.t1 and IbMYB113/g17108.t1) were relatively highly expressed in pigmented leaves and tuberous root flesh and skin, respectively; thus, they were identified to regulate tissue-specific anthocyanin accumulation in sweet potato. This study provides a basis for the evolution and function of the R2R3-MYB gene family in sweet potatoes and five other Ipomoea species.
Collapse
Affiliation(s)
- Maoxing Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
| | - Yuanping Zhou
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
| | - Kaifeng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
| | - Huachun Guo
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
| |
Collapse
|
9
|
Nie H, Park H, Kim S, Kim D, Kim S, Kwon SY, Kim SH. Genetic diversity assessment and genome-wide association study reveal candidate genes associated with component traits in sweet potato (Ipomoea batatas (L.) Lam). Mol Genet Genomics 2023; 298:653-667. [PMID: 36943475 DOI: 10.1007/s00438-023-02007-3] [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: 02/16/2022] [Accepted: 03/11/2023] [Indexed: 03/23/2023]
Abstract
The Korean sweet potatoes were bred by various cultivars introduced from Japanese, American, Porto Rico, China, and Burundi. This issue enriched their genetic diversity but also resulted in a mixture of cultivars. For genotyping, we collected and sequenced 66 sweet potato germplasms from different localities around Korea, including 36 modern cultivars, 5 local cultivars, and 25 foreign cultivars. This identified 447.6 million trimmed reads and 324.8 million mapping reads and provided 39,424 single nucleotide polymorphisms (SNPs) markers. Phylogenetic clustering and population structure analysis distinctly classified these germplasms into 5 genetic groups, group 1, group 2, group 3, group 4, and group 5, containing 20, 15, 10, 7, and 14 accessions, respectively. Sixty-three significant SNPs were selected by genome-wide association for sugar composition-related traits (fructose, glucose, and total sugars), total starch, amylose content, and total carotenoid of the storage root. A total of 37 candidate genes encompassing these significant SNPs were identified, among which, 7 genes were annotated to involve in sugar and starch metabolism, including galactose metabolism (itf04g30630), starch and sucrose metabolism (itf03g13270, itf15g09320), carbohydrate metabolism (itf14g10250), carbohydrate and amino acid metabolism (itf12g19270), and amino sugar and nucleotide sugar metabolism (itf03g21950, itf15g04880). This results indicated that sugar and starch are important characteristics to determine the genetic diversity of sweet potatoes. These findings not only illustrate the importance of component traits to genotyping sweet potatoes but also explain an important reason resulting in genetic diversity of sweet potato.
Collapse
Affiliation(s)
- Hualin Nie
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Hyungjun Park
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Sujung Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, 58545, Republic of Korea
| | - Doyeon Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, South Korea
| | - Sun-Hyung Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea.
| |
Collapse
|
10
|
Hou W, Yan P, Shi T, Lu P, Zhao W, Yang H, Zeng L, Yang J, Li Z, Fan W, Zhang L. Modulation of anthocyanin accumulation in storage roots of sweetpotato by transcription factor IbMYB1-2 through direct binding to anthocyanin biosynthetic gene promoters. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:868-879. [PMID: 36878161 DOI: 10.1016/j.plaphy.2023.02.050] [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: 11/22/2022] [Revised: 01/30/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The storage roots of purple-fleshed sweetpotato rich in anthocyanins are considered nutrient-rich foods with health effects. However, the molecular mechanism underlying anthocyanin biosynthesis and regulation remains to be revealed. In this study, IbMYB1-2 was isolated from purple-fleshed sweetpotato "Xuzishu8". The phylogenetic and sequence analysis indicated that IbMYB1-2 belongs to the SG6 subfamily with a conserved bHLH motif. Subcellular localization analysis and transcriptional activity assay revealed that IbMYB1-2 is a key transcriptional activator and is specific to the nucleus. Agrobacterium rhizogenes-mediated overexpression of IbMYB1-2 in sweetpotato through in vivo root transgenic system led to an increase in anthocyanins in the root of sweetpotato. qRT-PCR and transcriptome analysis depicted that the transcript levels of IbMYB1-2, IbbHLH42, and eight structural genes that are associated with the synthesis of anthocyanin were upregulated in overexpressed IbMYB1-2 transgenic roots. Dual-luciferase reporter (DLR) assay and yeast one-hybrid (Y1H) assay demonstrated IbMYB1-2 binding to the promoter regions of IbbHLH42 and other anthocyanin biosynthetic genes, including IbCHS, IbCHI, IbF3H, IbDFR, IbANS, IbGSTF12, IbUGT78D2, and IbUF3GT. Moreover, IbbHLH42 was shown to be an active enhancer for the formation of MYB-bHLH-WD40 (MBW) complex, which strongly supports the promoter activities of the IbCHS, IbANS, IbUGT78D2, and IbGSTF12 genes to induce anthocyanin accumulation. Taken together, our findings not only revealed the underlying regulatory molecular mechanism of IbMYB1-2 for anthocyanin accumulation in the storage roots of sweetpotato but also uncovered a potential mechanism by which IbbHLH42 modulated anthocyanin biosynthesis through a positive feedback regulatory loop.
Collapse
Affiliation(s)
- Wenqian Hou
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Street, Xuzhou, 221100, Jiangsu Province, People's Republic of China.
| | - Ping Yan
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Street, Xuzhou, 221100, Jiangsu Province, People's Republic of China.
| | - Tianye Shi
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Street, Xuzhou, 221100, Jiangsu Province, People's Republic of China.
| | - Pengzhou Lu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Street, Xuzhou, 221100, Jiangsu Province, People's Republic of China
| | - Weiwei Zhao
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Street, Xuzhou, 221100, Jiangsu Province, People's Republic of China
| | - Huimin Yang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Street, Xuzhou, 221100, Jiangsu Province, People's Republic of China
| | - Liqian Zeng
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Street, Xuzhou, 221100, Jiangsu Province, People's Republic of China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, People's Republic of China
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Street, Xuzhou, 221100, Jiangsu Province, People's Republic of China
| | - Weijuan Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, People's Republic of China.
| | - Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Street, Xuzhou, 221100, Jiangsu Province, People's Republic of China.
| |
Collapse
|
11
|
Li L, Jin Z, Huang R, Zhou J, Song F, Yao L, Li P, Lu W, Xiao L, Quan M, Zhang D, Du Q. Leaf physiology variations are modulated by natural variations that underlie stomatal morphology in Populus. PLANT, CELL & ENVIRONMENT 2023; 46:150-170. [PMID: 36285358 DOI: 10.1111/pce.14471] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 06/16/2023]
Abstract
Stomata are essential for photosynthesis and abiotic stress tolerance. Here, we used multiomics approaches to dissect the genetic architecture and adaptive mechanisms that underlie stomatal morphology in Populus tomentosa juvenile natural population (303 accessions). We detected 46 candidate genes and 15 epistatic gene-pairs, associated with 5 stomatal morphologies and 18 leaf development and photosynthesis traits, through genome-wide association studies. Expression quantitative trait locus mapping revealed that stomata-associated gene loci were significantly associated with the expression of leaf-related genes; selective sweep analysis uncovered significant differentiation in the allele frequencies of genes that underlie stomatal variations. An allelic regulatory network operating under drought stress and adequate precipitation conditions, with three key regulators (DUF538, TRA2 and AbFH2) and eight interacting genes, was identified that might regulate leaf physiology via modulation of stomatal shape and density. Validation of candidate gene variations in drought-tolerant and F1 hybrid populations of P. tomentosa showed that the DUF538, TRA2 and AbFH2 loci cause functional stabilisation of spatiotemporal regulatory, whose favourable alleles can be faithfully transmitted to offspring. This study provides insights concerning leaf physiology and stress tolerance via the regulation of stomatal determination in perennial plants.
Collapse
Affiliation(s)
- Lianzheng Li
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Zhuoying Jin
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Rui Huang
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Jiaxuan Zhou
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Fangyuan Song
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Liangchen Yao
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Peng Li
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Wenjie Lu
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Liang Xiao
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Mingyang Quan
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Deqiang Zhang
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Qingzhang Du
- National Engineering Research Center of Tree breeding and Ecological restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| |
Collapse
|
12
|
Integrated Analysis of Metabolome and Transcriptome Reveals the Difference in Flavonoid Biosynthesis between the Red- and White-Sarcocarp Pomelo Fruits. Metabolites 2022; 12:metabo12121161. [PMID: 36557200 PMCID: PMC9782486 DOI: 10.3390/metabo12121161] [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: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Flavonoids are bioactive secondary metabolites that play multiple roles in plants. However, studies on the flavonoid accumulation of the pomelo fruit are rare. In this study, we conducted a widely targeted metabolome analysis by using ultra-performance liquid chromatography and tandem mass spectrometry and identified 550 metabolites in the sarcocarp from red (C. maxima Merr. var. Tubtim Siam) and white pomelos (C. maxima (Burm.) Osbeck). A total of 263 significantly changed metabolites were detected from the 550 metabolites. Content analysis of the significantly changed metabolites (SCMs) showed that 138 SCMs were highly accumulated, whereas 125 SCMs were observed with lower content in red-sarcocarp pomelo. Importantly, 103 of the 263 SCMs were flavonoids, including 34 flavonoids, 29 flavonols, 18 flavonoid carbonosides, 9 dihydroflavones, 6 isoflavones, 5 anthocyanins, 1 dihydroflavonol, and 1 chalcone. Gene ontology analysis indicated that upregulated genes in red-sarcocarp pomelo were significantly enriched in GO terms related to flavonoids including flavonoid biosynthetic processes. Several important differentially expressed genes were detected in the correlation network, especially Cg2g009540 which is an orthologous gene of AtCHS, also detected in flavonoid biosynthesis networks, and which could be related to the high level of total flavonoids in the red-sarcocarp pomelo. Our study demonstrated the fluctuation of flavonoid biosynthesis in the two pomelo cultivars and laid a theoretical foundation for pomelo breeding to generate fruits with a high flavonoid content.
Collapse
|
13
|
Xiao S, Dai X, Zhao L, Zhou Z, Zhao L, Xu P, Gao B, Zhang A, Zhao D, Yuan R, Wang Y, Wang J, Li Q, Cao Q. Resequencing of sweetpotato germplasm resources reveals key loci associated with multiple agronomic traits. HORTICULTURE RESEARCH 2022; 10:uhac234. [PMID: 36643760 PMCID: PMC9832839 DOI: 10.1093/hr/uhac234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity, which limits gene mining for important agronomic traits. Here, 314 sweetpotato germplasm resources were deeply resequenced, and 4 599 509 SNPs and 846 654 InDels were generated, among which 196 124 SNPs were nonsynonymous and 9690 InDels were frameshifted. Based on the Indels, genome-wide marker primers were designed, and 3219 of 40 366 primer pairs were selected to construct the core InDel marker set. The molecular ID of 104 sweetpotato samples verified the availability of these primers. The sweetpotato population structures were then assessed through multiple approaches using SNPs, and diverse approaches demonstrated that population stratification was not obvious for most Chinese germplasm resources. As many as 20 important agronomic traits were evaluated, and a genome-wide association study was conducted on these traits. A total of 19 high-confidence loci were detected in both models. These loci included several candidate genes, such as IbMYB1, IbZEP1, and IbYABBY1, which might be involved in anthocyanin metabolism, carotenoid metabolism, and leaf morphogenesis, respectively. Among them, IbZEP1 and IbYABBY1 were first reported in sweetpotato. The variants in the promoter and the expression levels of IbZEP1 were significantly correlated with flesh color (orange or not orange) in sweetpotato. The expression levels of IbYABBY1 were also correlated with leaf shape. These results will assist in genetic and breeding studies in sweetpotato.
Collapse
Affiliation(s)
| | | | | | - Zhilin Zhou
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Lukuan Zhao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Pan Xu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Bingqian Gao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - An Zhang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Donglan Zhao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Rui Yuan
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Yao Wang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Jie Wang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Qinglian Li
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Qinghe Cao
- Correspondence: Qinghe Cao (); Tel.: 086-0516-82189205; Fax: 086-0516-82189205
| |
Collapse
|
14
|
Yan M, Nie H, Wang Y, Wang X, Jarret R, Zhao J, Wang H, Yang J. Exploring and exploiting genetics and genomics for sweetpotato improvement: Status and perspectives. PLANT COMMUNICATIONS 2022; 3:100332. [PMID: 35643086 PMCID: PMC9482988 DOI: 10.1016/j.xplc.2022.100332] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/17/2022] [Accepted: 05/02/2022] [Indexed: 05/14/2023]
Abstract
Sweetpotato (Ipomoea batatas (L.) Lam.) is one of the most important root crops cultivated worldwide. Because of its adaptability, high yield potential, and nutritional value, sweetpotato has become an important food crop, particularly in developing countries. To ensure adequate crop yields to meet increasing demand, it is essential to enhance the tolerance of sweetpotato to environmental stresses and other yield-limiting factors. The highly heterozygous hexaploid genome of I. batatas complicates genetic studies and limits improvement of sweetpotato through traditional breeding. However, application of next-generation sequencing and high-throughput genotyping and phenotyping technologies to sweetpotato genetics and genomics research has provided new tools and resources for crop improvement. In this review, we discuss the genomics resources that are available for sweetpotato, including the current reference genome, databases, and available bioinformatics tools. We systematically review the current state of knowledge on the polyploid genetics of sweetpotato, including studies of its origin and germplasm diversity and the associated mapping of important agricultural traits. We then outline the conventional and molecular breeding approaches that have been applied to sweetpotato. Finally, we discuss future goals for genetic studies of sweetpotato and crop improvement via breeding in combination with state-of-the-art multi-omics approaches such as genomic selection and gene editing. These approaches will advance and accelerate genetic improvement of this important root crop and facilitate its sustainable global production.
Collapse
Affiliation(s)
- Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Haozhen Nie
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yunze Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xinyi Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | | | - Jiamin Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Hongxia Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| |
Collapse
|
15
|
Dong W, Tang L, Peng Y, Qin Y, Lin Y, Xiong X, Hu X. Comparative transcriptome analysis of purple-fleshed sweet potato and its yellow-fleshed mutant provides insight into the transcription factors involved in anthocyanin biosynthesis in tuberous root. FRONTIERS IN PLANT SCIENCE 2022; 13:924379. [PMID: 36003808 PMCID: PMC9393619 DOI: 10.3389/fpls.2022.924379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
In various plant species, many transcription factors (TFs), such as MYB, bHLH, and WD40, have been identified as regulators of anthocyanin biosynthesis in underground organs. However, the regulatory elements of anthocyanin biosynthesis in the tuberous roots of sweet potato have not been elucidated yet. Here, we selected the purple-fleshed sweet potato cultivar "Zhezi1" (ZZ P ) and its spontaneous yellow-fleshed mutant "Xinli" (XL Y ) to investigate the regulatory mechanism of the anthocyanin biosynthesis in the tuberous roots of sweet potato. By analyzing the IbMYB1 genotype in ZZ P and XL Y , we found that the IbMYB1-2, a MYB TF involved in anthocyanin biosynthesis, was missing in the XL Y genome, which might lead to an extreme decrease in anthocyanins in XL Y . A comparative transcriptome analysis of ZZ P and XL Y was conducted to find the TFs involved in anthocyanin biosynthesis in ZZ P and XL Y . The anthocyanin structural genes were significantly enriched among the differentially expressed genes. Moreover, one MYB activator (IbMYB1), one bHLH (IbbHLH2), three WRKY activator candidates (IbWRKY21, IbWRKY24, and IbWRKY44), and two MYB repressors (IbMYB27 and IbMYBx-ZZ) were highly expressed in ZZ P accompanied with anthocyanin structural genes. We also tested the expression of these TFs in six purple- and two orange-fleshed sweet potato cultivars. Interestingly, most of these TFs were significantly positively correlated with anthocyanin contents in these cultivars. The function of the anthocyanin biosynthesis repression of IbMYB27 and IbMYBx-ZZ was verified through transient co-transformation with IbMYB1 into tobacco leaves. Further functional verification of the above TFs was conducted by Y2H, BiFC, and dual-luciferase assays. These tests showed that the MYB-bHLH-WD40/MYB-bHLH-WD40-WRKY complex activated the promoter of anthocyanin structural gene IbDFR and promoters for IbWRKY44, IbMYB27, and IbMYBx-ZZ, indicating reinforcement and feedback regulation to maintain the level of anthocyanin accumulation in the tuberous roots of purple-fleshed sweet potato. These results may provide new insights into the regulatory mechanism of anthocyanin biosynthesis and accumulation in underground organs of sweet potatoes.
Collapse
Affiliation(s)
- Wen Dong
- Hunan Provincial Engineering Research Center for Potatoes, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Linfei Tang
- Hunan Provincial Engineering Research Center for Potatoes, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Yali Peng
- Hunan Provincial Engineering Research Center for Potatoes, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Yuzhi Qin
- Hunan Provincial Engineering Research Center for Potatoes, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Yuan Lin
- Hunan Provincial Engineering Research Center for Potatoes, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xingyao Xiong
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinxi Hu
- Hunan Provincial Engineering Research Center for Potatoes, College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| |
Collapse
|
16
|
Yang Z, Dong T, Dai X, Wei Y, Fang Y, Zhang L, Zhu M, Nawaz G, Cao Q, Xu T. Comparative Analysis of Salt Responsive MicroRNAs in Two Sweetpotato [ Ipomoea batatas (L.) Lam.] Cultivars With Different Salt Stress Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:879819. [PMID: 35874022 PMCID: PMC9302446 DOI: 10.3389/fpls.2022.879819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Sweetpotato [Ipomoea batatas (L.) Lam.] is an important food, vegetable and economic crop, but its productivity is remarkably affected by soil salinity. MiRNAs are a class of endogenous non-coding small RNAs that play an important role in plant resistance to salt stress. However, the function of miRNAs still remains largely unknown in sweetpotato under salt stress. Previously, we identified salt-responsive miRNAs in one salt-sensitive sweetpotato cultivar "Xushu 32." In this study, we identified miRNAs in another salt-tolerant cultivar "Xushu 22" by high-throughput deep sequencing and compared the salt-responsive miRNAs between these two cultivars with different salt sensitivity. We identified 687 miRNAs in "Xushu 22," including 514 known miRNAs and 173 novel miRNAs. Among the 759 miRNAs from the two cultivars, 72 and 109 miRNAs were specifically expressed in "Xushu 32" and "Xushu 22," respectively, and 578 miRNAs were co-expressed. The comparison of "Xushu 32" and "Xushu 22" genotypes showed a total of 235 miRNAs with obvious differential expression and 177 salt-responsive miRNAs that were obviously differently expressed between "Xushu 32" and "Xushu 22" under salt stress. The target genes of the miRNAs were predicted and identified using the Target Finder tool and degradome sequencing. The results showed that most of the targets were transcription factors and proteins related to metabolism and stress response. Gene Ontology analysis revealed that these target genes are involved in key pathways related to salt stress response and secondary redox metabolism. The comparative analysis of salt-responsive miRNAs in sweetpotato cultivars with different salt sensitivity is helpful for understanding the regulatory pattern of miRNA in different sweetpotato genotypes and improving the agronomic traits of sweetpotato by miRNA manipulation in the future.
Collapse
Affiliation(s)
- Zhengmei Yang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Applied Biology, Chonnam National University, Gwangju, South Korea
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xibin Dai
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, China
| | - Yiliang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yujie Fang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Mingku Zhu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Ghazala Nawaz
- Department of Botanical and Environmental Sciences, Kohat University of Science and Technology, Kohat, Pakistan
| | - Qinghe Cao
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, China
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| |
Collapse
|
17
|
Zhang R, Li M, Tang C, Jiang B, Yao Z, Mo X, Wang Z. Combining Metabolomics and Transcriptomics to Reveal the Mechanism of Coloration in Purple and Cream Mutant of Sweet Potato ( Ipomoea batatas L.). FRONTIERS IN PLANT SCIENCE 2022; 13:877695. [PMID: 35599902 PMCID: PMC9116297 DOI: 10.3389/fpls.2022.877695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/24/2022] [Indexed: 05/27/2023]
Abstract
Purple sweet potato is considered as a healthy food because of its high anthocyanins. To understand the coloring mechanism and quality change between purple-fleshed sweet potato (cv. Xuzi201) and its cream fleshed mutant (M1001), a combined metabolomic and transcriptomic analysis was performed. The metabolome data showed that 4 anthocyanins, 19 flavones, 6 flavanones, and 4 flavonols dramatically decreased in M1001, while the contents of 3 isoflavones, 3 flavonols, 4 catechins, and 2 proanthocyanins increased. Transcriptomic analyses indicated that the expression of 49 structural genes in the flavonoid pathway and transcription factors (TFs) (e.g., bHLH2, R2R3-MYB, MYB1) inducting anthocyanin biosynthesis were downregulated, but the repressor MYB44 was upregulated. The IbMYB1-2 gene was detected as a mutation gene in M1001, which is responsible for anthocyanin accumulation in the storage roots. Thus, the deficiency of purple color in the mutant is due to the lack of anthocyanin accumulation which was regulated by IbMYB1. Moreover, the accumulation of starch and aromatic volatiles was significantly different between Xuzi201 and M1001. These results not only revealed the mechanism of color mutation but also uncovered certain health-promoting compounds in sweet potato.
Collapse
Affiliation(s)
- Rong Zhang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Ming Li
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Chaochen Tang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Bingzhi Jiang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Zhufang Yao
- Crops Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Xueying Mo
- Crops Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Zhangying Wang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| |
Collapse
|
18
|
Yang Y, Zhang X, Zou H, Chen J, Wang Z, Luo Z, Yao Z, Fang B, Huang L. Exploration of molecular mechanism of intraspecific cross-incompatibility in sweetpotato by transcriptome and metabolome analysis. PLANT MOLECULAR BIOLOGY 2022; 109:115-133. [PMID: 35338442 PMCID: PMC9072463 DOI: 10.1007/s11103-022-01259-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Cross-incompatibility, frequently happening in intraspecific varieties, has seriously restricted sweetpotato breeding. However, the mechanism of sweetpotato intraspecific cross-incompatibility (ICI) remains largely unexplored, especially for molecular mechanism. Treatment by inducible reagent developed by our lab provides a method to generate material for mechanism study, which could promote incompatible pollen germination and tube growth in the ICI group. Based on the differential phenotypes between treated and untreated samples, transcriptome and metabolome were employed to explore the molecular mechanism of sweetpotato ICI in this study, taking varieties 'Guangshu 146' and 'Shangshu 19', a typical incompatible combination, as materials. The results from transcriptome analysis showed oxidation-reduction, cell wall metabolism, plant-pathogen interaction, and plant hormone signal transduction were the essential pathways for sweetpotato ICI regulation. The differentially expressed genes (DEGs) enriched in these pathways were the important candidate genes to response ICI. Metabolome analysis showed that multiple differential metabolites (DMs) involved oxidation-reduction were identified. The most significant DM identified in comparison between compatible and incompatible samples was vitexin-2-O-glucoside, a flavonoid metabolite. Corresponding to it, cytochrome P450s were the most DEGs identified in oxidation-reduction, which were implicated in flavonoid biosynthesis. It further suggested oxidation-reduction play an important role in sweetpotato ICI regulation. To validate function of oxidation-reduction, reactive oxygen species (ROS) was detected in compatible and incompatible samples. The green fluorescence was observed in incompatible but not in compatible samples. It indicated ROS regulated by oxidation-reduction is important pathway to response sweetpotato ICI. The results in this study would provide valuable insights into molecular mechanisms for sweetpotato ICI.
Collapse
Affiliation(s)
- Yiling Yang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiongjian Zhang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Hongda Zou
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jingyi Chen
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zhangying Wang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zhongxia Luo
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zhufang Yao
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Boping Fang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lifei Huang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| |
Collapse
|
19
|
He F, Wang W, Rutter WB, Jordan KW, Ren J, Taagen E, DeWitt N, Sehgal D, Sukumaran S, Dreisigacker S, Reynolds M, Halder J, Sehgal SK, Liu S, Chen J, Fritz A, Cook J, Brown-Guedira G, Pumphrey M, Carter A, Sorrells M, Dubcovsky J, Hayden MJ, Akhunova A, Morrell PL, Szabo L, Rouse M, Akhunov E. Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat. Nat Commun 2022; 13:826. [PMID: 35149708 PMCID: PMC8837796 DOI: 10.1038/s41467-022-28453-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 01/26/2022] [Indexed: 12/23/2022] Open
Abstract
Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluate their effects on the population-scale variation in homoeolog expression dosage. The relative contribution of cis- and trans-eQTL to homoeolog expression variation is strongly affected by both selection and demographic events. Though trans-acting effects play major role in expression regulation, the expression dosage of homoeologs is largely influenced by cis-acting variants, which appear to be subjected to selection. The frequency and expression of homoeologous gene alleles showing strong expression dosage bias are predictive of variation in yield-related traits, and have likely been impacted by breeding for increased productivity. Our study highlights the importance of genomic variants affecting homoeolog expression dosage in shaping agronomic phenotypes and points at their potential utility for improving yield in polyploid crops.
Collapse
Affiliation(s)
- Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Wheat Genetic Resources Center, Kansas State University, Manhattan, KS, USA
| | - William B Rutter
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,USDA-ARS, U.S. Vegetable Laboratory, Charleston, SC, USA
| | - Katherine W Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Ellie Taagen
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Noah DeWitt
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA.,USDA-ARS SAA, Plant Science Research, Raleigh, NC, USA
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | | | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jyotirmoy Halder
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Sunish Kumar Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Shuyu Liu
- Texas A&M AgriLife Research, Amarillo, TX, USA
| | - Jianli Chen
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, USA
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Jason Cook
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Gina Brown-Guedira
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA.,USDA-ARS SAA, Plant Science Research, Raleigh, NC, USA
| | - Mike Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Arron Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Mark Sorrells
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Matthew J Hayden
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Les Szabo
- USDA-ARS Cereal Disease Lab, St. Paul, MN, USA
| | | | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA. .,Wheat Genetic Resources Center, Kansas State University, Manhattan, KS, USA.
| |
Collapse
|
20
|
Liu Z, Yang B, Huang R, Suo H, Zhang Z, Chen W, Dai X, Zou X, Ou L. Transcriptome- and proteome-wide Association of Real Isogenic Line Populations Identified Twelve Core QTLs for four fruit traits in pepper (Capsicum annuum L.). HORTICULTURE RESEARCH 2022; 9:uhac015. [PMID: 35147182 PMCID: PMC9016867 DOI: 10.1093/hr/uhac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Zhoubin Liu
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Bozhi Yang
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Renyan Huang
- Plant Protection Institute of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Huan Suo
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Zhuqing Zhang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha, 410125, China
| | - Wenchao Chen
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha, 410125, China
| | - Xiongze Dai
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Xuexiao Zou
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Lijun Ou
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| |
Collapse
|
21
|
Yan H, Ma M, Ahmad MQ, Arisha MH, Tang W, Li C, Zhang Y, Kou M, Wang X, Gao R, Song W, Li Z, Li Q. High-Density Single Nucleotide Polymorphisms Genetic Map Construction and Quantitative Trait Locus Mapping of Color-Related Traits of Purple Sweet Potato [ Ipomoea batatas (L.) Lam.]. FRONTIERS IN PLANT SCIENCE 2022; 12:797041. [PMID: 35069654 PMCID: PMC8770336 DOI: 10.3389/fpls.2021.797041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Flesh color (FC), skin color (SC), and anthocyanin content (AC) are three important traits being used for commodity evaluation in purple-fleshed sweet potato. However, to date, only a few reports are available on the inheritance of these traits. In this study, we used a biparental mapping population of 274 F1 progeny generated from a cross between a dark purple-fleshed (Xuzishu8) and white-fleshed (Meiguohong) sweet potato variety for genetic analyses. Correlation analysis showed a significant positive correlation among AC, SC, and FC. Medium-to-high heritability was observed for these traits. We detected single nucleotide polymorphisms (SNPs) by specific length amplified fragment sequencing (SLAF-seq) with the average sequencing depth of 51.72 and 25.76 for parents and progeny, respectively. Then we constructed an integrated genetic map consisting of 15 linkage groups (LGS) of sweet potato spanning on 2,233.66 cm with an average map distance of 0.71 cm between adjacent markers. Based on the linkage map, ten major quantitative trait loci (QTLs) associated to FC, SC, and AC were identified on LG12 between 0 and 64.97 cm distance, such as one QTL for SC and FC, respectively, which explained 36.3 and 45.9% of phenotypic variation; eight QTLs for AC, which explained 10.5-28.5% of the variation. These major QTLs were highly consistent and co-localized on LG12. Positive correlation, high heritability, and co-localization of QTLs on the same LG group confirm the significance of this study to establish a marker-assisted breeding program for sweet potato improvement.
Collapse
Affiliation(s)
- Hui Yan
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Meng Ma
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Mohamed Hamed Arisha
- Department of Horticulture, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Wei Tang
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Chen Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yungang Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Meng Kou
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Xin Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Runfei Gao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Weihan Song
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Zongyun Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Qiang Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| |
Collapse
|
22
|
Cai S, Shen Q, Huang Y, Han Z, Wu D, Chen Z, Nevo E, Zhang G. Multi-Omics Analysis Reveals the Mechanism Underlying the Edaphic Adaptation in Wild Barley at Evolution Slope (Tabigha). ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101374. [PMID: 34390227 PMCID: PMC8529432 DOI: 10.1002/advs.202101374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 06/27/2021] [Indexed: 06/13/2023]
Abstract
At the microsite "Evolution Slope", Tabigha, Israel, wild barley (Hordeum spontaneum) populations adapted to dry Terra Rossa soil, and its derivative abutting wild barley population adapted to moist and fungi-rich Basalt soil. However, the mechanisms underlying the edaphic adaptation remain elusive. Accordingly, whole genome bisulfite sequencing, RNA-sequencing, and metabolome analysis are performed on ten wild barley accessions inhabiting Terra Rossa and Basalt soil. A total of 121 433 differentially methylated regions (DMRs) and 10 478 DMR-genes are identified between the two wild barley populations. DMR-genes in CG context (CG-DMR-genes) are enriched in the pathways related with the fundamental processes, and DMR-genes in CHH context (CHH-DMR-genes) are mainly associated with defense response. Transcriptome and metabolome analysis reveal that the primary and secondary metabolisms are more active in Terra Rossa and Basalt wild barley populations, respectively. Multi-omics analysis indicate that sugar metabolism facilitates the adaptation of wild barley to dry Terra Rossa soil, whereas the enhancement of phenylpropanoid/phenolamide biosynthesis is beneficial for wild barley to inhabit moist and fungi pathogen-rich Basalt soil. The current results make a deep insight into edaphic adaptation of wild barley and provide elite genetic and epigenetic resources for developing barley with high abiotic stress tolerance.
Collapse
Affiliation(s)
- Shengguan Cai
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Qiufang Shen
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Yuqing Huang
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- Institute of Crop ScienceHangzhou Academy of Agricultural SciencesHangzhou310024China
| | - Zhigang Han
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Dezhi Wu
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Zhong‐Hua Chen
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaMount CarmelHaifa34988384Israel
| | - Guoping Zhang
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| |
Collapse
|
23
|
Miculan M, Nelissen H, Ben Hassen M, Marroni F, Inzé D, Pè ME, Dell’Acqua M. A forward genetics approach integrating genome-wide association study and expression quantitative trait locus mapping to dissect leaf development in maize (Zea mays). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1056-1071. [PMID: 34087008 PMCID: PMC8519057 DOI: 10.1111/tpj.15364] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/31/2021] [Indexed: 05/13/2023]
Abstract
The characterization of the genetic basis of maize (Zea mays) leaf development may support breeding efforts to obtain plants with higher vigor and productivity. In this study, a mapping panel of 197 biparental and multiparental maize recombinant inbred lines (RILs) was analyzed for multiple leaf traits at the seedling stage. RNA sequencing was used to estimate the transcription levels of 29 573 gene models in RILs and to derive 373 769 single nucleotide polymorphisms (SNPs), and a forward genetics approach combining these data was used to pinpoint candidate genes involved in leaf development. First, leaf traits were correlated with gene expression levels to identify transcript-trait correlations. Then, leaf traits were associated with SNPs in a genome-wide association (GWA) study. An expression quantitative trait locus mapping approach was followed to associate SNPs with gene expression levels, prioritizing candidate genes identified based on transcript-trait correlations and GWAs. Finally, a network analysis was conducted to cluster all transcripts in 38 co-expression modules. By integrating forward genetics approaches, we identified 25 candidate genes highly enriched for specific functional categories, providing evidence supporting the role of vacuolar proton pumps, cell wall effectors, and vesicular traffic controllers in leaf growth. These results tackle the complexity of leaf trait determination and may support precision breeding in maize.
Collapse
Affiliation(s)
- Mara Miculan
- Institute of Life SciencesScuola Superiore Sant’AnnaPisa56127Italy
| | - Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Manel Ben Hassen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Fabio Marroni
- IGA Technology ServicesUdine33100Italy
- Department of Agricultural, FoodAT, Environmental and Animal Sciences (DI4A)University of UdineUdine33100Italy
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Mario Enrico Pè
- Institute of Life SciencesScuola Superiore Sant’AnnaPisa56127Italy
| | | |
Collapse
|
24
|
Zhang G, Cui X, Niu J, Ma F, Li P. Visible light regulates anthocyanin synthesis via malate dehydrogenases and the ethylene signaling pathway in plum (Prunus salicina L.). PHYSIOLOGIA PLANTARUM 2021; 172:1739-1749. [PMID: 33665852 DOI: 10.1111/ppl.13383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/09/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Light regulates anthocyanins synthesis in plants. Upon exposure to visible light, the inhibition of photosynthetic electron transfer significantly lowered the contents of anthocyanins and the expression levels of key genes involved in anthocyanins synthesis in plum fruit peel. Meanwhile, the expression levels of PsmMDH2 (encoding the malate dehydrogenase in mitochondria) and PschMDH (encoding the malate dehydrogenase in chloroplasts) decreased significantly. The contents of anthocyanins and the levels of the key genes involved in anthocyanin synthesis decreased significantly with the treatment of 1-MCP (an inhibitor of ethylene perception) but were enhanced by the exogenous application of ethylene. The ethylene treatment could also recover the anthocyanin synthesis capacity lowered by the photosynthetic electron transfer inhibition. Silencing PsmMDH2 and PschMDH significantly lowered the contents of anthocyanins in plum fruit. At low temperature, visible light irradiation induced anthocyanin accumulation in Arabidopsis leaves. However, the mmdh, chmdh, and etr1-1 mutants had significantly lower anthocyanins content and expressions of the key genes involved in anthocyanins synthesis compared to wild type. Overall, the present study demonstrates that both photosynthesis and respiration were involved in the regulation of anthocyanin synthesis in visible light. The visible light regulates anthocyanin synthesis by controlling the malate metabolism via MDHs and the ethylene signaling pathway.
Collapse
Affiliation(s)
- Guojing Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Xiaohui Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Junping Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Pengmin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| |
Collapse
|
25
|
Xiao S, Xu P, Deng Y, Dai X, Zhao L, Heider B, Zhang A, Zhou Z, Cao Q. Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam). BMC Genomics 2021; 22:262. [PMID: 33849443 PMCID: PMC8042981 DOI: 10.1186/s12864-021-07544-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 03/22/2021] [Indexed: 02/08/2023] Open
Abstract
Background Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato. Results The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages. Conclusions Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07544-y.
Collapse
Affiliation(s)
- Shizhuo Xiao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Pan Xu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yitong Deng
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Xibin Dai
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Lukuan Zhao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Bettina Heider
- International Potato Center, Av.La Molina 1895, La Molina, Lima, Peru
| | - An Zhang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Zhilin Zhou
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China
| | - Qinghe Cao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China.
| |
Collapse
|
26
|
Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant. Genes (Basel) 2021; 12:genes12030341. [PMID: 33668977 PMCID: PMC7996550 DOI: 10.3390/genes12030341] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/12/2021] [Accepted: 02/23/2021] [Indexed: 12/02/2022] Open
Abstract
Eggplant is one of the most important vegetables worldwide. Prickles on the leaves, stems and fruit calyxes of eggplant may cause difficulties during cultivation, harvesting and transportation, and therefore is an undesirable agronomic trait. However, limited knowledge about molecular mechanisms of prickle morphogenesis has hindered the genetic improvement of eggplant. In this study, we performed the phenotypic characterization and transcriptome analysis on prickly and prickleless eggplant genotypes to understand prickle development at the morphological and molecular levels. Morphological analysis revealed that eggplant prickles were multicellular, lignified and layered organs. Comparative transcriptome analysis identified key pathways and hub genes involved in the cell cycle as well as flavonoid biosynthetic, photosynthetic, and hormone metabolic processes during prickle development. Interestingly, genes associated with flavonoid biosynthesis were up-regulated in developing prickles, and genes associated with photosynthesis were down-regulated in developing and matured prickles. It was also noteworthy that several development-related transcription factors such as bHLH, C2H2, MYB, TCP and WRKY were specifically down- or up-regulated in developing prickles. Furthermore, four genes were found to be differentially expressed within the Pl locus interval. This study provides new insights into the regulatory molecular mechanisms underlying prickle morphogenesis in eggplant, and the genes identified might be exploited in breeding programs to develop prickleless eggplant cultivars.
Collapse
|
27
|
Zhang D, Tan Y, Dong F, Zhang Y, Huang Y, Zhou Y, Zhao Z, Yin Q, Xie X, Gao X, Zhang C, Tu N. The Expression of IbMYB1 Is Essential to Maintain the Purple Color of Leaf and Storage Root in Sweet Potato [ Ipomoea batatas (L.) Lam]. FRONTIERS IN PLANT SCIENCE 2021; 12:688707. [PMID: 34630449 PMCID: PMC8495246 DOI: 10.3389/fpls.2021.688707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/16/2021] [Indexed: 05/14/2023]
Abstract
IbMYB1 was one of the major anthocyanin biosynthesis regulatory genes that has been identified and utilized in purple-fleshed sweet potato breeding. At least three members of this gene, namely, IbMYB1-1, -2a, and -2b, have been reported. We found that IbMYB1-2a and -2b are not necessary for anthocyanin accumulation in a variety of cultivated species (hexaploid) with purple shoots or purplish rings/spots of flesh. Transcriptomic and quantitative reverse transcription PCR (RT-qPCR) analyses revealed that persistent and vigorous expression of IbMYB1 is essential to maintain the purple color of leaves and storage roots in this type of cultivated species, which did not contain IbMYB1-2 gene members. Compared with IbbHLH2, IbMYB1 is an early response gene of anthocyanin biosynthesis in sweet potato. It cannot exclude the possibility that other MYBs participate in this gene regulation networks. Twenty-two MYB-like genes were identified from 156 MYBs to be highly positively or negatively correlated with the anthocyanin content in leaves or flesh. Even so, the IbMYB1 was most coordinately expressed with anthocyanin biosynthesis genes. Differences in flanking and coding sequences confirm that IbMYB2s, the highest similarity genes of IbMYB1, are not the members of IbMYB1. This phenomenon indicates that there may be more members of IbMYB1 in sweet potato, and the genetic complementation of these members is involved in the regulation of anthocyanin biosynthesis. The 3' flanking sequence of IbMYB1-1 is homologous to the retrotransposon sequence of TNT1-94. Transposon movement is involved in the formation of multiple members of IbMYB1. This study provides critical insights into the expression patterns of IbMYB1, which are involved in the regulation of anthocyanin biosynthesis in the leaf and storage root. Notably, our study also emphasized the presence of a multiple member of IbMYB1 for genetic improvement.
Collapse
Affiliation(s)
- Daowei Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- *Correspondence: Daowei Zhang,
| | - Yongjun Tan
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Fang Dong
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Ya Zhang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yanlan Huang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yizhou Zhou
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - ZhiJian Zhao
- Dryland Crop Research Institute, Shao Yang Academy of Agriculture Science, Shaoyang, China
| | - Qin Yin
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xuehua Xie
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiewang Gao
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Chaofan Zhang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Chaofan Zhang,
| | - Naimei Tu
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Naimei Tu,
| |
Collapse
|
28
|
Sun H, Mei J, Zhao W, Hou W, Zhang Y, Xu T, Wu S, Zhang L. Phylogenetic Analysis of the SQUAMOSA Promoter-Binding Protein-Like Genes in Four Ipomoea Species and Expression Profiling of the IbSPLs During Storage Root Development in Sweet Potato ( Ipomoea batatas). FRONTIERS IN PLANT SCIENCE 2021; 12:801061. [PMID: 35126426 PMCID: PMC8815303 DOI: 10.3389/fpls.2021.801061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/17/2021] [Indexed: 05/11/2023]
Abstract
As a major plant-specific transcription factor family, SPL genes play a crucial role in plant growth, development, and stress tolerance. The SPL transcription factor family has been widely studied in various plant species; however, systematic studies on SPL genes in the genus Ipomoea are lacking. Here, we identified a total of 29, 27, 26, and 23 SPLs in Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, and Ipomoea nil, respectively. Based on the phylogenetic analysis of SPL proteins from model plants, the Ipomoea SPLs were classified into eight clades, which included conserved gene structures, domain organizations and motif compositions. Moreover, segmental duplication, which is derived from the Ipomoea lineage-specific whole-genome triplication event, was speculated to have a predominant role in Ipomoea SPL expansion. Particularly, tandem duplication was primarily responsible for the expansion of SPL subclades IV-b and IV-c. Furthermore, 25 interspecific orthologous groups were identified in Ipomoea, rice, Arabidopsis, and tomato. These findings support the expansion of SPLs in Ipomoea genus, with most of the SPLs being evolutionarily conserved. Of the 105 Ipomoea SPLs, 69 were predicted to be the targets of miR156, with seven IbSPLs being further verified as targets using degradome-seq data. Using transcriptomic data from aboveground and underground sweet potato tissues, IbSPLs showed diverse expression patterns, including seven highly expressed IbSPLs in the underground tissues. Furthermore, the expression of 11 IbSPLs was validated using qRT-PCR, and two (IbSPL17/IbSPL28) showed significantly increased expression during root development. Additionally, the qRT-PCR analysis revealed that six IbSPLs were strongly induced in the roots under phytohormone treatments, particularly zeatin and abscisic acid. Finally, the transcriptomic data of storage roots from 88 sweet potato accessions were used for weighted gene co-expression network analysis, which revealed four IbSPLs (IbSPL16/IbSPL17/IbSPL21/IbSPL28) clusters with genes involved in "regulation of root morphogenesis," "cell division," "cytoskeleton organization," and "plant-type cell wall organization or biogenesis," indicating their potential role in storage root development. This study not only provides novel insights into the evolutionary and functional divergence of the SPLs in the genus Ipomoea but also lays a foundation for further elucidation of the potential functional roles of IbSPLs on storage root development.
Collapse
Affiliation(s)
- Haoyun Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingzhao Mei
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Weiwei Zhao
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Wenqian Hou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yang Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Tao Xu,
| | - Shaoyuan Wu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Shaoyuan Wu,
| | - Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Lei Zhang,
| |
Collapse
|
29
|
An Y, Chen L, Tao L, Liu S, Wei C. QTL Mapping for Leaf Area of Tea Plants ( Camellia sinensis) Based on a High-Quality Genetic Map Constructed by Whole Genome Resequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:705285. [PMID: 34394160 PMCID: PMC8358608 DOI: 10.3389/fpls.2021.705285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/07/2021] [Indexed: 05/08/2023]
Abstract
High-quality genetic maps play important roles in QTL mapping and molecular marker-assisted breeding. Tea leaves are not only important vegetative organs but are also the organ for harvest with important economic value. However, the key genes and genetic mechanism of regulating leaf area have not been clarified. In this study, we performed whole-genome resequencing on "Jinxuan," "Yuncha 1" and their 96 F1 hybrid offspring. From the 1.84 Tb of original sequencing data, abundant genetic variation loci were identified, including 28,144,625 SNPs and 2,780,380 indels. By integrating the markers of a previously reported genetic map, a high-density genetic map consisting of 15 linkage groups including 8,956 high-quality SNPs was constructed. The total length of the genetic map is 1,490.81 cM, which shows good collinearity with the genome. A total of 25 representative markers (potential QTLs) related to leaf area were identified, and there were genes differentially expressed in large and small leaf samples near these markers. GWAS analysis further verified the reliability of QTL mapping. Thirty-one pairs of newly developed indel markers located near these potential QTLs showed high polymorphism and had good discrimination between large and small leaf tea plant samples. Our research will provide necessary support and new insights for tea plant genetic breeding, quantitative trait mapping and yield improvement.
Collapse
Affiliation(s)
- Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Linbo Chen
- Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, China
| | - Lingling Tao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- *Correspondence: Chaoling Wei,
| |
Collapse
|