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Jiang G, Li Z, Ding X, Zhou Y, Lai H, Jiang Y, Duan X. WUSCHEL-related homeobox transcription factor SlWOX13 regulates tomato fruit ripening. PLANT PHYSIOLOGY 2024; 194:2322-2337. [PMID: 37995308 DOI: 10.1093/plphys/kiad623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023]
Abstract
Fruit ripening is a complex, genetically programmed process involving the action of critical transcription factors (TFs). Despite the established importance of WUSCHEL-related homeobox (WOX) TFs in plant development, the involvement of WOX and its underlying mechanism in the regulation of fruit ripening remain unclear. Here, we demonstrate that SlWOX13 regulates fruit ripening in tomato (Solanum lycopersicum). Overexpression of SlWOX13 accelerates fruit ripening, whereas loss-of-function mutation in SlWOX13 delays this process. Moreover, ethylene synthesis and carotenoid accumulation are significantly inhibited in slwox13 mutant fruit but accelerated in SlWOX13 transgenic fruit. Integrated analyses of RNA-seq and chromatin immunoprecipitation (ChIP)-seq identified 422 direct targets of SlWOX13, of which 243 genes are negatively regulated and 179 are positively regulated by SlWOX13. Electrophoretic mobility shift assay, RT-qPCR, dual-luciferase reporter assay, and ChIP-qPCR analyses demonstrated that SlWOX13 directly activates the expression of several genes involved in ethylene synthesis and signaling and carotenoid biosynthesis. Furthermore, SlWOX13 modulates tomato fruit ripening through key ripening-related TFs, such as RIPENING INHIBITOR (RIN), NON-RIPENING (NOR), and NAM, ATAF1, 2, and CUC2 4 (NAC4). Consequently, these effects promote fruit ripening. Taken together, these results demonstrate that SlWOX13 positively regulates tomato fruit ripening via both ethylene synthesis and signaling and by transcriptional regulation of key ripening-related TFs.
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Affiliation(s)
- Guoxiang Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiwei Li
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaochun Ding
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Yijie Zhou
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Hongmei Lai
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yueming Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuewu Duan
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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González AM, Lebrón R, Yuste-Lisbona FJ, Gómez-Martín C, Ortiz-Atienza A, Hackenberg M, Oliver JL, Lozano R, Santalla M. Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean. Int J Mol Sci 2022; 23:ijms232314783. [PMID: 36499112 PMCID: PMC9739310 DOI: 10.3390/ijms232314783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding to the vegetative and inflorescence meristems of two genotypes with different sensitivities to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and 1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting an evolutionary divergence of the transcriptional regulatory networks of the flowering process of both species. However, some genes belonging to the photoperiod and flower development pathways with evolutionarily conserved transcriptional profiles have been found. In addition, the flower meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as markers to distinguish between the vegetative and reproductive stages. Our data also indicated that the down-regulation of the photoperiodic genes seems to be directly associated with promoting floral transition under inductive short-day lengths. These findings provide valuable insight into the molecular factors that underlie meristematic development and contribute to understanding the photoperiod adaptation in the common bean.
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Affiliation(s)
- Ana M. González
- Genética del Desarrollo de Plantas, Misión Biológica de Galicia-CSIC, P.O. Box 28, 36080 Pontevedra, Spain
| | - Ricardo Lebrón
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Fernando J. Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Cristina Gómez-Martín
- Departamento de Genética, Facultad de Ciencias & Laboratorio de Bioinformática, Centro de Investigación Biomédica, Universidad de Granada, 18071 Granada, Spain
| | - Ana Ortiz-Atienza
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Michael Hackenberg
- Departamento de Genética, Facultad de Ciencias & Laboratorio de Bioinformática, Centro de Investigación Biomédica, Universidad de Granada, 18071 Granada, Spain
| | - José L. Oliver
- Departamento de Genética, Facultad de Ciencias & Laboratorio de Bioinformática, Centro de Investigación Biomédica, Universidad de Granada, 18071 Granada, Spain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Marta Santalla
- Genética del Desarrollo de Plantas, Misión Biológica de Galicia-CSIC, P.O. Box 28, 36080 Pontevedra, Spain
- Correspondence: ; Tel.: +34-986-596134; Fax: +34-986-851362
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Tanaka Y, Yokota M, Goto N, Goto T, Yoshida Y, Yasuba KI, Ohno S, Doi M. Morphological and gene expression characterization of maf-1, a floral chili pepper mutant caused by a nonsense mutation in CaLFY. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:32. [PMID: 37313508 PMCID: PMC10248606 DOI: 10.1007/s11032-022-01304-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Chili peppers are important as vegetables and ornamental crops, because of the variety of fruit shapes and colors. Understanding of flower and fruit development in Capsicum is limited compared with closely related Solanaceae crops such as tomato. This study reports a novel malformed fruit mutant named malformed fruit-1 (maf-1), which was isolated from an ethyl methanesulfonate-induced mutant population of chili pepper. maf-1 exhibited homeotic changes in the floral bud, which were characterized by conversion of petals and stamens into sepal-like and carpel-like organs, respectively. In addition, the indeterminate formation of carpel-like tissue was observed. Genetic analysis demonstrated that the causative gene in maf-1 is a nonsense mutation in CaLFY. This is the first characterization of an lfy mutant in Capsicum. Unlike tomatoes, the CaLFY mutation did not affect the architecture of sympodial unit or flowering time but mainly affected the formation of flower organs. Gene expression analysis suggested that a nonsense mutation in CaLFY led to decreased expression of multiple class B genes, resulting in homeotic changes in the flower and fruit. This maf-1 mutant may provide new insights at the molecular level in understanding flower organ formation and the genetic manipulation of fruit shape in chili peppers. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01304-w.
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Affiliation(s)
- Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho Sakyo-ku, Kyoto, 606-8502 Japan
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Mizuki Yokota
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho Sakyo-ku, Kyoto, 606-8502 Japan
| | - Naoto Goto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Tanjuro Goto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Yuichi Yoshida
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Ken-ichiro Yasuba
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Sho Ohno
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho Sakyo-ku, Kyoto, 606-8502 Japan
| | - Motoaki Doi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho Sakyo-ku, Kyoto, 606-8502 Japan
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Kim Y, Kim GW, Han K, Lee HY, Jo J, Kwon JK, Lemmon Z, Lippman Z, Kang BC. Identification of Genetic Factors Controlling the Formation of Multiple Flowers Per Node in Pepper ( Capsicum spp.). FRONTIERS IN PLANT SCIENCE 2022; 13:884338. [PMID: 35615119 PMCID: PMC9125326 DOI: 10.3389/fpls.2022.884338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Flower production provides the foundation for crop yield and increased profits. Capsicum annuum is a pepper species with a sympodial shoot structure with solitary flowers. By contrast, C. chinense produces multiple flowers per node. C. annuum accounts for 80% of pepper production worldwide. The identification of C. chinense genes that control multiple flowers and their transfer into C. annuum may open the way to increasing fruit yield. In this study, we dissected the genetic factors were dissected controlling the multiple-flower-per-node trait in Capsicum. 85 recombinant inbred lines (RILs) between the contrasting C. annuum 'TF68' and C. chinense 'Habanero' accessions were phenotyped and genotyped. Quantitative Trait Loci (QTL) analysis identified four novel QTLs on chromosomes 1, 2, 7, and 11 that accounted for 65% of the total phenotypic variation. Genome-wide association study was also performed on a panel of 276 genotyped and phenotyped C. annuum accessions, which revealed 28 regions significantly associated with the multiple-flower trait, of which three overlapped the identified QTLs. Five candidate genes involved in the development of the shoot and flower meristems were identified and these genes could cause multiple flowers per node in pepper. These results contribute to our understanding of multiple flower formation in Capsicum and will be useful to develop high-yielding cultivars.
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Affiliation(s)
- Youngin Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Geon Woo Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Hea-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jinkwan Jo
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | | | - Zachary Lippman
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York, NY, United States
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Yuan X, Fang R, Zhou K, Huang Y, Lei G, Wang X, Chen X. The APETALA2 homolog CaFFN regulates flowering time in pepper. HORTICULTURE RESEARCH 2021; 8:208. [PMID: 34719686 PMCID: PMC8558333 DOI: 10.1038/s41438-021-00643-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Flowering time is an important agronomic trait that contributes to fitness in plants. However, the genetic basis of flowering time has not been extensively studied in pepper. To understand the genetics underlying flowering time, we constructed an F2 population by crossing a spontaneous early flowering mutant and a late-flowering pepper line. Using bulked segregant RNA-seq, a major locus controlling flowering time in this population was mapped to the end of chromosome 2. An APETALA2 (AP2) homolog (CaFFN) cosegregated with flowering time in 297 individuals of the F2 population. A comparison between the parents revealed a naturally occurring rare SNP (SNP2T > C) that resulted in the loss of a start codon in CaFFN in the early flowering mutant. Transgenic Nicotiana benthamiana plants with high CaFFN expression exhibited a delay in flowering time and floral patterning defects. On the other hand, pepper plants with CaFFN silencing flowered early. Therefore, the CaFFN gene acts as a flowering repressor in pepper. CaFFN may function as a transcriptional activator to activate the expression of CaAGL15 and miR156e and as a transcriptional repressor to repress the expression of CaAG, CaAP1, CaSEP3, CaSOC1, and miR172b based on a qRT-PCR assay. Direct activation of CaAGL15 by CaFFN was detected using yeast one-hybrid and dual-luciferase reporter assays, consistent with the hypothesis that CaFFN regulates flowering time. Moreover, the CaFFN gene association analysis revealed a significant association with flowering time in a natural pepper population, indicating that the CaFFN gene has a broad effect on flowering time in pepper. Finally, the phylogeny, evolutionary expansion and expression patterns of CaFFN/AP2 homologs were analyzed to provide valuable insight into CaFFN. This study increases our understanding of the involvement of CaFFN in controlling flowering time in pepper, thus making CaFFN a target gene for breeding early maturing pepper.
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Affiliation(s)
- Xinjie Yuan
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Rong Fang
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Kunhua Zhou
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Yueqin Huang
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Gang Lei
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Xuejun Chen
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China.
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Tvorogova VE, Krasnoperova EY, Potsenkovskaia EA, Kudriashov AA, Dodueva IE, Lutova LA. What Does the WOX Say? Review of Regulators, Targets, Partners. Mol Biol 2021. [DOI: 10.1134/s002689332102031x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Hendelman A, Zebell S, Rodriguez-Leal D, Dukler N, Robitaille G, Wu X, Kostyun J, Tal L, Wang P, Bartlett ME, Eshed Y, Efroni I, Lippman ZB. Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection. Cell 2021; 184:1724-1739.e16. [PMID: 33667348 DOI: 10.1016/j.cell.2021.02.001] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/03/2021] [Accepted: 02/01/2021] [Indexed: 01/09/2023]
Abstract
Divergence of gene function is a hallmark of evolution, but assessing functional divergence over deep time is not trivial. The few alleles available for cross-species studies often fail to expose the entire functional spectrum of genes, potentially obscuring deeply conserved pleiotropic roles. Here, we explore the functional divergence of WUSCHEL HOMEOBOX9 (WOX9), suggested to have species-specific roles in embryo and inflorescence development. Using a cis-regulatory editing drive system, we generate a comprehensive allelic series in tomato, which revealed hidden pleiotropic roles for WOX9. Analysis of accessible chromatin and conserved cis-regulatory sequences identifies the regions responsible for this pleiotropic activity, the functions of which are conserved in groundcherry, a tomato relative. Mimicking these alleles in Arabidopsis, distantly related to tomato and groundcherry, reveals new inflorescence phenotypes, exposing a deeply conserved pleiotropy. We suggest that targeted cis-regulatory mutations can uncover conserved gene functions and reduce undesirable effects in crop improvement.
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Affiliation(s)
- Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Sophia Zebell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Noah Dukler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gina Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xuelin Wu
- The Salk Institute for Biological Research, San Diego, CA, USA
| | - Jamie Kostyun
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - Lior Tal
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Peipei Wang
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot, Israel
| | | | - Yuval Eshed
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Idan Efroni
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot, Israel.
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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Borovsky Y, Mohan V, Shabtai S, Paran I. CaFT-LIKE is a flowering promoter in pepper and functions as florigen in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110678. [PMID: 33218641 DOI: 10.1016/j.plantsci.2020.110678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/10/2020] [Accepted: 09/13/2020] [Indexed: 06/11/2023]
Abstract
We identified a pepper late-flowering mutant that is disrupted in the sequence of CaFT-LIKE, the ortholog of tomato SINGLE FLOWER TRUSS (SFT). Heterologous expression in tomato indicated that CaFT-LIKE has a conserved function as a flowering promoter and can rescue the wild-type phenotype of the tomato sft mutant. CaFT-LIKE confers a graft-transmissible signal for flowering initiation in tomato, implicating its function as a florigen. To test the relationship between CaFT-LIKE and FASCICULATE (FA), the ortholog of tomato SELF PRUNING (SP), we constructed the double mutant Caft-like fa. The phenotype of Caft-like fa resembled that of Caft-like, indicating epistasis of Caft-like over fa in controlling flowering time and sympodial shoot structure. To examine the association between the expression pattern of flowering genes and natural variation in flowering time, the expression levels of CaFT-LIKE and the flowering repressor CaAP2 were determined in a panel of early-flowering cultivars and late-flowering landraces and wild accessions. Strong positive and negative correlations between flowering time and expression levels of CaAP2 and CaFT-LIKE, respectively, were observed, indicating that high-expression alleles of CaFT-LIKE and low-expression alleles of CaAP2 were selected for early flowering during pepper domestication and breeding.
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Affiliation(s)
- Yelena Borovsky
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Vijee Mohan
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Sara Shabtai
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Ilan Paran
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel.
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Zhang XF, Wang GY, Dong TT, Chen B, Du HS, Li CB, Zhang FL, Zhang HY, Xu Y, Wang Q, Geng SS. High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.). BMC PLANT BIOLOGY 2019; 19:167. [PMID: 31035914 PMCID: PMC6489210 DOI: 10.1186/s12870-019-1753-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/31/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.). The trait is controlled by quantitative trait loci (QTL); however, studies have been limited on QTL mapping and genes contributing to the trait. RESULTS In this study, we developed a high density genetic map using specific-locus amplified fragment sequencing (SLAF-seq), a high-throughput strategy for de novo single nucleotide polymorphism discovery, based on 146 recombinant inbred lines (RILs) derived from an intraspecific cross between PM702 and FS871. The map contained 9328 SLAF markers on 12 linkage groups (LGs), and spanned a total genetic distance of 2009.69 centimorgan (cM) with an average distance of 0.22 cM. The sequencing depth for the map was 72.39-fold in the male parent, 57.04-fold in the female parent, and 15.65-fold in offspring. Using the genetic map, two major QTLs, named Ffn2.1 and Ffn2.2, identified on LG02 were strongly associated with FFN, with a phenotypic variance explanation of 28.62 and 19.56%, respectively. On the basis of the current annotation of C. annuum cv. Criollo de Morelos (CM334), 59 candidate genes were found within the Ffn2.1 and Ffn2.2 region, but only 3 of 59 genes were differentially expressed according to the RNA-seq results. Eventually we identified one gene associated with the FFN based on the function through GO, KEGG, and Swiss-prot analysis. CONCLUSIONS Our research showed that the construction of high-density genetic map using SLAF-seq is a valuable tool for fine QTL mapping. The map we constructed is by far the most saturated complete genetic map of pepper, and using it we conducted fine QTL mapping for the important trait, FFN. QTLs and candidate genes obtained in this study lay a good foundation for the further research on FFN-related genes and other genetic applications in pepper.
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Affiliation(s)
- Xiao-fen Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
- College of Horticulture, China Agricultural University, Beijing, 100097 People’s Republic of China
| | - Guo-yun Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Ting-ting Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Bin Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - He-shan Du
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Chang-bao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Feng-lan Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Hai-ying Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Yong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Qian Wang
- College of Horticulture, China Agricultural University, Beijing, 100097 People’s Republic of China
| | - San-sheng Geng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
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Zhu Z, Sun B, Wei J, Cai W, Huang Z, Chen C, Cao B, Chen G, Lei J. Construction of a high density genetic map of an interspecific cross of Capsicum chinense and Capsicum annuum and QTL analysis of floral traits. Sci Rep 2019; 9:1054. [PMID: 30705330 PMCID: PMC6355862 DOI: 10.1038/s41598-018-38370-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/27/2018] [Indexed: 11/09/2022] Open
Abstract
The yield of pepper plants (Capsicum spp.) is their most important trait and is affected by the flower number and flowering time. Capsicum annuum produces a single flower per node and has an early flowering habit. By contrast, Capsicum chinense yields multiple flowers per node and has a late flowering character. However, the genetic mechanism underlying the control of these floral traits remains largely unknown. In this study, 150 F2 populations from an interspecific cross between the inbred lines 740 (C. chinense) and CA1 (C. annuum) and their parents were used to construct a molecular genetic linkage map using the specific length amplified fragment sequencing (SLAF-seq) technique. This linkage map, spanning 1,586.78 cM in length, contained 9,038 markers on 12 chromosomes, with a mean marker distance of 0.18 cM. Phenotypic data on the flowering time and flower number per node were collected over multiple years, and QTL analysis identified 6 QTLs for the flowering time and flower number per node by composite interval mapping (CIM) and genome-wide composite interval mapping (GCIM) methods at least in two environments. The candidate genes within the major QTL were predicted. In the major flowering time QTL, the candidate gene Capana02g000700, which encodes the homeotic protein APETALA2, was identified. Quantitative reverse-transcription PCR (qRT-PCR) analysis indicated that its expression level in 740 was higher than that in CA1. Gene expression analysis indicated that the expression of Capana02g000700 was significantly upregulated in flowers, and many floral development-related genes were found to be coexpressed with Capana02g000700, supporting the function of this gene in association with flowering time in C. chinense and C. annuum species.
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Affiliation(s)
- Zhangsheng Zhu
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Binmei Sun
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianlang Wei
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wen Cai
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhubin Huang
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Changming Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Bihao Cao
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Guoju Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
| | - Jianjun Lei
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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11
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Mohan V, Borovsky Y, Kamara I, Zemach H, Paran I. CaVIL1, a plant homeodomain gene that promotes flowering in pepper. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2639-2649. [PMID: 30194521 DOI: 10.1007/s00122-018-3179-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
CaVIL1 is a homolog of VIL1, a regulator of vernalization response in Arabidopsis and acts as a flowering promoter in pepper which does not respond to vernalization and photoperiod. As part of our goal to study the genetic and molecular basis of transition to flowering in pepper, we isolated the late-flowering mutant E-2698. Aside from late flowering, multiple pleiotropic alterations of the shoot structure, such as enlarged and distorted leaves, weak apical dominance, and reduced angle of the lateral branches were observed, indicating a broad role for the mutated gene in pepper development. Genetic mapping and sequence analyses revealed that the disrupted gene in E-2698 is the pepper homolog of VERNALIZATION INSENSITIVE 3-LIKE 1 (VIL1) that acts as a regulator of vernalization in Arabidopsis through chromatin modification. The pepper gene, CaVIL1, contains a plant homeodomain motif associated with chromatin modification and a VERNALIZATION INSENSITIVE 3-interacting domain that is truncated in E-2698 and in two other allelic mutants. Because pepper flowering does not respond to vernalization, we postulate that CaVIL1 regulates flowering time via chromatin modification of unknown targets. Expression analysis indicated that CaVIL1 activates the flowering promoter CaFLOWERING LOCUS T and represses the flowering repressor CaAPETALA2. Furthermore, CaVIL1 represses several genes from the FLOWERING LOCUS C (FLC)-LIKE clade that are clustered together in the pepper genome. This indicates their possible involvement in flowering regulation in this species. Our results show that CaVIL1 is a major regulator of flowering and interacts with other flowering promoters and repressors, as well as with FLC-LIKE genes whose function in flowering regulation is not yet known in pepper.
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Affiliation(s)
- Vijee Mohan
- Institute of Plant Science, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Yelena Borovsky
- Institute of Plant Science, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Itzhak Kamara
- Institute of Plant Science, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Hanita Zemach
- Institute of Plant Science, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Ilan Paran
- Institute of Plant Science, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel.
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12
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Schorderet M, Duvvuru Muni RR, Fiebig A, Reinhardt D. Deregulation of MADS-box transcription factor genes in a mutant defective in the WUSCHEL-LIKE HOMEOBOX gene EVERGREEN of Petunia hybrida. PLANT SIGNALING & BEHAVIOR 2018; 13:e1471299. [PMID: 29995575 PMCID: PMC6207418 DOI: 10.1080/15592324.2018.1471299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 05/14/2023]
Abstract
Angiosperm inflorescences develop in two fundamentally different ways. In monopodial plants, for example in Arabidopsis thaliana, the flowers are initiated as lateral appendages of a central indeterminate inflorescence meristem. In sympodial plants, flowers arise by terminal differentiation of the inflorescence meristem, while further inflorescence development proceeds from new sympodial meristems that are generated at the flank of the terminal flower. We have used the sympodial model species Petunia hybrida to investigate inflorescence development. Here, we describe a mutant, bonsai (bns), which is defective in flower formation, inflorescence branching, and control of meristem size. Detailed microscopic analysis revealed that bns meristems retain vegetative charateristics including spiral phyllotaxis. Consistent with a block in flower formation, bns mutants exhibit a deregulated expression of various MADS-box genes. Molecular analysis revealed that the bns mutant carries a transposon insertion in the previously described EVERGREEN (EVG) gene, which belongs to the WUSCHEL-LIKE HOMEOBOX (WOX) transcription factor gene family. EVG falls in the WOX9 subfamily, which has diverse developmental functions in angiosperms. The comparison of WOX9 orthologues in five model species for flowering shows that these genes play functionally divergent roles in monopodial and sympodial plants, indicating that the WOX9 regulatory node may have played an important role in the evolution of shoot architecture.
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Affiliation(s)
- M. Schorderet
- Dept. of Biology, University of Fribourg, Fribourg, Switzerland
| | - R. R. Duvvuru Muni
- Dept. of Biology, University of Fribourg, Fribourg, Switzerland
- Monsanto Holdings Private Limited, Mfar Manyata Tech Park, Nagavara, Bangalore, India
| | - A. Fiebig
- Research Group Bioinformatics and Information Technology, Department Breeding Research, Leibniz Institute of Plant Genetics and CropPlant Research (IPK) Gatersleben, Seeland, Germany
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13
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Zhang X, Wang G, Chen B, Du H, Zhang F, Zhang H, Wang Q, Geng S. Candidate genes for first flower node identified in pepper using combined SLAF-seq and BSA. PLoS One 2018; 13:e0194071. [PMID: 29558466 PMCID: PMC5860747 DOI: 10.1371/journal.pone.0194071] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/23/2018] [Indexed: 02/05/2023] Open
Abstract
First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.), but the genetic mechanisms that control FFN are still poorly understood. In the present study, we developed 249 F2 plants derived from an intraspecific cross between the inbred pepper lines Z4 and Z5. Thirty plants with the highest FFN and 30 plants with the lowest FFN were chosen and their DNAs were pooled according to phenotype to construct two bulked DNA pools. Specific-locus amplified fragment sequencing (SLAF-seq) was combined with bulked segregant analysis (BSA) to identify candidate regions related to FFN. According to our genetic analysis, the FFN trait is quantitatively inherited. A total of 106,848 high-quality single nucleotide polymorphism (SNP) markers were obtained, and 393 high-quality SNP markers associated with FFN were detected. Ten candidate regions within an interval of 3.98 Mb on chromosome 12 harboring 23 candidate genes were identified as closely correlated with FFN. Five genes (CA12g15130, CA12g15160, CA12g15370, CA12g15360, and CA12g15390) are predicted based on their annotations to be associated with expression of the FFN trait. The present study demonstrates an efficient genetic mapping strategy and lays a good foundation for molecular marker-assisted breeding using SNP markers linked to FFN and for cloning and functional analysis of the key genes controlling FFN.
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Affiliation(s)
- Xiaofen Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- College of Horticulture, China Agricultural University, Beijing, P.R. China
| | - Guoyun Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Bin Chen
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Heshan Du
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Fenglan Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Haiying Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Qian Wang
- College of Horticulture, China Agricultural University, Beijing, P.R. China
- * E-mail: (SG); (QW)
| | - Sansheng Geng
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- * E-mail: (SG); (QW)
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14
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Lemmon ZH, Park SJ, Jiang K, Van Eck J, Schatz MC, Lippman ZB. The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation. Genome Res 2016; 26:1676-1686. [PMID: 27821409 PMCID: PMC5131819 DOI: 10.1101/gr.207837.116] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/27/2016] [Indexed: 12/28/2022]
Abstract
One of the most remarkable manifestations of plant evolution is the diversity for floral branching systems. These “inflorescences” arise from stem cell populations in shoot meristems that mature gradually to reproductive states in response to environmental and endogenous signals. The morphology of the shoot meristem maturation process is conserved across distantly related plants, raising the question of how diverse inflorescence architectures arise from seemingly common maturation programs. In tomato and related nightshades (Solanaceae), inflorescences range from solitary flowers to highly branched structures bearing hundreds of flowers. Since reproductive barriers between even closely related Solanaceae have precluded a genetic dissection, we captured and compared meristem maturation transcriptomes from five domesticated and wild species reflecting the evolutionary continuum of inflorescence complexity. We find these divergent species share hundreds of dynamically expressed genes, enriched for transcription factors. Meristem stages are defined by distinct molecular states and point to modified maturation schedules underlying architectural variation. These modified schedules are marked by a peak of transcriptome expression divergence during the reproductive transition, driven by heterochronic shifts of dynamic genes, including transcriptional regulators with known roles in flowering. Thus, evolutionary diversity in Solanaceae inflorescence complexity is determined by subtle modifications of transcriptional programs during a critical transitional window of meristem maturation, which we propose underlies similar cases of plant architectural variation. More broadly, our findings parallel the recently described transcriptome “inverse hourglass” model for animal embryogenesis, suggesting both plant and animal morphological variation is guided by a mid-development period of transcriptome divergence.
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Affiliation(s)
- Zachary H Lemmon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Soon Ju Park
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.,Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan, Jeonbuk 54538, Republic of Korea
| | - Ke Jiang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joyce Van Eck
- The Boyce Thompson Institute, Ithaca, New York 14853, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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15
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Cheng J, Qin C, Tang X, Zhou H, Hu Y, Zhao Z, Cui J, Li B, Wu Z, Yu J, Hu K. Development of a SNP array and its application to genetic mapping and diversity assessment in pepper (Capsicum spp.). Sci Rep 2016; 6:33293. [PMID: 27623541 PMCID: PMC5020730 DOI: 10.1038/srep33293] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/24/2016] [Indexed: 11/09/2022] Open
Abstract
The development and application of single nucleotide polymorphisms (SNPs) is in its infancy for pepper. Here, a set of 15,000 SNPs were chosen from the resequencing data to develop an array for pepper with 12,720 loci being ultimately synthesized. Of these, 8,199 (~64.46%) SNPs were found to be scorable and covered ~81.18% of the whole genome. With this array, a high-density interspecific genetic map with 5,569 SNPs was constructed using 297 F2 individuals, and genetic diversity of a panel of 399 pepper elite/landrace lines was successfully characterized. Based on the genetic map, one major QTL, named Up12.1, was detected for the fruit orientation trait. A total of 65 protein-coding genes were predicted within this QTL region based on the current annotation of the Zunla-1 genome. In summary, the thousands of well-validated SNP markers, high-density genetic map and genetic diversity information will be useful for molecular genetics and innovative breeding in pepper. Furthermore, the mapping results lay foundation for isolating the genes underlying variation in fruit orientation of Capsicum.
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Affiliation(s)
- Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Cheng Qin
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China.,Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Xin Tang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Huangkai Zhou
- Guangzhou Genedenovo Biotechnology Co., Ltd, Guangzhou 510006, China
| | - Yafei Hu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zicheng Zhao
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Junjie Cui
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Bo Li
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jiping Yu
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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16
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Borovsky Y, Sharma VK, Verbakel H, Paran I. CaAP2 transcription factor is a candidate gene for a flowering repressor and a candidate for controlling natural variation of flowering time in Capsicum annuum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1073-82. [PMID: 25748116 DOI: 10.1007/s00122-015-2491-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 02/27/2015] [Indexed: 05/26/2023]
Abstract
The APETALA2 transcription factor homolog CaAP2 is a candidate gene for a flowering repressor in pepper, as revealed by induced-mutation phenotype, and a candidate underlying a major QTL controlling natural variation in flowering time. To decipher the genetic control of transition to flowering in pepper (Capsicum spp.) and determine the extent of gene function conservation compared to model species, we isolated and characterized several ethyl methanesulfonate (EMS)-induced mutants that vary in their flowering time compared to the wild type. In the present study, we report on the isolation of an early-flowering mutant that flowers after four leaves on the primary stem compared to nine leaves in the wild-type 'Maor'. By genetic mapping and sequencing of putative candidate genes linked to the mutant phenotype, we identified a member of the APETALA2 (AP2) transcription factor family, CaAP2, which was disrupted in the early-flowering mutant. CaAP2 is a likely ortholog of AP2 that functions as a repressor of flowering in Arabidopsis. To test whether CaAP2 has an effect on controlling natural variation in the transition to flowering in pepper, we performed QTL mapping for flowering time in a cross between early and late-flowering C. annuum accessions. We identified a major QTL in a region of chromosome 2 in which CaAP2 was the most significant marker, explaining 52 % of the phenotypic variation of the trait. Sequence comparison of the CaAP2 open reading frames in the two parents used for QTL mapping did not reveal significant variation. In contrast, significant differences in expression level of CaAP2 were detected between near-isogenic lines that differ for the flowering time QTL, supporting the putative function of CaAP2 as a major repressor of flowering in pepper.
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Affiliation(s)
- Yelena Borovsky
- Institute of Plant Science, Agricultural Research Organization, The Volcani Center, P.O. Box 6, 50250, Bet Dagan, Israel
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17
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Tan S, Cheng JW, Zhang L, Qin C, Nong DG, Li WP, Tang X, Wu ZM, Hu KL. Construction of an interspecific genetic map based on InDel and SSR for mapping the QTLs affecting the initiation of flower primordia in pepper (Capsicum spp.). PLoS One 2015; 10:e0119389. [PMID: 25781878 PMCID: PMC4363154 DOI: 10.1371/journal.pone.0119389] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/30/2015] [Indexed: 01/18/2023] Open
Abstract
Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F2 population (n = 154) derived from a cross between BA3 (C. annuum) and YNXML (C. frutescens). Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. The BY map consisted of 13 linkage groups (LGs) and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle) were detected on chromosomes P2, P7, P10 and P11 in 2012. The major QTL on P2 was confirmed based on another subset of the same F2 population (n = 147) in 2014 with selective genotyping of markers from the BY map. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0), 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering time-related gene and other genetic applications for pepper.
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Affiliation(s)
- Shu Tan
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jiao-Wen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Li Zhang
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Cheng Qin
- College of Horticulture, South China Agricultural University, Guangzhou, China; Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou, China; Maize Research Institute of Sichuan Agricultural University / Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
| | - Ding-Guo Nong
- College of Agriculture, Guangxi University, Nanning, China
| | - Wei-Peng Li
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xin Tang
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Zhi-Ming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Kai-Lin Hu
- College of Horticulture, South China Agricultural University, Guangzhou, China
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