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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. J Exp Bot 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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Tan Q, Bu S, Chen G, Yan Z, Chang Z, Zhu H, Yang W, Zhan P, Lin S, Xiong L, Chen S, Liu G, Liu Z, Wang S, Zhang G. Reconstruction of the High Stigma Exsertion Rate Trait in Rice by Pyramiding Multiple QTLs. Front Plant Sci 2022; 13:921700. [PMID: 35747883 PMCID: PMC9209754 DOI: 10.3389/fpls.2022.921700] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/05/2022] [Indexed: 05/25/2023]
Abstract
Asian cultivated rice is a self-pollinating crop, which has already lost some traits of natural outcrossing in the process of domestication. However, male sterility lines (MSLs) need to have a strong outcrossing ability to produce hybrid seeds by outcrossing with restorer lines of male parents in hybrid rice seed production. Stigma exsertion rate (SER) is a trait related to outcrossing ability. Reconstruction of the high-SER trait is essential in the MSL breeding of rice. In previous studies, we detected eighteen quantitative trait loci (QTLs) for SER from Oryza sativa, Oryza glaberrima, and Oryza glumaepatula using single-segment substitution lines (SSSLs) in the genetic background of Huajingxian 74 (HJX74). In this study, eleven of the QTLs were used to develop pyramiding lines. A total of 29 pyramiding lines with 2-6 QTLs were developed from 10 SSSLs carrying QTLs for SER in the HJX74 genetic background. The results showed that the SER increased with increasing QTLs in the pyramiding lines. The SER in the lines with 5-6 QTLs was as high as wild rice with strong outcrossing ability. The epistasis of additive by additive interaction between QTLs in the pyramiding lines was less-than-additive or negative effect. One QTL, qSER3a-sat, showed minor-effect epistasis and increased higher SER than other QTLs in pyramiding lines. The detection of epistasis of QTLs on SER uncovered the genetic architecture of SER, which provides a basis for using these QTLs to improve SER levels in MSL breeding. The reconstruction of the high-SER trait will help to develop the MSLs with strong outcrossing ability in rice.
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Affiliation(s)
- Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guodong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhenguang Yan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zengyuan Chang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Penglin Zhan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Shaojun Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Liang Xiong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Songliang Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
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Amegbor IK, van Biljon A, Shargie N, Tarekegne A, Labuschagne MT. Heritability and Associations among Grain Yield and Quality Traits in Quality Protein Maize (QPM) and Non-QPM Hybrids. Plants (Basel) 2022; 11:713. [PMID: 35336595 PMCID: PMC8951685 DOI: 10.3390/plants11060713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Maize (Zea mays L.) is the main staple cereal food crop cultivated in southern Africa. Interactions between grain yield and biochemical traits can be useful to plant breeders in making informed decisions on the traits to be considered in breeding programs for high grain yield and enhanced quality. The objectives of this study were to estimate the heritability of grain yield and its related traits, as well as quality traits, and determine the association between quality protein maize (QPM) with non-QPM crosses. Grain yield, and agronomic and quality trait data were obtained from 13 field trials in two countries, for two consecutive seasons. Significant genotypic and phenotypic correlations were recorded for grain yield with protein content (rG = 0.38; rP = 0.25), and tryptophan with oil content (rG = 0.58; rP = 0.25), and negative rG and rP correlations were found for protein with tryptophan content and grain yield with tryptophan content. Path analysis identified ear aspect, ears per plant, and starch as the major traits contributing to grain yield. It is recommended that ear aspect should be considered a key secondary trait in breeding for QPM hybrids. The negative association between grain yield and tryptophan, and between protein and tryptophan, will make it difficult to develop hybrids with high grain yield and high tryptophan content. Hence, it is recommended that gene pyramiding should be considered for these traits.
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Affiliation(s)
- Isaac Kodzo Amegbor
- Department of Plant Sciences, University of the Free State, Bloemfontein 9301, South Africa;
- Maize Improvement Programme, CSIR-Savanna Agricultural Research Institute, Tamale P.O. Box TL 52, Ghana
| | - Angeline van Biljon
- Department of Plant Sciences, University of the Free State, Bloemfontein 9301, South Africa;
| | - Nemera Shargie
- ARC—Grain Crops Institute, Private Bag X1251, Potchefstroom 2520, South Africa;
| | - Amsal Tarekegne
- Zambia Seed Company Limited (Zamseed), Lusaka P.O. Box 35441, Zambia
| | - Maryke T. Labuschagne
- Department of Plant Sciences, University of the Free State, Bloemfontein 9301, South Africa;
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Beauchet A, Gévaudant F, Gonzalez N, Chevalier C. In search of the still unknown function of FW2.2/CELL NUMBER REGULATOR, a major regulator of fruit size in tomato. J Exp Bot 2021; 72:5300-5311. [PMID: 33974684 DOI: 10.1093/jxb/erab207] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/07/2021] [Indexed: 06/12/2023]
Abstract
The FW2.2 gene is associated with the major quantitative trait locus (QTL) governing fruit size in tomato, and acts by negatively controlling cell division during fruit development. FW2.2 belongs to a multigene family named the CELL NUMBER REGULATOR (CNR) family. CNR proteins harbour the uncharacterized PLAC8 motif made of two conserved cysteine-rich domains separated by a variable region that are predicted to be transmembrane segments, and indeed FW2.2 localizes to the plasma membrane. Although FW2.2 was cloned more than two decades ago, the molecular mechanisms of action remain unknown. In particular, how FW2.2 functions to regulate cell cycle and fruit growth, and thus fruit size, is as yet not understood. Here we review current knowledge on PLAC8-containing CNR/FWL proteins in plants, which are described to participate in organogenesis and the regulation of organ size, especially in fruits, and in cadmium resistance, ion homeostasis, and/or Ca2+ signalling. Within the plasma membrane FW2.2 and some CNR/FWLs are localized in microdomains, which is supported by recent data from interactomics studies. Hence FW2.2 and CNR/FWL could be involved in a transport function of signalling molecules across membranes, influencing organ growth via a cell to cell trafficking mechanism.
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Affiliation(s)
- Arthur Beauchet
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Frédéric Gévaudant
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Nathalie Gonzalez
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Christian Chevalier
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
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Wu B, Shen F, Wang X, Zheng WY, Xiao C, Deng Y, Wang T, Yu Huang Z, Zhou Q, Wang Y, Wu T, Feng Xu X, Hai Han Z, Zhong Zhang X. Role of MdERF3 and MdERF118 natural variations in apple flesh firmness/crispness retainability and development of QTL-based genomics-assisted prediction. Plant Biotechnol J 2021; 19:1022-1037. [PMID: 33319456 PMCID: PMC8131039 DOI: 10.1111/pbi.13527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 10/29/2020] [Accepted: 12/06/2020] [Indexed: 05/24/2023]
Abstract
Retention of flesh texture attributes during cold storage is critical for the long-term maintenance of fruit quality. The genetic variations determining flesh firmness and crispness retainability are not well understood. The objectives of this study are to identify gene markers based on quantitative trait loci (QTLs) and to develop genomics-assisted prediction (GAP) models for apple flesh firmness and crispness retainability. Phenotype data of 2664 hybrids derived from three Malus domestica cultivars and a M. asiatica cultivar were collected in 2016 and 2017. The phenotype segregated considerably with high broad-sense heritability of 83.85% and 83.64% for flesh firmness and crispness retainability, respectively. Fifty-six candidate genes were predicted from the 62 QTLs identified using bulked segregant analysis and RNA-seq. The genotype effects of the markers designed on each candidate gene were estimated. The genomics-predicted values were obtained using pyramiding marker genotype effects and overall mean phenotype values. Fivefold cross-validation revealed that the prediction accuracy was 0.5541 and 0.6018 for retainability of flesh firmness and crispness, respectively. An 8-bp deletion in the MdERF3 promoter disrupted MdDOF5.3 binding, reduced MdERF3 expression, relieved the inhibition on MdPGLR3, MdPME2, and MdACO4 expression, and ultimately decreased flesh firmness and crispness retainability. A 3-bp deletion in the MdERF118 promoter decreased its expression by disrupting the binding of MdRAVL1, which increased MdPGLR3 and MdACO4 expression and reduced flesh firmness and crispness retainability. These results provide insights regarding the genetic variation network regulating flesh firmness and crispness retainability, and the GAP models can assist in apple breeding.
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Affiliation(s)
- Bei Wu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Fei Shen
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xuan Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Wen Yan Zheng
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Chen Xiao
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Yang Deng
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Ting Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Zhen Yu Huang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Qian Zhou
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Yi Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Ting Wu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xue Feng Xu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Zhen Hai Han
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xin Zhong Zhang
- College of HorticultureChina Agricultural UniversityBeijingChina
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Kabas A, Ersoy A, Zengin S, Golukcu M. Assessment of quality attributes of hybrids developed from pure lines of cherry and cocktail-type tomatoes. AAlim 2021. [DOI: 10.1556/066.2020.00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
AbstractTomato is worldwide the most grown vegetable. The primary target of breeding programs is to develop new tomato cultivars that are resistant to pests and diseases, in combination with high quality and yield, well-adaptation and good firmness. Among the different tomato types, cherry and cocktail tomatoes are widely preferred by consumers due to their better taste and appearance. In this study, two female tester lines were crossed with four male lines to obtain new tomato hybrids. The eight F1 hybrids and two commercial hybrids were planted in a randomised complete block design with two replications in a greenhouse in Antalya. The tomatoes of the hybrids and lines were harvested at fully ripened stage to evaluate yield, total soluble solids (TSS), fruit firmness, lycopene content and fruit colour parameters. TSS values of the cultivars and lines ranged from 4.5 to 9.5 °Bx, fruit firmness from 7.94 to 11.85 kg cm−2, lycopene from 52.10 to 55.88 mg kg−1, yield from 554.3 to 1336.7 g/plant. Hybrid AK0020 was found the best for both yield and quality.
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Affiliation(s)
- A. Kabas
- 1Manavgat Vocational School, Akdeniz University, Antalya, Turkey
| | - A. Ersoy
- 2Antalya Directorate of Agricultural Quarantine, Antalya, Turkey
| | - S. Zengin
- 3Antalya Agriculture Production Consultancy and Marketing Company, Antalya, Turkey
| | - M. Golukcu
- 4Bati Akdeniz Agricultural Research Institute, Antalya, Turkey
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Jaiswal AK, Mengiste TD, Myers JR, Egel DS, Hoagland LA. Tomato Domestication Attenuated Responsiveness to a Beneficial Soil Microbe for Plant Growth Promotion and Induction of Systemic Resistance to Foliar Pathogens. Front Microbiol 2020; 11:604566. [PMID: 33391227 PMCID: PMC7775394 DOI: 10.3389/fmicb.2020.604566] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/01/2020] [Indexed: 11/13/2022] Open
Abstract
Crop domestication events followed by targeted breeding practices have been pivotal for improvement of desirable traits and to adapt cultivars to local environments. Domestication also resulted in a strong reduction in genetic diversity among modern cultivars compared to their wild relatives, though the effect this could have on tripartite relationships between plants, belowground beneficial microbes and aboveground pathogens remains undetermined. We quantified plant growth performance, basal resistance and induced systemic resistance (ISR) by Trichoderma harzianum, a beneficial soil microbe against Botrytis cinerea, a necrotrophic fungus and Phytophthora infestans, a hemi-biotrophic oomycete, in 25 diverse tomato genotypes. Wild tomato related species, tomato landraces and modern commercial cultivars that were conventionally or organically bred, together, representing a domestication gradient were evaluated. Relationships between basal and ISR, plant physiological status and phenolic compounds were quantified to identify potential mechanisms. Trichoderma enhanced shoot and root biomass and ISR to both pathogens in a genotype specific manner. Moreover, improvements in plant performance in response to Trichoderma gradually decreased along the domestication gradient. Wild relatives and landraces were more responsive to Trichoderma, resulting in greater suppression of foliar pathogens than modern cultivars. Photosynthetic rate and stomatal conductance of some tomato genotypes were improved by Trichoderma treatment whereas leaf nitrogen status of the majority of tomato genotypes were not altered. There was a negative relationship between basal resistance and induced resistance for both diseases, and a positive correlation between Trichoderma-ISR to B. cinerea and enhanced total flavonoid contents. These findings suggest that domestication and breeding practices have altered plant responsiveness to beneficial soil microbes. Further studies are needed to decipher the molecular mechanisms underlying the differential promotion of plant growth and resistance among genotypes, and identify molecular markers to integrate selection for responsiveness into future breeding programs.
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Affiliation(s)
- Amit K Jaiswal
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Tesfaye D Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - James R Myers
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Daniel S Egel
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Lori A Hoagland
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
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Salgon S, Raynal M, Lebon S, Baptiste JM, Daunay MC, Dintinger J, Jourda C. Genotyping by Sequencing Highlights a Polygenic Resistance to Ralstonia pseudosolanacearum in Eggplant (Solanum melongena L.). Int J Mol Sci 2018; 19:E357. [PMID: 29370090 PMCID: PMC5855579 DOI: 10.3390/ijms19020357] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 12/02/2022] Open
Abstract
Eggplant cultivation is limited by numerous diseases, including the devastating bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC). Within the RSSC, Ralstonia pseudosolanacearum (including phylotypes I and III) causes severe damage to all solanaceous crops, including eggplant. Therefore, the creation of cultivars resistant to R. pseudosolanacearum strains is a major goal for breeders. An intraspecific eggplant population, segregating for resistance, was created from the cross between the susceptible MM738 and the resistant EG203 lines. The population of 123 doubled haploid lines was challenged with two strains belonging to phylotypes I (PSS4) and III (R3598), which both bypass the published EBWR9 BW-resistance quantitative trait locus (QTL). Ten and three QTLs of resistance to PSS4 and to R3598, respectively, were detected and mapped. All were strongly influenced by environmental conditions. The most stable QTLs were found on chromosomes 3 and 6. Given their estimated physical position, these newly detected QTLs are putatively syntenic with BW-resistance QTLs in tomato. In particular, the QTLs' position on chromosome 6 overlaps with that of the major broad-spectrum tomato resistance QTL Bwr-6. The present study is a first step towards understanding the complex polygenic system, which underlies the high level of BW resistance of the EG203 line.
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Affiliation(s)
- Sylvia Salgon
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
- Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), Université de la Réunion, F-97410 Saint-Pierre, France.
- Association Réunionnaise pour la Modernisation de l'Economie Fruitière Légumière et Horticole (ARMEFLHOR), F-97410 Saint-Pierre, France.
| | | | - Sylvain Lebon
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
| | - Jean-Michel Baptiste
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
| | - Marie-Christine Daunay
- Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génétique et Amélioration des Fruits et Légumes (UR GAFL), F-84143 Montfavet, France.
| | - Jacques Dintinger
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
| | - Cyril Jourda
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
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Suneetha LM, Marsakatla P, Ravi GV, Sykam A, Raju R, Reddy PP, Hara Gopal VV, Jadhav R, Suneetha S. Phenotypic characterization of a pair of molecules in tissues confer to classical Mendelian or non Mendelian ratios. Med Hypotheses 2016; 94:112-7. [PMID: 27515215 DOI: 10.1016/j.mehy.2016.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 06/26/2016] [Accepted: 07/12/2016] [Indexed: 11/24/2022]
Abstract
Studies have reported a wide range of inflammatory responses in the nerve, skin and plasma of leprosy patients. The expression levels of each biomolecule was individualistic, however could be categorized as high and low based on their statistical mean level. Here we report for the first time, expression of a set of biomolecules relating with each other in a defined proportion. The hypothesis of this paper is that the segregation of high and low combinations of a set of biomolecules follows either classical Mendelian dihybrid ratio or epistatic ratios. This hypothesis was tested for 17 molecules in three tissues; nerve, skin and plasma and were confirmed to interact in 9:7, 9:3:4, 12:3:1, 13:3, 15:1 epistatic proportions. These findings suggest that there could be a significant role of networking of molecules in defined epistatic proportions and could be important in pathophysiology of peripheral nerve.
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Yang D, Liu Y, Cheng H, Chang L, Chen J, Chai S, Li M. Genetic dissection of flag leaf morphology in wheat (Triticum aestivum L.) under diverse water regimes. BMC Genet 2016; 17:94. [PMID: 27352616 PMCID: PMC4924301 DOI: 10.1186/s12863-016-0399-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/16/2016] [Indexed: 11/10/2022] Open
Abstract
Background Morphological traits related to flag leaves are determinant traits influencing plant architecture and yield potential in wheat (Triticum aestivum L.). However, little is known regarding their genetic controls under drought stress. One hundred and twenty F8-derived recombinant inbred lines from a cross between two common wheat cultivars Longjian 19 and Q9086 were developed to identify quantitative trait loci (QTLs) and to dissect the genetic bases underlying flag leaf width, length, area, length to width ratio and basal angle under drought stress and well-watered conditions consistent over four environments. Results A total of 55 additive and 51 pairs of epistatic QTLs were identified on all 21 chromosomes except 6D, among which additive loci were highly concentrated in a few of same or adjacent marker intervals in individual chromosomes. Two specific marker intervals of Xwmc694-Xwmc156 on chromosome 1B and Xbarc1072-Xwmc272 on chromosome 2B were co-located by additive QTLs for four tested traits. Twenty additive loci were repeatedly detected in more than two environments, suggestive of stable A-QTLs. A majority of QTLs involved significant additive and epistatic effects, as well as QTL × environment interactions (QEIs). Of these, 72.7 % of additive QEIs and 80 % of epistatic QEIs were related to drought stress with significant genetic effects decreasing phenotypic values. By contrast, additive and QEIs effects contributed more phenotypic variation than epistatic effects. Conclusions Flag leaf morphology in wheat was predominantly controlled by additive and QEIs effects, where more QEIs effects occurred in drought stress and depressed phenotypic performances. Several QTL clusters indicated tight linkage or pleiotropy in the inheritance of these traits. Twenty stable QTLs for flag leaf morphology are potentially useful for the genetic improvement of drought tolerance in wheat through QTL pyramiding.
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Affiliation(s)
- Delong Yang
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuan Liu
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Hongbo Cheng
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lei Chang
- School of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jingjing Chen
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shouxi Chai
- School of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Mengfei Li
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
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Abstract
Tomato (Solanum lycopersicum Mill.) represents a model species for all fleshy fruits due to its biological cycle and the availability of numerous genetic and molecular resources. Its importance in human nutrition has made it one of the most valuable worldwide commodities. Tomato fruit size results from the combination of cell number and cell size, which are determined by both cell division and expansion. As fruit growth is mainly driven by cell expansion, cells from the (fleshy) pericarp tissue become highly polyploid according to the endoreduplication process, reaching a DNA content rarely encountered in other plant species (between 2C and 512C). Both cell division and cell expansion are under the control of complex interactions between hormone signalling and carbon partitioning, which establish crucial determinants of the quality of ripe fruit, such as the final size, weight, and shape, and organoleptic and nutritional traits. This review describes the genes known to contribute to fruit growth in tomato.
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Affiliation(s)
- Lamia Azzi
- University of Bordeaux, UMR1332 Biologie du Fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882 Villenave d'Ornon cedex, France
| | - Cynthia Deluche
- University of Bordeaux, UMR1332 Biologie du Fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882 Villenave d'Ornon cedex, France
| | - Frédéric Gévaudant
- University of Bordeaux, UMR1332 Biologie du Fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882 Villenave d'Ornon cedex, France
| | - Nathalie Frangne
- University of Bordeaux, UMR1332 Biologie du Fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882 Villenave d'Ornon cedex, France
| | - Frédéric Delmas
- University of Bordeaux, UMR1332 Biologie du Fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882 Villenave d'Ornon cedex, France
| | - Michel Hernould
- University of Bordeaux, UMR1332 Biologie du Fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882 Villenave d'Ornon cedex, France
| | - Christian Chevalier
- INRA, UMR1332 Biologie du Fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882, Villenave d'Ornon cedex, France
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13
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Gur A, Zamir D. Mendelizing all Components of a Pyramid of Three Yield QTL in Tomato. Front Plant Sci 2015; 6:1096. [PMID: 26697048 PMCID: PMC4678209 DOI: 10.3389/fpls.2015.01096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 11/22/2015] [Indexed: 05/03/2023]
Abstract
Molecular markers allowed breeders to mendelize quantitative trait loci (QTL) providing another demonstration that quantitative traits are governed by the same principles as single qualitative genes. This research extends the QTL analysis to two and three QTL and tests our ability to mendelize an oligogenic trait. In tomato, agricultural yield is determined by the weight of the fruits harvested per unit area and the total soluble solids (% Brix)-sugars and acids. The current study explores the segregation of multiple independent yield-related QTL that were identified and mapped using introgression lines (IL) of Solanum pennellii in cultivated processing tomato (S. lycopersicum). We screened 45 different double and triple IL-QTL combinations for agricultural yield, to identify QTL pyramids that behaved in an additive manner and were suitable substrate for mendelizing an oligogenic trait. A pyramid of three independent QTL that significantly improved Brix(∗)Yield (BXY - the soluble solids output per unit area) compared to M82 was selected. In the progenies of the tri-hybrid we bred using markers a nearly isogenic 'immortalized F2.' While the common mode of QTL-QTL interactions across the 45 IL-QTLs combinations was less than additive, the three QTLs in the selected triple-stack performed in an additive manner which made it an exceptional material for breeding. This study demonstrates that using the phenotypic effect of all 27 possible QTL-alleles combinations it is possible to make reliable predictions about the genotypes that will maximize the yield.
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Sandhu N, Singh A, Dixit S, Sta Cruz MT, Maturan PC, Jain RK, Kumar A. Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress. BMC Genet 2014; 15:63. [PMID: 24885990 PMCID: PMC4048250 DOI: 10.1186/1471-2156-15-63] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Drought is one of the most important abiotic stresses that cause drastic reduction in rice grain yield (GY) in rainfed environments. The identification and introgression of QTL leading to high GY under drought have been advocated to be the preferred breeding strategy to improve drought tolerance of popular rice varieties. Genetic control of GY under reproductive-stage drought stress (RS) was studied in two BC1F4 mapping populations derived from crosses of Kali Aus, a drought-tolerant aus cultivar, with high-yielding popular varieties MTU1010 and IR64. The aim was to identify QTL for GY under RS that show a large and consistent effect for the trait. Bulk segregant analysis (BSA) was used to identify significant markers putatively linked with high GY under drought. RESULTS QTL analysis revealed major-effect GY QTL: qDTY1.2, qDTY2.2 and qDTY1.3, qDTY2.3 (DTY; Drought grain yield) under drought consistently over two seasons in Kali Aus/2*MTU1010 and Kali Aus/2*IR64 populations, respectively. qDTY1.2 and qDTY2.2 explained an additive effect of 288 kg ha-1 and 567 kg ha-1 in Kali Aus/2*MTU1010, whereas qDTY1.3 and qDTY2.3 explained an additive effect of 198 kg ha-1 and 147 kg ha-1 in Kali Aus/2*IR64 populations, respectively.Epistatic interaction was observed for DTF (days to flowering) between regions on chromosome 2 flanked by markers RM154-RM324 and RM263-RM573 and major epistatic QTL for GY showing interaction between genomic locations on chromosome 1 at marker interval RM488-RM315 and chromosome 2 at RM324-RM263 in 2012 DS and 2013 DS RS in Kali Aus/2*IR64 mapping populations. CONCLUSION The QTL, qDTY1.2, qDTY1.3, qDTY2.2, and qDTY2.3, identified in this study can be used to improve GY of mega varieties MTU1010 and IR64 under different degrees of severity of drought stress through marker-aided backcrossing and provide farmers with improved varieties that effectively combine high yield potential with good yield under drought. The observed epistatic interaction for GY and DTF will contribute to our understanding of the genetic basis of agronomically important traits and enhance predictive ability at an individualized level in agriculture.
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Affiliation(s)
| | | | | | | | | | | | - Arvind Kumar
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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15
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Abstract
The role of epistasis in the genetic architecture of quantitative traits is controversial, despite the biological plausibility that nonlinear molecular interactions underpin the genotype-phenotype map. This controversy arises because most genetic variation for quantitative traits is additive. However, additive variance is consistent with pervasive epistasis. In this Review, I discuss experimental designs to detect the contribution of epistasis to quantitative trait phenotypes in model organisms. These studies indicate that epistasis is common, and that additivity can be an emergent property of underlying genetic interaction networks. Epistasis causes hidden quantitative genetic variation in natural populations and could be responsible for the small additive effects, missing heritability and the lack of replication that are typically observed for human complex traits.
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Affiliation(s)
- Trudy F C Mackay
- Department of Biological Sciences, Campus Box 7614, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
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Haggard JE, Johnson EB, St Clair DA. Linkage relationships among multiple QTL for horticultural traits and late blight (P. infestans) resistance on chromosome 5 introgressed from wild tomato Solanum habrochaites. G3 (Bethesda) 2013; 3:2131-46. [PMID: 24122052 DOI: 10.1534/g3.113.007195] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
When the allele of a wild species at a quantitative trait locus (QTL) conferring a desirable trait is introduced into cultivated species, undesirable effects on other traits may occur. These negative phenotypic effects may result from the presence of wild alleles at other closely linked loci that are transferred along with the desired QTL allele (i.e., linkage drag) and/or from pleiotropic effects of the desired allele. Previously, a QTL for resistance to Phytophthora infestans on chromosome 5 of Solanum habrochaites was mapped and introgressed into cultivated tomato (S. lycopersicum). Near-isogenic lines (NILs) were generated and used for fine-mapping of this resistance QTL, which revealed coincident or linked QTL with undesirable effects on yield, maturity, fruit size, and plant architecture traits. Subsequent higher-resolution mapping with chromosome 5 sub-NILs revealed the presence of multiple P. infestans resistance QTL within this 12.3 cM region. In our present study, these sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over the course of two years. Each previously detected single horticultural trait QTL fractionated into two or more QTL. A total of 41 QTL were detected across all traits, with ∼30% exhibiting significant QTL × environment interactions. Colocation of QTL for multiple traits suggests either pleiotropy or tightly linked genes control these traits. The complex genetic architecture of horticultural and P. infestans resistance trait QTL within this S. habrochaites region of chromosome 5 presents challenges and opportunities for breeding efforts in cultivated tomato.
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Pirrello J, Bourdon M, Cheniclet C, Bourge M, Brown SC, Renaudin JP, Frangne N, Chevalier C. How fruit developmental biology makes use of flow cytometry approaches. Cytometry A 2013; 85:115-25. [PMID: 24273206 DOI: 10.1002/cyto.a.22417] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 09/20/2013] [Accepted: 10/26/2013] [Indexed: 12/15/2022]
Abstract
Fleshy fruit species such as tomato are important because of their nutritional and economic value. Several stages of fruit development such as ovary formation, fruit set, and fruit maturation have already been the subject of many developmental studies. However, fruit growth per se has been much less addressed. Fruit growth like all plant organs depends upon the developmental processes of cell division and cell expansion. The activity of cell divisions sets the number of cells that will compose the fruit; the cell expansion activity then determines its final size. Among the various mechanisms that may influence the determination of cell size, endopolyploidy by the means of endoreduplication, i.e. genome amplification in the absence of mitosis, appears to be of great importance in fleshy fruits. In tomato fruit, endoreduplication is associated with DNA-dependent cell expansion: cell size can reach spectacular levels such as hundreds of times its initial size (e.g. >0.5 mm in diameter), with as much as a 256-fold increase in nuclear DNA content. Using tomato fruit development as a model, recent investigations combining the use of flow cytometry, cellular imaging and molecular analyses have provided new data in favor of the long-standing karyoplasmic ratio theory, stating that cells tend to adjust their cytoplasmic volume to the nuclear DNA content. By establishing a highly structured cellular system where multiple physiological functions are integrated, endoreduplication acts as a morphogenetic factor supporting cell growth during tomato fruit development. In the context of plant breeding, deciphering the mechanisms controlling fruit growth, in particular those connecting the process of nuclear endoreduplication with modulation of gene expression, the regulation of cell size and final fruit size and composition, is necessary to understand better the establishment of fleshy fruit quality traits.
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Affiliation(s)
- Julien Pirrello
- INRA, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
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De Franceschi P, Stegmeir T, Cabrera A, van der Knaap E, Rosyara UR, Sebolt AM, Dondini L, Dirlewanger E, Quero-Garcia J, Campoy JA, Iezzoni AF. Cell number regulator genes in Prunus provide candidate genes for the control of fruit size in sweet and sour cherry. Mol Breed 2013; 32:311-326. [PMID: 23976873 PMCID: PMC3748327 DOI: 10.1007/s11032-013-9872-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/18/2013] [Indexed: 05/19/2023]
Abstract
Striking increases in fruit size distinguish cultivated descendants from small-fruited wild progenitors for fleshy fruited species such as Solanum lycopersicum (tomato) and Prunus spp. (peach, cherry, plum, and apricot). The first fruit weight gene identified as a result of domestication and selection was the tomato FW2.2 gene. Members of the FW2.2 gene family in corn (Zea mays) have been named CNR (Cell Number Regulator) and two of them exert their effect on organ size by modulating cell number. Due to the critical roles of FW2.2/CNR genes in regulating cell number and organ size, this family provides an excellent source of candidates for fruit size genes in other domesticated species, such as those found in the Prunus genus. A total of 23 FW2.2/CNR family members were identified in the peach genome, spanning the eight Prunus chromosomes. Two of these CNRs were located within confidence intervals of major quantitative trait loci (QTL) previously discovered on linkage groups 2 and 6 in sweet cherry (Prunus avium), named PavCNR12 and PavCNR20, respectively. An analysis of haplotype, sequence, segregation and association with fruit size strongly supports a role of PavCNR12 in the sweet cherry linkage group 2 fruit size QTL, and this QTL is also likely present in sour cherry (P. cerasus). The finding that the increase in fleshy fruit size in both tomato and cherry associated with domestication may be due to changes in members of a common ancestral gene family supports the notion that similar phenotypic changes exhibited by independently domesticated taxa may have a common genetic basis.
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Affiliation(s)
- P. De Franceschi
- Dipartimento di Scienze Agrarie, Università degli Studi di Bologna, Bologna, Italy
| | - T. Stegmeir
- Michigan State University, East Lansing, MI USA
| | - A. Cabrera
- Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH USA
| | - E. van der Knaap
- Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH USA
| | | | | | - L. Dondini
- Dipartimento di Scienze Agrarie, Università degli Studi di Bologna, Bologna, Italy
| | - E. Dirlewanger
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d’Ornon, France
- University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d’Ornon, France
| | - J. Quero-Garcia
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d’Ornon, France
- University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d’Ornon, France
| | - J. A. Campoy
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d’Ornon, France
- University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d’Ornon, France
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Sun YD, Liang Y, Wu JM, Li YZ, Cui X, Qin L. Dynamic QTL analysis for fruit lycopene content and total soluble solid content in a Solanum lycopersicum x S. pimpinellifolium cross. Genet Mol Res 2012; 11:3696-710. [PMID: 22930431 DOI: 10.4238/2012.august.17.8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fruit lycopene content and total soluble solid content are important factors determining fruit quality of tomatoes; however, the dynamic quantitative trait loci (QTL) controlling lycopene and soluble solid content have not been well studied. We mapped the chromosomal regions controlling these traits in different periods in F(2:3) families derived from a cross between the domestic and wild tomato species Solanum lycopersicum and S. pimpinellifolium. Fifteen QTLs for lycopene and soluble solid content and other related traits analyzed at three different fruit ripening stages were detected with a composite interval mapping method. These QTLs explained 7-33% of the individual phenotypic variation. QTLs detected in the color-changing period were different from those detected in the other two periods. On chromosome 1, the soluble solid content QTL was located in the same region during the color-changing and full-ripe periods. On chromosome 4, the same QTL for lycopene content was found during the color-changing and full-ripe periods. The QTL for lycopene content on chromosome 4 co-located with the QTL for soluble solid content during the full-ripe period. Co-location of lycopene content QTL and soluble solid content QTLs may be due to pleiotropic effects of a single gene or a cluster of genes via physiological relationships among traits. On chromosome 9, the same two QTLs for lycopene content at two different fruit ripening periods may reflect genes controlling lycopene content that are always expressed in tomato fruit development.
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Affiliation(s)
- Y D Sun
- Key Laboratory of Horticulture Plant Germplasm and Genetic Improvement, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, Shaanxi, China
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20
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Abstract
Background Grain yield is a key economic driver of successful wheat production. Due to its complex nature, little is known regarding its genetic control. The goal of this study was to identify important quantitative trait loci (QTL) directly and indirectly affecting grain yield using doubled haploid lines derived from a cross between Hanxuan 10 and Lumai 14. Methodology/Principal Findings Ten yield-associated traits, including yield per plant (YP), number of spikes per plant (NSP), number of grains per spike (NGS), one-thousand grain weight (TGW), total number of spikelets per spike (TNSS), number of sterile spikelets per spike (NSSS), proportion of fertile spikelets per spike (PFSS), spike length (SL), density of spikelets per spike (DSS) and plant height (PH), were assessed across 14 (for YP) to 23 (for TGW) year × location × water regime environments in China. Then, the genetic effects were partitioned into additive main effects (a), epistatic main effects (aa) and their environment interaction effects (ae and aae) by using composite interval mapping in a mixed linear model. Conclusions/Significance Twelve (YP) to 33 (PH) QTLs were identified on all 21 chromosomes except 6D. QTLs were more frequently observed on chromosomes 1B, 2B, 2D, 5A and 6B, and were concentrated in a few regions on individual chromosomes, exemplified by three striking yield-related QTL clusters on chromosomes 2B, 1B and 4B that explained the correlations between YP and other traits. The additive main-effect QTLs contributed more phenotypic variation than the epistasis and environmental interaction. Consistent with agronomic analyses, a group of progeny derived by selecting TGW and NGS, with higher grain yield, had an increased frequency of QTL for high YP, NGS, TGW, TNSS, PFSS, SL, PH and fewer NSSS, when compared to low yielding progeny. This indicated that it is feasible by marker-assisted selection to facilitate wheat production.
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Affiliation(s)
- Xianshan Wu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
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Huang Z, van der Knaap E. Tomato fruit weight 11.3 maps close to fasciated on the bottom of chromosome 11. Theor Appl Genet 2011; 123:465-74. [PMID: 21541852 DOI: 10.1007/s00122-011-1599-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 04/12/2011] [Indexed: 05/23/2023]
Abstract
Fruit weight is an important character in many crops. In tomato (Solanum lycopersicum), fruit weight is controlled by many loci, some of which have a major effect on the trait. Fruit weight 11.3 (fw11.3) and fasciated (fas) have been mapped to the same region on chromosome 11. We sought to determine whether these loci represent alleles of the same or separate genes. We show that fas and fw11.3 are not allelic and instead represent separate genes. The fw11.3 locus was fine-mapped to a 149-kb region comprised of 22 predicted genes. Unlike most fruit weight loci, gene action at fw11.3 indicates that the mutant allele is partially dominant over the wild allele. We also investigate the nature of the genome rearrangement at the fas locus and demonstrate that the mutation is due to a 294-kb inversion disrupting the YABBY gene known to underlie the fas locus.
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Affiliation(s)
- Zejun Huang
- Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691, USA
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22
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He Q, Zhang K, Xu C, Xing Y. Additive and additive × additive interaction make important contributions to spikelets per panicle in rice near isogenic (Oryza sativa L.) lines. J Genet Genomics 2010; 37:795-803. [PMID: 21193158 DOI: 10.1016/S1673-8527(09)60097-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 09/04/2010] [Accepted: 10/13/2010] [Indexed: 11/21/2022]
Abstract
Epistasis plays an important role in the genetic basis of rice yield traits. Taking interactions into account in breeding programs will help the development of high-yielding rice varieties. In this study, three sets of near isogenic lines (NILs) targeting three QTLs for spikelets per panicle (SPP), namely qSPP1, qSPP2 and qSPP7, which share the same Zhenshan 97 genetic background, were used to produce an F(2) population in which the three QTLs segregated simultaneously. The genotypes of the individual F(2) plants at the three QTLs were replaced with three markers that are closely linked to the corresponding QTLs. These QTLs were validated in the F(2) and F(3) populations at the single marker level. qSPP7 exhibited major pleiotropic effects on SPP, plant height and heading date. Multifactor analysis of variance was performed for the F(2) population and its progeny. Additive (additive interaction between qSPP2 and qSPP7 had significant effects on SPP in both the F(2) population and its progeny. Both additive and additive (additive interactions could explain about 73% of the total SPP phenotypic variance. The SPP performance of 27 three-locus combinations was ranked and favorable combinations were recommended for rice breeding in different ecosystems.
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Carli P, Barone A, Fogliano V, Frusciante L, Ercolano MR. Dissection of genetic and environmental factors involved in tomato organoleptic quality. BMC Plant Biol 2011; 11:58. [PMID: 21453463 PMCID: PMC3080294 DOI: 10.1186/1471-2229-11-58] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 03/31/2011] [Indexed: 05/25/2023]
Abstract
BACKGROUND One of the main tomato breeding objectives is to improve fruit organoleptic quality. However, this task is made somewhat challenging by the complex nature of sensory traits and the lack of efficient selection criteria. Sensory quality depends on numerous factors, including fruit colour, texture, aroma, and composition in primary and secondary metabolites. It is also influenced by genotypic differences, the nutritional regime of plants, stage of ripening at harvest and environmental conditions. In this study, agronomic, biochemical and sensory characterization was performed on six Italian heirlooms grown in different environmental conditions. RESULT We identified a number of links among traits contributing to fruit organoleptic quality and to the perception of sensory attributes. PCA analysis was used to highlight some biochemical, sensory and agronomic discriminating traits: this statistical test allowed us to identify which sensory attributes are more closely linked to environmental conditions and those, instead, linked to the genetic constitution of tomato. Sweetness, sourness, saltiness and tomato flavour are not only grouped in the same PCA factor, but also result in a clear discrimination of tomato ecotypes in the three different fields. The three different traditional varieties cluster on the basis of attributes like juiciness, granulosity, hardness and equatorial diameter, and are therefore more closely related to the genetic background of the cultivar. CONCLUSION This finding suggests that a different method should be undertaken to improve sensory traits related to taste perception and texture. Our results might be used to ascertain in what direction to steer breeding in order to improve the flavour characteristics of tomato ecotypes.
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Affiliation(s)
- Paola Carli
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples 'Federico II', Via Universita' 100, 80055 Portici (NA), Italy
| | - Amalia Barone
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples 'Federico II', Via Universita' 100, 80055 Portici (NA), Italy
| | - Vincenzo Fogliano
- Department of Food Science, University of Naples 'Federico II', Via Universita' 133, 80055 Portici (NA), Italy
| | - Luigi Frusciante
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples 'Federico II', Via Universita' 100, 80055 Portici (NA), Italy
| | - Maria R Ercolano
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples 'Federico II', Via Universita' 100, 80055 Portici (NA), Italy
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JIA JZ, TIAN LP, XUE L, WEI YN. Dynamic QTL and correlated characters of tomato soluble solid content. Hereditas (Beijing) 2011; 32:1077-83. [DOI: 10.3724/sp.j.1005.2010.01077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Fernandez-Silva I, Moreno E, Essafi A, Fergany M, Garcia-Mas J, Martín-Hernandez AM, Alvarez JM, Monforte AJ. Shaping melons: agronomic and genetic characterization of QTLs that modify melon fruit morphology. Theor Appl Genet 2010; 121:931-40. [PMID: 20506012 DOI: 10.1007/s00122-010-1361-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 05/12/2010] [Indexed: 05/03/2023]
Abstract
The consistency of quantitative trait locus (QTL) effects among genetic backgrounds is a key factor for introgressing QTLs from initial mapping experiments into applied breeding programs. We have selected four QTLs (fs6.4, fw4.3, fw4.4 and fw8.1) involved in melon fruit morphology that had previously been detected in a collection of introgression lines derived from the cross between a Spanish cultivar, "Piel de Sapo," and the Korean accession PI161375 (Songwan Charmi). Introgression lines harboring these QTLs were crossed with an array of melon inbred lines representative of the most important cultivar types. Hybrids of the introgression and inbred lines, with the appropriate controls, were evaluated in replicated agronomic trials. The effects of the QTLs were consistent among the different genetic backgrounds, demonstrating the utility of these QTLs for applied breeding programs in modifying melon fruit morphology. Three QTLs, fw4.4, fs6.4 and fs12.1 were subjected to further study in order to map them more accurately by substitution mapping using a new set of introgression lines with recombination events within the QTL chromosome region. The position of the QTLs was narrowed down to 36-5 cM, depending on the QTL. The results presented in the current study set the basis for the use of these QTLs in applied breeding programs and for the molecular characterization of the genes underlying them.
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Affiliation(s)
- Iria Fernandez-Silva
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348, Cabrils, Barcelona, Spain
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26
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Bertin N, Martre P, Génard M, Quilot B, Salon C. Under what circumstances can process-based simulation models link genotype to phenotype for complex traits? Case-study of fruit and grain quality traits. J Exp Bot 2010; 61:955-67. [PMID: 20038518 DOI: 10.1093/jxb/erp377] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Detailed information has arisen from research at gene and cell levels, but it is still incomplete in the context of a quantitative understanding of whole plant physiology. Because of their integrative nature, process-based simulation models can help to bridge the gap between genotype and phenotype and assist in deconvoluting genotype-by-environment (GxE) interactions for complex traits. Indeed, GxE interactions are emergent properties of simulation models, i.e. unexpected properties generated by complex interconnections between subsystem components and biological processes. They co-occur in the system with synergistic or antagonistic effects. In this work, different kinds of GxE interactions are illustrated. Approaches to link model parameters to genes or quantitative trait loci (QTL) are briefly reviewed. Then the analysis of GxE interactions through simulation models is illustrated with an integrated model simulation of peach (Prunus persica (L.) Batsch) fruit mass and sweetness, and with a model of wheat (Triticum aestivum L.) grain yield and protein concentration. This paper suggests that the management of complex traits such as fruit and grain quality may become possible, thanks to the increasing knowledge concerning the genetic and environmental regulation of organ size and composition and to the development of models simulating the complex aspects of metabolism and biophysical behaviours at the plant and organ levels.
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Affiliation(s)
- Nadia Bertin
- INRA, UR1115 Plantes et Systèmes de Culture Horticoles, F-84 914 Avignon, France.
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Dal Cin V, Kevany B, Fei Z, Klee HJ. Identification of Solanum habrochaites loci that quantitatively influence tomato fruit ripening-associated ethylene emissions. Theor Appl Genet 2009; 119:1183-92. [PMID: 19680624 DOI: 10.1007/s00122-009-1119-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 07/20/2009] [Indexed: 05/04/2023]
Abstract
The phytohormone ethylene is essential for ripening of climacteric fruits such as tomato. While many of the genes responsible for ethylene synthesis and perception have been identified, the regulatory network controlling autocatalytic climacteric ethylene synthesis is not well understood. In order to better understand the regulation of ripening-associated ethylene, we have exploited the genetic variation within Solanum Sect. Lycopersicon. In particular, we have used a near-isogenic population of S. habrochaites introgression lines to identify chromosome segments affecting ethylene emissions during ripening. S. habrochaites fruits produce much larger quantities of ethylene during ripening than do cultivated S. lycopersicum tomatoes. A total of 17 segments were identified; 3 had emissions more than twice the level of the tomato parent, 11 had less than a twofold increase and 3 had significantly reduced emissions at one or more ripening stages. While several of these segments co-segregate with known ethylene-related genes, many do not correspond to known genes. Thus, they may identify novel modes of regulation. These results illustrate the utility of wild relatives and their introgression lines to understand regulation of fruit ripening-related processes.
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Affiliation(s)
- Valeriano Dal Cin
- University of Florida, Horticultural Sciences, PO Box 110690, Gainesville, FL, 32611-0690, USA
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28
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Abstract
Epistasis, the nonadditive interaction between loci, is thought to play a role in many fundamental evolutionary processes, including adaptive differentiation and speciation. Focusing on species differences in ecophysiological traits, we examined the strength and direction of pairwise epistatic interactions between target chromosomal regions from one species, when co-introgressed into the genetic background of a foreign species. A full diallel cross was performed using 15 near-isogenic lines (NILs) constructed between two tomato species (Solanum habrochaites and Solanum lycopersicum) to compare the phenotypic effects of each chromosomal region singly and in combination with each other region. We detected main effect quantitative trait loci (QTLs) for two of our three focal traits. Epistatic effects accounted for c. 25% of detected effects on trait means, depending on the trait. Strikingly, all but two interactions were antagonistic, with the combined effect of chromosomal regions acting in the opposite direction from that of one or both individual chromosomal regions. Our study is one of the few to systematically examine pairwise epistatic effects in a nonmicrobial system. Our results suggest that epistatic interactions can contribute substantially to the genetic basis of traits involved in adaptive species differentiation, especially highly complex, multivariate traits.
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Affiliation(s)
- Christopher D Muir
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47401, USA
| | - Leonie C Moyle
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47401, USA
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Matas AJ, Gapper NE, Chung MY, Giovannoni JJ, Rose JKC. Biology and genetic engineering of fruit maturation for enhanced quality and shelf-life. Curr Opin Biotechnol 2009; 20:197-203. [PMID: 19339169 DOI: 10.1016/j.copbio.2009.02.015] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 02/23/2009] [Accepted: 02/28/2009] [Indexed: 01/20/2023]
Abstract
Commercial regulation of ripening is currently achieved through early harvest, by controlling the postharvest storage atmosphere and genetic selection for slow or late ripening varieties. Although these approaches are often effective, they are not universally applicable and often result in acceptable, but poor quality, products. With increased understanding of the molecular biology underlying ripening and the advent of genetic engineering technologies, researchers have pursued new strategies to address problems in fruit shelf-life and quality. These have been guided by recent insights into mechanisms by which ethylene and a complex network of transcription factors regulate ripening, and by an increased appreciation of factors that contribute to shelf-life, such as the fruit cuticle.
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Affiliation(s)
- Antonio J Matas
- Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
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Bertin N, Causse M, Brunel B, Tricon D, Génard M. Identification of growth processes involved in QTLs for tomato fruit size and composition. J Exp Bot 2009; 60:237-48. [PMID: 19033553 PMCID: PMC3071768 DOI: 10.1093/jxb/ern281] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 10/17/2008] [Accepted: 10/20/2008] [Indexed: 05/19/2023]
Abstract
Many quantitative trait loci (QTLs) for quality traits have been located on the tomato genetic map, but introgression of favourable wild alleles into large fruited species is hampered by co-localizations of QTLs with antagonist effects. The aim of this study was to assess the growth processes controlled by the main QTLs for fruit size and composition. Four nearly isogenic lines (NILs) derived from an intraspecific cross between a tasty cherry tomato (Cervil) and a normal-tasting large fruit tomato (Levovil) were studied. The lines carried one (L2, L4, and L9) or five (Lx) introgressions from Cervil on chromosomes 1, 2, 4, and 9. QTLs for fruit size could be mainly associated with cell division processes in L2 and L9, whereas cell expansion was rather homogeneous among the genotypes, except Cervil for which the low expansion rate was attributed to low cell plasticity. The link between endoreduplication and fruit size remained unclear, as cell or fruit sizes were positively correlated with the cell DNA content, but not with the endoreduplication factor. QTLs for fruit composition reflected differences in water accumulation rather than in sugar accumulation, except in L9 for which the up-regulation of sucrose unloading and hexose transport and/or starch synthesis was suggested. This may explain the increased amount of carbon allocated to cell structures in L9, which could be related to a QTL for fruit texture. In Lx, these effects were attenuated, except on fruit size and cell division. Finally, the region on top of chromosome 9 may control size and composition attributes in tomato, by a combination of QTL effects on cell division, cell wall synthesis, and carbon import and metabolism.
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Affiliation(s)
- Nadia Bertin
- INRA, UR1115 Plantes et systèmes de culture horticoles, INRA, F-84000 Avignon, France.
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Estañ MT, Villalta I, Bolarín MC, Carbonell EA, Asins MJ. Identification of fruit yield loci controlling the salt tolerance conferred by solanum rootstocks. Theor Appl Genet 2009; 118:305-12. [PMID: 18846361 DOI: 10.1007/s00122-008-0900-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 09/16/2008] [Indexed: 05/04/2023]
Abstract
The rootstock effect on the fruit yield of a grafted tomato variety was genetically analyzed under salinity using as rootstock two populations of F(9) lines developed from a salt sensitive genotype of Solanum lycopersicum var. cerasiforme, as female parent, and two salt tolerant lines, as male parents, from S. pimpinellifolium, the P population (123 lines), and S. cheesmaniae, the C population (100 lines). There were rootstock lines from the two populations (up to 65% in the P population) that raised the fruit yield of the commercial hybrid under saline conditions. It is shown that this salt tolerance rootstock effect is a heritable trait (h (2) near 0.3), governed by at least eight QTLs. The most relevant component was the number of fruits. Thus most detected QTLs correspond to this component. In general, QTL gene effects are medium-sized, with contributions from 8.5 up to 15.9% at most, and the advantageous allele comes from the wild, salt tolerant species. Only two fruit yield QTLs on chromosomes P9 and C11 might correspond to fruit yield QTLs of the non-grafted lines indicating their root system dependence. A fruit yield QTL on chromosome 3 is acting epistatically in both populations. The epistatic interactions found were dominant and they were unveiled using the associated marker as cofactor in the composite interval mapping methodology. Therefore, an efficient and profitable utilization of wild germplasm can be carried out through the improvement of rootstocks that confer salt tolerance in terms of fruit yield to the grafted variety.
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Affiliation(s)
- M T Estañ
- CEBAS, CSIC, Campus de Espinardo, 30100, Espinardo, Murcia, Spain
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32
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Abstract
Epistasis, or interactions between genes, has long been recognized as fundamentally important to understanding the structure and function of genetic pathways and the evolutionary dynamics of complex genetic systems. With the advent of high-throughput functional genomics and the emergence of systems approaches to biology, as well as a new-found ability to pursue the genetic basis of evolution down to specific molecular changes, there is a renewed appreciation both for the importance of studying gene interactions and for addressing these questions in a unified, quantitative manner.
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Cuevas HE, Staub JE, Simon PW, Zalapa JE, McCreight JD. Mapping of genetic loci that regulate quantity of beta-carotene in fruit of US Western Shipping melon (Cucumis melo L.). Theor Appl Genet 2008; 117:1345-59. [PMID: 18773190 DOI: 10.1007/s00122-008-0868-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 08/12/2008] [Indexed: 05/03/2023]
Abstract
Melon (Cucumis melo L.) is highly nutritious vegetable species and an important source of beta-carotene (Vitamin A), which is an important nutrient in the human diet. A previously developed set of 81 recombinant inbred lines (RIL) derived from Group Cantalupensis US Western Shipper market type germplasm was examined in two locations [Wisconsin (WI) and California (CA), USA] over 2 years to identify quantitative trait loci (QTL) associated with quantity of beta-carotene (QbetaC) in mature fruit. A moderately saturated 256-point RIL-based map [104 SSR, 7 CAPS, 4 SNP in putative carotenoid candidate genes, 140 dominant markers and one morphological trait (a) spanning 12 linkage groups (LG)] was used for QbetaC-QTL analysis. Eight QTL were detected in this evaluation that were distributed across four LG that explained a significant portion of the associated phenotypic variation for QbetaC (R (2) = 8 to 31.0%). Broad sense heritabilities for QbetaC obtained from RIL grown in WI. and CA were 0.56 and 0.68, respectively, and 0.62 over combined locations. The consistence of QbetaC in high/low RIL within location across years was confirmed in experiments conducted over 2 years. QTL map positions were not uniformly associated with putative carotenoid genes, although one QTL (beta-car6.1) interval was located 10 cM from a beta-carotene hydroxylase gene. These results suggest that accumulation of beta-carotene in melon is under complex genetic control. This study provides the initial step for defining the genetic control of QbetaC in melon leading to the development of varieties with enhanced beta-carotene content.
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Affiliation(s)
- H E Cuevas
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Unit, Department of Horticulture, University of Wisconsin, 1575 Linden Dr., Madison, WI 53706, USA,
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Abstract
The basic principle of Marker-Assisted Selection (MAS) is to exploit Linkage Disequilibrium (LD) between markers and QTLs. With strong enough LD, MAS should in theory be easier, faster, cheaper, or more efficient than classical (phenotypic) selection. I briefly review the major MAS methods, describing some 'success stories' where MAS was applied successfully in the context of plant breeding, and detailing other cases where efficiency was not as high as expected. I discuss the possible causes explaining the difference between theoretical expectations and practical observations. Finally, I review the principal challenges and issues that must be tackled to make marker-assisted selection in plants more effective in the future, namely: managing and controlling QTL stability to apply MAS to complex traits, and integrating MAS in traditional breeding practices to make it more economically attractive and applicable in developing countries.
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Affiliation(s)
- Frédéric Hospital
- INRA, UMR1236 Génétique et Diversité Animales, 78352, Jouy-en-Josas, France.
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35
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Abstract
The basic principle of Marker-Assisted Selection (MAS) is to exploit Linkage Disequilibrium (LD) between markers and QTLs. With strong enough LD, MAS should in theory be easier, faster, cheaper, or more efficient than classical (phenotypic) selection. I briefly review the major MAS methods, describing some 'success stories' where MAS was applied successfully in the context of plant breeding, and detailing other cases where efficiency was not as high as expected. I discuss the possible causes explaining the difference between theoretical expectations and practical observations. Finally, I review the principal challenges and issues that must be tackled to make marker-assisted selection in plants more effective in the future, namely: managing and controlling QTL stability to apply MAS to complex traits, and integrating MAS in traditional breeding practices to make it more economically attractive and applicable in developing countries.
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Affiliation(s)
- Frédéric Hospital
- INRA, UMR1236 Génétique et Diversité Animales, 78352, Jouy-en-Josas, France.
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36
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Jannink JL, Moreau L, Charmet G, Charcosset A. Overview of QTL detection in plants and tests for synergistic epistatic interactions. Genetica 2008; 136:225-36. [PMID: 18695990 DOI: 10.1007/s10709-008-9306-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Accepted: 07/17/2008] [Indexed: 12/01/2022]
Abstract
Improvements in the usefulness of QTL analysis arise from better statistical methods applied to the problem, ability to analyze more complex mating designs, and the fitting of less simplified genetic models. Here we review the advantages of different plant mating designs in QTL analysis and conclude that diallel designs have several favorable properties. We then turn to the detection of systematic genome-wide synergistic epistasis. This form of epistasis has important implications from evolutionary (maintenance of sexual reproduction and concealment of cryptic genetic variation) and practical perspectives (response to pyramided favorable alleles). We develop two methods for detecting systematic synergistic epistasis, one based on analyzing interactions between locus effects and predicted individual genotypic values and one based on analyzing pairwise locus interactions. Using the first method we detect synergistic epistasis in a barley and a wheat dataset but not in a maize dataset. We fail to detect synergistic epistasis with the second method. We discuss our results in the light of theoretical questions concerning the mechanisms of synergistic epistasis.
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Affiliation(s)
- Jean-Luc Jannink
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY 14853-2901, USA.
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Lippman ZB, Semel Y, Zamir D. An integrated view of quantitative trait variation using tomato interspecific introgression lines. Curr Opin Genet Dev 2007; 17:545-52. [PMID: 17723293 DOI: 10.1016/j.gde.2007.07.007] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Accepted: 07/17/2007] [Indexed: 02/02/2023]
Abstract
Resolving natural phenotypic variation into genetic and molecular components is a major objective in biology. Over the past decade, tomato interspecific introgression lines (ILs), each carrying a single 'exotic' chromosome segment from a wild species, have exposed thousands of quantitative trait loci (QTL) affecting plant adaptation, morphology, yield, metabolism, and gene expression. QTL for fruit size and sugar composition were isolated by map-based cloning, while others were successfully implemented in marker-assisted breeding programs. More recently, integrating the multitude of IL-QTL into a single database has unraveled some unifying principles about the architecture of complex traits in plants.
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Affiliation(s)
- Zachary B Lippman
- The Hebrew University of Jerusalem, Faculty of Agriculture, Institute of Plant Sciences, Rehovot, Israel.
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