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Berindean IV, Taoutaou A, Rida S, Ona AD, Stefan MF, Costin A, Racz I, Muntean L. Modern Breeding Strategies and Tools for Durable Late Blight Resistance in Potato. PLANTS (BASEL, SWITZERLAND) 2024; 13:1711. [PMID: 38931143 PMCID: PMC11207681 DOI: 10.3390/plants13121711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/08/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024]
Abstract
Cultivated potato (Solanum tuberosum) is a major crop worldwide. It occupies the second place after cereals (corn, rice, and wheat). This important crop is threatened by the Oomycete Phytophthora infestans, the agent of late blight disease. This pathogen was first encountered during the Irish famine during the 1840s and is a reemerging threat to potatoes. It is mainly controlled chemically by using fungicides, but due to health and environmental concerns, the best alternative is resistance. When there is no disease, no treatment is required. In this study, we present a summary of the ongoing efforts concerning resistance breeding of potato against this devastating pathogen, P. infestans. This work begins with the search for and selection of resistance genes, whether they are from within or from outside the species. The genetic methods developed to date for gene mining, such as effectoromics and GWAS, provide researchers with the ability to identify genes of interest more efficiently. Once identified, these genes are cloned using molecular markers (MAS or QRL) and can then be introduced into different cultivars using somatic hybridization or recombinant DNA technology. More innovative technologies have been developed lately, such as gene editing using the CRISPR system or gene silencing, by exploiting iRNA strategies that have emerged as promising tools for managing Phytophthora infestans, which can be employed. Also, gene pyramiding or gene stacking, which involves the accumulation of two or more R genes on the same individual plant, is an innovative method that has yielded many promising results. All these advances related to the development of molecular techniques for obtaining new potato cultivars resistant to P. infestans can contribute not only to reducing losses in agriculture but especially to ensuring food security and safety.
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Affiliation(s)
- Ioana Virginia Berindean
- Department of Crops Sciences: Genetics, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania; (I.V.B.)
| | - Abdelmoumen Taoutaou
- Laboratoire de Phytopathologie et Biologie Moléculaire, Département de Botanique, École Nationale, Supérieure Agronomique, Avenue Pasteur (ENSA-ES 1603), Hassan Badi, El-Harrach, Algiers 16200, Algeria
| | - Soumeya Rida
- Département d’Agronomie, Faculté des Sciences de la Nature et de la Vie (SNV), Université Chadli Bendjedid, BP N°73, El Tarf 36000, Algeria
| | - Andreea Daniela Ona
- Department of Crops Sciences: Plant Breeding, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania; (A.D.O.)
| | - Maria Floriana Stefan
- National Institute of Research and Development for Potato and Sugar Beet Braşov, Fundaturii Street 2, 500470 Braşov, Romania
| | - Alexandru Costin
- Department of Crops Sciences: Plant Breeding, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania; (A.D.O.)
| | - Ionut Racz
- Department of Crops Sciences: Genetics, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania; (I.V.B.)
| | - Leon Muntean
- Department of Crops Sciences: Plant Breeding, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania; (A.D.O.)
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Fan Y, Sun C, Yan K, Li P, Hein I, Gilroy EM, Kear P, Bi Z, Yao P, Liu Z, Liu Y, Bai J. Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:1400. [PMID: 38794470 PMCID: PMC11125032 DOI: 10.3390/plants13101400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.
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Affiliation(s)
- Youfang Fan
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Pengcheng Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Ingo Hein
- The James Hutton Institute, Dundee DD2 5DA, UK; (I.H.); (E.M.G.)
| | | | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing 102199, China;
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
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Wang F, Xia Z, Zou M, Zhao L, Jiang S, Zhou Y, Zhang C, Ma Y, Bao Y, Sun H, Wang W, Wang J. The autotetraploid potato genome provides insights into highly heterozygous species. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1996-2005. [PMID: 35767385 PMCID: PMC9491450 DOI: 10.1111/pbi.13883] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 05/19/2023]
Abstract
Potato (Solanum tuberosum L.) originated in the Andes and evolved its vegetative propagation strategy through short day-dependent tuber development. Herein, we present a high-quality, chromosome-scale reference genome sequence of a tetraploid potato cultivar. The total length of this genome assembly was 2.67 Gb, with scaffold N50 and contig N50 sizes of 46.24 and 2.19 Mb, respectively. In total, 1.69 Gb repetitive sequences were obtained through de novo annotation, and long terminal repeats were the main transposable elements. A total of 126 070 protein-coding genes were annotated, of which 125 077 (99.21%) were located on chromosomes. The 48 chromosomes were classified into four haplotypes. We annotated 31 506 homologous genes, including 5913 (18.77%) genes with four homologues, 11 103 (35.24%) with three homologues, 12 177 (38.65%) with two homologues and 2313 (7.34%) with one homologue. MLH3, MSH6/7 and RFC3, which are the genes involved in the mismatch repair pathway, were found to be significantly expanded in the tetraploid potato genome relative to the diploid potato genome. Genome-wide association analysis revealed that cytochrome P450, flavonoid synthesis, chalcone enzyme, glycosyl hydrolase and glycosyl transferase genes were significantly correlated with the flesh colours of potato tuber in 150 tetraploid potatoes. This study provides valuable insights into the highly heterozygous autotetraploid potato genome and may facilitate the development of tools for potato cultivar breeding and further studies on autotetraploid crops.
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Affiliation(s)
- Fang Wang
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
| | - Zhiqiang Xia
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Meiling Zou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Long Zhao
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
| | - Sirong Jiang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Yun Zhou
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
| | - Chenji Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Yongzhen Ma
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
| | - Yuting Bao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Haihong Sun
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
| | - Wenquan Wang
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Jian Wang
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
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Hyper-seq: A novel, effective and flexible marker-assisted selection and genotyping approach. Innovation (N Y) 2022; 3:100254. [PMID: 35602119 PMCID: PMC9118915 DOI: 10.1016/j.xinn.2022.100254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/26/2022] [Indexed: 11/21/2022] Open
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Zou M, Jiang S, Wang F, Zhao L, Zhang C, Bao Y, Chen Y, Xia Z. Feature Compression Applications of Genetic Algorithm. Front Genet 2022; 13:757524. [PMID: 35350241 PMCID: PMC8957834 DOI: 10.3389/fgene.2022.757524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
With the rapid development of molecular breeding technology and many new varieties breeding, a method is urgently needed to identify different varieties accurately and quickly. Using this method can not only help farmers feel convenient and efficient in the normal cultivation and breeding process but also protect the interests of breeders, producers and users. In this study, single nucleotide polymorphism (SNP) data of 533 Oryza sativa, 284 Solanum tuberosum and 247 Sus scrofa and 544 Manihot esculenta Crantz were used. The original SNPs were filtered and screened to remove the SNPs with deletion number more than 1% or the homozygous genotype 0/0 and 1/1 number less than 2. The correlation between SNPs were calculated, and the two adjacent SNPs with correlation R2 > 0.95 were retained. The genetic algorithm program was developed to convert the genotype format and randomly combine SNPs to calculate a set of a small number of SNPs which could distinguish all varieties in different species as fingerprint data, using Matlab platform. The successful construction of three sets of fingerprints showed that the method developed in this study was effective in animals and plants. The population structure analysis showed that the genetic algorithm could effectively obtain the core SNPs for constructing fingerprints, and the fingerprint was practical and effective. At present, the two-dimensional code of Manihot esculenta Crantz fingerprint obtained by this method has been applied to field planting. This study provides a novel idea for the Oryza sativa, Solanum tuberosum, Sus scrofa and Manihot esculenta Crantz identification of various species, lays foundation for the cultivation and identification of new varieties, and provides theoretical significance for many other species fingerprints construction.
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Affiliation(s)
- Meiling Zou
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.,Hainan University, Haikou, China
| | | | - Fang Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | - Long Zhao
- Hainan University, Haikou, China.,Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | | | | | | | - Zhiqiang Xia
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.,Hainan University, Haikou, China
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Yepuri V, Jalali S, Mudunuri V, Pothakani S, Kancharla N, Arockiasamy S. Genotyping by sequencing-based linkage map construction and identification of quantitative trait loci for yield-related traits and oil content in Jatropha (Jatropha curcas L.). Mol Biol Rep 2022; 49:4293-4306. [PMID: 35239140 DOI: 10.1007/s11033-022-07264-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/14/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Jatropha (Jatropha curcas L.) has been considered as a potential bioenergy crop and its genetic improvement is essential for higher seed yield and oil content which has been hampered due to lack of desirable molecular markers. METHODS AND RESULTS An F2 population was created using an intraspecific cross involving a Central American line RJCA9 and an Asiatic species RJCS-9 to develop a dense genetic map and for Quantitative trait loci (QTL) identification. The genotyping-by-sequencing (GBS) approach was used to genotype the mapping population of 136 F2 individuals along with the two parental lines for classification of the genotypes based on single nucleotide polymorphism (SNPs). NextSeq 2500 sequencing technology provided a total of 517.23 million clean reads, with an average of ~ 3.8 million reads per sample. We analysed 411 SNP markers and developed 11 linkage groups. The total length of the genetic map was 4092.3 cM with an average marker interval of 10.04 cM. We have identified a total of 83 QTLs for various yield and oil content governing traits. The percentage of phenotypic variation (PV) was found to be in the range of 8.81 to 65.31%, and a QTL showed the maximum PV of 65.3% for a total seed number on the 6th linkage group (LG). CONCLUSIONS The QTLs detected in this study for various phenotypic traits will lay down the path for marker-assisted breeding in the future and cloning of genes that are responsible for phenotypic variation.
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Affiliation(s)
- Vijay Yepuri
- Agronomy Division, Reliance Technology Group, Reliance Industries Ltd, Ghansoli, Navi Mumbai, 400701, India
| | - Saakshi Jalali
- Agronomy Division, Reliance Technology Group, Reliance Industries Ltd, Ghansoli, Navi Mumbai, 400701, India
| | - Vishwnadharaju Mudunuri
- Jatropha Breeding station, Reliance Industries Ltd, IDA-Peddapuram, ADB Road, Samalkota, Andhra Pradesh, 533440, India
| | - Sai Pothakani
- Jatropha Breeding station, Reliance Industries Ltd, IDA-Peddapuram, ADB Road, Samalkota, Andhra Pradesh, 533440, India
| | - Nagesh Kancharla
- Agronomy Division, Reliance Technology Group, Reliance Industries Ltd, Ghansoli, Navi Mumbai, 400701, India
| | - S Arockiasamy
- Agronomy Division, Reliance Technology Group, Reliance Industries Ltd, Ghansoli, Navi Mumbai, 400701, India.
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Wang F, Zou M, Zhao L, Xia Z, Wang J. Genome-Wide Association Mapping of Late Blight Tolerance Trait in Potato ( Solanum tuberosum L.). Front Genet 2021; 12:714575. [PMID: 34659338 PMCID: PMC8517323 DOI: 10.3389/fgene.2021.714575] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022] Open
Abstract
Uncovering the genetic basis and optimizing the late blight tolerance trait in potatoes (Solanum tuberosum L.) are crucial for potato breeding. Late blight disease is one of the most significant diseases hindering potato production. The traits of late blight tolerance were evaluated for 284 potato cultivars to identify loci significantly associated with the late blight tolerance trait. Of all, 37 and 15 were the most tolerant to disease, and 107 and 30 were the most susceptible. A total of 22,489 high-quality single-nucleotide polymorphisms and indels were identified in 284 potato cultivars. All the potato cultivars were clustered into eight subgroups using population structure analysis and principal component analysis, which were consistent with the results of the phylogenetic tree analysis. The average genetic diversity for all 284 potato cultivars was 0.216, and the differentiation index of each subgroup was 0.025–0.149. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about 0.9 kb. A genome-wide association study using a mixed linear model identified 964 loci significantly associated with the late blight tolerance trait. Fourteen candidate genes for late blight tolerance traits were identified, including genes encoding late blight tolerance protein, chitinase 1, cytosolic nucleotide-binding site–leucine-rich repeat tolerance protein, protein kinase, ethylene-responsive transcription factor, and other potential plant tolerance-related proteins. This study provides novel insights into the genetic architecture of late blight tolerance traits and will be helpful for late blight tolerance in potato breeding.
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Affiliation(s)
- Fang Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China.,National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China.,Key Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Xining, China.,Qinghai Provincial Key Laboratory of Potato Breeding, Xining, China
| | - Meiling Zou
- College of Tropical Crops, Hainan University, Haikou, China.,Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Long Zhao
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China.,National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China.,Key Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Xining, China.,Qinghai Provincial Key Laboratory of Potato Breeding, Xining, China
| | - Zhiqiang Xia
- College of Tropical Crops, Hainan University, Haikou, China.,Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Jian Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China.,National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China.,Key Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Xining, China.,Qinghai Provincial Key Laboratory of Potato Breeding, Xining, China
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Fang K, Xia Z, Li H, Jiang X, Qin D, Wang Q, Wang Q, Pan C, Li B, Wu H. Genome-wide association analysis identified molecular markers associated with important tea flavor-related metabolites. HORTICULTURE RESEARCH 2021; 8:42. [PMID: 33642595 PMCID: PMC7917101 DOI: 10.1038/s41438-021-00477-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 05/02/2023]
Abstract
The characteristic secondary metabolites in tea (theanine, caffeine, and catechins) are important factors contributing to unique tea flavors. However, there has been relatively little research on molecular markers related to these metabolites. Thus, we conducted a genome-wide association analysis of the levels of these tea flavor-related metabolites in three seasons. The theanine, caffeine, and catechin levels in Population 1 comprising 191 tea plant germplasms were examined, which revealed that their heritability exceeded 0.5 in the analyzed seasons, with the following rank order (highest to lowest heritabilities): (+)-catechin > (-)-gallocatechin gallate > caffeine = (-)-epicatechin > (-)-epigallocatechin-3-gallate > theanine > (-)-epigallocatechin > (-)-epicatechin-3-gallate > catechin gallate > (+)-gallocatechin. The SNPs detected by amplified-fragment SNP and methylation sequencing divided Population 1 into three groups and seven subgroups. An association analysis yielded 307 SNP markers related to theanine, caffeine, and catechins that were common to all three seasons. Some of the markers were pleiotropic. The functional annotation of 180 key genes at the SNP loci revealed that FLS, UGT, MYB, and WD40 domain-containing proteins, as well as ATP-binding cassette transporters, may be important for catechin synthesis. KEGG and GO analyses indicated that these genes are associated with metabolic pathways and secondary metabolite biosynthesis. Moreover, in Population 2 (98 tea plant germplasm resources), 30 candidate SNPs were verified, including 17 SNPs that were significantly or extremely significantly associated with specific metabolite levels. These results will provide a foundation for future research on important flavor-related metabolites and may help accelerate the breeding of new tea varieties.
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Affiliation(s)
- Kaixing Fang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Zhiqiang Xia
- Institute of Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570100, China
- Hainan University, Haikou, 570228, China
| | - Hongjian Li
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Xiaohui Jiang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Dandan Qin
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Qiushuang Wang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Qing Wang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Chendong Pan
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Bo Li
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China
| | - Hualing Wu
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, 510640, China.
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Mbanjo EGN, Rabbi IY, Ferguson ME, Kayondo SI, Eng NH, Tripathi L, Kulakow P, Egesi C. Technological Innovations for Improving Cassava Production in Sub-Saharan Africa. Front Genet 2021; 11:623736. [PMID: 33552138 PMCID: PMC7859516 DOI: 10.3389/fgene.2020.623736] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production.
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Affiliation(s)
| | | | | | | | - Ng Hwa Eng
- CGIAR Excellence in Breeding Platform, El Batan, Mexico
| | - Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- National Root Crops Research Institute, Umudike, Nigeria
- Department of Global Development, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
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Malik AI, Kongsil P, Nguyễn VA, Ou W, Sholihin, Srean P, Sheela MN, Becerra López-Lavalle LA, Utsumi Y, Lu C, Kittipadakul P, Nguyễn HH, Ceballos H, Nguyễn TH, Selvaraj Gomez M, Aiemnaka P, Labarta R, Chen S, Amawan S, Sok S, Youabee L, Seki M, Tokunaga H, Wang W, Li K, Nguyễn HA, Nguyễn VĐ, Hàm LH, Ishitani M. Cassava breeding and agronomy in Asia: 50 years of history and future directions. BREEDING SCIENCE 2020; 70:145-166. [PMID: 32523397 PMCID: PMC7272245 DOI: 10.1270/jsbbs.18180] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 09/29/2019] [Indexed: 09/29/2023]
Abstract
In Asia, cassava (Manihot esculenta) is cultivated by more than 8 million farmers, driving the rural economy of many countries. The International Center for Tropical Agriculture (CIAT), in partnership with national agricultural research institutes (NARIs), instigated breeding and agronomic research in Asia, 1983. The breeding program has successfully released high-yielding cultivars resulting in an average yield increase from 13.0 t ha-1 in 1996 to 21.3 t ha-1 in 2016, with significant economic benefits. Following the success in increasing yields, cassava breeding has turned its focus to higher-value traits, such as waxy cassava, to reach new market niches. More recently, building resistance to invasive pests and diseases has become a top priority due to the emergent threat of cassava mosaic disease (CMD). The agronomic research involves driving profitability with advanced technologies focusing on better agronomic management practices thereby maintaining sustainable production systems. Remote sensing technologies are being tested for trait discovery and large-scale field evaluation of cassava. In summary, cassava breeding in Asia is driven by a combination of food and market demand with technological innovations to increase the productivity. Further, exploration in the potential of data-driven agriculture is needed to empower researchers and producers for sustainable advancement.
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Affiliation(s)
- Al Imran Malik
- International Center for Tropical Agriculture (CIAT-Laos), Lao PDR Office, Dong Dok, Ban Nongviengkham, Vientiane, Lao PDR
| | - Pasajee Kongsil
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Vũ Anh Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Wenjun Ou
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Sholihin
- Indonesian Legume and Tuber Crops Research Institute, Kendalpayak Km 8, PO BOX 66, Malang 65101, Indonesia
| | - Pao Srean
- Faculty of Agriculture & Food Processing, University of Battambang, Battambang, Cambodia
| | - MN Sheela
- Central Tuber Crops Research Institute Sreekariyam, Thiruvananthapuram-605 017, Kerala, India
| | | | - Yoshinori Utsumi
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Cheng Lu
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Piya Kittipadakul
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Hữu Hỷ Nguyễn
- Hung Loc Agricultural Research Center, Institute for Agriculture in Southern Vietnam, 121 Nguyen Binh Khiem, District 1, HCM City, Vietnam
| | - Hernan Ceballos
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Trọng Hiển Nguyễn
- Root and Tuber Crop Research and Development Center, Food and Field Crop Research Institute, Vinh Quynh, Thanh Tri, Hanoi, Vietnam
| | - Michael Selvaraj Gomez
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Pornsak Aiemnaka
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Ricardo Labarta
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Songbi Chen
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Suwaluk Amawan
- Rayong Field Crops Research Center, Sukumvit Rd, Huaypong, Meang, Rayong 21150, Thailand
| | - Sophearith Sok
- International Center for Tropical Agriculture (CIAT-Asia), Phnom Penh, Cambodia
| | - Laothao Youabee
- International Center for Tropical Agriculture (CIAT-Laos), Lao PDR Office, Dong Dok, Ban Nongviengkham, Vientiane, Lao PDR
| | - Motoaki Seki
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroki Tokunaga
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Wenquan Wang
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Kaimian Li
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Hai Anh Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Văn Đồng Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Lê Huy Hàm
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Manabu Ishitani
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
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11
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Cerruti E, Comino C, Acquadro A, Marconi G, Repetto AM, Pisanu AB, Pilia R, Albertini E, Portis E. Analysis of DNA Methylation Patterns Associated with In Vitro Propagated Globe Artichoke Plants Using an EpiRADseq-Based Approach. Genes (Basel) 2019; 10:E263. [PMID: 30939865 PMCID: PMC6523903 DOI: 10.3390/genes10040263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 01/16/2023] Open
Abstract
Globe artichoke represents one of the main horticultural species of the Mediterranean basin, and 'Spinoso sardo' is the most widespread and economically relevant varietal type in Sardinia, Italy. In the last decades, in vitro culture of meristematic apices has increased the frequency of aberrant plants in open-field production. These off-type phenotypes showed highly pinnate-parted leaves and late inflorescence budding, and emerged from some branches of the true-to-type 'Spinoso sardo' plants. This phenomenon cannot be foreseen and is reversible through generations, suggesting the occurrence of epigenetic alterations. Here, we report an exploratory study on DNA methylation patterns in off-type/true-to-type globe artichoke plants, using a modified EpiRADseq technology, which allowed the identification of 2,897 differentially methylated loci (DML): 1,998 in CG, 458 in CHH, and 441 in CHG methylation contexts of which 720, 88, and 152, respectively, were in coding regions. Most of them appeared involved in primary metabolic processes, mostly linked to photosynthesis, regulation of flower development, and regulation of reproductive processes, coherently with the observed phenotype. Differences in the methylation status of some candidate genes were integrated with transcriptional analysis to test whether these two regulation levels might interplay in the emergence and spread of the 'Spinoso sardo' non-conventional phenotype.
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Affiliation(s)
- Elisa Cerruti
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
| | - Gianpiero Marconi
- Department of Agricultural, Food, and Environmental Sciences, University of Perugia, 06121 Perugia, Italy.
| | - Anna Maria Repetto
- Agris Sardegna-Agenzia Regionale per la Ricerca in Agricoltura-Servizio Ricerca sui Sistemi Colturali Erbacei, 09123 Cagliari, Italy.
| | - Anna Barbara Pisanu
- Agris Sardegna-Agenzia Regionale per la Ricerca in Agricoltura-Servizio Ricerca sui Sistemi Colturali Erbacei, 09123 Cagliari, Italy.
| | - Roberto Pilia
- Agris Sardegna-Agenzia Regionale per la Ricerca in Agricoltura-Servizio Ricerca sui Sistemi Colturali Erbacei, 09123 Cagliari, Italy.
| | - Emidio Albertini
- Department of Agricultural, Food, and Environmental Sciences, University of Perugia, 06121 Perugia, Italy.
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
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12
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Construction of a high-density linkage map and QTL mapping for important agronomic traits in Stylosanthes guianensis (Aubl.) Sw. Sci Rep 2019; 9:3834. [PMID: 30846860 PMCID: PMC6405868 DOI: 10.1038/s41598-019-40489-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 02/18/2019] [Indexed: 11/15/2022] Open
Abstract
Stylosanthes guianensis (Aubl.) Sw. is an economically important pasture and forage legume in tropical regions of the world. Genetic improvement of the crop can be enhanced through marker-assisted breeding. However, neither single nucleotide polymorphism (SNP) markers nor SNP-based genetic linkage map has been previously reported. In this study, a high-quality genetic linkage map of 2572 SNP markers for S. guianensis is generated using amplified-fragment single nucleotide polymorphism and methylation (AFSM) approach. The genetic map has 10 linkage groups (LGs), which spanned 2226.6 cM, with an average genetic distance of 0.87 cM between adjacent markers. Genetic mapping of quantitative trait loci (QTLs) for important agronomic traits such as yield-related and nutritional or quality-related traits was performed using F2 progeny of a cross between a male-sterile female parent TPRC1979 and male parent TPRCR273 with contrasting phenotypes for morphological and physiological traits. A total of 30 QTLs for 8 yield-related traits and 18 QTLs for 4 nutritional or quality-related traits are mapped on the linkage map. Both the high-quality genetic linkage map and the QTL mapping for important agronomic traits described here will provide valuable genetic resources for marker-assisted selection for S. guianensis.
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13
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Zhang J, Yang J, Yang Y, Luo J, Zheng X, Wen C, Xu Y. Transcription Factor CsWIN1 Regulates Pericarp Wax Biosynthesis in Cucumber Grafted on Pumpkin. FRONTIERS IN PLANT SCIENCE 2019; 10:1564. [PMID: 31850038 PMCID: PMC6895144 DOI: 10.3389/fpls.2019.01564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 11/07/2019] [Indexed: 05/21/2023]
Abstract
Pericarp wax of cucumber is an important economic trait, determining sales and marketing. Grafting of cucumber onto pumpkin rootstock (Cucurbita moschata) is an effective way to produce glossy cucumber fruits. However, the molecular regulation mechanism of this phenomenon remains largely unknown. In the present study, transcriptome analyses, genome-wide DNA methylation sequencing, and wax metabolite analysis were performed on the pericarp of self-rooted versus grafted cucumber. We identified the AP2/ERF-type transcription factor CsWIN1 as methylated and significantly upregulated in grafted cucumber compared to self-rooted cucumber. The increased expression of CsWIN1 was also positively correlated with several key wax biosynthesis genes, including CsCER1, CsCER1-1, CsCER4, CsKCS1, and the wax transporter gene CsABC. The transcriptome expression level of these genes was validated through qRT-PCR profiles. Furthermore, wax metabolite analysis showed that more wax ester (C20 fatty acid composition), but fewer alkanes (C29 and C31) were deposited in grafted cucumber pericarp. The higher expression of CsWIN1 and wax biosynthesis genes was reflected in the glossier appearance of grafted pericarp, possibly the result of higher wax ester content and higher integration of small trichomes in the pericarp. This study demonstrates that grafting can affect the content and composition of pericarp wax in cucumber grafted on pumpkin, and a unique regulation model of CsWIN1 for wax biosynthesis may exist in cucumber.
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Affiliation(s)
- Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
| | - Yang Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
| | - Jiang Luo
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
| | - Xuyang Zheng
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- *Correspondence: Changlong Wen, ; Yong Xu,
| | - Yong Xu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- *Correspondence: Changlong Wen, ; Yong Xu,
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14
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Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare). EPIGENOMES 2018. [DOI: 10.3390/epigenomes2020012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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15
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Mayne BT, Leemaqz SY, Buckberry S, Rodriguez Lopez CM, Roberts CT, Bianco-Miotto T, Breen J. msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data. Sci Rep 2018; 8:2190. [PMID: 29391490 PMCID: PMC5794748 DOI: 10.1038/s41598-018-19655-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/04/2018] [Indexed: 12/02/2022] Open
Abstract
Genotyping-by-sequencing (GBS) or restriction-site associated DNA marker sequencing (RAD-seq) is a practical and cost-effective method for analysing large genomes from high diversity species. This method of sequencing, coupled with methylation-sensitive enzymes (often referred to as methylation-sensitive restriction enzyme sequencing or MRE-seq), is an effective tool to study DNA methylation in parts of the genome that are inaccessible in other sequencing techniques or are not annotated in microarray technologies. Current software tools do not fulfil all methylation-sensitive restriction sequencing assays for determining differences in DNA methylation between samples. To fill this computational need, we present msgbsR, an R package that contains tools for the analysis of methylation-sensitive restriction enzyme sequencing experiments. msgbsR can be used to identify and quantify read counts at methylated sites directly from alignment files (BAM files) and enables verification of restriction enzyme cut sites with the correct recognition sequence of the individual enzyme. In addition, msgbsR assesses DNA methylation based on read coverage, similar to RNA sequencing experiments, rather than methylation proportion and is a useful tool in analysing differential methylation on large populations. The package is fully documented and available freely online as a Bioconductor package (https://bioconductor.org/packages/release/bioc/html/msgbsR.html).
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Affiliation(s)
- Benjamin T Mayne
- Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia. .,Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Shalem Y Leemaqz
- Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.,Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.,Plant Energy Biology, ARC Centre of Excellence, The University of Western Australia, Perth, WA, 6009, Australia
| | - Carlos M Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Claire T Roberts
- Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.,Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Tina Bianco-Miotto
- Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.,Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, 5005, Australia
| | - James Breen
- Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia. .,Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
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16
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Xia Z, Zhang S, Wen M, Lu C, Sun Y, Zou M, Wang W. Construction of an ultrahigh-density genetic linkage map for Jatropha curcas L. and identification of QTL for fruit yield. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:3. [PMID: 29321812 PMCID: PMC5759280 DOI: 10.1186/s13068-017-1004-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/22/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND As an important biofuel plant, the demand for higher yield Jatropha curcas L. is rapidly increasing. However, genetic analysis of Jatropha and molecular breeding for higher yield have been hampered by the limited number of molecular markers available. RESULTS An ultrahigh-density linkage map for a Jatropha mapping population of 153 individuals was constructed and covered 1380.58 cM of the Jatropha genome, with average marker density of 0.403 cM. The genetic linkage map consisted of 3422 SNP and indel markers, which clustered into 11 linkage groups. With this map, 13 repeatable QTLs (reQTLs) for fruit yield traits were identified. Ten reQTLs, qNF-1, qNF-2a, qNF-2b, qNF-2c, qNF-3, qNF-4, qNF-6, qNF-7a, qNF-7b and qNF-8, that control the number of fruits (NF) mapped to LGs 1, 2, 3, 4, 6, 7 and 8, whereas three reQTLs, qTWF-1, qTWF-2 and qTWF-3, that control the total weight of fruits (TWF) mapped to LGs 1, 2 and 3, respectively. It is interesting that there are two candidate critical genes, which may regulate Jatropha fruit yield. We also identified three pleiotropic reQTL pairs associated with both the NF and TWF traits. CONCLUSION This study is the first to report an ultrahigh-density Jatropha genetic linkage map construction, and the markers used in this study showed great potential for QTL mapping. Thirteen fruit-yield reQTLs and two important candidate genes were identified based on this linkage map. This genetic linkage map will be a useful tool for the localization of other economically important QTLs and candidate genes for Jatropha.
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Affiliation(s)
- Zhiqiang Xia
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Shengkui Zhang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Mingfu Wen
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Cheng Lu
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Yufang Sun
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Meiling Zou
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Wenquan Wang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
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17
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Zhang S, Chen X, Lu C, Ye J, Zou M, Lu K, Feng S, Pei J, Liu C, Zhou X, Ma P, Li Z, Liu C, Liao Q, Xia Z, Wang W. Genome-Wide Association Studies of 11 Agronomic Traits in Cassava ( Manihot esculenta Crantz). FRONTIERS IN PLANT SCIENCE 2018; 9:503. [PMID: 29725343 PMCID: PMC5917017 DOI: 10.3389/fpls.2018.00503] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/03/2018] [Indexed: 05/21/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 × 10-4 for all sampled landraces. This average nucleotide diversity was 1.97 × 10-4, 1.01 × 10-4, and 1.89 × 10-4 for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about ∼8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes.13G023300, Manes.16G000800, Manes.02G154700, Manes.02G192500, and Manes.09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes.05G164500, Manes.05G164600, Manes.04G057300, Manes.01G202000, and Manes.03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava.
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Affiliation(s)
- Shengkui Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xin Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Cheng Lu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianqiu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Meiling Zou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kundian Lu
- Wuming Agricultural Technology Extension Center, Nanning, China
| | - Subin Feng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jinli Pei
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chen Liu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xincheng Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ping’an Ma
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhaogui Li
- Wuming Agricultural Technology Extension Center, Nanning, China
| | - Cuijuan Liu
- Hepu Institute of Agricultural Science, Beihai, China
| | - Qi Liao
- Hepu Institute of Agricultural Science, Beihai, China
| | - Zhiqiang Xia
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Zhiqiang Xia, Wenquan Wang,
| | - Wenquan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Zhiqiang Xia, Wenquan Wang,
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18
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Zou M, Lu C, Zhang S, Chen Q, Sun X, Ma P, Hu M, Peng M, Ma Z, Chen X, Zhou X, Wang H, Feng S, Fang K, Xie H, Li Z, Liu K, Qin Q, Pei J, Wang S, Pan K, Hu W, Feng B, Fan D, Zhou B, Wu C, Su M, Xia Z, Li K, Wang W. Epigenetic map and genetic map basis of complex traits in cassava population. Sci Rep 2017; 7:41232. [PMID: 28120898 PMCID: PMC5264614 DOI: 10.1038/srep41232] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/16/2016] [Indexed: 11/13/2022] Open
Abstract
Cassava (Manihot esculenta Crantz) is an important tropical starchy root crop that is adapted to drought but extremely cold sensitive. A cold-tolerant, high-quality, and robust supply of cassava is urgently needed. Here, we clarify genome-wide distribution and classification of CCGG hemi-methylation and full-methylation, and detected 77 much candidate QTLsepi for cold stress and 103 much candidate QTLsepi for storage root quality and yield in 186 cassava population, generated by crossing two non-inbred lines with female parent KU50 and male parent SC124 (KS population). We developed amplified-fragment single nucleotide polymorphism and methylation (AFSM) genetic map in this population. We also constructed the AFSM QTL map, identified 260 much candidate QTL genes for cold stress and 301 much candidate QTL genes for storage root quality and yield, based on the years greenhouse and field trials. This may accounted for a significant amount of the variation in the key traits controlling cold tolerance and the high quality and yield of cassava.
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Affiliation(s)
- Meiling Zou
- Huazhong Agricultural University, Wuhan, China.,The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Cheng Lu
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Shengkui Zhang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Qing Chen
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Xianglai Sun
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Pingan Ma
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Meizhen Hu
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Ming Peng
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Zilong Ma
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Xin Chen
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Xincheng Zhou
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Haiyan Wang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Subin Feng
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Kaixin Fang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Hairong Xie
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Zaiyun Li
- Huazhong Agricultural University, Wuhan, China
| | - Kede Liu
- Huazhong Agricultural University, Wuhan, China
| | - Qiongyao Qin
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Jinli Pei
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Shujuan Wang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Kun Pan
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Wenbin Hu
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Binxiao Feng
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Dayong Fan
- Guangxi Academy of Agricultural Sciences, Guilin, China
| | - Bin Zhou
- Guangxi Academy of Agricultural Sciences, Guilin, China
| | - Chunling Wu
- Guangxi Academy of Agricultural Sciences, Guilin, China
| | - Ming Su
- Guangxi Academy of Agricultural Sciences, Guilin, China
| | - Zhiqiang Xia
- Huazhong Agricultural University, Wuhan, China.,The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Kaimian Li
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Wenquan Wang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
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19
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A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters (Crassostrea gigas × Crassostrea angulata) Using Genotyping-by-Sequencing. G3-GENES GENOMES GENETICS 2016; 6:1417-26. [PMID: 26994291 PMCID: PMC4856092 DOI: 10.1534/g3.116.026971] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Oysters are among the most important species in global aquaculture. Crassostrea gigas, and its subspecies C. angulata, are the major cultured species. To determine the genetic basis of growth-related traits in oysters, we constructed a second-generation linkage map from 3367 single-nucleotide polymorphisms (SNPs) based on genotyping-by-sequencing, genotyped from a C. gigas × C. angulata hybrid family. These 3367 SNPs were distributed on 1695 markers, which were assigned to 10 linkage groups. The genetic linkage map had a total length of 1084.3 cM, with an average of 0.8 cM between markers; it thus represents the densest genetic map constructed for oysters to date. Twenty-seven quantitative trait loci (QTL) for five growth-related traits were detected. These QTL could explain 4.2-7.7% (mean = 5.4%) of the phenotypic variation. In total, 50.8% of phenotypic variance for shell width, 7.7% for mass weight, and 34.1% for soft tissue weight were explained. The detected QTL were distributed among eight linkage groups, and more than half (16) were concentrated within narrow regions in their respective linkage groups. Thirty-eight annotated genes were identified within the QTL regions, two of which are key genes for carbohydrate metabolism. Other genes were found to participate in assembly and regulation of the actin cytoskeleton, signal transduction, and regulation of cell differentiation and development. The newly developed high-density genetic map, and the QTL and candidate genes identified provide a valuable genetic resource and a basis for marker-assisted selection for C. gigas and C. angulata.
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20
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Kitimu SR, Taylor J, March TJ, Tairo F, Wilkinson MJ, Rodríguez López CM. Meristem micropropagation of cassava (Manihot esculenta) evokes genome-wide changes in DNA methylation. FRONTIERS IN PLANT SCIENCE 2015; 6:590. [PMID: 26322052 PMCID: PMC4534864 DOI: 10.3389/fpls.2015.00590] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/16/2015] [Indexed: 05/25/2023]
Abstract
There is great interest in the phenotypic, genetic and epigenetic changes associated with plant in vitro culture known as somaclonal variation. In vitro propagation systems that are based on the use of microcuttings or meristem cultures are considered analogous to clonal cuttings and so widely viewed to be largely free from such somaclonal effects. In this study, we surveyed for epigenetic changes during propagation by meristem culture and by field cuttings in five cassava (Manihot esculenta) cultivars. Principal Co-ordinate Analysis of profiles generated by methylation-sensitive amplified polymorphism revealed clear divergence between samples taken from field-grown cuttings and those recovered from meristem culture. There was also good separation between the tissues of field samples but this effect was less distinct among the meristem culture materials. Application of methylation-sensitive Genotype by sequencing identified 105 candidate epimarks that distinguish between field cutting and meristem culture samples. Cross referencing the sequences of these epimarks to the draft cassava genome revealed 102 sites associated with genes whose homologs have been implicated in a range of fundamental biological processes including cell differentiation, development, sugar metabolism, DNA methylation, stress response, photosynthesis, and transposon activation. We explore the relevance of these findings for the selection of micropropagation systems for use on this and other crops.
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Affiliation(s)
- Shedrack R. Kitimu
- Plant Research Centre, School of Agriculture Food and Wine, Faculty of Sciences, University of AdelaideAdelaide, SA, Australia
| | - Julian Taylor
- Biometry Hub, School of Agriculture Food and Wine, Faculty of Sciences, University of AdelaideAdelaide, SA, Australia
| | - Timothy J. March
- School of Agriculture Food and Wine, Faculty of Sciences, University of AdelaideAdelaide, SA, Australia
| | - Fred Tairo
- Mikocheni Agricultural Research InstituteDar es Salaam, Tanzania
| | - Mike J. Wilkinson
- Plant Research Centre, School of Agriculture Food and Wine, Faculty of Sciences, University of AdelaideAdelaide, SA, Australia
| | - Carlos M. Rodríguez López
- Plant Research Centre, School of Agriculture Food and Wine, Faculty of Sciences, University of AdelaideAdelaide, SA, Australia
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