1
|
Poonam, Sharma R, Sharma P, Sharma NC, Kumar K, Singh KN, Bhardwaj V, Negi N, Chauhan N. Exploring genetic diversity and ascertaining genetic loci associated with important fruit quality traits in apple ( Malus × domestica Borkh.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1693-1716. [PMID: 38162921 PMCID: PMC10754789 DOI: 10.1007/s12298-023-01382-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Genetic diversity is the primary source of variability in any crop improvement program, and the diverse germplasm of any crop species represents an important genetic resource for gene or allele mining to meet future needs. Huge genetic and phenotypic diversity is present in the apple gene pool, even though, breeding programs have been mainly focused on a few traits of interests, which have resulted in the reduction of the diversity in the cultivated lines of apple. Therefore, the present study was carried out on 70 diverse apple genotypes with the objective of analyzing the genetic diversity and to identify the genetic loci associated with important fruit quality traits. A total of 140 SSR primers were used to characterize the 70 genotypes of apples, out of which only 88 SSRs were found to be polymorphic. The PIC values varied from 0.03 to 0.75. The value of MI, EMR, and RP varied from 0.03 to 3.5, 0.5 to 5.0, and 1.89 to 6.74, respectively. The dendrogram and structure analysis divided all the genotypes into two main groups. In addition to this, large phenotypic variability was observed for the fruit quality traits under study indicated the suitability of the genotypes for association studies. Altogether 71 novel MTAs were identified for 10 fruit quality traits, of which 15 for fruit length, 15 for fruit diameter, 12 for fruit weight, 2 for total sugar, 2 for TSS, 4 for reducing sugar, 5 for non-reducing sugar, 5 for fruit firmness, 5 for fruit acidity and 6 for anthocyanin, respectively. Consistent with the physicochemical evaluation of traits, there was a significant correlation coefficient among different fruit quality characters, and many common markers were found to be associated with these traits (fruit diameter, length, TSS, total sugar, acidity and anthocyanin, respectively) by using the different modeling techniques (GLM, MLM). The inferred genetic structure, diversity pattern and the identified MTAs will be serving as resourceful grounds for better predictions and understanding of apple genome towards efficient conservation and utilization of apple germplasm for facilitating genetic improvement of fruit quality traits. Furthermore, these findings also suggested that association mapping could be a viable alternative to the conventional QTL mapping approach in apple. Graphic abstract Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01382-w.
Collapse
Affiliation(s)
- Poonam
- Department of Biotechnology, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
- School of Bioengineering & Food Technology, Shoolini University, Solan, HP, 173 229, India
| | - Rajnish Sharma
- Department of Biotechnology, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
| | - Parul Sharma
- Department of Biotechnology, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
| | - Naveen C. Sharma
- Department of Fruit Science, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
| | - Kuldeep Kumar
- ICAR-Indian Institute of Pulses Research, Kanpur, UP 208 024 India
| | - Krishna Nand Singh
- Department of Botany, University of Delhi, North Campus, New Delhi, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, HP 171 004 India
| | - Narender Negi
- ICAR-NBPGR Regional Station, Phagli, Shimla, HP 171 004 India
| | - Neena Chauhan
- RHR&TS, Dr YS Parmar University of Horticulture & Forestry, Mashobra, Shimla, HP, 171 007 India
| |
Collapse
|
2
|
Qi X, Di Z, Li Y, Zhang Z, Guo M, Tong B, Lu Y, Zhang Y, Zheng J. Genome-Wide Identification and Expression Profiling of Heat Shock Protein 20 Gene Family in Sorbus pohuashanensis (Hance) Hedl under Abiotic Stress. Genes (Basel) 2022; 13:genes13122241. [PMID: 36553508 PMCID: PMC9778606 DOI: 10.3390/genes13122241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Small heat shock proteins (HSP20s) are a significant factor in plant growth and development in response to abiotic stress. In this study, we investigated the role of HSP20s' response to the heat stress of Sorbus pohuashanensis introduced into low-altitude areas. The HSP20 gene family was identified based on the genome-wide data of S. pohuashanensis, and the expression patterns of tissue specificity and the response to abiotic stresses were evaluated. Finally, we identified 38 HSP20 genes that were distributed on 16 chromosomes. Phylogenetic analysis of HSP20s showed that the closest genetic relationship to S. pohuashanensis (SpHSP20s) is Malus domestica, followed by Populus trichocarpa and Arabidopsis thaliana. According to phylogenetic analysis and subcellular localization prediction, the 38 SpHSP20s belonged to 10 subfamilies. Analysis of the gene structure and conserved motifs indicated that HSP20 gene family members are relatively conserved. Synteny analysis showed that the expansion of the SpHSP20 gene family was mainly caused by segmental duplication. In addition, many cis-acting elements connected with growth and development, hormones, and stress responsiveness were found in the SpHSP20 promoter region. Analysis of expression patterns showed that these genes were closely related to high temperature, drought, salt, growth, and developmental processes. These results provide information and a theoretical basis for the exploration of HSP20 gene family resources, as well as the domestication and genetic improvement of S. pohuashanensis.
Collapse
Affiliation(s)
- Xiangyu Qi
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Zexin Di
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Yuyan Li
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Zeren Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Miaomiao Guo
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Boqiang Tong
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Yizeng Lu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Yan Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Jian Zheng
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
- Correspondence:
| |
Collapse
|
3
|
Yao F, Song C, Wang H, Song S, Jiao J, Wang M, Zheng X, Bai T. Genome-Wide Characterization of the HSP20 Gene Family Identifies Potential Members Involved in Temperature Stress Response in Apple. Front Genet 2020; 11:609184. [PMID: 33240335 DOI: 10.3389/fgene.2020a.609184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/20/2020] [Indexed: 05/24/2023] Open
Abstract
Apple (Malus domestica Borkh.), an economically important tree fruit worldwide, frequently suffers from temperature stress during growth and development, which strongly affects the yield and quality. Heat shock protein 20 (HSP20) genes play crucial roles in protecting plants against abiotic stresses. However, they have not been systematically investigated in apple. In this study, we identified 41 HSP20 genes in the apple 'Golden Delicious' genome. These genes were unequally distributed on 15 different chromosomes and were classified into 10 subfamilies based on phylogenetic analysis and predicted subcellular localization. Chromosome mapping and synteny analysis indicated that three pairs of apple HSP20 genes were tandemly duplicated. Sequence analysis revealed that all apple HSP20 proteins reflected high structure conservation and most apple HSP20 genes (92.6%) possessed no introns, or only one intron. Numerous apple HSP20 gene promoter sequences contained stress and hormone response cis-elements. Transcriptome analysis revealed that 35 of 41 apple HSP20 genes were nearly unchanged or downregulated under normal temperature and cold stress, whereas these genes exhibited high-expression levels under heat stress. Subsequent qRT-PCR results showed that 12 of 29 selected apple HSP20 genes were extremely up-regulated (more than 1,000-fold) after 4 h of heat stress. However, the heat-upregulated genes were barely expressed or downregulated in response to cold stress, which indicated their potential function in mediating the response of apple to heat stress. Taken together, these findings lay the foundation to functionally characterize HSP20 genes to unravel their exact role in heat defense response in apple.
Collapse
Affiliation(s)
- Fuwen Yao
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Chunhui Song
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Hongtao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Shangwei Song
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Jian Jiao
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Miaomiao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Tuanhui Bai
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|
4
|
Yao F, Song C, Wang H, Song S, Jiao J, Wang M, Zheng X, Bai T. Genome-Wide Characterization of the HSP20 Gene Family Identifies Potential Members Involved in Temperature Stress Response in Apple. Front Genet 2020; 11:609184. [PMID: 33240335 PMCID: PMC7678413 DOI: 10.3389/fgene.2020.609184] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/20/2020] [Indexed: 11/13/2022] Open
Abstract
Apple (Malus domestica Borkh.), an economically important tree fruit worldwide, frequently suffers from temperature stress during growth and development, which strongly affects the yield and quality. Heat shock protein 20 (HSP20) genes play crucial roles in protecting plants against abiotic stresses. However, they have not been systematically investigated in apple. In this study, we identified 41 HSP20 genes in the apple ‘Golden Delicious’ genome. These genes were unequally distributed on 15 different chromosomes and were classified into 10 subfamilies based on phylogenetic analysis and predicted subcellular localization. Chromosome mapping and synteny analysis indicated that three pairs of apple HSP20 genes were tandemly duplicated. Sequence analysis revealed that all apple HSP20 proteins reflected high structure conservation and most apple HSP20 genes (92.6%) possessed no introns, or only one intron. Numerous apple HSP20 gene promoter sequences contained stress and hormone response cis-elements. Transcriptome analysis revealed that 35 of 41 apple HSP20 genes were nearly unchanged or downregulated under normal temperature and cold stress, whereas these genes exhibited high-expression levels under heat stress. Subsequent qRT-PCR results showed that 12 of 29 selected apple HSP20 genes were extremely up-regulated (more than 1,000-fold) after 4 h of heat stress. However, the heat-upregulated genes were barely expressed or downregulated in response to cold stress, which indicated their potential function in mediating the response of apple to heat stress. Taken together, these findings lay the foundation to functionally characterize HSP20 genes to unravel their exact role in heat defense response in apple.
Collapse
Affiliation(s)
- Fuwen Yao
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Chunhui Song
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Hongtao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Shangwei Song
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Jian Jiao
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Miaomiao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Tuanhui Bai
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|
5
|
Emeriewen OF, Richter K, Berner T, Keilwagen J, Schnable PS, Malnoy M, Peil A. Construction of a dense genetic map of the Malus fusca fire blight resistant accession MAL0045 using tunable genotyping-by-sequencing SNPs and microsatellites. Sci Rep 2020; 10:16358. [PMID: 33005026 PMCID: PMC7529804 DOI: 10.1038/s41598-020-73393-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
Although, the Pacific crabapple, Malus fusca, is a hardy and disease resistant species, studies relating to the genetics of its unique traits are very limited partly due to the lack of a genetic map of this interesting wild apple. An accession of M. fusca (MAL0045) of Julius Kühn-Institut collection in Germany is highly resistant to fire blight disease, incited by different strains of the causative pathogen—Erwinia amylovora. This is the most destructive bacterial disease of Malus of which most of the domesticated apples (Malus domestica) are susceptible. Using a scarcely dense genetic map derived from a population of 134 individuals of MAL0045 × ‘Idared’, the locus (Mfu10) controlling fire blight resistance mapped on linkage group 10 (LG10) and explained up to 66% of the phenotypic variance with different strains. Although the development of robust and tightly linked molecular markers on LG10 through chromosome walking approach led to the identification of a major candidate gene, any minor effect locus remained elusive possibly due to the lack of marker density of the entire genetic map. Therefore, we have developed a dense genetic map of M. fusca using tunable genotyping-by-sequencing (tGBS) approach. Of thousands of de novo SNPs identified, 2677 were informative in M. fusca and 90.5% of these successfully mapped. In addition, integration of SNP data and microsatellite (SSR) data resulted in a final map comprising 17 LGs with 613 loci spanning 1081.35 centi Morgan (cM). This map will serve as a template for mapping using different strains of the pathogen.
Collapse
Affiliation(s)
- Ofere Francis Emeriewen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326, Dresden, Germany.
| | - Klaus Richter
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Thomas Berner
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Jens Keilwagen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Patrick S Schnable
- Data2Bio LLC, Ames, IA, 50011-3650, USA.,Plant Sciences Institute, Iowa State University, 2035B Carver, Ames, IA, 50011-3650, USA
| | - Mickael Malnoy
- Research and Innovation Centre, Genomics and Biology of Fruit Crops Department, Fondazione Edmund Mach, Via E. Mach, 1, 38010, San Michele all 'Adige (Trentino), Italy
| | - Andreas Peil
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326, Dresden, Germany.
| |
Collapse
|
6
|
Cheng C, Che Q, Su S, Liu Y, Wang Y, Xu X. Genome-wide identification and characterization of Respiratory Burst Oxidase Homolog genes in six Rosaceae species and an analysis of their effects on adventitious rooting in apple. PLoS One 2020; 15:e0239705. [PMID: 32976536 PMCID: PMC7518606 DOI: 10.1371/journal.pone.0239705] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 09/12/2020] [Indexed: 11/25/2022] Open
Abstract
Adventitious root formation is essential for plant propagation, development, and response to various stresses. Reactive oxygen species (ROS) are essential for adventitious root formation. However, information on Respiratory Burst Oxidase Homolog (RBOH), a key enzyme that catalyzes the production ROS, remains limited in woody plants. Here, a total of 44 RBOH genes were identified from six Rosaceae species (Malus domestica, Prunus avium, Prunus dulcis 'Texas’, Rubus occidentalis, Fragaria vesca and Rosa chinensis), including ten from M. domestica. Their phylogenetic relationships, conserved motifs and gene structures were analyzed. Exogenous treatment with the RBOH protein inhibitor diphenyleneiodonium (DPI) completely inhibited adventitious root formation, whereas exogenous H2O2 treatment enhanced adventitious root formation. In addition, we found that ROS accumulated during adventitious root primordium inducing process. The expression levels of MdRBOH-H, MdRBOH-J, MdRBOH-A, MdRBOH-E1 and MdRBOH-K increased more than two-fold at days 3 or 9 after auxin treatment. In addition, cis-acting element analysis revealed that the MdRBOH-E1 promoter contained an auxin-responsive element and the MdRBOH-K promoter contained a meristem expression element. Based on the combined results from exogenous DPI and H2O2 treatment, spatiotemporal expression profiling, and cis-element analysis, MdRBOH-E1 and MdRBOH-K appear to be candidates for the control of adventitious rooting in apple.
Collapse
Affiliation(s)
- Chenxia Cheng
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Qinqin Che
- Qingdao Key Laboratory of Genetic Development and Breeding in Horticultural Plants, Qingdao Agricultural University, Qingdao, China
| | - Shenghui Su
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, China
| | - Yuan Liu
- Laixi Elite Cultivars Propagation Farm, Laixi, Qingdao, China
| | - Yongzhang Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Xiaozhao Xu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- * E-mail:
| |
Collapse
|
7
|
Genome-Wide Identification and Characterization of Apple P3A-Type ATPase Genes, with Implications for Alkaline Stress Responses. FORESTS 2020. [DOI: 10.3390/f11030292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The P3A-type ATPases play crucial roles in various physiological processes via the generation of a transmembrane H+ gradient (∆pH). However, the P3A-type ATPase superfamily in apple remains relatively uncharacterized. In this study, 15 apple P3A-type ATPase genes were identified based on the new GDDH13 draft genome sequence. The exon-intron organization of these genes, the physical and chemical properties, and conserved motifs of the encoded enzymes were investigated. Analyses of the chromosome localization and ω values of the apple P3A-type ATPase genes revealed the duplicated genes were influenced by purifying selection pressure. Six clades and frequent old duplication events were detected. Moreover, the significance of differences in the evolutionary rates of the P3A-type ATPase genes were revealed. An expression analysis indicated that all of the P3A-type ATPase genes were specifically expressed in more than one tissue. The expression of one P3A-type ATPase gene (MD15G1108400) was significantly upregulated in response to alkaline stress. Furthermore, a subcellular localization assay indicated that MD15G1108400 is targeted to the plasma membrane. These results imply that MD15G1108400 may be involved in responses to alkaline stress. Our data provide insights into the molecular characteristics and evolutionary patterns of the apple P3A-type ATPase gene family and provide a theoretical foundation for future in-depth functional characterizations of P3A-type ATPase genes under alkaline conditions.
Collapse
|
8
|
Ma B, Liao L, Fang T, Peng Q, Ogutu C, Zhou H, Ma F, Han Y. A Ma10 gene encoding P-type ATPase is involved in fruit organic acid accumulation in apple. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:674-686. [PMID: 30183123 PMCID: PMC6381788 DOI: 10.1111/pbi.13007] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/02/2018] [Accepted: 08/31/2018] [Indexed: 05/23/2023]
Abstract
Acidity is one of the main determinants of fruit organoleptic quality. Here, comparative transcriptome analysis was conducted between two cultivars that showed a significant difference in fruit acidity, but contained homozygous non-functional alleles at the major gene Ma1 locus controlling apple fruit acidity. A candidate gene for fruit acidity, designated M10, was identified. The M10 gene encodes a P-type proton pump, P3A -ATPase, which facilitates malate uptake into the vacuole. The Ma10 gene is significantly associated with fruit malate content, accounting for ~7.5% of the observed phenotypic variation in apple germplasm. Subcellular localization assay showed that the Ma10 is targeted to the tonoplast. Overexpression of the Ma10 gene can complement the defect in proton transport of the mutant YAK2 yeast strain and enhance the accumulation of malic acid in apple callus. Moreover, its ectopic expression in tomato induces a decrease in fruit pH. These results suggest that the Ma10 gene has the capacity for proton pumping and plays an important role in fruit vacuolar acidification in apple. Our study provides useful knowledge towards comprehensive understanding of the complex mechanism regulating apple fruit acidity.
Collapse
Affiliation(s)
- Baiquan Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden of the Chinese Academy of SciencesWuhanChina
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden of the Chinese Academy of SciencesWuhanChina
- Sino‐African Joint Research CenterChinese Academy of SciencesWuhanChina
| | - Ting Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden of the Chinese Academy of SciencesWuhanChina
- Graduate University of Chinese Academy of SciencesBeijingChina
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden of the Chinese Academy of SciencesWuhanChina
- Graduate University of Chinese Academy of SciencesBeijingChina
| | - Collins Ogutu
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden of the Chinese Academy of SciencesWuhanChina
- Graduate University of Chinese Academy of SciencesBeijingChina
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden of the Chinese Academy of SciencesWuhanChina
- Sino‐African Joint Research CenterChinese Academy of SciencesWuhanChina
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden of the Chinese Academy of SciencesWuhanChina
- Sino‐African Joint Research CenterChinese Academy of SciencesWuhanChina
| |
Collapse
|
9
|
Güney M, Kafkas S, Keles H, Aras S, Ercişli S. Characterization of hawthorn ( Crataegus spp.) genotypes by SSR markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:1221-1230. [PMID: 30425436 PMCID: PMC6214427 DOI: 10.1007/s12298-018-0604-6] [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: 05/13/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 06/09/2023]
Abstract
Hawthorn (Crataegus spp.) is an edible wild fruit that is used in traditional medicine, landscape studies, and food and beverage industries in many countries. It is an important wild plant species in Turkey and is numerous in the Yozgat Province. Genetic and breeding studies on hawthorn are very limited. Therefore, we aimed to characterize 91 hawthorn genotypes using simple sequence repeat (SSR) markers. The SSRs were developed from apple and pear and were screened in hawthorn for amplification and polymorphisms. A total of 265 alleles were detected from thirty-two SSR primer pairs, and those were used to identify genetic relationships. The number of alleles ranged from 2 to 21 alleles per locus with a mean value of 8.28. The Hi05b09 locus showed the highest allele number (Na = 21). The polymorphism information content (PIC) values ranged from 0.16 (CH03d10) to 0.89 (C6554) with a mean value of 0.60. An Unweighted Pair Group Method with Arithmetic Average method was used to cluster the genotypes, and four major clusters were obtained from the amplification of the SSRs. STRUCTURE software identified four populations (ΔK = 4) and eight sub-populations (ΔK = 8), and four major clusters similar results to UPGMA analysis. Our study showed that the SSR markers could be utilized as a reliable tool for the determination of genetic variations and relationships of hawthorn genotypes. A basic molecular analysis on the hawthorn genotypes identified in this study will promote the collection of germplasm collection and the selection of parents' in future cross-breeding studies.
Collapse
Affiliation(s)
- Murat Güney
- Department of Horticulture, Faculty of Agriculture, University of Yozgat Bozok, Yozgat, Turkey
| | - Salih Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Cukurova, Adana, Turkey
| | - Hakan Keles
- Department of Horticulture, Faculty of Agriculture, University of Yozgat Bozok, Yozgat, Turkey
| | - Servet Aras
- Department of Horticulture, Faculty of Agriculture, University of Yozgat Bozok, Yozgat, Turkey
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, University of Atatürk, Erzurum, Turkey
| |
Collapse
|
10
|
Ma B, Yuan Y, Gao M, Xing L, Li C, Li M, Ma F. Genome-wide Identification, Classification, Molecular Evolution and Expression Analysis of Malate Dehydrogenases in Apple. Int J Mol Sci 2018; 19:E3312. [PMID: 30356028 PMCID: PMC6274877 DOI: 10.3390/ijms19113312] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/23/2022] Open
Abstract
Malate dehydrogenase plays crucial roles in energy homeostasis, plant development and cold and salt tolerance, as it mediates the reversible conversion of malate to oxaloacetate. However, the evolutionary pattern of MDH genes in apple remains elusive. In this study, a total of 20 MDH genes were identified from the "Golden Delicious" apple draft genome. We revealed the physiological and biochemical properties, gene structure, and conserved motifs of MdMDH genes. Chromosomal localization and Ka/Ks ratio analysis of MdMDH genes revealed different selective pressures acted on duplicated MdMDH genes. Exploration of the phylogenetic relationships revealed six clades and similar frequencies between old and recent duplications, and significant differences in the evolutionary rates of the MDH gene family were observed. One MdMDH gene, MDP0000807458, which was highly expressed during apple fruit development and flower bud differentiation, was under positive selection. Thus, we speculated that MDP0000807458 is a likely candidate gene involved in regulation of flower bud differentiation and organic acid metabolism in apple fruits. This study provides a foundation for improved understanding of the molecular evolution of MdMDH genes and further facilitates the functional analysis of MDP0000807458 to unravel its exact role in flower bud differentiation and organic acid metabolism.
Collapse
Affiliation(s)
- Baiquan Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yangyang Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Meng Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Libo Xing
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Cuiying Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| |
Collapse
|
11
|
Ma B, Yuan Y, Gao M, Qi T, Li M, Ma F. Genome-Wide Identification, Molecular Evolution, and Expression Divergence of Aluminum-Activated Malate Transporters in Apples. Int J Mol Sci 2018; 19:E2807. [PMID: 30231490 PMCID: PMC6163302 DOI: 10.3390/ijms19092807] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 11/30/2022] Open
Abstract
Aluminum-activated malate transporters (ALMTs) play an important role in aluminum tolerance, stomatal opening, and fruit acidity in plants. However, the evolutionary pattern of the ALMT gene family in apples remains relatively unknown. In this study, a total of 25 MdALMT genes were identified from the apple reference genome of the "Golden Delicious" doubled-haploid tree (GDDH13). The physiological and biochemical properties, gene structure, and conserved motifs of MdALMT genes were examined. Chromosome location and gene-duplication analysis indicated that whole-genome duplication/segmental duplication played an important role in the expansion of the MdALMT gene family. The Ka/Ks ratio of duplicated MdALMT genes showed that members of this family have undergone strong purifying selection. Through exploration of the phylogenetic relationships, seven subgroups were classified, and higher old gene duplication frequency and significantly different evolutionary rates of the ALMT gene families were detected. In addition, the functional divergence of ALMT genes occurred during the evolutionary process of Rosaceae species. Furthermore, the functional divergence of MdALMT genes was confirmed by expression discrepancy and different subcellular localizations. This study provides the foundation to better understand the molecular evolution of MdALMT genes and further facilitate functional analysis to unravel their exact role in apples.
Collapse
Affiliation(s)
- Baiquan Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A and F University, Yangling 712100, China.
| | - Yangyang Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A and F University, Yangling 712100, China.
| | - Meng Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A and F University, Yangling 712100, China.
| | - Tonghui Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A and F University, Yangling 712100, China.
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A and F University, Yangling 712100, China.
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A and F University, Yangling 712100, China.
| |
Collapse
|
12
|
Yan M, Byrne DH, Klein PE, Yang J, Dong Q, Anderson N. Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map. HORTICULTURE RESEARCH 2018; 5:17. [PMID: 29619228 PMCID: PMC5878828 DOI: 10.1038/s41438-018-0021-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/03/2017] [Accepted: 01/22/2018] [Indexed: 05/09/2023]
Abstract
Roses, which have been cultivated for at least 5000 years, are one of the most important ornamental crops in the world. Because of the interspecific nature and high heterozygosity in commercial roses, the genetic resources available for rose are limited. To effectively identify markers associated with QTL controlling important traits, such as disease resistance, abundant markers along the genome and careful phenotyping are required. Utilizing genotyping by sequencing technology and the strawberry genome (Fragaria vesca v2.0.a1) as a reference, we generated thousands of informative single nucleotide polymorphism (SNP) markers. These SNPs along with known bridge simple sequence repeat (SSR) markers allowed us to create the first high-density integrated consensus map for diploid roses. Individual maps were first created for populations J06-20-14-3×"Little Chief" (J14-3×LC), J06-20-14-3×"Vineyard Song" (J14-3×VS) and "Old Blush"×"Red Fairy" (OB×RF) and these maps were linked with 824 SNPs and 13 SSR bridge markers. The anchor SSR markers were used to determine the numbering of the rose linkage groups. The diploid consensus map has seven linkage groups (LGs), a total length of 892.2 cM, and an average distance of 0.25 cM between 3527 markers. By combining three individual populations, the marker density and the reliability of the marker order in the consensus map was improved over a single population map. Extensive synteny between the strawberry and diploid rose genomes was observed. This consensus map will serve as the tool for the discovery of marker-trait associations in rose breeding using pedigree-based analysis. The high level of conservation observed between the strawberry and rose genomes will help further comparative studies within the Rosaceae family and may aid in the identification of candidate genes within QTL regions.
Collapse
Affiliation(s)
- Muqing Yan
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - David H. Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Patricia E. Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843 USA
| | - Jizhou Yang
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843 USA
- Present Address: Department of Computer Science, San Francisco State University, San Francisco, CA 94132 USA
| | - Qianni Dong
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
- Present Address: Monsanto Company, 700 Chesterfield Parkway West, Chesterfield, MO 63017 USA
| | - Natalie Anderson
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| |
Collapse
|
13
|
Zhen Q, Fang T, Peng Q, Liao L, Zhao L, Owiti A, Han Y. Developing gene-tagged molecular markers for evaluation of genetic association of apple SWEET genes with fruit sugar accumulation. HORTICULTURE RESEARCH 2018; 5:14. [PMID: 29581882 PMCID: PMC5859117 DOI: 10.1038/s41438-018-0024-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 05/09/2023]
Abstract
Sugar content is an important component of fruit quality. Although sugar transporters are known to be crucial for sugar accumulation, the role of genes encoding SWEET sugar transporters in fruit sugar accumulation remains elusive. Here we report the effect of the SWEET genes on fruit sugar accumulation in apple. A total of 25 MdSWEET genes were identified in the apple genome, and 9 were highly expressed throughout fruit development. Molecular markers of these 9 MdSWEET genes were developed and used for genotyping of 188 apple cultivars. The association of polymorphic MdSWEET genes with soluble sugar content in mature fruit was analyzed. Three genes, MdSWEET2e, MdSWEET9b, and MdSWEET15a, were significantly associated with fruit sugar content, with MdSWEET15a and MdSWEET9b accounting for a relatively large proportion of phenotypic variation in sugar content. Moreover, both MdSWEET9b and MdSWEET15a are located on chromosomal regions harboring QTLs for sugar content. Hence, MdSWEET9b and MdSWEET15a are likely candidates regulating fruit sugar accumulation in apple. Our study not only presents an efficient way of implementing gene functional study but also provides molecular tools for genetic improvement of fruit quality in apple-breeding programs.
Collapse
Affiliation(s)
- Qiaoling Zhen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Ting Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Li Zhao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Albert Owiti
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| |
Collapse
|
14
|
Development of CACTA transposon derived SCAR markers and their use in population structure analysis in Zea mays. Genetica 2017; 146:1-12. [PMID: 28916874 DOI: 10.1007/s10709-017-9985-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022]
Abstract
Molecular marker technologies have proven to be an important breakthrough for genetic studies, construction of linkage maps and population genetics analysis. Transposable elements (TEs) constitute major fractions of repetitive sequences in plants and offer a wide range of possible areas to be explored as molecular markers. Sequence characterized amplified region (SCAR) marker development provides us with a simple and time saving alternative approach for marker development. We employed the CACTA-TD to develop SCARs and then integrated them into linkage map and used them for population structure and genetic diversity analysis of corn inbred population. A total of 108 dominant SCAR markers were designed out of which, 32 were successfully integrated in to the linkage map of maize RIL population and the remaining were added to a physical map for references to check the distribution throughout all chromosomes. Moreover, 76 polymorphic SCARs were used for diversity analysis of corn accessions being used in Korean corn breeding program. The overall average polymorphic information content (PIC) was 0.34, expected heterozygosity was 0.324 and Shannon's information index was 0.491 with a percentage of polymorphism of 98.67%. Further analysis by associating with desirable traits may also provide some accurate trait specific tagged SCAR markers. TE linked SCARs can provide an added level of polymorphism as well as improved discriminating ability and therefore can be useful in further breeding programs to develop high yielding germplasm.
Collapse
|
15
|
Ma B, Liao L, Peng Q, Fang T, Zhou H, Korban SS, Han Y. Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:190-204. [PMID: 28093854 DOI: 10.1111/jipb.12522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/15/2017] [Indexed: 05/02/2023]
Abstract
Identifying DNA sequence variations is a fundamental step towards deciphering the genetic basis of traits of interest. Here, a total of 20 cultivated and 10 wild apples were genotyped using specific-locus amplified fragment sequencing, and 39,635 single nucleotide polymorphisms with no missing genotypes and evenly distributed along the genome were selected to investigate patterns of genome-wide genetic variations between cultivated and wild apples. Overall, wild apples displayed higher levels of genetic diversity than cultivated apples. Linkage disequilibrium (LD) decays were observed quite rapidly in cultivated and wild apples, with an r2 -value below 0.2 at 440 and 280 bp, respectively. Moreover, bidirectional gene flow and different distribution patterns of LD blocks were detected between domesticated and wild apples. Most LD blocks unique to cultivated apples were located within QTL regions controlling fruit quality, thus suggesting that fruit quality had probably undergone selection during apple domestication. The genome of the earliest cultivated apple in China, Nai, was highly similar to that of Malus sieversii, and contained a small portion of genetic material from other wild apple species. This suggested that introgression could have been an important driving force during initial domestication of apple. These findings will facilitate future breeding and genetic dissection of complex traits in apple.
Collapse
Affiliation(s)
- Baiquan Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Ting Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Schuyler S Korban
- Department of Biology, University of Massachusetts Boston, Boston Massachusetts 02184, USA
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| |
Collapse
|
16
|
Di Pierro EA, Gianfranceschi L, Di Guardo M, Koehorst-van Putten HJJ, Kruisselbrink JW, Longhi S, Troggio M, Bianco L, Muranty H, Pagliarani G, Tartarini S, Letschka T, Lozano Luis L, Garkava-Gustavsson L, Micheletti D, Bink MCAM, Voorrips RE, Aziz E, Velasco R, Laurens F, van de Weg WE. A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species. HORTICULTURE RESEARCH 2016; 3:16057. [PMID: 27917289 PMCID: PMC5120355 DOI: 10.1038/hortres.2016.57] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 10/25/2016] [Accepted: 10/25/2016] [Indexed: 05/18/2023]
Abstract
Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.
Collapse
Affiliation(s)
| | | | - Mario Di Guardo
- Plant Breeding, Wageningen University and Research, Wageningen 6700AJ, The Netherlands
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige 38010, Italy
| | | | | | - Sara Longhi
- Plant Breeding, Wageningen University and Research, Wageningen 6700AJ, The Netherlands
| | - Michela Troggio
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige 38010, Italy
| | - Luca Bianco
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige 38010, Italy
| | - Hélène Muranty
- IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, Beaucouzé 49071, France
| | - Giulia Pagliarani
- Department of Agricultural Sciences, University of Bologna, Bologna 40127, Italy
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna 40127, Italy
| | - Thomas Letschka
- Department of Molecular Biology, Laimburg Research Centre for Agriculture and Forestry, Ora 39040, Italy
| | - Lidia Lozano Luis
- Department of Molecular Biology, Laimburg Research Centre for Agriculture and Forestry, Ora 39040, Italy
| | | | - Diego Micheletti
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige 38010, Italy
| | - Marco CAM Bink
- Biometris, Wageningen University and Research, Wageningen 6700AA, The Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University and Research, Wageningen 6700AJ, The Netherlands
| | - Ebrahimi Aziz
- Plant Breeding, Wageningen University and Research, Wageningen 6700AJ, The Netherlands
| | - Riccardo Velasco
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all’Adige 38010, Italy
| | - François Laurens
- IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, Beaucouzé 49071, France
| | - W Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen 6700AJ, The Netherlands
- ()
| |
Collapse
|
17
|
Ma B, Liao L, Zheng H, Chen J, Wu B, Ogutu C, Li S, Korban SS, Han Y. Genes Encoding Aluminum-Activated Malate Transporter II and their Association with Fruit Acidity in Apple. THE PLANT GENOME 2015; 8:eplantgenome2015.03.0016. [PMID: 33228269 DOI: 10.3835/plantgenome2015.03.0016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/27/2015] [Indexed: 05/25/2023]
Abstract
A gene encoding aluminum-activated malate transporter (ALMT) was previously reported as a candidate for the Ma locus controlling acidity in apple (Malus × domestica Borkh.). In this study, we found that apple ALMT genes can be divided into three families and the Ma1 gene belongs to the ALMTII family. Duplication of ALMTII genes in apple is related to the polyploid origin of the apple genome. Divergence in expression has occurred between the Ma1 gene and its homologs in the ALMTII family and only the Ma1 gene is significantly associated with malic acid content. The Ma locus consists of two alleles, Ma1 and ma1. Ma1 resides in the tonoplast and its ectopic expression in yeast was found to increase the influx of malic acid into yeast cells significantly, suggesting it may function as a vacuolar malate channel. In contrast, ma1 encodes a truncated protein because of a single nucleotide substitution of G with A in the last exon. As this truncated protein resides within the cell membrane, it is deemed to be nonfunctional as a vacuolar malate channel. The frequency of the Ma1Ma1 genotype is very low in apple cultivars but is high in wild relatives, which suggests that apple domestication may be accompanied by selection for the Ma1 gene. In addition, variations in the malic acid content of mature fruits were also observed between accessions with the same genotype in the Ma locus. This suggests that the Ma gene is not the only genetic determinant of fruit acidity in apple.
Collapse
Affiliation(s)
- Baiquan Ma
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Liao Liao
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
| | - Hongyu Zheng
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Jie Chen
- Beijing Key Lab. of Grape Sciences and Enology, and Key Lab. of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Benhong Wu
- Beijing Key Lab. of Grape Sciences and Enology, and Key Lab. of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Collins Ogutu
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
- Graduate Univ. of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, P.R. China
| | - Shaohua Li
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
| | - Schuyler S Korban
- Dep. of Biology, Univ. of Massachusetts-Boston, Boston, MA, 02184, USA
| | - Yuepeng Han
- Key Lab. of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P.R. China
| |
Collapse
|
18
|
Sun R, Chang Y, Yang F, Wang Y, Li H, Zhao Y, Chen D, Wu T, Zhang X, Han Z. A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality. BMC Genomics 2015; 16:747. [PMID: 26437648 PMCID: PMC4595315 DOI: 10.1186/s12864-015-1946-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 09/22/2015] [Indexed: 02/05/2023] Open
Abstract
Background Genetic map based quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits in apple. To facilitate molecular breeding studies of fruit quality traits in apple, we aim to construct a high density map which was efficient for QTL mapping and possible to search for candidate genes directly in mapped QTLs regions. Methods A total of 1733 F1 seedlings derived from ‘Jonathan’ × ‘Golden Delicious’ was used for the map constructionand QTL analysis. The SNP markers were developed by restriction site-associated DNA sequencing (RADseq). Phenotyping data of fruit quality traits were calculated in 2008-2011. Once QTLs were mapped, candidate genes were searched for in the corresponding regions of the apple genome sequence underlying the QTLs. Then some of the candidate genes were validated using real-time PCR. Results A high-density genetic map with 3441 SNP markers from 297 individuals was generated. Of the 3441 markers, 2017 were mapped to ‘Jonathan’ with a length of 1343.4 cM and the average distance between markers was 0.67 cM, 1932 were mapped to ‘Golden Delicious’ with a length of 1516.0 cM and the average distance between markers was 0.78 cM. Twelve significant QTLs linked to the control of fruit weight, fruit firmness, sugar content and fruit acidity were mapped to seven linkage groups. Based on gene annotation, 80, 64 and 17 genes related to fruit weight, fruit firmness and fruit acidity, respectively, were analyzed.Among the 17 candidate genes associated with control of fruit acidity, changes in the expression of MDP0000582174 (MdMYB4) were in agreement with the pattern of changes in malic acid content in apple during ripening, and the relative expression of MDP0000239624 (MdME) was significantly correlated withfruit acidity. Conclusions We demonstrated the construction of a dense SNP genetic map in apple using next generation sequencing and that the increased resolution enabled the detection of narrow interval QTLs linked to the three fruit quality traits assessed. The candidate genes MDP0000582174 and MDP0000239624 were found to be related to fruit acidity regulation. We conclude that application of RADseq for genetic map construction improved the precision of QTL detection and should be utilized in future studies on the regulatory mechanisms of important fruit traits in apple. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1946-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rui Sun
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Yuansheng Chang
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Fengqiu Yang
- Changli Institute for Pomology, Hebei Academy of Agricultural and Forestry Science, Changli, Heibei 066600, China.
| | - Yi Wang
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Hui Li
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Yongbo Zhao
- Changli Institute for Pomology, Hebei Academy of Agricultural and Forestry Science, Changli, Heibei 066600, China.
| | - Dongmei Chen
- Changli Institute for Pomology, Hebei Academy of Agricultural and Forestry Science, Changli, Heibei 066600, China.
| | - Ting Wu
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Xinzhong Zhang
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Zhenhai Han
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
19
|
Zhang Q, Liu C, Liu Y, VanBuren R, Yao X, Zhong C, Huang H. High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers. DNA Res 2015; 22:367-75. [PMID: 26370666 PMCID: PMC4596402 DOI: 10.1093/dnares/dsv019] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/19/2015] [Indexed: 01/25/2023] Open
Abstract
Kiwifruit (Actinidia chinensis Planchon) is an important specialty fruit crop that suffers from narrow genetic diversity stemming from recent global commercialization and limited cultivar improvement. Here, we present high-density RAD-seq-based genetic maps using an interspecific F1 cross between Actinidia rufa ‘MT570001’ and A. chinensis ‘Guihai No4’. The A. rufa (maternal) map consists of 2,426 single-nucleotide polymorphism (SNP) markers with a total length of 2,651 cM in 29 linkage groups (LGs) corresponding to the 29 chromosomes. The A. chinensis (paternal) map consists of 4,214 SNP markers over 3,142 cM in 29 LGs. Using these maps, we were able to anchor an additional 440 scaffolds from the kiwifruit draft genome assembly. Kiwifruit is functionally dioecious, which presents unique challenges for breeding and production. Three sex-specific simple sequence repeats (SSR) markers can be used to accurately sex type male and female kiwifruit in breeding programmes. The sex-determination region (SDR) in kiwifruit was narrowed to a 1-Mb subtelomeric region on chromosome 25. Localizing the SDR will expedite the discovery of genes controlling carpel abortion in males and pollen sterility in females.
Collapse
Affiliation(s)
- Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Chunyan Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yifei Liu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | | | - Xiaohong Yao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Hongwen Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| |
Collapse
|
20
|
Falginella L, Cipriani G, Monte C, Gregori R, Testolin R, Velasco R, Troggio M, Tartarini S. A major QTL controlling apple skin russeting maps on the linkage group 12 of 'Renetta Grigia di Torriana'. BMC PLANT BIOLOGY 2015; 15:150. [PMID: 26084469 PMCID: PMC4472412 DOI: 10.1186/s12870-015-0507-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/27/2015] [Indexed: 05/23/2023]
Abstract
BACKGROUND Russeting is a disorder developed by apple fruits that consists of cuticle cracking followed by the replacement of the epidermis by a corky layer that protects the fruit surface from water loss and pathogens. Although influenced by many environmental conditions and orchard management practices, russeting is under genetic control. The difficulty in classifying offspring and consequent variable segregation ratios have led several authors to conclude that more than one genetic determinant could be involved, although some evidence favours a major gene (Ru). RESULTS In this study we report the mapping of a major genetic russeting determinant on linkage group 12 of apple as inferred from the phenotypic observation in a segregating progeny derived from 'Renetta Grigia di Torriana', the construction of a 20 K Illumina SNP chip based genetic map, and QTL analysis. Recombination analysis in two mapping populations restricted the region of interest to approximately 400 Kb. Of the 58 genes predicted from the Golden Delicious sequence, a putative ABCG family transporter has been identified. Within a small set of russeted cultivars tested with markers of the region, only six showed the same haplotype of 'Renetta Grigia di Torriana'. CONCLUSIONS A major determinant (Ru_RGT) for russeting development putatively involved in cuticle organization is proposed as a candidate for controlling the trait. SNP and SSR markers tightly co-segregating with the Ru_RGT locus may assist the breeder selection. The observed segregations and the analysis of the 'Renetta Grigia di Torriana' haplotypic region in a panel of russeted and non-russeted cultivars may suggest the presence of other determinants for russeting in apple.
Collapse
Affiliation(s)
- Luigi Falginella
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Guido Cipriani
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Corinne Monte
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Roberto Gregori
- Department of Agricultural Sciences, University of Bologna, Via Fanin 44, 40127, Bologna, Italy.
| | - Raffaele Testolin
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy.
| | - Riccardo Velasco
- Research and Innovation Centre - Fondazione Edmund Mach - Department of Genomics and Biology of Fruit Crop, Via E. Mach 1, 38010 S, Michele all'Adige TN, Italy.
| | - Michela Troggio
- Research and Innovation Centre - Fondazione Edmund Mach - Department of Genomics and Biology of Fruit Crop, Via E. Mach 1, 38010 S, Michele all'Adige TN, Italy.
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Via Fanin 44, 40127, Bologna, Italy.
| |
Collapse
|
21
|
Chen JJ, Wang Y. Microsatellite Development and Potential Application in Authentication, Conservation, and Genetic Improvement of Chinese Medicinal Plants. CHINESE HERBAL MEDICINES 2015. [DOI: 10.1016/s1674-6384(15)60029-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
22
|
Romanov D, Divashuk M, Havey MJ, Khrustaleva L. Tyramide-FISH mapping of single genes for development of an integrated recombination and cytogenetic map of chromosome 5 of Allium cepa. Genome 2015; 58:111-9. [PMID: 26158384 DOI: 10.1139/gen-2015-0019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Chromosome 5 of onion carries major quantitative trait loci (QTL) that control dry-matter content, pungency and storability of bulbs, amounts and types of epicuticular waxes, and resistances to abiotic factors, all of which are of interest to breeders. SNPs, SSRs, and RFLPs in expressed regions of the onion genome have been genetically mapped, and we used these clones and sequences from the NCBI database to develop DNA probes for in situ hybridization to integrate the genetic and physical maps of onion chromosome 5. We produced genomic amplicons from expressed regions of the onion genome that carried both exons and introns in order to increase the hybridization specificity of the probes and to enlarge the target DNA sizes. Tyramide-FISH technique was used to increase the detection sensitivity of relatively short target DNA regions, which range from 950 to 2100 bp. Through the integration of genetic and chromosomal maps, we were able to estimate the distribution of recombination events along onion chromosome 5. We demonstrated the efficiency of chromosomal in situ mapping of exon-intron genomic clones for the extremely large genome of onion.
Collapse
Affiliation(s)
- Dmitry Romanov
- a Center of Molecular Biotechnology, Russian State Agrarian University - MTAA, Moscow 127550, Russia
| | - Mikhail Divashuk
- a Center of Molecular Biotechnology, Russian State Agrarian University - MTAA, Moscow 127550, Russia
| | - Michael J Havey
- b USDA-ARS and Department of Horticulture, University of Wisconsin, Madison, WI 53706 USA
| | - Ludmila Khrustaleva
- a Center of Molecular Biotechnology, Russian State Agrarian University - MTAA, Moscow 127550, Russia
| |
Collapse
|
23
|
Pootakham W, Ruang-Areerate P, Jomchai N, Sonthirod C, Sangsrakru D, Yoocha T, Theerawattanasuk K, Nirapathpongporn K, Romruensukharom P, Tragoonrung S, Tangphatsornruang S. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS). FRONTIERS IN PLANT SCIENCE 2015; 6:367. [PMID: 26074933 PMCID: PMC4444744 DOI: 10.3389/fpls.2015.00367] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/09/2015] [Indexed: 05/18/2023]
Abstract
Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23-1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.
Collapse
Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Panthita Ruang-Areerate
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Kanikar Theerawattanasuk
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Kanlaya Nirapathpongporn
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Phayao Romruensukharom
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
- *Correspondence: Sithichoke Tangphatsornruang, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| |
Collapse
|
24
|
Wu J, Li LT, Li M, Khan MA, Li XG, Chen H, Yin H, Zhang SL. High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5771-81. [PMID: 25129128 PMCID: PMC4203118 DOI: 10.1093/jxb/eru311] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Pear (Pyrus spp) is an important fruit crop, grown in all temperate regions of the world, with global production ranked after grape and apples among deciduous tree crops. A high-density linkage map is a valuable tool for fine mapping quantitative trait loci (QTL) and map-based gene cloning. In this study, we firstly constructed a high-density linkage map of pear using SNPs integrated with SSRs, developed by the rapid and robust technology of restriction-associated DNA sequencing (RADseq). The linkage map consists of 3143 SNP markers and 98 SSRs, 3241 markers in total, spanning 2243.4 cM, with an average marker distance of 0.70 cM. Anchoring SSRs were able to anchor seventeen linkage groups to their corresponding chromosomes. Based on this high-density integrated pear linkage map and two years of fruit phenotyping, a total of 32 potential QTLs for 11 traits, including length of pedicel (LFP), single fruit weight (SFW), soluble solid content (SSC), transverse diameter (TD), vertical diameter (VD), calyx status (CS), flesh colour (FC), juice content (JC), number of seeds (NS), skin colour (SC), and skin smooth (SS), were identified and positioned on the genetic map. Among them, some important fruit-related traits have for the first time been identified, such as calyx status, length of pedicel, and flesh colour, and reliable localization of QTLs were verified repeatable. This high-density linkage map of pear is a worthy reference for mapping important fruit traits, QTL identification, and comparison and combination of different genetic maps.
Collapse
Affiliation(s)
- Jun Wu
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei-Ting Li
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Meng Li
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - M Awais Khan
- International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Xiu-Gen Li
- Zhengzhou Fruit Research Institute, Zhengzhou 450009, China
| | - Hui Chen
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Yin
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Shao-Ling Zhang
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
25
|
Saladié M, Wright LP, Garcia-Mas J, Rodriguez-Concepcion M, Phillips MA. The 2-C-methylerythritol 4-phosphate pathway in melon is regulated by specialized isoforms for the first and last steps. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5077-92. [PMID: 25013119 PMCID: PMC4144782 DOI: 10.1093/jxb/eru275] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway provides the precursors for the biosynthesis of plastidial isoprenoids, which include the carotenoid pigments of many fruits. We have analysed the genes encoding the seven enzymes of the MEP pathway in melon (Cucumis melo L.) and determined that the first one, 1-deoxyxylulose 5-phosphate synthase (DXS), and the last one, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (HDR), are represented in the genome as a small gene family and paralogous pair, respectively. In the case of DXS, three genes encode functional DXS activities which fall into previously established type I (CmDXS1) and II (CmDXS2a and CmDXS2b) categories, while a fourth DXS-like gene belonging to the type III group did not encode a protein with DXS activity. Their expression patterns and phylogenies suggest that CmDXS1 is functionally specialized for developmental and photosynthetic processes, while CmDXS2a and CmDXS2b are induced in flowers and ripening fruit of orange- (but not white-) fleshed varieties, coinciding with β-carotene accumulation. This is the first instance connecting type II DXS genes to specialized isoprenoid biosynthesis in the fruit of an agronomically important species. Two HDR paralogues were shown to encode functional enzymes, although only CmHDR1 was highly expressed in the tissues and developmental stages tested. Phylogenetic analysis showed that in cucurbits such as melon, these HDR paralogues probably arose through individual gene duplications in a common angiosperm ancestor, mimicking a prior division in gymnosperms, while other flowering plants, including apple, soy, canola, and poplar, acquired HDR duplicates recently as homoeologues through large-scale genome duplications. We report the influence of gene duplication history on the regulation of the MEP pathway in melon and the role of specialized MEP-pathway isoforms in providing precursors for β-carotene production in orange-fleshed melon varieties.
Collapse
Affiliation(s)
- Montserrat Saladié
- Plant and Animal Genomics Programme, Institut de Recerca i Tecnologia Agroalimentàries and Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Louwrance P Wright
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans Knöll Street 8, 07745 Jena, Germany
| | - Jordi Garcia-Mas
- Plant and Animal Genomics Programme, Institut de Recerca i Tecnologia Agroalimentàries and Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Manuel Rodriguez-Concepcion
- Plant Metabolism and Metabolic Engineering Programme, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Michael A Phillips
- Plant Metabolism and Metabolic Engineering Programme, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| |
Collapse
|
26
|
Fast and cost-effective genetic mapping in apple using next-generation sequencing. G3-GENES GENOMES GENETICS 2014; 4:1681-7. [PMID: 25031181 PMCID: PMC4169160 DOI: 10.1534/g3.114.011023] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Next-generation DNA sequencing (NGS) produces vast amounts of DNA sequence data, but it is not specifically designed to generate data suitable for genetic mapping. Recently developed DNA library preparation methods for NGS have helped solve this problem, however, by combining the use of reduced representation libraries with DNA sample barcoding to generate genome-wide genotype data from a common set of genetic markers across a large number of samples. Here we use such a method, called genotyping-by-sequencing (GBS), to produce a data set for genetic mapping in an F1 population of apples (Malus × domestica) segregating for skin color. We show that GBS produces a relatively large, but extremely sparse, genotype matrix: over 270,000 SNPs were discovered but most SNPs have too much missing data across samples to be useful for genetic mapping. After filtering for genotype quality and missing data, only 6% of the 85 million DNA sequence reads contributed to useful genotype calls. Despite this limitation, using existing software and a set of simple heuristics, we generated a final genotype matrix containing 3967 SNPs from 89 DNA samples from a single lane of Illumina HiSeq and used it to create a saturated genetic linkage map and to identify a known QTL underlying apple skin color. We therefore demonstrate that GBS is a cost-effective method for generating genome-wide SNP data suitable for genetic mapping in a highly diverse and heterozygous agricultural species. We anticipate future improvements to the GBS analysis pipeline presented here that will enhance the utility of next-generation DNA sequence data for the purposes of genetic mapping across diverse species.
Collapse
|
27
|
Yuan H, Meng D, Gu Z, Li W, Wang A, Yang Q, Zhu Y, Li T. A novel gene, MdSSK1, as a component of the SCF complex rather than MdSBP1 can mediate the ubiquitination of S-RNase in apple. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3121-31. [PMID: 24759884 PMCID: PMC4071834 DOI: 10.1093/jxb/eru164] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
As a core factor in S-RNase-based gametophytic self-incompatibility (GSI), the SCF (SKP1-Cullin1-F-box-Rbx1) complex (including pollen determinant SLF, S-locus-F-box) functions as an E3 ubiquitin ligase on non-self S-RNase. The SCF complex is formed by SKP1 bridging between SLF, CUL1, and Rbx1; however, it is not known whether an SCF complex lacking SKP1 can mediate the ubiquitination of S-RNase. Three SKP1-like genes from pollen were cloned based on the structural features of the SLF-interacting-SKP1-like (SSK) gene and the 'Golden Delicious' apple genome. These genes have a motif of five amino acids following the standard 'WAFE' at the C terminal and, in addition, contain eight sheets and two helices. All three genes were expressed exclusively in pollen. In the yeast two-hybrid and pull-down assays only one was found to interact with MdSFBB and MdCUL1, suggesting it is the SLF-interacting SKP1-like gene in apple which was named MdSSK1. In vitro experiments using MdSSK1, S2-MdSFBB1 (S2-Malus domestica S-locus-F-box brother) and MdCUL1 proteins incubated with S 2-RNase and ubiquitin revealed that the SCF complex ubiquitinylates S-RNase in vitro, while MdSBP1 (Malus domestica S-RNase binding protein 1) could not functionally replace MdSSK1 in the SCF complex in ubiquitinylating S-RNase. According to the above experiments, MdSBP1 is probably the only factor responsible for recognition with S-RNase, while not a component of the SCF complex, and an SCF complex containing MdSSK1 is required for mediating the ubiquitination of S-RNase.
Collapse
Affiliation(s)
- Hui Yuan
- Laboratory of Fruit Cell and Molecular Breeding, College of Agronomy and Bio-tech, China Agricultural University, Beijing 100193, China
| | - Dong Meng
- Laboratory of Fruit Cell and Molecular Breeding, College of Agronomy and Bio-tech, China Agricultural University, Beijing 100193, China
| | - Zhaoyu Gu
- Laboratory of Fruit Cell and Molecular Breeding, College of Agronomy and Bio-tech, China Agricultural University, Beijing 100193, China
| | - Wei Li
- Laboratory of Fruit Cell and Molecular Breeding, College of Agronomy and Bio-tech, China Agricultural University, Beijing 100193, China
| | - Aide Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Qing Yang
- Laboratory of Fruit Cell and Molecular Breeding, College of Agronomy and Bio-tech, China Agricultural University, Beijing 100193, China
| | - Yuandi Zhu
- Laboratory of Fruit Cell and Molecular Breeding, College of Agronomy and Bio-tech, China Agricultural University, Beijing 100193, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, College of Agronomy and Bio-tech, China Agricultural University, Beijing 100193, China
| |
Collapse
|
28
|
Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y, Azam S, Zhang Y, Jaganathan D, You FM, Gao J, Riera-Lizarazu O, Luo MC. Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Funct Integr Genomics 2014; 14:59-73. [PMID: 24610029 PMCID: PMC4273598 DOI: 10.1007/s10142-014-0363-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/27/2014] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
Abstract
Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.
Collapse
Affiliation(s)
- Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Reyazul Rouf Mir
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Yuqin Hu
- University of California, Davis, USA
| | - Sarwar Azam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Frank M. You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Canada
| | | | - Oscar Riera-Lizarazu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Dow AgroSciences, Pullman, USA
| | | |
Collapse
|
29
|
Satovic Z, Avila CM, Cruz-Izquierdo S, Díaz-Ruíz R, García-Ruíz GM, Palomino C, Gutiérrez N, Vitale S, Ocaña-Moral S, Gutiérrez MV, Cubero JI, Torres AM. A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.). BMC Genomics 2013; 14:932. [PMID: 24377374 PMCID: PMC3880837 DOI: 10.1186/1471-2164-14-932] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/12/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. RESULTS A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. CONCLUSION We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different marker technologies. Combined with syntenic approaches, the consensus map will increase marker density in selected genomic regions and will be useful for future faba bean molecular breeding applications.
Collapse
Affiliation(s)
- Zlatko Satovic
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Present addresses: Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Carmen M Avila
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Serafin Cruz-Izquierdo
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Colegio de Postgraduados, Recursos Genéticos y Productividad – Genética, Campus Montecillo, Km 36.5 Carretera México-Texcoco, C.P., Texcoco, Edo. de México 56230, México
| | - Ramón Díaz-Ruíz
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Colegio de Postgraduados, Campus Puebla, Km 125.5 Carretera México-Puebla, C.P., Puebla, Pue 72760, México
| | - Gloria M García-Ruíz
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Carmen Palomino
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Natalia Gutiérrez
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Stefania Vitale
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Sara Ocaña-Moral
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - María Victoria Gutiérrez
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - José I Cubero
- Departamento de Mejora Genética, IAS-CSIC, Apdo. 4084, Córdoba 14080, Spain
| | - Ana M Torres
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| |
Collapse
|
30
|
Kopecký D, Studer B. Emerging technologies advancing forage and turf grass genomics. Biotechnol Adv 2013; 32:190-9. [PMID: 24309540 DOI: 10.1016/j.biotechadv.2013.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 11/20/2022]
Abstract
Grassland is of major importance for agricultural production and provides valuable ecosystem services. Its impact is likely to rise in changing socio-economic and climatic environments. High yielding forage grass species are major components of sustainable grassland production. Understanding the genome structure and function of grassland species provides opportunities to accelerate crop improvement and thus to mitigate the future challenges of increased feed and food demand, scarcity of natural resources such as water and nutrients, and high product qualities. In this review, we will discuss a selection of technological developments that served as main drivers to generate new insights into the structure and function of nuclear genomes. Many of these technologies were originally developed in human or animal science and are now increasingly applied in plant genomics. Our main goal is to highlight the benefits of using these technologies for forage and turf grass genome research, to discuss their potentials and limitations as well as their relevance for future applications.
Collapse
Affiliation(s)
- David Kopecký
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371, Olomouc-Holice, Czech Republic
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetsstrasse 2, 8092 Zurich, Switzerland.
| |
Collapse
|
31
|
Vimolmangkang S, Han Y, Wei G, Korban SS. An apple MYB transcription factor, MdMYB3, is involved in regulation of anthocyanin biosynthesis and flower development. BMC PLANT BIOLOGY 2013; 13:176. [PMID: 24199943 PMCID: PMC3833268 DOI: 10.1186/1471-2229-13-176] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 11/04/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Red coloration of fruit is an important trait in apple, and it is mainly attributed to the accumulation of anthocyanins, a class of plant flavonoid metabolites. Anthocyanin biosynthesis is genetically determined by structural and regulatory genes. Plant tissue pigmentation patterns are mainly controlled by expression profiles of regulatory genes. Among these regulatory genes are MYB transcription factors (TFs), wherein the class of two-repeats (R2R3) is deemed the largest, and these are associated with the anthocyanin biosynthesis pathway. Although three MdMYB genes, almost identical in nucleotide sequences, have been identified in apple, it is likely that there are other R2R3 MYB TFs that are present in the apple genome that are also involved in the regulation of coloration of red color pigmentation of the skin of apple fruits. RESULTS In this study, a novel R2R3 MYB gene has been isolated and characterized in apple. This MYB gene is closely related to the Arabidopsis thaliana AtMYB3, and has been designated as MdMYB3. This TF belongs to the subgroup 4 R2R3 family of plant MYB transcription factors. This apple MdMYB3 gene is mapped onto linkage group 15 of the integrated apple genetic map. Transcripts of MdMYB3 are detected in all analyzed tissues including leaves, flowers, and fruits. However, transcripts of MdMYB3 are higher in excocarp of red-skinned apple cultivars than that in yellowish-green skinned apple cultivars. When this gene is ectopically expressed in Nicotiana tabacum cv. Petite Havana SR1, flowers of transgenic tobacco lines carrying MdMYB3 have exhibited increased pigmentation and accumulate higher levels of anthocyanins and flavonols than wild-type flowers. Overexpression of MdMYB3 has resulted in transcriptional activation of several flavonoid pathway genes, including CHS, CHI, UFGT, and FLS. Moreover, peduncles of flowers and styles of pistils of transgenic plants overexpressing MdMYB3 are longer than those of wild-type plants, thus suggesting that this TF is involved in regulation of flower development. CONCLUSIONS This study has identified a novel MYB transcription factor in the apple genome. This TF, designated as MdMYB3, is involved in transcriptional activation of several flavonoid pathway genes. Moreover, this TF not only regulates the accumulation of anthocyanin in the skin of apple fruits, but it is also involved in the regulation of flower development, particularly that of pistil development.
Collapse
Affiliation(s)
- Sornkanok Vimolmangkang
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Moshan, Wuhan 430074, P. R C
| | - Guochao Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Moshan, Wuhan 430074, P. R C
| | - Schuyler S Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
- Department of Biology, University of Massachusetts, Boston, Boston, MA 02125, USA
| |
Collapse
|
32
|
Khan MA, Zhao YF, Korban SS. Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping. PHYSIOLOGIA PLANTARUM 2013; 148:344-53. [PMID: 23627651 DOI: 10.1111/ppl.12068] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/15/2013] [Accepted: 04/20/2013] [Indexed: 05/20/2023]
Abstract
Fire blight, incited by the enterobacterium Erwinia amylovora, is a destructive disease of Rosaceae, particularly of apples and pears. There are reports on the molecular mechanisms underlying E. amylovora pathogenesis and how the host activates its resistance mechanism. The host's resistance mechanism is quantitatively controlled, although some major genes might also be involved. Thus far, quantitative trait loci (QTL) mapping and differential expression studies have been used to elucidate those genes and/or genomic regions underlying quantitative resistance present in the apple genome. In this study, an effort is undertaken to dissect the genetic basis of fire blight resistance in apple using both QTL and genome-wide association mapping. On the basis of an F1 pedigree of 'Coop 16' × 'Coop 17' and a genome-wide association study (GWAS) mapping population of Malus accessions (species, old and new cultivars and selections), new QTLs and associations have been identified. A total of three QTLs for resistance to fire blight, with above 95% significant logarithm of odds threshold value of 2.5, have been identified on linkage groups (LGs) 02, 06, and 15 of the apple genome with phenotypic variation explained values of 14.7, 20.1 and 17.4, respectively. Although elevated P-values with signals for marker-trait associations are observed for some LGs, these are not found to be significant. However, a total of 34 significant associations, with P-values ≥0.02, have been detected including 8 for lesion length at 7 days following inoculation (PL1), 14 for lesion length at 14 days following inoculation (PL2), and 12 for shoot length.
Collapse
Affiliation(s)
- M Awais Khan
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA
| | | | | |
Collapse
|
33
|
Jiang SY, González JM, Ramachandran S. Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice. PLoS One 2013; 8:e63551. [PMID: 23696832 PMCID: PMC3656045 DOI: 10.1371/journal.pone.0063551] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 04/03/2013] [Indexed: 12/20/2022] Open
Abstract
Tandem and segmental duplications significantly contribute to gene family expansion and genome evolution. Genome-wide identification of tandem and segmental genes has been analyzed before in several plant genomes. However, comparative studies in functional bias, expression divergence and their roles in species domestication are still lacking. We have carried out a genome-wide identification and comparative analysis of tandem and segmental genes in the rice genome. A total of 3,646 and 3,633 pairs of tandem and segmental genes, respectively, were identified in the genome. They made up around 30% of total annotated rice genes (excluding transposon-coding genes). Both tandem and segmental duplicates showed different physical locations and exhibited a biased subset of functions. These two types of duplicated genes were also under different functional constrains as shown by nonsynonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analysis. They are also differently regulated depending on the tissues and abiotic and biotic stresses based on transcriptomics data. The expression divergence might be related to promoter differentiation and DNA methylation status after tandem or segmental duplications. Both tandem and segmental duplications differ in their contribution to genetic novelty but evidence suggests that they play their role in species domestication and genome evolution.
Collapse
Affiliation(s)
- Shu-Ye Jiang
- Temasek Life Sciences Laboratory, The National University of Singapore, Singapore, Singapore
| | - José M. González
- Department of Microbiology, University of La Laguna, La Laguna, Tenerife, Spain
| | - Srinivasan Ramachandran
- Temasek Life Sciences Laboratory, The National University of Singapore, Singapore, Singapore
- * E-mail:
| |
Collapse
|
34
|
Cloutier S, Ragupathy R, Miranda E, Radovanovic N, Reimer E, Walichnowski A, Ward K, Rowland G, Duguid S, Banik M. Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1783-95. [PMID: 22890805 PMCID: PMC3493668 DOI: 10.1007/s00122-012-1953-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/21/2012] [Indexed: 05/06/2023]
Abstract
Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1-52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence.
Collapse
Affiliation(s)
- Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Yang M, Han Y, VanBuren R, Ming R, Xu L, Han Y, Liu Y. Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar. BMC Genomics 2012; 13:653. [PMID: 23170872 PMCID: PMC3564711 DOI: 10.1186/1471-2164-13-653] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 11/07/2012] [Indexed: 01/18/2023] Open
Abstract
Background The genus Nelumbo Adans. comprises two living species, N. nucifera Gaertan. (Asian lotus) and N. lutea Pers. (American lotus). A genetic linkage map is an essential resource for plant genetic studies and crop improvement but has not been generated for Nelumbo. We aimed to develop genomic simple sequence repeat (SSR) markers from the genome sequence and construct two genetic maps for Nelumbo to assist genome assembly and integration of a genetic map with the genome sequence. Results A total of 86,089 SSR motifs were identified from the genome sequences. Di- and tri-nucleotide repeat motifs were the most abundant, and accounted for 60.73% and 31.66% of all SSRs, respectively. AG/GA repeats constituted 51.17% of dinucleotide repeat motifs, followed by AT/TA (44.29%). Of 500 SSR primers tested, 386 (77.20%) produced scorable alleles with an average of 2.59 per primer, and 185 (37.00%) showed polymorphism among two parental genotypes, N. nucifera ‘Chinese Antique’ and N. lutea ‘AL1’, and six progenies of their F1 population. The normally segregating markers, which comprised 268 newly developed SSRs, 37 previously published SSRs and 53 sequence-related amplified polymorphism markers, were used for genetic map construction. The map for Asian lotus was 365.67 cM with 47 markers distributed in seven linkage groups. The map for American lotus was 524.51 cM, and contained 177 markers distributed in 11 genetic linkage groups. The number of markers per linkage group ranged from three to 34 with an average genetic distance of 3.97 cM between adjacent markers. Moreover, 171 SSR markers contained in linkage groups were anchored to 97 genomic DNA sequence contigs of ‘Chinese Antique’. The 97 contigs were merged into 60 scaffolds. Conclusion Genetic mapping of SSR markers derived from sequenced contigs in Nelumbo enabled the associated contigs to be anchored in the linkage map and facilitated assembly of the genome sequences of ‘Chinese Antique’. The present study reports the first construction of genetic linkage maps for Nelumbo, which can serve as reference linkage maps to accelerate characterization germplasm, genetic mapping for traits of economic interest, and molecular breeding with marker-assisted selection.
Collapse
Affiliation(s)
- Mei Yang
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | | | | | | | | | | | | |
Collapse
|
36
|
Khan MA, Han Y, Zhao YF, Troggio M, Korban SS. A multi-population consensus genetic map reveals inconsistent marker order among maps likely attributed to structural variations in the apple genome. PLoS One 2012; 7:e47864. [PMID: 23144832 PMCID: PMC3489900 DOI: 10.1371/journal.pone.0047864] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 09/19/2012] [Indexed: 12/26/2022] Open
Abstract
Genetic maps serve as frameworks for determining the genetic architecture of quantitative traits, assessing structure of a genome, as well as aid in pursuing association mapping and comparative genetic studies. In this study, a dense genetic map was constructed using a high-throughput 1,536 EST-derived SNP GoldenGate genotyping platform and a global consensus map established by combining the new genetic map with four existing reliable genetic maps of apple. The consensus map identified markers with both major and minor conflicts in positioning across all five maps. These major inconsistencies among marker positions were attributed either to structural variations within the apple genome, or among mapping populations, or genotyping technical errors. These also highlighted problems in assembly and anchorage of the reference draft apple genome sequence in regions with known segmental duplications. Markers common across all five apple genetic maps resulted in successful positioning of 2875 markers, consisting of 2033 SNPs and 843 SSRs as well as other specific markers, on the global consensus map. These markers were distributed across all 17 linkage groups, with an average of 169±33 marker per linkage group and with an average distance of 0.70±0.14 cM between markers. The total length of the consensus map was 1991.38 cM with an average length of 117.14±24.43 cM per linkage group. A total of 569 SNPs were mapped onto the genetic map, consisting of 140 recombinant individuals, from our recently developed apple Oligonucleotide pool assays (OPA). The new functional SNPs, along with the dense consensus genetic map, will be useful for high resolution QTL mapping of important traits in apple and for pursuing comparative genetic studies in Rosaceae.
Collapse
Affiliation(s)
- Muhammad Awais Khan
- Department of Natural Resources & Environmental Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Moshan, Wuhan, People's Republic of China
| | - Youfu Frank Zhao
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Michela Troggio
- Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, Trento, Italy
| | - Schuyler S. Korban
- Department of Natural Resources & Environmental Sciences, University of Illinois, Urbana, Illinois, United States of America
| |
Collapse
|
37
|
Zhao L, Yuanda L, Caiping C, Xiangchao T, Xiangdong C, Wei Z, Hao D, Xiuhua G, Wangzhen G. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information. BMC Genomics 2012; 13:539. [PMID: 23046547 PMCID: PMC3557173 DOI: 10.1186/1471-2164-13-539] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 09/23/2012] [Indexed: 01/02/2023] Open
Abstract
Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource for tetraploid cotton genome assembly, for cloning genes related to superior agronomic traits, and for further comparative genomic analyses in Gossypium.
Collapse
Affiliation(s)
- Liang Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing 210095, China
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Zhang Q, Ma B, Li H, Chang Y, Han Y, Li J, Wei G, Zhao S, Khan MA, Zhou Y, Gu C, Zhang X, Han Z, Korban SS, Li S, Han Y. Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple. BMC Genomics 2012; 13:537. [PMID: 23039990 PMCID: PMC3704940 DOI: 10.1186/1471-2164-13-537] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 10/04/2012] [Indexed: 11/10/2022] Open
Abstract
Background Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled contig sequences of the apple genome. Results A total of 28,538 SSRs have been identified in the apple genome, with an overall density of 40.8 SSRs per Mb. Di-nucleotide repeats are the most frequent microsatellites in the apple genome, accounting for 71.9% of all microsatellites. AT/TA repeats are the most frequent in genomic regions, accounting for 38.3% of all the G-SSRs, while AG/GA dimers prevail in transcribed sequences, and account for 59.4% of all EST-SSRs. A total set of 310 SSRs is selected to amplify eight apple genotypes. Of these, 245 (79.0%) are found to be polymorphic among cultivars and wild species tested. AG/GA motifs in genomic regions have detected more alleles and higher PIC values than AT/TA or AC/CA motifs. Moreover, AG/GA repeats are more variable than any other dimers in apple, and should be preferentially selected for studies, such as genetic diversity and linkage map construction. A total of 54 newly developed apple SSRs have been genetically mapped. Interestingly, clustering of markers with distorted segregation is observed on linkage groups 1, 2, 10, 15, and 16. A QTL responsible for malic acid content of apple fruits is detected on linkage group 8, and accounts for ~13.5% of the observed phenotypic variation. Conclusions This study demonstrates that di-nucleotide repeats are prevalent in the apple genome and that AT/TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. All SSR motifs identified in this study as well as those newly mapped SSRs will serve as valuable resources for pursuing apple genetic studies, aiding the apple breeding community in marker-assisted breeding, and for performing comparative genomic studies in Rosaceae.
Collapse
Affiliation(s)
- Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, People's Republic of China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Jiao Y, Jia HM, Li XW, Chai ML, Jia HJ, Chen Z, Wang GY, Chai CY, van de Weg E, Gao ZS. Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra). BMC Genomics 2012; 13:201. [PMID: 22621340 PMCID: PMC3505174 DOI: 10.1186/1471-2164-13-201] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 04/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in recent years has stimulated its extension in China and introduction to Australia. A limited number of co-dominant markers have been developed and applied in genetic diversity and identity studies. Here we report, for the first time, a survey of whole genome shotgun data to develop a large number of simple sequence repeat (SSR) markers to analyse the genetic diversity of the common cultivated Chinese bayberry and the relationship with three other Myrica species. RESULTS The whole genome shotgun survey of Chinese bayberry produced 9.01Gb of sequence data, about 26x coverage of the estimated genome size of 323 Mb. The genome sequences were highly heterozygous, but with little duplication. From the initial assembled scaffold covering 255 Mb sequence data, 28,602 SSRs (≥5 repeats) were identified. Dinucleotide was the most common repeat motif with a frequency of 84.73%, followed by 13.78% trinucleotide, 1.34% tetranucleotide, 0.12% pentanucleotide and 0.04% hexanucleotide. From 600 primer pairs, 186 polymorphic SSRs were developed. Of these, 158 were used to screen 29 Chinese bayberry accessions and three other Myrica species: 91.14%, 89.87% and 46.84% SSRs could be used in Myrica adenophora, Myrica nana and Myrica cerifera, respectively. The UPGMA dendrogram tree showed that cultivated Myrica rubra is closely related to Myrica adenophora and Myrica nana, originating in southwest China, and very distantly related to Myrica cerifera, originating in America. These markers can be used in the construction of a linkage map and for genetic diversity studies in Myrica species. CONCLUSION Myrica rubra has a small genome of about 323 Mb with a high level of heterozygosity. A large number of SSRs were identified, and 158 polymorphic SSR markers developed, 91% of which can be transferred to other Myrica species.
Collapse
Affiliation(s)
- Yun Jiao
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Hui-min Jia
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Xiong-wei Li
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Ming-liang Chai
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Hui-juan Jia
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Zhe Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Guo-yun Wang
- Fruit Research Institute, Yuyao, Ningbo, 315400, China
| | - Chun-yan Chai
- Forestry Technology Extension Center, Cixi Ningbo, 315300, China
| | - Eric van de Weg
- Plant Breeding-Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Zhong-shan Gao
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
40
|
Han Y, Vimolmangkang S, Soria-Guerra RE, Korban SS. Introduction of apple ANR genes into tobacco inhibits expression of both CHI and DFR genes in flowers, leading to loss of anthocyanin. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2437-47. [PMID: 22238451 PMCID: PMC3346214 DOI: 10.1093/jxb/err415] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/11/2011] [Accepted: 11/16/2011] [Indexed: 05/03/2023]
Abstract
Three genes encoding anthocyanidin reductase (ANR) in apple (Malus×domestica Borkh.), designated MdANR1, MdANR2a, and MdANR2b, have been cloned and characterized. MdANR1 shows 91% identity in coding DNA sequences with MdANR2a and MdANR2b, while MdANR2a and MdANR2b are allelic and share 99% nucleotide sequence identity in the coding region. MdANR1 and MdANR2 genes are located on linkage groups 10 and 5, respectively. Expression levels of both MdANR1 and MdANR2 genes are generally higher in yellow-skinned cv. Golden Delicious than in red-skinned cv. Red Delicious. Transcript accumulation of MdANR1 and MdANR2 genes in fruits gradually decreased throughout fruit development. Ectopic expression of apple MdANR genes in tobacco positively and negatively regulates the biosynthesis of proanthocyanidins (PAs) and anthocyanin, respectively, resulting in white, pale pink-coloured, and white/red variegated flowers. The accumulation of anthocyanin is significantly reduced in all tobacco transgenic flowers, while catechin and epicatechin contents in transgenic flowers are significantly higher than those in flowers of wild-type plants. The inhibition of anthocyanin synthesis in tobacco transgenic flowers overexpressing MdANR genes is probably attributed to down-regulation of CHALCONE ISOMERASE (CHI) and DIHYDROFLAVONOL-4-REDUCTASE (DFR) genes involved in the anthocyanin pathway. Interestingly, several transgenic lines show no detectable transcripts of the gene encoding leucoanthocyanidin reductase (LAR) in flowers, but accumulate higher levels of catechin in flowers of transgenic plants than those of wild-type plants. This finding suggests that the ANR gene may be capable of generating catechin via an alternative route, although this mechanism is yet to be further elucidated.
Collapse
Affiliation(s)
- Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Moshan, Wuhan, 430074 PR China
| | - Sornkanok Vimolmangkang
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
| | - Ruth Elena Soria-Guerra
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
| | - Schuyler S. Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
| |
Collapse
|
41
|
Cheng J, Khan MA, Qiu WM, Li J, Zhou H, Zhang Q, Guo W, Zhu T, Peng J, Sun F, Li S, Korban SS, Han Y. Diversification of genes encoding granule-bound starch synthase in monocots and dicots is marked by multiple genome-wide duplication events. PLoS One 2012; 7:e30088. [PMID: 22291904 PMCID: PMC3264551 DOI: 10.1371/journal.pone.0030088] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 12/13/2011] [Indexed: 11/18/2022] Open
Abstract
Starch is one of the major components of cereals, tubers, and fruits. Genes encoding granule-bound starch synthase (GBSS), which is responsible for amylose synthesis, have been extensively studied in cereals but little is known about them in fruits. Due to their low copy gene number, GBSS genes have been used to study plant phylogenetic and evolutionary relationships. In this study, GBSS genes have been isolated and characterized in three fruit trees, including apple, peach, and orange. Moreover, a comprehensive evolutionary study of GBSS genes has also been conducted between both monocots and eudicots. Results have revealed that genomic structures of GBSS genes in plants are conserved, suggesting they all have evolved from a common ancestor. In addition, the GBSS gene in an ancestral angiosperm must have undergone genome duplication ∼251 million years ago (MYA) to generate two families, GBSSI and GBSSII. Both GBSSI and GBSSII are found in monocots; however, GBSSI is absent in eudicots. The ancestral GBSSII must have undergone further divergence when monocots and eudicots split ∼165 MYA. This is consistent with expression profiles of GBSS genes, wherein these profiles are more similar to those of GBSSII in eudicots than to those of GBSSI genes in monocots. In dicots, GBSSII must have undergone further divergence when rosids and asterids split from each other ∼126 MYA. Taken together, these findings suggest that it is GBSSII rather than GBSSI of monocots that have orthologous relationships with GBSS genes of eudicots. Moreover, diversification of GBSS genes is mainly associated with genome-wide duplication events throughout the evolutionary course of history of monocots and eudicots.
Collapse
Affiliation(s)
- Jun Cheng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Muhammad Awais Khan
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Wen-Ming Qiu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jing Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wenwu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tingting Zhu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Junhua Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, Georgia, United States of America
| | - Shaohua Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Schuyler S. Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail: (SK); (YH)
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail: (SK); (YH)
| |
Collapse
|
42
|
Khan MA, Han Y, Zhao YF, Korban SS. A high-throughput apple SNP genotyping platform using the GoldenGate™ assay. Gene 2011; 494:196-201. [PMID: 22209719 DOI: 10.1016/j.gene.2011.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 10/14/2022]
Abstract
EST data generated from 14 apple genotypes were downloaded from NCBI and mapped against a reference EST assembly to identify Single Nucleotide Polymorphisms (SNPs). Mapping of these SNPs was undertaken using 90% of sequence similarity and minimum coverage of four reads at each SNP position. In total, 37,807 SNPs were identified with an average of one SNP every 187 bp from a total of 6888 unique EST contigs. Identified SNPs were checked for flanking sequences of ≥ 60 bp along both sides of SNP alleles for reliable design of a custom high-throughput genotyping assay. A total of 12,299 SNPs, representing 6525 contigs, fit the selected criterion of ≥ 60 bp sequences flanking a SNP position. Of these, 1411 SNPs were validated using four apple genotypes. Based on genotyping assays, it was estimated that 60% of SNPs were valid SNPs, while 26% of SNPs might be derived from paralogous regions.
Collapse
Affiliation(s)
- M Awais Khan
- Department of Natural Resources & Environmental Sciences, University of Illinois, Urbana, IL 61801, USA
| | | | | | | |
Collapse
|