1
|
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
|
2
|
Huang J, Ma Q, Cai Z, Xia Q, Li S, Jia J, Chu L, Lian T, Nian H, Cheng Y. Identification and Mapping of Stable QTLs for Seed Oil and Protein Content in Soybean [ Glycine max (L.) Merr.]. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6448-6460. [PMID: 32401505 DOI: 10.1021/acs.jafc.0c01271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This research aimed to identify stable quantitative trait loci (QTL) associated with oil and protein content in soybean. A population of 196 recombinant inbred lines (RILs) derived from Huachun 2 × Wayao was used to evaluate these target traits. A high-density genetic linkage map was constructed by using high-throughput genome-wide sequencing technology, which contained 3413 recombination bin markers and spanned 5400.4 cM with an average distance of 1.58 cM between markers. Eighteen stable QTLs controlling oil and protein content were detected. Among them, qOil-11-1 was identified for the first time as a novel QTL, while qOil-5-1, qPro-10-1, and qPro-14-1 were strong and stable QTLs with high log-likelihood (LOD) values. Sixteen differentially expressed genes (DEGs) within these four QTLs were shown to be highly expressed during seed development based on RNA sequencing (RNA-seq) data analysis. Our results may contribute toward gene mining and marker-assisted selection (MAS) for breeding a high-quality soybean in the future.
Collapse
Affiliation(s)
- Jinghua Huang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Qiuju Xia
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, People's Republic of China
| | - Shuxian Li
- United States Department of Agriculture, Agricultural Research Service, Crop Genetics Research Unit, 141 Experiment Station Road, P.O. Box 345, Stoneville, Mississippi 38776, United States
| | - Jia Jia
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Li Chu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China
| |
Collapse
|
3
|
Li S, Yang G, Yang S, Just J, Yan H, Zhou N, Jian H, Wang Q, Chen M, Qiu X, Zhang H, Dong X, Jiang X, Sun Y, Zhong M, Bendahmane M, Ning G, Ge H, Hu JY, Tang K. The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose. Sci Rep 2019; 9:5985. [PMID: 30979937 PMCID: PMC6461668 DOI: 10.1038/s41598-019-42428-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/07/2019] [Indexed: 01/11/2023] Open
Abstract
Roses are important woody plants featuring a set of important traits that cannot be investigated in traditional model plants. Here, we used the restriction-site associated DNA sequencing (RAD-seq) technology to develop a high-density linkage map of the backcross progeny (BC1F1) between Rosa chinensis ‘Old Blush’ (OB) and R. wichuraiana ‘Basyes’ Thornless’ (BT). We obtained 643.63 million pair-end reads and identified 139,834 polymorphic tags that were distributed uniformly in the rose genome. 2,213 reliable markers were assigned to seven linkage groups (LGs). The length of the genetic map was 1,027.425 cM in total with a mean distance of 0.96 cM per marker locus. This new linkage map allowed anchoring an extra of 1.21/23.14 Mb (12.18/44.52%) of the unassembled OB scaffolds to the seven reference pseudo-chromosomes, thus significantly improved the quality of assembly of OB reference genome. We demonstrate that, while this new linkage map shares high collinearity level with strawberry genome, it also features two chromosomal rearrangements, indicating its usefulness as a resource for understanding the evolutionary scenario among Rosaceae genomes. Together with the newly released genome sequences for OB, this linkage map will facilitate the identification of genetic components underpinning key agricultural and biological traits, hence should greatly advance the studies and breeding efforts of rose.
Collapse
Affiliation(s)
- Shubin Li
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Guoqian Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China.,Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shuhua Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jeremy Just
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69364, Lyon, France
| | - Huijun Yan
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Ningning Zhou
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Hongying Jian
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Qigang Wang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Min Chen
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Xianqin Qiu
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Hao Zhang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Xue Dong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiaodong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Yibo Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Micai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69364, Lyon, France
| | - Guogui Ning
- Key laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Ge
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Kaixue Tang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China.
| |
Collapse
|
4
|
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
|
5
|
Wu D, Koch J, Coggeshall M, Carlson J. The first genetic linkage map for Fraxinus pennsylvanica and syntenic relationships with four related species. PLANT MOLECULAR BIOLOGY 2019; 99:251-264. [PMID: 30604323 DOI: 10.1007/s11103-018-0815-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/15/2018] [Indexed: 06/09/2023]
Abstract
The genetic linkage map for green ash (Fraxinus pennsylvanica) contains 1201 DNA markers in 23 linkage groups spanning 2008.87cM. The green ash map shows stronger synteny with coffee than tomato. Green ash (Fraxinus pennsylvanica) is an outcrossing, diploid (2n = 46) hardwood tree species, native to North America. Native ash species in North America are being threatened by the rapid spread of the emerald ash borer (EAB, Agrilus planipennis), an invasive pest from Asia. Green ash, the most widely distributed ash species, is severely affected by EAB infestation, yet few genomic resources for genetic studies and improvement of green ash are available. In this study, a total of 5712 high quality single nucleotide polymorphisms (SNPs) were discovered using a minimum allele frequency of 1% across the entire genome through genotyping-by-sequencing. We also screened hundreds of genomic- and EST-based microsatellite markers (SSRs) from previous de novo assemblies (Staton et al., PLoS ONE 10:e0145031, 2015; Lane et al., BMC Genom 17:702, 2016). A first genetic linkage map of green ash was constructed from 90 individuals in a full-sib family, combining 2719 SNP and 84 SSR segregating markers among the parental maps. The consensus SNP and SSR map contains a total of 1201 markers in 23 linkage groups spanning 2008.87 cM, at an average inter-marker distance of 1.67 cM with a minimum logarithm of odds of 6 and maximum recombination fraction of 0.40. Comparisons of the organization the green ash map with the genomes of asterid species coffee and tomato, and genomes of the rosid species poplar and peach, showed areas of conserved gene order, with overall synteny strongest with coffee.
Collapse
Affiliation(s)
- Di Wu
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jennifer Koch
- USDA Forest Service, Northern Research Station, Project NRS-16, 359 Main Road, Delaware, OH, 43015, USA
| | - Mark Coggeshall
- Department of Forestry, Center for Agroforestry, University of Missouri, Columbia, MO, 65211, USA
- USDA Forest Service, Northern Research Station, Hardwood Tree Improvement and Regeneration Center, Project NRS-14, 715 W. State Street, West Lafayette, IN, 47907, USA
| | - John Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA.
| |
Collapse
|
6
|
Marconi G, Ferradini N, Russi L, Concezzi L, Veronesi F, Albertini E. Genetic Characterization of the Apple Germplasm Collection in Central Italy: The Value of Local Varieties. FRONTIERS IN PLANT SCIENCE 2018; 9:1460. [PMID: 30364143 PMCID: PMC6191466 DOI: 10.3389/fpls.2018.01460] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/12/2018] [Indexed: 05/06/2023]
Abstract
In the last 50 years, intensive farming systems have been boosted by modern agricultural techniques and newly bred cultivars. The massive use of few and related cultivars has dramatically reduced the apple genetic diversity of local varieties, confined to marginal areas. In Central Italy a limited spread of intensive fruit orchards has made it possible to preserve much of the local genetic diversity, but at the same time the coexistence of both modern and ancient varieties has generated some confusion. The characterization and clarification of possible synonyms, homonyms, and/or labeling errors in old local genetic resources is an issue in the conservation and management of living collections. 175 accessions provided by 10 apple collections, mainly local varieties, some of unknown origin, and well-known modern and ancient varieties, were studied by using 19 SSRs, analyzed by STRUCTURE, Ward's clustering and parentage analysis. We were able to identify 25 duplicates, 9 synonyms, and 9 homonyms. As many as 37 unknown accession were assigned to well known local or commercial varieties. Polyploids made up 20%. Some markers were found to be significantly correlated with morphological traits and the loci associated with the fruit over color were related to QTLs for resistance to biotic stresses, aroma compounds, stiffness, and acidity. In conclusion the gene pool of Central Italy seems to be rather consistent and highly differentiated compared with other European studies (F ST = 0.147). The importance of safeguarding this diversity and the impact on the management of the germplasm living collection is discussed.
Collapse
Affiliation(s)
- Gianpiero Marconi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Nicoletta Ferradini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Luigi Russi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | | | - Fabio Veronesi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università degli Studi di Perugia, Perugia, Italy
- *Correspondence: Emidio Albertini,
| |
Collapse
|
7
|
He Y, Yuan W, Dong M, Han Y, Shang F. The First Genetic Map in Sweet Osmanthus ( Osmanthus fragrans Lour.) Using Specific Locus Amplified Fragment Sequencing. FRONTIERS IN PLANT SCIENCE 2017; 8:1621. [PMID: 29018460 PMCID: PMC5614988 DOI: 10.3389/fpls.2017.01621] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/05/2017] [Indexed: 05/23/2023]
Abstract
Osmanthus fragrans is an ornamental plant of substantial commercial value, and no genetic linkage maps of this species have previously been reported. Specific-locus amplified fragment sequencing (SLAF-seq) is a recently developed technology that allows massive single nucleotide polymorphisms (SNPs) to be identified and high-resolution genotyping. In our current research, we generated the first genetic map of O. fragrans using SLAF-seq, which is composed with 206.92 M paired-end reads and 173,537 SLAF markers. Among total 90,715 polymorphic SLAF markers, 15,317 polymorphic SLAFs could be used for genetic map construction. The integrated map contained 14,189 high quality SLAFs that were grouped in 23 genetic linkage groups, with a total length of 2962.46 cM and an average distance of 0.21 cM between two adjacent markers. In addition, 23,664 SNPs were identified from the mapped markers. As far as we know, this is the first of the genetic map of O. fragrans. Our results are further demonstrate that SLAF-seq is a very effective method for developing markers and constructing high-density linkage maps. The SNP markers and the genetic map reported in this study should be valuable resource in future research.
Collapse
Affiliation(s)
- Yanxia He
- Plant Germplasm Resources and Genetic Laboratory, College of Life Sciences, Henan UniversityKaifeng, China
| | - Wangjun Yuan
- Institute of Pharmacy, Pharmaceutical College of Henan UniversityKaifeng, China
| | - Meifang Dong
- Plant Germplasm Resources and Genetic Laboratory, College of Life Sciences, Henan UniversityKaifeng, China
| | - Yuanji Han
- Plant Germplasm Resources and Genetic Laboratory, College of Life Sciences, Henan UniversityKaifeng, China
| | - Fude Shang
- Plant Germplasm Resources and Genetic Laboratory, College of Life Sciences, Henan UniversityKaifeng, China
- Woe Key Laboratory of Plant Stress Biology, Henan UniversityKaifeng, China
| |
Collapse
|
8
|
Zarei A, Erfani-Moghadam J, Mozaffari M. Phylogenetic analysis among some pome fruit trees of Rosaceae family using RAPD markers. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2016.1276414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Abdolkarim Zarei
- Department of Biotechnology, Faculty of Agriculture, Jahrom University, Jahrom, Iran
| | - Javad Erfani-Moghadam
- Department of Horticultural Sciences, Faculty of Agriculture, Ilam University, Ilam, Iran
| | - Mohsen Mozaffari
- Department of Horticultural Sciences, Faculty of Agriculture, Ilam University, Ilam, Iran
| |
Collapse
|
9
|
Kunihisa M, Moriya S, Abe K, Okada K, Haji T, Hayashi T, Kawahara Y, Itoh R, Itoh T, Katayose Y, Kanamori H, Matsumoto T, Mori S, Sasaki H, Matsumoto T, Nishitani C, Terakami S, Yamamoto T. Genomic dissection of a 'Fuji' apple cultivar: re-sequencing, SNP marker development, definition of haplotypes, and QTL detection. BREEDING SCIENCE 2016; 66:499-515. [PMID: 27795675 PMCID: PMC5010306 DOI: 10.1270/jsbbs.16018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/19/2016] [Indexed: 05/03/2023]
Abstract
'Fuji' is one of the most popular and highly-produced apple cultivars worldwide, and has been frequently used in breeding programs. The development of genotypic markers for the preferable phenotypes of 'Fuji' is required. Here, we aimed to define the haplotypes of 'Fuji' and find associations between haplotypes and phenotypes of five traits (harvest day, fruit weight, acidity, degree of watercore, and flesh mealiness) by using 115 accessions related to 'Fuji'. Through the re-sequencing of 'Fuji' genome, total of 2,820,759 variants, including single nucleotide polymorphisms (SNPs) and insertions or deletions (indels) were detected between 'Fuji' and 'Golden Delicious' reference genome. We selected mapping-validated 1,014 SNPs, most of which were heterozygous in 'Fuji' and capable of distinguishing alleles inherited from the parents of 'Fuji' (i.e., 'Ralls Janet' and 'Delicious'). We used these SNPs to define the haplotypes of 'Fuji' and trace their inheritance in relatives, which were shown to have an average of 27% of 'Fuji' genome. Analysis of variance (ANOVA) based on 'Fuji' haplotypes identified one quantitative trait loci (QTL) each for harvest time, acidity, degree of watercore, and mealiness. A haplotype from 'Delicious' chr14 was considered to dominantly cause watercore, and one from 'Ralls Janet' chr1 was related to low-mealiness.
Collapse
Affiliation(s)
- Miyuki Kunihisa
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
- Corresponding author (e-mail: )
| | - Shigeki Moriya
- NARO Institute of Fruit Tree Science,
92-24 Shimokuriyagawa, Morioka, Iwate 020-0123,
Japan
| | - Kazuyuki Abe
- NARO Institute of Fruit Tree Science,
92-24 Shimokuriyagawa, Morioka, Iwate 020-0123,
Japan
| | - Kazuma Okada
- NARO Institute of Fruit Tree Science,
92-24 Shimokuriyagawa, Morioka, Iwate 020-0123,
Japan
| | - Takashi Haji
- NARO Institute of Fruit Tree Science,
92-24 Shimokuriyagawa, Morioka, Iwate 020-0123,
Japan
| | - Takeshi Hayashi
- NARO Agricultural Research Center,
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666,
Japan
| | - Yoshihiro Kawahara
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602,
Japan
| | - Ryutaro Itoh
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602,
Japan
- DYNACOM Co., Ltd.,
E-25F, WBG, 2-6-1 Nakase, Mihama-ku, Chiba 261-7125,
Japan
| | - Takeshi Itoh
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602,
Japan
| | - Yuichi Katayose
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602,
Japan
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602,
Japan
| | - Toshimi Matsumoto
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602,
Japan
| | - Satomi Mori
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602,
Japan
| | - Harumi Sasaki
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602,
Japan
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305- 8602,
Japan
| | - Chikako Nishitani
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Shingo Terakami
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Toshiya Yamamoto
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| |
Collapse
|
10
|
The first genetic linkage map of Primulina eburnea (Gesneriaceae) based on EST-derived SNP markers. J Genet 2016; 95:377-82. [PMID: 27350682 DOI: 10.1007/s12041-016-0650-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Primulina eburnea is a promising candidate for domestication and floriculture, since it is easy to culture and has beautiful flowers. An F₂ population of 189 individuals was established for the construction of first-generation linkage maps based on expressed sequence tags-derived single-nucleotide polymorphism markers using the massARRAY genotyping platform. Of the 232 screened markers, 215 were assigned to 18 LG according to the haploid number of chromosomes in the species. The linkage map spanned a total of 3774.7 cM with an average distance of 17.6 cM between adjacent markers. This linkage map provides a framework for identification of important genes in breeding programmes.
Collapse
|
11
|
Montanari S, Brewer L, Lamberts R, Velasco R, Malnoy M, Perchepied L, Guérif P, Durel CE, Bus VGM, Gardiner SE, Chagné D. Genome mapping of postzygotic hybrid necrosis in an interspecific pear population. HORTICULTURE RESEARCH 2016; 3:15064. [PMID: 26770810 PMCID: PMC4702180 DOI: 10.1038/hortres.2015.64] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 05/22/2023]
Abstract
Deleterious epistatic interactions in plant inter- and intraspecific hybrids can cause a phenomenon known as hybrid necrosis, characterized by a typical seedling phenotype whose main distinguishing features are dwarfism, tissue necrosis and in some cases lethality. Identification of the chromosome regions associated with this type of incompatibility is important not only to increase our understanding of the evolutionary diversification that led to speciation but also for breeding purposes. Development of molecular markers linked to the lethal genes will allow breeders to avoid incompatible inbred combinations that could affect the expression of important agronomic tratis co-segregating with these genes. Although hybrid necrosis has been reported in several plant taxa, including Rosaceae species, this phenomenon has not been described previously in pear. In the interspecific pear population resulting from a cross between PEAR3 (Pyrus bretschneideri × Pyrus communis) and 'Moonglow' (P. communis), we observed two types of hybrid necrosis, expressed at different stages of plant development. Using a combination of previously mapped and newly developed genetic markers, we identified three chromosome regions associated with these two types of lethality, which were genetically independent. One type resulted from a negative epistatic interaction between a locus on linkage group 5 (LG5) of PEAR3 and a locus on LG1 of 'Moonglow', while the second type was due to a gene that maps to LG2 of PEAR3 and which either acts alone or more probably interacts with another gene of unknown location inherited from 'Moonglow'.
Collapse
Affiliation(s)
- Sara Montanari
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige (TN), Italy
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Lester Brewer
- The New Zealand Institute for Plant & Food Research Limited, Motueka Research Centre, Motueka, New Zealand
| | - Robert Lamberts
- The New Zealand Institute for Plant & Food Research Limited, Motueka Research Centre, Motueka, New Zealand
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige (TN), Italy
| | - Mickael Malnoy
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige (TN), Italy
| | - Laure Perchepied
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
- Institut de Recherche en Horticulture et Semences - UMR1345, Université d’Angers, F-49045 Angers, France
| | - Philippe Guérif
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
- Institut de Recherche en Horticulture et Semences - UMR1345, Université d’Angers, F-49045 Angers, France
| | - Charles-Eric Durel
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
- Institut de Recherche en Horticulture et Semences - UMR1345, Université d’Angers, F-49045 Angers, France
| | - Vincent G M Bus
- The New Zealand Institute for Plant & Food Research Limited, Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
- ()
| |
Collapse
|
12
|
Yamamoto T, Terakami S. Genomics of pear and other Rosaceae fruit trees. BREEDING SCIENCE 2016; 66:148-59. [PMID: 27069399 PMCID: PMC4780798 DOI: 10.1270/jsbbs.66.148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/12/2016] [Indexed: 05/04/2023]
Abstract
The family Rosaceae includes many economically important fruit trees, such as pear, apple, peach, cherry, quince, apricot, plum, raspberry, and loquat. Over the past few years, whole-genome sequences have been released for Chinese pear, European pear, apple, peach, Japanese apricot, and strawberry. These sequences help us to conduct functional and comparative genomics studies and to develop new cultivars with desirable traits by marker-assisted selection in breeding programs. These genomics resources also allow identification of evolutionary relationships in Rosaceae, development of genome-wide SNP and SSR markers, and construction of reference genetic linkage maps, which are available through the Genome Database for the Rosaceae website. Here, we review the recent advances in genomics studies and their practical applications for Rosaceae fruit trees, particularly pear, apple, peach, and cherry.
Collapse
Affiliation(s)
- Toshiya Yamamoto
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Shingo Terakami
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| |
Collapse
|
13
|
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
|
14
|
Gaur R, Jeena G, Shah N, Gupta S, Pradhan S, Tyagi AK, Jain M, Chattopadhyay D, Bhatia S. High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea. Sci Rep 2015; 5:13387. [PMID: 26303721 PMCID: PMC4548218 DOI: 10.1038/srep13387] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/29/2015] [Indexed: 01/07/2023] Open
Abstract
This study presents genome-wide discovery of SNPs through next generation sequencing of the genome of Cicer reticulatum. Mapping of the C. reticulatum sequenced reads onto the draft genome assembly of C. arietinum (desi chickpea) resulted in identification of 842,104 genomic SNPs which were utilized along with an additional 36,446 genic SNPs identified from transcriptome sequences of the aforementioned varieties. Two new chickpea Oligo Pool All (OPAs) each having 3,072 SNPs were designed and utilized for SNP genotyping of 129 Recombinant Inbred Lines (RILs). Using Illumina GoldenGate Technology genotyping data of 5,041 SNPs were generated and combined with the 1,673 marker data from previously published studies, to generate a high resolution linkage map. The map comprised of 6698 markers distributed on eight linkage groups spanning 1083.93 cM with an average inter-marker distance of 0.16 cM. Utility of the present map was demonstrated for improving the anchoring of the earlier reported draft genome sequence of desi chickpea by ~30% and that of kabuli chickpea by 18%. The genetic map reported in this study represents the most dense linkage map of chickpea , with the potential to facilitate efficient anchoring of the draft genome sequences of desi as well as kabuli chickpea varieties.
Collapse
Affiliation(s)
- Rashmi Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Ganga Jeena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Niraj Shah
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Shefali Gupta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Seema Pradhan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Mukesh Jain
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| |
Collapse
|
15
|
Bushakra JM, Bryant DW, Dossett M, Vining KJ, VanBuren R, Gilmore BS, Lee J, Mockler TC, Finn CE, Bassil NV. A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag(4) conferring resistance to the aphid Amphorophora agathonica. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1631-46. [PMID: 26037086 PMCID: PMC4477079 DOI: 10.1007/s00122-015-2541-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/18/2015] [Indexed: 05/07/2023]
Abstract
We have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance. Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace. Few genetic resources are readily available and little improvement has been achieved through breeding efforts to address production challenges involved in growing this crop. Contributing to its lack of improvement is low genetic diversity in elite cultivars and an untapped reservoir of genetic diversity from wild germplasm. In the Pacific Northwest, where most production is centered, the current standard commercial cultivar is highly susceptible to the aphid Amphorophora agathonica Hottes, which is a vector for the Raspberry mosaic virus complex. Infection with the virus complex leads to a rapid decline in plant health resulting in field replacement after only 3-4 growing seasons. Sources of aphid resistance have been identified in wild germplasm and are used to develop mapping populations to study the inheritance of these valuable traits. We have constructed a genetic linkage map using single-nucleotide polymorphism and transferable (primarily simple sequence repeat) markers for F1 population ORUS 4305 consisting of 115 progeny that segregate for aphid resistance. Our linkage map of seven linkage groups representing the seven haploid chromosomes of black raspberry consists of 274 markers on the maternal map and 292 markers on the paternal map including a morphological locus for aphid resistance. This is the first linkage map of black raspberry and will aid in developing markers for marker-assisted breeding, comparative mapping with other Rubus species, and enhancing the black raspberry genome assembly.
Collapse
Affiliation(s)
- Jill M Bushakra
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Rd., Corvallis, OR, 97333, USA,
| | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Wang G, Guo Y, Zhao Y, Su K, Zhang J. Construction of a molecular genetic map for hawthorn based on SRAP markers. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1018322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
17
|
Cavagnaro PF, Iorizzo M, Yildiz M, Senalik D, Parsons J, Ellison S, Simon PW. A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation. BMC Genomics 2014; 15:1118. [PMID: 25514876 PMCID: PMC4378384 DOI: 10.1186/1471-2164-15-1118] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. Informative, saturated linkage maps associated with well characterized populations segregating for anthocyanin pigmentation have not been developed. To investigate the genetic architecture conditioning anthocyanin pigmentation we scored root color visually, quantified root anthocyanin pigments by high performance liquid chromatography in segregating F2, F3 and F4 generations of a mapping population, mapped quantitative trait loci (QTL) onto a dense gene-derived single nucleotide polymorphism (SNP)-based linkage map, and performed comparative trait mapping with two unrelated populations. RESULTS Root pigmentation, scored visually as presence or absence of purple coloration, segregated in a pattern consistent with a two gene model in an F2, and progeny testing of F3-F4 families confirmed the proposed genetic model. Purple petiole pigmentation was conditioned by a single dominant gene that co-segregates with one of the genes conditioning root pigmentation. Root total pigment estimate (RTPE) was scored as the percentage of the root with purple color.All five anthocyanin glycosides previously reported in carrot, as well as RTPE, varied quantitatively in the F2 population. For the purpose of QTL analysis, a high resolution gene-derived SNP-based linkage map of carrot was constructed with 894 markers covering 635.1 cM with a 1.3 cM map resolution. A total of 15 significant QTL for all anthocyanin pigments and for RTPE mapped to six chromosomes. Eight QTL with the largest phenotypic effects mapped to two regions of chromosome 3 with co-localized QTL for several anthocyanin glycosides and for RTPE. A single dominant gene conditioning anthocyanin acylation was identified and mapped.Comparative mapping with two other carrot populations segregating for purple color indicated that carrot anthocyanin pigmentation is controlled by at least three genes, in contrast to monogenic control reported previously. CONCLUSIONS This study generated the first high resolution gene-derived SNP-based linkage map in the Apiaceae. Two regions of chromosome 3 with co-localized QTL for all anthocyanin pigments and for RTPE, largely condition anthocyanin accumulation in carrot roots and leaves. Loci controlling root and petiole anthocyanin pigmentation differ across diverse carrot genetic backgrounds.
Collapse
Affiliation(s)
- Pablo F Cavagnaro
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
- />CONICET, Facultad de Ciencias Agrarias – Universidad Nacional de Cuyo, and INTA E.E.A. La Consulta, Ex Ruta 40. km 96, La Consulta CC 8, Mendoza, 5567 Argentina
| | - Massimo Iorizzo
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
| | - Mehtap Yildiz
- />Department of Agricultural Biotechnology, Faculty of Agriculture, Yuzuncu Yil University, 65080 Van, Turkey
| | - Douglas Senalik
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
- />USDA-Agricultural Research Service, Vegetable Crops Unit, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
| | - Joshua Parsons
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
| | - Shelby Ellison
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
| | - Philipp W Simon
- />Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
- />USDA-Agricultural Research Service, Vegetable Crops Unit, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706 USA
| |
Collapse
|
18
|
Verdu CF, Guyot S, Childebrand N, Bahut M, Celton JM, Gaillard S, Lasserre-Zuber P, Troggio M, Guilet D, Laurens F. QTL analysis and candidate gene mapping for the polyphenol content in cider apple. PLoS One 2014; 9:e107103. [PMID: 25271925 PMCID: PMC4182701 DOI: 10.1371/journal.pone.0107103] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 08/12/2014] [Indexed: 11/25/2022] Open
Abstract
Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed.
Collapse
Affiliation(s)
- Cindy F. Verdu
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
- Université d'Angers, EA921 Laboratoire de Substances d'Origine Naturelle et Analogues Structuraux, SFR 4207 Quasav, PRES L'UNAM, Angers, France
| | - Sylvain Guyot
- INRA, UR1268 Biopolymères, Interactions & Assemblages, Equipe « Polyphénols, Réactivité & Procédés », Le Rheu, France
| | - Nicolas Childebrand
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Muriel Bahut
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Jean-Marc Celton
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Sylvain Gaillard
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Pauline Lasserre-Zuber
- INRA-UBP, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, TN, Italy
| | - David Guilet
- Université d'Angers, EA921 Laboratoire de Substances d'Origine Naturelle et Analogues Structuraux, SFR 4207 Quasav, PRES L'UNAM, Angers, France
| | - François Laurens
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| |
Collapse
|
19
|
Kunihisa M, Moriya S, Abe K, Okada K, Haji T, Hayashi T, Kim H, Nishitani C, Terakami S, Yamamoto T. Identification of QTLs for fruit quality traits in Japanese apples: QTLs for early ripening are tightly related to preharvest fruit drop. BREEDING SCIENCE 2014; 64:240-51. [PMID: 25320559 PMCID: PMC4154613 DOI: 10.1270/jsbbs.64.240] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/24/2014] [Indexed: 05/03/2023]
Abstract
Many important apple (Malus × domestica Borkh.) fruit quality traits are regulated by multiple genes, and more information about quantitative trait loci (QTLs) for these traits is required for marker-assisted selection. In this study, we constructed genetic linkage maps of the Japanese apple cultivars 'Orin' and 'Akane' using F1 seedlings derived from a cross between these cultivars. The 'Orin' map consisted of 251 loci covering 17 linkage groups (LGs; total length 1095.3 cM), and the 'Akane' map consisted of 291 loci covering 18 LGs (total length 1098.2 cM). We performed QTL analysis for 16 important traits, and found that four QTLs related to harvest time explained about 70% of genetic variation, and these will be useful for marker-assisted selection. The QTL for early harvest time in LG15 was located very close to the QTL for preharvest fruit drop. The QTL for skin color depth was located around the position of MYB1 in LG9, which suggested that alleles harbored by 'Akane' are regulating red color depth with different degrees of effect. We also analyzed soluble solids and sugar component contents, and found that a QTL for soluble solids content in LG16 could be explained by the amount of sorbitol and fructose.
Collapse
Affiliation(s)
- Miyuki Kunihisa
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
- Corresponding author (e-mail: )
| | - Shigeki Moriya
- Apple Research Station, NARO Institute of Fruit Tree Science,
Shimokuriyagawa, Morioka, Iwate 020-0123,
Japan
| | - Kazuyuki Abe
- Apple Research Station, NARO Institute of Fruit Tree Science,
Shimokuriyagawa, Morioka, Iwate 020-0123,
Japan
| | - Kazuma Okada
- Apple Research Station, NARO Institute of Fruit Tree Science,
Shimokuriyagawa, Morioka, Iwate 020-0123,
Japan
| | - Takashi Haji
- Apple Research Station, NARO Institute of Fruit Tree Science,
Shimokuriyagawa, Morioka, Iwate 020-0123,
Japan
| | - Takeshi Hayashi
- NARO Agricultural Research Center,
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666,
Japan
| | - Hoytaek Kim
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Chikako Nishitani
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Shingo Terakami
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Toshiya Yamamoto
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| |
Collapse
|
20
|
Abstract
In accordance with pseudo-testcross strategy, the first genetic linkage map of Eucommia ulmoides Oliv. was constructed by an F1 population of 122 plants using amplified fragment length polymorphism (AFLP) markers. A total of 22 AFLP primer combinations generated 363 polymorphic markers. We selected 289 markers segregating as 1:1 and used them for constructing the parent-specific linkage maps. Among the candidate markers, 127 markers were placed on the maternal map LF and 108 markers on the paternal map Q1. The maternal map LF spanned 1116.1 cM in 14 linkage groups with a mean map distance of 8.78 cM; the paternal map Q1 spanned 929.6 cM in 12 linkage groups with an average spacing of 8.61 cM. The estimated coverage of the genome through two methods was 78.5 and 73.9% for LF, and 76.8 and 71.2% for Q1, respectively. This map is the first linkage map of E. ulmoides and provides a basis for mapping quantitative-trait loci and breeding applications.
Collapse
Affiliation(s)
- Dawei Wang
- College of Forestry, Northwest A and F University, Yangling, Shaanxi 712100, People's Republic of China.
| | | | | | | | | |
Collapse
|
21
|
Tan LQ, Wang LY, Wei K, Zhang CC, Wu LY, Qi GN, Cheng H, Zhang Q, Cui QM, Liang JB. Floral transcriptome sequencing for SSR marker development and linkage map construction in the tea plant (Camellia sinensis). PLoS One 2013; 8:e81611. [PMID: 24303059 PMCID: PMC3841144 DOI: 10.1371/journal.pone.0081611] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/14/2013] [Indexed: 11/18/2022] Open
Abstract
Despite the worldwide consumption and high economic importance of tea, the plant (Camellia sinensis) is not well studied in molecular biology. Under the few circumstances in which the plant is studied, C. sinensis flowers, which are important for reproduction and cross-breeding, receive less emphasis than investigation of its leaves or roots. Using high-throughput Illumina RNA sequencing, we analyzed a C. sinensis floral transcriptome, and 26.9 million clean reads were assembled into 75,531 unigenes averaging 402 bp. Among them, 50,792 (67.2%) unigenes were annotated with a BLAST search against the NCBI Non-Redundant (NR) database and 10,290 (16.67%) were detected that contained one or more simple sequence repeats (SSRs). From these SSR-containing sequences, 2,439 candidate SSR markers were developed and 720 were experimentally tested, validating 431 (59.9%) novel polymorphic SSR markers for C. sinensis. Then, a consensus SSR-based linkage map was constructed that covered 1,156.9 cM with 237 SSR markers distributed in 15 linkage groups. Both transcriptome information and the genetic map of C. sinensis presented here offer a valuable foundation for molecular biology investigations such as functional gene isolation, quantitative trait loci mapping, and marker-assisted selection breeding in this important species.
Collapse
Affiliation(s)
- Li-Qiang Tan
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
- College of Horticulture, Sichuan Agricultural University, Yaan, P. R. China
| | - Li-Yuan Wang
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
- * E-mail: (HC); (LYW); (GNQ)
| | - Kang Wei
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
| | - Cheng-Cai Zhang
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
| | - Li-Yun Wu
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
| | - Gui-Nian Qi
- College of Horticulture, Sichuan Agricultural University, Yaan, P. R. China
- * E-mail: (HC); (LYW); (GNQ)
| | - Hao Cheng
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, P. R. China
- * E-mail: (HC); (LYW); (GNQ)
| | - Qiang Zhang
- Tea Research Institute, Enshi Academy of Agricultural Sciences, Enshi, P. R. China
| | - Qing-Mei Cui
- Tea Research Institute, Enshi Academy of Agricultural Sciences, Enshi, P. R. China
| | - Jin-Bo Liang
- Tea Research Institute, Enshi Academy of Agricultural Sciences, Enshi, P. R. China
| |
Collapse
|
22
|
Di Guardo M, Tadiello A, Farneti B, Lorenz G, Masuero D, Vrhovsek U, Costa G, Velasco R, Costa F. A multidisciplinary approach providing new insight into fruit flesh browning physiology in apple (Malus x domestica Borkh.). PLoS One 2013; 8:e78004. [PMID: 24205065 PMCID: PMC3799748 DOI: 10.1371/journal.pone.0078004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/09/2013] [Indexed: 11/18/2022] Open
Abstract
In terms of the quality of minimally processed fruit, flesh browning is fundamentally important in the development of an aesthetically unpleasant appearance, with consequent off-flavours. The development of browning depends on the enzymatic action of the polyphenol oxidase (PPO). In the 'Golden Delicious' apple genome ten PPO genes were initially identified and located on three main chromosomes (2, 5 and 10). Of these genes, one element in particular, here called Md-PPO, located on chromosome 10, was further investigated and genetically mapped in two apple progenies ('Fuji x Pink Lady' and 'Golden Delicious x Braeburn'). Both linkage maps, made up of 481 and 608 markers respectively, were then employed to find QTL regions associated with fruit flesh browning, allowing the detection of 25 QTLs related to several browning parameters. These were distributed over six linkage groups with LOD values spanning from 3.08 to 4.99 and showed a rate of phenotypic variance from 26.1 to 38.6%. Anchoring of these intervals to the apple genome led to the identification of several genes involved in polyphenol synthesis and cell wall metabolism. Finally, the expression profile of two specific candidate genes, up and downstream of the polyphenolic pathway, namely phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO), provided insight into flesh browning physiology. Md-PPO was further analyzed and two haplotypes were characterised and associated with fruit flesh browning in apple.
Collapse
Affiliation(s)
- Mario Di Guardo
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Alice Tadiello
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Brian Farneti
- Department of Fruit Trees & Woody Plant Science, University of Bologna, Bologna, Italy
| | - Giorgia Lorenz
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Domenico Masuero
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Urska Vrhovsek
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Guglielmo Costa
- Department of Fruit Trees & Woody Plant Science, University of Bologna, Bologna, Italy
| | - Riccardo Velasco
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
| | - Fabrizio Costa
- Genomics and Crop Biology Department Research and Innovation Centre, Fondazione Edmund, Mach, San Michele all’Adige (Trento), Italy
- * E-mail:
| |
Collapse
|
23
|
Costa F, Cappellin L, Zini E, Patocchi A, Kellerhals M, Komjanc M, Gessler C, Biasioli F. QTL validation and stability for volatile organic compounds (VOCs) in apple. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 211:1-7. [PMID: 23987805 DOI: 10.1016/j.plantsci.2013.05.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 05/28/2013] [Accepted: 05/31/2013] [Indexed: 05/22/2023]
Abstract
The aroma trait in apple is a key factor for fruit quality strongly affecting the consumer appreciation, and its detection and analysis is often an extremely laborious and time consuming procedure. Molecular markers associated to this trait can to date represent a valuable selection tool to overcome these limitations. QTL mapping is the first step in the process of targeting valuable molecular markers to be employed in marker-assisted breeding programmes (MAB). However, a validation step is usually required before a newly identified molecular marker can be implemented in marker-assisted selection. In this work the position of a set of QTLs associated to volatile organic compounds (VOCs) was confirmed and validated in three different environments in Switzerland, namely Wädenswil, Conthey and Cadenazzo, where the progeny 'Fiesta×Discovery' was replicated. For both QTL identification and validation, the phenotypic data were represented by VOCs produced by mature apple fruit and assessed with a Proton Transfer Reaction-Mass Spectrometer (PTR-MS) instrument. The QTL-VOC combined analysis performed among these three locations validated the presence of important QTLs in three specific genomic regions, two located in the linkage group 2 and one in linkage group 15, respectively, for compounds related to esters (m/z 43, 61 and 131) and to the hormone ethylene (m/z 28). The QTL set presented here confirmed that in apple some compounds are highly genetically regulated and stable across environments.
Collapse
Affiliation(s)
- Fabrizio Costa
- Research and Innovation Centre, Foundation Edmund Mach, Via Mach 1, San Michele all'Adige (TN), Italy.
| | | | | | | | | | | | | | | |
Collapse
|
24
|
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
|
25
|
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
|
26
|
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
|
27
|
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
|
28
|
Patzak J, Paprštein F, Henychová A, Sedlák J. Comparison of genetic diversity structure analyses of SSR molecular marker data within apple (Malus×domestica) genetic resources. Genome 2012; 55:647-65. [PMID: 22954156 DOI: 10.1139/g2012-054] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to compare traditional hierarchical clustering techniques and principal coordinate analysis (PCoA) with the model-based Bayesian cluster analyses in relation to subpopulation differentiation based on breeding history and geographical origin of apple (Malus×domestica Borkh.) cultivars and landraces. We presented the use of a set of 10 microsatellite (SSR) loci for genetic diversity structure analyses of 273 apple accessions from national genetic resources. These SSR loci yielded a total of 113 polymorphic SSR alleles, with 5-18 alleles per locus. SSR molecular data were successfully used in binary and allelic input format for all genetic diversity analyses, but allelic molecular data did not reveal reliable results with the NTSYS-pc and BAPS softwares. A traditional cluster analysis still provided an easy and effective way for determining genetic diversity structure in the apple germplasm collection. A model-based Bayesian analysis also provided the clustering results in accordance to traditional cluster analysis, but the analyses were distorted by the presence of a dominant group of apple genetic resources owing to the narrow origin of the apple genome. PCoA confirmed that there were no noticeable differences in genetic diversity structure of apple genetic resources during the breeding history. The results of our analyses are useful in the context of enhancing apple collection management, sampling of core collections, and improving breeding processes.
Collapse
Affiliation(s)
- Josef Patzak
- Hop Research Institute Co. Ltd., Kadaňská 2525, 438 46 Žatec, Czech Republic.
| | | | | | | |
Collapse
|
29
|
Schouten HJ, van de Weg WE, Carling J, Khan SA, McKay SJ, van Kaauwen MPW, Wittenberg AHJ, Koehorst-van Putten HJJ, Noordijk Y, Gao Z, Rees DJG, Van Dyk MM, Jaccoud D, Considine MJ, Kilian A. Diversity arrays technology (DArT) markers in apple for genetic linkage maps. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2012; 29:645-660. [PMID: 22408382 PMCID: PMC3285764 DOI: 10.1007/s11032-011-9579-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 04/09/2011] [Indexed: 05/18/2023]
Abstract
Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Henk J. Schouten
- Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - W. Eric van de Weg
- Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Jason Carling
- Diversity Arrays Technology, PO Box 7141, Yarralumla, ACT 2600 Australia
| | - Sabaz Ali Khan
- Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Steven J. McKay
- Department of Horticultural Science, University of Minnesota, Alderman Hall, 1970 Folwell Ave, St. Paul, MN 55108 USA
| | | | | | | | - Yolanda Noordijk
- Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Zhongshan Gao
- Department of Horticulture, Zhejiang University, Hangzhou, 310029 China
| | - D. Jasper G. Rees
- ARC: Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, Pretoria, 0110 South Africa
| | - Maria M. Van Dyk
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028 South Africa
| | - Damian Jaccoud
- Diversity Arrays Technology, PO Box 7141, Yarralumla, ACT 2600 Australia
| | - Michael J. Considine
- School of Plant Biology, and the Institute of Agriculture, University of Western Australia, M084, Crawley, WA 6009 Australia
- Department of Agriculture and Food Western Australia, South Perth, WA 6151 Australia
| | - Andrzej Kilian
- Diversity Arrays Technology, PO Box 7141, Yarralumla, ACT 2600 Australia
| |
Collapse
|
30
|
Cruz-Hernández A, Paredes-lópez O. Fruit Quality: New Insights for Biotechnology. Crit Rev Food Sci Nutr 2012; 52:272-89. [DOI: 10.1080/10408398.2010.499844] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
31
|
Longhi S, Moretto M, Viola R, Velasco R, Costa F. Comprehensive QTL mapping survey dissects the complex fruit texture physiology in apple (Malus x domestica Borkh.). JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1107-21. [PMID: 22121200 DOI: 10.1093/jxb/err326] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Fruit ripening is a complex physiological process in plants whereby cell wall programmed changes occur mainly to promote seed dispersal. Cell wall modification also directly regulates the textural properties, a fundamental aspect of fruit quality. In this study, two full-sib populations of apple, with 'Fuji' as the common maternal parent, crossed with 'Delearly' and 'Pink Lady', were used to understand the control of fruit texture by QTL mapping and in silico gene mining. Texture was dissected with a novel high resolution phenomics strategy, simultaneously profiling both mechanical and acoustic fruit texture components. In 'Fuji × Delearly' nine linkage groups were associated with QTLs accounting from 15.6% to 49% of the total variance, and a highly significant QTL cluster for both textural components was mapped on chromosome 10 and co-located with Md-PG1, a polygalacturonase gene that, in apple, is known to be involved in cell wall metabolism processes. In addition, other candidate genes related to Md-NOR and Md-RIN transcription factors, Md-Pel (pectate lyase), and Md-ACS1 were mapped within statistical intervals. In 'Fuji × Pink Lady', a smaller set of linkage groups associated with the QTLs identified for fruit texture (15.9-34.6% variance) was observed. The analysis of the phenotypic variance over a two-dimensional PCA plot highlighted a transgressive segregation for this progeny, revealing two QTL sets distinctively related to both mechanical and acoustic texture components. The mining of the apple genome allowed the discovery of the gene inventory underlying each QTL, and functional profile assessment unravelled specific gene expression patterns of these candidate genes.
Collapse
Affiliation(s)
- Sara Longhi
- Research and Innovation Centre, Foundation Edmund Mach, Via Mach 1, I-38010 San Michele all'Adige, Trento, Italy
| | | | | | | | | |
Collapse
|
32
|
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
|
33
|
Han Y, Zheng D, Vimolmangkang S, Khan MA, Beever JE, Korban SS. Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genome. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:5117-30. [PMID: 21743103 PMCID: PMC3193016 DOI: 10.1093/jxb/err215] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A total of 355 simple sequence repeat (SSR) markers were developed, based on expressed sequence tag (EST) and bacterial artificial chromosome (BAC)-end sequence databases, and successfully used to construct an SSR-based genetic linkage map of the apple. The consensus linkage map spanned 1143 cM, with an average density of 2.5 cM per marker. Newly developed SSR markers along with 279 SSR markers previously published by the HiDRAS project were further used to integrate physical and genetic maps of the apple using a PCR-based BAC library screening approach. A total of 470 contigs were unambiguously anchored onto all 17 linkage groups of the apple genome, and 158 contigs contained two or more molecular markers. The genetically mapped contigs spanned ∼421 Mb in cumulative physical length, representing 60.0% of the genome. The sizes of anchored contigs ranged from 97 kb to 4.0 Mb, with an average of 995 kb. The average physical length of anchored contigs on each linkage group was ∼24.8 Mb, ranging from 17.0 Mb to 37.73 Mb. Using BAC DNA as templates, PCR screening of the BAC library amplified fragments of highly homologous sequences from homoeologous chromosomes. Upon integrating physical and genetic maps of the apple, the presence of not only homoeologous chromosome pairs, but also of multiple locus markers mapped to adjacent sites on the same chromosome was detected. These findings demonstrated the presence of both genome-wide and segmental duplications in the apple genome and provided further insights into the complex polyploid ancestral origin of the apple.
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
| | - Danman Zheng
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
| | - Sornkanok Vimolmangkang
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
| | - Muhammad A. Khan
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
| | - Jonathan E. Beever
- Department of Animal 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
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
34
|
Flachowsky H, Le Roux PM, Peil A, Patocchi A, Richter K, Hanke MV. Application of a high-speed breeding technology to apple (Malus × domestica) based on transgenic early flowering plants and marker-assisted selection. THE NEW PHYTOLOGIST 2011; 192:364-77. [PMID: 21736565 DOI: 10.1111/j.1469-8137.2011.03813.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Breeding of apple (Malus × domestica) remains a slow process because of protracted generation cycles. Shortening the juvenile phase to achieve the introgression of traits from wild species into prebreeding material within a reasonable time frame is a great challenge. In this study, we evaluated early flowering transgenic apple lines overexpressing the BpMADS4 gene of silver birch with regard to tree morphology in glasshouse conditions. Based on the results obtained, line T1190 was selected for further analysis and application to fast breeding. The DNA sequences flanking the T-DNA were isolated and the T-DNA integration site was mapped on linkage group 4. The inheritance and correctness of the T-DNA integration were confirmed after meiosis. A crossbred breeding programme was initiated by crossing T1190 with the fire blight-resistant wild species Malus fusca. Transgenic early flowering F(1) seedlings were selected and backcrossed with 'Regia' and 98/6-10 in order to introgress the apple scab Rvi2, Rvi4 and powdery mildew Pl-1, Pl-2 resistance genes and the fire blight resistance quantitative trait locus FB-F7 present in 'Regia'. Three transgenic BC'1 seedlings pyramiding Rvi2, Rvi4 and FB-F7, as well as three other BC'1 seedlings combining Pl-1 and Pl-2, were identified. Thus, the first transgenic early flowering-based apple breeding programme combined with marker-assisted selection was established.
Collapse
Affiliation(s)
- Henryk Flachowsky
- Institute for Breeding Research on Horticultural and Fruit Crops, Dresden, Germany
| | | | | | | | | | | |
Collapse
|
35
|
Genomic resources in horticultural crops: Status, utility and challenges. Biotechnol Adv 2011; 29:199-209. [DOI: 10.1016/j.biotechadv.2010.11.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2010] [Revised: 09/04/2010] [Accepted: 09/26/2010] [Indexed: 01/02/2023]
|
36
|
Genetic mapping of 14 avirulence genes in an EU-B04×1639 progeny of Venturia inaequalis. Fungal Genet Biol 2011; 48:166-76. [DOI: 10.1016/j.fgb.2010.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 09/03/2010] [Accepted: 09/05/2010] [Indexed: 02/01/2023]
|
37
|
Le Roux PMF, Khan MA, Broggini GAL, Duffy B, Gessler C, Patocchi A. Mapping of quantitative trait loci for fire blight resistance in the apple cultivars 'Florina' and 'Nova Easygro'. Genome 2011; 53:710-22. [PMID: 20924420 DOI: 10.1139/g10-047] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fire blight is a devastating bacterial disease of rosaceous plants. Its damage to apple production is a major concern, since no existing control option has proven to be completely effective. Some commercial apple varieties, such as 'Florina' and 'Nova Easygro', exhibit a consistent level of resistance to fire blight. In this study, we used an F1 progeny of 'Florina' × 'Nova Easygro' to build parental genetic maps and identify quantitative trait loci (QTLs) related to fire blight resistance. Linkage maps were constructed using a set of microsatellites and enriched with amplified fragment length polymorphism (AFLP) markers. In parallel, progeny plants were artificially inoculated with Erwinia amylovora strain CFBP 1430 in a quarantine glasshouse. Shoot length measured 7 days after inoculation (DAI) and lesion length measured 7 and 14 DAI were used to calculate the lesion length as a percentage of the shoot length (PLL1 and PLL2, respectively). Percent lesion length data were log10-transformed (log10(PLL)) and used to perform the Kruskal-Wallis test, interval mapping (IM), and multiple QTL mapping (MQM). Two significant fire blight resistance QTLs were detected in 'Florina'. One QTL was mapped on linkage group 10 by IM and MQM; it explained 17.9% and 15.3% of the phenotypic variation by MQM with log10(PLL1) and log10(PLL2) data, respectively. A second QTL was identified on linkage group 5 by MQM with log10(PLL2) data; it explained 10.1% of the phenotypic variation. Genotyping the plants of 'Florina' pedigree with the microsatellites flanking the QTLs showed that the QTLs on linkage groups 5 and 10 were inherited from 'Jonathan' and 'Starking' (a 'Red Delicious' sport mutation), respectively. Other putative QTLs (defined as QTLs with LOD scores above the chromosomal threshold and below the genome-wide threshold) were detected by IM on linkage groups 5 and 9 of 'Nova Easygro'.
Collapse
Affiliation(s)
- P-M F Le Roux
- Plant Pathology, IBZ, ETH Zürich, 8092 Zürich, Switzerland
| | | | | | | | | | | |
Collapse
|
38
|
Stolle E, Wilfert L, Schmid-Hempel R, Schmid-Hempel P, Kube M, Reinhardt R, Moritz RFA. A second generation genetic map of the bumblebee Bombus terrestris (Linnaeus, 1758) reveals slow genome and chromosome evolution in the Apidae. BMC Genomics 2011; 12:48. [PMID: 21247459 PMCID: PMC3034698 DOI: 10.1186/1471-2164-12-48] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 01/19/2011] [Indexed: 12/30/2022] Open
Abstract
Background The bumblebee Bombus terrestris is an ecologically and economically important pollinator and has become an important biological model system. To study fundamental evolutionary questions at the genomic level, a high resolution genetic linkage map is an essential tool for analyses ranging from quantitative trait loci (QTL) mapping to genome assembly and comparative genomics. We here present a saturated linkage map and match it with the Apis mellifera genome using homologous markers. This genome-wide comparison allows insights into structural conservations and rearrangements and thus the evolution on a chromosomal level. Results The high density linkage map covers ~ 93% of the B. terrestris genome on 18 linkage groups (LGs) and has a length of 2'047 cM with an average marker distance of 4.02 cM. Based on a genome size of ~ 430 Mb, the recombination rate estimate is 4.76 cM/Mb. Sequence homologies of 242 homologous markers allowed to match 15 B. terrestris with A. mellifera LGs, five of them as composites. Comparing marker orders between both genomes we detect over 14% of the genome to be organized in synteny and 21% in rearranged blocks on the same homologous LG. Conclusions This study demonstrates that, despite the very high recombination rates of both A. mellifera and B. terrestris and a long divergence time of about 100 million years, the genomes' genetic architecture is highly conserved. This reflects a slow genome evolution in these bees. We show that data on genome organization and conserved molecular markers can be used as a powerful tool for comparative genomics and evolutionary studies, opening up new avenues of research in the Apidae.
Collapse
Affiliation(s)
- Eckart Stolle
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.
| | | | | | | | | | | | | |
Collapse
|
39
|
Zhao Y, Guo Y, Fu J, Huang S, Lu B, Zhou J, Hu G, iu C. Molecular Genetic Map Construction and QTL Analysis for Fruit Maturation Period in Litchi. BIOTECHNOL BIOTEC EQ 2011. [DOI: 10.5504/bbeq.2011.0046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
40
|
Hong Y, Chen X, Liang X, Liu H, Zhou G, Li S, Wen S, Holbrook CC, Guo B. A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome. BMC PLANT BIOLOGY 2010; 10:17. [PMID: 20105299 PMCID: PMC2835713 DOI: 10.1186/1471-2229-10-17] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 01/27/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND The construction of genetic linkage maps for cultivated peanut (Arachis hypogaea L.) has and continues to be an important research goal to facilitate quantitative trait locus (QTL) analysis and gene tagging for use in a marker-assisted selection in breeding. Even though a few maps have been developed, they were constructed using diploid or interspecific tetraploid populations. The most recently published intra-specific map was constructed from the cross of cultivated peanuts, in which only 135 simple sequence repeat (SSR) markers were sparsely populated in 22 linkage groups. The more detailed linkage map with sufficient markers is necessary to be feasible for QTL identification and marker-assisted selection. The objective of this study was to construct a genetic linkage map of cultivated peanut using simple sequence repeat (SSR) markers derived primarily from peanut genomic sequences, expressed sequence tags (ESTs), and by "data mining" sequences released in GenBank. RESULTS Three recombinant inbred lines (RILs) populations were constructed from three crosses with one common female parental line Yueyou 13, a high yielding Spanish market type. The four parents were screened with 1044 primer pairs designed to amplify SSRs and 901 primer pairs produced clear PCR products. Of the 901 primer pairs, 146, 124 and 64 primer pairs (markers) were polymorphic in these populations, respectively, and used in genotyping these RIL populations. Individual linkage maps were constructed from each of the three populations and a composite map based on 93 common loci were created using JoinMap. The composite linkage maps consist of 22 composite linkage groups (LG) with 175 SSR markers (including 47 SSRs on the published AA genome maps), representing the 20 chromosomes of A. hypogaea. The total composite map length is 885.4 cM, with an average marker density of 5.8 cM. Segregation distortion in the 3 populations was 23.0%, 13.5% and 7.8% of the markers, respectively. These distorted loci tended to cluster on LG1, LG3, LG4 and LG5. There were only 15 EST-SSR markers mapped due to low polymorphism. By comparison, there were potential synteny, collinear order of some markers and conservation of collinear linkage groups among the maps and with the AA genome but not fully conservative. CONCLUSION A composite linkage map was constructed from three individual mapping populations with 175 SSR markers in 22 composite linkage groups. This composite genetic linkage map is among the first "true" tetraploid peanut maps produced. This map also consists of 47 SSRs that have been used in the published AA genome maps, and could be used in comparative mapping studies. The primers described in this study are PCR-based markers, which are easy to share for genetic mapping in peanuts. All 1044 primer pairs are provided as additional files and the three RIL populations will be made available to public upon request for quantitative trait loci (QTL) analysis and linkage map improvement.
Collapse
Affiliation(s)
- Yanbin Hong
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - Xiaoping Chen
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
- US Department of Agriculture, Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA 31793, USA
- University of Georgia, Department of Plant Pathology, Tifton, GA 31793, USA
| | - Xuanqiang Liang
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - Haiyan Liu
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - Guiyuan Zhou
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - Shaoxiong Li
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - Shijie Wen
- Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
| | - C Corley Holbrook
- US Department of Agriculture, Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA 31793, USA
| | - Baozhu Guo
- US Department of Agriculture, Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA 31793, USA
| |
Collapse
|
41
|
Cavanna M, Torello Marinoni D, Beccaro GL, Bounous G. Microsatellite-based evaluation of Ribes spp. germplasm. Genome 2009; 52:839-48. [DOI: 10.1139/g09-057] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
There is a lack of published microsatellite data which characterizes Ribes spp. To address this, an initial study of simple sequence repeat (SSR) variation was undertaken in 41 cultivars belonging to four species of the genus Ribes to evaluate its genetic variability. The cultivars were collected in Piedmont, northwest Italy, together with one cultivar from Switzerland. Twenty SSRs were screened for amplification and polymorphism. Seven failed to amplify, and therefore the remaining 13 were selected and used to fingerprint all the cultivars. Microsatellite analysis resulted in the identification of 38 genotypes, suggesting the existence of possible clonal genotypes and synonyms. Among the cultivars analyzed, two tetraploid accessions were found. The evaluation of genetic variability in Ribes is of fundamental importance for future nutritional breeding programs and to preserve genetic resources, as cultivar characterization permits better management of plant collections.
Collapse
Affiliation(s)
- M. Cavanna
- Dipartimento di Colture Arboree, Università degli Studi di Torino, Via Leonardo da Vinci 44, 10095, Grugliasco (Torino), Italy
| | - D. Torello Marinoni
- Dipartimento di Colture Arboree, Università degli Studi di Torino, Via Leonardo da Vinci 44, 10095, Grugliasco (Torino), Italy
| | - G. L. Beccaro
- Dipartimento di Colture Arboree, Università degli Studi di Torino, Via Leonardo da Vinci 44, 10095, Grugliasco (Torino), Italy
| | - G. Bounous
- Dipartimento di Colture Arboree, Università degli Studi di Torino, Via Leonardo da Vinci 44, 10095, Grugliasco (Torino), Italy
| |
Collapse
|
42
|
Celton JM, Chagné D, Tustin SD, Terakami S, Nishitani C, Yamamoto T, Gardiner SE. Update on comparative genome mapping between Malus and Pyrus. BMC Res Notes 2009; 2:182. [PMID: 19747407 PMCID: PMC2749866 DOI: 10.1186/1756-0500-2-182] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 09/14/2009] [Indexed: 11/13/2022] Open
Abstract
Background Comparative genome mapping determines the linkage between homologous genes of related taxa. It has already been used in plants to characterize agronomically important genes in lesser studied species, using information from better studied species. In the Maloideae sub-family, which includes fruit species such as apple, pear, loquat and quince, genome co-linearity has been suggested between the genera Malus and Pyrus; however map comparisons are incomplete to date. Findings Genetic maps for the apple rootstocks 'Malling 9' ('M.9') (Malus × domestica) and 'Robusta 5' ('R5') (Malus × robusta), and pear cultivars 'Bartlett' and 'La France' (Pyrus communis) were constructed using Simple Sequence Repeat (SSR) markers developed from both species, including a new set of 73 pear Expressed Sequence Tag (EST) SSR markers. Integrated genetic maps for apple and pear were then constructed using 87 and 131 SSR markers in common, respectively. The genetic maps were aligned using 102 markers in common, including 64 pear SSR markers and 38 apple SSR markers. Of these 102 markers, 90 anchor markers showed complete co-linearity between the two genomes. Conclusion Our alignment of the genetic maps of two Malus cultivars of differing species origin with two Pyrus communis cultivars confirms the ready transferability of SSR markers from one genus to the other and supports a high level of co-linearity within the sub-family Maloideae between the genomes of Malus and Pyrus.
Collapse
Affiliation(s)
- Jean-Marc Celton
- University of Western Cape, Biotechnology Department, Modderdam Road, Bellville, Cape Town, 7535, South Africa.
| | | | | | | | | | | | | |
Collapse
|
43
|
Blas AL, Yu Q, Chen C, Veatch O, Moore PH, Paull RE, Ming R. Enrichment of a papaya high-density genetic map with AFLP markers. Genome 2009; 52:716-25. [DOI: 10.1139/g09-043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A high-density genetic linkage map of papaya, previously developed using an F2mapping population derived from the intraspecific cross AU9 × SunUp, was enriched with AFLP markers. The comprehensive genetic map presented here spans 945.2 cM and covers 9 major and 5 minor linkage groups containing 712 SSR, 277 AFLP, and 1 morphological markers. The average marker density for the 9 major linkage groups is 0.9 cM between adjacent markers, and the total number of gaps >5 cM was reduced from 48 to 27 in the current map. AFLPs generated by EcoRI/MseI primer combinations were distributed throughout the 14 linkage groups and resulted in several large locus order rearrangements within the 9 major linkage groups. Integration of AFLP markers provided tighter linkage association between loci, leading to a reduction in map distance on LGs 1, 2, and 4, which were inflated in the previous map, and correction of the marker order on LG8. Suppression of recombination in the male-specific Y region (MSY) of LG1 is further validated by the addition of 27 sex co-segregating AFLP markers. A large region of distorted segregation surrounding the MSY spans 54.4 cM and represents ∼71% of the linkage group. This comprehensive high-density genetic map provides a framework for mapping quantitative trait loci and for fine mapping as well as for comparative genomic studies of crop plant development and evolution.
Collapse
Affiliation(s)
- Andrea L. Blas
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Qingyi Yu
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Cuixia Chen
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Olivia Veatch
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Paul H. Moore
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Robert E. Paull
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Ray Ming
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| |
Collapse
|
44
|
Broggini GAL, Galli P, Parravicini G, Gianfranceschi L, Gessler C, Patocchi A. HcrVf paralogs are present on linkage groups 1 and 6 of Malus. Genome 2009; 52:129-38. [PMID: 19234561 DOI: 10.1139/g08-115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular markers derived from resistance gene analogs of HcrVf2, the first apple resistance gene cloned, may pave the way to the cloning of additional apple scab resistance genes. The Malus xdomestica 'Florina' (Vf) bacterial artificial chromosome (BAC) genomic library was screened by hybridization using HcrVf2 as a probe. Positive BAC clones were assembled into contigs and microsatellite markers developed from each contig mapped. Only linkage groups 1 and 6 contained HcrVf2 paralogs. On linkage group 1, five loci in addition to the Vf locus were identified. A single locus was detected on linkage group 6. Representative BAC clones of these loci including the Vf locus were sequenced and the gene structure compiled. A total of 22 sequences, showing high sequence similarity to HcrVf2, were identified. Nine sequences were predicted to encode all seven protein domains described in HcrVf2, while three were truncated. Transcriptional analysis indicated that six genes with a complete HcrVf-like structure were constitutively expressed in young uninfected leaves of 'Florina'. The map position of each HcrVf analog was compared with the location of the major apple scab resistance genes. None of the major genes conferring scab resistance co-localized with HcrVf paralogs, indicating that they are unlikely to belong to the leucine-rich repeat - transmembrane class, which includes the Vf gene.
Collapse
|
45
|
Terakami S, Kimura T, Nishitani C, Sawamura Y, Saito T, Hirabayashi T, Yamamoto T. Genetic Linkage Map of the Japanese Pear ‘Housui’ Identifying Three Homozygous Genomic Regions. ACTA ACUST UNITED AC 2009. [DOI: 10.2503/jjshs1.78.417] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
46
|
Moriya S, Iwanami H, Kotoda N, Takahashi S, Yamamoto T, Abe K. Development of a Marker-assisted Selection System for Columnar Growth Habit in Apple Breeding. ACTA ACUST UNITED AC 2009. [DOI: 10.2503/jjshs1.78.279] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
47
|
Han Y, Chagné D, Gasic K, Rikkerink EHA, Beever JE, Gardiner SE, Korban SS. BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple. Genomics 2008; 93:282-8. [PMID: 19059473 DOI: 10.1016/j.ygeno.2008.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 11/05/2008] [Accepted: 11/06/2008] [Indexed: 11/26/2022]
Abstract
A genome-wide BAC physical map of the apple, Malus x domestica Borkh., has been recently developed. Here, we report on integrating the physical and genetic maps of the apple using a SNP-based approach in conjunction with bin mapping. Briefly, BAC clones located at ends of BAC contigs were selected, and sequenced at both ends. The BAC end sequences (BESs) were used to identify candidate SNPs. Subsequently, these candidate SNPs were genetically mapped using a bin mapping strategy for the purpose of mapping the physical onto the genetic map. Using this approach, 52 (23%) out of 228 BESs tested were successfully exploited to develop SNPs. These SNPs anchored 51 contigs, spanning approximately 37 Mb in cumulative physical length, onto 14 linkage groups. The reliability of the integration of the physical and genetic maps using this SNP-based strategy is described, and the results confirm the feasibility of this approach to construct an integrated physical and genetic maps for apple.
Collapse
Affiliation(s)
- Yuepeng Han
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA
| | | | | | | | | | | | | |
Collapse
|
48
|
Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink EHA, Gardiner SE, Korban SS. Development of a set of SNP markers present in expressed genes of the apple. Genomics 2008; 92:353-8. [PMID: 18721872 DOI: 10.1016/j.ygeno.2008.07.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 07/28/2008] [Accepted: 07/29/2008] [Indexed: 11/25/2022]
Abstract
Molecular markers associated with gene coding regions are useful tools for bridging functional and structural genomics. Due to their high abundance in plant genomes, single nucleotide polymorphisms (SNPs) are present within virtually all genomic regions, including most coding sequences. The objective of this study was to develop a set of SNPs for the apple by taking advantage of the wealth of genomics resources available for the apple, including a large collection of expressed sequenced tags (ESTs). Using bioinformatics tools, a search for SNPs within an EST database of approximately 350,000 sequences developed from a variety of apple accessions was conducted. This resulted in the identification of a total of 71,482 putative SNPs. As the apple genome is reported to be an ancient polyploid, attempts were made to verify whether those SNPs detected in silico were attributable either to allelic polymorphisms or to gene duplication or paralogous or homeologous sequence variations. To this end, a set of 464 PCR primer pairs was designed, PCR was amplified using two subsets of plants, and the PCR products were sequenced. The SNPs retrieved from these sequences were then mapped onto apple genetic maps, including a newly constructed map of a Royal Gala x A689-24 cross and a Malling 9 x Robusta 5, map using a bin mapping strategy. The SNP genotyping was performed using the high-resolution melting (HRM) technique. A total of 93 new markers containing 210 coding SNPs were successfully mapped. This new set of SNP markers for the apple offers new opportunities for understanding the genetic control of important horticultural traits using quantitative trait loci (QTL) or linkage disequilibrium analysis. These also serve as useful markers for aligning physical and genetic maps, and as potential transferable markers across the Rosaceae family.
Collapse
Affiliation(s)
- David Chagné
- The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, Palmerston North 4442, New Zealand
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Gong L, Stift G, Kofler R, Pachner M, Lelley T. Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:37-48. [PMID: 18379753 PMCID: PMC2413107 DOI: 10.1007/s00122-008-0750-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Accepted: 03/10/2008] [Indexed: 05/04/2023]
Abstract
Until recently, only a few microsatellites have been available for Cucurbita, thus their development is highly desirable. The Austrian oil-pumpkin variety Gleisdorfer Olkürbis (C. pepo subsp. pepo) and the C. moschata cultivar Soler (Puerto Rico) were used for SSR development. SSR-enriched partial genomic libraries were established and 2,400 clones were sequenced. Of these 1,058 (44%) contained an SSR at least four repeats long. Primers were designed for 532 SSRs; 500 primer pairs produced fragments of expected size. Of these, 405 (81%) amplified polymorphic fragments in a set of 12 genotypes: three C. moschata, one C. ecuadorensis, and eight C. pepo representing all eight cultivar groups. On an average, C. pepo and C. moschata produced 3.3 alleles per primer pair, showing high inter-species transferability. There were 187 SSR markers detecting polymorphism between the USA oil-pumpkin variety "Lady Godiva" (O5) and the Italian crookneck variety "Bianco Friulano" (CN), which are the parents of our previous F(2) mapping population. It has been used to construct the first published C. pepo map, containing mainly RAPD and AFLP markers. Now the updated map comprises 178 SSRs, 244 AFLPs, 230 RAPDs, five SCARs, and two morphological traits (h and B). It contains 20 linkage groups with a map density of 2.9 cM. The observed genome coverage (Co) is 86.8%.
Collapse
Affiliation(s)
- L. Gong
- University of Natural Resources and Applied Life Sciences (BOKU), Vienna, Austria
- Department of Agrobiotechnology, IFA-Tulln, Konrad Lorenz Str. 20, 3430 Tulln, Austria
| | - G. Stift
- University of Natural Resources and Applied Life Sciences (BOKU), Vienna, Austria
- Department of Agrobiotechnology, IFA-Tulln, Konrad Lorenz Str. 20, 3430 Tulln, Austria
| | - R. Kofler
- University of Natural Resources and Applied Life Sciences (BOKU), Vienna, Austria
- Department of Agrobiotechnology, IFA-Tulln, Konrad Lorenz Str. 20, 3430 Tulln, Austria
| | - M. Pachner
- University of Natural Resources and Applied Life Sciences (BOKU), Vienna, Austria
- Department of Agrobiotechnology, IFA-Tulln, Konrad Lorenz Str. 20, 3430 Tulln, Austria
| | - T. Lelley
- University of Natural Resources and Applied Life Sciences (BOKU), Vienna, Austria
- Department of Agrobiotechnology, IFA-Tulln, Konrad Lorenz Str. 20, 3430 Tulln, Austria
| |
Collapse
|
50
|
Malnoy M, Xu M, Borejsza-Wysocka E, Korban SS, Aldwinckle HS. Two receptor-like genes, Vfa1 and Vfa2, confer resistance to the fungal pathogen Venturia inaequalis inciting apple scab disease. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:448-58. [PMID: 18321190 DOI: 10.1094/mpmi-21-4-0448] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The Vf locus, originating from the crabapple species Malus floribunda 821, confers resistance to five races of the fungal pathogen Venturia inaequalis, the causal agent of apple scab disease. Previously, a cluster of four receptor-like genes, Vfa1, Vfa2, Vfa3, and Vfa4, was identified within the Vf locus. Because the amino-acid sequence of Vfa3 is truncated, it was deemed nonfunctional. In this study, each of the three full-length Vfa genes was introduced into a plant cloning vector, pCAMBIA2301, and used for Agrobacterium-mediated transformation of two apple cultivars, Galaxy and McIntosh, to assess functionality of these genes and to characterize their roles in resistance to V. inaequalis. Transformed apple lines carrying each of Vfa1, Vfa2, or Vfa4 were developed, analyzed for the presence of the transgene using polymerase chain reaction and Southern blotting, and assayed for resistance to apple scab following inoculation with V. inaequalis. Transformed lines expressing Vfa4 were found to be susceptible to apple scab, whereas those expressing either Vfa1 or Vfa2 exhibited partial resistance to apple scab. Based on Western blot analysis as well as microscopic analysis of plant resistance reactions, the roles of Vfa1 and Vfa2 in apple scab disease resistance response are discussed.
Collapse
Affiliation(s)
- Mickael Malnoy
- Department of Plant Pathology, Cornell University, Geneva, NY 14456, USA
| | | | | | | | | |
Collapse
|