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Lee JH, Venkatesh J, Jo J, Jang S, Kim GW, Kim JM, Han K, Ro N, Lee HY, Kwon JK, Kim YM, Lee TH, Choi D, Van Deynze A, Hill T, Kfir N, Freiman A, Davila Olivas NH, Elkind Y, Paran I, Kang BC. High-quality chromosome-scale genomes facilitate effective identification of large structural variations in hot and sweet peppers. HORTICULTURE RESEARCH 2022; 9:uhac210. [PMID: 36467270 PMCID: PMC9715575 DOI: 10.1093/hr/uhac210] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Pepper (Capsicum annuum) is an important vegetable crop that has been subjected to intensive breeding, resulting in limited genetic diversity, especially for sweet peppers. Previous studies have reported pepper draft genome assemblies using short read sequencing, but their capture of the extent of large structural variants (SVs), such as presence-absence variants (PAVs), inversions, and copy-number variants (CNVs) in the complex pepper genome falls short. In this study, we sequenced the genomes of representative sweet and hot pepper accessions by long-read and/or linked-read methods and advanced scaffolding technologies. First, we developed a high-quality reference genome for the sweet pepper cultivar 'Dempsey' and then used the reference genome to identify SVs in 11 other pepper accessions and constructed a graph-based pan-genome for pepper. We annotated an average of 42 972 gene families in each pepper accession, defining a set of 19 662 core and 23 115 non-core gene families. The new pepper pan-genome includes informative variants, 222 159 PAVs, 12 322 CNVs, and 16 032 inversions. Pan-genome analysis revealed PAVs associated with important agricultural traits, including potyvirus resistance, fruit color, pungency, and pepper fruit orientation. Comparatively, a large number of genes are affected by PAVs, which is positively correlated with the high frequency of transposable elements (TEs), indicating TEs play a key role in shaping the genomic landscape of peppers. The datasets presented herein provide a powerful new genomic resource for genetic analysis and genome-assisted breeding for pepper improvement.
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Affiliation(s)
| | | | - Jinkwan Jo
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Siyoung Jang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Geon Woo Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jung-Min Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Hea-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Doil Choi
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Theresa Hill
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Nir Kfir
- NRGene, 5 Golda Meir St., Ness Ziona 7403649, Israel
| | - Aviad Freiman
- Top Seeds International Ltd. Moshav Sharona, 1523200, Israel
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Lozada DN, Nunez G, Lujan P, Dura S, Coon D, Barchenger DW, Sanogo S, Bosland PW. Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.). BMC PLANT BIOLOGY 2021; 21:601. [PMID: 34922461 PMCID: PMC8684135 DOI: 10.1186/s12870-021-03387-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/07/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between 'Criollo de Morellos-334' (CM-334), a resistant landrace from Mexico, and 'Early Jalapeno', a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified. RESULTS Development of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified. CONCLUSIONS Results support the genetic complexity of the P. capsici-Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.
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Affiliation(s)
- Dennis N Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Guillermo Nunez
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Phillip Lujan
- Extension Plant Sciences, Plant Diagnostic Clinic, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Srijana Dura
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Danise Coon
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA
| | | | - Soumaila Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Paul W Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA
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Cheng J, Chen Y, Hu Y, Zhou Z, Hu F, Dong J, Chen W, Cui J, Wu Z, Hu K. Fine mapping of restorer-of-fertility gene based on high-density genetic mapping and collinearity analysis in pepper (Capsicum annuum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:889-902. [PMID: 31863157 DOI: 10.1007/s00122-019-03513-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/13/2019] [Indexed: 05/24/2023]
Abstract
The pepper restorer-of-fertility (CaRf) gene was fine mapped based on conjoint analysis of recombinants and collinearity between the two pepper reference genomes. Capana06g003028, encoding an Rf-like PPR protein, was proposed as the strongest candidate for pepper CaRf based on sequence comparison and expression analysis. The cytoplasmic male sterility (CMS)/restorer-of-fertility (Rf) system not only provides an excellent model to dissect genetic interactions between the mitochondria and nucleus but also plays a vital role in high-efficiency hybrid seed production in crops including pepper (Capsicum spp.). Although two important CMS candidate genes, orf507 and Ψatp6-2, have previously been suggested, the pepper Rf gene (CaRf) has not yet been isolated. In this study, a high-density genetic map comprising 7566 SNP markers in 1944 bins was first constructed with the array genotyping results from 317 F2 individuals. Based on this map, the CaRf gene was preliminarily mapped to a region of 1.15 Mb in length at the end of chromosome P6. Then, by means of a conjoint analysis of recombinants and collinearity between the two pepper reference genomes, an important candidate interval with 270.10 kb in length was delimited for CaRf. Finally, Capana06g003028, which encodes an Rf-like PPR protein, was proposed as the strongest candidate for CaRf based on sequence analysis and expression characteristics in sterile and fertile plants. The high-density genetic map and fine mapping results provided here lay a foundation for the application of molecular breeding, as well as cloning and functional analysis of CaRf, in pepper.
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Affiliation(s)
- Jiaowen Cheng
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Yijian Chen
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Yafei Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Ziyan Zhou
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Fang Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Jichi Dong
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Weili Chen
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Junjie Cui
- Department of Horticulture, College of Food Science and Engineering, Foshan University, Foshan, 528200, Guangdong, China
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China.
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Tello J, Roux C, Chouiki H, Laucou V, Sarah G, Weber A, Santoni S, Flutre T, Pons T, This P, Péros JP, Doligez A. A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2237-2252. [PMID: 31049634 DOI: 10.1007/s00122-019-03351-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/20/2019] [Indexed: 05/21/2023]
Abstract
A half-diallel population involving five elite grapevine cultivars was generated and genotyped by GBS, and highly-informative segregation data was used to construct a high-density genetic map for Vitis vinifera L. Grapevine is one of the most relevant fruit crops in the world. Deeper genetic knowledge could assist modern grapevine breeding programs to develop new wine grape varieties able to face climate change effects. To assist in the rapid identification of markers for crop yield components, grape quality traits and adaptation potential, we generated a large Vitis vinifera L. population (N = 624) by crossing five red wine cultivars in a half-diallel scheme, which was subsequently sequenced by an efficient GBS procedure. A high number of fully informative genetic variants was detected using a novel mapping approach capable of reconstructing local haplotypes from adjacent biallelic SNPs, which were subsequently used to construct the densest consensus genetic map available for the cultivated grapevine to date. This 1378.3-cM map integrates 10 bi-parental consensus maps and orders 4437 markers in 3353 unique positions on 19 chromosomes. Markers are well distributed all along the grapevine reference genome, covering up to 98.8% of its genomic sequence. Additionally, a good agreement was observed between genetic and physical orders, adding confidence in the quality of this map. Collectively, our results pave the way for future genetic studies (such as fine QTL mapping) aimed to understand the complex relationship between genotypic and phenotypic variation in the cultivated grapevine. In addition, the method used (which efficiently delivers a high number of fully informative markers) could be of interest to other outbred organisms, notably perennial fruit crops.
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Affiliation(s)
- Javier Tello
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Catherine Roux
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Hajar Chouiki
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Valérie Laucou
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Gautier Sarah
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Audrey Weber
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Sylvain Santoni
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Timothée Flutre
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Thierry Pons
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Patrice This
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Jean-Pierre Péros
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Agnès Doligez
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France.
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France.
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Gonda I, Ashrafi H, Lyon DA, Strickler SR, Hulse-Kemp AM, Ma Q, Sun H, Stoffel K, Powell AF, Futrell S, Thannhauser TW, Fei Z, Van Deynze AE, Mueller LA, Giovannoni JJ, Foolad MR. Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection. THE PLANT GENOME 2019; 12:180010. [PMID: 30951101 DOI: 10.3835/plantgenome2018.02.0010] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Genotyping-by-sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato ( L.) recombinant inbred line (RIL) population, derived from a cross between cultivar NC EBR-1 and the wild tomato L. accession LA2093. A pipeline was developed to convert single nucleotide polymorphism (SNP) data into genomic bins, which could be used for fine mapping of quantitative trait loci (QTL) and identification of candidate genes. The pipeline, implemented in a python script named SNPbinner, adopts a hidden Markov model approach for calculation of recombination breakpoints followed by genomic bins construction. The total length of the newly developed high-resolution genetic map was 1.2-fold larger than previously estimated based on restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR)-based markers. The map was used to verify and refine QTL previously identified for two fruit quality traits in the RIL population, fruit weight (FW) and fruit lycopene content (LYC). Two well-described FW QTL ( and ) were localized precisely at their known underlying causative genes, and the QTL intervals were decreased by two- to tenfold. A major QTL for LYC content () was verified at high resolution and its underlying causative gene was determined to be ζ (). The RIL population, the high resolution genetic map, and the easy-to-use genotyping pipeline, SNPbinner, are made publicly available.
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Zhu Z, Sun B, Wei J, Cai W, Huang Z, Chen C, Cao B, Chen G, Lei J. Construction of a high density genetic map of an interspecific cross of Capsicum chinense and Capsicum annuum and QTL analysis of floral traits. Sci Rep 2019; 9:1054. [PMID: 30705330 PMCID: PMC6355862 DOI: 10.1038/s41598-018-38370-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/27/2018] [Indexed: 11/09/2022] Open
Abstract
The yield of pepper plants (Capsicum spp.) is their most important trait and is affected by the flower number and flowering time. Capsicum annuum produces a single flower per node and has an early flowering habit. By contrast, Capsicum chinense yields multiple flowers per node and has a late flowering character. However, the genetic mechanism underlying the control of these floral traits remains largely unknown. In this study, 150 F2 populations from an interspecific cross between the inbred lines 740 (C. chinense) and CA1 (C. annuum) and their parents were used to construct a molecular genetic linkage map using the specific length amplified fragment sequencing (SLAF-seq) technique. This linkage map, spanning 1,586.78 cM in length, contained 9,038 markers on 12 chromosomes, with a mean marker distance of 0.18 cM. Phenotypic data on the flowering time and flower number per node were collected over multiple years, and QTL analysis identified 6 QTLs for the flowering time and flower number per node by composite interval mapping (CIM) and genome-wide composite interval mapping (GCIM) methods at least in two environments. The candidate genes within the major QTL were predicted. In the major flowering time QTL, the candidate gene Capana02g000700, which encodes the homeotic protein APETALA2, was identified. Quantitative reverse-transcription PCR (qRT-PCR) analysis indicated that its expression level in 740 was higher than that in CA1. Gene expression analysis indicated that the expression of Capana02g000700 was significantly upregulated in flowers, and many floral development-related genes were found to be coexpressed with Capana02g000700, supporting the function of this gene in association with flowering time in C. chinense and C. annuum species.
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Affiliation(s)
- Zhangsheng Zhu
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Binmei Sun
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianlang Wei
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wen Cai
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhubin Huang
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Changming Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Bihao Cao
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Guoju Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
| | - Jianjun Lei
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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Haenel Q, Laurentino TG, Roesti M, Berner D. Meta-analysis of chromosome-scale crossover rate variation in eukaryotes and its significance to evolutionary genomics. Mol Ecol 2018; 27:2477-2497. [PMID: 29676042 DOI: 10.1111/mec.14699] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 01/02/2023]
Abstract
Understanding the distribution of crossovers along chromosomes is crucial to evolutionary genomics because the crossover rate determines how strongly a genome region is influenced by natural selection on linked sites. Nevertheless, generalities in the chromosome-scale distribution of crossovers have not been investigated formally. We fill this gap by synthesizing joint information on genetic and physical maps across 62 animal, plant and fungal species. Our quantitative analysis reveals a strong and taxonomically widespread reduction of the crossover rate in the centre of chromosomes relative to their peripheries. We demonstrate that this pattern is poorly explained by the position of the centromere, but find that the magnitude of the relative reduction in the crossover rate in chromosome centres increases with chromosome length. That is, long chromosomes often display a dramatically low crossover rate in their centre, whereas short chromosomes exhibit a relatively homogeneous crossover rate. This observation is compatible with a model in which crossover is initiated from the chromosome tips, an idea with preliminary support from mechanistic investigations of meiotic recombination. Consequently, we show that organisms achieve a higher genome-wide crossover rate by evolving smaller chromosomes. Summarizing theory and providing empirical examples, we finally highlight that taxonomically widespread and systematic heterogeneity in crossover rate along chromosomes generates predictable broad-scale trends in genetic diversity and population differentiation by modifying the impact of natural selection among regions within a genome. We conclude by emphasizing that chromosome-scale heterogeneity in crossover rate should urgently be incorporated into analytical tools in evolutionary genomics, and in the interpretation of resulting patterns.
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Affiliation(s)
- Quiterie Haenel
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | - Marius Roesti
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
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Li N, Yin Y, Wang F, Yao M. Construction of a high-density genetic map and identification of QTLs for cucumber mosaic virus resistance in pepper ( Capsicum annuum L.) using specific length amplified fragment sequencing (SLAF-seq). BREEDING SCIENCE 2018; 68:233-241. [PMID: 29875607 PMCID: PMC5982177 DOI: 10.1270/jsbbs.17063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/13/2017] [Indexed: 05/09/2023]
Abstract
Pepper (Capsicum) is one of the most important vegetable and spice crops. Aphid-transmitted cucumber mosaic virus (CMV) causes significant damage to pepper crops across the world. The genetic basis of CMV resistance in pepper is complex, and the mechanisms underlying resistance remain largely unknown. Here, we employed a SLAF-seq approach to generate a high-density genetic map of pepper. The map spanned 1,785.46 cM, containing 12,727 markers on 12 chromosomes, with a mean marker distance of 0.16 cM between adjacent markers. We used this map and the interval mapping (IM) and multiple QTL mapping (MQM) procedures to detect genetic regions associated with quantitative trait for CMV resistance. Three QTLs, qcmv11.1, qcmv11.2 and qcmv12.1, conferred resistance to CMV and showed trait variation of 10.2%, 19.2% and 7.3% respectively. Our results will help to develop markers linked to CMV-resistant QTLs to improve pepper resistance to CMV.
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Affiliation(s)
| | | | - Fei Wang
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences,
Wuhan 430064,
China
| | - Minghua Yao
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences,
Wuhan 430064,
China
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Hulse-Kemp AM, Maheshwari S, Stoffel K, Hill TA, Jaffe D, Williams SR, Weisenfeld N, Ramakrishnan S, Kumar V, Shah P, Schatz MC, Church DM, Van Deynze A. Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library. HORTICULTURE RESEARCH 2018; 5:4. [PMID: 29423234 PMCID: PMC5798813 DOI: 10.1038/s41438-017-0011-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/13/2017] [Accepted: 11/16/2017] [Indexed: 05/19/2023]
Abstract
Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes, however, the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5-gigabase (Gb) diploid pepper (Capsicum annuum) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion. The Supernova software generated a highly ordered, more contiguous sequence assembly than all currently available C. annuum reference genomes. Over 83% of the final assembly was anchored and oriented using four publicly available de novo linkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F1 sample that represents pungent and nonpungent peppers, as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes. The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.
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Affiliation(s)
- Amanda M. Hulse-Kemp
- Department of Plant Sciences, University of California, Davis, CA USA
- USDA-ARS Genomics and Bioinformatics Research Unit, Raleigh, NC USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC USA
| | | | - Kevin Stoffel
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Theresa A. Hill
- Department of Plant Sciences, University of California, Davis, CA USA
| | - David Jaffe
- 10x Genomics, Inc, 7068 Koll Center Parkway, Suite 401, Pleasanton, CA USA
| | | | - Neil Weisenfeld
- 10x Genomics, Inc, 7068 Koll Center Parkway, Suite 401, Pleasanton, CA USA
| | | | - Vijay Kumar
- 10x Genomics, Inc, 7068 Koll Center Parkway, Suite 401, Pleasanton, CA USA
| | - Preyas Shah
- 10x Genomics, Inc, 7068 Koll Center Parkway, Suite 401, Pleasanton, CA USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD USA
| | - Deanna M. Church
- 10x Genomics, Inc, 7068 Koll Center Parkway, Suite 401, Pleasanton, CA USA
| | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, CA USA
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Hill TA, Chunthawodtiporn J, Ashrafi H, Stoffel K, Weir A, Van Deynze A. Regions Underlying Population Structure and the Genomics of Organ Size Determination in Capsicum annuum. THE PLANT GENOME 2017; 10. [PMID: 29293816 DOI: 10.3835/plantgenome2017.03.0026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fruits, as an important part of the human diet, have been under strong selection during domestication. In general, continued directed selection has led to varieties having larger fruit with greater shape variation and tremendous increases in fruit mass. Common cultivated peppers ( L.) are found in a wide range of sizes and shapes. Analysis of genetic relatedness and population structure has shown that the large-fruited, nonpungent types have reduced diversity and comprise a highly structured group. To explore this population structure, a statistical method for detecting fixation within subpopulations was applied to a set of 21 pungent and 19 nonpungent lines that represent the pepper breeding germplasm. We have identified 17 blocks within the pepper genome that are conserved among nonpungent large-fruited varieties. To determine if these regions were fixed by selection on fruit size or pungency, quantitative trait loci (QTLs) from seven studies along with capsaicin biosynthesis genes and homologs of organ size regulatory genes were mapped onto the current pepper genome assembly. Of the 17 fixed regions, 14 overlapped with fruit size or shape QTLs. There were seven putative organ size regulators and seven capsaicin biosynthetic genes within these regions. This work defines genomic regions that underly structure within the nonpungent pepper germplasm and QTLs or genes that may have been selected for during the development of large-fruited nonpungent pepper varieties.
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11
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Building Ultra-High-Density Linkage Maps Based on Efficient Filtering of Trustable Markers. Genetics 2017; 206:1285-1295. [PMID: 28512186 DOI: 10.1534/genetics.116.197491] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/09/2017] [Indexed: 12/18/2022] Open
Abstract
The study is focused on addressing the problem of building genetic maps in the presence of ∼103-104 of markers per chromosome. We consider a spectrum of situations with intrachromosomal heterogeneity of recombination rate, different level of genotyping errors, and missing data. In the ideal scenario of the absence of errors and missing data, the majority of markers should appear as groups of cosegregating markers ("twins") representing no challenge for map construction. The central aspect of the proposed approach is to take into account the structure of the marker space, where each twin group (TG) and singleton markers are represented as points of this space. The confounding effect of genotyping errors and missing data leads to reduction of TG size, but upon a low level of these effects surviving TGs can still be used as a source of reliable skeletal markers. Increase in the level of confounding effects results in a considerable decrease in the number or even disappearance of usable TGs and, correspondingly, of skeletal markers. Here, we show that the paucity of informative markers can be compensated by detecting kernels of markers in the marker space using a clustering procedure, and demonstrate the utility of this approach for high-density genetic map construction on simulated and experimentally obtained genotyping datasets.
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Cheng J, Qin C, Tang X, Zhou H, Hu Y, Zhao Z, Cui J, Li B, Wu Z, Yu J, Hu K. Development of a SNP array and its application to genetic mapping and diversity assessment in pepper (Capsicum spp.). Sci Rep 2016; 6:33293. [PMID: 27623541 PMCID: PMC5020730 DOI: 10.1038/srep33293] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/24/2016] [Indexed: 11/09/2022] Open
Abstract
The development and application of single nucleotide polymorphisms (SNPs) is in its infancy for pepper. Here, a set of 15,000 SNPs were chosen from the resequencing data to develop an array for pepper with 12,720 loci being ultimately synthesized. Of these, 8,199 (~64.46%) SNPs were found to be scorable and covered ~81.18% of the whole genome. With this array, a high-density interspecific genetic map with 5,569 SNPs was constructed using 297 F2 individuals, and genetic diversity of a panel of 399 pepper elite/landrace lines was successfully characterized. Based on the genetic map, one major QTL, named Up12.1, was detected for the fruit orientation trait. A total of 65 protein-coding genes were predicted within this QTL region based on the current annotation of the Zunla-1 genome. In summary, the thousands of well-validated SNP markers, high-density genetic map and genetic diversity information will be useful for molecular genetics and innovative breeding in pepper. Furthermore, the mapping results lay foundation for isolating the genes underlying variation in fruit orientation of Capsicum.
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Affiliation(s)
- Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Cheng Qin
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China.,Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Xin Tang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Huangkai Zhou
- Guangzhou Genedenovo Biotechnology Co., Ltd, Guangzhou 510006, China
| | - Yafei Hu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zicheng Zhao
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Junjie Cui
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Bo Li
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jiping Yu
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Hulse-Kemp AM, Ashrafi H, Plieske J, Lemm J, Stoffel K, Hill T, Luerssen H, Pethiyagoda CL, Lawley CT, Ganal MW, Van Deynze A. A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding. HORTICULTURE RESEARCH 2016; 3:16036. [PMID: 27602231 PMCID: PMC4962762 DOI: 10.1038/hortres.2016.36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/06/2016] [Accepted: 07/08/2016] [Indexed: 05/18/2023]
Abstract
The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land. These conditions require increased efficiency in pepper breeding to deal with these imminent challenges. Through resequencing of inbred lines we have completed a valuable haplotype map (HapMap) for the pepper genome based on single-nucleotide polymorphisms (SNP). The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines. A selection of one marker per gene model was utilized to create the PepperSNP16K array, which simultaneously genotyped 16 405 SNPs, of which 90.7% were found to be informative. A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F2 individuals were utilized to validate the array. Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups. The interspecific population created between Tabasco (C. frutescens chile type) and P4 (C. annuum blocky type) produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM. This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper. As a standardized tool for genetic analyses, the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers. Data and information on the array are available through the Solanaceae Genomics Network.
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Affiliation(s)
- Amanda M Hulse-Kemp
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Hamid Ashrafi
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Joerg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Jana Lemm
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Kevin Stoffel
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Theresa Hill
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Hartmut Luerssen
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | | | - Cindy T Lawley
- Illumina Incorporated, 5200 Illumina Way, San Diego, CA 92122, USA
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Allen Van Deynze
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
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Rinaldi R, Van Deynze A, Portis E, Rotino GL, Toppino L, Hill T, Ashrafi H, Barchi L, Lanteri S. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL. FRONTIERS IN PLANT SCIENCE 2016; 7:1031. [PMID: 27486463 PMCID: PMC4948011 DOI: 10.3389/fpls.2016.01031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/30/2016] [Indexed: 05/20/2023]
Abstract
Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous chromosomal regions. Our results highlight that the availability of genome sequences for an increasing number of crop species and the development of "ultra-dense" physical maps provide new and key tools for detailed syntenic and orthology studies between related plant species.
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Affiliation(s)
- Riccardo Rinaldi
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Ezio Portis
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
| | | | - Laura Toppino
- CREA-ORL Research Unit for Vegetable CropsMontanaso Lombardo, Italy
| | - Theresa Hill
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Lorenzo Barchi
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
- *Correspondence: Lorenzo Barchi
| | - Sergio Lanteri
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
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